Neotropical Plant Evolution: Assembling the Big Picture

Aguiar, 2009, Global patterns of speciation and diversity, Nature, 460, 384, 10.1038/nature08168

Alfaro, 2009, Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates, Proceedings of the National Academy of Sciences of the United States of America, 106, 13410, 10.1073/pnas.0811087106

Antonelli, 2009, Tracing the impact of the Andean uplift on Neotropical plant evolution, Proceedings of the National Academy of Sciences, 106, 9749, 10.1073/pnas.0811421106

Antonelli, 2010, Climate cooling promoted the expansion and radiation of a threatened group of South American orchids (Epidendroideae: Laeliinae), Biological Journal of the Linnean Society, 100, 597, 10.1111/j.1095-8312.2010.01438.x

Antonelli, 2011, Why are there so many plant species in the Neotropics?, Taxon, 60, 403, 10.1002/tax.602010

Arakaki, 2011, Contemporaneous and recent radiations of the world's major succulent plant lineages, Proceedings of the National Academy of Sciences of the United States of America, 108, 8379, 10.1073/pnas.1100628108

Ayres, 1992, River boundaries and species range size in Amazonian primates, American Naturalist, 140, 531, 10.1086/285427

Bacon, 2012, Testing geological models of evolution of the Isthmus of Panama in a phylogenetic framework, Botanical Journal of the Linnean Society, 171, 287, 10.1111/j.1095-8339.2012.01281.x

Bardon, 2012, Origin and evolution of the Chrysobalanaceae family: insights into the evolution of plants in the Neotropics, Botanical Journal of the Linnean Society, 171, 19, 10.1111/j.1095-8339.2012.01289.x

Barraclough, 2010, Evolving entities: towards a unified framework for understanding diversity at the species and higher levels, Philosophical Transactions of the Royal Society B, 1547, 1801, 10.1098/rstb.2009.0276

Bates, 2004, Avian mitochondrial DNA sequence divergence across a headwater stream of the Rio Tapajos, a major Amazonian river, Journal of Ornithology, 145, 199, 10.1007/s10336-004-0039-4

Burnham, 1999, The history of Neotropical vegetation: new developments and status, Annals of the Missouri Botanical Garden, 86, 546, 10.2307/2666185

Burnham, 2004, South American paleobotany and the origins of neotropical rainforests, Philosophical Transactions of the Royal Society B, 359, 1595, 10.1098/rstb.2004.1531

Cavender-Bares, 2009, The merging of community ecology and phylogenetic biology, Ecology Letters, 12, 693, 10.1111/j.1461-0248.2009.01314.x

Christenhusz, 2012, Biogeographical patterns of plants in the Neotropics - dispersal rather than tectonics is most explanatory, Botanical Journal of the Linnean Society, 171, 277, 10.1111/j.1095-8339.2012.01301.x

Cody, 2010, The great American biotic interchange revisited, Ecography, 33, 326, 10.1111/j.1600-0587.2010.06327.x

Crisp, 2009, Phylogenetic biome conservatism on a global scale, Nature, 458, 754, 10.1038/nature07764

Crisp, 2012, Phylogenetic niche conservatism: what are the underlying evolutionary and ecological causes?, New Phytologist, 196, 681, 10.1111/j.1469-8137.2012.04298.x

Cronn, 2012, Targeted enrichment strategies for next-generation plant biology, American Journal of Botany, 99, 291, 10.3732/ajb.1100356

Cusimano, 2010, Slowdowns in diversification rates from real phylogenies may not be real, Systematic Biology, 59, 458, 10.1093/sysbio/syq032

Donoghue, 2008, A phylogenetic perspective on the distribution of plant diversity, Proceedings of the National Academy of Sciences, 105, 11549, 10.1073/pnas.0801962105

Drew, 2012, Phylogenetics, biogeography and evolution of dioecy in South American Lepechinia (Lamaiaceae), Botanical Journal of the Linnean Society, 171, 171, 10.1111/j.1095-8339.2012.01325.x

