Pleistocene impacts on the phylogeography of the desert Pocket Mouse (Chaetodipus Penicillatus)

Journal of Mammalogy

Volumn 90, Issue 2, 2009, Pages 306-320

  Jezkova, Tereza ^a   Jaeger, Jef R ^a   Marshall, Zane L ^b   Riddle, Brett R ^a  

^a UNIVERSITY OF NEVADA   (United States)

^b SOUTHERN NEVADA WATER AUTHORITY   (United States)

Author keywords

Chaetodipus penicillatus; Desert pocket mouse; Ecological niche modeling; Mitochondrial DNA; Mojave Desert; Phylogeography; Sonoran Desert; Subspecies

Indexed keywords

ALLOZYME; CHROMOSOME; EVOLUTIONARY BIOLOGY; LAST GLACIAL MAXIMUM; LONGEVITY; MITOCHONDRIAL DNA; PHYLOGEOGRAPHY; PLEISTOCENE; RANGE EXPANSION; RODENT;

COLORADO RIVER [NORTH AMERICA]; MOJAVE DESERT; NORTH AMERICA; SONORAN DESERT; UNITED STATES;

CHAETODIPUS PENICILLATUS;

EID: 65949122939     PISSN: 00222372     EISSN: None     Source Type: Journal    
DOI: 10.1644/08-MAMM-A-243.1     Document Type: Article

References (65)

