Mammals

Division of Mammals

open weekdays 8am - 5pm
visitors welcome by appointment
information for visitors

phone: (505) 277-1360
fax: (505) 277-1351
museum administrator


DOM logo

mailing:

Division of Mammals
Museum of Southwestern Biology
1 University of New Mexico
MSC03-2020
Albuquerque, NM 87131
shipping:
Division of Mammals
Museum of Southwestern Biology
CERIA Building 83 Room 204
302 Yale Blvd NE
University of New Mexico
Albuquerque, NM 87131

Joseph A. Cook

Joseph A. Cook

Professor of Biology
Curator of Mammals
Curator of Genomic Resources
Cook Molecular Evolution and Ecology Lab

Ph.D. 1990 - Biology, University of New Mexico
Dissertation: Rapid chromosomal evolution and the systematics of the Bolivian tuco-tucos (Rodentia: Ctenomyidae).

M.S. 1982 - Biology, University of New Mexico
Thesis: The Mammals of the Animas Mountains, Hidalgo County, New Mexico

B.S. 1980 - Zoology, Western New Mexico University

download Joe Cook's CV


Research Interests

  • Biotic Conservation
  • Historical Biogeography
  • Molecular & Morphological Evolution
  • Systematics, Speciation, Natural History of Subterranean Mammals

Publications

view on Google Scholar

Books and Monographs

MacDonald, S. O. and J. A. Cook. 2009. Recent Mammals of Alaska. University of Alaska Press, Fairbanks. 387pp.

MacDonald, S. O. and J. A. Cook. 2007. The Mammals and Amphibians of Southeast Alaska. Museum of Southwestern Biology, Special Publication 8, 191pp.

Cook, J. A. 1986. The Mammals of the Animas Mountains. Occasional Papers of The Museum of Southwestern Biology. No. 4, 45 pp.

Book Chapters

Cook, J. A., C. Brochmann, S. L. Talbot, V. Fedorov, E. B. Taylor, R. Väinölä, E.P. Hoberg, M. Kholodova, K. P. Magnusson. 2013. Genetic Perspectives on Arctic Biodiversity. Pp. 459-483 In Arctic Biodiversity Assessment. Conservation of Arctic Fauna and Flora Committee, Copenhagen.

Hoberg, E. P., S. J. Kutz, J. A. Cook. K. Galaktionov, V. Haukisalmi, H. Henttonen, and S. Laaksonen. 2013. Parasites in Terrestrial, Freshwater, and Marine Environments. Pp. 420-449 In Arctic Biodiversity Assessment. Conservation of Arctic Fauna and Flora Committee, Copenhagen.

Meltofte, H., T. Barry, D. Berteaux, H. Bultmann, J. S. Christiansen, J. A. Cook, A. Dahlberg, F. J.A. Daniëls, D. Ehrich, J. Fjeldså, F. Radisson, B. Ganter, A. J. Gaston, L. J. Gillespie, L. Grenoble, E. P. Hoberg, I. D. Hodkinson, H. P. Huntington, R. A. Ims, A. B. Josefson, S. J. Kutz, S. L. Kuzmin, K. L. Laidre, D. R. Lassuy, P. N. Lewis, C. Lovejoy, C. Michel, V. Mokievsky, T. Mustonen, D. C. Payer, M. Poulin, D. G. Reid, J. D. Reist, D. F. Tessler and F. J. Wrona. 2013. Synthesis: implications for conservation. Pp. 22-65 In Arctic Biodiversity Assessment. Conservation of Arctic Fauna and Flora Committee, Copenhagen.

Cook, J. A. and S. O. MacDonald. 2013. Island life: Coming to grips with the insular nature of North Pacific Coastal Forests. Pp. 19-42, In Conservation of North Pacific Coastal Forests, Orians, G. H., and J. W. Schoen, eds. Univ. Washington Press, Seattle.

Dawson, N. G. and J. A. Cook. 2012. Behind the genes: Diversification of North American marten (Martes americana and Martes caurina). Pp. 23-38 In Biology and Conservation of Marten, Sables and Fisher. A New Synthesis. In Aubry, K., W. J. Zielinski, M. G. Raphael, G. Proulx, and S. W. Buskirk, eds.

Hoberg, E., A.V.A. Koehler, and J. A. Cook. 2012. Complex host-parasite systems in Martes: Implications for conservation biology of endemic faunas. Accepted Pp. 39-57. In Biology and Conservation of Marten, Sables and Fisher. A New Synthesis. Aubry, K., W. J. Zielinski, M. G. Raphael, G. Proulx, and S. W. Buskirk, eds.

Cook, J. A., and V. Fedorov. 2010. Arctic genetic diversity: heavily shaped by past climate change. In Arctic Biodiversity and Climate Change Assessment Highlights, Conservation of Arctic Fauna and Flora Committee. Copenhagen.

Dawson, N. G., S. O. MacDonald and J. A. Cook. 2007.  Endemic Mammals of the Alexander Archipelago. Chapter 6.7, Pp. 1-11. In J. Schoen and E. Dovichin (eds). The Coastal Forests and Mountains Ecoregion of Southeastern Alaska and the Tongass National Forest: A conservation Assessment and resource synthesis. Audubon & Nature Conservancy, Special Publication.

Cook, J. A., and J. Salazar-Bravo. 2004. Heterochromatin variation among the chromosomally diverse tuco-tucos (Rodentia: Ctenomyidae) from Bolivia. Pp. 129-142 In Sánchez-Cordero, V. and Medellín, R. A. (Eds.) Contribuciones Mastozoológicos en Homenaje a Bernardo Villa. Instituto de Biología e Instituto de Ecología, UNAM, México.

Cook, J. A., E. P. Lessa, and E. A. Hadly. 2000. Paleontology, phylogenetic patterns, and macroevolutionary processes in subterranean rodents. Pp. 332-369 In E. Lacey, J. L. Patton, and G. Cameron, eds. Life Underground: The Biology of Subterranean Rodents, University of Chicago Press.

Yensen, E., D. J. Hafner, and J. A. Cook. 1998.  Conservation priorities, action plans, and conservation strategies for North American rodents.  Pp. 125-145 In North American Rodents: Action Plans for Species of Conservation Concern (D. J. Hafner, E. Yensen, and G. L. Kirkland, Jr., eds.).  IUCN---the World Conservation Union, Gland, Switzerland.