Drummond, 2012, Multiple continental radiations and correlates of diversification in Lupinus (Leguminosae): testing for key innovation with incomplete taxon sampling, Systematic Biology, 61, 443, 10.1093/sysbio/syr126

Drummond, 2007, BEAST: Bayesian evolutionary analysis by sampling trees, BMC Evolutionary Biology, 7, 8, 10.1186/1471-2148-7-214

Edwards, 2010, The origins of C4 grasslands: integrating evolutionary and ecosystem science, Science, 328, 587, 10.1126/science.1177216

Edwards, 2010, Phylogenetic analyses reveal the shady history of C4 grasses, Proceedings of the National Academy of Sciences of the United States of America, 107, 2532, 10.1073/pnas.0909672107

Eiserhardt, 2012, Separating environmental and geographical determinants of phylogenetic community structure in Amazonian palms (Arecaceae), Botanical Journal of the Linnean Society, 171, 244, 10.1111/j.1095-8339.2012.01276.x

Erkens, 2007, A rapid diversification of rainforest trees (Guatteria; Annonaceae) following dispersal from Central into South America, Molecular Phylogenetics and Evolution, 44, 399, 10.1016/j.ympev.2007.02.017

Etienne, 2012, Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record, Proceedings of the Royal Society B, 279, 1300, 10.1098/rspb.2011.1439

Eva, 2004, A land cover map of South America, Global Change Biology, 10, 731, 10.1111/j.1529-8817.2003.00774.x

Farris, 2011, Fracturing of the Panamanian Isthmus during initial collision with South America, Geology, 39, 1007, 10.1130/G32237.1

Fine, 2004, Herbivores promote habitat specialization by trees in Amazonian forests, Science, 305, 663, 10.1126/science.1098982

Fine, 2005, The contribution of edaphic heterogeneity to the evolution and diversity of Burseraceae trees in the western Amazon, Evolution, 59, 1464

Fregonezi, 2012, Biogeographic history and diversification of Petunia and Calibrachoa (Solanaceae) in the Neotropical Pampas grassland, Botanical Journal of the Linnean Society, 171, 140, 10.1111/j.1095-8339.2012.01292.x

Garzione, 2008, Rise of the Andes, Science, 320, 1304, 10.1126/science.1148615

Gentry, 1982, Neotropical floristic diversity: phytogeographical connections between Central and South America, Pleistocene climatic fluctuations, or an accident of the Andean orogeny?, Annals of the Missouri Botanical Garden, 69, 557, 10.2307/2399084

Gentry, 1989, Tropical forests: botanical dynamics, speciation and diversity, 113, 10.1016/B978-0-12-353550-4.50017-4

Govindarajulu, 2011, Phylogenetic and population genetic analyses of diploid Leucaena (Leguminosae; Mimosoideae) reveal cryptic species diversity and patterns of divergent allopatric speciation, American Journal of Botany, 98, 2049, 10.3732/ajb.1100259

Graham, 2010, Late Cretaceous and Cenozoic history of Latin American vegetation and terrestrial environments

Graham, 2011, The age and diversification of terrestrial New World ecosystems through Cretaceous and Cenozoic time, American Journal of Botany, 98, 336, 10.3732/ajb.1000353

Grover, 2012, Targeted sequence capture as a powerful tool for evolutionary analysis, American Journal of Botany, 99, 312, 10.3732/ajb.1100323

Gustafsson, 2010, Reassessing the temporal evolution of orchids with new fossils and a Bayesian relaxed clock, with implications for the diversification of the rare South American genus Hoffmannseggella (Orchidaceae: Epidendroideae), BMC Evolutionary Biology, 10, 177, 10.1186/1471-2148-10-177

Gustafsson, 2003, Evolution of morphological diversity and resin secretion in flowers of Clusia L. (Clusiaceae): insights from ITS sequence variation, Nordic Journal of Botany., 22, 183, 10.1111/j.1756-1051.2002.tb01364.x

