(a) Refereed journal research papers

A1. PENNINGTON, R.T. & de Lima, H.C. (1995). Two new species of Andira from Bahia Brazil, and the influence of dispersal in determining their distributions. Kew Bulletin 50: 557-566.

A2. PENNINGTON, R.T. (1995). Cladistic analysis of chloroplast DNA restriction site characters in Andira (Leguminosae: Dalbergieae). American Journal of Botany 82: 526-534.

A3. PENNINGTON, R.T. (1996). Molecular and morphological data provide resolution at different hierarchical levels in Andira. Systematic Biology 45: 496-515.

A4. PENNINGTON, R.T., Aymard, G & Cuello, N. (1997). A new species of Andira from the Venezuelan Guayana. Novon 7(1): 72-74.

A5. Zamora, N, PENNINGTON, R.T & Stirton, C.S. (1999). Dussia atropurpurea (Leguminosae), a new species from Central America and notes on sarcotesta coloration in Dussia systematics. Edinburgh Journal of Botany 56: 175-180.

A6. Ireland, H. & PENNINGTON, R.T. (1999). A revision of Geoffroea Leguminosae-Dalbergieae. Edinburgh Journal of Botany 56: 329-347.

A7. PENNINGTON, R.T., Prado, D.A. & Pendry, C. (2000). Neotropical seasonally dry forests and Pleistocene vegetation changes. Journal of Biogeography 27: 261-273.

A8. Lavin, M., Thulin, M., Labat, J-N. & PENNINGTON, R.T. (2000). Africa, the odd man out: molecular biogeography of dalbergioid legumes (Fabaceae) suggests otherwise. Systematic Botany 25: 449-467.

A9. PENNINGTON, R.T., Lewis, G.P., Marsh, M. (2000). Andira inermis subsp. inermis (Leguminosae-Papilionoideae). Curtis Botanical Magazine 17: 188-194.

A10. PENNINGTON, R.T. & Gemeinholzer, B. (2000). Cryptic clades, fruit wall morphology and biology of Andira (Leguminosae-Papilionoideae). Botanical Journal of the Linnean Society 134: 267-286.

A11. Lavin, M., PENNINGTON, R.T., Klitgaard, B.B., Sprent, J.I., de Lima, H.C. & Gasson, P.E. (2001). The dalbergioid legumes (Fabaceae): Delimitation of a pantropical monophyletic clade. American Journal of Botany 88: 503-533.

A12. PENNINGTON, R.T., Lavin, M., Ireland, H.E., Klitgaard, B. & Preston, J. (2001). Phylogenetic relationships of primitive papilionoid legumes based upon sequences of the chloroplast intron trnL. Systematic Botany 26: 537-556.

A13. Richardson, J.E., PENNINGTON, R.T., Pennington, T.D. & Hollingsworth, P.M. (2001). Rapid diversification of a species-rich genus of Neotropical rain forest trees. Science 293: 2242-2245

A14. Warwick, M. & PENNINGTON, R.T. (2002). A revision of Cyclolobium (Leguminosae-Papilionoideae). Edinburgh Journal of Botany 59: 247-258.

A15. PENNINGTON, R.T. (2002). Proposal to change the authorship of Andira nom. cons. (Leguminosae-Papilionoideae) and to conserve it with a conserved type. Taxon 51: 385-386.

A16. Moylan, E.C., PENNINGTON, R.T. & Scotland, R.W. (2002). Taxonomic account of Hemigraphis Nees (Strobilanthinae-Acanthaceae) from the Philippines. Kew Bulletin 57: 769-825.

A17. Lewis, G.P., Knudsen, J.T., Klitgaard, B. & PENNINGTON, R.T. (2003). The floral scent of Cyathostegia mathewsii (Benth.) Schery and preliminary observations on its reproductive biology. Biochemical Systematics and Ecology 31: 951-962.

A18. Bridgewater, S., PENNINGTON, R.T., Reynel, C., Daza, A. & Pennington, T.D. (2003). A preliminary floristic and phytogeographic analysis of the woody flora of seasonally dry forests in northern Peru. Candollea 58: 129-148.

A19. Citerne, H., Luo, D., PENNINGTON, R.T., Coen, E. & Cronk, Q.C.B. (2003). A phylogenomic investigation of CYC-like TCP genes in Leguminosae. Plant Physiology 131: 1042-1053.

A20. PENNINGTON, R.T. (2003). A monograph of Andira (Leguminosae-Papilionoideae). Systematic Botany Monographs 64 (145pp.; illus. 44 b+w).

A21. Linares-Palomino, R., PENNINGTON, R.T. & Bridgewater, S. (2003). The phytogeography of seasonally dry tropical forests in Equatorial Pacific South America. Candollea 58: 473-499.

A22. Kite, G.C. and PENNINGTON, R.T. (2003). Quinolizidine alkaloid status of Styphnolobium and Cladrastis (Leguminosae). Biochemical Systematics and Ecology 31: 1409-1416.

A23. PENNINGTON, R. T., Pendry, C.A., Goodall-Copestake, W., O’Sullivan, S. (2004). Phylogenetic analysis of Ruprechtia. In Pendry, C.A. A monograph of Ruprecthia (Polygonaceae). Systematic Botany Monographs 67: 12-17.

A24. Bramley, G.L.C., PENNINGTON, R.T., Zakaria, R., Sudarmiyati Tjitrosoedirdjo, S. & Cronk, Q.C.B. (2004). Assembly of tropical plant diversity on a local scale: Cyrtandra (Gesneriaceae) on Mount Kerinci, Sumatra. Biological Journal of the Linnean Society 81: 49-62.

A25. PENNINGTON, R.T., Lavin, M. Prado, D.E., Pendry, C.A., Pell, S. & Butterworth, C.A. (2004). Historical climate change and speciation: Neotropical seasonally dry forest plants show patterns of both Tertiary and Quaternary diversification. Philosophical Transactions of the Royal Society (Biological Sciences) 359: 515-538.

