Beringian Coevolution Project Publications, Theses, & Manuscripts

NSF0196095(9972154) & NSF0415668

 

  1. 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.

  2. 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.
  3. Asmundsson I, Nadler SA, Hoberg EP, Carreno RA, Kuchboev A.  A molecular phylogeny for the Protostrongylidae (Nematoda: Metastrongylina). Journal of Parasitology, submitted.
  4. Bidlack, A. 2000. Phylogeography and population genetics of northern flying squirrels (Glaucomys sabrinus) in Southeast Alaska. M. S. Thesis. University of Alaska.
  5. 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.
  6. 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.
  7. Brooks DR, and Hoberg EP. 2000. Triage for the biosphere: The need and rationale for taxonomic inventories and phylogenetic studies of parasites. Comparative Parasitology 67: 1-25.
  8. Brooks DR, and Hoberg EP. 2001. Parasite systematics in the 21st Century: Opportunities and obstacles. Trends in Parasitology 17: 273-275.
  9. Brooks DR, Hoberg EP.  2006. Systematics and emerging infectious diseases: From management to solution. Journal of Parasitology. 92: 426-429.
  10. Brooks DR, Hoberg EP. 2007. How will climate change affect host-parasite assemblages? Trends in Parasitology 23: 571-574.
  11. 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.
  12. Carreno R, and Hoberg EP. 1999. Evolutionary relationships among the Protostrongylidae (Nematoda: Metastrongyloidea) as inferred from morphological characters, with consideration of parasite-host coevolution. Journal of Parasitology 85: 638-648. (a foundation paper for the BCP submitted in late 1998)
  13. Chernyavsky F.B., Dokuchaev N.E. 2000. Diversity of the terrestrial mammals in North-East Asia (The taxonomy problems and Beringian connections) /Biodiversity and dynamics of ecosystems in North Eurasia. Vol 1. Novosibirsk, Russia. August 21-26, 2000. IC&G, Novosibirsk. P. 19-20.
  14. Conroy, C. J., and J. A. Cook.  2000.  Systematics of a Holarctic rodent: Microtus (Muridae). Journal of Mammalogy 81:344-359.
  15. 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(6):332-344.
  16. 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.
  17. Conroy, C. J. and J. A. Cook. 2000. Phylogeography of a post-glacial colonizer: Microtus longicaudus (Muridae: Rodentia). Molecular Ecology 9:165-175.
  18. 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.
  19. 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.
  20. 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.
  21. Cook, J.A., N. Dawson, S. MacDonald, and A. Runck. 2004. Mammal Diversity: Inventories of Alaska National Parks Stimulate New Perspectives. Alaska Park Science 3:23-28.
  22. 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.
  23. Cook, J. A., M. Kholodova, C. Brochmann, V. Fedorov, S. L. Talbot, E. B. Taylor, R. Väinölä, E.P. Hoberg, K. P. Magnusson. In Press. Genetic Perspectives on Arctic Biodiversity. In Arctic Biodiversity Assessment. Conservation of Arctic Fauna and Flora Committee, Copenhagen.
  24. Cook, J. A., and V. Fedorov. 2010. Arctic genetic diversity: heavily shaped by past climate change. Genetic Diversity. in Arctic Biodiversity and Climate Change Assessment Highlights, Conservation of Arctic Fauna and Flora Committee. Copenhagen.
  25. Cook. J.A., Hoberg, E.P., Koehler, A., Henttonen, H., Wickström, L., Haukisalmi, V., Galbreath, K.,  Chernyavski, F., Dokuchaev, N., Lahzuhtkin, A., MacDonald, S.O.,  Hope, A., Waltari, E., Runck, A., Veitch, A., Popko, R., Jenkins, E., Kutz, S. and Eckerlin, R.  2005. Beringia:  intercontinental exchange and diversification of high latitude mammals and their parasites during the Pliocene and Quaternary. Mammal Study 30:S33-44.
  26. 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.
  27. Cook, J. A. and S. O. MacDonald. In Press. Island life: Coming to grips with the insular nature of North Pacific Coastal Forests. Chapter in Conservation of North Pacific Coastal Forests, G. Orians, J. Schoen, and J. Franklin, eds. Univ. Washington Press.