Parker, D., J. A. Cook, and S. Lewis. 1996.  Effects of timber harvest on bat activity in southeastern Alaska’s temperate rainforest. Pp. 277-292 In Bats and Forests Symposium, R. Barclay and M. Brigham (eds), Res. Branch, Ministry of Forests, Victoria, 23:1-292.

Yates, T. L., C. Jones, and J. A. Cook. 1996.  Preservation of voucher specimens. Pp. 265-274 In Measuring and Monitoring Biological Diversity: Standard Methods for Mammals (D. Wilson, F. R. Cole, J. D. Nichols, R. Rudran, M. S. Foster. Eds.)  Smithsonian Institution Press Washington, DC. 409 p. 

Journal Articles/Reviews

Lessa, EP, Cook JA, D’Elía G, and. Opazo JC. 2014. Rodent diversity in South America: transitioning into the genomics era. Frontiers in Ecology and Evolution. 2 (39):1-7.

Barker, B. S., Joseph A. Cook, J. Rodríguez-Robles. Accepted. Climate as a driver of tropical insular diversity: comparative phylogeography of two ecologically distinctive frogs in Puerto Rico. Ecography.

Bradley, R. D., L. K. Ammerman, R. J. Baker, L. C. Bradley, J. A. Cook, R. C. Dowler, C. Jones, D. J. Schmidly, F. B. Stangl, Jr., R. A. Van Den Bussche, and B. Würsig. 2014. Revised Checklist of North American mammals North of Mexico, 2014. Texas Tech University Press.

Kohli, B. A., V. B. Fedorov, E. C. Waltari, and J. A. Cook. 2014.

Phylogeography of a Holarctic rodent (Clethrionomys rutilus): Testing high-latitude biogeographic hypotheses and the dynamics of range shifts. Journal of Biogeography.

Powers, K. E., L. A. Prather, J. A. Cook, J. Woolley, H. L. Bart, Jr., A. K. Monfils, M. Blackwell, and P. Sierwald. 2014. Revolutionizing the Use of Natural History Collections in Education. The Science Education Review.

Kohli, B. A., K. A. Speer, C. W. Kilpatrick, N. Batsaikhan, D. Damdinbaza, J. A. Cook. 2014. Evolution in the subarctic: Multilocus systematics of a recent radiation of boreal rodents (Arvicolinae: Myodini). Molecular Phylogenetics and Evolution 76:18-29.

Hope, A. G., S, Y. W. Ho, J. L. Malaney, J. A. Cook, S. L. Talbot. 2014. Calibrating molecular evolutionary rates for comparative demographic inference of multiple species. Evolution. 68: 2689-2700.

Gardner, S. L., J. Salazar-Bravo, and J. A. Cook. 2014. New species of Ctenomys Blainville 1826 (Rodentia: Ctenomyidae) from the lowlands and central highlands of Bolivia. Special Publications, Museum of Texas Tech University, 62:1-34.

Hope, A.G., N. Panter, J. A. Cook, S. L. Talbot, and D. Nagorsen. 2014. Multi-locus phylogeography and systematic revision of North American water shrews (genus: Sorex). Journal of Mammalogy. 95: 722-738.

Gu, S.H., B. K. Lim, B. Kadjo, S. Arai, J.-W. Song, J.-A. Kim, V. Nicolas, C. Denys, J. A. Cook, S. R. Dominguez, K. V. Holmes, and R. Yanagihara. 2014. Molecular phylogeny of hantaviruses harbored by insectivorous bats in Côte d’Ivoire and Vietnam. Viruses 6:1897-1910.

Cook, J.A., S. V. Edwards, E. Lacey, R. P. Guralnick, P. S. Soltis, D. E. Soltis, C. Welch, K. C. Bell, K. E. Galbreath, C. Himes, J. M. Allen, T. A. Heath, A. C. Carnaval, K. L. Cooper, M. Liu, J. Hanken, and S. Ickert-Bond. 2014. Natural History Collections as Emerging Resources for Innovative Education in Biology. BioScience 64:725-734.

Ryan, M. J., M. Fuller, N. J. Scott, J. A. Cook, S. Poe, B. Willink, G. Chaves, and F. Bolaños. 2014. Individualistic population responses of five frog species over 42-years in two changing tropical environments. PLoS One 9(5):e98351.

Dawson, N. G., A. G. Hope, S. L. Talbot, and J. A. Cook. 2014. A multi-locus evaluation of ermine (Mustela erminea) across the Holarctic, testing hypotheses of Pleistocene diversification in response to climate change. Journal of Biogeography 41:464-475.

Malaney, J. L. and J. A. Cook. 2013. Using biogeographic history to inform conservation: The case of Preble’s jumping mouse. Molecular Ecology 22:6000-6017.

Greiman, S. E., V. V. Tkach, and J. A. Cook. 2013. Description and molecular differentiation of a new Staphylocystoides (Cyclophyllidea: Hymenolepididae) from the dusky shrew Sorex monticolus in Southeast Alaska. Journal of Parasitology 99: 1045-1049.

Ho, S-H. and J. A. Cook. 2013. Co-Evolving Pedagogies. ARID: A Journal of Desert Art, Design and Ecology. Vol. 2 published online (http://aridjournal.com/co-evolving-pedagogies-szu-han-ho-and-joseph-a-cook/)

Deardorff, E.R., R. A. Nofchissey, J. A. Cook, A. G. Hope, A. Tsvetkova, S. L. Talbot, G. D. Ebel. 2013. Serological Evidence of Powassan Virus in Mammals from Russia, Alaska and New Mexico, 2004-2007. Emerging and Infectious Diseases. 19:2012-2016.

Hope, A. G., E. C. Waltari, D. C. Payer, J. A. Cook, and S. L. Talbot. 2013. Future distribution of tundra refugia in Alaska. Nature Climate Change 3:931-938.

Malaney, J. L., C. J. Conroy, L. A. Moffitt, H. D. Spoonhunter, J. L. Patton, and J. A. Cook. 2013. Phylogeography of the western jumping mouse (Zapus princeps) detects deep structure in the southwestern United States. Journal of Mammalogy, 94:1016-1029.

Cook, J. A. 2013. A Splendid Southern Synthesis. Bioscience 63:304-305.