A26. Plana, V., Gascoigne, A., Forrest, L.L., Harris, D., & PENNINGTON, R.T. (2004). Pleistocene and pre-Pleistocene Begonia speciation in Africa. Molecular Phylogenetics and Evolution 31: 449-461.

A27. Cortés-Burns, H., Schrire, B. D., PENNINGTON, R. T. & Miller, A. G. (2004). A taxonomic revision of Socotran Indigofereae Benth. (Leguminosae – Papilionoideae) with insights into the phytogeographical links of the Socotran Archipelago. Nordic Journal of Botany 22: 693-711.

A28. Lavin, M., Schrire, B., Lewis, G., PENNINGTON, R.T., Delgado-Salinas, A., Thulin, M., Hughes, C. & Wojciechowski, M.F. (2004). Metacommunity process rather than continental tectonic history better explains geographically structured phylogenies in legumes. Philosophical Transactions of the Royal Society (Biological Sciences) 359: 1509-1522.

A29. PENNINGTON, R.T. & Dick, C.W. (2004). The role of immigrants in the assembly of the Amazonian tree flora. Philosophical Transactions of the Royal Society (Biological Sciences) 359: 1611-1622.

A30. PENNINGTON, R.T., Richardson, J.E. & Cronk, Q.C.B. (2004). Plant phylogeny and the origin of major biomes: introduction and synthesis.  Philosophical Transactions of the Royal Society (Biological Sciences) 359: 1455-1465.

A31. Hollingsworth, P. M., Dawson, I. K., Goodall-Copestake, W. P., Richardson, J. E., Weber, J. C., Sotelo Montes, C. & Pennington, R.T. (2005). Do farmers reduce genetic diversity when they domesticate tropical trees? A case study from Amazonia. Molecular Ecology 14: 497-501.

A32. Kenicer, G., Kajita, T., PENNINGTON, R.T. & Murata, J. (2005). Systematics and biogeography of Lathyrus based upon internal transcribed spacer and cpDNA sequence data. American Journal of Botany 92: 1199-1209.

A33. Naciri-Graven, Y., Caetano, S., Prado, D., PENNINGTON, R.T. & 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 5: 542-545.

A34. Coley, P. D., Lokvam, J., Rudolph, K., Bromberg, K., Wright, L., Dvorett, D., Ring, S., Ponge, A., Baptiste, C., PENNINGTON, R. T. & Kursar, T. A.  (2005). Divergent defensive strategies of young leaves in two Neotropical species of Inga.  Ecology 86: 2633-2643

A35. Cronk, Q.C.B., Ojeda, I. & PENNINGTON, R.T. (2005). Legume comparative genomics: progress in phylogenetics and phylogenomics. Current Opinion in Plant Biology 9: 1-5.

A36. Wilkie, P., Ponge, A., PENNINGTON, R.T., Cheek, M., Bayer, C. & Wilcock, C. (2006). A phylogenetic analysis of subfamily Sterculioideae (Malvaceae /Sterculiaceae – Sterculieae) using the chloroplast gene ndhF. Systematic Botany 31: 160-170.

A37. Citerne, H., PENNINGTON, R.T. & Cronk, Q.C.B. (2006). An apparent reversal in floral symmetry in the legume Cadia is a homeotic transformation. Proceedings of the National Academy of Sciences, USA 103: 12017-12020.

A38. PENNINGTON, R.T., Richardson, J.A., Lavin M. (2006). Insights into the historical construction of species-rich biomes from dated plant phylogenies, phylogenetic community structure and neutral ecological theory. New Phytologist (invited Tansley Review) 172: 605-616.

A39. Särkinen, T.E., Newman, M.F., Maas, P.J.M., Maas, H., Poulsen, A.D., Harris, D.J., Richardson, J.E., Clark, A., Hollingsworth, M. & PENNINGTON, R.T. (2007). Recent oceanic long-distance dispersal and divergence in the amphi-Atlantic rain forest genus Renealmia L.f. (Zingiberaceae). Molecular Phylogenetics and Evolution 44: 968-980.

A40. PENNINGTON, R.T. (2007). In Flora Neotropica Monograph 100. Proteaceae (Prance, G.T., Edwards, K., Plana, V. & PENNINGTON, R.T.): accounts of Gevuina, Embothrium, Oreocallis and Lomatia, pp.22-36.

A41. Linares Palomino, R. & PENNINGTON R.T. (2007). Annotated checklist of the woody plants in Peruvian seasonally dry forests - a new web-based tool for taxonomic, ecological and biodiversity studies. Arnaldoa 14: 149-152.

A42. Dawson, I.K., Hollingsworth, P., Doyle, J.J., Kresovich, S., Weber, J.C., Sotelo Montes, C., Pennington, T.D., PENNINGTON, R.T. (2008). Origins and genetic conservation of tropical trees in agroforestry systems: a case study from the Peruvian Amazon. Conservation Genetics 9: 361-372.

A43. Caetano, S., D. Prado, R.T. PENNINGTON, S. Beck, A. Oliveira-Filho, R. Spichiger and Y. Naciri. 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 17:3147-3159.

A44. PENNINGTON, R.T. & Wojciechowski, M.J. (2008). The status of Sophora. The Plantsman 7: 186-189

A45. Honorio, E.N. R.T. PENNINGTON, L.A. Freitas, G. Nebel & T.R. Baker. (2008). Análisis de la composición florística de los bosques de Jenaro Herrera, Loreto, Perú. Revista Peruana de Biologia.

A46. Pirie, M.D., B.B. Klitgaard & R.T. PENNINGTON. (2009). Revision and biogeography of Centrolobium. Systematic Botany 34: 345-359

A47. PENNINGTON, R.T., Lavin, M & Oliveira-Filho A. (2009). Plant diversity, evolution and ecology in the tropics: perspectives from seasonally dry tropical forests. Annual Review of Ecology, Evolution and Systematics 40: 437-457.