  28. 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.
  29. Dawson, N. G. 2008. Vista Norteña: Tracking historical diversification and contemporary structure in high latitude mesocarnivores. Doctoral Dissertation, University of New Mexico.
  30. 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.

  31. 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.
  32. Dalerum, F., J. Loxterman, B. Shults, K. Kunkel, J. A. Cook. 2007. Microsatellite markers suggest delayed female dispersal in a solitary carnivore, the wolverine. J. Mammalogy 88:793-800.
  33. 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.
  34. Demboski, J. R. and J. A. Cook. 2003. Phylogenetic diversification within the Sorex cinereus complex (Insectivora: Soricidae). Journal of Mammalogy 84:144-158.
  35. Demboski, J. R., K. D. Stone, and J. A. Cook. 1999. Further perspectives on the Haida Gwaii glacial refugium hypothesis. Evolution 53:2008-2012.
  36. Dokuchaev N.E. 2000. The taxonomy and biogeography questions of the shrews (Sorex) in Eastern Asia // Proceedings of international meetings of biodiversity in Asia 2000. September. Tokyo-Hayama-Sapporo-Osaka. P. 14-15.
  37. Dokuchaev N.E. 2000. Problems of taxonomy, zoogeography and protection of the small mammals in Kamchatka // Conservation of biodiversity of Kamchatka and coastal waters: Materials of regional scientific conference Petropavlovsk-Kamchatsky, April 11-12, 2000. Petropavlovsk-Kamchatsky. P. 26-27. (in Russian).
  38. Dokuchaev N.E. 2001. Significance of shrews as paratenic hosts of nematodes Soboliphyme baturini. Overall results and prospects of the development of the mammalogy in Siberia (Proceedings of the first scientific conference. Irkutsk, May 24-26, 2001). Irkutsk. P. 237-240. (in Russian).
  39. Dokuchaev N.E., Atrashkevich G.I. 2001. The first discovery of Alcefilaria abramovi (NEMATODA, FILARIIDAE) in farthest of North East Asia: Overall results and prospects of the development of the mammalogy in Siberia (Proceedings of the first scientific conference. Irkutsk, May 24-26, 2001). Irkutsk. P. 240-242. (in Russian).
  40. Dowling, A.P.G., van Veller, M.P.G., Hoberg, E.P., Brooks, D.R. 2003. A priori and a posteriori methods in comparative evolutionary studies of host-parasite associations. Cladistics 19: 240-253.
  41. Durette-Desset M-C, Galbreath KE, Hoberg EP. 2010 Discovery of new Ohbayashinema spp. (Heligmosomidae: Nematoda) in Ochotona princeps and O. cansus (Lagomorpha: Ochotonidae) from western North America and central Asia, with consideration of historical biogeography. Journal of Parasitology. 96: 569-579.
  42. Duszynski, D.W., A.J. Lynch, 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.
  43. 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.
  44. Eddingsaas, A. 2003. The effects of Pleistocene glacial process on Beringia: the evolutionary history of the arctic ground squirrel (Spermophilus parryii). Master’s thesis, Idaho State University. 107 pp.
  45. 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.
  46. 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.
  47. Fleming, M. A. and J. A. Cook. 2002. Phylogeography of endemic ermine (Mustela erminea) in southeast Alaska. Molecular Ecology 11:795-808.
  48. Frances, Jose. 2008.  Differentiation of peripheral populations of wolverine. Master’s Thesis, University of New Mexico.
  49. Galbreath, K. 2002. Genetic consequences of Pleistocene glaciations for the tundra vole (Microtus oeconomus) in Beringia. MS Thesis, UAF.
  50. Galbreath, K. 2009. Of pikas and parasites: historical biogeography of an alpine host-parasite assemblage. Doctoral Dissertation, Cornell University.
  51. Galbreath, K., and J. Cook. 2004. Genetic consequences of Pleistocene glaciations for the tundra vole (Microtus oeconomus) in Beringia. Molecular Ecology 13:135-148.
  52. 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.

  53. Galbreath, K. E., J. A. Cook, and E. P. Hoberg. 2012. Climate’s role in polar bear past. Science 336:1230.
  54. Galbreath, K. E., and E. P. Hoberg. 2011. Return to Beringia: parasites reveal cryptic biogeographic history of North American pikas.  Proceedings of the Royal Society B 279:371-378.