Hope, A. G., N. Takebayashi, K. E. Galbreath, S, L. Talbot, and J. A. Cook. 2013. Temporal dynamics of speciation among amphi-Beringian small mammals. Journal of Biogeography 40:415-429.

Haas, G. E., J. Kucera, S. O. MacDonald and J. A. Cook. 2012. First flea (Siphonaptera) records for Kanuti National Wildlife Refuge and review of historical records from nearby villages, Central Alaska. Journal of the Entomological Society of British Columbia. 109:6-11.

Dunnum, J. L., and J. A. Cook. 2012. Gerrit Smith Miller: His influence on the enduring legacy of natural history collections. Mammalia, 76:365-373.

Sonsthagen, S., G. Sage, M. Fowler, A. Hope, J. A. Cook, S. L. Talbot. 2013. Development and characterization of 21 polymorphic microsatellite markers for the barren-ground shrew, Sorex ugyunak (Mammalia: Sorcidae), through next-generation sequencing, and cross-species amplification in the masked shrew, S. cinereus. Conservation Genetics Resources. 5: 315-318.

Barker, B. S., J. Rodríguez-Robles, V. S. Aran, A. Montoya, R. B. Waide, and J. A. Cook. 2012. Sea level, topography, and island diversity: phylogeography of the Puerto Rican Red-eyed Coquí, Eleutherodactylus antillensis. Molecular Ecology 21:6033-6052.

Galbreath, K. E., J. A. Cook, and E. P. Hoberg. 2012. Climate’s role in polar bear past. Science 336:1230.

Hope, A.G., K. A. Speer, J. R. Demboski, S. L. Talbot, and J. A. Cook. 2012. A climate for speciation: rapid spatial diversification among the Sorex cinereus complex of shrews. Molecular Phylogenetics and Evolution 64:671-684.

Hoberg, E. P., K. E. Galbreath, J. A. Cook, S. J. Kutz, and L. Polley. 2012. Northern Host–Parasite Assemblages: History and Biogeography on the Borderlands of Episodic Climate and Environmental Transition. Advances in Parasitology 79:1-97.

Malaney, J.L., J. K. Frey, J. A. Cook. 2012. The biogeographic legacy of an imperiled taxon provides a foundation for assessing lineage diversification, demography and conservation genetics. Diversity and Distributions 18:689-703.

Sumbicay, L., B. Kadjo, S. H. Gu, H. J. Kang, B. K. Lim, J. A. Cook, J.-W. Song and R. Yanagihara. 2012. Divergent lineage of a novel hantavirus in the banana pipistrelle (Neoromcia nanus) in Cote d’Ivoire. Virology Journal 9:34 

Torres-Perez, F., B. Hjelle, E. C. Holmes, and J.A. Cook. 2011. Spatial but not Temporal Co-divergence of a Virus and its Mammalian Host. Molecular Ecology 20:4109-4122.

Torres-Pérez, F., M. Acuna-Retamar, J. A. Cook, A. Bacigalupo, A. García, P. E. Cattan. 2011. Statistical phylogeography and population dynamics of Chagas disease vector Triatoma infestans: testing biogeographic hypotheses of dispersal. Infection, Genetics, and Evolution. 11:167-174.

Weckworth, B.V., N. G. Dawson, S. L. Talbot, M. J. Flamme, J. A. Cook. 2011. Going coastal: Shared evolutionary history between coastal British Columbia and Southeast Alaska wolves (Canis lupus). PLoS One 6: e19582.

Barker, B. R., R. Waide, and J. A. Cook. 2011. Deep intra-island divergence of a montane forest endemic: phylogeography of the Puerto Rican frog Eleutherodactylus portoricensis (Anura: Eleutherodactylidae). Journal of Biogeography 38:2311-2325.

Galbreath, K. E., J. A. Cook, A. A. Eddingsaas, E. G. DeChaine. 2011. Multi-locus tests of paleodistributional models reveal different facets of the complex demographic history of arctic ground squirrels in Beringia. Evolution 65:1879-1896.

Hope, A.G., E. Waltari, V. B. Fedorov, A. V. Goropashnaya, S. L. Talbot, and J. A. Cook. 2011. Persistence and diversification of the Holarctic shrew, Sorex tundrensis (Family Soricidae), in response to climate change. Molecular Ecology. 20:4346-4370.

Kang, H. J., S. N. Bennett, A. G. Hope, J. A. Cook, R. Yanagihara. 2011. Shared Ancestry Between a Newfound Mole-Borne Hantavirus and Hantaviruses Harbored by Cricetid Rodents. Journal of Virology 85:7496-7503.

Kang HJ, Arai S, Hope AG, Cook JA, Yanagihara R. 2010. Novel Hantavirus in the Flat-Skulled Shrew (Sorex roboratus). Vector Borne Zoonotic Diseases. 10: 593-597.

Cook, J. A., A. A. Eddingsaas, J. L. Loxterman, S. Ebbert, and S.O. MacDonald. 2010. Insular ground squirrels of the North Pacific: Indigenous or Exotic? Journal of Mammalogy 91:1401-1412.

Gonzalez, P., Y. E. Sawyer, M. Avila, A. Armien, B. Armien, J. A. Cook. 2010. Variation in Cytochrome-b Haplotypes Suggests a New Species of Zygodontomys (Rodentia: Cricetidae) on Isla Coiba, Veraguas, Panama. Zoologia 27:660-665.

Hope, A. G., E. Waltari, N. E. Dokuchaev, S. Abramov, T. Dupral, H. Henttonen, S. O. MacDonald, and J. A. Cook. 2010. Diversification of the Eurasian least shrew and Alaska tiny shrew (Soricidae) at high latitudes. Journal of Mammalogy. 91:1041-1057.

Matsumoto, K., J. A. Cook, H. K. Goethert, and S. R. Telford, III. 2010. Bartonella sp. infection of voles trapped from an Interior Alaskan site where ticks are absent. Journal of Wildlife Diseases 46:173-178.

Esteva, M., F. A. Cervantes, S. V. Brant, and J. A. Cook. 2010. Molecular phylogeny of long-tailed shrews (genus Sorex) from México and Guatemala. Zootaxa 2615:47-65.

Weckworth, B., S. Talbot, J. A. Cook. 2010. Phylogeography of wolves (Canis lupus) in the Pacific Northwest. Journal of Mammalogy. 91:363-375.

