Toby Pennington

Toby Pennington

Email: Toby Pennington

Phone: +44 (0)131 248 2818

Fax: +44 (0)131 248 2901

My research has aimed to address one of the fundamental questions of tropical biology – how and when did the huge species numbers in the tropics arise? It is grounded in fundamental, descriptive taxonomic, inventory and phylogenetic research, which provides the foundation to address evolutionary and biogeographic questions.


Most taxonomic research has concentrated upon Leguminosae, which dominates the tropical forests of the Americas and Africa. Much work has been carried out via supervision of MSc and PhD students, and it has led to monographic accounts of Berlinia, Centrolobium, Proteaceae for Flora Neotropica, and an account of Berberis for Nepal. These taxonomic accounts are fundamental for species definition and identification, and therefore important for the conservation and sustainable use of plant species.

Applied research: inventory

In biodiverse countries such as Peru that are not covered by a national flora project and lack well-curated, comprehensive herbaria, there is a clear need for simple identification tools that suit both specialist and non-specialist workers. Following earlier guides to Amazonian and Andean trees, I have co-authored a third book covering 105 dry forest species from northern Peru.
    With support from a recent grant from the Leverhulme Trust, work on seasonally dry tropical forests has been expanded to cover the entire New World Tropics by the foundation of an international network of researchers. The “Latin American Seasonally Dry Tropical Forest Floristic Network” (DRYFLOR) will be coordinated from RBGE and include partner institutions from five Latin American countries that support significant areas of dry forest: Brazil, Argentina, Peru, Colombia and Mexico. The DRYFLOR network aims to pinpoint areas of high plant species diversity and endemism that are an essential basis for conservation strategies. For more details click here.

Phylogeny, biogeography and environmental change

(a) neotropical seasonally dry forests – a molecular view of past environmental change
It has been generally assumed that cool-dry glacial climates during the Pleistocene favoured more widespread savanna formations. This view, however, neglected the possibility that SDTF may also have increased in extent, which I have addressed by population genetic study of widespread SDTF species. Chloroplast and nuclear microsatellite data for two SDTF tree species with disjunct distributions across South America have been gathered in collaboration with the Geneva Botanical Garden (funded by the Swiss National Science Foundation) and give evidence for recent (potentially Pleistocene) population expansion in eastern Brazil and recent dispersal to the Galapagos islands. However, connections between Brazilian SDTF and those of dry Andean valleys were demonstrated to be more ancient, matching their low floristic similarity. Within the dry interAndean valleys, we demonstrated extraordinary antiquity (c. 5 million years) of conspecific populations of the legume shrub Cyathostegia matthewsii. This result has considerable implications for the scientific understanding and conservation of the Andean biodiversity hotpot, and was a research highlight in PNAS.

(b) rain forests: how has herbivore pressure influenced plant speciation?
A focus genus for my research on diversification in tropical rain forests over the past decade has been Inga (Leguminosae), which is species-rich (300 spp.), widely distributed, and has consistently high local abundance and species diversity. It therefore provides an ideal system to investigate the origin and maintenance of tropical diversity and is used as a model for studying the evolutionary ecology of anti-herbivory strategies in tropical plants by the ecologists Phyllis Coley and Thomas Kursar (University of Utah, USA and Smithsonian Tropical Research Institute, Panama). Over the past five years, collaboration with Coley and Kursar has been facilitated by producing a better resolved phylogeny for Inga. In a paper published in PNAS we have demonstrated that there is little phylogenetic signal for defence chemistry in Inga, which is in contrast to the prevailing orthodoxy in coevolutionary theory that related species have similar defences. Work in this area is now supported by a US National Science Foundation Dimensions of Biodiversity grant.

(c) rain forests: how have plants moved over biogeographic boundaries and corridors?
In one of the first biogeographic meta-analyses for a tropical region (published in Ecography), we demonstrated that whilst most animal groups did not cross the dispersal corridor of the Panama Isthmus until it became a land connection c. 3 million years ago, many plants crossed by long-distance dispersal over water before this date. These conclusions of more long-distance dispersal for plants have considerable implications for models of biome assembly and co-evolution, implying a resident fauna continually having to adapt to newly arriving flora over evolutionary timescales.

(d) is evolution and biogeography biome-specific?
There has been a tendency to view the tropics as uniformly covered by rain forests, but this neglects huge areas of tropical savannas and SDTF, which have been a focus of research at RBGE for five decades. Work in my research group has demonstrated that the tempo and mode of evolution differs among distinct biomes. For example, phylogenies of clades endemic to SDTF show older, geographically structured patterns, contrasting more recent, geographically unstructured rain forest diversifications. Such results suggest that a fruitful route to understanding tropical hyperdiversity is to examine diversification separately in different major biomes in order to build an overall picture.
In collaboration with the University of Leeds, RBGE has received a grant from the Natural Environment Research Council to investigate more deeply the evolutionary timing and rate of biome switching in tropical South American plant lineages. We will link floristic inventory data with phylogenetic information to provide a more general picture of niche evolution. We aim to investigate how many times lineages of trees have switched between different biomes, which will deliver important knowledge for future studies of evolutionary diversification and also for conservation. If lineages have rarely switched between biomes, then each biome will contain a distinct subset of evolutionary diversity, and destruction of a single biome could wipe out an entire part of evolutionary history. Such scenarios of the destruction of an entire biome are not unlikely for the highly threatened savannas and SDTF.