A48. Hollingsworth, M.L., Clark, A., Forrest, L.L., Richardson, J., PENNINGTON, R.T., Long, D.G., Cowan, R., Chase, M.W., Gaudeul, M., Hollingsworth, P.M. (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, 9: 439-457. 

A49. Honorio E.N., Baker, T.R., Phillips, O.L., Pitman, N.C.A., PENNINGTON R.T. et al. (2009). Integrating regional and continental scale comparisons of tree composition in Amazonian terra firme forests. Biogeosciences Discussions 6: 1-31.

A50. Kursar, T.A., Dexter, K.G., Lokvam, J., PENNINGTON R.T., Richardson, J.E., Weber, M.G., Murakami, E, Drake, C., McGregor, R. & Coley, P.D. (2009). The importance of plant-herbivore interactions for diversification and coexistence in the tropical tree genus Inga. Proceedings of the National Academy of Sciences, USA. 106: 18073-18078. doi: 10.1073/pnas.0904786106

A51. Simon, M., Grether, R., de Queiroz L.P., Skema C., PENNINGTON, R.T. & C.E. Hughes . (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, USA 106:  20359-20364.

A52. Smith, G.F., Figueiredo, E., PENNINGTON, R.T., Davila, P. (2009).  Getting that grant: how to convince an evaluation panel that your proposal is worthy of funding. Taxon, 58: 675-677. A. 2.36

A53. Ireland, H.E., Kite G.C., Veitch, N.C., Chase, M.W., Schrire, B., Lavin, M., PENNINGTON, R.T. (2010). Biogeographic, ecological, and morphological structure of a phylogenetic analysis of Ateleia (Swartzieae-Leguminosae) derived from combined molecular and morphological/chemical data. Botanical Journal of the Linnean Society 162: 39-53

A54. Cody, S., Richardson, J.E., Rull, V., Ellis, C. & PENNINGTON, R.T. (2010). The Great American Biotic Interchange Revisited. Ecography 33: 1-7.    

A55. PENNINGTON R.T., Lavin M, Hughes C., Sarkinen T, Lewis G, Klitgaard B. (2010). Differing diversification histories in the Andean biodiversity hotspot. Proceedings of the National Academy of Sciences, USA 107: 13783-13787.

A56. MacKinder, B. & PENNINGTON R.T. (2011). A monograph of Berlinia (Leguminosae: Caesalpinioideae). Systematic Botany Monographs 91 (117 pp.)

A57. Milliken, W., Zappi D., Sasaki D., Hopkins M. & PENNINGTON R.T. (2011). Amazon vegetation: how much don’t we know and how much does it matter? Kew Bulletin 65: 1-19.

A58. PENNINGTON, R.T., Daza A & Lavin M. (2011). Poissonia eriantha (Leguminosae) From Cuzco, Peru: An Overlooked Species Underscores a Pattern of Narrow Endemism Common to Seasonally Dry Neotropical Vegetation Poissonia. Systematic Botany 36:59-68.

A59. Barlow, J., Ewers, R.M., Anderson L., Aragao, L.E.O.C., Baker, T., Boyd E., Feldpausch T., Gloor E., Hall A., Malhi Y., Milliken W., Mulligan M., Parry L., PENNINGTON R.T., Peres C.A., Phillips O., Roman-Cuesta R.M., Tobias J. & Gardner T.A.. (2011) Using learning networks to understand complex systems: a case study of biological, geophysical and social research in the Amazon. Biological Reviews 86:.457-474.

A60. Jones, H., Mayle, F.E., PENNINGTON, R.T. & Killeen, T. (2011). Characterization of neotropical savanna ecosystems by their modern pollen rain and implication for fossil pollen records. Review of Palaeobotany and Palynology 164: 223-237

A61. Whitney, B.S., Mayle, F.E., Punysena, S.W., Fitzpatrick, K.A., Burn, M.J., Guillen, R., Chavez, E., Mann, D.G., PENNINGTON, R.T., & Metcalfe, S.E. (2011). A 45 kyr palaeoclimate record from the heart of tropical South America. Palaeography, Palaeoclimatology, Palaeoecology 307: 177-192.

A62. Cardenas, M.L., Gosling, W.D., Sherlock, S.C., Poole, I., PENNINGTON, R.T. & Mothes P. (2011). The response of vegetation at the Andean flank in western Amazonia to Pleistocene climate change. Science 331: 1055-1058.

A63. Cardenas, M.L., Gosling, W.D., Sherlock, S.C., Poole, I., PENNINGTON, R.T. & Mothes P. (2011).Response to Comment on “The Response of Vegetation on the Andean Flank in Western Amazonia to Pleistocene Climate Change”. Science 333: 1825.

A64. Iganci, J.R.V, Heiden G., Miotto, S.T.S. & PENNINGTON R. T. (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: 378–393. DOI: 10.1111/j.1095-8339.2011.01182.x

A65. Dick C.W. & PENNINGTON, R.T. (2011). Molecular systematic perspectives on biome origins and dynamics. New Phytologist 193(1): 9-11.

A66. Särkinen, T., J. L. Marcelo Peña, A. Daza Yomona, M. F. Simon, R. T. Pennington, and C. E. Hughes ( 2011 ) Underestimated endemic species diversity in the dry inter-Andean valley of the Río Marañón, northern Peru: An example from Mimosa (Leguminosae, Mimosoideae). Taxon 60: 139-150 .

A67. Särkinen, T., PENNINGTON, R.T., Lavin, M., Simon, M.F. & Hughes, C.E. (2011). Evolutionary islands in the Andes: persistence and isolation explain high endemism in Andean dry tropical forests. Journal of Biogeography 39: 884–900.