Torres-Pérez, F., R. E. Palma, M. Ferres, B. Hjelle, J. A. Cook. 2010. Andes virus infection in the rodent reservoir and in humans varies across contrasting landscapes in Chile. Infection, Genetics and Evolution. 10:820-825.

Kang, H. J., Arai, S., Hope, A., Song, J.-W., Cook, J. A., Yanagihara, R. 2009. Genetic diversity and phylogeography of Seewis virus in Eurasian common shrew in Finland and Hungary. Virology Journal 6:208.

Galindo, E., L. Broncho, E. Keeley, R. Inouye, S. Galindo, V. Winston, L. Farrell, J. Cook. 2009. Compassion: A Hearts-on Paradigm for Transiting Native American Students into a STEM University Environment. Journal of Mathematics and Culture 4:1-22.

Kang, H. J., S. Bennett, L Sumbicay, S. Arai, A. G. Hope, G. Mocz, J-W. Song, J. A. Cook, and R. Yanagihara.  2009. Evolutionary insights from a genetically divergent hantavirus harbored by the European common mole (Talpa europaea). PLoS ONE 4(7): e6149. doi:10.1371/journal.pone.0006149.

Medina, R. A., F. Torres-Perez, H. Galeno, M. Navarrete, P. A.Vial, R. E. Palma, M. Ferres, J. A. Cook, and B. Hjelle. 2009. Ecology, Genetic Diversity and Phylogeographic Structure of Andes virus in humans and rodents in Chile. Journal of Virology. 83:2446-2459.

Runck, A., M. Matocq, and J. A. Cook. 2009. Historic hybridization and persistence of a novel mito-nuclear combination in red-backed voles (genus Myodes). BMC Evolutionary Biology 9:114.

MacDonald, S. O., E. Waltari, R. Nofchissey, Y. Sawyer, and J. A. Cook. 2009. First records of deermice in southcentral Alaska. Northwestern Naturalist. 90:243-247.

Koehler, A. V. A., E. P. Hoberg, N. E. Dokuchaev, N. A. Tranbenkova, J. S. Whitman, D. W. Nagorsen, and J. A. Cook. 2009. Phylogeography of a Holarctic nematode, Soboliphyme baturini among mustelids: Climate change, episodic colonization, and diversification in a complex host-parasite system. Biological Journal of the Linnaean Society. 96:651-663.

Koehler A. V. A., E. P. Hoberg, F. Torres-Pérez and J. A. Cook. 2009. A molecular view of the superfamily Dioctophymatoidea (Nematoda). Comparative Parasitology 76:100-104.

Baker, R. J., D. J. Schmidly, J. A. Cook, J. S. Bravo, H. Genoways. 2008. Obituary: Terry Lamon Yates 1950-2007.  Journal of Mammalogy 89:1557-1569.

Fedorov, V. B., A. V. Goropashnaya, G. G. Boeskorov and J. A. Cook. 2008. Comparative phylogeography and demographic history of the wood lemming (Myopus schisticolor): implications for late Quaternary history of the taiga species in Eurasia. Molecular Ecology 17:598-610.

Arai, S., S. Bennett, L. Sumibacay, J. A. Cook, J. Song, A. Hope, C. Parmenter, V. R. Nerurkar, T.L. Yates, and R. Yanagihara. 2008. Phylogenetically distinct hantaviruses in the masked shrew (Sorex cinereus) and montane shrew (Sorex monticolus) in the United States. American Journal of Tropical Medicine and Hygiene 78:348-351.

Arai, S., Jin-Won Song, Laarni Sumibcay, Vivek R. Nerurkar, Shannon N. Bennett, Cheryl Parmenter, Joseph A. Cook, Terry L. Yates, Richard Yanagihara. 2007. Hantavirus in the short-tailed shrew, North America. Emerging Infectious Diseases 13:1420-1423.

Lucid, M. K. and J. A. Cook. 2007. Cytochrome b haplotypes suggest an undescribed Peromyscus species from the Yukon. Canadian Journal of Zoology, 85:916-919.

Koehler, A. V. A., E. P. Hoberg, N. E. Dokuchaev and J. A. Cook. 2007. Geographic and host range of the nematode Soboliphyme baturini across Beringia. Journal of Parasitology. 93:1070-1083.

Duszynski, D.W., A.J. Lynch, and J.A. Cook. 2007. Coccidia (Apicomplexa: Eimeriidae) infecting cricetid rodents from Alaska, U.S.A., and Northeastern Siberia, Russia, and description of a new Eimeria species from Myodes rutilus, the northern red-backed vole. Comparative Parasitology, 74:294-311.

Lynch, A.J., D.W. Duszynski, and J.A. Cook. 2007. Species of Coccidia (Apicomplexa: Eimeriidae) Infecting Pikas from Alaska, U.S.A. and Northeastern Siberia, Russia. Journal of Parasitology 93:1230-1234.

Dalerum, F., J. Loxterman, B. Shults, K. Kunkel and J. A. Cook. 2007. Microsatellite markers suggest delayed female dispersal in a solitary carnivore, the wolverine. Journal of Mammalogy 88:793-800.

Waltari, E., E. P. Hoberg, E. P. Lessa and J. A. Cook. 2007. Eastward Ho: phylogeographic perspectives on colonization across the Beringian nexus. Journal of Biogeography 34:561-574.

Cook, J. A., N. G. Dawson and S. O. MacDonald. 2006. Conservation of highly fragmented systems: the north temperate Alexander Archipelago. Biological Conservation. 133:1-15.

Goethert, H. K., J. A. Cook, E. W. Lance, and S. R. Telford III. 2006. Fay and Rausch 1969 Revisited: Babesia microti in Alaskan small mammals. Journal of Parasitology. 92:826-831.

Glass, G. E., T. M. Shields, R. R. Parmenter, D. Goade, J. N. Mills, J. Cheek, J. Cook, and T. L. Yates. 2006. Hantavirus risk in 2006 for U. S. Southwest. Occasional Papers, Texas Tech University. 255:1-16.

Dragoo, J., A. Lackey, K. Moore, E. Lessa, J. A. Cook, and T. Yates. 2006. Phylogeography of the deer mouse (Peromyscus maniculatus) provides a predictive framework for research on hantaviruses. Journal of General Virology. 87: 1997-2003.