Haffer, 1969, Speciation in Amazonian forest birds, Science, 165, 131, 10.1126/science.165.3889.131

Harrison, 2011, Next-generation sequencing and systematics: what can a billion base pairs of DNA sequence data do for you?, Taxon, 60, 1552, 10.1002/tax.606002

Hollingsworth, 2011, Refining the DNA barcode for land plants, Proceedings of the National Academy of Sciences of the United States of America, 108, 19451, 10.1073/pnas.1116812108

Hoorn, 2010, Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversity, Science, 330, 927, 10.1126/science.1194585

Hubbell, 2001, The unified neutral theory of biodiversity and biogeography

Hughes, 2006, Island radiation on a continental scale: exceptional rates of plant diversification after uplift of the Andes, Proceedings of the National Academy of Sciences of the United States of America, 103, 10334, 10.1073/pnas.0601928103

Humboldt A. 1820 Voyage aux regions equinoxiales du Nouveau Continent

Iganci, 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, 378, 10.1111/j.1095-8339.2011.01182.x

Jabaily, 2012, Historical biogeography and life history evolution of Andean Puya (Bromeliaceae), Botanical Journal of the Linnean Society, 171, 201, 10.1111/j.1095-8339.2012.01307.x

Jacobs, 2004, Paleobotanical Studies from tropical Africa: relevance to the evolution of forest, woodland, and savanna biomes, Philosophical Transactions of the Royal Society of London Series B Biological Sciences, 359, 1574, 10.1098/rstb.2004.1533

Jaramillo, 2006, Cenozoic plant diversity in the Neotropics, Science, 311, 1893, 10.1126/science.1121380

Kay, 2005, Rapid speciation and the evolution of hummingbird pollination in Neotropical Costus subgenus Costus (Costaceae): evidence from nrDNA its and ETS sequences, American Journal of Botany, 92, 1899, 10.3732/ajb.92.11.1899

Kreft, 2010, A framework for delineating biogeographical regions based on species distributions, Journal of Biogeography, 37, 2029, 10.1111/j.1365-2699.2010.02375.x

Kissling, 2012, Cenozoic imprints on the phylogenetic structure of palm species assemblages worldwide, Proceedings of the National Academy of Sciences of the United States of America, 109, 7379, 10.1073/pnas.1120467109

Kursar, 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, 106, 18073, 10.1073/pnas.0904786106

Lavin, 2006, Neotropical savannas and seasonally dry forests: plant biodiversity, biogeography and conservation, 433, 10.1201/9781420004496.ch19

Lavin, 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, 359, 1509, 10.1098/rstb.2004.1536

Linares-Palomino, 2011, Seasonally dry tropical forests: ecology and conservation, 3, 10.5822/978-1-61091-021-7_1

Linder, 2012, The partitioning of Africa: statistically defined biogeographical regions in sub-Saharan Africa, Journal of Biogeography, 39, 1189, 10.1111/j.1365-2699.2012.02728.x

Lohmann, 2012, Pattern and timing of biogeographic history in the Neotropical tribe Bignonieae (Bignoniaceae), Botanical Journal of the Linnean Society, 171, 154, 10.1111/j.1095-8339.2012.01311.x

Lugo, 2006, Neotropical savannas and seasonally dry forests: plant biodiversity, biogeography and conservation, 359, 10.1201/9781420004496.ch15

Lu-Irving, 2012, Untangling the evolution of problematic taxa using multiple loci: an example from Lantaneae (Verbenaceae), Botanical Journal of the Linnean Society, 171, 103, 10.1111/j.1095-8339.2012.01305.x

Luteyn, 1999, Páramos: a checklist of plant diversity, geographical distribution, and botanical literature, Memoirs of the New York Botanical Garden, 84, 1

