Publications by year
Pennington T, Griffith DM, Lehmann CER, Stromberg CER, Parr CL, Sankaran M, Ratnam J, Still CJ, Powell RL, Hanan NP, et al (In Press). Comment on “The extent of forest in dryland biomes”
Griffith, D.M. Lehmann, C.E.R. Strömberg, C.A.E. Parr, C.L. PENNINGTON, R.T. Sankaran, M. Ratnam, J. Still, C.J. Powell, R.L. Hanan, N.P. Nippert, J.B. Osborne, C.P. Good, S.P. Anderson, M. Holdo, R.M. Veldman, J.W. Durigan, G. Tomlinson, K.W. Hoffmann, W.A. Archibald, S. Bond, W.J. Science
Françoso R, Dexter KG, Machado RB, Pennington T, Pinto JRR, Brandao RA, Ratter JA (In Press). Delimiting floristic biogeographic districts in the Cerrado and assessing their
conservation status. Biodiversity and Conservation
Barros FDV, Lewis K, Robertson AD, Pennington RT, Hill TC, Matthews C, Lira-Martins D, Mazzochini GG, Oliveira RS, Rowland L, et al (2023). Cost-effective restoration for carbon sequestration across Brazil's biomes. Science of the Total Environment, 876, 162600-162600.
Correa DF, Stevenson PR, Umaña MN, Coelho LDS, Lima Filho DDA, Salomão RP, Amaral ILD, Wittmann F, Matos FDDA, Castilho CV, et al
(2023). Geographic patterns of tree dispersal modes in Amazonia and their ecological correlates. Global Ecology and Biogeography
Geographic patterns of tree dispersal modes in Amazonia and their ecological correlates
Aim: to investigate the geographic patterns and ecological correlates in the geographic distribution of the most common tree dispersal modes in Amazonia (endozoochory, synzoochory, anemochory and hydrochory). We examined if the proportional abundance of these dispersal modes could be explained by the availability of dispersal agents (disperser-availability hypothesis) and/or the availability of resources for constructing zoochorous fruits (resource-availability hypothesis). Time period: Tree-inventory plots established between 1934 and 2019. Major taxa studied: Trees with a diameter at breast height (DBH) ≥ 9.55 cm. Location: Amazonia, here defined as the lowland rain forests of the Amazon River basin and the Guiana Shield. Methods: We assigned dispersal modes to a total of 5433 species and morphospecies within 1877 tree-inventory plots across terra-firme, seasonally flooded, and permanently flooded forests. We investigated geographic patterns in the proportional abundance of dispersal modes. We performed an abundance-weighted mean pairwise distance (MPD) test and fit generalized linear models (GLMs) to explain the geographic distribution of dispersal modes. Results: Anemochory was significantly, positively associated with mean annual wind speed, and hydrochory was significantly higher in flooded forests. Dispersal modes did not consistently show significant associations with the availability of resources for constructing zoochorous fruits. A lower dissimilarity in dispersal modes, resulting from a higher dominance of endozoochory, occurred in terra-firme forests (excluding podzols) compared to flooded forests. Main conclusions: the disperser-availability hypothesis was well supported for abiotic dispersal modes (anemochory and hydrochory). The availability of resources for constructing zoochorous fruits seems an unlikely explanation for the distribution of dispersal modes in Amazonia. The association between frugivores and the proportional abundance of zoochory requires further research, as tree recruitment not only depends on dispersal vectors but also on conditions that favour or limit seedling recruitment across forest types. Abstract
Osborne OG, Dobreva MP, Papadopulos AST, de Moura MSB, Brunello AT, de Queiroz LP, Pennington RT, Lloyd J, Savolainen V
(2023). Mapping the root systems of individual trees in a natural community using genotyping-by-sequencing. New Phytol
Mapping the root systems of individual trees in a natural community using genotyping-by-sequencing.
The architecture of root systems is an important driver of plant fitness, competition and ecosystem processes. However, the methodological difficulty of mapping roots hampers the study of these processes. Existing approaches to match individual plants to belowground samples are low throughput and species specific. Here, we developed a scalable sequencing-based method to map the root systems of individual trees across multiple species. We successfully applied it to a tropical dry forest community in the Brazilian Caatinga containing 14 species. We sequenced all 42 individual shrubs and trees in a 14 × 14 m plot using double-digest restriction site-associated sequencing (ddRADseq). We identified species-specific markers and individual-specific haplotypes from the data. We matched these markers to the ddRADseq data from 100 mixed root samples from across the centre (10 × 10 m) of the plot at four different depths using a newly developed R package. We identified individual root samples for all species and all but one individual. There was a strong significant correlation between belowground and aboveground size measurements, and we also detected significant species-level root-depth preference for two species. The method is more scalable and less labour intensive than the current techniques and is broadly applicable to ecology, forestry and agricultural biology. Abstract
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Silva TT, de Lima RB, de Souza RLF, Moonlight PW, Cardoso D, Santos HKV, de Oliveira CP, Veenendaal E, de Queiroz LP, Rodrigues PMS, et al (2023). Mapping wood volume in seasonally dry vegetation of Caatinga in Bahia State, Brazil. Scientia Agricola, 80
Ringelberg JJ, Koenen EJM, Sauter B, Aebli A, Rando JG, Iganci JR, de Queiroz LP, Murphy DJ, Gaudeul M, Bruneau A, et al
(2023). Precipitation is the main axis of tropical plant phylogenetic turnover across space and time. Sci Adv
Precipitation is the main axis of tropical plant phylogenetic turnover across space and time.
Early natural historians-Comte de Buffon, von Humboldt, and De Candolle-established environment and geography as two principal axes determining the distribution of groups of organisms, laying the foundations for biogeography over the subsequent 200 years, yet the relative importance of these two axes remains unresolved. Leveraging phylogenomic and global species distribution data for Mimosoid legumes, a pantropical plant clade of c. 3500 species, we show that the water availability gradient from deserts to rain forests dictates turnover of lineages within continents across the tropics. We demonstrate that 95% of speciation occurs within a precipitation niche, showing profound phylogenetic niche conservatism, and that lineage turnover boundaries coincide with isohyets of precipitation. We reveal similar patterns on different continents, implying that evolution and dispersal follow universal processes. Abstract
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Viana Santos H, Borges De Lima R, Figueiredo De Souza R, Cardoso D, Moonlight P, Teixeira Silva T, Pereira De Oliveira C, Alves Júnior F, Veenendaal E, Paganucci De Queiroz L, et al (2023). Spatial distribution of aboveground biomass stock in tropical dry forest in Brazil. iForest - Biogeosciences and Forestry, 16(2), 116-126.
Ramos G, Zartman CE, de Lima HC, Toby Pennington R, Cardoso DBOS
(2022). A Taxonomic Synopsis of <i>Aldina</i>, a Florally Distinctive and Poorly Collected Amazonian Genus of Papilionoid Legumes. Systematic Botany
A Taxonomic Synopsis of Aldina, a Florally Distinctive and Poorly Collected Amazonian Genus of Papilionoid Legumes
Abstract— We present a taxonomic synopsis of Aldina (Leguminosae, Papilionoideae), a poorly known Neotropical genus of predominantly Amazonian trees with unusual, non-papilionate flowers. Aldina is characterized by the combination of odd-foliolate leaves Abstract
and flowers with radial symmetry, free and undifferentiated petals, an entire calyx, and free, numerous stamens. Difficulty accessing species in remote areas has led to poor representation in herbaria, and species descriptions based on scant material have led to a doubtful and confused taxonomy.
Eighteen species are recognized here: A. aurea, A. auyantepuiensis, A. barnebyana, A. berryi, A. discolor, A. diplogyne, A. elliptica, A. heterophylla, A. insignis, A. kunhardtiana, A. latifolia, A. macrophylla, A. microphylla, A.
occidentalis, A. paulberryi, A. petiolulata, A. polyphylla, and A. reticulata. The names A. amazonica, A. latifolia var. pubescens, A. insignis var. retusa, A. stergiosii, A. aquae-negrae, A. rio-negrae, and A.
speciosa are newly synonymized. We lectotypify A. discolor, A. heterophylla, A. macrophylla, A. occidentalis, and A. polyphylla, and make a new combination, Aldina auyantepuiensis. All Aldina species are found in the Amazon basin. An identification
key for all species, a color plate, diagnostic illustrations, and a map of geographic distribution of the genus are also presented.
Torke BM, Cardoso D, Chang H, Li S-J, Niu M, Pennington RT, Stirton CH, Xu W-B, Zartman CE, Chung K-F, et al
(2022). A dated molecular phylogeny and biogeographical analysis reveals the evolutionary history of the trans-pacifically disjunct tropical tree genus Ormosia (Fabaceae). Mol Phylogenet Evol
A dated molecular phylogeny and biogeographical analysis reveals the evolutionary history of the trans-pacifically disjunct tropical tree genus Ormosia (Fabaceae).
The papilionoid legume genus Ormosia (Fabaceae) comprises about 150 species of trees and exhibits a striking disjunct geographical distribution between the New World- and Asian and Australasian wet tropics and subtropics. Modern classifications of Ormosia are not grounded on a well-substantiated phylogenetic hypothesis and have been limited to just portions of the geographical range of the genus. The lack of an evolutionarily-based foundation for systematic studies has hindered taxonomic work on the genus and prevented the testing of biogeographical hypotheses related to the origin of the Old World/New World disjunction and the individual dispersal histories within both areas. Here, we present the most comprehensively sampled molecular phylogeny of Ormosia to date, based on analysis of both nuclear (ITS) and plastid (matK and trnL-F) DNA sequences from 82 species of the genus. Phylogenetically-based divergence times and ancestral range estimations are employed to test hypotheses related to the biogeographical history of the genus. We find strong support for the monophyly of Ormosia and the grouping of all sampled Asian species of the genus into two comparably sized clades, one of which is sister to another large clade containing all sampled New World species. Within the New World clade, additional resolution supports the grouping of most species into three mutually exclusive subordinate clades. The remaining New World species form a fourth well-supported clade in the analyses of plastid sequences, but that result is contradicted by the analysis of ITS. With few exceptions the supported clades have not been previously recognized as taxonomic groups. The biogeographical analysis suggests that Ormosia originated in continental Asia and dispersed to the New World in the Oligocene or early Miocene via long-distance trans-oceanic dispersal. We reject the hypothesis that the inter-hemispheric disjunction in Ormosia resulted from fragmentation of a more continuous "Boreotropical" distribution since the dispersal post-dates Eocene climatic maxima. Both of the Old World clades appear to have originated in mainland Asia and subsequently dispersed into the Malay Archipelago and beyond, at least two lineages dispersing across Wallace's Line as far as the Solomon Islands and northeastern Australia. In the New World, the major clades all originated in Amazonia. Dispersal from Amazonia into peripheral areas in Central America, the Caribbean, and Extra-Amazonian Brazil occurred multiple times over varying time scales, the earliest beginning in the late Miocene. In a few cases, these dispersals were followed by local diversification, but not by reverse migration back to Amazonia. Within each of the two main areas of distribution, multiple modest bouts of oceanic dispersal were required to achieve the modern distributions. Abstract
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Keith DA, Ferrer-Paris JR, Nicholson E, Bishop MJ, Polidoro BA, Ramirez-Llodra E, Tozer MG, Nel JL, Mac Nally R, Gregr EJ, et al
(2022). A function-based typology for Earth’s ecosystems. Nature
A function-based typology for Earth’s ecosystems
As the United Nations develops a post-2020 global biodiversity framework for the Convention on Biological Diversity, attention is focusing on how new goals and targets for ecosystem conservation might serve its vision of ‘living in harmony with nature’1,2. Advancing dual imperatives to conserve biodiversity and sustain ecosystem services requires reliable and resilient generalizations and predictions about ecosystem responses to environmental change and management3. Ecosystems vary in their biota4, service provision5 and relative exposure to risks6, yet there is no globally consistent classification of ecosystems that reflects functional responses to change and management. This hampers progress on developing conservation targets and sustainability goals. Here we present the International Union for Conservation of Nature (IUCN) Global Ecosystem Typology, a conceptually robust, scalable, spatially explicit approach for generalizations and predictions about functions, biota, risks and management remedies across the entire biosphere. The outcome of a major cross-disciplinary collaboration, this novel framework places all of Earth’s ecosystems into a unifying theoretical context to guide the transformation of ecosystem policy and management from global to local scales. This new information infrastructure will support knowledge transfer for ecosystem-specific management and restoration, globally standardized ecosystem risk assessments, natural capital accounting and progress on the post-2020 global biodiversity framework. Abstract
Silveira FAO, Ordonez-Parra CA, Moura LC, Schmidt IB, Andersen AN, Bond W, Buisson E, Durigan G, Fidelis A, Oliveira RS, et al
(2022). Biome Awareness Disparity is BAD for tropical ecosystem conservation and restoration. JOURNAL OF APPLIED ECOLOGY
(8), 1967-1975. Author URL
Forrister DL, Endara M, Soule AJ, Younkin GC, Mills AG, Lokvam J, Dexter KG, Pennington RT, Kidner CA, Nicholls JA, et al (2022). Diversity and divergence: evolution of secondary metabolism in the tropical tree genus. <i>Inga</i>. New Phytologist, 237(2), 631-642.
Rickenback J, Pennington RT, Lehmann CER (2022). Diversity in habit expands the environmental niche of. <i>Ziziphus</i>. (Rhamnaceae). Biotropica, 54(5), 1285-1299.
Lewis K, Barros FDV, Moonlight PW, Hill TC, Oliveira RS, Schmidt IB, Sampaio AB, Pennington RT, Rowland L
(2022). Identifying hotspots for ecosystem restoration across heterogeneous tropical savannah-dominated regions. Philosophical Transactions of the Royal Society B: Biological Sciences
Identifying hotspots for ecosystem restoration across heterogeneous tropical savannah-dominated regions
. There is high potential for ecosystem restoration across tropical savannah-dominated regions, but the benefits that could be gained from this restoration are rarely assessed. This study focuses on the Brazilian Cerrado, a highly species-rich savannah-dominated region, as an exemplar to review potential restoration benefits using three metrics: net biomass gains, plant species richness and ability to connect restored and native vegetation. Localized estimates of the most appropriate restoration vegetation type (grassland, savannah, woodland/forest) for pasturelands are produced. Carbon sequestration potential is significant for savannah and woodland/forest restoration in the seasonally dry tropics (net biomass gains of 58.2 ± 37.7 and 130.0 ± 69.4 Mg ha
. ). Modelled restoration species richness gains were highest in the central and south-east of the Cerrado for savannahs and grasslands, and in the west and north-west for woodlands/forests. The potential to initiate restoration projects across the whole of the Cerrado is high and four hotspot areas are identified. We demonstrate that landscape restoration across all vegetation types within heterogeneous tropical savannah-dominated regions can maximize biodiversity and carbon gains. However, conservation of existing vegetation is essential to minimizing the cost and improving the chances of restoration success.
. This article is part of the theme issue ‘Understanding forest landscape restoration: reinforcing scientific foundations for the UN Decade on Ecosystem Restoration’.
Pérez-Escobar OA, Zizka A, Bermúdez MA, Meseguer AS, Condamine FL, Hoorn C, Hooghiemstra H, Pu Y, Bogarín D, Boschman LM, et al (2022). The Andes through time: evolution and distribution of Andean floras. Trends in Plant Science, 27(4), 364-378.
Fernandes MF, Cardoso D, Pennington RT, de Queiroz LP
(2022). The Origins and Historical Assembly of the Brazilian Caatinga Seasonally Dry Tropical Forests. Frontiers in Ecology and Evolution
The Origins and Historical Assembly of the Brazilian Caatinga Seasonally Dry Tropical Forests
The Brazilian Caatinga is considered the richest nucleus of the Seasonally Dry Tropical Forests (SDTF) in the Neotropics, also exhibiting high levels of endemism, but the timing of origin and the evolutionary causes of its plant diversification are still poorly understood. In this study, we integrate comprehensive sampled dated molecular phylogenies of multiple flowering plant groups and estimations of ancestral areas to elucidate the forces driving diversification and historical assembly in the Caatinga flowering plants. Our results show a pervasive floristic exchange between Caatinga and other neotropical regions, particularly those adjacent. While some Caatinga lineages arose in the Eocene/Oligocene, most dry-adapted endemic plant lineages found in region emerged from the middle to late Miocene until the Pleistocene, indicating that only during this period the Caatinga started to coalesce into a SDTF like we see today. Our findings are temporally congruent with global and regional aridification events and extensive denudation of thick layers of sediments in Northeast (NE) Brazil. We hypothesize that global aridification processes have played important role in the ancient plant assembly and long-term Caatinga SDTF biome stability, whereas climate-induced vegetation shifts, as well as the newly opened habitats have largely contributed as drivers of in situ diversification in the region. Patterns of phylogenetic relatedness of Caatinga endemic clades revealed that much modern species diversity has originated in situ and likely evolved via recent (Pliocene/Pleistocene) ecological specialization triggered by increased environmental heterogeneity and the exhumation of edaphically disparate substrates. The continuous assembly of dry-adapted flora of the Caatinga has been complex, adding to growing evidence that the origins and historical assembly of the distinct SDTF patches are idiosyncratic across the Neotropics, driven not just by continental-scale processes but also by unique features of regional-scale geological history. Abstract
Endara M-J, Soule AJ, Forrister DL, Dexter KG, Pennington RT, Nicholls JA, Loiseau O, Kursar TA, Coley PD
(2022). The role of plant secondary metabolites in shaping regional and local plant community assembly. JOURNAL OF ECOLOGY
(1), 34-45. Author URL
Bacon CD, Gutierrez-Pinto N, Flantua S, Castellanos Suarez D, Jaramillo C, Pennington RT, Antonelli A
(2022). The seasonally dry tropical forest species Cavanillesia chicamochae has a middle Quaternary origin. BIOTROPICA
(1), 91-99. Author URL
Silva MC, Moonlight P, Oliveira RS, Pennington RT, Rowland L
(2022). Toward diverse seed sourcing to upscale ecological restoration in the Brazilian Cerrado. Frontiers in Ecology and Evolution
Toward diverse seed sourcing to upscale ecological restoration in the Brazilian Cerrado
Seed markets are vital to scaling up ecosystem restoration in the Brazilian Cerrado, home of the world’s most species-rich grasslands and savannas. We compiled lists of species traded by four major Cerrado seed supply systems to investigate the representativeness of the species currently available for seed-based restoration. We also identified whether dominant ground-layer species are being sourced for seed production. Seeds from 263 Cerrado species can be purchased for restoration, of which 68% are trees, particularly legumes (24%). 63% of the traded species were found in only one seed supply system. The five most dominant graminoids of the Cerrado ground layer were available for sale, but two additional species uncommon in old-growth areas represented 44% of the sales of a key seed trader in Central Brazil. The expansion of Cerrado seed supply systems should be supported to further increase the number of species on the market. Sourcing seeds from a diversity of herbaceous species is central to facilitating the restoration of species-rich grasslands and savannas in the Cerrado. Recovering the diversity and functioning of old-growth open ecosystems through seeds will depend on increasing the supply and demand for species typical of Cerrado’s ground layer. Abstract
Serrano J, Richardson JE, Milne RI, Mondragon GA, Hawkins JA, Bartish IV, Gonzalez M, Chave J, Madriñán S, Cárdenas D, et al
(2021). Andean orogeny and the diversification of lowland neotropical rain forest trees: a case study in Sapotaceae. Global and Planetary Change
Andean orogeny and the diversification of lowland neotropical rain forest trees: a case study in Sapotaceae
Understanding how species diversify and evolve in species-rich areas like the lowland rain forest in the Neotropics is critical for conservation in times of unprecedented threats. To determine how the Andean uplift, the formation of the Panama land bridge, and Pleistocene climatic fluctuations affected dispersal and diversification in the Sapotaceae subfamily Chrysophylloideae, we collected 146 Chrysophylloideae accessions in previously under-explored areas, generating one of the most geographically complete data sets for neotropical Sapotaceae. Sapotaceae is a good model to test diversification hypotheses in lowland neotropical rain forests as it predominantly occurs Abstract
Cardoso D, Moonlight PW, Ramos G, Oatley G, Dudley C, Gagnon E, Queiroz LPD, Pennington RT, Särkinen TE
(2021). Defining Biologically Meaningful Biomes Through Floristic, Functional, and Phylogenetic Data. Frontiers in Ecology and Evolution
Defining Biologically Meaningful Biomes Through Floristic, Functional, and Phylogenetic Data
While we have largely improved our understanding on what biomes are and their utility in global change ecology, conservation planning, and evolutionary biology is clear, there is no consensus on how biomes should be delimited or mapped. Existing methods emphasize different aspects of biomes, with different strengths and limitations. We introduce a novel approach to biome delimitation and mapping, based upon combining individual regionalizations derived from floristic, functional, and phylogenetic data linked to environmentally trained species distribution models. We define “core Biomes” as areas where independent regionalizations agree and “transition zones” as those whose biome identity is not corroborated by all analyses. We apply this approach to delimiting the neglected Caatinga seasonally dry tropical forest biome in northeast Brazil. We delimit the “core Caatinga” as a smaller and more climatically limited area than previous definitions, and argue it represents a floristically, functionally, and phylogenetically coherent unit within the driest parts of northeast Brazil. “Caatinga transition zones” represent a large and biologically important area, highlighting that ecological and evolutionary processes work across environmental gradients and that biomes are not categorical variables. We discuss the differences among individual regionalizations in an ecological and evolutionary context and the potential limitations and utility of individual and combined biome delimitations. Our integrated ecological and evolutionary definition of the Caatinga and associated transition zones are argued to best describe and map biologically meaningful biomes. Abstract
Schley RJ, Twyford AD, Pennington RT (2021). Hybridization: a ‘double-edged sword’ for Neotropical plant diversity. Botanical Journal of the Linnean Society, 199(1).