(e) palaeoecology: how did Ice Age climate fluctuations affect South American biomes?
An additional research area since has been collaborations in palaeoecology with two groups from the University of Edinburgh and the Open University. These draw on expertise at RBGE in the floristics and contemporary ecology of neotropical rain forests, SDTF and savannas in order to make palaeoenvironmental reconstructions based largely upon fossil pollen proxies. A lake core from Bolivia suggests that the lowland, tropical South American climate may have been de-coupled from that of the High Andes (where most climate records originate) in some periods following the Last Glacial Maximum (published by Whitney et al., in Palaeography, Palaeoclimatology, Palaeoecology ). A second record from Ecuador, published in Science (by Cardenas et al.), helps to reveal the nature of vegetation in Amazonia in a previous interglacial, and demonstrates a strong effect of temperature on floristic composition.

Other duties

I am Head of the Tropical Diversity section at RBGE and a Visiting Professor at the School of Biological Sciences, University of Edinburgh. I have served on the Natural Environment Research Council, Peer Review College (2008-2011) and have evaluated grants for Biology for the Danish Agency for Science, Technology and Innovation (2012 -). I attend the University of Edinburgh/RBGE MSc in Plant Taxonomy and Biodiversity steering committee. I teach Phylogenetics, Plant Geography and Leguminosae to MSc and undergraduate students at the University of Edinburgh.


Researchers (core funded RBGE staff not listed)

Dr Kyle Dexter (US NSF Overseas Postdoctoral Fellow; 100% from Sept 2011 – Dec 2012) Phylogeny and biogeography (niche evolution of South American trees)

Ms Julia Weintritt (Band C; Leverhulme Trust; 60% from May 2012): Floristic inventory and conservation of neotropical dry forests (network facilitator for Leverhulme-funded DRYFLOR International Network)

Ms Alexandra Clark (Band C; NERC, 40% from Sept 2012): Lab technician (niche evolution of South American trees)

Dr Terry Pennington (Consultant; Oct-Dec 2011): Peruvian floristics

Sabbatical visitors

Dr Haroldo Cavalcante de Lima, Rio de Janeiro Botanical Garden, Brazil (2009-2010; Brazilian government funded). Leguminosae of the Brazilian coastal Atlantic rain forests

Dr Susana Magallón, Universidad Autonoma de México (2009-2010; Mexican government funded) Phylogenetic structure of tropical forest communities.

Dr Marcelo Nascimento, Universidade Federal de Rio de Janeiro, Brazil (2012-2013; Brazilian government funded). Floristic relationships of dry tropical forest of Rio de Janeiro State.

PhD Students (Funding sources indicated)

Danilo Neves, Universidade Federal de Minas Gerais, Brazil (2011-2012)
Phenology, structure, dynamics and floristic patterns of the vegetation of the southern Pantanal
One year sandwich visit funded by Brazilian government (CAPES)

Marcelo Bueno, Universidade Federal de Minas Gerais, Brazil (2011-2012)
Phytogeographic patterns of the central Brazilian tree flora
One year sandwich visit funded by Brazilian government (CAPES)

Vanessa Pontara, Universidade Federal de Minas Gerais, Brazil (2011-2012)
Dynamics, growth and recruitment of Dalbergia nigra (Vellozo) Freire Allemão ex Bentham.
One year sandwich visit funded by Brazilian government (CAPES)

Oswaldo Cruz Neto, Universidade Federal do Rio Grande do Sul (2012)
Reproductive success of Inga vera Willd. (Leguminosae) in the Brazilian northeastern Atlantic forest
Six month sandwich visit funded by Brazilian government (CAPES)

Roosevelt García, University of Edinburgh (2011-2014).
Biogeography of the white sand forests of the Amazon
Supervisors: Toby Pennington, James Richardson, Kyle Dexter
University of Edinburgh Principal’s Career Development Scholarship

María-Camila Gómez, University of Edinburgh (2010-2013)
Evolution of the páramo flora
Supervisors: James Richardson, Richard Milne, Toby Pennington
University of Edinburgh

Euridice Honorio, University of Leeds (2009-2012)
Integrating ecological and molecular information of widespread species in western Amazonia
Supervisors: Oliver Phillips, Simon Lewis (Leeds), Toby Pennington
Programa de Ciencia y Tecnologia – FINCyT, Peru, and University of Leeds

Faten Filimban, University of Edinburgh (2009-2012)
Systematics and biogeography of Senna (Leguminosae) in Arabia.
Supervisors: Toby Pennington, Barbara MacKinder
Saudi Arabian government

