Landscape genetics of California mule deer (Odocoileus hemionus): The roles of ecological and historical factors in generating differentiation

Molecular Ecology

Volumn 18, Issue 9, 2009, Pages 1848-1862

  Pease, Katherine M ^a   Freedman, Adam H ^a   Pollinger, John P ^a   McCormack, John E ^a   Buermann, Wolfgang ^a   Rodzen, Jeff ^b   Banks, Jim ^b   Meredith, Erin ^b   Bleich, Vernon C ^b   Schaefer, Robert J ^b   Jones, Ken ^c   Wayne, Robert K ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b CALIFORNIA DEPARTMENT OF FISH AND GAME   (United States)

^c Genetic Identification Services   (United States)

Author keywords

Landscape genetics; Microsatellites; MtDNA; Mule deer; Niche modelling

Indexed keywords

CERVIDAE; ODOCOILEUS HEMIONUS;

MICROSATELLITE DNA; MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; CLUSTER ANALYSIS; DEER; DNA SEQUENCE; ECOSYSTEM; ENVIRONMENT; FEMALE; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; HAPLOTYPE; MALE; MOLECULAR EVOLUTION; POPULATION DYNAMICS; POPULATION GENETICS; SEQUENCE ALIGNMENT; UNITED STATES;

ANIMALS; CALIFORNIA; CLUSTER ANALYSIS; DEER; DNA, MITOCHONDRIAL; ECOSYSTEM; ENVIRONMENT; EVOLUTION, MOLECULAR; FEMALE; GENETIC VARIATION; GENETICS, POPULATION; GEOGRAPHY; HAPLOTYPES; MALE; MICROSATELLITE REPEATS; MODELS, GENETIC; POPULATION DYNAMICS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 65549097104     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2009.04112.x     Document Type: Article

References (60)