  55. 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.
  56. 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.
  57. 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.
  58. Haukisalmi, V. 2009. A taxonomic revision of the genus Anoplocephaloides Baer, 1923 sensu Rausch (1976), with the description of four new genera (Cestoda: Anoplocephalidae). Zootaxa 2057: 1–31.
  59. Haukisalmi, V., L. M. Hardman, P. Foronda, C. Feliu, H. Henttonen. 2010. Systematic relationships of Mosgovoyia Spasski, 1951 (Cestoda: Anoplocephalidae) and related genera inferred from mitochondrial and nuclear sequence data. Systematic Parasitology 77: 71-79.
  60. Haukisalmi, V., L. M. Hardman, M. Hardman, J. Laakkonen, J. Niemimaa, H. Henttonen. 2007. Morphological and molecular characterization of Paranoplocephala buryatiensis n. sp. and P. longivaginata Chechulin & Gulyaev, 1998 (Cestoda: Anoplocephalidae) in voles of the genus Clethrionomys. Systematic Parasitology 66:55-71.
  61. Haukisalmi, V.,  Hardman, L.M., Hardman, M., Rausch, R.L. & Henttonen, H. 2008. Molecular systematics of the Holarctic Anoplocephaloides variabilis (Douthitt, 1915) complex, with the proposal of Microcephaloides n. g. (Cestoda: Anoplocephalidae). Syst. Parasitology 70: 15-26.
  62. Haukisalmi,V., Hardman, L.M., Henttonen, H., Laakkonen, J., Niemimaa, J., Hardman, M. &  Gubányi, A. 2009. Molecular systematics and morphometrics of Anoplocephaloides dentata (Cestoda, Anoplocephalidae) and related species in voles and lemmings. – Zool. Scripta 38: 199-220.
  63. Haukisalmi, V. L. M. Hardman, J. Niemimaa, H. Henttonen. 2007. Taxonomy and genetic divergence of Paranoplocephala kalelai (Tenora, Haukisalmi et Henttonen, 1985) (Cestoda, Anoplocephalidae) in the grey-sided vole Myodes rufocanus in northern Fennoscandia. Acta Parasitologica, 52:335–341
  64. Haukisalmi, V. and Henttonen, H.  2000. Paranoplocephala serrata  sp. n. (Cestoda, Anoplocephalidae) in  collared lemmings (Dicrostonyx spp., Arvicolinae) from Arctic Siberia and North America. Syst. Parasitol. 45:219-231.
  65. Haukisalmi, V. and Henttonen, H.  2001. Biogeography of helminth parasitism in Lemmus Link (Arvicolinae), with the description of Paranoplocephala fellmani n.sp. (Cestoda: Anoplocephalidae) from the Norwegian lemming L. lemmus (Linnaeus). Syst. Parasitol. 49:7-22.
  66. Haukisalmi, V. and Henttonen H. 2003. What is Paranoplocephala macrocephala (Douthitt, 1915) (Cestoda: Anoplocephalidae)? Syst. Parasitology 54:53-69.
  67. Haukisalmi, V. and Henttonen H. 2007. A taxonomic revision of the Paranoplocephala primordialis (Douthitt) complex (Cestoda: Anoplocephalidae) in voles and squirrels. Zootaxa 1548:51-68.
  68. Haukisalmi, V., Henttonen, H. and Hardman, L.M.  2006. Taxonomy, diversity and zoogeography of Paranoplocephala spp. (Cestoda: Anoplocephalidae) in voles and lemmings of Beringia, with a description of three new species. Biol. J. Linnean Soc. 89:277-299.
  69. Haukisalmi, V., Henttonen, H., Hardman, L.M., Hardman, M., Laakkonen, J., Murueva, G., Niemimaa, J., Shulunov, S., Vapalahti, O. and Yampilova, Z. 2009. Review of tapeworms of rodents in the Republic of Buryatia, with emphasis on anoplocephalid cestodes. ZooKeys 8:1-18.
