Conservation genetics of the sonoma tree vole (Arborimus pomo) based on mitochondrial and amplified fragment length polymorphism markers

Journal of Mammalogy

Volumn 87, Issue 5, 2006, Pages 950-960

  Blois, Jessica L ^a,b   Arbogast, Brian S ^a  

^a HUMBOLDT STATE UNIVERSITY   (United States)

^b STANFORD UNIVERSITY   (United States)

Author keywords

Amplified fragment length polymorphism (AFLP); Arborimus pomo; Genetic diversity; Mitochondrial DNA (mtDNA); Sonoma tree vole

Indexed keywords

COMPARATIVE STUDY; CONSERVATION GENETICS; GEOGRAPHICAL VARIATION; MITOCHONDRIAL DNA; MITOCHONDRION; POLYMORPHISM; POPULATION SIZE; RODENT; SPECIES DIVERSITY;

NORTH AMERICA; PACIFIC OCEAN; PACIFIC OCEAN (NORTHWEST);

ARBORIMUS POMO; MAMMALIA; MURIDAE;

EID: 33750419044     PISSN: 00222372     EISSN: None     Source Type: Journal    
DOI: 10.1644/05-MAMM-A-321R1.1     Document Type: Article

References (76)

1. ADAM, M. D., AND J. P. HAYES. 1998. Arborimus pomo. Mammalian Species 593:1-5.
2. ANIMAL CARE AND USE COMMITTEE. 1998. Guidelines for the capture, handling, and care of mammals as approved by the American Society of Mammalogists. Journal of Mammalogy 79:1416-1431.
3. ARBOGAST, B. S., AND G. J. KENAGY. 2001. Comparative phylogeography as an integrative approach to historical biogeography. Journal of Biogeography 28:819-825.
4. AUSUBEL, F. M., AND R. BRENT. 1992. Short protocols in molecular biology: a compendium of methods from current protocols in molecular biology. 2nd ed. Greene Publishing Associates, New York.
5. AVISE, J. C. 2000. Phylogeography: the history and formation of species. Harvard University Press, Cambridge, Massachusetts.
6. AVISE, J. C. 2004. Molecular markers, natural history, and evolution. 2nd ed. Sinauer Associates, Inc., Publishers, Sunderland, Massachusetts.
7. AVISE, J. C., ET AL. 1987. Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology and Systematics 18:489-522.
8. BALLARD, J. W. O., AND M. C. WHITLOCK. 2004. The incomplete natural history of mitochondria. Molecular Ecology 13:729-744.
9. BELLINGER, R., S. HAIG, E. FORSMAN, AND T. MULLINS. 2005. Taxonomic relationships among Phenacomys voles endemic to western United States. Journal of Mammalogy 86:201-210.
10. BENSCH, S., AND M. AKESSON. 2005. Ten years of AFLP in ecology and evolution: why so few animals? Molecular Ecology 14: 2899-2914.
11. BENSON, S. B., AND A. E. BORELL. 1931. Notes on the life history of the red tree mouse, Phenacomys longicaudus. Journal of Mammalogy 12:226-233.
12. BIDLACK, A. L., 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.
13. BLEARS, M. J., S. A. DE GRANDIS, H. LEE, AND J. T. TREVORS. 1998. Amplified fragment length polymorphism (AFLP): a review of the procedure and its applications. Journal of Industrial Microbiology and Biotechnology 21:99-114.
14. BLOIS, J. L. 2005. A multilocus assessment of the genetic structure and diversity within an endemic, arboreal vole, Arborimus pomo, in northern California. M.A. thesis, Humboldt State University, Arcata, California.
15. BOWEN, B. W. 1999. Preserving genes, species, or ecosystems? Healing the fractured foundations of conservation policy. Molecular Ecology 8:S5-S10.
16. BYRNES, D. G. P. 1999. AFLP fingerprinting the bats of New Britain (Papua New Guinea): taxonomic, phylogeographic, and conservation applications. Bat Research News 40:165.
17. CAREY, A. B. 1991. The biology of arboreal rodents in Douglas-fir forest. United States Department of Agriculture, Forest Service, Pacific Northwest Research Station, General Technical Report PNW-GTR-276:1-46.
18. CAREY, A. B., B. BISWELL, AND J. W. WITT. 1991. Methods for measuring populations of arboreal rodents. United States Department of Agriculture, Forest Service, Pacific Northwest Research Station, General Technical Report PNW-GTR-273:1-24.
19. CHAPPELL, D. E., R. A. VAN DEN BUSSCHE, J. KRIZAN, AND B. PATTERSON. 2004. Contrasting levels of genetic differentiation among populations of wolverines (Gulo gulo) from northern Canada revealed by nuclear and mitochondrial loci. Conservation Genetics 5:759-767.
20. CREER, S., R. THORPE, A. MALHOTRA, W. CHOU, AND A. STENSON. 2004. The utility of AFLPs for supporting mitochondrial DNA phylogeographical analyses in the Taiwanese bamboo viper, Trimeresurus stejnegeri. Journal of Evolutionary Biology 17:100-107.
