Curator and Section Head, Life Sciences
Negaunee Integrative Research Center
- 312.665.7730 (office)
- 312.665.7754 (fax)
The tropics harbor the highest species diversity on the planet. I am most intrigued by evolution at the tips of the tree of life. 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 students working with me and my wife Shannon Hackett and other museum curators also have studied amphibians and small mammals (bats and rodents) and more recently internal, external and blood parasites (e.g., Lutz et al. 2015, Block et al. 2015, Patitucci et al. 2016). Research in the our 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, Dantas et al. 2015). Phylogeographic work has sought to understand comparative patterns of divergence at level of population and species across different biomes (Bates et al 2003, Bates et al. 2004, Bowie et al. 2006, I. Caballero dissertation research, Block et al. 2015, Winger and Bates 2015, Lawson et al. 2015). 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, e.g., Voelker et al. 2010, Engel et al. 2014), the Eastern Arc Mountains (Lawson dissertation research, Lawson et al. 2015), the Philippines (T. Roberts and S. Weyandt dissertation research) and South America, particularly the Amazon (Savit dissertation research, Savit and Bates 2015, Figueiredo et al. 2013), and we are entering into the genomic realm focusing initially on Andean (Winger et al. 2015) and Amazonian birds (through our NSF Dimensions of Diversity grant). Shane DuBay is doing his dissertation research in the Himalayas on physiological plasticity in Tarsiger Bush Robins. Nick Crouch, who I co-advise at U. Illinois, Chicago with Roberta Mason-Gamer, 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). João Capurucho (U. Illinois, Chicago, co-advised with Mary Ashley) is studying phlylogeography of Amazonian white sand specialist birds and Natalia Piland (Committee on Evolutionary Biology, U. Chicago) is studying the impact of urbanization on Neotropical birds. New graduate student Valentina Gomez Bahamon (U. Illinois, Chicago) is also working Boris Igic and me, after doing her Master Degree in her native Colombia on genomics and the evolution of migrating Fork-tailed Flycatchers (Tyrannus savana). Jacob Cooper (Committee on Evolutionary Biology, U. Chicago) is studying the diversification of birds in Afromonte forests
Josh Engel and I are working up multi-species phylogeographic studies of birds across the Albertine Rift, based the Bird Division's long term research throughout the region. We are working up similar data sets for Malawian 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. These large collaborative projects are providing new perspectives on the history of Amazonia.
Education and Work
Ph.D., Louisiana State University, 1993.
M.S., University of Arizona, 1987.
B.S., University of Arizona, 1983.
Primary Research (since 2002)
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 156:330–340.
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.
Ritter, C. D., C. M. E. Figueiredo, C. Gubili, K. A. Feldheim, J. M. Bates, C. Cornelius, C. C. Ribas. 2014. Isolation and characterization of seventeen microsatellite DNA markers from Eleania ruficeps (Aves: Tyrannidae). Conservation Genetic Resources 6:1015-1018.
Winger, B. and J. M. Bates. 2015. The tempo of trait divergence in humid montane forests: Avian speciation across the Marañon valley of Peru. Evolution 69:772-787.
Lutz, H.L., Hochachka, W.M., Engel, J.I., Bell, J.A., Tkach, V.V., Bates, J.M., Hackett, S.J., Weckstein, J.D. 2015. Parasite prevalence corresponds to host life history in a diverse assemblage of Afrotropical birds and haemosporidian parasites. PLOS ONE. DOI: 10.1371/journal.pone.0121254.
Bates, J. M. and G. Voelker. 2015. Scientific collecting in Malawi, a response to Dowsett-Lemaire et al. Bird Conservation International, Available on CJO 2015 doi:10.1017/S0959270914000434.
Lawson, L. P., J. M. Bates, M. Menegon, and S. Loader. 2015. Divergence at the edges: Peripatric isolation in the montane Spiny-throated Reed Frog complex. BMC Evolutionary Biology 15 (1), 128.
Block, N. L, S. M. Goodman, S. J. Hackett, J. M. Bates, and M. J. Raherilalao. 2015. Potential merger of ancient lineages in a passerine bird discovered on evidence from host-specific ectoparasites. Ecology and Evolution, 5(17) 3743-3755.