  70. Haukisalmi, V., Henttonen, H., Niemimaa, J. and Rausch, R.L.  2002. Paranoplocephala etholeni n.sp. (Cestoda: Anoplocephalidae) in Microtus pennsylvanicus from Alaska, with a synopsis of Paranoplocephala-species in Holarctic rodents. Parasite 9:305-314.
  71. Haukisalmi, V., Rausch, R. L. & Henttonen, H. 2005: Morphological characterization of Paranoplocephala bairdi (Schad, 1954) (Cestoda:  Anoplocephalidae) in heather voles Phenacomys spp. and tree voles Arborimus spp., and related species in voles and lemmings (Muridae: Arvicolinae). - Folia Parasitol. 52:311-321.
  72. Haukisalmi, V., Wickström, L.M., Hantula, J. and Henttonen, H. 2001. Taxonomy, genetic differentiation and Holarctic biogeography of Paranoplocephala spp. (Cestoda: Anoplocephalidae) in collared lemmings (Dicrostonyx; Arvicolinae). Biol. J. Linnean Society 74:171-196.
  73. Haukisalmi, V., Wickström, L.M., Henttonen, H., Hantula, J. and  Gubányi, A..  2004. Molecular and morphological evidence for multiple species  within Paranoplocephala omphalodes (Hermann, 1783) (Cestoda:  Anoplocephalidae) in  Microtus-voles (Arvicolinae). Zool Scripta 33:277-290.
  74. Henttonen, H. & Burek, K.A. 2001. Parasitism: an underestimated stressor of arctic fauna? - In: Huntington, H.P. (ed.). Arctic flora and fauna. Status and conservation. Arctic Council Program for the Conservation of Arctic Flora and Fauna (CAFF). Edita, Helsinki. p. 145.
  75. Hoberg EP. 2002. Foundations for an integrative parasitology: Collections, archives and biodiversity informatics. Comparative Parasitology. 69: 124-131.
  76. Hoberg EP. 2005. Coevolution and biogeography among Nematodirinae (Nematoda: Trichostrongylina), Lagomorpha and Artiodactyla (Mammalia): Exploring determinants of history and structure for the northern fauna across the Holarctic.  Journal of Parasitology. 91: 358-369.
  77. Hoberg, EP. 2010. Invasive processes, mosaics, and the structure of helminth parasite faunas. Revue Scientifique et Technique Office International des Épizooties 29: 255-271.
  78. Hoberg EP, and Adams A. 2000. Phylogeny, history and biodiversity: Understanding faunal structure and biogeography in the marine realm. Bulletin of the Scandinavian Society of Parasitology 10: 19-37.
  79. Hoberg EP, Brooks DR. 2008. Structuring the biosphere: Episodic host-switching, geographic colonization, and diversification in complex host-parasite systems. Journal of Biogeography. 35:1533–1550.
  80. Hoberg EP, Brooks DR. 2010. Beyond Vicariance: Integrating Taxon Pulses, Ecological Fitting and Oscillation in Evolution and Historical Biogeography. In The Geography of Host/Parasite Interactions. Morand, S., and R. Poulin, eds. Oxford University Press. pp. 7-20.
  81. 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.
  82. Hoberg EP, Jenkins EJ, Rosenthal BM, Wong M, Erbe E, Kutz SJ, Polley L. 2005. Caudal polymorphism and cephalic morphology for first stage larvae of Parelaphostrongylus odocoilei (Protostrongylidae: Elaphostrongylinae) in Dall’s sheep from the Mackenzie Mountains, Canada.  Journal of Parasitology 91:1318-1325.
  83. Hoberg, E., A.V.A. Koehler, and J. A. Cook. 2012. Complex host-parasite systems in Martes: Implications for conservation biology of endemic faunas. In Biology and Conservation of Marten, Sables and Fisher. A New Synthesis. Pp. 39-57. In Aubry, K., W. J. Zielinski, M. G. Raphael, G. Proulx, and S. W. Buskirk, eds.
  84. Hoberg EP, Lichtenfels JR, Gibbons L. 2004. Phylogeny for genera of   Nematodirinae (Nematoda: Trichostrongylina).  Journal of Parasitology 90:382-389.