21. DRAGOO, J. W., J. SALAZAR-BRAVO, L. J. LAYNE, AND T. L. YATES. 2003. Relationships within the Calomys callosus species group based on amplified fragment length polymorphisms. Biochemical Systematics and Ecology 31:703-713.
22. EDWARDS, S. V., AND P. BEERLI. 2000. Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 54:1839-1854.
23. EXCOFFIER, L., P. E. SMOUSE, AND J. M. QUATTRO. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479-491.
24. FRANKHAM, R. 1996. Relationship of genetic variation to population size in wildlife. Conservation Biology 10:1500-1508.
25. FRANKHAM, R., J. D. BALLOU, AND D. A. BRISCOE. 2002. Introduction to conservation genetics. Cambridge University Press, Cambridge, United Kingdom.
26. FRANKHAM, R., K. LEES, M. E. MONTGOMERY, P. R. ENGLAND, E. H. LOWE, AND D. A. BRISCOE. 1999. Do population size bottlenecks reduce evolutionary potential? Animal Conservation 2:255-260.
27. GAINES, M. S., J. E. DIFFENDORFER, R. H. TAMATIN, AND T. S. WHITTAM. 1997. The effects of habitat fragmentation on the genetic structure of small mammal populations. Journal of Heredity 88:294-304.
28. GALBREATH, K. E., AND J. A. COOK. 2004. Genetic consequences of Pleistocene glaciations for the tundra vole (Microtus oeconomus) in Beringia. Molecular Ecology 13:135-148.
29. HAMILTON, W. J., III. 1939. American mammals. Their lives, habits, and economic relations. McGraw-Hill Book Co., Inc., New York.
30. HAMMOND, P. M. 1994. Practical approaches to the estimation of the extent of biodiversity in speciose groups. Philosophical Transactions of the Royal Society of London, B. Biological Sciences 345:119-136.
31. HUELSENBECK, J. P., AND F. RONQUIST. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755.
32. IRWIN, D. E. 2002. Phylogeographic breaks without geographic barriers to gene flow. Evolution 56:2383-2394.
33. IRWIN, D. E., S. BENSCH, J. H. IRWIN, AND T. D. PRICE. 2005. Speciation by distance in a ring species. Science 307:414-416.
34. JOHNSON, M. L., AND S. B. GEORGE. 1991. Species limits within the Arborimus longicaudus species-complex (Mammalia: Rodentia) with a description of a new species from California. Contributions in Science, Natural History Museum of Los Angeles County 429:1-16.
35. KINGSTON, S., AND P. ROSEL. 2004. Genetic differentiation among recently diverged delphinid taxa determined using AFLP markers. Journal of Heredity 95:1-10.
36. KOCHER, T. D., J. A. CONROY, K. R. MCKAYE, AND J. R. STAUFFER. 1993. Similar morphologies of cichlid fish in lakes Tanganyika and Malawi are due to convergence. Molecular Phylogenetics and Evolution 2:158-165.
37. KOH, L. P., R. R. DUNN, N. S. SODHI, R. K. COLWELL, H. C. PROCTOR, AND V. S. SMITH. 2004. Species coextinctions and the biodiversity crisis. Science 305:1632-1634.
38. LANDE, R. 1988. Genetics and demography in biological conservation. Science 241:1455-1460.
39. LARIZZA, A., G. PESOLE, A. REYES, E. SBISÀ, AND C. SACCONE. 2002. Lineage specificity of the evolutionary dynamics of the mtDNA D-loop region in rodents. Journal of Molecular Evolution 54:145-155.
40. LYNCH, M., AND B. G. MULLIGAN. 1994. Analysis of population genetic structure with RAPD markers. Molecular Ecology 3:91-99.
41. MAY, R. M. 1990. How many species? Philosophical Transactions of the Royal Society of London, B. Biological Sciences 330:293-303.
42. MEISELMAN, N., AND A. T. DOYLE. 1996. Habitat and microhabitat use by the red tree vole (Phenacomys longicaudus). American Midland Naturalist 135:33-42.
43. MILLER, M. P., M. R. BELLINGER, E. D. FORSMAN, AND S. M. HAIG. 2006. Effects of historical climate change, habitat connectivity, and vicariance on genetic structure and diversity across the range of the red tree vole (Phenacomys longicaudus) in the Pacific Northwestern United States. Molecular Ecology 15:145-159.
44. MILLER, M. P., S. M. HAIG, AND R. S. WAGNER. 2005. Conflicting patterns of genetic structure produced by nuclear and mitochondrial markers in the Oregon slender salamander (Batrachoseps wrighti): implications for conservation efforts and species management. Conservation Genetics 6:275.
45. MILLS, L. S., AND P. E. SMOUSE. 1994. Demographic consequences of inbreeding in remnant populations. American Naturalist 144: 412-431.
46. MORITZ, C. 1994. Defining 'evolutionarily significant units' for conservation. Trends in Ecology and Evolution 9:373-375.
47. MURRAY, M. A. 1995. Biochemical systematics of the genus Arborimus. M.A. thesis, Humboldt State University, Arcata, California.
48. NEI, M. 1987. Molecular evolutionary genetics. Columbia University Press, New York.