Oliveira-Filho AT, Dexter KG, Pennington RT, Simon MF, Bueno ML, Neves DM
(2021). On the floristic identity of Amazonian vegetation types. Biotropica
On the floristic identity of Amazonian vegetation types
The Amazon forest is far from uniform, containing different forest types and even savannas, but quantitative analyses of this variation are lacking. Here, we applied ordination analyses to test the floristic differentiation among Amazonian vegetation types using data for virtually all known tree species occurring in the Amazon (8224), distributed across 1584 sites. We also performed multiple regressions to assess the role of climate and substrate in shaping continental-scale patterns of community composition across Amazonia. We find that the traditional classification of Amazonian vegetation types is consistent with quantitative patterns of tree species composition. High elevation and the extremes of substrate-related factors underpin the floristic segregation of environmentally “marginal” vegetation types and terra firme forests with climatic factors being relatively unimportant. These patterns hold at continental scales, with sites of similar vegetation types showing higher similarity between them regardless of geographic distance, which contrasts with the idea of large-scale variation among geographic regions (e.g. between the Guiana Shield and southwestern Amazon) representing the dominant floristic pattern in the Amazon. In contrast to other tropical biomes in South America, including the Mata Atlântica (second largest rain forest biome in the neotropics), the main floristic units in the Amazon are not geographically separated, but are edaphically driven and spatially interdigitated across Amazonia. Two thirds of terra firme tree species are restricted to this vegetation type, while among marginal vegetation types, only white-sand forests (campinaranas) have a substantial proportion of restricted species, with other vegetation types sharing large numbers of species. Abstract
Pezzini FF, Dexter KG, De Carvalho-Sobrinho JG, Kidner CA, Nicholls JA, De Queiroz LP, Pennington RT (2021). Phylogeny and biogeography of Ceiba Mill. (Malvaceae, Bombacoideae). Frontiers of Biogeography, 13(2).
Pennington RT, Baker TR (2021). Plants, people and long-term ecological monitoring in the tropics. Plants People Planet, 3(3), 222-228.
Pilon NAL, Durigan G, Rickenback J, Pennington RT, Dexter KG, Hoffmann WA, Abreu RCR, Lehmann CER
(2021). Shade alters savanna grass layer structure and function along a gradient of canopy cover. Journal of Vegetation Science
Shade alters savanna grass layer structure and function along a gradient of canopy cover
Aim: in savannas, a grass-dominated ground layer is key to ecosystem function via grass–fire feedbacks that maintain open ecosystems. With woody encroachment, tree density increases, thereby decreasing light in the ground layer and potentially altering ecosystem function. We investigated how light availability can filter individual grass species distributions and whether different functional traits are associated with response to a shade gradient in a landscape experiencing woody encroachment. Location: Savanna–forest mosaic in the Cerrado domain, southeastern Brazil. Methods: Along an encroachment gradient of increasing tree leaf area index (LAI) and shade, we determined how changing light availability alters grass diversity and ground layer structure relative to grass cover and grass functional traits (photosynthetic pathway, underground storage organs, bud protection and traits related to grass shape, size and leaf dimensions). Results: Increasing shade led to a decrease in grass cover and grass species richness, and also compositional and functional changes. We found that where tree LAI reached 1, grass cover was reduced by 50% and species richness by 30%. While C4 grass species abundances decreased with increasing shade, the opposite pattern was true for C3 grasses. There were only small differences in light preferences among C4 subtypes, with phosphoenolpyruvate carboxykinase (PCK) species tolerating slightly more shaded conditions. Persistence of some C4 species under more shaded conditions was possible, likely due to an ability to store starch reserves via underground storage organs. Conclusions: Woody encroachment changes diversity and structure of the grassy layer that is critical to the functioning of savanna ecosystems, highlighting the dependence of the diverse grass layer on open and sunny conditions. Our results suggest a threshold of tree cover close to LAI ≈ 1 as being critical to cerrado grassy layer conservation. Abstract
Pos E, de Souza Coelho L, de Andrade Lima Filho D, Salomão RP, Amaral IL, de Almeida Matos FD, Castilho CV, Phillips OL, Guevara JE, de Jesus Veiga Carim M, et al (2021). Unraveling Amazon tree community assembly using Maximum Information Entropy: a quantitative analysis of tropical forest ecology.
Ter Steege H, Prado PI, Lima RAFD, Pos E, de Souza Coelho L, de Andrade Lima Filho D, Salomão RP, Amaral IL, de Almeida Matos FD, Castilho CV, et al
(2020). Biased-corrected richness estimates for the Amazonian tree flora. Sci Rep
Biased-corrected richness estimates for the Amazonian tree flora.
Amazonian forests are extraordinarily diverse, but the estimated species richness is very much debated. Here, we apply an ensemble of parametric estimators and a novel technique that includes conspecific spatial aggregation to an extended database of forest plots with up-to-date taxonomy. We show that the species abundance distribution of Amazonia is best approximated by a logseries with aggregated individuals, where aggregation increases with rarity. By averaging several methods to estimate total richness, we confirm that over 15,000 tree species are expected to occur in Amazonia. We also show that using ten times the number of plots would result in an increase to just ~50% of those 15,000 estimated species. To get a more complete sample of all tree species, rigorous field campaigns may be needed but the number of trees in Amazonia will remain an estimate for years to come. Abstract
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Neves DM, Dexter KG, Baker TR, Coelho de Souza F, Oliveira-Filho AT, Queiroz LP, Lima HC, Simon MF, Lewis GP, Segovia RA, et al
(2020). Evolutionary diversity in tropical tree communities peaks at intermediate precipitation. Scientific Reports
Evolutionary diversity in tropical tree communities peaks at intermediate precipitation
Global patterns of species and evolutionary diversity in plants are primarily determined by a temperature gradient, but precipitation gradients may be more important within the tropics, where plant species richness is positively associated with the amount of rainfall. The impact of precipitation on the distribution of evolutionary diversity, however, is largely unexplored. Here we detail how evolutionary diversity varies along precipitation gradients by bringing together a comprehensive database on the composition of angiosperm tree communities across lowland tropical South America (2,025 inventories from wet to arid biomes), and a new, large-scale phylogenetic hypothesis for the genera that occur in these ecosystems. We find a marked reduction in the evolutionary diversity of communities at low precipitation. However, unlike species richness, evolutionary diversity does not continually increase with rainfall. Rather, our results show that the greatest evolutionary diversity is found in intermediate precipitation regimes, and that there is a decline in evolutionary diversity above 1,490 mm of mean annual rainfall. If conservation is to prioritise evolutionary diversity, areas of intermediate precipitation that are found in the South American ‘arc of deforestation’, but which have been neglected in the design of protected area networks in the tropics, merit increased conservation attention. Abstract
Moonlight PW, Banda‐R K, Phillips OL, Dexter KG, Pennington RT, Baker TR, C. de Lima H, Fajardo L, González‐M. R, Linares‐Palomino R, et al (2020). Expanding tropical forest monitoring into Dry Forests: the DRYFLOR protocol for permanent plots. PLANTS, PEOPLE, PLANET, 3(3), 295-300.
Segovia RA, Pennington RT, Baker TR, Coelho de Souza F, Neves DM, Davis CC, Armesto JJ, Olivera-Filho AT, Dexter KG
(2020). Freezing and water availability structure the evolutionary diversity of trees across the Americas. Science Advances
Freezing and water availability structure the evolutionary diversity of trees across the Americas
Freezing temperatures and water availability shape the distribution of evolutionary lineages of angiosperm trees in the Americas. Abstract
Koenen EJM, Kidner C, de Souza ÉR, Simon MF, Iganci JR, Nicholls JA, Brown GK, de Queiroz LP, Luckow M, Lewis GP, et al
(2020). Hybrid capture of 964 nuclear genes resolves evolutionary relationships in the mimosoid legumes and reveals the polytomous origins of a large pantropical radiation. American Journal of Botany
Hybrid capture of 964 nuclear genes resolves evolutionary relationships in the mimosoid legumes and reveals the polytomous origins of a large pantropical radiation
PREMISE: Targeted enrichment methods facilitate sequencing of hundreds of nuclear loci to enhance phylogenetic resolution and elucidate why some parts of the “tree of life” are difficult (if not impossible) to resolve. The mimosoid legumes are a prominent pantropical clade of ~3300 species of woody angiosperms for which previous phylogenies have shown extensive lack of resolution, especially among the species-rich and taxonomically challenging ingoids. METHODS: We generated transcriptomes to select low-copy nuclear genes, enrich these via hybrid capture for representative species of most mimosoid genera, and analyze the resulting data using de novo assembly and various phylogenomic tools for species tree inference. We also evaluate gene tree support and conflict for key internodes and use phylogenetic network analysis to investigate phylogenetic signal across the ingoids. RESULTS: Our selection of 964 nuclear genes greatly improves phylogenetic resolution across the mimosoid phylogeny and shows that the ingoid clade can be resolved into several well-supported clades. However, nearly all loci show lack of phylogenetic signal for some of the deeper internodes within the ingoids. CONCLUSIONS: Lack of resolution in the ingoid clade is most likely the result of hyperfast diversification, potentially causing a hard polytomy of six or seven lineages. The gene set for targeted sequencing presented here offers great potential to further enhance the phylogeny of mimosoids and the wider Caesalpinioideae with denser taxon sampling, to provide a framework for taxonomic reclassification, and to study the ingoid radiation. Abstract
Schley RJ, Pennington RT, Pérez-Escobar OA, Helmstetter AJ, de la Estrella M, Larridon I, Sabino Kikuchi IAB, Barraclough TG, Forest F, Klitgård B, et al
(2020). Introgression across evolutionary scales suggests reticulation contributes to Amazonian tree diversity. Mol Ecol
Introgression across evolutionary scales suggests reticulation contributes to Amazonian tree diversity.
Hybridization has the potential to generate or homogenize biodiversity and is a particularly common phenomenon in plants, with an estimated 25% of plant species undergoing interspecific gene flow. However, hybridization in Amazonia's megadiverse tree flora was assumed to be extremely rare despite extensive sympatry between closely related species, and its role in diversification remains enigmatic because it has not yet been examined empirically. Using members of a dominant Amazonian tree family (Brownea, Fabaceae) as a model to address this knowledge gap, our study recovered extensive evidence of hybridization among multiple lineages across phylogenetic scales. More specifically, using targeted sequence capture our results uncovered several historical introgression events between Brownea lineages and indicated that gene tree incongruence in Brownea is best explained by reticulation, rather than solely by incomplete lineage sorting. Furthermore, investigation of recent hybridization using ~19,000 ddRAD loci recovered a high degree of shared variation between two Brownea species that co-occur in the Ecuadorian Amazon. Our analyses also showed that these sympatric lineages exhibit homogeneous rates of introgression among loci relative to the genome-wide average, implying a lack of selection against hybrid genotypes and persistent hybridization. Our results demonstrate that gene flow between multiple Amazonian tree species has occurred across temporal scales, and contrasts with the prevailing view of hybridization's rarity in Amazonia. Overall, our results provide novel evidence that reticulate evolution influenced diversification in part of the Amazonian tree flora, which is the most diverse on Earth. Abstract
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Koenen EJM, Ojeda DI, Steeves R, Migliore J, Bakker FT, Wieringa JJ, Kidner C, Hardy OJ, Pennington RT, Bruneau A, et al
(2020). Large-scale genomic sequence data resolve the deepest divergences in the legume phylogeny and support a near-simultaneous evolutionary origin of all six subfamilies. New Phytol
Large-scale genomic sequence data resolve the deepest divergences in the legume phylogeny and support a near-simultaneous evolutionary origin of all six subfamilies.
Phylogenomics is increasingly used to infer deep-branching relationships while revealing the complexity of evolutionary processes such as incomplete lineage sorting, hybridization/introgression and polyploidization. We investigate the deep-branching relationships among subfamilies of the Leguminosae (or Fabaceae), the third largest angiosperm family. Despite their ecological and economic importance, a robust phylogenetic framework for legumes based on genome-scale sequence data is lacking. We generated alignments of 72 chloroplast genes and 7621 homologous nuclear-encoded proteins, for 157 and 76 taxa, respectively. We analysed these with maximum likelihood, Bayesian inference, and a multispecies coalescent summary method, and evaluated support for alternative topologies across gene trees. We resolve the deepest divergences in the legume phylogeny despite lack of phylogenetic signal across all chloroplast genes and the majority of nuclear genes. Strongly supported conflict in the remainder of nuclear genes is suggestive of incomplete lineage sorting. All six subfamilies originated nearly simultaneously, suggesting that the prevailing view of some subfamilies as 'basal' or 'early-diverging' with respect to others should be abandoned, which has important implications for understanding the evolution of legume diversity and traits. Our study highlights the limits of phylogenetic resolution in relation to rapid successive speciation. Abstract
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Draper FC, Baker TR, Baraloto C, Chave J, Costa F, Martin RE, Pennington RT, Vicentini A, Asner GP
(2020). Quantifying Tropical Plant Diversity Requires an Integrated Technological Approach. Trends Ecol Evol
Quantifying Tropical Plant Diversity Requires an Integrated Technological Approach.
Tropical biomes are the most diverse plant communities on Earth, and quantifying this diversity at large spatial scales is vital for many purposes. As macroecological approaches proliferate, the taxonomic uncertainties in species occurrence data are easily neglected and can lead to spurious findings in downstream analyses. Here, we argue that technological approaches offer potential solutions, but there is no single silver bullet to resolve uncertainty in plant biodiversity quantification. Instead, we propose the use of artificial intelligence (AI) approaches to build a data-driven framework that integrates several data sources - including spectroscopy, DNA sequences, image recognition, and morphological data. Such a framework would provide a foundation for improving species identification in macroecological analyses while simultaneously improving the taxonomic process of species delimitation. Abstract
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Koenen EJM, Ojeda DI, Bakker FT, Wieringa JJ, Kidner C, Hardy OJ, Pennington RT, Herendeen PS, Bruneau A, Hughes CE, et al
(2020). The Origin of the Legumes is a Complex Paleopolyploid Phylogenomic Tangle Closely Associated with the Cretaceous–Paleogene (K–Pg) Mass Extinction Event. Systematic Biology
The Origin of the Legumes is a Complex Paleopolyploid Phylogenomic Tangle Closely Associated with the Cretaceous–Paleogene (K–Pg) Mass Extinction Event
. The consequences of the Cretaceous–Paleogene (K–Pg) boundary (KPB) mass extinction for the evolution of plant diversity remain poorly understood, even though evolutionary turnover of plant lineages at the KPB is central to understanding assembly of the Cenozoic biota. The apparent concentration of whole genome duplication (WGD) events around the KPB may have played a role in survival and subsequent diversification of plant lineages. To gain new insights into the origins of Cenozoic biodiversity, we examine the origin and early evolution of the globally diverse legume family (Leguminosae or Fabaceae). Legumes are ecologically (co-)dominant across many vegetation types, and the fossil record suggests that they rose to such prominence after the KPB in parallel with several well-studied animal clades including Placentalia and Neoaves. Furthermore, multiple WGD events are hypothesized to have occurred early in legume evolution. Using a recently inferred phylogenomic framework, we investigate the placement of WGDs during early legume evolution using gene tree reconciliation methods, gene count data and phylogenetic supernetwork reconstruction. Using 20 fossil calibrations we estimate a revised timeline of legume evolution based on 36 nuclear genes selected as informative and evolving in an approximately clock-like fashion. To establish the timing of WGDs we also date duplication nodes in gene trees. Results suggest either a pan-legume WGD event on the stem lineage of the family, or an allopolyploid event involving (some of) the earliest lineages within the crown group, with additional nested WGDs subtending subfamilies Papilionoideae and Detarioideae. Gene tree reconciliation methods that do not account for allopolyploidy may be misleading in inferring an earlier WGD event at the time of divergence of the two parental lineages of the polyploid, suggesting that the allopolyploid scenario is more likely. We show that the crown age of the legumes dates to the Maastrichtian or early Paleocene and that, apart from the Detarioideae WGD, paleopolyploidy occurred close to the KPB. We conclude that the early evolution of the legumes followed a complex history, in which multiple auto- and/or allopolyploidy events coincided with rapid diversification and in association with the mass extinction event at the KPB, ultimately underpinning the evolutionary success of the Leguminosae in the Cenozoic. [Allopolyploidy; Cretaceous–Paleogene (K–Pg) boundary; Fabaceae, Leguminosae; paleopolyploidy; phylogenomics; whole genome duplication events]
Amador-Jiménez M, Millner N, Palmer C, Pennington RT, Sileci L
(2020). The Unintended Impact of Colombia’s Covid-19 Lockdown on Forest Fires. Environmental and Resource Economics
The Unintended Impact of Colombia’s Covid-19 Lockdown on Forest Fires
AbstractThe covid-19 pandemic led to rapid and large-scale government intervention in economies and societies. A common policy response to covid-19 outbreaks has been the lockdown or quarantine. Designed to slow the spread of the disease, lockdowns have unintended consequences for the environment. This article examines the impact of Colombia’s lockdown on forest fires, motivated by satellite data showing a particularly large upsurge of fires at around the time of lockdown implementation. We find that Colombia’s lockdown is associated with an increase in forest fires compared to three different counterfactuals, constructed to simulate the expected number of fires in the absence of the lockdown. To varying degrees across Colombia’s regions, the presence of armed groups is correlated with this fire upsurge. Mechanisms through which the lockdown might influence fire rates are discussed, including the mobilisation of armed groups and the reduction in the monitoring capacity of state and conservation organisations during the covid-19 outbreak. Given the fast-developing situation in Colombia, we conclude with some ideas for further research. Abstract
Cardoso D, Moonlight PW, de Miranda PLS, Dexter KG, Oliveira-Filho AT, Pennington RT, Ramos G, Sarkinen TE
(2020). The strengths and weaknesses of species distribution models in biome delimitation. GLOBAL ECOLOGY AND BIOGEOGRAPHY
(10), 1770-1784. Author URL
Zizka A, Carvalho-Sobrinho JG, Pennington RT, Queiroz LP, Alcantara S, Baum DA, Bacon CD, Antonelli A
(2020). Transitions between biomes are common and directional in Bombacoideae (Malvaceae). Journal of Biogeography
Transitions between biomes are common and directional in Bombacoideae (Malvaceae)
Aim: to quantify evolutionary transitions between tropical evergreen rain forest and seasonally dry biomes, to test whether biome transitions affect lineage diversification and to examine the robustness of these results to methodological choices. Location: the tropics. Time period: the Cenozoic. Major taxa studied: the plant subfamily Bombacoideae (Malvaceae). Methods: We inferred ancestral biomes based on a fossil-dated molecular phylogeny of 103 species (59% of the clade) and recorded the number of transitions among biomes using biogeographical stochastic mapping based on the dispersal-extinction-cladogenesis model. We then estimated diversification rates using state-specific speciation and extinction rate (SSE) methods. Furthermore, we tested the sensitivity of the results to model choice, phylogenetic uncertainty, measurement error and biome definition. Results: We found numerous transitions from evergreen rain forest to seasonally dry biomes, and fewer in the opposite direction. These results were robust to methodological choices. Biome type did not influence diversification rates, although this result was subject to uncertainty, especially related to model choice and biome definition. Main conclusions: Our results contradict the idea of evolutionary biome conservatism in Bombacoideae, and support previous findings that evergreen rain forests serve as a source for the flora of seasonally dry biomes. The impact of biome classification and biome definition on the results suggest caution when using a biome concept for biogeographical reconstruction and diversification rate analysis. Abstract
Honorio Coronado EN, Dexter KG, Hart ML, Phillips OL, Pennington RT
(2019). Comparative phylogeography of five widespread tree species: Insights into the history of western Amazonia. Ecology and Evolution
Comparative phylogeography of five widespread tree species: Insights into the history of western Amazonia
Various historical processes have been put forth as drivers of patterns in the spatial distribution of Amazonian trees and their population genetic variation. We tested whether five widespread tree species show congruent phylogeographic breaks and similar patterns of demographic expansion, which could be related to proposed Pleistocene refugia or the presence of geological arches in western Amazonia. We sampled Otoba parvifolia/glycycarpa (Myristicaceae), Clarisia biflora, Poulsenia armata, Ficus insipida (all Moraceae), and Jacaratia digitata (Caricaceae) across the western Amazon Basin. Plastid DNA (trnH–psbA; 674 individuals from 34 populations) and nuclear ribosomal internal transcribed spacers (ITS; 214 individuals from 30 populations) were sequenced to assess genetic diversity, genetic differentiation, population genetic structure, and demographic patterns. Overall genetic diversity for both markers varied among species, with higher values in populations of shade-tolerant species than in pioneer species. Spatial analysis of molecular variance (SAMOVA) identified three genetically differentiated groups for the plastid marker for each species, but the areas of genetic differentiation were not concordant among species. Fewer SAMOVA groups were found for ITS, with no detectable genetic differentiation among populations in pioneers. The lack of spatially congruent phylogeographic breaks across species suggests no common biogeographic history of these Amazonian tree species. The idiosyncratic phylogeographic patterns of species could be due instead to species-specific responses to geological and climatic changes. Population genetic patterns were similar among species with similar biological features, indicating that the ecological characteristics of species impact large-scale phylogeography. Abstract
Coelho de Souza F, Dexter KG, Phillips OL, Pennington RT, Neves D, Sullivan MJP, Alvarez-Davila E, Alves Á, Amaral I, Andrade A, et al
(2019). Evolutionary diversity is associated with wood productivity in Amazonian forests. Nat Ecol Evol
Evolutionary diversity is associated with wood productivity in Amazonian forests.