  85. Hoberg EP, Monsen K, Kutz, S, and Blouin M.  1999. Structure, biodiversity, and historical biogeography of nematode faunas in Holarctic ruminants: Morphological and molecular diagnoses for Teladorsagia boreoarcticus sp.n. (Nematoda: Ostertagiinae) a dimorphic cryptic species in muskoxen (Ovibos moschatus). Journal of Parasitology 85: 910-934.
  86. Hoberg EP, Kocan A , Rickard LG. 2001. Gastrointestinal strongyles in wild ruminants from North America. In: Parasitic Diseases of Wild Mammals. W. Samuel, M. Pybus and A. Kocan, eds. Iowa State University Press. pp. 193-227.
  87. 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.
  88. Hoberg EP, Kutz S., Nagy, J., Jenkins, E., Elkin, B. Branigan, M. and Cooley, D. 2002.   Protostrongylus stilesi, ecological isolation and host switching between muskoxen and Dall’s sheep in a contact zone. Comparative Parasitology 69: 1-9.
  89. Hoberg EP, Klassen GJ. 2002 Revealing the faunal tapestry: Coevolution and historical biogeography of hosts and parasites in marine systems. Parasitology. Suppl. 125. S3-S22.
  90. Hoberg, E.P., Pilitt, P.A., and K.E. Galbreath. 2009. Why museums matter: A tale of pinworms (Oxyuroidea: Heteroxynematidae) among pikas (Ochotona princeps and O. collaris) in the American west.  Journal of Parasitology 95:490-501.
  91. Hoberg EP, Polley L, Jenkins EJ, Kutz SJ, Veitch A, Elkin B. 2008.Integrated approaches and empirical models for investigation of parasitic diseases in northern wildlife. Emerging Infectious Diseases. 14: 10-17.
  92. Hoberg EP, Polley L, Jenkins EJ, Kutz SJ. 2008. Pathogens of domestic and free-ranging ungulates: Global climate change in temperate to boreal latitudes across North America. Revue Scientifique et Technique Office International des Épizooties. 27: 511-528.
  93. Hope, A. G. 2011.  Spatiotemporal evolution in high latitude soricine shrews. Doctoral Dissertation, University of New Mexico.
  94. 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.
  95. 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.
  96. 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.

  97. 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.
  98. Jenkins EJ, Hoberg EP, Veitch A, Schwantje H, Toweill D, Kutz SJ, Polley L.  2004. Parasite fauna of mountain goats (Oreamnos americana) in the Northwest Territories, British Columbia and Idaho. Proceedings of the Northern Wild Sheep and Goat Council. 14: 141-158.
  99. Jenkins EJ, Appleyard GD, Hoberg EP, Rosenthal BM, Kutz SJ, Veitch A, Schwantje H, Polley L. 2005. Geographic distribution of the muscle dwelling nematode Parelaphostrongylus odocoilei (Protostrongylidae: Elaphostrongylinae) in North America using molecular identification of first stage larvae.  Journal of Parasitology 91:574-584.
  100. Jenkins EJ, Veitch AM, Kutz SJ, Hoberg EP, Polley L. 2006. Climate change and the epidemiology of protostrongylid nematodes in northern ecosystems: Parelaphostrongylus odocoilei and Protostrongylus stilesi in Dall’s sheep (Ovis dalli dalli). Parasitology. 132: 387-401.
  101. Kang HJ, Arai S, Hope AG, Cook JA, Yanagihara R. 2010. Novel Hantavirus in the Flat-Skulled Shrew (*Sorex roboratus*). Vector Borne Zoonotic Diseases. 2010 10:593-597.
  102. 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.
  103. Karpenko, S. V., N. E. Dokuchaev, and E. P. Hoberg. 2007. Nearctic shrews, Sorex spp., as paratenic hosts of Soboliphyme baturini (Nematoda: Soboliphymidae). Comparative Parasitology 74: 1-7.
  104. Koehler, A. V. A. 2006. Systematics, Phylogeography, Distribution, and Life Cycle of Soboliphyme baturini. M. S. Thesis, University of New Mexico.
  105. 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.
  106. 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.
  107. Koehler Anson V. A., Eric P. Hoberg, Fernando Torres-Pérez and Joseph A. Cook. 2009. A molecular view of the superfamily Dioctophymatoidea (Nematoda). J. Comparative Parasitology. 76:100-104.