A68. Caetano, S., Currat, M., PENNINGTON, R.T., Prado, D., Excoffier, L., & Naciri, Y. (2012). Recent colonization of the Galapagos by the tree Geoffroea spinosa Jacq. (Leguminosae). Molecular Ecology 21(11): 2743-2760. doi: 10.1111/j.1365-294X.2012.05562.x

A69. Simon, M.F. & PENNINGTON, R.T. (2012). The evolution of adaptations of woody plants in the savannas of the Brazilian cerrado. International Journal of Plant Sciences 173: 711-723

A70. Cardoso, D., de Lima, H.C., Schütz Rodrigues R., de Queiroz, L.P., PENNINGTON, R.T. & Lavin, M. (2012). The Bowdichia clade of Genistoid legumes: phylogenetic analysis of combined molecular (ITS, matK and trnL intron) and morphological data and a recircumscription of Diplotropis. Taxon 61: 1074-1087.

A71. Cardoso, D., de Lima, H.C., Schütz Rodrigues R., de Queiroz, L.P., PENNINGTON, R.T. & Lavin, M. (2012). The realignment of Acosmium sensu stricto with the Dalbergioid clade (Leguminosae, Papilionoideae) reveals a proneness for independent evolution of radial floral symmetry among early branching papilionoid legumes. Taxon 61: 1057-1073.

A72. Schaefer, H., Hechenleitner, P., Santos-Guerra, A., de Sequeira, M. M., PENNINGTON, R. T., Kenicer, G., & Carine, M. A. (2012)  Systematics, biogeography, and character evolution of the legume tribe Fabeae with special focus on the middle-Atlantic island lineages. BMC Evolutionary Biology 12.

A73. Adhikari, B.,  Pendry, C. A., PENNINGTON, R. T. & Milne, R. I. (2012)  A revision of Berberis, s.s. (Berberidaceae) in Nepal. Edinburgh Journal of Botany 69: 447-522.

A74. Cardoso, D. de Queiroz, L., PENNINGTON, R.T., de Lima, H.C., Fonty, E., Wojciechowski, M.F. & Lavin, M. (2013). Revisiting the phylogeny of papilionoid legumes: new insights from comprehensively sampled early-branching lineages. American Journal of Botany 1991-2013.

A75. Hughes, C.E., PENNINGTON, R.T. & Antonelli, A. (2013). Neotropical Plant Evolution - Assembling the Big Picture'. Botanical Journal of the Linnean Society 171: 1-18.

A76. Whitney, B.S., Mayle, F.E., Burn, M.J., Guillén, R., Chavez, E., & PENNINGTON, R.T. (2013). Sensitivity of Bolivian seasonally-dry tropical forest to precipitation and temperature changes over glacial-interglacial timescales. Vegetation History and Archaeobotany. DOI 10.1007/s00334-013-0395-1

A77. Legume Phylogeny Working Group (2013). Legume phylogeny and classification in the 21st century: progress, prospects and lessons. Taxon.(This paper was compiled by Anne Bruneau, Jeff Doyle, Patrick Herendeen, Colin Hughes, Greg Kenicer, Gwilym Lewis, Barbara Mackinder, R.T. PENNINGTON*, Michael Sanderson and Martin Wojciechowski who were equally responsible and listed here in alphabetical order only, with contributions from Stephen Boatwright, Gillian Brown, Domingos Cardoso, Michael Crisp, Ashley Egan, Renee Fortunato, Julie Hawkins, Tadashi Kajita, Bente Klitgaard, Erik Koenen, Matt Lavin, Melissa Luckow, Brigitte Marazzi, Michelle McMahon, Joseph T. Miller, Daniel J. Murphy, Hiroyoshi Ohashi, Luciano P. de Queiroz, Lourdes Rico, Tiina Särkinen, Brian Schrire, Marcelo F. Simon, Elvia R. Souza, Kelly Steele, Benjamin Torke, Jan J. Wieringa, Ben-Erik Van Wyk. Taxon 62: 217–248. *Corresponding author.

A78. Iganci, J.R.V, Miotto, S.T.S., Souza-Chies, T.T., Särkinen, T.E., Simpson, B.B., Simon, M.F., & PENNINGTON, R.T. (2013). Diversification history of Adesmia ser. psoraleoides (Leguminosae): Evolutionary processes and the colonization of the southern Brazilian highland grasslands. South African Journal of Botany 89:257–264

A79. Vatanparast, M. Klitgård, B.B., Adema, F.A.C.B., PENNINGTON, R.T., Yahara, T. & Kajita, T. (2013). First molecular phylogeny of the pantropical genus Dalbergia: implications for infrageneric circumscription and biogeography. South African Journal of Botany. 89:143-149.

A80. Oliveira-Filho, A.T., Cardoso D., Schrire, B.D., Lewis, G.P., PENNINGTON, R.T., Brummer, T.J., 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. 89: 42-57.

A81. Coronado, E., Dexter, K.G., Poelchau, M.F, Hollingsworth, P.M., Phillips, O.L., & Pennington R.T. (2014). Ficus insipida subsp. insipida (Moraceae) reveals the role of ecology in the phylogeography of widespread neotropical rain forest tree species. Journal of Biogeography. doi:10.1111/jbi.12326

A82. Baker, T.R., PENNINGTON, R.T., S. Magallon, W.F. Laurance,  M. Alexiades, E. Alvarez, A. Araujo, E.J.M.M. Arets, G. Aymard, A.A. de Oliveira, I. Amaral, L. Arroyo, D. Bonal, R.J.W. Brienen, J. Chave, A. Di Fiore, E. Eler, T.R. Feldpausch, L. Ferreira, G. Lopez-Gonzalez, G. van der Heijden-Corr, N. Higuchi, E. Honorio1, I. Hamantupa, T.J. Killeen, S. Laurance, C. Leaño, S.L. Lewis, Y. Malhi, B.S. Marimon, B.H. Marimon Junior, A. Monteagudo Mendoza, D. Neill, M.-C. Peñuela Mora, N. Pitman, A. Prieto, C.A. Quesada, F. Ramírez, H. Ramírez Angulo, A. Rudas, A. Ruschel, R.P. Salomão, F. Santos, A. Segalin de Andrade, J.N.M. Silva, M. Silveira, W. Spironello, H. ter Steege, J. Terborgh, M. Toledo, A. Torres-Lezama, R.Vasquez, I.C.  Guimarães Vieira, E. Vilanova, V.A. Vos, O.L. Phillips. (2014) Rapid turnover promotes high diversification of Amazonian trees. Ecology Letters 17: 527–536