1. ALEXANDER, L. F., AND B. R. RIDDLE. 2005. Phylogenetics of the New World rodent family Heteromyidae. Journal of Mammalogy 86:366-379.
2. BANDELT, H. J., P. FORSTER, AND A. ROHL. 1999. Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution 16:37-48.
3. BENTANCOURT, J. L., T. R. VAN DEVENDER, AND P. S. MARTIN. 1990a. Introduction. Pp. 2-11 in Packrat middens: the last 40,000 years of biotic change (J. L. Bentancourt, T. R. Van Devender, and P. S. Martin, eds.). University of Arizona Press, Tucson.
4. BENTANCOURT, J. L., T. R. VAN DEVENDER, AND P. S. MARTIN. 1990b. Synthesis and Prospectus. Pp. 435-447 in Packrat middens: the last 40,000 years of biotic change (J. L. Bentancourt, T. R. Van Devender, and P. S. Martin, eds.). University of Arizona Press, Tucson.
5. CARSTENS, B. C., AND C. L. RICHARDS. 2007. Integrating coalescent and ecological niche modeling in comparative phylogeography. Evolution 61:1439-1454.
6. CRANDALL, K. A., AND A. R. TEMPLETON. 1996. Applications of intraspecific phylogenetics. Pp. 81-99 in New uses for new phylogenies (P. H. Harvey, A. J. Leigh Brown, J. Maynard Smith, and S. Nee, eds.). Oxford University Press, Oxford, United Kingdom.
7. CRONIN, M. A. 2007. The Preble's meadow jumping mouse: subjective subspecies, advocacy, and management. Animal Conservation 10:159-161.
8. DOUGLAS, M. E., M. R. DOUGLAS, G. W. SCHUETT, AND L. W. PORRAS. 2006. Evolution of rattlesnakes (Viperidae; Crotalus) in the warm deserts of western North America shaped by Neogene vicariance and Quaternary climate change. Molecular Ecology 15:3353-3374.
9. DUPANLOUP, I., S. SCHNEIDER, AND L. EXCOFFIER. 2002. A simulated annealing approach to define the genetic structure of populations. Molecular Ecology 11:2571-2581.
10. ENZEL, Y., S. G. WELLS, AND N. LANCASTER. 2003. Late Pleistocene lakes along the Mojave River, southeastern California. Pp. 61-77 in Paleoenvironments and paleohydrology of the Mojave and southern Great Basin deserts (Y. Enzel, S. G. Wells, and N. Lancaster, eds.). Special Paper 368, The Geological Society of America, Boulder, Colorado.
11. EXCOFFIER, L., G. LAVAL, AND S. SCHNEIDER. 2005. Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1:47-50.
12. FIELDING, A. H., AND J. F. BELL. 1997. A review of methods for the assessment of prediction errors in conservation presence/absence models. Environmental Conservation 24:38-49.
13. GANNON, W. L., R. S. SIKES, AND THE ANIMAL CARE AND Use COMMITTEE of THE AMERICAN SOCIETY of MAMMALOGISTS. 2007. Guidelines of the American Society of Mammalogists for the use of wild mammals in research. Journal of Mammalogy 88:809-823.
14. HAFNER, J. C., AND M. S. HAFNER. 1983. Evolutionary relationships in heteromyid rodents. Great Basin Naturalist Memoirs 7:3-29.
15. HAFNER, J. C., et al. 2007. Basal clades and molecular systematics of heteromyid rodents. Journal of Mammalogy 88:1129-1145.
16. HALL, E. R. 1981. The mammals of North America. Vol. I. 2nd ed. John Wiley & Sons, Inc., New York.
17. HEWITT, G. M. 1996. Some genetic consequences of ice ages, and their role in divergence and speciation. Biological Journal of the Linnean Society 58:247-276.
18. HEWITT, G. M. 2000. The genetic legacy of the Quaternary ice ages. Nature 405:907-913.
19. HUMANS, R. J., S. E. CAMERON, J. L. PARRA, P. G. JONES, AND A. JARVIS. 2005. Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology 25: 1965-1978.
20. HOFFMEISTER, D. F. 1986. Mammals of Arizona. University of Arizona Press, Tucson.
21. HOFFMEISTER, D. F., AND M. R. LEE. 1967. Revision of pocket mice Perognathus penicillatus. Journal of Mammalogy 48:361-380.
22. JAEGER, J. R., B. R. RIDDLE, AND D. F. BRADFORD. 2005. Cryptic Neogene vicariance and Quaternary dispersal of the red-spotted toad (Bufo punctatus): insights on the evolution of North American warm desert biotas. Molecular Ecology 14:3033-3048.
23. JONES, K. B. 1995. Phylogeography of the desert horned lizard (Phrynosoma platyrhinos) and the short-horned lizard (Phrynosoma douglassi): patterns of divergence and diversity. Ph.D. dissertation, University of Nevada, Las Vegas.
24. KOCHER, T. D., et al. 1989. Dynamics of mitochondrial-DNA evolution in animals - amplification and sequencing with conserved primers. Proceedings of the National Academy of Sciences 86:6196-6200.
25. KUMAR, S., K. TAMURA, AND M. NEI. 2004. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinformatics 5:150-163.
26. LAMB, T., T. R. JONES, AND J. C. AVISE. 1992. Phylogeographic histories of representative herpetofauna of the southwestern United States - mitochondrial-DNA variation in the desert iguana (Dipsosaurus dorsalis) and the chuckwalla (Sauromalus obesus). Journal of Evolutionary Biology 5:465-480.
27. LEACHE, A. D., AND T. W. REEDER. 2002. Molecular systematics of the eastern fence lizard (Sceloporus undulatus): a comparison of parsimony, likelihood, and Bayesian approaches. Systematic Biology 51:44-68.
28. LEE, T. E., B. R. RIDDLE, AND P. L. LEE. 1996. Speciation in the desert pocket mouse (Chaetodipus penicillatus Woodhouse). Journal of Mammalogy 77:58-68.
29. LOBO, J. M., A. JIMENEZ-VALVERDE, AND R. REAL. 2008. AUC: a misleading measure of the performance of predictive distribution models. Global Ecology and Biogeography 17:145-151.
30. LONGMIRE, J. L., M. MALTBIE, AND R. J. BAKER. 1997. Use of lysis buffer in DNA isolation and its implication for museum collections. Occasional Papers, The Museum, Texas Tech University 163:1-3.
31. MANNI, F., E. GUERARD, AND E. HEYER. 2004. Geographic patterns of (genetic, morphologic, linguistic) variation: how barriers can be detected by using Monmonier's algorithm. Human Biology 76: 173-190.
32. MANTEL, N. 1967. The detection of disease clustering and a generalized regression approach. Cancer Research 27:209-220.
33. MANTOOTH, S. L., AND T. L. BEST. 2005. Chaetodipus penicillatus. Mammalian Species 767:1-7.