Higher levels of taxonomic and evolutionary diversity are expected to maximize ecosystem function, yet their relative importance in driving variation in ecosystem function at large scales in diverse forests is unknown. Using 90 inventory plots across intact, lowland, terra firme, Amazonian forests and a new phylogeny including 526 angiosperm genera, we investigated the association between taxonomic and evolutionary metrics of diversity and two key measures of ecosystem function: aboveground wood productivity and biomass storage. While taxonomic and phylogenetic diversity were not important predictors of variation in biomass, both emerged as independent predictors of wood productivity. Amazon forests that contain greater evolutionary diversity and a higher proportion of rare species have higher productivity. While climatic and edaphic variables are together the strongest predictors of productivity, our results show that the evolutionary diversity of tree species in diverse forest stands also influences productivity. As our models accounted for wood density and tree size, they also suggest that additional, unstudied, evolutionarily correlated traits have significant effects on ecosystem function in tropical forests. Overall, our pan-Amazonian analysis shows that greater phylogenetic diversity translates into higher levels of ecosystem function: tropical forest communities with more distantly related taxa have greater wood productivity. Abstract
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Dick CW, Pennington RT
(2019). History and Geography of Neotropical Tree Diversity. Annual Review of Ecology, Evolution, and Systematics
History and Geography of Neotropical Tree Diversity
Early botanical explorers invoked biogeographic history to explain the remarkable tree diversity of Neotropical forests. In this context, we review the history of Neotropical tree diversity over the past 100 million years, focusing on biomes with significant tree diversity. We evaluate hypotheses for rain forest origins, intercontinental disjunctions, and models of Neotropical tree diversification. To assess the impact of biotic interchange on the Amazon tree flora, we examined biogeographic histories of trees in Ecuador's Yasuní Forest, which suggest that nearly 50% of its species descend from immigrant lineages that colonized South America during the Cenozoic. Long-distance and intercontinental dispersal, combined with trait filtering and niche evolution, are important factors in the community assembly of Neotropical forests. We evaluate the role of pre-Columbian people on Neotropical tree diversity and discuss the future of Neotropical forests in the Anthropocene. Abstract
Coley PD, Endara M-J, Ghabash G, Kidner CA, Nicholls JA, Pennington T, Mills AG, Soule AJ, Stone GN, Lemes MR, et al (2019). Macroevolutionary patterns in overexpression of tyrosine: an anti‐herbivore defence in a speciose tropical tree genus, Inga
(Fabaceae). Journal of Ecology
ter Steege H, Henkel TW, Helal N, Marimon BS, Marimon-Junior BH, Huth A, Groeneveld J, Sabatier D, Coelho LDS, Filho DDAL, et al
(2019). Rarity of monodominance in hyperdiverse Amazonian forests. Scientific Reports
Rarity of monodominance in hyperdiverse Amazonian forests
Tropical forests are known for their high diversity. Yet, forest patches do occur in the tropics where a single tree species is dominant. Such “monodominant” forests are known from all of the main tropical regions. For Amazonia, we sampled the occurrence of monodominance in a massive, basin-wide database of forest-inventory plots from the Amazon Tree Diversity Network (ATDN). Utilizing a simple defining metric of at least half of the trees ≥ 10 cm diameter belonging to one species, we found only a few occurrences of monodominance in Amazonia, and the phenomenon was not significantly linked to previously hypothesized life history traits such wood density, seed mass, ectomycorrhizal associations, or Rhizobium nodulation. In our analysis, coppicing (the formation of sprouts at the base of the tree or on roots) was the only trait significantly linked to monodominance. While at specific locales coppicing or ectomycorrhizal associations may confer a considerable advantage to a tree species and lead to its monodominance, very few species have these traits. Mining of the ATDN dataset suggests that monodominance is quite rare in Amazonia, and may be linked primarily to edaphic factors. Abstract
da Cruz DT, Idarraga A, Banda K, Cogollo A, van den Berg C, de Queiroz L, Pennington T, Lavin M, Cardoso D (2018). Ancient speciation of the papilionoid legume Luetzelburgia jacana,
a newly discovered species in an inter-Andean seasonally dry valley
of Colombia. Taxon
Pennington T, de Lima HC, Inches F, Watherston N (2018). Andira anthelmia. Curtis Botanical Magazine, 35, 125-133.
Endara M, Coley PD, Wiggins NL, Forrister DL, Younkin GC, Nicholls JA, Pennington RT, Dexter KG, Kidner CA, Stone GN, et al (2018). Chemocoding as an identification tool where morphological‐ and. <scp>DNA</scp>. ‐based methods fall short:. <i>Inga</i>. as a case study. New Phytologist, 218(2), 847-858.
Lavin M, Pennington T, Hughes CE, Lewis GP, Delgado-Salinas A, Duno de Stefano R, de Queiroz LP, Cardoso D, Wojciechowski MF (2018). DNA Sequence Variation among Conspecific Accessions of the Legume Coursetia caribaea Reveals Geographically Localized Clades Here Ranked as Species. Systematic Botany, 43, 664-675.
Dexter KG, Pennington T, Oliveira-Filho AT, Bueno ML, Silva de Miranda PL, Neves D (2018). Inserting Tropical Dry Forests into the Discussion on Biome Transitions in the Tropics. Frontiers in Ecology and Evolution
Neves DM, Dexter KG, Pennington RT, Bueno ML, de Miranda PLS, Oliveira-Filho AT
(2018). Lack of floristic identity in campos rupestres—A hyperdiverse mosaic of rocky montane savannas in South America. Flora: Morphology, Distribution, Functional Ecology of Plants
Lack of floristic identity in campos rupestres—A hyperdiverse mosaic of rocky montane savannas in South America
The rocky montane savannas of South America, known as campos rupestres in Brazil, where they largely occur, represent a hyperdiverse habitat housing c.15% of the Brazilian vascular flora in less than 1% of the Brazilian territory. Amongst other factors, the remarkable plant diversity in campos rupestres has been attributed to its occurrence as many isolated patches and to floristic influences from surrounding habitats, including lowland woody savannas (cerrado), Atlantic rain forests, seasonally dry woodlands and Amazonian rain forests. However, no study has assessed the degree to which the putative floristic influence from surrounding habitats drives compositional variation in campos rupestres. Here, we used a dataset on the composition of South American woody plant communities (4,637 community surveys, with 115 representing campos rupestres), combined with environmental data, with the aim of characterising and explaining compositional variation of the campos rupestres woody flora. Our results showed that all campos rupestres, including the sites occurring in Amazonian ironstone formations, are more similar to cerrado woody savannas than to any other South American vegetation formations covered in our dataset. Also, multiple campo rupestre floristic groups may be recognized based on distinct species composition and environmental conditions, primarily related to substrate and climate. We stress the importance of considering this floristic heterogeneity in conservation, management and research planning. Abstract
Gomes VHF, IJff SD, Raes N, Amaral IL, Salomão RP, de Souza Coelho L, de Almeida Matos FD, Castilho CV, de Andrade Lima Filho D, López DC, et al
(2018). Species Distribution Modelling: Contrasting presence-only models with plot abundance data. Sci Rep
Species Distribution Modelling: Contrasting presence-only models with plot abundance data.
Species distribution models (SDMs) are widely used in ecology and conservation. Presence-only SDMs such as MaxEnt frequently use natural history collections (NHCs) as occurrence data, given their huge numbers and accessibility. NHCs are often spatially biased which may generate inaccuracies in SDMs. Here, we test how the distribution of NHCs and MaxEnt predictions relates to a spatial abundance model, based on a large plot dataset for Amazonian tree species, using inverse distance weighting (IDW). We also propose a new pipeline to deal with inconsistencies in NHCs and to limit the area of occupancy of the species. We found a significant but weak positive relationship between the distribution of NHCs and IDW for 66% of the species. The relationship between SDMs and IDW was also significant but weakly positive for 95% of the species, and sensitivity for both analyses was high. Furthermore, the pipeline removed half of the NHCs records. Presence-only SDM applications should consider this limitation, especially for large biodiversity assessments projects, when they are automatically generated without subsequent checking. Our pipeline provides a conservative estimate of a species' area of occupancy, within an area slightly larger than its extent of occurrence, compatible to e.g. IUCN red list assessments. Abstract
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Nazre M, Newman MF, Pennington T, Middleton D (2018). Taxonomic Revision of Garcinia Section Garcinia (Clusiaceae). Phytotaxa
Bueno ML, Dexter KG, Pennington RT, Pontara V, Neves DM, Ratter JA, de Oliveira-Filho AT (2018). The environmental triangle of the Cerrado Domain: Ecological factors driving shifts in tree species composition between forests and savannas. Journal of Ecology, 106(5), 2109-2120.
Endara M-J, Nicholls J, Coley PD, Forrister DL, Younkin GC, Dexter KG, Kidner CA, Pennington T, Stone G, Kursar TA, et al (2018). Tracking of host defenses and phylogeny during the radiation of neotropical Inga-feeding sawflies. Frontiers in Plant Science
Pennington RT, Lehmann CER, Rowland LM
(2018). Tropical savannas and dry forests. Current Biology
Tropical savannas and dry forests
In the tropics, research, conservation and public attention focus on rain forests, but this neglects that half of the global tropics have a seasonally dry climate. These regions are home to dry forests and savannas (Figures 1 and 2), and are the focus of this Primer. The attention given to rain forests is understandable. Their high species diversity, sheer stature and luxuriance thrill biologists today as much as they did the first explorers in the Age of Discovery. Although dry forest and savanna may make less of a first impression, they support a fascinating diversity of plant strategies to cope with stress and disturbance including fire, drought and herbivory. Savannas played a fundamental role in human evolution, and across Africa and India they support iconic megafauna. Pennington et al. introduce seasonally dry biomes in the tropics – savannahs and dry forests. Abstract
Silva de Miranda P, Oliveira Filho A, Pennington T, Neves D, Baker T, Dexter KG (2018). Using tree species inventories to map biomes and assess their climatic overlaps in lowland tropical South America. Global Ecology and Biogeography, 27, 899-912.
Pennington RT, Quintana C, Ulloa Ulloa C, Balslev H (2017). BIOGEOGRAPHIC BARRIERS IN THE ANDES: IS THE AMOTAPE – HUANCABAMBA ZONE a DISPERSAL BARRIER FOR DRY FOREST PLANTS?. Annals of the Missouri Botanical Garden, 102, 542-550.
Endara M-J, Coley PD, Ghabash G, Nicholls JA, Dexter KG, Donoso DA, Stone GN, Pennington RT, Kursar TA (2017). Coevolutionary arms race versus host defense chase in a tropical herbivore–plant system. Proceedings of the National Academy of Sciences, 114(36), E7499-E7505.
Griffith DM, Lehmann CER, Stromberg CAE, Parr CL, Pennington T, Sankaran M, Ratnam J, Still CJ, Powell RL, Hanan NP, et al (2017). Comment on “The extent of forest in dryland biomes”. Science
Dexter KG, Lavin M, Torke BM, Twyford AD, Kursar TA, Coley PD, Drake C, Hollands R, Pennington RT (2017). Dispersal assembly of rain forest tree communities across the Amazon basin. Proceedings of the National Academy of Sciences, 114(10), 2645-2650.
Toby Pennington R, Lavin M
(2017). Dispersal, isolation and diversification with continued gene flow in an Andean tropical dry forest. Mol Ecol
Dispersal, isolation and diversification with continued gene flow in an Andean tropical dry forest.
The Andes are the world's longest mountain chain, and the tropical Andes are the world's richest biodiversity hot spot. The origin of the tropical Andean cordillera is relatively recent because the elevation of the mountains was relatively low (400-2500 m palaeoelevations) only 10 MYA with final uplift being rapid. These final phases of the Andean orogeny are thought to have had a fundamental role in shaping processes of biotic diversification and biogeography, with these effects reaching far from the mountains themselves by changing the course of rivers and deposition of mineral-rich Andean sediments across the massive Amazon basin. In a recent issue of Molecular Ecology, Oswald, Overcast, Mauck, Andersen, and Smith (2017) investigate the biogeography and diversification of bird species in the Andes of Peru and Ecuador. Their study is novel in its focus on tropical dry forests (Figure 1) rather than more mesic biomes such as rain forests, cloud forests and paramos, which tend to be the focus of science and conservation in the Andean hot spot. It is also able to draw powerful conclusions via the first deployment of genomic approaches to a biogeographic question in the threatened dry forests of the New World. Abstract
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Neves DM, Dexter KG, Pennington RT, Valente ASM, Bueno ML, Eisenlohr PV, Fontes MAL, Miranda PLS, Moreira SN, Rezende VL, et al
(2017). Dissecting a biodiversity hotspot: the importance of environmentally marginal habitats in the Atlantic Forest Domain of South America. Diversity and Distributions
Dissecting a biodiversity hotspot: the importance of environmentally marginal habitats in the Atlantic Forest Domain of South America
Aim: We aimed to assess the contribution of marginal habitats to the tree species richness of the Mata Atlântica (Atlantic Forest) biodiversity hotspot. In addition, we aimed to determine which environmental factors drive the occurrence and distribution of these marginal habitats. Location: the whole extension of the South American Atlantic Forest Domain plus forest intrusions into the neighbouring Cerrado and Pampa Domains, which comprises rain forests (“core” habitat) and five marginal habitats, namely high elevation forests, rock outcrop dwarf-forests, riverine forests, semideciduous forests and restinga (coastal white-sand woodlands). Methods: We compiled a dataset containing 366,875 occurrence records of 4,431 tree species from 1,753 site-checklists, which were a priori classified into 10 main vegetation types. We then performed ordination analyses of the species-by-site matrix to assess the floristic consistency of this classification. In order to assess the relative contribution of environmental predictors to the community turnover, we produced models using 26 climate and substrate-related variables as environmental predictors. Results: Ordination diagrams supported the floristic segregation of vegetation types, with those considered as marginal habitats placed at the extremes of ordination axes. These marginal habitats are associated with the harshest extremes of five limiting factors: temperature seasonality (high elevation and subtropical riverine forests), flammability (rock outcrop dwarf-forests), high salinity (restinga), water deficit severity (semideciduous forests) and waterlogged soils (tropical riverine forests). Importantly, 45% of all species endemic to the Atlantic Domain only occur in marginal habitats. Main conclusions: Our results showed the key role of the poorly protected marginal habitats in contributing to the high species richness of the Atlantic Domain. Various types of environmental harshness operate as environmental filters determining the distribution of the Atlantic Domain habitats. Our findings also stressed the importance of fire, a previously neglected environmental factor. Abstract
Bueno ML, Pennington RT, Dexter KG, Kamino LHY, Pontara V, Neves DM, Ratter JA, de Oliveira-Filho AT
(2017). Effects of Quaternary climatic fluctuations on the distribution of Neotropical savanna tree species. Ecography
Effects of Quaternary climatic fluctuations on the distribution of Neotropical savanna tree species
In order to develop niche models for tree species characteristic of the cerrado vegetation (woody savannas) of central South America, and to hindcast their distributions during the Last Glacial Maximum and Last Inter-Glacial, we compiled a dataset of tree species checklists for typical cerrado vegetation (n = 282) and other geographically co-occurring vegetation types, e.g. seasonally dry tropical forest (n = 355). We then performed an indicator species analysis to select ten species that best characterize typical cerrado vegetation and developed niche models for them using the Maxent algorithm. We used these models to assess the probability of occurrence of each species across South America at the following time slices: Current (0 ka pre-industrial), Holocene (6 ka BP), Last Glacial Maximum (LGM – 21 ka BP), and Last Interglacial (LIG – 130 ka BP). The niche models were robust for all species and showed the highest probability of occurrence in the core area of the Cerrado Domain. The palaeomodels suggested changes in the distributions of cerrado tree species throughout the Quaternary, with expansion during the LIG into the adjacent Amazonian and Atlantic moist forests, as well as connections with other South American savannas. The LGM models suggested a retraction of cerrado vegetation to inter-tableland depressions and slopes of the Central Brazilian Highlands. Contrary to previous hypotheses, such as the Pleistocene refuge theory, we found that the widest expansion of cerrado tree species seems to have occurred during the LIG, most probably due to its warmer climate. On the other hand, the postulated retractions during the LGM were likely related to both decreased precipitation and temperature. These results are congruent with palynological and phylogeographic studies in the Cerrado Domain. Abstract
DRYFLOR, Pennington RT, Banda-R K, Delgado-Salinas A, Dexter KG, Linares-Palomino R, Olivera-Filho A, Prado D, Quintana C, Riina R, et al (2017). Forest conservation: Humans' handprints—Response. Science, 355(6324), 467-467.
DRYFLOR, Pennington RT, Banda-R K, Delgado-Salinas A, Dexter KG, Galetti L, Linares-Palomino R, Maturo HM, Mogni V, Oakley L, et al (2017). Forest conservation: Remember Gran Chaco—Response. Science, 355(6324), 465-466.
Gómez-Gutiérrez MC, Pennington RT, Neaves LE, Milne RI, Madriñán S, Richardson JE (2017). Genetic diversity in the Andes: variation within and between the South American species of Oreobolus R. Br. (Cyperaceae). Alpine Botany, 127(2), 155-170.