Paulina Hechenleitner, University of Aberdeen (2009-2012).
Systematics and biogeography of neotropical Vicia (Leguminosae).
Supervisors: Toby Pennington, David Burslem (Aberdeen), Gwilym Lewis (RBG Kew)
ORSAS and RBGE Conifer Conservation Programme

Macarena Cardenas, Dept. Earth and Environmental Sciences, Open University (2007-2010). Climate change impacts on hyper-diverse Amazonian ecosystems.
Supervisors: William Gosling, Sarah Sherlock, Vincent Gauci (OU), Imogen Poole (Utrecht), Toby Pennington
NERC CASE studentship

Katherine Fitzpatrick, Dept. Geography, University of Edinburgh (2007-2010).
Multi-proxy based Late Quaternary environmental reconstruction in lowland tropical South America. Supervisors: Francis Mayle (UoE), Toby Pennington.

Tiina Sarkinen, Department of Plant Sciences, University of Oxford (2006-2009).
Systematics of Amicia (Leguminosae) and plant diversification in the Andes.
Supervisors: Colin Hughes, John Pannell (Oxford), Toby Pennington
Oskar Huttusen Saatio, Helsingin Sanomat Saatio, Ella ja Georg Ehrnroothin Saatio (private Finnish Foundations)

Bhaskar Adhikari, University of Edinburgh (2006-2009).
Investigating the evolution of large genera: how did Berberis speciate in Nepal?
Supervisors: Richard Milne (UoE), Colin Pendry, Toby Pennington
University of Edinburgh Torrance Bequest, Royal Horticultural Society, RBGE

Bronwen Whitney, Dept. Geography, University of Edinburgh (2006-2009).
Palaeoecology of the Pantanal: Late Quaternary vegetation and climate change in Eastern Bolivia.
Supervisors: Francis Mayle (UoE), Toby Pennington

Huw Jones Dept. Geography, University of Edinburgh (2006-2009).
Characterisation of neotropical savanna ecosystems by their modern pollen rain.
Supervisors: Francis Mayle (UoE), Jim Ratter, Toby Pennington

Sofia Caetano, University of Geneva (2003-2007).
South American seasonally dry tropical forests: are they current refugia or the result of long distance dispersal?
Supervisors: Yamama Naciri, Rodolphe Spichiger (Geneva), Toby Pennington
Swiss National Science Foundation

MSc students

Loic Cecilio, University of Edinburgh and RBGE MSc student (2011)
Isolation and gene flow across the Amazonian basin: illustration through species within the recently radiated genus Inga
Supervisors: Toby Pennington, James Richardson, Kyle Dexter

Cathy King, University of Edinburgh and RBGE MSc student (2009)
Systematics and biogeography of Dussia
Supervisors: Toby Pennington, Tiina Särkinen:

Sarah Cody, University of Edinburgh and RBGE MSc student 2008)
The use of plant and animal dated phylogenies to explore the effects of the closure of the Panama Isthmus
Supervisors: Toby Pennington , J. Richardson


(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 IngaEcology 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., 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.

A67. 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 .

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 doi: 10.1111/j.1365-294X.2012.05562.x

A70. 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

A71. Cardoso, D., de Lima, H.C., Schütz Rodrigues R., de Queiroz, L.P., PENNINGTON, R.T. & Lavin, M. (submitted). 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.

A72. Cardoso, D., de Lima, H.C., Schütz Rodrigues R., de Queiroz, L.P., PENNINGTON, R.T. & Lavin, M. (submitted). 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.

A69. Oliviera-Filho, A.T., PENNINGTON, R.T., Rotella, J. & Lavin, M. (submitted). Exploring evolutionarily meaningful vegetation definitions in the tropics: a community phylogenetic approach. Ecological Reviews.

A70. Cardoso, D. de Queiroz, L., PENNINGTON, R.T., de Lima, H.C., Fonty, E., Wojciechowski, M.F. & Lavin, M. (submitted). Revisiting the phylogeny of papilionoid legumes: new insights from comprehensively sampled early-branching lineages. American Journal of Botany.

A71. Legume Phylogeny Working Group (submitted). 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. *Corresponding author.


(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, in press). Neotropical Plant Evolution - Assembling the Big Picture. Botanical Journal of the Linnean Society (contains 17 papers)


(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

(d) Web

D1. Linares-Palomino, R. (supervised by PENNINGTON, R.T., Hughes, C.E., Pennington, T.D. & Ratter, J.A.). (2005). Annotated Checklist of the woody plants in Peruvian seasonally dry forests.

D2. Ratter, J.A., Bridgewater S., Milliken W., Pullan M., Oliveira-Filho, A., Ribeiro F., & PENNINGTON R.T. (2011). (website for floristic surveys and general botanical information about Brazilian cerrado vegetation; includes downloadable data and publications)

D3. PENNINGTON, R.T. (2011) (blog for WWF Save the Cerrado Campaign, “The Forgotten Forest that Moved Underground”).

D4. Weintritt, J. & PENNINGTON, R.T. (2012). (Website for DRYFLOR project: A Latin American Seasonally Dry Tropical Forest Floristic Network)

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