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John Bates

Assoc. Curator and Section Head

Integrative Research Center
Environmental Conservation
Evolutionary Biology

Contact Information

The tropics harbor the highest species diversity on the planet.  My students and I study genetic structure in tropical birds and other organisms to address how this diversity evolved and how it continues to evolve as climates change and humans continue to alter landscapes.

We study comparative genetic structure and evolution primarily in the Afrotropics the Neotropics, and the Asian tropics.  I am an ornithologist, but my students also have studied amphibians and small mammals (bats and rodents).  Research in the my lab has involved gathering and interpreting genetic data in both phylogeographic and phylogenetic frameworks. Phylogenetic work on Neotropical birds has focused on rates of diversification and comparative biogeography (Tello and Bates 2007, Pantané et al 2009, Patel et al. 2011, Lutz et al. 2013).  Phylogeographic work has sought to understand comparative patterns across different biomes (Bates et al 2003, Bates et al. 2004, Bowie et al. 2006, I. Caballero dissertation research).  We also have used genetic data to better understand evolutionary patterns in relation to climate change across landscapes (e.g., Carnaval and Bates 2007) that include the Albertine Rift (through our MacArthur Grants), the Eastern Arc Mountains (Lawson dissertation research), the Philippines (T. Roberts and S. Weyandt dissertation research) and South America, particularly the Amazon (A. Savit dissertation research, Figueiredo et al. 2013), and we are entering into the genomic realm focusing initially on Andean (Ben Winger dissertation research) and Amazonian birds (through our NSF Dimensions of Diversity grant). Shane DuBay has initiated his dissertation research in the Himalayas on physiological plasticity in Tarsiger Bush Robins.  Nick Crouch, who I co-advise at U. Illinois, Chicago with Boris Igic, is studying specialization in birds from a modern phylogenetic perspective.  We seek to create a broader understanding of diversification in the tropics from a comparative biogeographic framework (Silva and Bates 2002, Kahindo et al, 2007, Bates et al. 2008, Antonelli et al. 2009).  Beginning in the Fall of 2014 Two new students, João Caparucho (U. Illinois, Chicago) and Natalia Piland (Committee on Evolutionary Biology, U. Chicago) have joined our research group. 

Josh Engel and I are working up multi-species phylogeographic studies of birds across the Albertine Rift, based the Bird Divsion's long term research throughout the region.  We are working up similar data sets for Malwian birds.  Our current NSF Dimensions of Diversity grant on the assembly of the Amazonian biota and our NSF grant to survey birds and their parasites across the southern Amazon are generating genomic data for analysis in collaboration with paleoecologists, climatologists, geologists, and remote sensing experts from the U.S. and Brazil.  This large collaboration will provide new perspectives on the history of Amazonia.

Recent Blog Posts

Additional Information


Ph.D., Louisiana State University, 1993.

M.S., University of Arizona, 1987.

B.S., University of Arizona, 1983.


Primary Research

Silva, J. M. C. and J. M. Bates. 2002. Biogeographic patterns in the South American Cerrado: a tropical savanna hotspot. BioScience 52:225-233.

Griffiths, C. S. and J. M. Bates. 2002. Morphology, genetics and the value of voucher specimens: an example with Cathartes vultures. Journal of Raptor Biology 36:183-187.

Bates, J. M., J. G. Tello, and J. M. Cardoso da Silva. 2003. An initial assessment of genetic diversity in ten bird species of South American Cerrado. Studies on Neotropical Fauna and the Environment 38:87-94.

Bates, J. M., J. Haffer and E. Grismer. 2004. Avian Mitochondrial DNA sequence divergence across as headwater stream of the Rio Tapajos, a major Amazonian river. Journal of Ornithology 145:199-205.

Braun, M. J., M. L. Isler, P. Isler, J. M. Bates, and M. B. Robbins. 2005. Avian speciation in the Pantepui: the case of Percnostola [Schistocichla] "leucostigma" saturata. Condor 107:329-343.