Malhi, 2009, Exploring the likelihood and mechanism of a climate-change-induced dieback of the Amazon rainforest, Proceedings of the National Academy of Sciences, USA, 106, 20610, 10.1073/pnas.0804619106

Mason, 2011, Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens, Genome Research, 21, 1695, 10.1101/gr.120196.111

McKenna, 2006, Tropical forests are both evolutionary cradles and museums of leaf beetle diversity, Proceedings of the National Academy of Sciences, 103, 10947, 10.1073/pnas.0602712103

Michelangeli, 2012, Phylogenetic relationships and distribution of New World Melastomeae (Melastomataceae), Botanical Journal of the Linnean Society, 171, 38, 10.1111/j.1095-8339.2012.01295.x

Montes, 2012, Evidence for middle Eocene and younger land emergence in central Panama: implications for Isthmus closure, Geological Society of America Bulletin, 124, 780, 10.1130/B30528.1

Morlon, 2011, Reconciling molecular phylogenies with the fossil record, Proceedings of the National Academy of Sciences of the United States of America, 108, 16327, 10.1073/pnas.1102543108

Mucina, 1997, Nomenclature of vegetation types and the code: a few concluding remarks, Folia Geobotanica, 32, 421, 10.1007/BF02821951

Murphy, 1986, Ecology of tropical dry forest, Annual Review of Ecology & Systematics, 17, 67, 10.1146/annurev.es.17.110186.000435

Murphy, 1995, Seasonally dry tropical forests, 146

Myers, 2000, Biodiversity hotspots for conservation priorities, Nature, 403, 853, 10.1038/35002501

Nagalingum, 2011, Recent synchronous radiation of a living fossil, Science, 334, 796, 10.1126/science.1209926

Olmstead, 2012, Phylogeny and biogeography in Solanaceae, Verbenaceae and Bignoniaceae: a comparison of continental and intercontinental diversification patterns, Botanical Journal of the Linnean Society, 171, 80, 10.1111/j.1095-8339.2012.01306.x

Oliveira-Filho, In press, Exploring evolutionarily meaningful vegetation definitions in the tropics: a community phylogenetic approach, Ecological Reviews

Pennington, 2004, The role of immigrants in the assembly of the South American rainforest tree flora, Philosophical Transactions of the Royal Society B: Biological Sciences, 359, 1611, 10.1098/rstb.2004.1532

Pennington, 2010, Amazonia, landscape and species evolution, 1st edition, 373

Pennington, 2004a, Historical climate change and speciation: Neotropical seasonally dry forest plants show patterns of both Tertiary and Quaternary diversification, Philosophical Transactions of the Royal Society B: Biological Sciences, 359, 515, 10.1098/rstb.2003.1435

Pennington, 2004b, Introduction and synthesis: plant phylogeny and the origin of major biomes, Philosophical Transactions of the Royal Society B: Biological Sciences, 359, 1455, 10.1098/rstb.2004.1539

Pennington, 2000, Neotropical seasonally dry forests and Pleistocene vegetation changes, Journal of Biogeography, 27, 261, 10.1046/j.1365-2699.2000.00397.x

Pennington, 2006a, Neotropical savannas and seasonally dry forests: plant biodiversity, biogeography and conservation, 1, 10.1201/9781420004496.ch1

Pennington, 2006b, Insights into the historical construction of species-rich biomes from dated plant phylogenies, neutral ecological theory and phylogenetic community structure, New Phytologist, 172, 605, 10.1111/j.1469-8137.2006.01902.x

Pennington, 2009, Woody plant diversity, evolution, and ecology in the tropics: perspectives from seasonally dry tropical forests, Annual Review of Ecology, Evolution, and Systematics, 437, 10.1146/annurev.ecolsys.110308.120327

Pennington, 2010, Contrasting plant diversification histories within the Andean biodiversity hotspot, Proceedings of the National Academy of Sciences, 107, 13783, 10.1073/pnas.1001317107