Cook, J. A., E. P. Hoberg, A. Koehler, S. O. MacDonald, H. Henttonen, L. Wickstrom, V. Haukisalmi, K. Galbreath, F. Chernyavski, N. Dokuchaev, A. Lahzuhtkin, A. Hope, E. Waltari, A. Runck, A. Veitch, R. Popko, E. Jenkins, S. Kutz, and R. Eckerlin. 2005. Beringia: Intercontinental exchange and diversification of high latitude mammals and their parasites during the Pliocene and Quaternary. Mammal Science 30:S33-S44.

Haas, G. E., J. R. Kucera, A. Runck, S. O. MacDonald, and J. A. Cook. 2005. Mammal Fleas (Siphonaptera) new for Alaska and the Southeastern mainland collection during seven years of a field survey of small mammals. Journal of the Entomological Society of British Columbia. 102:65-75.

Waltari, E. and J. Cook. 2005. Historical demographics and phylogeography of arctic hares (Lepus): genetic signatures test glacial refugia hypotheses. Molecular Ecology 14:3005-3016.

Runck, A., and J. Cook. 2005. Post-glacial expansion of the southern red-backed vole (Clethrionomys gapperi) in North America. Molecular Ecology 14:1445-1456.

Weckworth B., S. Talbot, G. Sage, D. Person, and J. Cook. 2005. A signal for independent coastal and continental histories for North American wolves. Molecular Ecology 14:917-931.

Tomasik, E., and J. Cook. 2005. Mitochondrial phylogeography and conservation genetics of wolverine (Gulo gulo) in Northwestern North America. Journal of Mammalogy 86:386-396.

Lucid, M., and J. Cook. 2004. Phylogeography of Keen’s mouse (Peromyscus keeni) in a naturally fragmented landscape. Journal of Mammalogy. 85:1149-1159.

Eddingsaas, A., B. Jacobsen, E. Lessa, J. Cook. 2004. Evolutionary history of the arctic ground squirrel (Spermophilus parryii) in Nearctic Beringia. Journal of Mammalogy. 85:591-600.

Waltari, E., J. R. Demboski, D. Klein, and J. A. Cook. 2004. A molecular perspective on the historical biogeography of the northern high latitudes. Journal of Mammalogy 85:601-610.

Cook, J. A., A. Runck, and C. J. Conroy. 2004. Historical biogeography at the crossroads of the northern continents: molecular phylogenetics of red-backed voles (Rodentia: Arvicolinae). Molecular Phylogenetics and Evolution 30:767-777.

Galbreath, K., and J. Cook. 2004. Genetic consequences of Pleistocene glaciations for the tundra vole (Microtus oeconomus) in Beringia. Molecular Ecology 13:135-148.

MacDonald, S. O., A. M. Runck, and J. A. Cook. 2004. The heather vole (genus Phenacomys) in Alaska. Canadian Field-Naturalist. 118:438-440.

Cook, J., N. Dawson, S. MacDonald, and A. Runck. 2004. Mammal Diversity: Inventories of Alaska National Parks Stimulate New Perspectives. Alaska Park Science 3:22-27.

Murrell, B. P., L. A. Durden, and J. A. Cook. 2003. Host associations of the tick, Ixodes angustus, on Alaskan mammals. Journal of Medical Entomology 40:682-685.

Lessa, E. P., J. A. Cook, and J. L. Patton. 2003. Genetic footprints of demographic expansion in North America, but not Amazonia, following the Late Pleistocene. Proceedings of the National Academy of Sciences, USA 100: 10331-10334.

Hoberg, E. P., S. J. Kutz, K. E. Galbreath, and J. Cook. 2003. Arctic biodiversity: From discovery to faunal baselines—revealing the history of a dynamic system. Journal of Parasitology 89:S84-S95.

Demboski, J. R. and J. A. Cook. 2003. Phylogenetic diversification within the Sorex cinereus complex (Insectivora: Soricidae). Journal of Mammalogy 84:144-158.

Fedorov, V. B., A. V. Goropashnaya, M. Jaarola & J. A. Cook. 2003. Phylogeography of lemmings (Lemmus): no evidence for post-glacial colonization of Arctic from the Beringian refugium. Molecular Ecology 12:725-732.

Brunhoff, C., K. E. Galbreath, V. B. Fedorov, J. A. Cook and M. Jaarola. 2003. Holarctic phylogeography of the root vole (Microtus oeconomus): implications for late Quaternary biogeography of high latitudes. Molecular Ecology 12: 957-968.

Small, M.P., K. D. Stone, and J.A. Cook. 2003. American marten (Martes americana) population structure across a landscape fragmented in time and space. Molecular Ecology 12:89-103.

Stone, K. and J. Cook. 2002. Molecular evolution of the Holarctic genus Martes. Molecular Phylogenetics and Evolution. 24:169-179.

Pyare, S., W. Smith, J. Nicholls, and J Cook. 2002. Diets of northern flying squirrels, Glaucomys sabrinus, in southeast Alaska. Canadian Field-Naturalist 116:98-103.

Stone, K., R. Flynn, and J. Cook. 2002. Post-glacial colonization of northwestern North America by the forest associated American marten (Martes americana). Molecular Ecology 11:2049-2064.

Fleming, M. A. and J. A. Cook. 2002. Phylogeography of endemic ermine (Mustela erminea) in southeast Alaska. Molecular Ecology 11:795-808.

Bidlack, A. L. and J. A. Cook. 2002. A nuclear perspective on endemism in northern flying squirrels (Glaucomys sabrinus) of the Alexander Archipelago, Alaska. Conservation Genetics 3:247-259.

Slamovits, C. H., J. A. Cook, E. P. Lessa, and M. S. Rossi. 2001. Recurrent amplifications and deletions of satellite DNA accompanied chromosomal diversification in South American tuco-tucos (genus Ctenomys, Rodentia: Octodontidae): A phylogenetic approach. Molecular Biology and Evolution 18:1708-1719.

Bidlack, A., and J. A. Cook. 2001. Reduced genetic variation in insular northern flying squirrels (Glaucomys sabrinus) along the North Pacific Coast. Animal Conservation 4:283-290.

Demboski, J., and J. Cook. 2001. Phylogeography of the dusky shrew, Sorex monticolus (Insectivora, Soricidae): Insight into deep and shallow history in northwestern North America. Molecular Ecology 10:1227-1240.