Dantas, S., J. D. Weckstein, J. M. Bates, N. K. Krabbe, C. D. Cadena, M. B. Robbins, E. Valderrama, and A. Aleixo. 2015. Molecular phylogeny of the new world screech-owls (Megascops: Aves, Strigidae). Biogeographic and taxonomic implications. Molecular Phylogenetics and Evolution 94:626-634.
Winger, B. M., P. A. Hosner, G. A. Bravo, A. M. Cuervo, N. Aristizábal, L. E. Cueto and J. M Bates. 2015. Inferring the geographic history of speciation in the Andes with genotyping-by-sequencing: an example in the bay-backed antpittas (Aves; Grallariidae; Grallaria hypoleuca s. l.). Molecular Ecology doi: 10.1111/mec.13477.
Savit, A. V. and J. M. Bates. 2015. Right around the Amazon: The origin of the circum-Amazonian distribution in Tangara cayana. Folia Zoolgica 64 (3):273-283.
Dantas, S.M., Weckstein, J.D., Bates, J.M., Krabbe, N.K., Cadena, C.D., Robbins, M.B., Valderrama, E. and Aleixo, A., 2016. Molecular systematics of the new world screech-owls (Megascops: Aves, Strigidae): biogeographic and taxonomic implications. Molecular Phylogenetics and Evolution 94:626-634.
Wogan, G.O., Feldheim, K.A., Tsai, A.S., Brown, A.A., Kapelke, J., Galinato, M., Tung, J.N., Bates, J.M., Kaliba, P., Voelker, G. and Bowie, R.C., 2016. New genetic resources and a preliminary multi-locus assessment of species boundaries in the Batis capensis species complex (Passeriformes: Platysteridae). Biochemical Systematics and Ecology 65:83-88.
Gubili, C., Ritter, C.D., Motta, J., Farias, I.P., Bates, J., Canton, R., Capurucho, J.M., Cornelius, C., Feldheim, K.A. and Ribas, C.C., 2016. Isolation and characterization of polymorphic microsatellite DNA Markers from an Amazonian white-sand vegetation specialist bird, Xenopipo atronitens(Aves: Pipridae). The Wilson Journal of Ornithology, 128(3):668-672.
Caballero I. C., J. M. Bates, M. Hennen and M. V. Ashley. 2016. Sex in the City: Breeding Behavior of Urban Peregrine Falcons in the Midwestern U.S. PLoS ONE 11(7): e0159054. doi:10.1371/journal.pone.0159054.De Silva, T.N., A. T. Peterson, J. M. Bates, S. W. Fernando, and M. G. Girard. 2017. Phylogenetic relationships of weaverbirds (Aves: Ploceidae): A first robust phylogeny based on mitochondrial and nuclear markers. Molecular Phylogenetics and Evolution, 109:21-32.
Kahindo, C., J. M. Bates, and R. C. K. Bowie. 2017. Population Genetic structure of Grauer’s Swamp Warbler Bradypterus graueri, a flagship Albertine Rift endemic. The Ibis, 159: 415-429.
Kyriazis, C. C., J. M. Bates, and L. R. Heaney. 2017. Dynamics of genetic and morphological diversification in an incipient intra-island radiation of Philippine rodents (Muridae: Bullimus). Journal of Biogeography: Version of Record online: 11 JUL 2017, DOI: 10.1111/jbi.13063.
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.
Patitucci, K. F., J. M. Bates and V. V. Tkach. 2016. Mosesia ovalis n. sp. (Digenea: Phaneropsolidae) from the green manakin Xenopipo holochlora from Peruvian Amazon with notes on morphology of Mosesia mosesi Travassos, 1921. Comparative Parasitology 83:49-53.
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.
Engel, J. D. Parelius, and J. M. Bates. 2014. The Parelius bird collection from Ivory Coast at the Field Museum of Natural History, and the first country record of Rufous Cisticola (Cisticola rufus). Malimbus 36:119-122.
Engel, J. L., D. E. Willard, P M. Kabila, L Mazibuko, and J. M. Bates. 2015. First record for Malawi of Kenrick’s Starling (Poeoptera kenricki Shelley, 1894) (Aves: Sturnidae). Checklist 11(6):1818.
Engel, J. I., D. Parelius, and J. M. Bates. 2015. Clarification: Black-bellied Seedcracker Pyrenestes ostrinus specimens from Ivory Coast include males. Malimbus 37 (1):26-27.