1. Birungi J, Arctander P (2000) Large sequence divergence of mitochondrial DNA genotypes of the control region within populations of the African antelope, kob (Kobus kob). Molecular Ecology, 9, 1997 2008. (Pubitemid 32053334)
2. Bonnet E, Van de Peer Y (2002) zt: a software tool for simple and partial Mantel tests. Journal of Statistical Software, 7, 1 12. (Pubitemid 39217779)
3. Boutin-Ganache I, Raposo M, Raymond M, Deschepper CF (2001) M13-tailed primers improve the readability and usability of microsatellite analyses performed with two different allele-sizing methods. Biotechniques, 31, 24 28. (Pubitemid 32645903)
4. ter Braak CJF, Smilauer P (2002) Canoco reference manual and Canodraw for Windows user's guide: software for canonical community ordination, Version 4.5. Microcomputer Power, Ithaca, New York.
5. Brown DM, Brenneman RA, Koepfli KP et al 2007) Extensive population genetic structure in the giraffe. BMC Biology, 5, 57.
6. Bunnell FL, Harestad AS (1983) Dispersal and dispersion of black-tailed deer: models and observations. Journal of Mammology, 64, 201 209.
7. Calsbeek R, Thompson JN, Richardson JE (2003) Patterns of molecular evolution and diversification in a biodiversity hotspot: the California Floristic Province. Molecular Ecology, 12, 1021 1029. (Pubitemid 36524294)
8. Courtois R, Bernatchez L, Ouellet JP, Breton L (2003) Significance of caribou (Rangifer tarandus) ecotypes from a molecular genetics viewpoint. Conservation Genetics, 4, 393 404. (Pubitemid 36761639)
9. Cowan IM (1956) What and where are the mule and black-tailed deer? In : The Deer of North America (ed. Taylor WP pp. 334 359. Stackpole Books, Harrisburg, Pennsylvania.
10. Crandall KA, Bininda-Emonds ORP, Mace GM, Wayne RK (2000) Considering evolutionary processes in conservation biology. Trends in Ecology and Evolution, 15, 290 295. (Pubitemid 30409541)
11. Dasmann WP (1975) Big Game of California. State of California Department of Fish and Game, Sacramento, California.
12. Davis FW, Stoms DM, Hollander AD et al 1998) The California Gap Analysis Project-Final Report. University of California, Santa Barbara, California. [ http://www.biogeog.ucsb.edu/projects/gap/gap-rep.html ].
13. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software Structure: a simulation study. Molecular Ecology, 14, 2611 2620. (Pubitemid 40886055)
14. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics, 164, 1567 1587. (Pubitemid 37102217)
15. Feldman CR, Spicer GS (2006) Comparative phylogeography of woodland reptiles in California: repeated patterns of cladogenesis and population expansion. Molecular Ecology, 15, 2201 2222. (Pubitemid 43876461)
16. Geffen E, Anderson MJ, Wayne RK (2004) Climate and habitat barriers to dispersal in the highly mobile grey wolf. Molecular Ecology, 13, 2481 2490. (Pubitemid 38946436)
17. Goudet J (1995) fstat (version 1.2): a computer program to calculate F-statistics. Journal of Heredity, 86, 485 486.
18. Hamlin KL, Mackie RJ (1989) Mule deer in the Missouri River Breaks, Montana: A Study of Population Dynamics in a Fluctuating environment (Final Report, Federal Aid in Wildlife Restoration Project W-120-R). Montana Department of Fish, Wildlife and Parks, Helena, Montana.
19. Hansen MC, DeFries RS, Townshend JRG, Sohlberg R, Dimiceli C, Carroll M (2002) Towards an operational MODIS continuous field of percent tree cover algorithm: examples using AVHRR and MODIS data. Remote Sensing of the Environment, 83, 303 319. (Pubitemid 35307475)
20. Hey J, Nielsen R (2004) Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics, 167, 747 760. (Pubitemid 38931862)
21. Hickman JC (1993) The Jepson Manual: Higher Plants of California. University of California Press, Berkeley, California.
22. Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A (2005) Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology, 25, 1965 1978. (Pubitemid 43013915)
23. Hoss M, Kohn M, Paabo S, Knauer F, Schroder W (1992) Excrement analysis by PCR. Nature, 359, 199.
24. Huelsenbeck JP, Ronquist F (2001) MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics, 17, 754 755. (Pubitemid 32851390)
25. Hugall A, Moritz C, Moussalli A, Stanisic J (2002) Reconciling paleodistribution models and comparative phylogeography in the Wet Tropics rainforest land snail Gnarosophia bellendenkerensis (Brazier 1875). Proceedings of the National Academy of Sciences, USA, 99, 6112 6117. (Pubitemid 34493274)
26. Jacobs DK, Haney TA, Louie KD (2004) Genes, diversity, and geologic process on the Pacific coast. Annual Review of Earth and Planetary Sciences, 32, 601 652. (Pubitemid 38836380)
27. Jobb G, von Haeseler A, Strimmer K (2004) TreeFinder: a powerful graphical analysis environment for molecular phylogenetics. BMC Evolutionary Biology, 4, 18. (Pubitemid 40205271)
28. Jones KC, Levine KF, Banks JD (2000) DNA-based genetic markers in black-tailed and mule deer for forensic application. California Fish and Game, 86, 115 126. (Pubitemid 32217960)
29. Justice CO, Vermote E, Townshend JRG et al 1998) The moderate resolution imaging spectroradiometer (MODIS): land remote sending for global change research. IEEE Transactions on Geoscience and Remote Sensing, 36, 1228 1249. (Pubitemid 128748531)