Rezende VL, Dexter KG, Pennington RT, Oliveira-Filho AT
(2017). Geographical variation in the evolutionary diversity of tree communities across southern South America. Journal of Biogeography
Geographical variation in the evolutionary diversity of tree communities across southern South America
Aim: to determine the principal drivers of variation in the evolutionary diversity of forest tree communities, with a focus on the temperate forests of South America. Location: Forests across southern South America, extending from tropical forests in southern Brazil, to the temperate forests of southern Chile and Argentina. Methods: We compiled a database of 742 forest tree community inventories spread over six countries and 12 biomes, or major vegetation types. In total, these inventories covered 3075 species of shrubs and trees. We combined this dataset with a temporally calibrated phylogeny that included all species. For each community, we evaluated multiple measures of evolutionary diversity, including phylogenetic diversity sensu stricto (PD), which is the sum of the branch lengths of a phylogeny that includes all species in a community, and its equivalent standardized for variation in species richness (ses.PD), which we refer to as lineage diversity. Results: We found that biome affiliation is the most important determinant of the evolutionary diversity of woody plant communities, with climate also showing a significant influence. Communities in wet evergreen tropical forest have the highest species richness and the highest PD, but the lowest lineage diversity, while temperate forests in southern South America show the lowest species richness and PD, but the highest lineage diversity. Main conclusions: Our results contradict the idea that temperate floras represent recently derived, evolutionarily poor subsets of tropical floras. Rather, the high lineage diversity we find in the temperate forest communities supports the ‘austral conservatism hypothesis’, which states that the flora of southern South america has evolved independently from the Neotropical Domain over tens of millions of years. Our identification of the evolutionary distinctness and richness of this flora suggests that it deserves as much conservation attention as the more species-rich tropical forests of South America and that southern South American forests should not be lumped into the Neotropical Floristic Province. Abstract
Baker TR, Pennington RT, Dexter KG, Fine PVA, Fortune-Hopkins H, Honorio EN, Huamantupa-Chuquimaco I, Klitgård BB, Lewis GP, de Lima HC, et al (2017). Maximising Synergy among Tropical Plant Systematists, Ecologists, and Evolutionary Biologists. Trends in Ecology & Evolution, 32(4), 258-267.
Heckenhauer J, Abu Salim K, Chase MW, Dexter KG, Pennington RT, Tan S, Kaye ME, Samuel R (2017). Plant DNA barcodes and assessment of phylogenetic community structure of a tropical mixed dipterocarp forest in Brunei Darussalam (Borneo). PLOS ONE, 12(10), e0185861-e0185861.
Dunning LT, Liabot A-L, Olofsson JK, Smith EK, Vorontsova MS, Besnard G, Simpson KJ, Lundgren MR, Addicott E, Gallagher RV, et al (2017). The recent and rapid spread of <i>Themeda triandra</i>. Botany Letters, 164(4), 327-337.
García-Villacorta R, Dexter KG, Pennington T
(2016). Amazonian White-Sand Forests Show Strong Floristic Links with Surrounding Oligotrophic Habitats and the Guiana Shield. Biotropica
Amazonian White-Sand Forests Show Strong Floristic Links with Surrounding Oligotrophic Habitats and the Guiana Shield
Amazonian white-sand forests occur on quartzitic sandy soils, are distributed as an archipelago of habitat islands across the rain forests of Amazonia and contain many endemic plant species. Surprisingly, we found that only 23 percent of plant species in western Amazon white-sand forests are white-sand specialists, while the remaining species (77%) also occur in other habitat types. Overall, our analyses revealed: (1) somewhat unexpected composition similarity of white-sand forests with nearby non-white-sand forests; (2) phytogeographical connections among distant white-sand forests; and (3) a large proportion of western Amazon white-sand specialists occurring in floras of the western and central Guiana Shield region (7-43%). These results suggest that dispersal from both neighboring oligotrophic non-white-sand habitats and distant white-sand forests is fundamental in shaping western Amazonian white-sand forests' species composition and diversity. Although endemism in Amazonian white-sand forests may be lower than previously estimated, conservation of this unique and fragile environment should remain a priority. Such conservation will require the maintenance of regional dispersal processes that connect these archipelagos of habitat islands and other ecologically similar oligotrophic habitats across the Amazon and the Guiana Shield. Abstract
Galetti LA, Mogni VY, Oakley LJ, Pennington RT, Prado DE
(2016). Cynophalla polyantha (Capparaceae), new record for the Argentine flora. Boletin de la Sociedad Argentina de Botanica
Cynophalla polyantha (Capparaceae), new record for the Argentine flora
This paper records for the first time the presence in the Argentine flora of the small tree Cynophalla polyantha (Triana & Planch.) Cornejo & Iltis (Capparaceae), which was recently found in the north of the province of Salta, close to the Bolivian border. Abstract
Richardson JE, Pennington RT (2016). Editorial: Origin of tropical diversity: from clades to communities. Frontiers in Genetics, 7(OCT).
Coelho de Souza F, Dexter KG, Phillips OL, Brienen RJW, Chave J, Galbraith DR, Lopez Gonzalez G, Monteagudo Mendoza A, Pennington RT, Poorter L, et al
(2016). Evolutionary heritage influences Amazon tree ecology. Proceedings. Biological sciences
Evolutionary heritage influences Amazon tree ecology
Lineages tend to retain ecological characteristics of their ancestors through time. However, for some traits, selection during evolutionary history may have also played a role in determining trait values. To address the relative importance of these processes requires large-scale quantification of traits and evolutionary relationships among species. The Amazonian tree flora comprises a high diversity of angiosperm lineages and species with widely differing life-history characteristics, providing an excellent system to investigate the combined influences of evolutionary heritage and selection in determining trait variation. We used trait data related to the major axes of life-history variation among tropical trees (e.g. growth and mortality rates) from 577 inventory plots in closed-canopy forest, mapped onto a phylogenetic hypothesis spanning more than 300 genera including all major angiosperm clades to test for evolutionary constraints on traits. We found significant phylogenetic signal (PS) for all traits, consistent with evolutionarily related genera having more similar characteristics than expected by chance. Although there is also evidence for repeated evolution of pioneer and shade tolerant life-history strategies within independent lineages, the existence of significant PS allows clearer predictions of the links between evolutionary diversity, ecosystem function and the response of tropical forests to global change. Abstract
Pontara V, Bueno ML, Garcia LE, Oliveira-Filho AT, Pennington TR, Burslem DFRP, Lemos-Filho JP
(2016). Fine-scale variation in topography and seasonality determine radial growth of an endangered tree in Brazilian Atlantic forest. Plant and Soil
Fine-scale variation in topography and seasonality determine radial growth of an endangered tree in Brazilian Atlantic forest
Aims: We use dendroecological methods to test the hypothesis that variation in topographic position is related to radial growth and phenology for individuals of the endangered tropical tree Dalbergia nigra under uniform conditions of climate and irradiance, and to examine effects of seasonality on plant phenology and growth periodicity. Methods: Dendrometer-based measurements of stem diameter change over 26 months and local measurements of soil nutrient and water availability were compared for 24 individuals of D. nigra distributed equally between summit and valley positions within a topographically heterogeneous fragment of Atlantic Forest in southeastern Brazil. Results: Soil water and nutrient availability, and cumulative radial growth, were greater for trees in valley than summit positions. Monthly diameter increment was seasonal and positively related to monthly rainfall. D. nigra was seasonal in all phenophases, regardless of topographic position, and there were no differences in the frequency, timing or intensity of phenophases among topographic positions. Conclusions: We conclude that low soil nutrient and/or moisture availability reduce radial growth of D. nigra individuals growing in summit positions, while trees growing in valleys exhibit faster annual growth. Vegetative phenology is unaffected by fine-scale variation in topography. Abstract
Banda-R K, Delgado-Salinas A, Dexter KG, Linares-Palomino R, Oliveira-Filho A, Prado D, Pullan M, Quintana C, Riina R, Rodriguez M. GM, et al (2016). Plant diversity patterns in neotropical dry forests and their conservation implications. Science, 353(6306), 1383-1387.
Pennington RT, Lavin M
(2016). The contrasting nature of woody plant species in different neotropical forest biomes reflects differences in ecological stability. New Phytologist
The contrasting nature of woody plant species in different neotropical forest biomes reflects differences in ecological stability
A fundamental premise of this review is that distinctive phylogenetic and biogeographic patterns in clades endemic to different major biomes illuminate the evolutionary process. In seasonally dry tropical forests (SDTFs), phylogenies are geographically structured and multiple individuals representing single species coalesce. This pattern of monophyletic species, coupled with their old species stem ages, is indicative of maintenance of small effective population sizes over evolutionary timescales, which suggests that SDTF is difficult to immigrate into because of persistent resident lineages adapted to a stable, seasonally dry ecology. By contrast, lack of coalescence in conspecific accessions of abundant and often widespread species is more frequent in rain forests and is likely to reflect large effective population sizes maintained over huge areas by effective seed and pollen flow. Species nonmonophyly, young species stem ages and lack of geographical structure in rain forest phylogenies may reflect more widespread disturbance by drought and landscape evolution causing resident mortality that opens up greater opportunities for immigration and speciation. We recommend full species sampling and inclusion of multiple accessions representing individual species in phylogenies to highlight nonmonophyletic species, which we predict will be frequent in rain forest and savanna, and which represent excellent case studies of incipient speciation. Abstract
Neves DM, Dexter KG, Pennington RT, Bueno ML, Oliveira Filho AT
(2015). Environmental and historical controls of floristic composition across the South American Dry Diagonal. Journal of Biogeography
Environmental and historical controls of floristic composition across the South American Dry Diagonal
Aim: the aim of this study was to test the role of environmental factors and spatially autocorrelated processes, such as historical fragmentation and dispersal limitation, in driving floristic variation across seasonally dry tropical forests (SDTFs) in eastern South America. Location: SDTFs extending from the Caatinga phytogeographical domain of north-eastern Brazil to the Chaco phytogeographical domain of northern Argentina, an area referred to as the Dry Diagonal. Methods: We compiled a database of 282 inventories of woody vegetation in SDTFs from across the Dry Diagonal and combined this with data for 14 environmental variables. We assessed the relative contribution of spatially autocorrelated processes and environmental factors to the floristic turnover among SDTFs across the Dry Diagonal using variation partitioning methods. In addition, we used multivariate analyses to determine which environmental factors were most important in explaining the turnover. Results: We found that the environmental factors measured (temperature, precipitation and edaphic conditions) explained 21.3% of the variation in species composition, with 14.1% of this occurring independently of spatial autocorrelation. A spatially structured fraction of 4.2% could not be accounted for by the environmental factors measured. The main axis of compositional variation was significantly correlated with a north-south gradient in temperature regime. At the extreme south of the Dry Diagonal, a cold temperature regime, in which frost occurred, appeared to underlie floristic similarities between chaco woodlands and southern SDTFs. Main conclusions: Environmental variables, particularly those related to temperature regime, seem to be the most significant factors affecting variation in species composition of SDTFs. Thus historical fragmentation and isolation alone cannot explain the turnover in species composition within SDTFs, as is often assumed. Compositional and environmental heterogeneity needs to be taken into account both to understand the past distribution of SDTFs and to manage and conserve this key tropical biome. Abstract
Cardoso D, São-Mateus WMB, da Cruz DT, Zartman CE, Komura DL, Kite G, Prenner G, Wieringa JJ, Clark A, Lewis G, et al
(2015). Filling in the gaps of the papilionoid legume phylogeny: the enigmatic Amazonian genus Petaladenium is a new branch of the early-diverging Amburaneae clade. Molecular Phylogenetics and Evolution
Filling in the gaps of the papilionoid legume phylogeny: the enigmatic Amazonian genus Petaladenium is a new branch of the early-diverging Amburaneae clade
Recent deep-level phylogenies of the basal papilionoid legumes (Leguminosae, Papilionoideae) have resolved many clades, yet left the phylogenetic placement of several genera unassessed. The phylogenetically enigmatic Amazonian monospecific genus Petaladenium had been believed to be close to the genera of the Genistoid Ormosieae clade. In this paper we provide the first DNA phylogenetic study of Petaladenium and show it is not part of the large Genistoid clade, but is a new branch of the Amburaneae clade, one of the first-diverging lineages of the Papilionoideae phylogeny. This result is supported by the chemical observation that the quinolizidine alkaloids, a chemical synapomorphy of the Genistoids, are absent in Petaladenium. Parsimony and Bayesian phylogenetic analysis of nuclear ITS/5.8S and plastid matK and trnL intron agree with a new interpretation of morphology that Petaladenium is sister to Dussia, a genus comprising ~18 species of trees largely confined to rainforests in Central America and northern South America. Petaladenium, Dussia, and Myrospermum have papilionate flowers in a clade otherwise with radial floral symmetry, loss of petals or incompletely differentiated petals. Our phylogenetic analyses also revealed well-supported resolution within the three main lineages of the ADA clade (Angylocalyceae, Dipterygeae, and Amburaneae). We also discuss further molecular phylogenetic evidence for the undersampled Amazonian genera Aldina and Monopteryx, and the tropical African Amphimas, Cordyla, Leucomphalos, and Mildbraediodendron. Abstract
Zappi DC, Ranzato Filardi FL, Leitman P, Souza VC, Walter BMT, Pirani JR, Morim MP, Queiroz LP, Cavalcanti TB, Mansano VF, et al
(2015). Growing knowledge: an overview of Seed Plant diversity in Brazil. Rodriguesia
Growing knowledge: an overview of Seed Plant diversity in Brazil
An updated inventory of Brazilian seed plants is presented and offers important insights into the country's biodiversity. This work started in 2010, with the publication of the Plants and Fungi Catalogue, and has been updated since by more than 430 specialists working online. Brazil is home to 32,086 native Angiosperms and 23 native Gymnosperms, showing an increase of 3% in its species richness in relation to 2010. The Amazon Rainforest is the richest Brazilian biome for Gymnosperms, while the Atlantic Rainforest is the richest one for Angiosperms. There was a considerable increment in the number of species and endemism rates for biomes, except for the Amazon that showed a decrease of 2.5% of recorded endemics. However, well over half of Brazillian seed plant species (57.4%) is endemic to this territory. The proportion of life-forms varies among different biomes: trees are more expressive in the Amazon and Atlantic Rainforest biomes while herbs predominate in the Pampa, and lianas are more expressive in the Amazon, Atlantic Rainforest, and Pantanal. This compilation serves not only to quantify Brazilian biodiversity, but also to highlight areas where there information is lacking and to provide a framework for the challenge faced in conserving Brazil's unique and diverse flora. Abstract
Honorio Coronado EN, Dexter KG, Pennington RT, Chave J, Lewis SL, Alexiades MN, Alvarez E, Alves de Oliveira A, Amaral IL, Araujo-Murakami A, et al
(2015). Phylogenetic diversity of Amazonian tree communities. Diversity and Distributions
Phylogenetic diversity of Amazonian tree communities
Aim: to examine variation in the phylogenetic diversity (PD) of tree communities across geographical and environmental gradients in Amazonia. Location: Two hundred and eighty-three c. 1 ha forest inventory plots from across Amazonia. Methods: We evaluated PD as the total phylogenetic branch length across species in each plot (PDss), the mean pairwise phylogenetic distance between species (MPD), the mean nearest taxon distance (MNTD) and their equivalents standardized for species richness (ses.PDss, ses.MPD, ses.MNTD). We compared PD of tree communities growing (1) on substrates of varying geological age; and (2) in environments with varying ecophysiological barriers to growth and survival. Results: PDss is strongly positively correlated with species richness (SR), whereas MNTD has a negative correlation. Communities on geologically young- and intermediate-aged substrates (western and central Amazonia respectively) have the highest SR, and therefore the highest PDss and the lowest MNTD. We find that the youngest and oldest substrates (the latter on the Brazilian and Guiana Shields) have the highest ses.PDss and ses.MNTD. MPD and ses.MPD are strongly correlated with how evenly taxa are distributed among the three principal angiosperm clades and are both highest in western Amazonia. Meanwhile, seasonally dry tropical forest (SDTF) and forests on white sands have low PD, as evaluated by any metric. Main conclusions: High ses.PDss and ses.MNTD reflect greater lineage diversity in communities. We suggest that high ses.PDss and ses.MNTD in western Amazonia results from its favourable, easy-to-colonize environment, whereas high values in the Brazilian and Guianan Shields may be due to accumulation of lineages over a longer period of time. White-sand forests and SDTF are dominated by close relatives from fewer lineages, perhaps reflecting ecophysiological barriers that are difficult to surmount evolutionarily. Because MPD and ses.MPD do not reflect lineage diversity per se, we suggest that PDss, ses.PDss and ses.MNTD may be the most useful diversity metrics for setting large-scale conservation priorities. Abstract
Adhikari B, Milne R, Pennington RT, Särkinen T, Pendry CA
(2015). Systematics and biogeography of Berberis s.l. inferred from nuclear ITS and chloroplast ndhF gene sequences. Taxon
Systematics and biogeography of Berberis s.l. inferred from nuclear ITS and chloroplast ndhF gene sequences
Berberis is the largest genus in the Berberidaceae, comprising more than 500 species. It is now recognised to include all of the compound-leaved species formally ascribed to Mahonia, as well as simple-leaved species comprising Berberis s.str. Berberis s.l. has a mainly Northern Hemisphere distribution, with a centre of diversity in the Sino-Himalaya region, while Berberis s.str. extends into South America where it has a secondary centre of diversity. We analyzed nuclear ITS and chloroplast ndhF sequence data from 68 accessions of Berberis s.l. The results support the monophyly of Berberis s.l. but compound-leaved Berberis are shown to be paraphyletic. The analysis supports Berberis higginsae, a member of North American B. sect. Horridae, as sister to all other Berberis species. Our results, interpreted in the light of fossil evidence, suggest a North American origin of Berberis s.l. but the area of origin of the simple-leaved group remains uncertain. Abstract
Pennington RT, Hughes M, Moonlight PW
(2015). The Origins of Tropical Rainforest Hyperdiversity. Trends in Plant Science
The Origins of Tropical Rainforest Hyperdiversity
Traditional models for tropical species richness contrast rainforests as 'museums' of old species or 'cradles' of recent speciation. High plant species diversity in rainforests may be more likely to reflect high episodic evolutionary turnover of species-a scenario implicating high rates of both speciation and extinction through geological time. Abstract
Nicholls JA, Pennington RT, Koenen EJM, Hughes CE, Hearn J, Bunnefeld L, Dexter KG, Stone GN, Kidner CA
(2015). Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae). Frontiers in Plant Science
Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae)
Evolutionary radiations are prominent and pervasive across many plant lineages in diverse geographical and ecological settings; in neotropical rainforests there is growing evidence suggesting that a significant fraction of species richness is the result of recent radiations. Understanding the evolutionary trajectories and mechanisms underlying these radiations demands much greater phylogenetic resolution than is currently available for these groups. The neotropical tree genus Inga (Leguminosae) is a good example, with ~300 extant species and a crown age of 2-10 MY, yet over 6kb of plastid and nuclear DNA sequence data gives only poor phylogenetic resolution among species. Here we explore the use of larger-scale nuclear gene data obtained though targeted enrichment to increase phylogenetic resolution within Inga. Transcriptome data from three Inga species were used to select 264 nuclear loci for targeted enrichment and sequencing. Following quality control to remove probable paralogs from these sequence data, the final dataset comprised 259,313 bases from 194 loci for 24 accessions representing 22 Inga species and an outgroup (Zygia). Bayesian phylogenies reconstructed using either all loci concatenated or a gene-tree/species-tree approach yielded highly resolved phylogenies. We used coalescent approaches to show that the same targeted enrichment data also have significant power to discriminate among alternative within-species population histories within the widespread species I. umbellifera. In either application, targeted enrichment simplifies the informatics challenge of identifying orthologous loci associated with de novo genome sequencing. We conclude that targeted enrichment provides the large volumes of phylogenetically-informative sequence data required to resolve relationships within recent plant species radiations, both at the species level and for within-species phylogeographic studies. Abstract
Baker TR, Pennington RT, Magallon S, Gloor E, Laurance WF, Alexiades M, Alvarez E, Araujo A, Arets EJMM, Aymard G, et al
(2014). Fast demographic traits promote high diversification rates of Amazonian trees. Ecol Lett
Fast demographic traits promote high diversification rates of Amazonian trees.