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.
Bates, J. M. 2017. Museum (pp. 100- 102). In: Wildlife Professions: Becoming Marketable for Employment [Scott E. Henke and Paul R. Krausman, eds]**. **Johns Hopkins University Press, pp. 100-102.
Webster, M.S., Cicero, C., Bates, J., Hackett, S. and L. Joseph. 2017. Ornithological Collections in the 21st Century. In: The Extended Specimen: Emerging Frontiers in Collections-Based Ornithological Research.
Bates, J. M. 2017. Forward, In: The Peregrine Returns: The Art and Architecture of and Urban Raptor Recovery (M. Hennen and M. Macnamara). University of Chicago Press.
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.
Bates, J. M. 2017. Forward, In: The Peregrine Returns: The Art and Architecture of and Urban Raptor Recovery (M. Hennen and M. Macnamara). 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.
Rocha, L. and 115 additional authors (including J. M. Bates). 2014. Collecting biological specimens is essential in science and conservation. Science 344 (6186):814-815.
**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 on Wild Shores: Portraits of the Natural World by K. Winker. Two Harbors Press, Minneapolis, MN, USA. Wilson Journal of Ornithology 126:409.
Bates, J. M. 2017. Review of Magellanic sub-Antarctic Ornithology: First decade of long-term bird studies at the Omora Ethnobotanical Park, Cape Horn Biosphere Reserve, Chile. By: Ricardo Rozzi and Jaime E. Jiménez (editors). Sub-Antarctic Biocultural Conservation Program, University of North Texas,/Universidad de Magallenes, Denton, TX /Punta Arenas, Chile. 2014: i-xx + 364 pages. Wilson J. of Ornithology: 129:652.
Earlier publications (Pre-2002)
Mills, G. S., J. B. Dunning, Jr., and J. M. Bates. 1988. Effects of urbanization on breeding bird community structure in southwestern desert habitats. Condor 91: 416-428.
Bennet, G. F., M. C. Garvin, and J. M. Bates. 1991. Avian hematozoa from east-central Bolivia. J. Parasitology 77: 207-211.
Mills, G. S., J. B. Dunning, and J. M. Bates. 1991. The relationship between breeding bird density and vegetation volume. Wilson Bulletin 103: 468-479.
Bates, J. M., M. C. Garvin, D. C. Schmitt, and C. G Schmitt. 1991. Notes on bird distribution in northeastern Dpto. Santa Cruz, Bolivia, with 15 new species to Bolivia. Bull. Brit. Orn. Club 109: 236-244.
Bates, J. M., T. A. Parker, III, A. P. Capparella and T. J. Davis. 1992. Observations on the campo, cerrado, and forest avifaunas of eastern Dpto. Santa Cruz, Bolivia, including 21 species new to the country. Bull. Brit. Orn. Club 112:86-98.
Parker, T. A., III, J. M. Bates, and G. Cox. 1992. Rediscovery of the Bolivian Recurvebill (Simoxenops striatus; Furnariidae) with notes on other little-known species of the Bolivian Andes. Wilson Bulletin 104: 173-178.
Bates, J. M. 1992. Winter territorial behavior of Gray Vireos. Wilson Bulletin 104: 425-433.
Bates, J. M. 1992. Frugivory on Bursera microphylla (Burseracae) by wintering Gray Vireos (Vireo vicinior, Vireonidae) in the coastal deserts of Sonora, Mexico. Southwestern Naturalist 37: 252-257.
Bates, J. M. and R. M. Zink. 1992. Seasonal variation in gene frequencies in the House Sparrow (Passer domesticus). The Auk 109: 658-662.
Bates, J. M. 1993. Review of "Birds of Southwestern Brazil: Catalogue and Guide to the Birds of the Pantanal of Mato Grosso and its Border Areas" by Balthasar Dubs. The Auk 110: 661.
Bates, J. M. 1993. Studying ways to teach evolution: the importance of practicing what we preach. Proceedings of the LSU/NSF Evolution Research Conference (R. A. Good, J. E. Trowbridge, S. S. Demastes, J. H. Wundersee, M. S. Hafner, and C. L. Cummins, Eds.) Baton Rouge, LA.