Cook, J. A., A. L. Bidlack, C. J. Conroy, J. R. Demboski, M. A. Fleming, A. M. Runck, K. D. Stone, and S. O. MacDonald.  2001. A phylogeographic perspective on endemism in the Alexander Archipelago of the North Pacific. Biological Conservation 97:215-227.

Cook, J. A., and S. O. MacDonald. 2001. Should endemism be a focus of conservation efforts along the North Pacific Coast of North America? Biological Conservation 97:207-213.

Conroy, C. J., Y. Hortelano, F. Cervantes, and J. A. Cook. 2001. The phylogenetic position of southern relictual species of Microtus. Mammalian Biology (Zeitschrift für Säugetierkunde) 66:332-344.

Conroy, C. J., and J. A. Cook.  2000.  Systematics of a Holarctic rodent: Microtus (Muridae). Journal of Mammalogy 81:344-359.

Stone, K. D. and J. A. Cook.  2000. Phylogeography of black bears (Ursus americanus) from the Pacific Northwest. Canadian Journal of Zoology 78:1-6.

Conroy, C. J. and J. A. Cook. 2000. Phylogeography of a post-glacial colonizer: Microtus longicaudus (Muridae: Rodentia). Molecular Ecology 9:165-175.

Demboski, J. R., K. D. Stone, and J. A. Cook. 1999. Further perspectives on the Haida Gwaii glacial refugium hypothesis. Evolution 53:2008-2012.

Fitzgerald, L. A., J. A. Cook, and A. L. Aquino. 1999. Phylogenetics and conservation of Tupinambis (Sauria: Teiidae). Copeia 1999:894-905.

Fleming, M. A., E. A. Ostrander, and J. A. Cook.  1999. Microsatellite primers for American mink (Mustela vison) and ermine (Mustela erminea). Molecular Ecology 8:1352-1354.

Conroy, C. J. and Cook, J. A.  1999.  MtDNA evidence for repeated pulses of speciation within arvicoline and murid rodents.  Journal of Mammalian Evolution 6:221-245.

Vapalahti, O., Å. Lundkvist, V. Fedorov, C. J. Conroy, S. Hirvonen, A. Plyusnina, K. Nemirov, K. Fredga, J. A. Cook, J. Niemimaa, A. Kaikusalo, H. Henttonen, A. Vaheri and A. Plyusnin. 1999. Isolation and characterization of a hantavirus from Lemmus sibiricus: evidence for host-switch during hantavirus evolution. Journal of Virology. 73:5586-5592.

Conroy, C. J., J. R. Demboski & J. A. Cook. 1999. Mammalian biogeography of the Alexander Archipelago of Alaska: a north temperate nested fauna. Journal of Biogeography. 26:343-352.

D’Elia, G., E. P. Lessa, and J. A. Cook. 1999. Molecular phylogeny of tuco-tucos, genus Ctenomys (Rodentia: Octodontidae): Evaluation of the mendocinus species group and the evolution of asymmetric sperm. Journal of Mammalian Evolution 6:19-38.

Halanych, K.M, Demboski, J.R., van Vuuren, B.J., Klein, D.R., and Cook, J.A. 1999. Cytochrome b phylogeny of North American hares and jackrabbits (Lepus, Lagomorpha) and the effects of mutational saturation in outgroup taxa. Molecular Phylogenetics and Evolution. 11:213-221.

Conroy, C. and J. A. Cook. 1999. Microtus xanthognathus. Mammalian Species 627:1-5.

Demboski, J. R., B. K. Jacobsen, and J. A. Cook. 1998. Endemism in the Alexander Archipelago: an assessment of genetic variation in flying squirrels (Rodentia: Glaucomys sabrinus). Canadian Journal of Zoology 76:1771-1777.

Cook, J. A., and E. P. Lessa. 1998. Are rates of diversification in subterranean South American tuco-tucos (genus Ctenomys, Rodentia: Octodontidae) unusually high? Evolution 52:1521-1527

D’Elia, G., E. P. Lessa, and J. A. Cook. 1998. Geographic structure, gene flow and maintenance of melanism in Ctenomys rionegrensis (Rodentia: Octodontidae). Z. für Säugetierkunde (International J. Mammalian Biology) 63:285-296.

Lessa, E. P., and J. A. Cook.  1998. The molecular phylogenetics of tuco-tucos (genus Ctenomys, Rodentia: Octodontidae) suggests an early burst of speciation.  Molecular Phylogenetics and Evolution, 9:88-99.

Lance, E. W., and J. A. Cook.  1998. Phylogeography of tundra voles (Microtus oeconomus): Beringia region and southcoastal Alaska.  J. Mammalogy 79:53-65.

Cook, J. A., C. J. Conroy, and J. Herriges.  1997. Northern record of the water shrew, Sorex palustris, in Alaska.  Canadian Field-Naturalist 111:638-640.

Parker, D., B. Lawhead, and J. A. Cook. 1997. Latitudinal limits of bats in Alaska. Arctic 50:256-265.

Parker, D. and J. A. Cook. 1996.  Keen’s long-eared bat (Myotis keenii, Vespertilionidae) confirmed in Southeast Alaska.  Canadian Field-Naturalist 110:611-614.

MacDonald, S. O., and J. A. Cook. 1996.  The Land Mammal Fauna of Southeast Alaska. Canadian Field-Naturalist 110:571-599.

Cook, J. A.  1995.  The University of Alaska Mammal Collection. Cultural Resource Management, National Park Service 18:15-16.

Mouchaty, S. K., J. A. Cook, and G. F. Shields. 1995.  Phylogenetic analysis of northern hair seals based on nucleotide sequences of the mitochondrial cytochrome b gene. Journal of Mammalogy 76:1178-1185

Houseal, T., J. A. Cook, W. Modi, and D. Hale. 1995. Identification of highly conserved genomic loci by genome painting. Chromosome Research, 3:175-181.

Cook, J. A. and T. L. Yates. 1994. Systematic relationships of the Bolivian tuco-tucos, genus Ctenomys (Rodentia: Ctenomyidae). Journal of Mammalogy, 75:583-600.

Anderson, S., B. Riddle, T. Yates, and J. A. Cook.  1993. Mamiferos en la region del Parque Nacional de Amboro y Santa Cruz de la Sierra, Bolivia. Special Publication, The Museum of Southwestern Biology 2:1-58 (in Spanish).