  108. Kutz SJ, Asmundsson IM, Hoberg EP, Appleyard GD, Jenkins EJ, Lankester MW, Beckmen K, Branigan M, Huby-Chilton F, Cooley D, Elkin B, Johnson D, Kuchboev A, Nagy J, Oakley M, Olsen B, Popko R, Scheer A, Veitch A.  2007. Serendipitous discovery of a novel protostrongylid (Nematoda: Metastrongyloidea) associated with caribou (Rangifer tarandus), muskoxen (Ovibos moschatus) and moose (Alces alces) from high latitudes of North America based on DNA sequence comparisons.  Canadian Journal of Zoology. 85: 1143-1156.
  109. Kutz, S. J., A. P. Dobson, and E. P. Hoberg. 2009. Where are the parasites? Science 326:1187-1188.
  110. Kutz SJ, Hoberg EP, Polley L, Jenkins EJ. 2005. Global warming is changing the dynamics of Arctic host-parasite systems. Proceedings of the Royal Society London, B. 272: 2571-2576.
  111. Kutz, S., Hoberg, E.P., Nagy, J., and L. Polley. 2004. Emerging parasitic infections in Arctic ungulates. Integrative and Comparative Biology 44: 109-118.
  112. Kutz S, Hoberg EP, Polley L. 2001 A new lungworm in muskoxen: An exploration in Arctic parasitology. Trends in Parasitology 17:276-280.
  113. Kutz SJ, Veitch A, Hoberg EP, Elkin B, Jenkins EJ, Polley L. 2001. New host and geographic records for the protostrongylid nematodes Protostrongylus stilesi and Parelaphostrongylus odocoilei in Dall’s sheep (Ovis dalli dalli). Journal of Wildlife Diseases. 37: 761-774.
  114. Laakkonen J, Henttonen H, Hastriter MW, Niemimma J, and Jarrell GH. 2002. Hemoparasites and fleas of shrews and rodents from Alaska. Acta Parasitologica 47: 255-257.
  115. Laakkonen, J., Smith, A., Hildebrandt, K., Niemimaa, J. & Henttonen, H. 2005. Significant morphological, but little molecular differences between Trypanosoma of rodents from Alaska. Journal of Parasitology 91:201-203.
  116. 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.
  117. 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.
  118. Lynch, A. 2004. Coccidia of Mammals from Beringia: A survey and inventory. M.S. Thesis, University of New Mexico. 141pp.
  119. 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. J. Parasitology. 93:1230-1234.
  120. Lynch, A. and D.W. Duszynski. 2008. Species of Coccidia (Apicomplexa: Eimeriidae) in Shrews from Alaska, U.S.A., and Northeastern Siberia, Russia, with Description of Two New Species. Journal of Parasitology 94:883-888.
  121. MacDonald, S. O. 2003. Identification guide to Alaska’s shrews and small rodents. University of Alaska Museum 45 pp.
  122. MacDonald, S. O. and J. A. Cook. 2007. The Mammals and Amphibians of Southeast Alaska. Museum of Southwestern Biology, Special Publication 8:1-191.
  123. MacDonald, S. O., and J. A. Cook. 2009. Catalog of the Recent Mammals of Alaska. University of Alaska Press. 389 p.
  124. MacDonald, S. O., A. M. Runck, and J. A. Cook. 2004. The heather vole (genus Phenacomys) in Alaska. Canadian Field-Naturalist. 118:438-440.
  125. 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.
  126. 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.
  127. Pozio E, E. Hoberg, G. La Rosa and D. S. Zarlenga. 2009. Molecular taxonomy, phylogeny and biogeography of nematodes belonging to the Trichinella genus. Infection, Genetics, and Evolution. 9:606-616.
  128. Runck, A. M. 2001. Molecular and morphological perspectives on post-glacial colonization of Clethrionomys rutilus and Clethrionomys gapperi in Southeast Alaska. MS Thesis, UAF.
  129. Runck, A. M. 2006. Dynamics across a broad hybrid zone between Myodes rutilus and M. gapperi. Ph.D. dissertation, Idaho State University.
  130. 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.
  131. 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 9:114-122.