30. Kiehl JT, Gent PR (2004) The community climate system model, version 2. Journal of Climate, 17, 3666 3682. (Pubitemid 39500320)
31. Knowles LL, Carstens BC, Keat ML (2007) Coupling genetic and ecological-niche models to examine how past population distributions contribute to divergence. Current Biology, 17, 940 946. (Pubitemid 46839179)
32. Kocher TD, Thomas WK, Meyer A et al 1989) Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proceedings of the National Academy of Sciences, USA, 86, 6196 6200. (Pubitemid 19210622)
33. Kohn MH, Wayne RK (1997) Facts from feces revisited. Trends in Ecology & Evolution., 12, 223 227. (Pubitemid 27420009)
34. Kozak KH, Wiens JJ (2006) Does niche conservatism promote speciation? A case study in North American salamanders. Evolution, 12, 2604 2621. (Pubitemid 46220868)
35. Lapointe FJ, Rissler LJ (2005) Congruence, consensus, and the comparative phylogeography of codistributed species in California. The American Naturalist, 166, 290 299. (Pubitemid 41076651)
36. Mackie RJ, Kie JG, Pac DF, Hamlin KL (2003) Mule deer. In : Wild Mammals of North America (eds Feldhamer GA, Thompson BC, Chapman JA pp. 889 905. The Johns Hopkins University Press, Baltimore, Maryland.
37. Maldonado JE, Vila C, Wayne RK (2001) Tripartite genetic subdivisions in the ornate shrew (Sorex ornatus). Molecular Ecology, 10, 127 147. (Pubitemid 32097535)
38. Manel S, Schwartz MK, Luikart G, Taberlet P (2003) Landscape genetics: combining landscape ecology and population genetics. Trends in Ecology and Evolution, 18, 189 197. (Pubitemid 36345738)
39. Nei M (1972) Genetic distance between populations. The American Naturalist, 106, 283 292.
40. Niemiller ML, Fitzpatrick BM, Miller BT (2008) Recent divergence with gene flow in Tennessee cave salamanders (Plethodontidae: Gyrinophilus) inferred from gene genealogies. Molecular Ecology, 17, 2258 2275.
41. Peakall R, Smouse PE (2006) GenAlEx 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6, 288 295. (Pubitemid 43373825)
42. Phillips SJ, Anderson RP, Schapire RE (2006) Maximum entropy modeling of species geographic distributions. Ecological Modelling, 190, 231 259. (Pubitemid 41680650)
43. Pilot M, Jedrzejewski W, Branicki W et al 2006) Ecological factors influence population genetic structure of European grey wolves. Molecular Ecology, 15, 4533 4553.
44. Posada D (1999) Collapse, Version 1.2. Department of Zoology, Brigham Young University, Salt Lake City, Utah.
45. Posada D, Crandall KA (1998) ModelTest: testing the model of DNA substitution. Bioinformatics, 14, 817 818. (Pubitemid 28552116)
46. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945 959. (Pubitemid 30397141)
47. Raymond M, Rousset F (1995) GenePop (version 1.2): population genetics software for exact tests and ecumenicism. Journal of Heredity, 86, 248 249.
48. Rice WR (1989) Analyzing tables of statistical tests. Evolution, 43, 223 225.
49. Richards CL, Carstens BC, Knowles LL (2007) Distribution modelling and statistical phylogeography: an integrative framework for generating and testing alternative biogeographical hypotheses. Journal of Biogeography, 34, 1833 1845. (Pubitemid 47610616)
50. Rissler LJ, Apodaca JJ (2007) Adding more ecology into species delimitation: ecological niche models and phylogeography help define cryptic species in the black salamander (Aneides flavipunctatus). Systematic Biology, 56, 924 942.
51. Rozas J, Sanchez-De I, Barrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19, 2496 2497. (Pubitemid 38016658)
52. Sacks BN, Brown SK, Ernest HB (2004) Population structure of California coyotes corresponds to habitat-specific breaks and illuminates species history. Molecular Ecology, 13, 1265 1275. (Pubitemid 38504429)
53. Shields GF, Kocher TD (1991) Phylogenetic relationships of North American ursids based on analysis of mitochondrial DNA. Evolution, 45, 218 221.
54. Stenseth NC, Ehrich D, Rueness EK et al 2004) The effect of climate forcing on population synchrony and genetic structuring of the Canadian lynx. Proceedings of the National Academy of Sciences, USA, 101, 6056 6061. (Pubitemid 38520527)
55. Storfer A, Murphy MA, Evans JS et al 2007) Putting the 'landscape' in landscape genetics. Heredity, 98, 128 142. (Pubitemid 46321417)
56. Swofford DL (2002) paup*: Phylogenetic Analysis Using Parsimony (*and Other Methods) Version 4.0b10. Sinauer Associates, Sunderland, Massachusetts.
57. Wallmo OC (1978) Mule and black-tailed deer in. In : Big Game of North America, Ecology and Management (eds Schmidt JL, Gilbert DL pp. 31 41. Stackpole Books, Harrisburg, Pennsylvania.
58. Waltari E, Hijmans RJ, Townsend Peterson A et al 2007) Locating Pleistocene refugia: comparing phylogeographic and ecological niche model predictions. PLoS One, 2, e563.
59. Wiens JJ, Graham CH (2005) Niche conservatism: integrating evolution, ecology, and conservation biology. Annual Review of Ecology, Evolution, and Systematics, 36, 519 539. (Pubitemid 43068869)
60. Wilson GA, Rannala B (2003) Bayesian inference of recent migration rates using multilocus genotypes. Genetics, 163, 1177 1191. (Pubitemid 36417957)