34. MARTINEZ-MEYER, E., A. T. PETERSON, AND W. W. HARGROVE. 2004. Ecological niches as stable distributional constraints on mammal species, with implications for Pleistocene extinctions and climate change projections for biodiversity. Global Ecology and Biogeography 13:305-314.
35. MC GUIRE, J. A., et al. 2007. Mitochondrial introgression and incomplete lineage sorting through space and time: phylogenetics of crotaphytid lizards. Evolution 61:2879-2897.
36. MILLER, M. P. 2005. Alleles In Space (AIS): computer software for the joint analysis of interindividual spatial and genetic information. Journal of Heredity 96:722-724.
37. 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.
38. MULCAHY, D. G., A. W. SPAULDING, J. R. MENDELSON III, AND E. D. BRODIE, JR. 2006. Phylogeography of the flat-tailed horned lizard (Phrynosoma mcallii) and systematics of the P. mcallii-platyrhinos mtDNA complex. Molecular Ecology 15:1807-1826.
39. MURPHY, R. W., T. L. TREPANIER, AND D. J. MORAFKA. 2006. Conservation genetics, evolution and distinct population segments of the Mojave fringe-toed lizard, Uma scoparia. Journal of Arid Environments 67:226-247.
40. NYLANDER, J. A. A., F. RONQUIST, J. P. HUELSENBECK, AND J. L. NIEVES-ALDREY. 2004. Bayesian phylogenetic analysis of combined data. Systematic Biology 53:47-67.
41. PATTON, J. L. 1969. Karyotypic variation in the pocket mouse, Perognathus penicillatus Woodhouse (Rodentia-Heteromyidae). Caryologia 22:351-358.
42. PATTON, J. L., S. W. SHERWOOD, AND S. Y. YANG. 1981. Biochemical systematics of chaetodipine pocket mice, genus Perognathus. Journal of Mammalogy 62:477-492.
43. PEARSON, R. G., C. RAXWORTHY, M. NAKAMURA, AND A. T. PETERSON. 2007. Predicting species' distributions from small numbers of occurrence records: a test case using cryptic geckos in Madagascar. Journal of Biogeography 34:102-117.
44. PETERSON, A. T. 2001. Predicting species' geographic distributions based on ecological niche modeling. Condor 103:599-605.
45. PHILLIPS, S. J., R. P. anderson, AND R. E. SCHAPIRE. 2006. Maximum entropy modeling of species geographic distributions. Ecological Modelling 190:231-259.
46. PHILLIPS, S. J., M. DUDIK, AND R. E. SCHAPIRE. 2004. A maximum entropy approach to species distribution modeling. Pp. 655-662 in Proceedings of the Twenty-First International Conference on Machine Learning. Association for Computing Machinery, New York.
47. POLZIN, T., AND S. V. DANESCHMAND. 2003. On Steiner trees and minimum spanning trees in hypergraphs. Operations Research Letters 31:12-20.
48. RAES, N., AND H. TER STEEGE. 2007. A null-model for significance testing of presence-only species distribution models. Ecography 0:727-736.
49. RIDDLE, B. R. 1995. Molecular biogeography in the pocket mice (Perognathus and Chaetodipus) and grasshopper mice (Onychomys): the late Cenozoic development of a North American aridlands rodent guild. Journal of Mammalogy 76:283-301.
50. RIDDLE, B. R., D. J. HAFNER, AND L. F. ALEXANDER. 2000. Comparative phylogeography of Bailey's pocket mouse (Chaetodipus baileyi) and Peromyscus eremicus species group: historical vicariance of the Baja California Peninsular Desert. Molecular Phylogenetics and Evolution 17:161-172.
51. RONQUIST, F., AND J. P. HUELSENBECK. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
52. SAMBROOK, J., E. F. FRITSCH, AND T. MANIATIS. 1989. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Plainview, New York.
53. SCHNEIDER, S., AND L. EXCOFFIER. 1999. Estimation of demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: application to human mitochondrial DNA. Genetics 152:1079-1089.
54. SMITH, S. D., R. K. MONSON, AND J. E. anderson. 1997. Physiological ecology of North American desert plants. Springer-Verlag, Berlin, Germany.
55. SMITH, M. F., AND J. L. PATTON. 1980. Relationships of pocket gopher (Thomomys bottae) populations of the Lower Colorado River. Journal of Mammalogy 61:681-696.
56. SOBERON, J., AND A. T. PETERSON. 2005. Interpretation of models of fundamental ecological niches and species' distributional areas. Biodiversity Informatics 2:1-10.
57. SPAULDING, W. G. 1990. Vegetational and climatic development of the Mojave Desert: the last glacial maximum to the present. Pp. 166-199 in Packrat middens: the last 40,000 years of biotic change (J. L. Bentancourt, T. R. Van Devender, and P. S. Martin, eds.). University of Arizona Press, Tucson.
58. SPRADLING, T. A., M. S. HAFNER, AND J. W. DEMASTES. 2001. Differences in rate of cytochrome-I evolution among species of rodents. Journal of Mammalogy 82:65-80.
59. THOMPSON, R. S., and K. H. anderson. 2000. Biomes of western North America at 18,000, 6000 and 014C yr BP reconstructed from pollen and packrat midden data. Journal of Biogeography 27: 555-584.
60. THORNE, J. L., AND H. KISHINO. 2002. Divergence time and evolutionary rate estimation with multilocus data. Systematic Biology 51:689-702.
61. VAN DEVENDER, T. R. 1990. Late Quaternary vegetation and climate of the Chihuahuan Desert, United States and Mexico. Pp. 104-133 in Packrat middens: the last 40,000 years of biotic change (J. L. Bentancourt, T. R. Van Devender, and P. S. Martin, eds.). University of Arizona Press, Tucson.
62. WAHLERT, J. H. 1993. The fossil record. Pp. 1-37 in Biology of the Heteromyidae (H. H. Genoways and J. H. Brown, eds.). Special Publication 10, The American Society of Mammalogists.
63. WALTARI, E., R. J. HIJMANS, A. T. PETERSON, A. S. NYA'RI, S. L. PERKINS, AND R. P. GURALNICK. 2007. Locating Pleistocene refugia: comparing phylogeographic and ecological niche model predictions. PLoS ONE 2:e563.
64. WIENS, J. J., AND C. H. GRAHAM. 2005. Niche conservatism: integrating evolution, ecology, and conservation biology. Annual Review of Ecology and Systematics 36:519-539.
65. WINKER, K., D. A. ROCQUE, T. M. BRAILE, AND C. L. PRUETT. 2007. Vainly beating the air: species-concept debates need not impede progress in science or conservation. Ornithological Monographs 63:30-44.