A83. Cruz Neto, O., Aguiar, Antonio V., Twyford, A. D.,  Neaves, L. E.,  Pennington, R.T. & Lopes, A.V. (2014). Genetic and ecological outcomes of Inga vera subsp. affinis (Leguminosae) tree plantations in a fragmented tropical landscape. PloS One 9: e99903

A84. PENNINGTON, R.T. & Hughes, C.E. (2014). The remarkable congruence of New and Old Wold savannah origins. New Phytologist (2014) 204: 4–6

A85. Filimban, F., MacKinder, B., Knees, S. & Pennington, R.T. (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 71: 117-132

A86.  Banda-R ,K.  Weintritt, J., R. T. Pennington (2016). Caribbean Dry Forest Networking, an Opportunity for Conservation. Caribbean Naturalist, Special Issue 1: 63–72

A87. Cardoso, D., Sao-Mateus, W.M.B., da Cruz, D.T., Zartman, C.E., Komura, D.L., Kite, G., Prenner, G., Wieringa, J.J., Clark, A., Lewis, G.P., PENNINGTON, R.T., de Quieroz, L.P. (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. 84: 112-124

A88. Adhikari,B., Milne,R., PENNINGTON, R.T., Särkinen, T. & Pendry, C.A. (2015) Systematics and biogeography of Berberis s.l. inferred from nuclear ITS and chloroplast ndhF gene sequences. Taxon 64: 39-48

A89. Dexter, K.G., Smart, B., Baldauf, C., Baker, T.R., [50 additional co-authors], & PENNINGTON, R.T. (2015). Vegetation in seasonally dry regions of the tropics: floristics and biogeography. International Forestry Review 17(2) : 10-32

A90. Sunderland, T., Apgaua, D., Baldauf, C., Blackie, R., Colfer, C., Cunningham, A.B., Dexter, K.G., Djoudi, H., Gautier, D., Gumbo, D., Ickowitz, A., Kassa, H., Parthasarathy, N., PENNINGTON, R.T., Paumgarten, F., Pulla, S., Sola, P., Tng, D., Waeber, P., & Wilmé, L. (2015). Global dry forests : a prologue. International Forestry Review 17(2) : 1-9

A91.  Neves, D., Dexter, K.G., Pennington, R.T., Bueno, M.L., & Oliveira Filho, A.T.  (2015). Environmental controls of β-diversity across the South American Dry Diagonal. Journal of Biogeography. 42: 1566–1576. DOI: 10.1111/jbi.12529

A92. Coronado, E., Dexter, K.G., PENNINGTON, R.T., Lewis, S.L., Alexiades, M.N., [44 additional co-authors] & Phillips, O.L. (2015). Phylogenetic diversity of Amazon Tree Communities. Diversity and Distributions 21: 1295–1307

A93. Bueno, M., PENNINGTON, R.T., Dexter, K.G., Yoshino Kamino, L.H., Pontara, V., Neves, D.R.M., Ratter, J.A., & Oliveira-Filho, A. (2015) Effects of Quaternary Climatic Fluctuations on the Distribution of Neotropical Savanna Tree Species. Ecography.

A94. Nicholls, J.A., PENNINGTON, R.T., Koenen, E.J.M., Hughes, C.E., Hearn, J., Bunnefeld, L., Dexter, K.G., Stone. G.N., Kidner, C.A. (2015). Recent radiations robustly resolved: a case study using targeted enrichment of nuclear genes within the neotropical rain forest genus Inga (Leguminosae: Mimosoideae). Frontiers in Plant Science http://dx.doi.org/10.3389/fpls.2015.00710

A95. PENNINGTON, R.T. & Lavin, M. (2015). The contrasting nature of woody plant species in different neotropical forest biomes reflects differences in ecological stability. New Phytologist (invited Tansley review paper). doi 10.1111/nph.13724

A96. PENNINGTON, R.T., Hughes, M. & Moonlight, P.W. (2015). The origins of tropical rainforest hyper-diversity. Trends in Plant Science. (Invited spotlight article) http://dx.doi.org/10.1016/j.tplants.2015.10.005

A97. Garcia-Villacorta, R., Dexter, K.G. & PENNINGTON, R.T. (2016). Amazonian White-Sand Forests Show Strong Floristic Links with Surrounding Oligotrophic Habitats and the Guiana Shield. Biotropica 48: 47–57.

A98. Pontara, V., Bueno, M.L., Garcia, L.E., Oliveira-Filho, A.T., PENNINGTON, R.T., Burslem, D.F.R.P., Lemos-Filho, J.P. (2016).  Fine-scale variation in topography and seasonality determine radial growth of an endangered tree in Brazilian Atlantic Forest. Plant and Soil. DOI 10.1007/s11104-016-2795-3.

A99. DRYFLOR (54 authors; PENNINGTON, R.T. senior author; 2016). Plant diversity patterns and their conservation implications in neotropical dry forests. Science 353: 1383-1387.

A100. DRYFLOR (PENNINGTON, R.T., Banda, K., Delgado-Salinas, A., Dexter, K.G., Galetti, L., Linares-Palomino, R., Maturo, H.M., Mogni, V., Oakley, L., Oliveira-Filho, A., Prado, D., Quintana, C., Riina, R., Sarkinen, T.; 2017). Response to “Forest conservation: Remember the Gran Chaco). Science 355: 465-466.

A101. DRYFLOR (PENNINGTON, R.T., Banda, K., Delgado-Salinas, A., Dexter, K.G., Linares-Palomino, R., Oliveira-Filho, A., Prado, D., Quintana, C., Riina, R., Sarkinen, T.; 2017). Response to “Forest conservation: Humans’ handprints. Science 355: 467.