Pennington, 2011, Poissonia eriantha (Leguminosae) from Cuzco, Peru: an overlooked species underscores a pattern of narrow endemism common to seasonally dry neotropical vegetation, Systematic Botany, 36, 59, 10.1600/036364411X553135

Pennington, 1997, The genus Inga: botany

Perret, 2012, Temporal and spatial origin of Gesneriaceae in the New World inferred from plastid DNA sequences, Botanical Journal of the Linnean Society, 171, 61, 10.1111/j.1095-8339.2012.01303.x

Pirie, 2012, Dating clades with fossils and molecules: the case of Annonaceae, Botanical Journal of the Linnean Society, 169, 84, 10.1111/j.1095-8339.2012.01234.x

Pirie, 2012, Model uncertainty in ancestral area reconstruction: a parsimonious solution?, Taxon, 61, 652, 10.1002/tax.613013

Poore, 1955, The use of phytosociological methods in ecological investigations: I. The Braun-Blanquet system, Journal of Ecology, 43, 226, 10.2307/2257132

Potter, 2009, Global Miocene tectonics and the modern world, Earth-Science Reviews, 96, 279, 10.1016/j.earscirev.2009.07.003

Prado, 1993a, What is the Gran Chaco vegetation in South America? I. A review. Contribution to the study of flora and vegetation of the Chaco. V, Candollea, 48, 145

Prado, 1993b, What is the Gran Chaco vegetation in South America? II. A redefinition. Contribution to the study of flora and vegetation of the Chaco. VII, Candollea, 48, 615

Prado, 2000, Seasonally dry forests of tropical South America: from forgotten ecosystems to a new phytogeographic unit, Edinburgh Journal of Botany, 57, 437, 10.1017/S096042860000041X

Ratter, 1997, The Brazilian Cerrado vegetation and threats to its biodiversity, Annals of Botany, 80, 223, 10.1006/anbo.1997.0469

Ree, 2009, Prospects and challenges for parametric models in historical biogeographical inference, Journal of Biogeography, 36, 1211, 10.1111/j.1365-2699.2008.02068.x

Renner, 2004, Plant dispersal across the tropical Atlantic by wind and sea currents, International Journal of Plant Sciences, 165, S23, 10.1086/383334

Reynel, 1997, El género Inga en el Perú: morfología, distribución y usos

Richardson, 2001, Rapid diversification of a species-rich genus of neotropical rain forest trees, Science, 293, 2242, 10.1126/science.1061421

Rohland, 2012, Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture, Genome Research, 22, 939, 10.1101/gr.128124.111

Roncal, 2012, Cenozoic colonization and diversification patterns of tropical American palms: evidence from Astrocaryum (Arecaceae), Botanical Journal of the Linnean Society, 171, 120, 10.1111/j.1095-8339.2012.01297.x

Rull, 2008, Speciation timing and Neotropical biodiversity: the Tertiary-Quaternary debate in the light of molecular phylogenetic evidence, Molecular Ecology, 17, 2722, 10.1111/j.1365-294X.2008.03789.x

Rull, 2011, Neotropical biodiversity: timing and potential drivers, Trends in Ecology and Evolution, 26, 508, 10.1016/j.tree.2011.05.011

Sanderson, 2010, Phylogenomics with incomplete taxon coverage: the limits to inference, BMC Evolutionary Biology, 10, 155, 10.1186/1471-2148-10-155

Särkinen, 2007, Recent oceanic long-distance dispersal and divergence in the amphi-Atlantic rain forest genus Renealmia L.f. (Zingiberaceae), Molecular Phylogenetics and Evolution, 44, 968, 10.1016/j.ympev.2007.06.007

Särkinen, 2011a, Underestimated endemic species diversity in the dry inter-Andean valley of the Río Marañón, northern Peru: an example from Mimosa (Leguminosae, Mimosoideae), Taxon, 60, 139, 10.1002/tax.601012