Bates, J. M., S. J. Hackett, and R. M. Zink. 1993. Tecnicas y materiales para la preservación de tejidos congelados. Pp. 75-78 in Curación moderna de colecciones ornitolólogicas (P. Escalante-Pliego, Ed.) American Ornithologists' Union, Washington, D. C.
Bates, J. M. 1994. Review of "On the biology of five species of swifts (Apodidae, Cypselinoidinae) in Costa Rica" by Manuel Marin A. and F. Gary Stiles. The Auk 111: 717.
Bates, J. M. and R. M. Zink. 1994. Evolution into the Andes: species relationships in the flycatcher genus Leptopogon. The Auk 111: 507-515.
Hackett, S. J., C. S. Griffiths, J. M. Bates, and N. K. Klein. 1995. A commentary on the use of sequence data for phylogeny reconstruction. Mol. Phylogenet. Evol. 4:350-353.
Bates, J. M. 1996. Review of "Status, Distribution and Biogeography of the Birds of Paraguay " by Floyd E. Hayes. The Auk 113:727-728.
Bates, J. M. and T. S. Schulenberg. 1996. In Memorium: Theodore A. Parker, III. The Auk 114:110.
Bates, J. M. 1997. Distribution and geographic variation in three South American grassquits (Emberizinae, Tiaris). Ornithological Monographs 48:91-110.
Garvin, M. C., J. M. Bates, and J. M. Kinsella. 1997. Field techniques for collecting and preserving helminth parasites from birds, with new geographic and host records of parasitic nematodes from Bolivia. Ornithological Monographs 48:261-266.
Hackett, S. J. and J. M. Bates. 1997. Review of “Molecular Systematics” edited by D. M. Hillis, C. Moritz, and B. K. Mable. The Auk 114:802-803.
Bates, J. M. 1998. Review of “Handbook of Birds of the World, Volume 4 (Sandgrouse to Cuckoos)”, J. Del Hoyo, A Elliot and J. Sargatal (eds.). Condor 100:769-775.
Bates, J. M., J. Cracraft and S. J. Hackett. 1998. Area-relationships in the Neotropical lowlands: An hypothesis based on raw distributions of Passerine birds. Jrnl. of Biogeography 25:783-793.
Bates, J. M., D. F. Stotz, and T. S. Schulenberg. 1998. Avifauna of Parque Nacional Noel Kempff Mercado. Pp. 120-128. In: A Biological Assessment of Parque Nacional Noel Kempff Mercado, Bolivia. RAP Working papers 10. Conservation International, Washington, D. C.
Bates, J. M. and T. A. Parker, III. 1998. The avifauna of Parque Nacional Noel Kempff Mercado and surrounding areas. Pp. 317-340. In: A Biological Assessment of Parque Nacional Noel Kempff Mercado, Bolivia. RAP Working papers 10. Conservation International, Washington, D. C.
Bates, J. M., S. J. Hackett and J. Goerck. 1999. High levels of mitochondrial DNA differentiation in two lineages of antbirds (Drymophila and Hypocnemis). The Auk 116:1093-1106.
Bates, J. M. 2000. Allozyme genetic structure and natural habitat fragmentation: Data for five species of Amazonian forest birds. Condor 102:770-783.
Kirchman, J. J., S. J. Hackett, S. M. Goodman, and J. M. Bates. 2001. Phylogeny and systematics of the ground rollers (Brachypteraciidae) of Madagascar. The Auk 118:849-863.
Bates, J. M. 2001. Avian diversification in Amazonia: evidence for historical complexity and a vicariance model for a basic pattern of diversification. Pp. 119-138 in: Diversidade Biológica e Cultural da Amazônia (I. Viera, M. A. D'Incao, J. M. Cardoso da Silva and D. Oren, editors). Museu Paraense Emilio Goeldi, Belém, Pará, Brazil.
Bates, J. M. and T. C. Demos. 2001. Do we need to devalue Amazonia and other large tropical forests? Diversity and Distribution 7:249-255.
Bober, S. O., M. Herremans, M. Louette, J. C. Kerbis Peterhans and J. M. Bates. 2001. Geographical and altitudinal distribution of endemic birds in the Albertine Rift. Ostrich Supplement 15 (July 2001):189-196.
Graves, G. R., A. W. Kratter, and J. M. Bates. 2001. The first nesting record of Black-billed Cuckoo (Coccyzus erthythropthalmus) in the lower Mississippi Valley. Journal of Louisiana Ornithology 5:46-48.