Ruedas, L., J. A. Cook, T. Yates, and J. Bickham. 1993. Conservative genome size evolution in tuco-tucos. (Rodentia: Ctenomyidae). Genome 36: 449-458.         

Cook, J. A., K. R. Bestgen, D. L. Propst, T. L. Yates. 1992. Allozymic divergence and systematic status of the Rio Grande Silvery Minnow (Hybognathus amarus, Cypriniformes: Cyprinidae). Copeia 1992:36-44

Cook, J. A., F. Caceres, and C. Miranda. 1991. Cariotipo del quirquincho (Chaetophractus nationi). Ecologia en Bolivia, Revista del Instituto de Ecologia, La Paz, Bolivia, 18:21-27 (in Spanish).

Kelt, D., E. Palma, M. Gallardo, and J. Cook. 1991. Confirmation of the identity of Eligmodontia morgani, with notes on the karyotype of E. puerulus. Z. fur Säugetierkunde 56:352-358.

Vitullo, A. D. and J.A. Cook. 1991. The role of sperm morphology in the evolution of tuco-tucos Ctenomys (Rodentia: Ctenomyidae): confirmation of results from Bolivian species. Z. fur Säugetierkunde, 56:359-364.

Cook, J. A., S. Anderson, and T. L. Yates. 1990. Notes on Bolivian mammals 6: The genus Ctenomys (Rodentia: Ctenomyidae) in the highlands. American Museum of Natural History Novitates. 2980:1-27.

 Lessa, E. P., and J. Cook. 1989. Interspecific variation of penial morphology of tuco-tucos (Rodentia: Octodontidae). Journal of Mammalogy, 70:984-987.

Anderson, S., T. L. Yates, and J. A. Cook. 1987. Notes on Bolivian mammals 4: The genus Ctenomys (Rodentia: Ctenomyidae) in the lowlands. American Museum of Natural History Novitates 2891:1-19.

Best, T. L., R. M. Sullivan, J. A. Cook and T. L. Yates.  1986. Chromosomal, genic and morphologic variation in the agile kangaroo rat, Dipodomys agilis (Rodentia: Heteromyidae). Systematic Zoology 35:311-324.

Bednarz, J. C., and J. A. Cook. 1984. Distribution and numbers of the white-sided jackrabbit (Lepus callotis gaillardii) in New Mexico. Southwestern Naturalist 29:358-360.

Species Accounts, Endangered Species Status Reports and Other Articles

Hanken, J., L. McDade, J. Beach, J. Cook, L.S. Ford, K. Joyce, B. Theirs. 2013. Implementation Plan for the Network Integrated Biocollections Alliance. American Institute of Biological Sciences. Reston, VA, USA. [http://www.aibs.org/public-policy/biocollections.html]

Sawyer, Y.E., D. Banks-Richardson, S.O. MacDonald, and J.A. Cook. 2009. Introduction of exotic species on islands: Peromyscus found on Shemya Island of the far western Aleutian Islands of Alaska. Peromyscus Newsletter, 44:27-28.

MacDonald, S. O. and J. A. Cook. 2007. Checklist of the Land Mammals of Beringia. 4pp

Frey, J. K., S. O. MacDonald, and J. A. Cook. 2006. Checklist to the Mammals of New Mexico. 4pp

Jarrell, G., S. O. MacDonald, and J. A. Cook. 2005. Checklist to the Mammals of Alaska. University of Alaska Museum. 5pp.

Cook, J. A., and D. R. Klein. 1999. Microtus abbreviatus. pp. 623-624 in "The Smithsonian book of North American mammals", D Wilson and S. Ruff, eds. Smithsonian Institution Press.

Demboski, J., G. Kirkland, and J. A. Cook. 1998. Glaucomys sabrinus. pp. 37-39 in D. J. Hafner, E. Yensen, and G. L. Kirkland, Jr. (eds). North American rodents: Status survey and conservation action plan. IUCN/SSC Rodent Specialist Group. Gland, Switzerland and Cambridge, UK. x + 171 pp.

Cook, J. A. 1998. Spermophilus parryii pp. 49-50 in D. J. Hafner, E. Yensen, and G. L. Kirkland, Jr. (eds). North American rodents: Status survey and conservation action plan. IUCN/SSC Rodent Specialist Group. Gland, Switzerland and Cambridge, UK. x + 171 pp.

Cook, J. A.  1998. Marmota caligata. pp. 39-40 in D. J. Hafner, E. Yensen, and G. L. Kirkland, Jr. (eds). North American rodents: Status survey and conservation action plan. IUCN/SSC Rodent Specialist Group. Gland, Switzerland and Cambridge, UK. x + 171 pp.

Cook, J. A. 1998. Dicrostonyx unalascensis. pp. 89 in D. J. Hafner, E. Yensen, and G. L. Kirkland, Jr. (eds). North American rodents: Status survey and conservation action plan. IUCN/SSC Rodent Specialist Group. Gland, Switzerland and Cambridge, UK. x + 171 pp.

Cook, J. A. 1998. Dicrostonyx exsul. pp. 87-88 in D. J. Hafner, E. Yensen, and G. L. Kirkland, Jr. (eds). North American rodents: Status survey and conservation action plan. IUCN/SSC Rodent Specialist Group. Gland, Switzerland and Cambridge, UK. x + 171 pp.

Cook, J. A. 1998. Microtus abbreviatus pp. 89-90 in D. J. Hafner, E. Yensen, and G. L. Kirkland, Jr. (eds). North American rodents: Status survey and conservation action plan. IUCN/SSC Rodent Specialist Group. Gland, Switzerland and Cambridge, UK. x + 171 pp.

Conroy, C. J., and J. A. Cook. 1998. Microtus longicaudus pp. 93-95 in D. J. Hafner, E. Yensen, and G. L. Kirkland, Jr. (eds). North American rodents: Status survey and conservation action plan. IUCN/SSC Rodent Specialist Group. Gland, Switzerland and Cambridge, UK. x + 171 pp.

MacDonald, S. O., J. A. Cook, G. Kirkland, Jr., and E. Yensen. 1998. Microtus pennsylvanicus. pp. 99-101 in D. J. Hafner, E. Yensen, and G. L. Kirkland, Jr. (eds). North American rodents: Status survey and conservation action plan. IUCN/SSC Rodent Specialist Group. Gland, Switzerland and Cambridge, UK. x + 171 pp.