The Amazon rain forest sustains the world's highest tree diversity, but it remains unclear why some clades of trees are hyperdiverse, whereas others are not. Using dated phylogenies, estimates of current species richness and trait and demographic data from a large network of forest plots, we show that fast demographic traits--short turnover times--are associated with high diversification rates across 51 clades of canopy trees. This relationship is robust to assuming that diversification rates are either constant or decline over time, and occurs in a wide range of Neotropical tree lineages. This finding reveals the crucial role of intrinsic, ecological variation among clades for understanding the origin of the remarkable diversity of Amazonian trees and forests. Abstract
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Honorio Coronado EN, Dexter KG, Poelchau MF, Hollingsworth PM, Phillips OL, Pennington RT
(2014). Ficus insipida subsp. insipida (Moraceae) reveals the role of ecology in the phylogeography of widespread Neotropical rain forest tree species. Journal of Biogeography
Ficus insipida subsp. insipida (Moraceae) reveals the role of ecology in the phylogeography of widespread Neotropical rain forest tree species
Aim: to examine the phylogeography of Ficus insipida subsp. insipida in order to investigate patterns of spatial genetic structure across the Neotropics and within Amazonia. Location: Neotropics. Methods: Plastid DNA (trnH-psbA; 410 individuals from 54 populations) and nuclear ribosomal internal transcribed spacer (ITS; 85 individuals from 27 populations) sequences were sampled from Mexico to Bolivia, representing the full extent of the taxon's distribution. Divergence of plastid lineages was dated using a Bayesian coalescent approach. Genetic diversity was assessed with indices of haplotype and nucleotide diversities, and genetic structure was examined using spatial analysis of molecular variance (SAMOVA) and haplotype networks. Population expansion within Amazonia was tested using neutrality and mismatch distribution tests. Results: trnH-psbA sequences yielded 19 haplotypes restricted to either Mesoamerica or Amazonia; six haplotypes were found among ITS sequences. Diversification of the plastid DNA haplotypes began c. 14.6 Ma. Haplotype diversity for trnH-psbA was higher in Amazonia. Seven genetically differentiated SAMOVA groups were described for trnH-psbA, of which two were also supported by the presence of unique ITS sequences. Population expansion was suggested for both markers for the SAMOVA group that contains most Amazonian populations. Main conclusions: Our results show marked population genetic structure in F. insipida between Mesoamerica and Amazonia, implying that the Andes and seasonally dry areas of northern South America are eco-climatic barriers to its migration. This pattern is shared with other widespread pioneer species affiliated to wet habitats, indicating that the ecological characteristics of species may impact upon large-scale phylogeography. Ficus insipida also shows genetic structure in north-western Amazonia potentially related to pre-Pleistocene historical events. In contrast, evident population expansion elsewhere in Amazonia, in particular the presence of genetically uniform populations across the south-west, indicate recent colonization. Our findings are consistent with palaeoecological data that suggest recent post-glacial expansion of Amazonian forests in the south. © 2014 the Authors. Journal of Biogeography Published by John Wiley & Sons Ltd. Abstract
Cárdenas ML, Gosling WD, Pennington RT, Poole I, Sherlock SC, Mothes P
(2014). Forests of the tropical eastern Andean flank during the middle Pleistocene. Palaeogeography, Palaeoclimatology, Palaeoecology
Forests of the tropical eastern Andean flank during the middle Pleistocene
Inter-bedded volcanic and organic sediments from Erazo (Ecuador) indicate the presence of four different forest assemblages on the eastern Andean flank during the middle Pleistocene. Radiometric dates (40Ar-39Ar) obtained from the volcanic ash indicate that deposition occurred between 620,000 and 192,000years ago. Examination of the organic sediment composition and the fossil pollen, wood and charcoal it contains provides insight into depositional environment, vegetation assemblage and fire history. The high organic content and abundance of macro fossils found throughout the sediment suggest that during the period of deposition the local environment was either a swamp or a shallow water body. The correlation of fire activity (peaks in charcoal abundance) with volcanic ash deposits through most of the record suggests that volcanoes were the main source of ignition. The low abundance of grass (typically Abstract
Whitney BS, Mayle FE, Burn MJ, Guillén R, Chavez E, Pennington RT
(2014). Sensitivity of Bolivian seasonally-dry tropical forest to precipitation and temperature changes over glacial-interglacial timescales. Vegetation History and Archaeobotany
Sensitivity of Bolivian seasonally-dry tropical forest to precipitation and temperature changes over glacial-interglacial timescales
We used fossil pollen to investigate the response of the eastern Chiquitano seasonally-dry tropical forest (SDTF), lowland Bolivia, to high-amplitude climate change associated with glacial-interglacial cycles. Changes in the structure, composition and diversity of the past vegetation are compared with palaeoclimate data previously reconstructed from the same record, and these results shed light on the biogeographic history of today's highly disjunct blocks of SDTF across South America. We demonstrate that lower glacial temperatures limited tropical forest in the Chiquitanía region, and suggest that SDTF was absent or restricted at latitudes below 17°S, the proposed location of the majority of the hypothesized 'Pleistocene dry forest arc' (PDFA). At 19500 yrs b.p. warming supported the establishment of a floristically-distinct SDTF, which showed little change throughout the glacial-Holocene transition, despite a shift to significantly wetter conditions beginning ca. 12500-12200 yrs b.p. Anadenanthera colubrina, a key SDTF taxon, arrived at 10000 yrs b.p. which coincides with the onset of drought associated with an extended dry season. Lasting until 3000 yrs b.p. Holocene drought caused a floristic shift to more drought-tolerant taxa and a reduction in α-diversity (shown by declining palynological richness), but closed-canopy forest was maintained throughout. In contrast to the PDFA, the modern distribution of SDTF most likely represents the greatest spatial coverage of these forests in southern South America since glacial times. We find that temperature is a key climatic control upon the distribution of lowland South American SDTF over glacial-interglacial timescales, and seasonality of rainfall exerts a strong control on their floristic composition. © 2013 Springer-Verlag Berlin Heidelberg. Abstract
Filimban FZ, Mackinder B, Knees SG, Pennington RT
(2014). Studies in the Flora of Arabia: XXX. A Synopsis of the native and naturalised species of Senna (Leguminosae: Caesalpinioideae) in the Arabian Peninsula. Edinburgh Journal of Botany
Studies in the Flora of Arabia: XXX. A Synopsis of the native and naturalised species of Senna (Leguminosae: Caesalpinioideae) in the Arabian Peninsula
A synopsis of the native and naturalised species of Senna (Leguminosae: Caesalpinioideae) in the Arabian Peninsula is provided. Nine species are recognised. A key to the species is presented. For each species the accepted name with selected synonymy is given, followed by a diagnostic morphological description, the geographical distribution, details of habitat preference, and citation of specimens studied. Preliminary regional conservation assessments are given for all species. © Trustees of the Royal Botanic Garden Edinburgh (2014). Abstract
Pennington RT, Hughes CE (2014). The remarkable congruence of New and Old World savanna origins. New Phytologist, 204(1), 4-6.
Iganci JRV, Miotto STS, Souza-Chies TT, Särkinen TE, Simpson BB, Simon MF, Pennington RT
(2013). Diversification history of Adesmia ser. psoraleoides (Leguminosae): Evolutionary processes and the colonization of the southern Brazilian highland grasslands. South African Journal of Botany
Diversification history of Adesmia ser. psoraleoides (Leguminosae): Evolutionary processes and the colonization of the southern Brazilian highland grasslands
A molecular phylogeny is used to analyze the diversification history of Adesmia ser. psoraleoides, and its implications for understanding the historical assembly of the grasslands in the highlands of southern Brazil. All species of A. ser. psoraleoides were sampled, including multiple accessions for each species, plus representative species of the rest of Adesmia covering its geographic distribution. Phylogenetic analyses were based on nuclear and plastid DNA sequences, and a plastid matK phylogeny was dated. A. ser. psoraleoides is a well-supported monophyletic group, nested within the series bicolores, muricatae, subnudae, longisetae and candidae. The stem of A. ser. psoraleoides is c. 11. Mya, but most extant species diversified c. 3-5. Mya, suggesting that the flora of the subtropical grasslands of southern Brazil was assembled recently, co-incident with the expansion of other tropical grassland systems globally. © 2013 South African Association of Botanists. Abstract
Vatanparast M, Klitgård BB, Adema FACB, Pennington RT, Yahara T, Kajita T
(2013). First molecular phylogeny of the pantropical genus Dalbergia: Implications for infrageneric circumscription and biogeography. South African Journal of Botany
First molecular phylogeny of the pantropical genus Dalbergia: Implications for infrageneric circumscription and biogeography
The genus Dalbergia with c. 250 species has a pantropical distribution. In spite of the high economic and ecological value of the genus, it has not yet been the focus of a species level phylogenetic study. We utilized ITS nuclear sequence data and included 64 Dalbergia species representative of its entire geographic range to provide a first phylogenetic framework of the genus to evaluate previous infrageneric classifications based on morphological data. The phylogenetic analyses performed suggest that Dalbergia is monophyletic and that it probably originated in the New World. Several clades corresponding to sections of these previous classifications are revealed. Taking into account that there is not a complete correlation between geography and phylogeny, and the estimation that the Dalbergia stem and crown clades are 40.4-43.3 mya and 3.8-12.7 mya, respectively, it is plausible that several long distance dispersal events underlie the pantropical distribution of the genus. © 2013 South African Association of Botanists. Abstract
Yahara T, Javadi F, Onoda Y, de Queiroz LP, Faith DP, Prado DE, Akasaka M, Kadoya T, Ishihama F, Davies S, et al
(2013). Global legume diversity assessment: Concepts, key indicators, and strategies. Taxon
Global legume diversity assessment: Concepts, key indicators, and strategies
While many plant species are considered threatened under anthropogenic pressure, it remains uncertain how rapidly we are losing plant species diversity. To fill this gap, we propose a Global Legume Diversity Assessment (GLDA) as the first step of a global plant diversity assessment. Here we describe the concept of GLDA and its feasibility by reviewing relevant approaches and data availability. We conclude that Fabaceae is a good proxy for overall angiosperm diversity in many habitats and that much relevant data for GLDA are available. As indicators of states, we propose comparison of species richness with phylogenetic and functional diversity to obtain an integrated picture of diversity. As indicators of trends, species loss rate and extinction risks should be assessed. Specimen records and plot data provide key resources for assessing legume diversity at a global scale, and distribution modeling based on these records provide key methods for assessing states and trends of legume diversity. GLDA has started in Asia, and we call for a truly global legume diversity assessment by wider geographic collaborations among various scientists. Abstract
Hughes CE, Pennington RT, Antonelli A
(2013). Neotropical Plant Evolution: Assembling the Big Picture. Botanical Journal of the Linnean Society
Neotropical Plant Evolution: Assembling the Big Picture
This paper and this issue attempt to address how, when and why the phenomenal c. 100,000 species of seed plants in tropical America (the Neotropics) arose. It is increasingly clear that an approach focusing on individual major biomes rather than a single aggregate view is useful because of evidence for differing diversification histories among biomes. Phylogenetic evidence suggests that Neotropical-scale diversification patterns are structured more ecologically than geographically, with a key role for phylogenetic niche or biome conservatism. Lower geographical structure reflects the fact that long-distance dispersal, inferred from dated phylogenetic trees, has overcome many supposed dispersal barriers. Overall, high rates of species turnover as inferred from palaeontological and molecular data have been the hallmark of plant evolutionary dynamics in the Neotropics throughout the Cenozoic, with most extant species diversity post-dating the Mid- to Late Miocene, perhaps reflecting the conjunction of both global climatic changes and geological upheavals such as the Neogene uplift of the tropical Andes. Future studies of Neotropical diversification will be facilitated by taxonomically and genetically better sampled phylogenetic analyses, their integration with palaeontological, geological and ecological data, and improved methods to estimate biogeographic history and diversification dynamics at different spatial and temporal scales. Future biome-focused approaches would benefit greatly from better delimitation and mapping of Neotropical biomes. © 2012 the Linnean Society of London. Abstract
Cardoso D, Pennington RT, de Queiroz LP, Boatwright JS, Van Wyk BE, Wojciechowski MF, Lavin M
(2013). Reconstructing the deep-branching relationships of the papilionoid legumes. South African Journal of Botany
Reconstructing the deep-branching relationships of the papilionoid legumes
Resolving the phylogenetic relationships of the deep nodes of papilionoid legumes (Papilionoideae) is essential to understanding the evolutionary history and diversification of this economically and ecologically important legume subfamily. The early-branching papilionoids include mostly Neotropical trees traditionally circumscribed in the tribes Sophoreae and Swartzieae. They are more highly diverse in floral morphology than other groups of Papilionoideae. For many years, phylogenetic analyses of the Papilionoideae could not clearly resolve the relationships of the early-branching lineages due to limited sampling. In the eight years since the publication of Legumes of the World, we have seen an extraordinary wealth of new molecular data for the study of Papilionoideae phylogeny, enabling increasingly greater resolution and many surprises. This study draws on recent molecular phylogenetic studies and a new comprehensive Bayesian phylogenetic analysis of 668 plastid matK sequences. The present matK phylogeny resolves the deep-branching relationships of the papilionoids with increased support for many clades, and suggests that taxonomic realignments of some genera and of numerous tribes are necessary. The potentially earliest-branching papilionoids fall within an ADA clade, which includes the recircumscribed monophyletic tribes Angylocalyceae, Dipterygeae, and Amburanae. The genera Aldina and Amphimas represent two of the nine main but as yet unresolved lineages comprising the large 50-kb inversion clade. The quinolizidine-alkaloid-accumulating Genistoid s.l. clade is expanded to include Dermatophyllum and a strongly supported and newly circumscribed tribe Ormosieae. Sophoreae and Swartzieae are dramatically reorganized so as to comprise monophyletic groups within the Core Genistoid clade and outside the 50-kb inversion clade, respectively. Acosmium is excluded from the Genistoids s.l. and strongly resolved within the newly circumscribed tribe Dalbergieae. By providing a better resolved phylogeny of the earliest-branching papilionoids, this study, in combination with other recent evidence, will lead to a more stable phylogenetic classification of the Papilionoideae. © 2013 South African Association of Botanists. Abstract
Oliveira-Filho AT, Cardoso D, Schrire BD, Lewis GP, Pennington RT, Brummer TJ, Rotella J, Lavin M
(2013). Stability structures tropical woody plant diversity more than seasonality: Insights into the ecology of high legume-succulent-plant biodiversity. South African Journal of Botany
Stability structures tropical woody plant diversity more than seasonality: Insights into the ecology of high legume-succulent-plant biodiversity
Phylogenies of legume taxa are ecologically structured along a tropical seasonality gradient, which suggests phylogenetic niche conservatism. This seasonality gradient spans Neotropical wet forests, savannas, and highly seasonal drought-prone woody vegetation known as the succulent biome. Ecological phylogenetic structure was investigated using a community phylogenetic approach. We further analyzed bioclimatic and other independent variables that potentially explained phylogenetic beta diversity among 466 floristic sites that spanned the savanna and succulent biomes in eastern South America. Explanatory variables were selected using variance inflation factors, information criteria, and the ability to explain both species and phylogenetic beta diversity. A model involving annual precipitation suggests that a threshold of Abstract
Borges L, Bruneau A, Cardoso D, Crisp M, Delgado-Salinas A, Doyle JJ, Egan A, Herendeen PS, Hughes C, Kenicer G, et al
(2013). Towards a new classification system for legumes: Progress report from the 6th International Legume Conference. South African Journal of Botany
Towards a new classification system for legumes: Progress report from the 6th International Legume Conference
Legume systematists have been making great progress in understanding evolutionary relationships within the Leguminosae (Fabaceae), the third largest family of flowering plants. As the phylogenetic picture has become clearer, so too has the need for a revised classification of the family. The organization of the family into three subfamilies and 42 tribes is outdated and evolutionarily misleading. The three traditionally recognized subfamilies, Caesalpinioideae, Mimosoideae, and Papilionoideae, do not adequately represent relationships within the family. The occasion of the Sixth International Legume Conference in Johannesburg, South Africa in January 2013, with its theme "Towards a new classification system for legumes," provided the impetus to move forward with developing a new classification. A draft classification, based on current phylogenetic results and a set of principles and guidelines, was prepared in advance of the conference as the basis for discussion. The principles, guidelines, and draft classification were presented and debated at the conference. The objectives of the discussion were to develop consensus on the principles that should guide the development of the classification, to discuss the draft classification's strengths and weaknesses and make proposals for its revision, and identify and prioritize phylogenetic deficiencies that must be resolved before the classification could be published. This paper describes the collaborative process by a large group of legume systematists, publishing under the name Legume Phylogeny Working Group, to develop a new phylogenetic classification system for the Leguminosae. The goals of this paper are to inform the broader legume community, and others, of the need for a revised classification, and spell out clearly what the alternatives and challenges are for a new classification system for the family. © 2013 South African Association of Botanists. Abstract
Adhikari B, Pendry CA, Pennington RT, Milne RI
(2012). A revision of berberis S.S. (Berberidaceae) in Nepal. Edinburgh Journal of Botany
A revision of berberis S.S. (Berberidaceae) in Nepal
The genus Berberis (Berberidaceae) in Nepal is revised and 21 species are recognised. Two species, Berberis pendryi Bh.Adhikari and Berberis karnaliensis Bh.Adhikari, are newly described and 11 taxa are lectotypified. A key to species is provided and all species are fully described and illustrated, and their distributions within Nepal mapped. An IUCN conservation assessment is given for each species. ©2012 Copyright Trustees of the Royal Botanic Garden Edinburgh. Abstract
Simon MF, Pennington T
(2012). Evidence for adaptation to fire regimes in the tropical savannas of the Brazilian Cerrado. International Journal of Plant Sciences
Evidence for adaptation to fire regimes in the tropical savannas of the Brazilian Cerrado
A recent controversy concerns whether plant traits that are assumed to be adaptations to fire originally evolved in response to selective factors other than fire. We contribute to this debate by investigating the evolution of the endemic woody flora of the fire-prone Cerrado of central Brazil, the most species-rich savanna in the world. We review evidence from dated phylogenies and show that Cerrado lineages started to diversify less than 10 million years ago. These Cerrado lineages are characterized by fire-resistant traits such as thick, corky bark and root sprouting, which have been considered to have evolved as adaptations to drought or nutrient-deficient soils. However, the fact that the lineages carrying these features arose coincident with the rise to dominance of flammable C4 grasses and expansion of the savanna biome worldwide, and postdating the earlier origin of seasonal climates and the nutrient-poor, acid Cerrado soils suggests that such traits should be considered as adaptations to fire regimes. The nature of these features as adaptations to fire is further suggested by their absence or poor development in related lineages found in fire-free environments with similar edaphic conditions to the Cerrado and by their repeated independent origin in diverse lineages. We present evidence to demonstrate that the evolutionary barrier to entry to the Cerrado is a weak one, presumably because of the ease of evolution of the necessary adaptations to fire regimes for lineages inhabiting neighboring fire-free biomes. © 2012 by the University of Chicago. All rights reserved. Abstract
Särkinen T, Pennington RT, Lavin M, Simon MF, Hughes CE
(2012). Evolutionary islands in the Andes: Persistence and isolation explain high endemism in Andean dry tropical forests. Journal of Biogeography
Evolutionary islands in the Andes: Persistence and isolation explain high endemism in Andean dry tropical forests
Aim the tropical Andes are a world biodiversity hotspot. With diverse biomes and dramatic, geologically recent mountain uplift, they offer a system to study the relative contributions of geological and biome history to species richness. There are preliminary indications that historical species assembly in the Andes has been influenced by physiographical heterogeneity and that distinct biomes have evolved in relative isolation despite physical proximity. Here we test this 'Andean biotic separation hypothesis' by focusing on the low-elevation, seasonally dry tropical forest (SDTF) biome to determine whether patterns of plant diversification within the SDTF differ from those in mid- and high-elevation biomes. Location Tropical Andes, South America. Methods Densely sampled time-calibrated phylogenies for five legume genera (Amicia, Coursetia, Cyathostegia, Mimosa and Poissonia) containing species endemic to the Andean SDTF biome were used to investigate divergence times and levels of geographical structure. Geographical structure was measured using isolation-by-distance methods. Meta-analysis of time-calibrated phylogenies of Andean plant groups was used to compare the pattern and tempo of endemic species diversification between the major Andean biomes. Results Long-term persistence of SDTF in the Andes is suggested by old stem ages (5-27Ma) of endemic genera/clades within genera, and deep divergences coupled with strong geographical structure among and within species. Comparison of species diversification patterns among different biomes shows that the relatively old, geographically confined pattern of species diversification in SDTF contrasts with the high-elevation grasslands that show rapid and recent radiations driven by ecological opportunities. Main conclusions the SDTF biome has a long history in the Andes. We suggest that the diverse SDTF flora has been assembled gradually over the past c.19Ma from lineages exhibiting strong phylogenetic niche conservatism. These patterns suggest that Andean SDTFs have formed stable and strongly isolated 'islands' despite the upheavals of Andean uplift. Indeed, the Andean SDTFs may represent some of the most isolated and evolutionarily persistent continental plant communities, similar in many respects to floras of remote oceanic islands. © 2011 Blackwell Publishing Ltd. Abstract
Caetano S, Currat M, Pennington RT, Prado D, Excoffier L, Naciri Y
(2012). Recent colonization of the Galápagos by the tree Geoffroea spinosa Jacq. (Leguminosae). Molecular Ecology
Recent colonization of the Galápagos by the tree Geoffroea spinosa Jacq. (Leguminosae)
This study puts together genetic data and an approximate bayesian computation (ABC) approach to infer the time at which the tree Geoffroea spinosa colonized the Galápagos Islands. The genetic diversity and differentiation between Peru and Galápagos population samples, estimated using three chloroplast spacers and six microsatellite loci, reveal significant differences between two mainland regions separated by the Andes mountains (Inter Andean vs. Pacific Coast) as well as a significant genetic differentiation of island populations. Microsatellites identify two distinct geographical clusters, the Galápagos and the mainland, and chloroplast markers show a private haplotype in the Galápagos. The nuclear distinctiveness of the Inter Andean populations suggests current restricted pollen flow, but chloroplast points to cross-Andean dispersals via seeds, indicating that the Andes might not be an effective biogeographical barrier. The ABC analyses clearly point to the colonization of the Galápagos within the last 160 000 years and possibly as recently as 4750 years ago (475 generations). Founder events associated with colonization of the two islands where the species occurs are detected, with Española having been colonized after Floreana. We discuss two nonmutually exclusive possibilities for the colonization of the Galápagos, recent natural dispersal vs. human introduction. © 2012 Blackwell Publishing Ltd. Abstract
Schaefer H, Hechenleitner P, Santos-Guerra A, De Sequeira MM, Pennington RT, Kenicer G, Carine MA
(2012). Systematics, biogeography, and character evolution of the legume tribe Fabeae with special focus on the middle-Atlantic island lineages. BMC Evolutionary Biology
Systematics, biogeography, and character evolution of the legume tribe Fabeae with special focus on the middle-Atlantic island lineages
Background: Tribe Fabeae comprises about 380 legume species, including some of the most ancient and important crops like lentil, pea, and broad bean. Breeding efforts in legume crops rely on a detailed knowledge of closest wild relatives and geographic origin. Relationships within the tribe, however, are incompletely known and previous molecular results conflicted with the traditional morphology-based classification. Here we analyse the systematics, biogeography, and character evolution in the tribe based on plastid and nuclear DNA sequences. Results: Phylogenetic analyses including c. 70% of the species in the tribe show that the genera Vicia and Lathyrus in their current circumscription are not monophyletic: Pisum and Vavilovia are nested in Lathyrus, the genus Lens is nested in Vicia. A small, well-supported clade including Vicia hirsuta, V. sylvatica, and some Mediterranean endemics, is the sister group to all remaining species in the tribe. Fabeae originated in the East Mediterranean region in the Miocene (23-16 million years ago (Ma)) and spread at least 39 times into Eurasia, seven times to the Americas, twice to tropical Africa and four times to Macaronesia. Broad bean (V. faba) and its sister V. paucijuga originated in Asia and might be sister to V. oroboides. Lentil (Lens culinaris ssp. culinaris) is of Mediterranean origin and together with eight very close relatives forms a clade that is nested in the core Vicia, where it evolved c. 14 Ma. The Pisum clade is nested in Lathyrus in a grade with the Mediterranean L. gloeosperma, L. neurolobus, and L. nissolia. The extinct Azorean endemic V. dennesiana belongs in section Cracca and is nested among Mediterranean species. According to our ancestral character state reconstruction results, ancestors of Fabeae had a basic chromosome number of 2n=14, an annual life form, and evenly hairy, dorsiventrally compressed styles. Conclusions: Fabeae evolved in the Eastern Mediterranean in the middle Miocene and spread from there across Eurasia, into Tropical Africa, and at least seven times to the Americas. The middle-Atlantic islands were colonized four times but apparently did not serve as stepping-stones for Atlantic crossings. Long-distance dispersal events are relatively common in Fabeae (seven per ten million years). Current generic and infrageneric circumscriptions in Fabeae do not reflect monophyletic groups and should be revised. Suggestions for generic level delimitation are offered. © 2012 Schaefer et al.; licensee BioMed Central Ltd. Abstract
Whitney BS, Mayle FE, Punyasena SW, Fitzpatrick KA, Burn MJ, Guillen R, Chavez E, Mann D, Pennington RT, Metcalfe SE, et al (2011). A 45kyr palaeoclimate record from the lowland interior of tropical South America. Palaeogeography, Palaeoclimatology, Palaeoecology, 307(1-4), 177-192.