Systematics, genetic structure, and geographic variation in the tropics.
My research focuses on genetic structure of tropical birds, primarily at the level of populations and species. At a continental scale, I use data from DNA sequences to uncover patterns of history among lineages of South American, African, and Malagasy birds. Multi-taxon studies, in which samples of different taxa are obtained at each geographic site provide insightful comparative data sets. Coupled with an understanding of distribution and ecology, we can search for correlations between molecular differentiation and other aspects of the biology of these birds such as morphological differentiation, ecology (e.g., habitat selection, foraging guild membership, breeding system, degree of seasonal movement) and phylogenetic relationships (phylogenetic constraints). With Shannon Hackett and TFM research scientist Jason Weckstein, I have been studying co-evolutionary patterns in birds, their parasites and pathogens. In addition to addressing evolutionary questions, I have focused research efforts on demonstating how patterns of genetic structure have relevance to conservation biology.
My former students have studied similar questions in birds and other organisms throughout the tropics (e.g., flycatchers and antbirds in the neotropical lowlands, Jose Tello; Albertine Rift warblers, Charles Kahindo; Ana Carnaval, frogs of northeastern Brazil; Philippine Fruit bats, Trina Roberts; East African frogs, Lucinda Lawson; Philippine insectivorous bats, Sara Weyandt.). Recently graduates Ben Winger and Aaron Savit (University of Chicago) studied the evolution of South American birds (Winger and Bates 2015, Winger et al. 2015, Savit and Bates 2015), and Isabel Caballero (Univeristy of Illinois, Chicago) studied population genetics of Peregrine Falcons (Caballero et al. 2016). Current students are working on loss of migration in Neotropical birds (Valentina Gomez, U. I. Chicago), Evolution of white sand birds (Joao Capurucho, U. I. Chicago), Evolution of specialization (Nick Crouch, U. I. Chicago), Evolution and physiology of elevational migration in Himalayan bush robins (Tarsiger) (Shane DuBay, U. Chicago), Effects of urbanization on Neotropical birds (Natalia Piland, U. Chicago), and the Evolution of Afro-montane forest birds (Jacob Cooper, U. Chicago).
At the local geographic scale, I have studied genetic structure in populations of five forest understory species from continuous forest and from forest fragments in northeastern Bolivia. The sites in continuous forest and the forest fragments are all within 200 km of one another, yet genetic differentiation appears to have developed in the forest fragments for three of the species studied. This work also has implications for the design of nature reserves and for conservation planning, because my data indicate that genetic structure in these forest species can be affected by forest fragmentation.
I also study geographic variation using traditional museum specimens and computerized databases. One such study of geographic variation in some South American finches (genus Tiaris) uncovered misconceptions about traditional species limits and diagnosable populations. Another led to the description of a new species of hanging parrot (Loriculus camiguinensis), which is endemic to the small island of Camiguin in the Philippines. This description was based on a series of specimens collected in the 1960s and deposited in the Field Museum's collections. A colalborative project with Research Associate Guy Kirwan used Field Museum specimens to document a previously unrecognized pattern of migration in Eurpoean stonechats (Saxicola torquata). In 2010, a collaborative project led by Research Associate Gary Voelker described a new species of Bush-shrike, Laniarius willardi, based on a detailed anaylsis of both modern and historical Field Museum specimens. The new species, named in honor of our retired Collections Manager of Birds David Willard, is only known from mid-elevations of Albertine Rift forests in central Africa and appears highly endangered based on our ongoing assessments of the niche of this species.
Such studies demonstrate the vital importance of museum collections and, along with results of molecular studies, emphasize that additional inventory work on birds is sorely needed. Collaborative fieldwork by the division over the last 10 years has included Malawi, the Democratic Republic of Congo, South Africa, Uganda, Central African Republic, Gabon, Peru, Brazil, Bolivia, Madagascar and Bhutan. In all countries where we work, building capacity for collections-based ornithological science is a primary goal of our efforts because collections everywhere can be used for teaching and research, telling us now and in the future so much about the birds with which we share the planet.
With Dr. Charles Kahindo and the Centre de Recherche en Sciences Naturelles (CRSN), Lwiro bird crew at Tshibati, Democratic Republic of Congo, 2005.