Cook, J. A. and G. Kirkland.  1998. Clethrionomys gapperi. pp. 87 in D. J. Hafner, E. Yensen, and G. L. Kirkland, Jr. (eds). North American rodents: Status survey and conservation action plan. IUCN/SSC Rodent Specialist Group. Gland, Switzerland and Cambridge, UK. x + 171 pp.

Lance, E. W. and J. A. Cook. 1998. Microtus oeconomus. pp. 97-99 in D. J. Hafner, E. Yensen, and G. L. Kirkland, Jr. (eds). North American rodents: Status survey and conservation action plan. IUCN/SSC Rodent Specialist Group. Gland, Switzerland and Cambridge, UK. x + 171 pp.

MacDonald, S. O. and J. A. Cook. 1998. Castor canadensis. pp. 59-60 in D. J. Hafner, E. Yensen, and G. L. Kirkland, Jr. (eds). North American rodents: Status survey and conservation action plan. IUCN/SSC Rodent Specialist Group. Gland, Switzerland and Cambridge, UK. x + 171 pp.

Yensen, E., J. A. Cook, and D. W. Nagorsen.  1998.  Rodents of northwestern North America.  Pp. 5-9, in North American rodents: action plans for species of conservation concern (D. J. Hafner, E. Yensen, and G. L. Kirkland, Jr., eds.).  IUCN---the World Conservation Union, Gland, Switzerland.

Weintraub, E. L., and J. A. Cook. 1995. Microtus oeconomus elymocetes. U.S. Fish and Wildlife Service, Endangered Species Status Report. 37pp.

Conroy, C.J., J. A. Cook. S. O. MacDonald, and K. J. Bagne. 1993. Discovery of black morph Peromyscus in Southeast Alaska. Peromyscus Newsletter 15:30-31.

Professional Experience

2011 -  2015: Director, Museum of Southwestern Biology, University of New Mexico

2007 - present: Curator of Genomic Resource, Museum of Southwestern Biology, University of New Mexico

2004 - present: Professor of Biolgy, University of New Mexico

2003 - present: Curator of Mammals, Museum of Southwestern Biology, University of New Mexico

2000 - 2003: Chair and Professor of Biology, Idaho State University

1999 - 2001: Associate Editor, Journal of Mammalogy

2000 - 2001: Professor of Biology, University of Alaska

1998 - 2000: Chief Curator, University of Alaska Museum

1995 - 2000:

  • Associate Professor of Biology, University of Alaska
  • Curator of Mammals and Alaska Frozen Tissue Collection, UA Museum
  • Faculty Affiliate, Biochemistry and Molecular Biology Program
  • Research Associate, Institute of Arctic Biology

1993 - present:

  • World Conservation Union (IUCN), Member of the Species Survival Commission,
  • Alaska Representative, Rodent Specialist Group

1997: Faculty Affiliate, Universidad Gabriel Rene Moreno-Santa Cruz, Bolivia

1993 - 1995: Faculty Affiliate, Universidad de la Republica, Facultad de Ciencias, Montevideo, Uruguay

1993: J. William Fulbright Fellowship (Uruguay)

1990 - 1995: Assistant Professor of Biology and Curator of Mammals, University of Alaska

Grants and Funding

Various sources of support have kept our operation running including the National Science Foundation, USDA Forest Service, US Fish and Wildlife Service, Coastal Marine Institute, and the Hayward Fund for Mammalogy.

Advising

  • Past and Present Graduate Students
  • Post-Doctoral Fellows
  • Undergraduates

Mentoring and Instruction

Formal Courses

University of New Mexico

  • Mammalogy - BIO 489 (8X)
  • Advanced Mammalogy - BIO 402/502 (3X)
  • Advanced Field Methods in Tropical Biology - BIO 402/502 (Panama)
  • Introduction to Tropical Biology - BIO 461 (Belize, Costa Rica (5X), Panama (2X)
  • Ecology and Evolution - BIO 203 (2X)
  • Basic Graduate Evolution - BIO 517 (2X)
  • Art and Natural History - BIO 402/502, Honors, Art (co-taught w/ Szu-Han Ho)
  • Lab Topics - BIO 402-502 1 hour seminar (16X)
  • UnO Seminar - BIO 402, 1 hour seminar (8X)
  • AIM-UP Seminars - BIO 402/502 (5X)

Idaho State University

  • Molecular Evolution - BIOS 499/599
  • Host Parasite Coevolution - BIOS 499/599 (with Walt Boeger)
  • Phylogeography and Coalescent Theory - BIOS 499/599 (with Enrique Lessa)
  • Advanced Topics in Genetics - BIOS 659

University of Alaska Fairbanks

  • Evolution - BIOL 308
  • Systematic and Comparative Biology - BIOL 615/497
  • Mammalogy - BIOL 425
  • Tropical Field Ecology - BIOL 678 (Paraguay)
  • Wildlife Field Trip - WLF 612 (with Dave Klein to Southeast Alaska)

Universidad de la Republica, Montevideo

  • Análisis Filogenético (1997) (with Enrique Lessa)

Universidad Gabriel Rene Moreno-Santa Cruz, Bolivia

  • Biología de la Conservación: La Perspectiva Genética y Evolutiva (1997)

Individual Studies & Discussion Courses

Biology and Wildlife Readings and Discussions

  • Readings in Evolution
  • Molecular Systematics
  • Rodent Biogeography
  • Biogeography Alaska Bats
  • Canid Phylogenies
  • Island Biology
  • Readings in Mammalogy
  • Analysis of Genetic Data (w/ Chris Conroy)
  • Population Genetics II (w/ Karen Stone)

Museum Studies

  • Phocid Curation - BIOL 697
  • Research Collection Management - BIOS 499

Field and Foreign Experience

Pacific Northwest of North America 1980, 1983, 1990 - 2014
Bolivia 1984 - 1988, 1990 - 1993, 1997
Mexico 1980, 1976 - 1982
Paraguay 1996
Russia 1991, 2004, 2006
Uruguay 1993, 1997, 2013
US Southwest 197
Panama 2005, 2000 - 2011, 2013
Canada 2006, 2010 - 2014