Milliken W, Zappi D, Sasaki D, Hopkins M, Pennington RT (2011). Amazon vegetation: how much don’t we know and how much does it matter?. Kew Bulletin, 65(4), 691-709.
IGANCI JRV, HEIDEN G, MIOTTO STS, PENNINGTON RT (2011). Campos de Cima da Serra: the Brazilian Subtropical Highland Grasslands show an unexpected level of plant endemism. Botanical Journal of the Linnean Society, 167(4), 378-393.
Jones HT, Mayle FE, Pennington RT, Killeen TJ
(2011). Characterisation of Bolivian savanna ecosystems by their modern pollen rain and implications for fossil pollen records. Review of Palaeobotany and Palynology
Characterisation of Bolivian savanna ecosystems by their modern pollen rain and implications for fossil pollen records
The majority of vegetation reconstructions from the Neotropics are derived from fossil pollen records extracted from lake sediments. However, the interpretation of these records is restricted by limited knowledge of the contemporary relationships between the vegetation and pollen rain of Neotropical ecosystems, especially for more open vegetation such as savannas. This research aims to improve the interpretation of these records by investigating the vegetation and modern pollen rain of different savanna ecosystems in Bolivia using vegetation inventories, artificial pollen traps and surface lake sediments. Two types of savanna were studied, upland savannas (cerrado), occurring on well drained soils, and seasonally-inundated savannas occurring on seasonally water-logged soils. Quantitative vegetation data are used to identify taxa that are floristically important in the different savanna types and to allow modern pollen/vegetation ratios to be calculated. Artificial pollen traps from the upland savanna site are dominated by Moraceae (35%), Poaceae (30%), Alchornea (6%) and Cecropia (4%). The two seasonally-inundated savanna sites are dominated by Moraceae (37%), Poaceae (20%), Alchornea (8%) and Cecropia (7%), and Moraceae (25%), Cyperaceae (22%), Poaceae (19%) and Cecropia (9%), respectively. The modern pollen rain of seasonally-inundated savannas from surface lake sediments is dominated by Cyperaceae (35%), Poaceae (33%), Moraceae (9%) and Asteraceae (5%). Upland and seasonally-flooded savannas were found to be only subtly distinct from each other palynologically. All sites have a high proportion of Moraceae pollen due to effective wind dispersal of this pollen type from areas of evergreen forest close to the study sites. Modern pollen/vegetation ratios show that many key woody plant taxa are absent/under-represented in the modern pollen rain (e.g. Caryocar and Tabebuia). The lower-than-expected percentages of Poaceae pollen, and the scarcity of savanna indicators, in the modern pollen rain of these ecosystems mean that savannas could potentially be overlooked in fossil pollen records without consideration of the full pollen spectrum available. © 2011 Elsevier B.V. Abstract
Pennington RT, Dick CW
(2011). Diversification of the Amazonian Flora and its Relation to key Geological and Environmental Events: a Molecular Perspective. In (Ed) Amazonia: Landscape and Species Evolution: a look into the past
Diversification of the Amazonian Flora and its Relation to key Geological and Environmental Events: a Molecular Perspective
Pennington RT, Daza A, Reynel C, Lavin M
(2011). Poissonia eriantha (Leguminosae) from Cuzco, Peru: an overlooked species underscores a pattern of narrow endemism common to seasonally dry neotropical vegetation. Systematic Botany
Poissonia eriantha (Leguminosae) from Cuzco, Peru: an overlooked species underscores a pattern of narrow endemism common to seasonally dry neotropical vegetation
The Peruvian Poissonia eriantha is segregated from peripatric Poissonia orbicularis and reinstated as the third unifoliolate species of Poissonia and the second from the Apurimac River basin in Peru. Poissonia eriantha is distinguished phenotypically and by DNA sequences from the ITS and cpDNA trnD-T region and morphology. This overlooked species is known from the type specimen and a recent collection from north of the Apurimac River in westcentral Cuzco where seasonally dry tropical forest vegetation predominates that is rich in succulent taxa (e.g. Cactaceae). Poissonia orbicularis is known from downstream along the Apurimac River and is disjunct further north along the Mantaro River, all within the same kind of seasonally dry vegetation. This seemingly small geographic distinction belies large genetic and phenotypic differences, a finding that may be most common to species groups confined to seasonally dry Neotropical forest vegetation. The case of Poissonia eriantha exemplifies the potentially high degree of niche conservatism and dispersal limitation that seasonally dry succulent-rich woodlands can impose on its constituent lineages. © Copyright 2011 by the American Society of Plant Taxonomists. Abstract
Cárdenas ML, Gosling WD, Sherlock SC, Poole I, Pennington RT, Mothes P
(2011). Response to comment on "The response of vegetation on the Andean flank in Western Amazonia to Pleistocene climate change". Science
Response to comment on "The response of vegetation on the Andean flank in Western Amazonia to Pleistocene climate change"
Puyasena et al. question our interpretation of climate-driven vegetation change on the Andean flank in western Amazonia during the middle Pleistocene and suggest that the use of Podocarpus spp. as a proxy of past climate change should be reassessed. We defend our assertion that vegetation change at the Erazo study site was predominantly driven by climate change due to concomitant changes recorded by multiple taxa in the fossil record. Abstract
Cárdenas ML, Gosling WD, Sherlock SC, Poole I, Pennington RT, Mothes P
(2011). The response of vegetation on the Andean Flank in Western Amazonia to Pleistocene climate change. Science
The response of vegetation on the Andean Flank in Western Amazonia to Pleistocene climate change
A reconstruction of past environmental change from Ecuador reveals the response of lower montane forest on the Andean flank in western Amazonia to glacial-interglacial global climate change. Radiometric dating of volcanic ash indicates that deposition occurred ∼324,000 to 193,000 years ago during parts of Marine Isotope Stages 9, 7, and 6. Fossil pollen and wood preserved within organic sediments suggest that the composition of the forest altered radically in response to glacial-interglacial climate change. The presence of Podocarpus macrofossils °1000 meters below the lower limit of their modern distribution indicates a relative cooling of at least 5°C during glacials and persistence of wet conditions. Interglacial deposits contain thermophilic palms suggesting warm and wet climates. Hence, global temperature change can radically alter vegetation communities and biodiversity in this region. Abstract
Barlow J, Ewers RM, Anderson L, Aragao LEOC, Baker TR, Boyd E, Feldpausch TR, Gloor E, Hall A, Malhi Y, et al
(2011). Using learning networks to understand complex systems: a case study of biological, geophysical and social research in the Amazon. Biol Rev Camb Philos Soc
Using learning networks to understand complex systems: a case study of biological, geophysical and social research in the Amazon.
Developing high-quality scientific research will be most effective if research communities with diverse skills and interests are able to share information and knowledge, are aware of the major challenges across disciplines, and can exploit economies of scale to provide robust answers and better inform policy. We evaluate opportunities and challenges facing the development of a more interactive research environment by developing an interdisciplinary synthesis of research on a single geographic region. We focus on the Amazon as it is of enormous regional and global environmental importance and faces a highly uncertain future. To take stock of existing knowledge and provide a framework for analysis we present a set of mini-reviews from fourteen different areas of research, encompassing taxonomy, biodiversity, biogeography, vegetation dynamics, landscape ecology, earth-atmosphere interactions, ecosystem processes, fire, deforestation dynamics, hydrology, hunting, conservation planning, livelihoods, and payments for ecosystem services. Each review highlights the current state of knowledge and identifies research priorities, including major challenges and opportunities. We show that while substantial progress is being made across many areas of scientific research, our understanding of specific issues is often dependent on knowledge from other disciplines. Accelerating the acquisition of reliable and contextualized knowledge about the fate of complex pristine and modified ecosystems is partly dependent on our ability to exploit economies of scale in shared resources and technical expertise, recognise and make explicit interconnections and feedbacks among sub-disciplines, increase the temporal and spatial scale of existing studies, and improve the dissemination of scientific findings to policy makers and society at large. Enhancing interaction among research efforts is vital if we are to make the most of limited funds and overcome the challenges posed by addressing large-scale interdisciplinary questions. Bringing together a diverse scientific community with a single geographic focus can help increase awareness of research questions both within and among disciplines, and reveal the opportunities that may exist for advancing acquisition of reliable knowledge. This approach could be useful for a variety of globally important scientific questions. Abstract
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Ireland HE, Kite GC, Veitch NC, Chase MW, Schrire B, Lavin M, Linares J, Pennington RT
(2010). Biogeographical, ecological and morphological structure in a phylogenetic analysis of Ateleia (Swartzieae, Fabaceae) derived from combined molecular, morphological and chemical data. Botanical Journal of the Linnean Society
Biogeographical, ecological and morphological structure in a phylogenetic analysis of Ateleia (Swartzieae, Fabaceae) derived from combined molecular, morphological and chemical data
A phylogenetic analysis of combined morphological, chemical and ITS/5.8S sequence data reveals that species of Ateleia are often more genetically than morphologically divergent, and that species thought to be most closely related morphologically are distant relatives within the genus. Ateleia shows niche conservatism, with most species confined to seasonally dry tropical forest in Central America and the Caribbean, and fewer species in the same biome in South America. Four independent transitions to wet forests may have occurred in the genus. The estimated ages of Ateleia lineages spanning Central and South America are either older or younger than the estimated age of closure of the Isthmus of Panama. The older dates clearly suggest that over-water dispersal is responsible for the distribution of Ateleia that includes the Caribbean Islands. © 2010 the Linnean Society of London. Abstract
Pennington T, Ratter J, Gibby M, Blackmore S (2010). Brazilian agriculture. Economist, 396(8699).
Pennington RT, Dick CW
(2010). Diversification of the Amazonian Flora and its Relation to key Geological and Environmental Events: a Molecular Perspective. In (Ed) Amazonia, Landscape and Species Evolution: a Look into the Past
Diversification of the Amazonian Flora and its Relation to key Geological and Environmental Events: a Molecular Perspective
Cody S, Richardson JE, Rull V, Ellis C, Pennington RT
(2010). The great American biotic interchange revisited. Ecography
The great American biotic interchange revisited
The "Great American Biotic Interchange" (GABI) is regarded as a defining event in the biogeography of the Americas. It is hypothesized to have occurred when the Isthmus of Panama closed ca three million years ago (Ma), ending the isolation of South America and permitting the mixing of its biota with that of North America. This view of the GABI is based largely upon the animal fossil record, but recent molecular biogeographic studies of plants that show repeated instances of long-distance dispersal over major oceanic barriers suggest that perhaps the land bridge provided by the isthmus may have been less necessary for plant migration. Here we show that plants have significantly earlier divergence time estimates than animals for historical migration events across the Isthmus of Panama region. This difference in timing indicates that plants had a greater propensity for dispersal over the isthmus before its closure compared with animals. The GABI was therefore asynchronous for plants and animals, which has fundamental implications for the historical assembly of tropical biomes in the most species-rich forests on the planet. © 2010 the Authors. Journal compilation © 2010 Ecography. Abstract
Smith GF, Figueiredo E, Pennington T, Davila P
(2009). Getting that grant: How to convince an evaluation panel that your proposal is worthy of funding. Taxon
Getting that grant: How to convince an evaluation panel that your proposal is worthy of funding
For some years the International Association for Plant Taxonomy (IAPT) has sponsored research grants in plant systematics to young scientists, predominantly from developing countries. At the meeting of Council, held on 12 January 2008 in Pretoria, South Africa, the first such meeting held in Africa, it was decided to review the programme and to provide applicants with advice on how to write a successful proposal. Guidelines for proposal writing are given here. Abstract
Honorio Coronado EN, Baker TR, Phillips OL, Pitman NCA, Pennington RT, Vásquez Martínez R, Monteagudo A, Mogollón H, Dávila Cardozo N, Ríos M, et al
(2009). Multi-scale comparisons of tree composition in Amazonian terra firme forests. Biogeosciences
Multi-scale comparisons of tree composition in Amazonian terra firme forests
We explored the floristic composition of terra firme forests across Amazonia using 55 plots. Firstly, we examined the floristic patterns using both genus-and specieslevel data and found that the species-level analysis more clearly distinguishes among forests. Next, we compared the variation in plot floristic composition at regional-and continental-scales, and found that average among-pair floristic similarity and its decay with distance behave similarly at regional-and continental-scales. Nevertheless, geographical distance had different effects on floristic similarity within regions at distances Abstract
Simon MF, Grether R, De Queiroz LP, Skemae C, Pennington RT, Hughes CE
(2009). Recent assembly of the Cerrado, a neotropical plant diversity hotspot, by in situ evolution of adaptations to fire. Proceedings of the National Academy of Sciences of the United States of America
Recent assembly of the Cerrado, a neotropical plant diversity hotspot, by in situ evolution of adaptations to fire
The relative importance of local ecological and larger-scale historical processes in causing differences in species richness across the globe remains keenly debated. To gain insight into these questions, we investigated the assembly of plant diversity in the Cerrado in South America, the world's most species-rich tropical savanna. Time-calibrated phylogenies suggest that Cerrado lineages started to diversify less than 10 Mya, with most lineages diversifying at 4 Mya or less, coinciding with the rise to dominance of flammable C4 grasses and expansion of the savanna biome worldwide. These plant phylogenies show that Cerrado lineages are strongly associated with adaptations to fire and have sister groups in largely fire-free nearby wet forest, seasonally dry forest, subtropical grassland, or wetland vegetation. These findings imply that the Cerrado formed in situ via recent and frequent adaptive shifts to resist fire, rather than via dispersal of lineages already adapted to fire. The location of the Cerrado surrounded by a diverse array of species-rich biomes, and the apparently modest adaptive barrier posed by fire, are likely to have contributed to its striking species richness. These findings add to growing evidence that the origins and historical assembly of species-rich biomes have been idiosyncratic, driven in large part by unique features of regional- and continental-scale geohistory and that different historical processes can lead to similar levels of modern species richness. Abstract
Pirie MD, Klitgaard BB, Pennington RT
(2009). Revision and biogeography of Centrolobium (Leguminosae - Papilionoideae). Systematic Botany
Revision and biogeography of Centrolobium (Leguminosae - Papilionoideae)
A taxonomic revision and biogeographic study of the genus Centrolobium (Leguminosae - Papilionoideae) is presented. Centrolobium includes important timber trees distributed disjunctly in seasonally dry tropical forests and rain forests in Central and South America, from Panama to south-eastern Brazil. It is characterized by large samaroid pods with a spiny seed case and an abundance of orange peltate glands covering the leaves and inflorescences. Taxonomic distinctions between some species of Centrolobium have been a source of con- fusion. Here, seven species are recognized: C. robustum, C. microchaete, C. tomentosum, C. ochroxylum, C. sclerophyllum, C. paraense, and C. yavi- zanum. Previously recognized varieties of C. paraense, C. paraense var. paraense and C. paraense var. orinocense, are not maintained. Phylogenetic analysis of DNA sequence data from the internal transcribed spacer region of nuclear ribosomal DNA and the plastid matK gene and trnL-trnF intron and spacer support the monophyly of the genus. Different molecular dating methods indicate that the Centrolobium crown group and lineages found to the west and east of the Andes diverged before the Pleistocene. Divergences between species occurring east of the Andes, particularly in Bolivia and south-eastern Brazil are more recent, but nevertheless unlikely to be explained by Pleistocene climatic changes. © Copyright 2009 by the American Society of Plant Taxonomists. Abstract
Hollingsworth ML, Andra Clark A, Forrest LL, Richardson J, Pennington RT, Long DG, Cowan R, Chase MW, Gaudeul M, Hollingsworth PM, et al
(2009). Selecting barcoding loci for plants: Evaluation of seven candidate loci with species-level sampling in three divergent groups of land plants. Molecular Ecology Resources
Selecting barcoding loci for plants: Evaluation of seven candidate loci with species-level sampling in three divergent groups of land plants
There has been considerable debate, but little consensus regarding locus choice for DNA barcoding land plants. This is partly attributable to a shortage of comparable data from all proposed candidate loci on a common set of samples. In this study, we evaluated the seven main candidate plastid regions (rpoC1, rpoB, rbcL, matK, trnH-psbA, atpF-atpH, psbK-psbI) in three divergent groups of land plants [Inga (angiosperm); Araucaria (gymnosperm); Asterella s.l. (liverwort)]. Across these groups, no single locus showed high levels of universality and resolvability. Interspecific sharing of sequences from individual loci was common. However, when multiple loci were combined, fewer barcodes were shared among species. Evaluation of the performance of previously published suggestions of particular multilocus barcode combinations showed broadly equivalent performance. Minor improvements on these were obtained by various new three-locus combinations involving rpoC1, rbcL, matK and trnH-psbA, but no single combination clearly outperformed all others. In terms of absolute discriminatory power, promising results occurred in liverworts (e.g. c. 90% species discrimination based on rbcL alone). However, Inga (rapid radiation) and Araucaria (slow rates of substitution) represent challenging groups for DNA barcoding, and their corresponding levels of species discrimination reflect this (upper estimate of species discrimination = 69% in Inga and only 32% in Araucaria; mean = 60% averaging all three groups). © 2009 Blackwell Publishing Ltd. Abstract
Kursar TA, Dexter KG, Lokvam J, Pennington RT, Richardson JE, Weber MG, Murakami ET, Drake C, McGregor R, Coley PD, et al
(2009). The evolution of antiherbivore defenses and their contribution to species coexistence in the tropical tree genus Inga. Proceedings of the National Academy of Sciences of the United States of America
The evolution of antiherbivore defenses and their contribution to species coexistence in the tropical tree genus Inga
Plants and their herbivores constitute more than half of the organisms in tropical forests. Therefore, a better understanding of the evolution of plant defenses against their herbivores may be central for our understanding of tropical biodiversity. Here, we address the evolution of antiherbivore defenses and their possible contribution to coexistence in the Neotropical tree genus Inga (Fabaceae). Inga has >300 species, has radiated recently, and is frequently one of the most diverse and abundant genera at a given site. For 37 species from Panama and Peru we characterized developmental, ant, and chemical defenses against herbivores. We found extensive variation in defenses, but little evidence of phylogenetic signal. Furthermore, in a multivariate analysis, developmental, ant, and chemical defenses varied independently (were orthogonal) and appear to have evolved independently of each other. Our results are consistent with strong selection for divergent defensive traits, presumably mediated by herbivores. In an analysis of community assembly, we found that Inga species co-occurring as neighbors are more different in antiherbivore defenses than random, suggesting that possessing a rare defense phenotype increases fitness. These results imply that interactions with herbivores may be an important axis of niche differentiation that permits the coexistence of many species of Inga within a single site. Interactions between plants and their herbivores likely play a key role in the generation and maintenance of the conspicuously high plant diversity in the tropics. Abstract
Pennington RT, Lavin M, Oliveira-Filho A
(2009). Woody plant diversity, evolution, and ecology in the tropics: Perspectives from seasonally dry tropical forests. Annual Review of Ecology, Evolution, and Systematics
Woody plant diversity, evolution, and ecology in the tropics: Perspectives from seasonally dry tropical forests
This review suggests that the ecology and patchy global distribution of seasonally dry tropical forest (SDTF) has distinctively structured the evolutionary history and biogeography of woody plant groups that are confined to it. SDTFs have few widespread woody plant species causing high Β-diversity between separate areas of forests. These separate areas contain geologically old, monophyletic clades of endemic plant species that often have geographically structured intraspecific genetic variation. These patterns of diversity, endemism, and phylogeny indicate a stable, dispersal-limited SDTF system. SDTF species tend to belong to larger clades confined to this vegetation, exemplifying phylogenetic niche conservatism, and we argue that this is evidence that the SDTF is a metacommunity (biome) for woody plant clades. That phylogenetic, population genetic, biogeographic, and community ecological patterns differ in woody plants from tropical rain forests and savannas suggests a hypothesis that broad ecological settings strongly influence plant diversification in the tropics. Copyright © 2009 by Annual Reviews. All rights reserved. Abstract
Honorio EN, Pennington TR, Freitas LA, Nebel G, Baker TR (2008). Análisis de la composición florística de los bosques de Jenaro Herrera, Loreto, Perú. Revista Peruana de Biología, 15(1), 53-60.