A102. Coelho F, Dexter KG, Phillips OL, Brienen RJW, Chave J, Galbraith DR, Lopez Gonzalez G, Monteagudo A, PENNIGNTON RT (+ 50 other authors). (2016). Evolutionary heritage shapes Amazon tree ecology. Proceedings of the Royal Society of London – Series B. https://doi.org/10.1098/rspb.2016.1587

A103. Dexter, K.G, Coley, P., Drake, C., Hollands, R., Kursar, T., Lavin, M., Torke, B., Twyford T. PENNINGTON, R.T. (2017). Dispersal assembly of rain forest tree communities across the Amazon basin.  Proceedings of the National Academy of Sciences, USA. 114 : 2645–2650. doi: 10.1073/pnas.1613655114

A104. Baker, T.R., PENNINGTON R.T. Dexter, K. G., Fine, P. V., Fortune-hopkins, H., Honorio, E. N., Huamantupa-chuquimaco, I., Klitgård, B. B., Lewis, G. P., De Lima, H. C., Ashton, P., Baraloto, C., Davies, S., Donoghue, M. J., Kaye, M., Kress, W. J., Lehmann, C. E., Monteagudo, A., Phillips, O. L. & Vasquez, R. (joint first authors with 18 co-authors; accepted). Maximising synergy amongst tropical plant systematists, ecologists and evolutionary biologists. Trends in Ecology and Evolution. doi.org/10.1016/j.tree.2017.01.007

A105. Legume Phylogeny Working Group (LPWG; 2017). A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny. Taxon. [This is a group authorship with 100 coauthors]. https://doi.org/10.12705/661.3

A106. Rezende V, Dexter KG, PENNINGTON RT, Oliveira-Filho AT. (2017). Evolutionary diversity patterns across southern South America. Journal of Biogeography 44: 2365–2375. 10.1111/jbi.13013

A107. Oliveira-Filho AT, Dexter KG, PENNINGTON RT, Valente AS, Bueno M, Eisenlohr P, Fontes MA, Moreira S, Rezende V, Saiter F, Neves DMR. (2017). Dissecting a biodiversity hotspot: the importance of environmentally marginal habitats in the Atlantic Forest Domain of South America. Diversity and Distributions 23: 898–909. 10.1111/ddi.12581

A108. Neves, D.M., Dexter, K.G., Pennington, R.T., Bueno, M.L., Miranda, P.L.S., Oliveira-Filho, A.T. (2017). Lack of floristic identity in campos rupestres – a hyperdiverse mosaic of rocky montane savannas of in South America. Flora. https://doi.org/10.1016/j.flora.2017.03.011

A109. PENNINGTON, R.T., Lavin, M. (2017). Dispersal, isolation, and diversification with continued gene flow in an Andean tropical dry forest. Molecular Ecology 26: 3327–3329. 10.1111/mec.14182

A110. Quintana, C., PENNINGTON, R.T., Ulloa Ulloa, C., Balslev, H. (2017). Biogeographic barriers in the Andes: is the Huancabamba depresspion a dispersal barrier for dry forest plants? Annals of the Missouri Botanical Garden 102:542-550. https://doi.org/10.3417/D-17-00003A

A111. Endara, M-J., Coley, P.D., Ghabasha, G., Nicholls, J.A., Dexter, K.G., Donosog, D.A., Stone, G.N., PENNINGTON, R.T., Kursar, T.A. (2017). Coevolutionary arms race versus host defense chase in a tropical herbivore–plant system Proceedings of the National Academy of Sciences, USA. doi: 10.1073/pnas.1707727114.

A112. 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. (2017). Comment on “The extent of forest in dryland biomes”. Science 358, eaao1309

A113. Heckenhauer, J., Abu Salim, K., Chase, M.W., Dexter, K.G., Pennington, R.T., Tan, S., Kaye, M.E., 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. https://doi.org/10.1371/journal.pone.0185861

A114. Gómez-Gutiérrez, M.C., PENNINGTON, R.T., Neave, L.E., Milne, R.I., Madriñán, Richardson, J.E. . (2017) Genetic diversity in the Andes: variation within and between the South American species of Oreobolus R. Br. (Cyperaceae). Alpine Botany 127:155–170. DOI 10.1007/s00035-017-0192-z. Available at: http://rdcu.be/vBkg

A115. Luke T. Dunning, Anne-Lise Liabot, Jill K. Olofsson, Emma K. Smith, Maria S. Vorontsova, Guillaume Besnard, Kimberley J. Simpson, Marjorie R. Lundgren, Eda Addicott, Rachael V. Gallagher, Yingying Chu, PENNINGTON, R.T., Pascal-Antoine Christin & Caroline E. R. Lehmann (2017): The recent and rapid spread of Themeda triandra, Botany Letters, DOI: 10.1080/23818107.2017.1391120

A116. Endara, M.J., Coley, P.D., Wiggins, N.L., Forrister, D.L., Younkin, G.C., Nicholls, J.A., PENNINGTON, R.T., Dexter, K.G., Kidner, C.A., Stone, G.N., Kursar, T.A. (2018) Chemocoding as an identification tool where morphological‐ and DNA‐based methods fall short: Inga as a case study. New Phytologist. https://doi.org/10.1111/nph.15020

A117. Bueno, M.L., Dexter, K.G., PENNINGTON, R.T., Pontara, V., Neves, D.M., Ratter, J.A., Oliveira‐Filho, A.T. (2018) The environmental triangle of the Cerrado Domain: Ecological factors driving shifts in tree species composition between forests and savannas. Journal of Ecology https://doi.org/10.1111/1365-2745.12969

A118. PENNINGTON, R.T., Lehmann, C.E., Rowland, L. Tropical savannas and dry forests. Current Biology 28: R541 - R545. https://doi.org/10.1016/j.cub.2018.03.014

A119. Silva de Miranda, P., Oliveira-Filho, A.T., PENNINGTON, R.T., Neves, D., Baker, T. & Dexter, K.D. (2018). Using tree species inventories to map biomes and assess their climatic overlaps in lowland tropical South America. Global Ecology and Biogeography.