Bowie, C. K. R., J Fjeldså, S. J. Hackett, J. M. Bates, and T. M. Crowe. 2006. Coalescent models reveal the relative roles of ancestral polymorphism, vicariance, and dispersal in shaping phylogeographical structure of an African montane forest robin. Molecular Phylogenetics and Evolution 38:171-188.

Carnaval, A. C. O. Q., and J. M. Bates. 2007. Amphibian DNA shows marked genetic structure and tracks Pleistocene climate change in northeastern Brazil. Evolution 61:2942-2957.

Cadena, C. D., B. López-Lanús, J. M. Bates, N. Krabbe, N. H. Rice, F. G. Stiles, J. D. Palacio, and P. Salaman. 2007. Second Record of Hybridization in the Tracheophone Suboscines: Grallaria nuchalis x G. ruficapilla in a Fragmented Andean Landscape. Ibis 149:814-825.

Tello, J. G. and J. M. Bates. 2007. Molecular phylogenetics of the Flatbill and Tody-tyrant assemblage of Tyrant flycatchers (Aves: Tyrannidae). The Auk 124:1-21.

Tobias, J. A., J. M. Bates, S. J. Hackett, and N. Seddon. 2008. Comment on “The latitudinal gradient in recent speciation and extinction rates of birds and mammals.: Science 319:901c.

Bates, J. M., C. D. Cadena, J. G. Tello, and R. T. Brumfield. 2008. Diversification in the Neotropics: phylogenetic patterns and historical processes. Proceedings of the VIIIth Neotropical Ornithological Congress. Ornitología Neotropical 19 (suppl.): 427-432.

Bueter, C. J., J. Weckstein, J. M. Bates, K. P. Johnson, and C. E. Gordon. 2009. Comparative phylogenetic histories of two louse genera found on Catharus thrushes and other birds. Journal of Parasitology 95:295-307.

Pantané, J. S. L., J. D. Weckstein, A. Aleixo, and J. M. Bates. 2009. Evolutionary history of Ramphastos toucans: Molecular phylogenetics, temporal diversification and biogeography. Molecular Phylogenetics and Evolution 53:923-934.

Patel, S., J. D. Weckstein, J. S. L. Patané, J. M. Bates, and A. Aleixo. 2011. Temporal and spatial diversification of Pteroglossus Aracaris (Aves Ramphastidae) in the Neotropics: Constant rate of diversification does not support an increase in radiation during the Pleistocene. Molecular Phylogenetics and Evolution 58:105-115.

Yojanan Lobo-y-Henriques, J. C., J. Bates, and D. Willard. 2013. First record for the Black-and-white Tanager (Conothraupis speculigera) in Colombia. Conservación Colombiana 17:45-51.

Lutz, H. L., J. D. Weckstein, J. S. L. Patané, J. M. Bates, and A. Aleixo. 2013. Biogeography and spatio-temporal diversification of Selenidera and Andigena Toucans (Aves: Ramphastidae). Molecular Phylogenetics and Evolution 69:873–883.

Diehl, R. H., J. M. Bates, D. E. Willard, and T. P. Gnoske. 2014. Bird mortality during migration over Lake Michigan: a case study. Wilson Bulletin 126:19-29.

Engel, J., K. Byamana, C. Kahindo, J. M. Bates, and J. Fjeldså. 2014. Genetic structure and species limits in the Barred Long-tailed Cuckoo (Cercococcyx montanus) complex. Ibis doi: 10.1111/ibi.12145.

Tello, J. G., M. Raposo, J. Bates, D. Cadena, G. Bravo, and M. Maldanado 2014. Cryptic genetic diversity in birds: the polyphyly of the widespread Neotropical genus Cercomacra (Aves, Thamnophilidae). Zoological Journal of the Linnean Society, 2014, 170:546–565.