Dawson IK, Hollingsworth PM, Doyle JJ, Kresovich S, Weber JC, Sotelo Montes C, Pennington TD, Pennington RT
(2008). Origins and genetic conservation of tropical trees in agroforestry systems: a case study from the Peruvian Amazon. Conservation Genetics
Origins and genetic conservation of tropical trees in agroforestry systems: a case study from the Peruvian Amazon
Hundreds of native tree species are currently found in extensive agroforestry ecosystems in the Peruvian Amazon, forming an important reservoir of biodiversity. To further promote conservation, farmers are encouraged to supplement intra-specific genetic diversity in these populations with seed collected from local forests. For some tree species, however, this approach may be inappropriate, as stands of these taxa already found on-farm may not be of local origin. Despite this issue being of importance for conservation, little information is available on the history of cultivated trees in the region, a situation that we here rectify for the important fruit tree Inga edulis. Based on nuclear SSR and chloroplast DHPLC analyses of closely geographically matched natural and planted stands at five sites, it appears that cultivated material of I. edulis is primarily of non-local origin, indicating that conservation based on new wide-scale infusions from local wild stands into farms may be inappropriate in the region. Although nuclear and chloroplast diversity were both lower in planted stands, values were still relatively high (∼80 and 70% of natural stands, respectively), indicating that when farmers plant trees, good collection practice of seed from already cultivated I. edulis should be an effective means for ensuring long-term conservation on farms. © 2007 Springer Science+Business Media B.V. Abstract
Caetano S, Prado D, Pennington RT, Beck S, Oliveira-Filho A, Spichiger R, Naciri Y
(2008). The history of Seasonally Dry Tropical Forests in eastern South America: Inferences from the genetic structure of the tree Astronium urundeuva (Anacardiaceae). Molecular Ecology
The history of Seasonally Dry Tropical Forests in eastern South America: Inferences from the genetic structure of the tree Astronium urundeuva (Anacardiaceae)
Today, the Seasonally Dry Tropical Forests (SDTF) of eastern South America occur as large, well-defined nuclei (e.g. Caatinga in the northeast) and as smaller enclaves within other vegetations (e.g. Cerrado and Chaco). In order to infer the way the present SDTF distribution was attained, the genetic structure of Astronium urundeuva, a tree confined to SDTF, was assessed using two chloroplast spacers and nine microsatellite loci. Five haplotypes were identified, whose distribution was spatially structured. The distribution of the two most common and divergent haplotypes suggested former vicariance and progressive divergence due to isolation. More recent range expansions of these two lineages subsequently occurred, leading to a secondary contact at the southern limit of the Caatinga SDTF nucleus. The multilocus-Bayesian approach using microsatellites consistently identified three groups of populations (Northeast, Central and Southwest). Isolation by distance was found in Northeast and Southwest groups whereas admixture was detected in the Central group, located at the transition between Caatinga and Cerrado domains. All together, the results support the existence of range expansions and secondary contact in the Central group. This study provides arguments that favour the existence of a previously more continuous formation of SDTF in eastern South America. © 2008 the Authors. Abstract
Citerne HL, Pennington RT, Cronk QCB
(2006). An apparent reversal in floral symmetry in the legume Cadia is a homeotic transformation. Proceedings of the National Academy of Sciences of the United States of America
An apparent reversal in floral symmetry in the legume Cadia is a homeotic transformation
Within papilionoid legumes, characterized by flowers with strong bilateral symmetry, a derived condition within angiosperms, Cadia (Cadia porpurea) has reverted to radially symmetrical flowers. Here, we investigate the genetic basis of this morphological reversal. Two orthologues of the floral symmetry gene CYCLOIDEA (CYC) demarcate the adaxial (dorsal) region of the flower in typical papilionoid legumes. In the model legume Lotus japonicus, one of these LegCYC genes has been shown, like CYC, to be required for the establishment of floral bilateral symmetry. This study shows that these genes are expressed in the adaxial region of the typical papilionoid flower of Lupinus, which belongs to the same papilionoid subclade as Cadia. In Cadia, these genes also are expressed, but the expression pattern of one of these has expanded from the adaxial to the lateral and abaxial regions of the corolla. This result suggests that the radial flowers of Cadia are dorsalized and, therefore, are not a true evolutionary reversal but an innovative homeotic transformation, where, in this case, all petals have acquired dorsal identity. This study raises a question over other putative reversals in animals and plants, which also may be cryptic innovations. © 2006 by the National Academy of Sciences of the USA. Abstract
Pennington RT, Richardson JE, Lavin M
(2006). Insights into the historical construction of species-rich biomes from dated plant phylogenies, neutral ecological theory and phylogenetic community structure. New Phytologist
Insights into the historical construction of species-rich biomes from dated plant phylogenies, neutral ecological theory and phylogenetic community structure
Analytical methods are now available that can date all nodes in a molecular phylogenetic tree with one calibration, and which correct for variable rates of DNA substitution in different lineages. Although these techniques are approximate, they offer a new tool to investigate the historical construction of species-rich biomes. Dated phylogenies of globally distributed plant families often indicate that dispersal, even across oceans, rather than plate tectonics, has generated their wide distributions. By contrast, there are indications that animal lineages have undergone less long distance dispersal. Dating the origin of biome-specific plant groups offers a means of estimating the age of the biomes they characterize. However, rather than a simple emphasis on biome age, we stress the importance of studies that seek to unravel the processes that have led to the accumulation of large numbers of species in some biomes. The synthesis of biological inventory, systematics and evolutionary biology offered by the frameworks of neutral ecological theory and phylogenetic community structure offers a promising route for future work. © the Authors (2006). Abstract
Cronk Q, Ojeda I, Pennington RT
(2006). Legume comparative genomics: Progress in phylogenetics and phylogenomics. Current Opinion in Plant Biology
Legume comparative genomics: Progress in phylogenetics and phylogenomics
The legumes are the focus of numerous rapidly expanding genomic projects, all of which involve members of one part of the Leguminosae, the subfamily Papilionoideae. This subfamily is monophyletic, and recent studies concur on a series of clades within it that are well supported and have received informal names. These include the Cladrastis clade, the genistoids (including Lupinus), the mirbelioids, the dalbergioids (including Arachis), the millettioids (including Glycine and Phaseolus), and the hologalegina (galegoid) legumes, which comprise the robinioids (including Lotus) and the inverted repeat loss (IRL) clade (including Medicago and Pisum). The canavanine-accumulating legumes appear to fall into a single clade, consistent with the idea that the production of this toxic amino acid evolved only once. Recent advances in analytical techniques for dating phylogenies support an 'early explosion hypothesis', suggesting that much of the morphological diversity of the legume family evolved rapidly around 50-60 million years ago. Within the papilionoids, the divergence between Glycine and Medicago is estimated to have taken place around 54 million years ago. There is strong evidence for a palaeoduplication event that affected both Glycine (a millettioid) and Medicago (from the IRL clade). As more genomic data are forthcoming for Arachis, it will be possible to test whether this event extends to the dalbergioids. © 2005 Elsevier Ltd. All rights reserved. Abstract
Wilkie P, Clark A, Pennington RT, Cheek M, Bayer C, Wilcock CC
(2006). Phylogenetic relationships within the subfamily sterculioideae (Malvaceae/Sterculiaceae-Sterculieae) using the chloroplast gene ndhF. Systematic Botany
Phylogenetic relationships within the subfamily sterculioideae (Malvaceae/Sterculiaceae-Sterculieae) using the chloroplast gene ndhF
A parsimony analysis of ndhF nucleotide sequences representing 24 species and 13 genera of Sterculioideae strongly supports (100% bootstrap) the monophyly of the group. Within the Sterculioideae clade four major clades are recognized with good bootstrap support but relationships among them are not resolved. This analysis suggests the recognition of Argyrodendron as separate from Heritiera, supports Acropogon as separate from Sterculia, and Tarrietia as part of Heritiera. The current circumscriptions of Hildegardia and Firmiana are not supported. The use of fruit characters in the delimitation of genera within Sterculioideae may not be appropriate in some cases and other morphological characters need to be found. © Copyright 2006 by the American Society of Plant Taxonomists. Abstract
Naciri-Graven Y, Caetano S, Prado D, Pennington RT, Spichiger R
(2005). Development and characterization of 11 microsatellite markers in a widespread Neotropical seasonally dry forest tree species, Geoffroea spinosa Jacq. (Leguminosae). Molecular Ecology Notes
Development and characterization of 11 microsatellite markers in a widespread Neotropical seasonally dry forest tree species, Geoffroea spinosa Jacq. (Leguminosae)
Eleven dinucleotide microsatellites were developed in Geoffroea spinosa (Leguminosae), a widespread tree of the seasonally dry Neotropical forests, and characterized on six populations from Peru, Argentina and Paraguay. Four of them amplified on the Peruvian populations only, probably because of mutations in the microsatellite flanking regions in the other populations. Ten microsatellites were found polymorphic, with within population gene diversities ranging from 0.17 to 0.95, and a number of alleles varying from seven to 19. A significant overall genetic differentiation was also found (θ = 0.212; P < 0.01). © 2005 Blackwell Publishing Ltd. Abstract
Coley PD, Lokvam J, Rudolph K, Bromberg K, Sackett TE, Wright L, Brenes-Arguedas T, Dvorett D, Ring S, Clark A, et al
(2005). Divergent defensive strategies of young leaves in two species of Inga. Ecology
Divergent defensive strategies of young leaves in two species of Inga
In the recently radiated genus Inga (Fabaceae), few nucleotide substitutions have accumulated among species, yet large divergences have occurred in defensive phenotypes, suggesting strong selection by herbivores. We compared herbivory and defenses of young leaves for I. goldmanii, a more derived species that follows a "defense" strategy, and I. umbellifera, a more basal species that follows an "escape" strategy. The two species suffered similar rates of herbivory (22% of the leaf area eaten during expansion) but were attacked by different communities of herbivores. I. goldmanii relied heavily on extra-floral nectaries and on a diversity of effective secondary metabolites, while I. umbellifera minimized damage through rapid leaf expansion and synchronous flushing. The major classes of secondary compounds in both species were flavanoids and non-protein amino acids; however, there were large differences in structure, biosynthetic pathways, and efficacy against herbivores. Growth rates of lepidopteran larvae were significantly lower when fed artificial diets with crude extracts from I. goldmanii as compared to I. umbellifera. Flavanoids accounted for the majority of growth reduction in both species. I. umbellifera had more unusual flavanoids and a non-protein amino acid not reported from plants, but the more common flavanoids found in I. goldmanii were more bioactive against herbivores. I. goldmanii also had greater ant visitation to extrafloral nectaries, suggesting that there was no trade-off between biotic and chemical defenses. In contrast, young leaves of I. umbellifera expanded more rapidly, minimizing the window of vulnerability before toughening. Resources for rapid expansion may have been reallocated from chloroplast development as I. umbellifera delayed the greening process until after full leaf expansion. Leaves were also produced synchronously, which can satiate herbivores and reduce damage. These defense differences, are reflected in almost completely nonoverlapping herbivore faunas and the more frequent occurrence of generalists on I. umbellifera. To understand why defenses have evolved, it is important to view them in light of the herbivore community as well as in the context of the other co-occurring traits. We hypothesize that the effectiveness of chemical defenses determines whether a species follows the evolutionary path of "defense" or "escape" strategies. © 2005 by the Ecological Society of America. Abstract
Hollingsworth PM, Dawson IK, Goodall-Copestake WP, Richardson JE, Weber JC, Montes CS, Pennington RT
(2005). Do farmers reduce genetic diversity when they domesticate tropical trees? a case study from Amazonia. Molecular Ecology
Do farmers reduce genetic diversity when they domesticate tropical trees? a case study from Amazonia
Agroforestry ecosystems may be an important resource for conservation and sustainable use of tropical trees, but little is known of the genetic diversity they contain. Inga edulis, a widespread indigenous fruit tree in South America, is used as a model to assess the maintenance of genetic diversity in five planted vs. five natural stands in the Peruvian Amazon. Analysis of five SSR (simple sequence repeat) loci indicated lower allelic variation in planted stands [mean corrected allelic richness 31.3 (planted) and 39.3 (natural), P = 0.009]. Concerns regarding genetic erosion in planted Amazonian tree stands appear valid, although allelic variation on-farm is still relatively high. Abstract
Kenicer GJ, Kajita T, Pennington RT, Murata J
(2005). Systematics and biogeography of Lathyrus (Leguminosae) based on internal transcribed spacer and cpDNA sequence data. American Journal of Botany
Systematics and biogeography of Lathyrus (Leguminosae) based on internal transcribed spacer and cpDNA sequence data
Lathyrus (Leguminosae; Papilionoideae) is the largest genus in tribe Fabeae and exhibits an intriguing extratropical distribution. We studied the systematics and biogeography of Lathyrus using sequence data, from accessions representing 53 species, for the internal transcribed spacer plus 5.8S-coding region of nuclear ribosomal DNA as well as the trnL-F and trnS-G regions of chloroplast DNA. Our results generally supported recent morphology-based classifications, resolving clades corresponding to sections Lathyrus and Lathyrostylis, but question the monophyly of the large, widespread section Orobus sensu Asmussen and Liston. Sections Orobus, Aphaca, and Pratensis form a predominantly northern Eurasian-New World clade. Within this clade, the North American and eastern Eurasian species, including both Holarctic species (L. palustris and L. japonicus), form a transberingian clade of relatively recent origin and diversification. The South American Notolathyrus group is distant from this transberingian lineage and should be reinstated as a distinct section within the northern Eurasian-New World clade. The Notolathyrus lineage reached the New World most probably through long-distance dispersal from Eurasia. The remaining sections in the genus are centered on the Mediterranean region. Abstract
Bramley GLC, Pennington RT, Zakaria R, Tjitrosoedirdjo SS, Cronk QCB
(2004). Assembly of tropical plant diversity on a local scale: Cyrtandra (Gesneriaceae) on Mount Kerinci, Sumatra. Biological Journal of the Linnean Society
Assembly of tropical plant diversity on a local scale: Cyrtandra (Gesneriaceae) on Mount Kerinci, Sumatra
At a regional scale, the high species numbers (gamma diversity) of tropical forests have been explained by either a gradual accumulation of species through time (museum hypothesis) or, by contrast, rapid recent speciation in large genera. However, the origins of local rain forest diversity (alpha diversity) have been given little attention. Cyrtandra (Gesneriaceae), an understorey genus in the highly species-rich Indo-Malayan rain forest, has considerable capacity for producing local endemics, making it particularly suitable for studying diversity on a local scale. We sampled Cyrtandra species from one community on Mount Kerinci, Sumatra, and phylogenetic analyses of ITS sequences suggest that this community is an assembly of three distinct phyletic lineages: (1) a group of herbaceous or subshrub plants of Bornean affinity, (2) one member of a group of widespread shrubs forming Cyrtandra section Dissimiles and (3) a second group of shrubs. The evolutionary origin of this community is therefore not a result of rapid and recent speciation: it is assembled from species resulting from a gradual accumulation of diversity through time (museum hypothesis), although one lineage shows evidence of more recent, continuing speciation than the other two. The community includes two distantly related, apparently endemic species, but there is no evidence for a local adaptive radiation. The protection of representative species from each lineage would allow the conservation of genetic diversity. © 2004 the Linnean Society of London, Biological Journal of the Linnean Society, 2004, 81, 49-62. Abstract
Pennington RT, Lavin M, Prado DE, Pendry CA, Pell SK, Butterworth CA
(2004). Historical climate change and speciation: Neotropical seasonally dry forest plants show patterns of both Tertiary and Quaternary diversification.