A120. PENNINGTON, R.T, de Lima, H.C., Inches, F., Watherston, N. (2018, in press). Andira anthelmia. Curtis Botanical Magazine.

A121. Dexter, K.G., PENNINGTON, R.T., Oliveira-Filho, A.T., Bueno, M.L., Silva de Miranda, P., Neves, D.M. (2018) Inserting Tropical Dry Forests into the Discussion on Biome Transitions in the Tropics. Frontiers in Ecology and Evolution. doi: 10.3389/fevo.2018.00104

A122. Lavin, M. PENNINGTON, R.T. Hughes, C.E., Lewis, G.P., Delgado-Salinas, A., Duno de Stefano, R., de Queiroz, L.P., Cardoso, D., Wojciechowski, M.F. 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.

A123. Endara, M.-J., Nicholls, J. Coley, P.D., Forrister, D.L., Younkin, G.C., Dexter, K.G., Kidner, C.A., PENNINGTON, R.T., Stone, G., Kursar, T.A. Tracking of host defenses and phylogeny during the radiation of neotropical Inga-feeding sawflies (Hymenoptera; Argidae). Frontiers in Plant Science. https://doi.org/10.3389/fpls.2018.01237

A124. Gomes, V. H. F., Ijff, S. D., Raes, N., Amaral, I. L., Salomão, R. P., Coelho, L. D. S., .PENNINGTON, R.T. . . De Souza, F. C. (2018). Species Distribution Modelling: Contrasting presence-only models with plot abundance data. Scientific Reports, 8(1). doi:10.1038/s41598-017-18927-1


(b) Books and volumes authored or edited

B1. Scotland, R.W. & PENNINGTON, R.T. (eds.) (2000). Homology in Systematics: Coding Characters for Phylogenetic Analysis. Taylor and Francis, London. 288pp: illus. 58 b+w.

B2. Reynel, C., Pennington, T.D., PENNINGTON, R.T., Daza, A. & Flores, C. (2003). Árboles útiles de la Amazonia Peruana y sus usos (Useful Trees of the Peruvian Amazon). Tarea Gráfica Educativa, Perú. 509 pp: illus 150 b+w, 20 colour.

B3. PENNINGTON, R.T., Richardson, J.E. & Cronk, Q.C.B. (eds). (2004). Plant phylogeny and the origin of major biomes. Philosophical Transactions of the Royal Society, Series B 359: 1453-1656.

B4. PENNINGTON, R.T., Lewis, G. & Ratter, J.A. (eds.) (2006). Neotropical savannas and dry forests: plant diversity, biogeography and conservation.  CRC Press, Florida. 484 pp.

B5. Reynel, C., Pennington, T.D., PENNINGTON, R.T., Marcelo, J. & Daza, A. (2007). Arboles útiles del ande peruano (Useful Trees of the Peruvian Andes). Tarea Gráfica Educativa, Perú. 462 pp: illus 130 b+w, 20 colour.

B6. Marcelo Peña, J.L., PENNINGTON R.T. & Reynel, C (2010). Guia ilustrada de la flora leñosa de los bosques estacionalmente secos de Jaén. Tarea Gráfica Educativa, Perú. 286pp. illus 13 b+w, 338 colour.

B7. Antonelli, A., Hughes, C.E., PENNINGTON R.T. & Fay, M (eds.) (2013). Neotropical Plant Evolution - Assembling the Big Picture. Botanical Journal of the Linnean Society 171: 1-300 (contains 17 papers)

B8. Reynel, C., PENNINGTON, R.T., Särkinen, T. 2013. Cómo se formó la diversidad ecológica del Perú. Jesús Bellido, Lima, Peru. 412 pp. Illus 27.

B9. Richardson, J. PENNINGTON,R.T. & (eds) (2015). Origin of tropical diversity: from clades to communities. Frontiers in Genetics, “Research Topic”. http://journal.frontiersin.org/researchtopic/1485/origin-of-tropical-diversity-from-clades-to-communities (22 articles by 126 authors). 91,000 article views (April 2017) [Now available as an ebook: Richardson, J. E., Pennington, R. T., eds. (2016). Origin of Tropical Diversity: From
Clades to Communities. Lausanne: Frontiers Media. doi: 10.3389/978-2-88945-050-3]

B10. Reynel, C., Pennington, T.D., PENNINGTON, R.T. (2016). Árboles del Peru. Tarea Gráfica Educativa, Perú. 800 pp: illus 450 b+w.


(c) Book chapters (all peer reviewed)

C1. PENNINGTON, R.T. (2000). Introduction. In R.W. Scotland & R.T. Pennington (eds.). Homology in Systematics: Coding Characters for Phylogenetic Analysis. pp. 1-9. Taylor and Francis, London.

C2. PENNINGTON R.T., Klitgaard, B., Ireland, H.E. & Lavin, M. (2000). New insights into floral evolution of basal Papilionoideae from molecular phylogenies. In: P. Herendeen & A. Bruneau (eds.). Advances in legume systematics. Part 9. pp. 233-248. Royal Botanic Gardens, Kew.

C3. Ireland, H., PENNINGTON, R.T. & Preston, J. (2000). Molecular Systematics of the Swartzieae. In: P. Herendeen & A. Bruneau (eds). Advances in legume systematics. Part 9. pp. 217-232. Royal Botanic Gardens, Kew.

C4. PENNINGTON, R.T., Lavin, M., Prado, D.E., Pendry C.A. & Pell, S. (2005). Climate change and speciation. In Y. Malhi and O.L. Phillips (eds.), Tropical forests and global atmospheric change. pp. 199-214. Oxford University Press

C5. PENNINGTON, R.T., Stirton, C.S. & Schrire, B.D. (2005). Sophoreae. In G.P.Lewis, B.D. Schrire, B. MacKinder & J.M. Lock (eds). Legumes of the World. pp. 227-249. Royal Botanic Gardens, Kew.