49. NEI, M., T. MARUYAMA, AND R. CHAKRABORTY. 1975. The bottleneck effect and genetic variability in populations. Evolution 29:1-10.
50. NIELSEN, J. L. 1999. The evolutionary history of steelhead (Oncorhynchus mykiss) along the US Pacific Coast: developing a conservation strategy using genetic diversity. ICES Journal of Marine Science 56:449-458.
51. NORSE, E. A. 1990. Ancient forests of the Pacific Northwest. Island Press, Washington, D.C.
52. O'BRIEN, S. J. 1994. A role for molecular genetics in biological conservation. Proceedings of the National Academy of Sciences 91:5748-5755.
53. O'BRIEN, S. J., ET AL. 1985. Genetic basis for species vulnerability in the cheetah. Science 227:1428-1434.
54. OKSANEN, J., R. KINDT, AND R. B. O'HARA. 2005. Vegan: community ecology package. R Foundation for Statistical Computing, Vienna, Austria.
55. OLSEN, J. B., S. J. MILLER, W. J. SPEARMAN, AND J. K. WENBURG. 2003. Patterns of intra- and inter-population genetic diversity in Alaskan coho salmon: implications for conservation. Conservation Genetics 4:557-569.
56. PATTON, J. L., AND M. F. SMITH. 1994. Paraphyly, polyphyly, and the nature of species boundaries in pocket gophers (genus Thomomys). Systematic Biology 43:11-26.
57. PERRY, D. R. 1978. A method of access into the crowns of emergent and canopy trees. Biotropica 10:155-157.
58. POLYAKOV, A., A. BEHARAV, A. AVIVI, AND E. NEVO. 2004. Mammalian microevolution in action: adaptive edaphic genomic divergence in blind subterranean mole-rats. Proceedings of the Royal Society of London, B. Biological Sciences 271:8156-5159.
59. POSADA, D., AND K. A. CRANDALL. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817-818.
60. PRIMACK, R. B. 2002. Essentials of conservation biology. 3rd ed. Sinauer Associates, Inc., Publishers, Sunderland, Massachusetts.
61. R DEVELOPMENT CORE TEAM. 2005. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
62. RYDER, O. A. 1986. Species conservation and systematics: the dilemma of subspecies. Trends in Ecology and Evolution 1:9-10.
63. SCHNEIDER, S., D. ROESSLI, AND L. EXCOFFIER. 2000. Arlequin: a software for population genetics data analysis. Genetics and Biometry Lab, Department of Anthropology, University of Geneva.
64. SCHÖNSWETTER, P., A. TRIBSCH, M. BARFUSS, AND H. NIKFELD. 2002. Several Pleistocene refugia detected in the high alpine plant Phyteuma globulariifolium Sternb. & Hoppe (Campanulaceae) in the European Alps. Molecular Ecology 11:2637-2647.
65. SHAW, K. L. 2002. Conflict between nuclear and mitochondrial DNA phylogenies of a recent species radiation: what mtDNA reveals and conceals about modes of speciation in Hawaiian crickets. Proceedings of the National Academy of Sciences 99:16122-16127.
66. SIPE, T. W., AND R. A. BROWNE. 2004. Phylogeography of masked (Sorex cinereus) and smoky shrews (Sorex fumeus) in the southern Appalachians. Journal of Mammalogy 85:875-885.
67. SPIELMAN, D., B. W. BROOK, AND R. FRANKHAM. 2004. Most species are not driven to extinction before genetic factors impact them. Proceedings of the National Academy of Sciences 101:15261-15264.
68. SWINGLE, J. K., E. D. FORSMAN, AND S. G. SOVERN. 2004. A method for live-trapping tree voles. Northwestern Naturalist 85:134-135.
69. SWOFFORD, D. 2003. PAUP*: phylogenetic analysis using parsimony (*and other methods). Sinauer Associates, Inc., Publishers, Sunderland, Massachusetts.
70. TAJIMA, F. 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics 105:437-460.
71. TEAR, T. H., J. M. SCOTT, P. H. HAYWARD, AND B. GRIFFITH. 1995. Recovery plans and the Endangered Species Act: are criticisms supported by data? Conservation Biology 9:182-195.
72. THOMAS, J. A., ET AL. 2004. Comparative losses of British butterflies, birds, and plants and the global extinction crisis. Science 303:1879-1881.
73. THOMPSON, J. L., AND L. V. DILLER. 2002. Relative abundance, nest site characteristics, and nest dynamics of Sonoma tree voles on managed timberlands in coastal northwest California. Northwestern Naturalist 83:91-100.
74. VEKEMANS, X. 2002. AFLP-SURV. Laboratoire de Génétique et Ecologie Végétale, Université Libre de Bruxelles, Bruxelles, Belgium.
75. VOS, P., ET AL. 1995. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Research 23:4407-4414.
76. WAPLES, R. S. 1991. Pacific salmon, Oncorhynchus spp., and the definition of "species" under the Endangered Species Act. Marine Fisheries Review 53:11-22.