Särkinen, 2011b, Forgotten forests-issues and prospects in biome mapping using seasonally dry tropical forests as a case study, BMC Ecology, 11, 27, 10.1186/1472-6785-11-27

Särkinen, 2012a, Evolutionary islands in the Andes: persistence and isolation explain high endemism in Andean dry tropical forests, Journal of Biogeography, 39, 884, 10.1111/j.1365-2699.2011.02644.x

Särkinen, 2012b, How to open the treasure chest? Optimising DNA extraction from herbarium specimens, PLoS One, 7, e43808, 10.1371/journal.pone.0043808

Sarmiento, 1992, . Nature and dynamics of forest-savanna boundaries, 583

Schrire, 2005, Global distribution patterns of the Leguminosae: insights from recent phylogenies, Biologiske Skrifter, 55, 375

Silvestro, 2011, A Bayesian framework to estimate diversification rates and their variation through time and space, BMC Evolutionary Biology, 11, 311, 10.1186/1471-2148-11-311

Simon, 2000, Phytogeographic patterns of Mimosa (Mimosoideae, Leguminosae) in the Cerrado biome of Brazil: an indicator genus of high altitude centers of endemism, Biological Conservation, 96, 279, 10.1016/S0006-3207(00)00085-9

Simon, 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, 106, 20359, 10.1073/pnas.0903410106

Simon, 2012, The evolution of adaptations of woody plants in the savannas of the Brazilian Cerrado, International Journal of Plant Sciences, 173, 711, 10.1086/665973

Simpson, 1980, Splendid isolation: the curious history of South American mammals

Sklenář, 2011, Tropical and temperate: evolutionary history of páramo flora, The Botanical Review, 77, 71, 10.1007/s12229-010-9061-9

Stadler, 2011, Inferring speciation and extinction processes from extant species data, Proceedings of the National Academy of Sciences of the United States of America, 108, 16145, 10.1073/pnas.1113242108

Stebbins, 1974, Evolution above the species level, 10.4159/harvard.9780674864856

Stehli, 1985, The Great American biotic interchange, 10.1007/978-1-4684-9181-4

Straub, 2012, Navigating the tip of the genomic iceberg: next-generation sequencing for plant systematics, American Journal of Botany, 99, 349, 10.3732/ajb.1100335

Torke, 2008, Molecular phylogenetics of the species-rich neotropical genus Swartzia (Leguminosae, Papilionoideae) and related genera of the swartzioid clade, American Journal of Botany, 95, 215, 10.3732/ajb.95.2.215

Tripp, 2008, Evolutionary relationships within the species-rich genus Ruellia, Systematic Botany, 32, 628, 10.1600/036364407782250625

Trovó, 2012, Molecular phylogeny and biogeography of Neotropical Paepalanthoideae Ruhland with emphasis on Brazilian Paepalanthus Mart. (Eriocaulaceae), Botanical Journal of the Linnean Society, 171, 225, 10.1111/j.1095-8339.2012.01310.x

Webb, 2002, Phylogenies and community ecology, Annual Review of Ecology and Systematics, 33, 475, 10.1146/annurev.ecolsys.33.010802.150448

Wesselingh, 2002, Lake Pebas: a palaeoecological reconstruction of a Miocene, long-lived lake complex in western Amazonia, Cenozoic Research, 1, 35

Wesselingh, 2010, Hoorn, C., Wesselingh, F.P.: Amazonia, Landscape and Species Evolution, 421

White, 1983, The vegetation of Africa: a descriptive memoir to accompany the UNESCO/AETFAT/UNSO vegetation map of Africa

White, 1993, The AETFAT chorological classification of Africa: history, methods and applications, Bulletin du Jardin Botanique Nationale de Belgique, 62, 225, 10.2307/3668279

Wiens, 2004, Historical biogeography, ecology, and species richness, Trends in Ecology and Evolution, 19, 639, 10.1016/j.tree.2004.09.011