New species

Joseph, L. and J. M. Bates. 2002. Pyrrhura snethalgeae sp. nov. Pp. 354-355 in Joseph, L. Geographical variation, taxonomy, and distribution of some Amazonian Pyrrhura parakeets. Ornithólogia Neotropical 13:337-363.

Tello, J. G., J. F. Degner, J. M. Bates, and D. E. Willard. 2006. A new species of Hanging-Parrot (Loriculus) from Camiguin Island, Philippines, pp. 58-72. In Heaney, L. R., ed., The Mammals and Birds of Camiguin Island, Philippines, a Distinctive Center of Biodiversity. Fieldiana Zoology, n.s., 106:1-72.

Voelker, G., Robert K. Outlaw, Sushma Reddy, Michael Tobler, John M. Bates, Shannon J. Hackett, Charles Kahindo, Ben D. Marks, Julian Kerbis Peterhans, and Thomas P. Gnoske. 2010. A new species of black boubou from the Albertine Rift (Passeriformes: Laniidae: Laniarius). The Auk 127:678-689.

Stanley, W. T., L. W. Robbins, J. M. Malekani, J. B. Doty, B. P. Monroe, Y. J. Nakazawa, D. Carroll, J. C. Kerbis Peterhans, J. M. Bates, and J. A. Esselstyn. 2013. A new hero emerges: a second shrew (Soricidae) with interlocking vertebrae and a hypothesis regarding their adaptive significance. Biology Letters 9: 20130486. http://dx.doi.org/10.1098/rsbl.2013.0486.

Aleixo, A., C. E. B. Portes, A. Whittaker, J. D. Weckstein, L. P. Gonzaga, K. J. Zimmer, C. C. Ribas and J. M. Bates. 2013. Molecular systematics and taxonomic revision of the Curve-billed Scythebill complex (Campylorhamphus procurvoides: Dendrocolaptidae), with description of a new species from western Amazonian Brazil. In: Handbook of the Birds of the World, Special Volume: New Species and Global Index [J. del Hoyo, A. Elliott e D. Christie, eds.]. Lynx Edicions, Barcelona, Spain, pp. 253-257. urn:lsid:zoobank.org:pub:293EDAE0-93B1-4E64-B1F5-C5B4977543FB.

Portes, C. E. B., A. Aleixo, K. J. Zimmer, A. Whittaker, J. D. Weckstein, L. P. Gonzaga, C. C. Ribas, J. M. Bates and A. C. Lees. 2013. A new species of Campylorhamphus (Aves: Dendrocolaptidae) from the Tapajós – Xingu interfluve in Amazonian Brazil. In: Handbook of the Birds of the World, Special Volume: New Species and Global Index [J. del Hoyo, A. Elliott and D. Christie, eds.]. Lynx Edicions, Barcelona, Spain, pp. 258-262. urn:lsid:zoobank.org:pub:5B0FCF37-D5F6-4520-9531-AE2461607F08.

Faunal Surveys and Natural History

Fraga, R. M. and J. M. Bates. 2005. Two unreported specimens of Ochre-breasted Pipit, Anthus nattereri, from a new Brazilian locality. Bull. Brit. Orn. Club 125:66-68.

Bates, J. M. 2006. The seasonal movements of southern populations of Dull-colored Grassquit (Tiaris obscura obscura). Bull. Brit. Orn. Club 126:50-53.

Aleixo, A., Rodrigues, E. B., Faccio, M. S., Weckstein, J. D. & Bates, J. M. 2007. Aves do Cacuajó, FLONA de Caxiuanã, p. 70-72. Em Resumos Expandidos do I Seminário Científico do PPBIO. Belém: Museu Paraense Emílio Goeldi. http://marte.museu-goeldi.br/ppbio/index.php?option=com_content&task=view&id=27&Itemid=39 (consultado em 30/08/2007).

Kaleme, P. K., J. M. Bates, J. Kerbis Peterhans, M. M. Jaques, and B. R. Ndara. 2007. Small mammal diversity and habitat requirements in the Kahuzi-Biega National Park and surrounding areas, eastern Democratic Republic of Congo. Integrative Zoology 2:239-246.