Historical climate change and speciation: Neotropical seasonally dry forest plants show patterns of both Tertiary and Quaternary diversification
Pennington RT, Cronk QCB, Richardson JA
(2004). Introduction and synthesis: plant phylogeny and the origin of major biomes. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences
Introduction and synthesis: plant phylogeny and the origin of major biomes
. Phylogenetic trees based upon DNA sequence data, when calibrated with a dimension of time, allow inference of: (i) the pattern of accumulation of lineages through time; (ii) the time of origin of monophyletic groups; (iii) when lineages arrived in different geographical areas; (iv) the time of origin of biome–specific morphologies. This gives a powerful new view of the history of biomes that in many cases is not provided by the incomplete plant fossil record. Dated plant phylogenies for angiosperm families such as Leguminoaceae (Fabaceae), Melastomataceae
. sensu stricto
. Annonaceae and Rhamnaceae indicate that long–distance, transoceanic dispersal has played an important role in shaping their distributions, and that this can obscure any effect of tectonic history, previously assumed to have been the major cause of their biogeographic patterns. Dispersal from other continents has also been i mportant in the assembly of the Amazonian rainforest flora and the Australian flora. Comparison of dated biogeographic patterns of plants and animals suggests that recent long–distance dispersal might be more prevalent in plants, which has major implications for community assembly and coevolution. Dated plant phylogenies also reveal the role of past environmental changes on the evolution of lineages in species–rich biomes, and show that recent Plio–Pleistocene diversification has contributed substantially to their current species richness. Because of the critical role of fossils and morphological characters in assigning ages to nodes in phylogenetic trees, future studies must include careful morphological consideration of fossils and their extant relatives in a phylogenetic context. Ideal study systems will be based upon DNA sequence data from multiple loci and multiple fossil calibrations. This allows cross–validation both of age estimates from different loci, and from different fossil calibrations. For a more complete view of biome history, future studies should emphasize full taxon sampling in ecologically important groups, and should focus on geographical areas for which few species–level phylogenies are available, such as tropical Africa and Asia. These studies are urgent because understanding the history of biomes can both inform conservation decisions, and help predict the effects of future environmental changes at a time when biodiversity is being impacted on an unprecedented scale.
Lavin M, Schrire BP, Lewis G, Pennington RT, Delgado–Salinas A, Thulin M, Hughes CE, Matos AB, Wojciechowski MF
(2004). Metacommunity process rather than continental tectonic history better explains geographically structured phylogenies in legumes. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences
Metacommunity process rather than continental tectonic history better explains geographically structured phylogenies in legumes
Penalized likelihood estimated ages of both densely sampled intracontinental and sparsely sampled transcontinental crown clades in the legume family show a mostly Quaternary to Neogene age distribution. The mode ages of the intracontinental crown clades range from 4–6 Myr ago, whereas those of the transcontinental crown clades range from 8–16 Myr ago. Both of these young age estimates are detected despite methodological approaches that bias results toward older ages. Hypotheses that resort to vicariance or continental history to explain continental disjunct distributions are dismissed because they require mostly Palaeogene and older tectonic events. An alternative explanation centring on dispersal that may well explain the geographical as well as the ecological phylogenetic structure of legume phylogenies is Hubbell's unified neutral theory of biodiversity and biogeography. This is the only dispersalist theory that encompasses evolutionary time and makes predictions about phylogenetic structure. Abstract
Plana V, Gascoigne A, Forrest LL, Harris D, Pennington RT
(2004). Pleistocene and pre-Pleistocene Begonia speciation in Africa. Molecular Phylogenetics and Evolution
Pleistocene and pre-Pleistocene Begonia speciation in Africa
This paper presents a historical biogeographic analysis of African Begonia based on combined internal transcribed spacer (ITS) and trnL intron sequences. Age range estimates for Begonia in Africa ranged from only 1.5 Ma for some terminal nodes to 27 Ma for basal nodes when the ages of Réunion (2 Ma) and Mayotte (5.4 Ma) were used to date the split between Begonia salaziensis and Begonia comorensis. Assuming a more recent origin age for Begonia salaziensis (2 Ma) provided age estimates in other parts of the phylogeny which agreed with patterns observed in other African organisms. A large proportion of the Begonia diversity seen today in Africa is of pre-Pleistocene origin. Species of Pleistocene origin are concentrated in species-rich groups such as sections Loasibegonia, Scutobegonia, and Tetraphila, which have their centre of diversity in western Central Africa. Phylogenetically isolated taxa such as Begonia longipetiolata, Begonia iucunda, and Begonia thomeana date to the late Miocene, a period of extended aridification on the African continent that had severe effects on African rain forest species. A general pattern is identified where phylogenetically isolated species occur outside the main identified rain forest refuges. Endemic species on the island of São Tomé such as Begonia baccata, Begonia molleri, and Begonia subalpestris appear to be palaeoendemics. of these species, the most recent age estimate is for B. baccata, which is dated at ca. 3 Ma. Therefore, São Tomé appears to have functioned as an important (if previously unrecognised) pre-Pleistocene refuge. On the mainland, areas such as the Massif of Chaillu in Gabon, southern Congo (Brazzaville), and far western areas of Congo (Kinshasa) have played similar roles to São Tomé. © 2003 Elsevier Inc. All rights reserved. Abstract
Pennington RT, Dick CW
(2004). The role of immigrants in the assembly of the South American rainforest tree flora.
The role of immigrants in the assembly of the South American rainforest tree flora
Citerne HL, Luo D, Pennington RT, Coen E, Cronk QCB
(2003). A phylogenomic investigation of CYCLOIDEA-like TCP genes in the leguminosae. Plant Physiology
A phylogenomic investigation of CYCLOIDEA-like TCP genes in the leguminosae
Numerous TCP genes (transcription factors with a TCP domain) occur in legumes. Genes of this class in Arabidopsis (TCP1) and snapdragon (Antirrhinum majus; CYCLOIDEA) have been shown to be asymmetrically expressed in developing floral primordia, and in snapdragon, they are required for floral zygomorphy (bilaterally symmetrical flowers). These genes are therefore particularly interesting in Leguminosae, a family that is thought to have evolved zygomorphy independently from other zygomorphic angiosperm lineages. Using a phylogenomic approach, we show that homologs of TCP1/CYCLOIDEA occur in legumes and may be divided into two main classes (LEGCYC group I and II), apparently the result of an early duplication, and each class is characterized by a typical amino acid signature in the TCP domain. Furthermore, group I genes in legumes may be divided into two subclasses (LEGCYC IA and IB), apparently the result of a duplication near the base of the papilionoid legumes or below. Most papilionoid legumes investigated have all three genes present (LEGCYC IA, IB, and II), inviting further work to investigate possible functional difference between the three types. However, within these three major gene groups, the precise relationships of the paralogs between species are difficult to determine probably because of a complex history of duplication and loss with lineage sorting or heterotachy (within-site rate variation) due to functional differentiation. The results illustrate both the potential and the difficulties of orthology determination in variable gene families, on which the phylogenomic approach to formulating hypotheses of function depends. Abstract
Bridgewater S, Pennington RT, Reynel CA, Daza A, Pennington TD
(2003). A preliminary floristic and phytogeographic analysis of the woody flora of seasonally dry forests in northern Peru. CANDOLLEA
(1), 129-148. Author URL
Bridgewater S, Pennington RT, Reynel CA, Daza A, Pennington TD
(2003). A preliminary floristic and phytogeographic analysis of the woody flora of seasonally dry forests in northern Peru. Candollea
(PART 1), 129-148.
A preliminary floristic and phytogeographic analysis of the woody flora of seasonally dry forests in northern Peru
Inventory data and general woody floristic lists are presented for northern Peruvian seasonally dry tropical forests (SDTFs). These preliminary data record ca. 250 woody species for the SDTFs around Tumbes, the inter-andean valleys and around Tarapoto. High levels of endemism are shown in these SDTFs, with between 13-20% of their tree species recognised as narrow regional endemics. A comparison of disjunct SDTF patches on the Pacific coast, in the Marañon drainage and around Tarapoto reveals only low floristic similarity (ca. 2-10%) between them, suggesting considerable barriers to species movement. Present day barriers arc represented by the Eastern and Western Andean Massifs. However, an examination of the disjunct species distribution patterns suggest that either species migration between the Marañon drainage and the Pacific region over the Andes has recently occurred via the Porculla Gap, or these areas were once continuous before the uplift of the Andes. A comparison of Peruvian dry forest plot data with inventories from southern Ecuador and Bolivia indicates that the northern Peruvian Tumbes and Marañon dry forests, and those of southern Ecuador may constitute a distinct phytogeographical unit. Abstract
Kite GC, Pennington RT
(2003). Quinolizidine alkaloid status of Styphnolobium and Cladrastis (Leguminosae). Biochemical Systematics and Ecology
Quinolizidine alkaloid status of Styphnolobium and Cladrastis (Leguminosae)
Reports of quinolizidine alkaloids in Styphnolobium Schott and Cladrastis Raf. (Leguminosae) conflict with their position in recent molecular phylogenies because they are not members of a major clade of quinolizidine alkaloid-accumulating taxa. The alkaloid status of these two genera was therefore re-investigated using gas chromatography-mass spectrometry. Quinolizidine alkaloids could not be detected in extracts of leaves, flowers or seeds of S. japonicum (L.) Schott, nor in leaves of S. affine (Torrey & A. Gray) Walp. C. delavayi (Franch.) Prain, C. kentukea (Dum.-Cours.) Rudd or C. platycarpa Mak. In contrast, Calia secundiflora (Ortega) Yakovlev, also currently placed outside the major clade of quinolizidine alkaloid-producing genera in molecular phylogenies, was confirmed to accumulate a range of quinolizidine alkaloids. © 2003 Elsevier Ltd. All rights reserved. Abstract
Lewis GP, Knudsen JT, Klitgaard BB, Pennington RT
(2003). The floral scent of Cyathostegia mathewsii (Leguminosae, Papilionoideae) and preliminary observations on reproductive biology. Biochemical Systematics and Ecology
The floral scent of Cyathostegia mathewsii (Leguminosae, Papilionoideae) and preliminary observations on reproductive biology
The chemical composition of the floral scent of two populations of Cyathostegia mathewsii (Benth.) Schery (Leguminosae, Papilionoideae, Swartzieae) were studied to test if the species is wind pollinated (as is reported for its close relative Ateleia herbert-smithii Pittier), beetle pollinated, or possesses a mixed pollination syndrome. Studies of flower visitors suggest that at night, the species might be pollinated by beetles. Only one species of beetle (Phyllophaga sp. Scarabaeidae, Melolonthinae) was caught on all individuals observed. Floral scent, collected in situ with headspace methods from flowers of three individuals of C. mathewsii, mainly contained unsaturated fatty acid derivatives, including heptadecene, and oxygenated monoterpenes, such as linalool and its oxides, as well as minor amounts of benzenoid compounds and sesquiterpenes. The composition of the scent does not preclude beetles as one of the pollinators of C. mathewsii, but it does not point towards beetles as the sole pollinators. Beetle pollination has previously only been reported from one other legume genus, Acacia (Bernhardt, 1989; Hawkeswood, 1983, 1989; Tybirk, 1993). This paper represents a second legume-beetle relationship within this diverse plant family. © 2003 Elsevier Science Ltd. All rights reserved. Abstract
Pennington RT (2002). (1533) Proposal to change the authorship of Andira, nom. cons. (Leguminosae-Papilionoideae) and to conserve it with a conserved type. Taxon, 51(2), 385-386.
Cortés-Burns H, Schrire BD, Pennington RT, Miller AG
(2002). A taxonomic revision of Socotran Indigofereae (Leguminosae - Papilionoideae) with insights into the phytogeographical links of the Socotran archipelago. Nordic Journal of Botany
A taxonomic revision of Socotran Indigofereae (Leguminosae - Papilionoideae) with insights into the phytogeographical links of the Socotran archipelago
This revision of Socotran Indigofereae (Leguminosae) treats two genera, Microcharis and Indigofera, and 16 species, one with two varieties. Indigofera coerulea var. coerulea and I. nugalensis are new records for the archipelago. Indigofera nephrocarpoides, I. marmorata (lectotypified here) and I. socotrana are endemic, whilst Microcharis disjuncta var. fallax and Indigofera nugalensis are near-endemic to the Socotran islands. This study indicates that the closest relatives of the Socotran Indigofereae are to be found in African lineages. The strongest affinities are between Socotra and extreme NE Somalia (Indigofera pseudointricata, I. nugalensis) and, to a lesser extent, with SW Oman (Microcharis disjuncta var. fallax), SW Pakistan (I. nephrocarpa) and Southern Yemen. Socotran Indigofereae are mainly derived from Tertiary African palaeotropical and drought-adapted lineages. We also suggest that following the separation of the islands from mainland Africa some Indigofereae would have reached the archipelago as a result of recent, long-distance dispersal events. Abstract
Warwick MC, Pennington RT
(2002). Revision of Cyclolobium (Leguminosae-Papilionoideae). Edinburgh Journal of Botany
Revision of Cyclolobium (Leguminosae-Papilionoideae)
Cyclolobium (Leguminosae-Papilionoideae-Millettieae) has traditionally comprised six species, but doubts have been expressed as to their distinctness. Analysis of morphological variation across the range of the genus indicates Cyclolobium comprises a single species, C. brasiliense Benth. Abstract
Moylan EC, Pennington RT, Scotland RW
(2002). Taxonomic account of Hemigraphis Nees (Strobilanthinae-Acanthaceae) from the Philippines. Kew Bulletin
Taxonomic account of Hemigraphis Nees (Strobilanthinae-Acanthaceae) from the Philippines
A taxonomic account of Hemigraphis Nees from the Philippines is provided. A pattern-based species concept is adopted and 18 species of Hemigraphis from the Philippines are recognised. Six species have an extended distribution beyond the Philippine archipelago. Three species are archipelagic endemics and nine species are restricted island endemics. One new species, Hemigraphis zwickeyae, is described from the islands of Luzon and Mindanao. Abstract
Pennington RT, Lavin M, Ireland H, Klitgaard B, Preston J, Hu JM
(2001). Phylogenetic relationships of basal Papilionoid legumes based upon sequences of the chloroplast trnL intron. Systematic Botany
Phylogenetic relationships of basal Papilionoid legumes based upon sequences of the chloroplast trnL intron
The Swartzieae, Sophoreae, Dipterygeae, and Dalbergieae are considered the most basal tribes of the subfamily Papilionoideae (Leguminosae). Nucleotide sequences from the chloroplast trnL intron for the majority of genera of these tribes were analyzed cladistically together with placeholder representatives of more derived tribes. Preliminary results indicate radical changes are necessary for papilionoid classification because Swartzieae, Sophoreae, and Dalbergieae are polyphyletic. Their constituent genera are mixed in a series of monophyletic groups, many of which have never been proposed previously, and the relationships amongst which are poorly resolved. Some of these groups, such as the genistoid and dalbergioid clades, are species-rich because they contain major papilionoid radiations. In other cases, putatively basal genera form small clades with no derived taxa included. There is weak evidence that Bobgunnia, Swartzia, Cyathostegia, Bocoa, and Ateleia (all Swartzieae) may be the sister group to all other papilionoids, and that a large clade is congruent with a 50kb inversion in the chloroplast large single copy (LSC) region. Abstract
Richardson JE, Pennington RT, Pennington TD, Hollingsworth PM
(2001). Rapid Diversification of a Species-Rich Genus of Neotropical Rain Forest Trees. Science
Rapid Diversification of a Species-Rich Genus of Neotropical Rain Forest Trees
. Species richness in the tropics has been attributed to the gradual accumulation of species over a long geological period in stable equatorial climates or, conversely, to speciation in response to late Tertiary geological events and unstable Pleistocene climates. DNA sequence data are consistent with recent diversification in
. a species-rich neotropical tree genus. We estimate that speciation was concentrated in the past 10 million years, with many species arising as recently as 2 million years ago. This coincides with the more recent major uplifts of the Andes, the bridging of the Isthmus of Panama, and Quaternary glacial cycles.
. may be representative of other species-rich neotropical genera with rapid growth and reproduction, which contribute substantially to species numbers in the world's most diverse flora.
Lavin M, Pennington RT, Klitgaard BB, Sprent JI, De Lima HC, Gasson PE
(2001). The dalbergioid legumes (fabaceae): Delimitation of a pantropical monophyletic clade. American Journal of Botany
The dalbergioid legumes (fabaceae): Delimitation of a pantropical monophyletic clade
A monophyletic pantropical group of papilionoid legumes, here referred to as the "dalbergioid" legumes, is circumscribed to include all genera previously referred to the tribes Aeschynomeneae and Adesmieae, the subtribe Bryinae of the Desmodieae, and tribe Dalbergieae except Andira, Hymenolobium, Vatairea, and Vataireopsis. This previously undetected group was discovered with phylogenetic analysis of DNA sequences from the chloroplast trnK (including matK) and trnL introns, and the nuclear ribosomal 5.8S and flanking internal transcribed spacers 1 and 2. All dalbergioids belong to one of three well-supported subclades, the Adesmia, Dalbergia, and Pterocarpus clades. The dalbergioid clade and its three main subclades are cryptic in the sense that they are genetically distinct but poorly, if at all, distinguished by nonmolecular data. Traditionally important taxonomic characters, such as arborescent habit, free stamens, and lomented pods, do not provide support for the major clades identified by the molecular analysis. Short shoots, glandular-based trichomes, bilabiate calyces, and aeschynomenoid root nodules, in contrast, are better indicators of relationship at this hierarchical level. The discovery of the dalbergioid clade prompted a re-analysis of root nodule structure and the subsequent finding that the aeschynomenoid root nodule is synapomorphic for the dalbergioids. Abstract
Lavin M, Thulin M, Labat J-N, Pennington RT (2000). Africa, the Odd Man Out: Molecular Biogeography of Dalbergioid Legumes (Fabaceae) Suggests Otherwise. Systematic Botany, 25(3), 449-449.
PENNINGTON R, GEMEINHOLZER B (2000). Cryptic clades, fruit wall morphology and biology of (Leguminosae: Papilionoideae). Botanical Journal of the Linnean Society, 134(1-2), 267-286.
Ireland H, Pennington RT
(1999). A revision of Geoffroea (Leguminosae-Papilionoideae). Edinburgh Journal of Botany
A revision of Geoffroea (Leguminosae-Papilionoideae)
Geoffroea (Leguminosae-Papilionoideae) has traditionally comprised three species. In this revision the number of species is reduced to two because G. striata (Willd.) Morong is considered indistinct from G. spinosa Jacq. and is placed in synonymy. No significant morphological variation is found between the five isolated areas of distribution of G. spinosa, which occurs in the disjunct seasonally dry tropical forests of South America, and there is certainly no basis for recognizing separate taxa. Abstract
Pennington RT, Aymard G, Cuello N (1997). A New Species of Andira (Leguminosae, Papilionoideae) from the Venezuelan Guayana. Novon, 7(1), 72-72.
Pennington RT (1996). Molecular and Morphological Data Provide Phylogenetic Resolution at Different Hierarchical Levels in Andira. Systematic Biology, 45(4), 496-515.
(1996). Molecular and morphological data provide phylogenetic resolution at different hierarchical levels in Andira. SYSTEMATIC BIOLOGY
(4), 496-515. Author URL
Pennington T, De Lima HC
(1996). Two new species of Andira (Leguminosae) from Brazil and the influence of dispersal in determining their distributions. Kew Bulletin
Two new species of Andira (Leguminosae) from Brazil and the influence of dispersal in determining their distributions
Two new Brazilian species of Andira (Leguminosae, Papilionoideae, tribe Dalbergieae), A. carvalhoi and A. cordata, are described and illustrated. The possible influence of dispersal by either large rodents or bats respectively in determining their distributions is discussed. Abstract
Pennington RT (1995). Cladistic analysis of chloroplast DNA restriction site characters in Andira (Leguminosae: Dalbergieae). American Journal of Botany, 82(4), 526-534.