  132. Runck, A.R., M. Matocq, and J. A. Cook. In revision. Do contact zones evolve over time? A case of readily hybridizing red-backed voles (Genus Myodes). Molecular Ecology
  133. Seville, R.S., C.E. Oliver, A.J. Lynch, M.C. Bryant, D.W. Duszynski.  2005. Eimeria species (Apicomplexa: Eimeriidae) from Arctic ground squirrels (Spermophilus parryii) and red squirrels (Tamiasciurus hudsonicus) in Alaska and in Siberia, Russia. Journal of Parasitology 91:857-862.
  134. 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.
  135. Sonsthagen, S., G. Sage, M. Fowler, A. Hope, J. A. Cook, S. L. Talbot. 2012. 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. Published online: 10 October 2012. DOI 10.1007/s12686-012-9792-5.

  136. Stone, K. D. 2000. Molecular evolution of martens (genus Martes). Ph. D. dissertation, UAF.

  137. Stone, K. and J. Cook. 2002. Molecular evolution of the Holarctic genus Martes. Molecular Phylogenetics and Evolution. 24:169-179.
  138. 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.
  139. Stone, K. D. and J. A. Cook.  2000. Phylogeography of black bears (Ursus americanus) from the Pacific Northwest. Canadian Journal Zoology 78:1-6.
  140. Telford SR, Korenberg EI, Goethert HK, Kovalevski YV, Gorelova N, Spielman, A.  2002. Detection of natural foci of Babesiosis and granulocytic ehrlichiosis in Russia. Siberia.  J. Microbiology and Epidemiology and Immunology. 6:21-25.
  141. Tomasik, E. 2003 A mitochondrial view of geographic variation in wolverine (Gulo gulo) of northwestern North America. Master’s thesis. Idaho State University.
  142. 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.
  143. 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.
  144. Waltari, E. 2005. Evolution of two high latitude mammals: phylogeography and historical demography of arctic hares (Lepus spp.) and shrews of the Sorex cinereus complex. Ph. D. Dissertation, Idaho State University. 159 pp.
  145. 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.
  146. 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.
  147. Waltari E., E. P. Hoberg, E. P. Lessa, and J. A. Cook.  2007. Eastward Ho: phylogeographic perspectives of trans-Beringian colonization. Journal of Biogeography 34: 561-574.
  148. Weckworth, B. V. 2003. Phylogeography and population dynamics of wolves of the Pacific Northwest. Master’s thesis. Idaho State University. 98 pp.
  149. 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

  150. Weckworth B.V., S.L. Talbot, G. Sage, D. Person, and J.A. Cook. 2005. A signal for independent coastal and continental histories for North American wolves. Molecular Ecology 14:917-931.
  151. Weckworth, B.V., S.L. Talbot, J. A. Cook. 2010. Phylogeography of wolves (Canis lupus) in the Pacific Northwest. Journal of Mammalogy. 91:363-375.
  152. Wickström, L.M. 2004.  Phylogeny, phyletic coevolution and phylogeography of Anoplocephaline cestodes in mammals.  PhD Dissertation. University of Helsinki.
  153. Wickström, L.M., Hantula, J., Haukisalmi, V. and Henttonen, H. 2001. Genetic and morphometric variation in the circumpolar helminth parasite Andrya arctica (Cestoda, Anoplocephalidae) in relation to the divergence of its lemming hosts (Dicrostonyx spp.). - Zool. J. Linnaean Society 131:443-457.
  154. Wickström, LM, Haukisalmi, V, Varis, S, Hantula, J, Fedorov, VB, Henttonen, H. 2003. Phylogeography of the circumpolar Paranoplocephala arctica species complex (Cestoda: Anoplocephalidae) parasitizing collared lemmings (Dicrostonyx spp.) Molecular Ecology 12:3359-3371.
  155. Wickström, L.M., Haukisalmi, V., Varis, S., Hantula, J. and Henttonen, H. 2005.  A molecular phylogeny of anoplocephaline cestodes in rodents and lagomorphs. Systematic Parasitology 62:83-99.
  156. Zarlenga DS, Rosenthal B, Pozio E, La Rosa G, Hoberg EP. 2006. Post-Miocene expansion, colonization, and host switching drove speciation among extant nematodes of the archaic genus Trichinella. Proceedings of the National Academy of Sciences (US) 103: 7354-7359.