C6. PENNINGTON, R.T., Ratter, J.A. & Lewis, G.P. (2006). An overview of the plant diversity, biogeography and conservation of neotropical savannas and seasonally dry forests. In R.T. Pennington, G.P. Lewis & J.A. Ratter (eds). Neotropical savannas and seasonally dry forests: plant diversity, biogeography and conservation. pp. 1-29. CRC Press, Florida.

C7. Naciri, Y., Caetano, S., PENNINGTON, R.T., Prado, D. & Spichiger, R. (2006). Population genetics and inference of ecosystem history: an example using two neotropical seasonally dry forest species. In R.T. Pennington, G.P. Lewis & J.A. Ratter (eds). Neotropical savannas and seasonally dry forests: plantdiversity, biogeography and conservation. pp. 417-432. CRC Press, Florida.

C8. PENNINGTON, R.T. & Dick, C.W. (2010).  Diversification of the Amazonian flora and its relation to key geological and environmental events: a molecular perspective. In C. Hoorn, H. Vonhof, F. Wesselingh (eds). Amazonia, Landscape and Species Evolution: a Look into the Past. pp. 373-385. Blackwell.

C9. Linares, R., Oliveira Filho A.T. & PENNINGTON, R.T. (2011). Neotropical Seasonally Dry Forests: Diversity, Endemism and Biogeography of Woody Plants. In R. Dirzo, H. Mooney, G. Ceballos, H. Young (eds). Latin American Seasonally Dry Tropical Forests. Pp. 3-21. Island Press

C10. Meir, P. & Pennington, R.T. (2011). Climate change and seasonally dry tropical forests. In R. Dirzo, H. Mooney, G. Ceballos, H. Young (eds). Latin American Seasonally Dry Tropical Forests. Island Press

C11. Oliveira-Filho, A.T., PENNINGTON, R.T., Rotella, J. & Lavin, M. (2013). Exploring evolutionarily meaningful vegetation definitions in the tropics: a community phylogenetic approach. In D.A. Coomes, D.F.R.P. Burslem and William D. Simonsen (eds).  Forests and Global Change. Pp. 239-260. Cambridge University Press (Ecological Reviews series).

C12. Winterton, C., Richardson, J.E., Hollingsworth, M., Clark, A., Zamora, N. & Pennington, R.T. (2014) Historical biogeography of the neotropical legume genus Dussia: the Andes, the Panama Isthmus and the Chocó. In Stevens, W. D., O. M. Montiel & P. H. Raven. 2014. Paleobotany and Biogeography: A Festschrift for Alan Graham in His 80th Year. Missouri Botanical Garden Press, St. Louis, MO. 128.pp.

C13. Magallon, S., PENNINGTON, R.T., Villaseñor, J.L., Rodríguez, P., Honorio, E.N., Foster, R., Harris, D., Wieringa, J. (2014) The influence of regional history and ecologicalaffinity in the angiosperm composition of Mexican lowland tropical rainforests. In Stevens, W. D., O. M. Montiel & P. H. Raven (eds.) Paleobotany and Biogeography: A Festschrift for Alan Graham in His 80th Year. Pp. 287-325. Missouri Botanical Garden Press, St. Louis, MO.


(d) Other publications

D1. PENNINGTON, R.T. (1993). The Commonwealth and Government of Guyana Iwokrama Rain Forest Programme ‑ Botanical Studies ‑ Final Report. Natural Resources Institute, Chatham, UK. 40pp.

D2. PENNINGTON, R.T. (1994). The Commonwealth and Government of Guyana Iwokrama Rain Forest Programme ‑ Botanical Studies. Flora of the Guianas Newsletter 10 (Special Workshop Issue): 12-14.

D3. Sidwell, K & PENNINGTON, R.T. (1995). Report of SA2000 Meeting. The Systematics Association Newsletter 2: 3

D4. PENNINGTON, R.T. (1995). Book Review: The diversity and evolutionary biology of tropical flowers, by Peter Endress (1994) Annals of Botany 75: 325-327.

D5. PENNINGTON, R.T. (1995).  Proteaceae. In B.T. Stannard (ed.). Flora of Pico das Almas. pp. 543-544. Royal Botanic Gardens, Kew.

D6. Aymard, G., Cuello, N & PENNINGTON, R.T. (1999) Andira.  In J.A. Steyermark, P.E. Berry & B.K. Holst (eds). The Flora of the Venezuelan Guayana. pp. 259-262. Missouri Botanical Garden and Timber Press .

D7. PENNINGTON, R.T. (2001). Book Review: The origin, expansion and demise of plant species, by Donald A. Levin (2000) Annals of Botany 87: 284-286.

D8. PENNINGTON, R.T. & Pennington, T.D. (2002). The INGA investigation: DNA and the evolution of the tropical forests. Tree News (Sylva), Spring/Summer 2002: 5-6

D9. PENNINGTON, R.T. (2002). Book Review: The evolution of plants, by K.J. Willis and J.C. McElwain (2002). Annals of Botany.

D10. PENNINGTON, R.T. (2005). Book review. Advances in legume systematics, part 10, Higher level systematics, edited by B. Klitgaard and Anne Bruneau. Plant Systematics and Evolution 252: 116-119.

D11. PENNINGTON, R.T., A.M. de Carvalho & H.C. de Lima (submitted). Andira. In Flora of Sao Paulo State, Brazil.

D12. Bridgewater S. & PENNINGTON, R.T. (2010). A scottish botanist in Brazil; Flora Peruviana et Chilensis; Flora Brasiliensis. In On the Edge of the World. British Council, ISBN 978-086355-637-1 (Catalogue to accompany art exhibition).

D13. PENNINGTON, R.T. (2013) A race against time to define our world. Scotsman newspaper, double page opinion piece, 20th August 2013.

D14. PENNINGTON, R.T. (2013) Prologue to introduce a special issue of Biota Colombiana covering dry forests in Colombia