Maillard, O., J. M. Bates, J. G. Tello, and M. A. Aponte. 2007. Avifauna del Rio Manupare y Cráter Iturralde, un bosque Amazonico en el Departamento de La Paz, Bolivia. Ornitología Neotropical 18:519-534.

Kizungu, R. B., J. M. Bates, and B. Murhabale. 2007. A nest of Collared Apalis (Apalis ruwenzori) in Kahuzi-Biega National Park, Democratic Republic of Congo. Journal of the African Bird Club 14:69-71.

Kirwan, G. M. and J. M. Bates. 2008. The status of European Stonechat Saxicola rubicola in the Islamic Republic of Iran. Sandgrouse 30:113-116.

Engel J. E., J. M. Bates, J. D. Weckstein, P. M. Kaliba, T. P. Gnoske. 2012. An avifaunal survey of Vwaza Marsh Wildlife Reserve, Malawi. Journal East African Natural History 101:223-240.

Book Chapters

Tello, J. G., J. M. Bates, and I. Caballero. 2004. Species accounts for the flycatcher genera Rhynchocyclus, Tolmomyias, and Platyrinchus. Pp. 337-343 in Handbook of Birds of the World, Vol. 9 (Eds, J. de Hoyo, A. Elliot, and D. Christie). Lynx Edicions, Barcelona, Spain.

Antonelli, A., A. Quijada-Mascareñas, A. J. Crawford, J. M. Bates, P. M. Velazco and W. Wüster. 2009. Molecular studies and phylogeography of Amazonian tetrapods and their relation to geological and climatic models. Pp 388-404 in: Neogene history of Western Amazonia and its significance for modern biodiversity. C. Hoorn, H. Vonhof, and F. Wesselingh (Eds.).

Bates, J. M. 2010. Studying birds in the Sonoran Desert. Pp. 49-57. In: Moments of Discovery: Natural History Narratives from Mexico and Central America. K. Winker (Ed.). Univ. Florida Press.

Popular Books
MacNamara, P., J. M. Bates, and J. H. Boone. 2008. Architecture by birds and insects: a natural art. Chicago, University of Chicago Press.

MacNamara, P., J. M. Bates, and J. H. Boone. 2013. Seasonality in the mid-western crossroads: Movements of birds and insects through a year in the Chicago region. University of Chicago Press.

Hauber, M. 2014. The Book of Eggs. B. Becker and J. M. Bates, editors. University of Chicago Press.

Conservation related publications

Bates, J. M. 2005. Conservationists: Don’t forget academics. Letter to editor. Worldwatch 2005(Nov./Dec.): 4.

Kahindo, C., J. M. Bates, and R. C. K. Bowie. 2007. The relevance of data on genetic diversity for the conservation of Afro-montane regions. Biological Conservation 134:262-270.

Book Reviews

Bates, J. M. 2003. Review of People and Forests: Communities, Institutions, and Governance (C. C. Gibson, M. A. McKean, and E. Ostrom; Editors). The Quarterly Review of Biology 78:113-114.

Bates, J. M. 2008. Review of The Clements Checklist of Birds of the World by J. F. Clements. The Quarterly Review of Biology 83(2):227.

Bates, J. M. 2014. Review of Walking Wild Shores by K. Winker. Wilson Bulletin (in press).

Work experience

Member, Committee on Evolutionary Biology, University of Chicago.

Adjunct Professor, Dept. of Biological Sciences, University of Illinois, Chicago.

External Lecturer, Makerere University, Kampala, Uganda

Project Leader, Programme Biodiversite des Ecosystemes Aquatiques et Terrestres dans le Rift Albertin (PBEATRA), Dem. Rep. of Congo.

Past Head, current member of TFM Pritzker Laboratory for Molecular Systematics and Evolution management committee