Phylogeography of the ground squirrel subgenus Xerospermophilus and assembly of the Mojave Desert biota

Journal of Biogeography

Volumn 37, Issue 2, 2010, Pages 363-378

  Bell, Kayce C ^a,e   Hafner, David J ^b   Leitner, Philip ^c   Matocq, Marjorie D ^d  

^a Nucl Eng Idaho State University   (United States)

^b UNIVERSITY OF NEW MEXICO   (United States)

^c CALIFORNIA STATE UNIVERSITY   (United States)

^d UNIVERSITY OF NEVADA   (United States)

^e DENVER MUSEUM OF NATURE AND SCIENCE   (United States)

Author keywords

Conservation biogeography; Mitochondrial DNA; Mojave Desert; Phylogeography; South western North America; Spermophilus; Xerospermophilus mohavensis; Xerospermophilus tereticaudus

Indexed keywords

ARID REGION; BAYESIAN ANALYSIS; CYTOCHROME; ENDEMIC SPECIES; EVOLUTIONARY BIOLOGY; GENE; HYPOTHESIS TESTING; MITOCHONDRIAL DNA; PHYLOGEOGRAPHY; RODENT;

MOJAVE DESERT; UNITED STATES;

SCIURIDAE; SPERMOPHILUS; SPERMOPHILUS MOHAVENSIS;

EID: 74949108517     PISSN: 03050270     EISSN: 13652699     Source Type: Journal    
DOI: 10.1111/j.1365-2699.2009.02202.x     Document Type: Article

References (100)

1. Adest, G. A. (1978) The relations of the sand lizards Uma, Callisaurus and Holbrookia (Sauria: Iguanidae): an electrophoretic study. PhD Thesis, University of California, Los Angeles, CA.
2. Akaike, H. (1974) A new look at the statistical model identification. IEEE Transactions on Automatic Control, 19, 716 723.
3. Axelrod, D. I. (1950) Evolution of desert vegetation in western North America. Carnegie Institute of Washington Publications, 590 VI, 215 306.
4. Axelrod, D. I. (1958) Evolution of the Madro-Tertiary geoflora. Botanical Review, 24, 433 509.
5. Axelrod, D. I. (1979) Age and origin of Sonoran Desert vegetation. Occasional Papers, California Academy of Sciences, 132, 1 74.
6. Axelrod, D. I. (1983) Paleobotanical history of the western deserts. Origin and evolution of deserts (ed. by S. G. Wells D. R. Haragan pp. 113 129. University of New Mexico Press, Albuquerque, NM.
7. Bailey, R. G. (1997) Ecoregions of North America. USDA Forest Service, Miscellaneous Publication 1548, Ecosystem Management Analysis Center, United States Department of Agriculture Forest Service, Fort Collins, CO.
8. Berry, K. H. (1997) The Desert Tortoise Recovery Plan: an ambitious effort to conserve biodiversity in the Mojave and Colorado deserts of the United States. Proceedings: Conservation, Restoration, and Management of Tortoises and Turtles - An International Conference (ed. by J. Van Abbema pp 430 440. New York Turtle and Tortoise Society and WCS Turtle Recovery Program, New York.
9. Best, T. L. (1995) Spermophilus mohavensis. Mammalian Species, 509, 1 7.
10. Boehm, M. C. (1984) An overview of the lithostratigraphy, biostratigraphy, and paleoenvironments of the Late Neogene San Felipe marine sequence, Baja California, Mexico. Geology of the Baja California Peninsula (ed. by V. A. Frizzell Jr. Vol. 39, pp. 253 265. Society of Economic Paleontologists and Mineralogists, Pacific Section, Los Angeles, CA.
11. Buising, A. V. (1990) The Bouse Formation and bracketing units, southeastern California and western Arizona: implications for the evolution of the proto-Gulf of California and the lower Colorado River. Journal of Geophysical Research, 95, 20,111, 20,132.
12. Cargill, M., Altshuler, D., Ireland, J., Sklar, P., Ardlie, K., Patil, N., Lane, C. R., Lim, E. P., Kalyanaraman, N., Nemesh, J., Ziaugra, L., Friedland, L., Rolfe, A., Warrington, J., Lipshutz, R., Daley, G. Q. Lander, E. S. (1999) Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nature Genetics, 22, 231 238.
13. CDFG (2005) The status of rare, threatened, and endangered plants and animals of California 2000-2004. California Department of Fish and Game (CDFG), Sacramento, CA.
14. Cox, B. F., Hillhouse, J. W. Owen, L. A. (2003) Pliocene and Pleistocene evolution of the Mojave River, and associated tectonic development of the Transverge Ranges and Mojave Desert, based on borehole stratigraphy studies and mapping of landforms and sediments near Victorville, California. Paleoenvironments and paleohydrology of the Mojave and southern Great Basin deserts (ed. by Y. Enzel, S. G. Wells N. Lancaster pp. 1 42. Geological Society of America Special Paper 368, Boulder, CO.
15. Eddingsaas, A. A., Jacobsen, B. K., Lessa, E. P. Cook, J. A. (2004) Evolutionary history of the Arctic ground squirrel (Spermophilus parryii) in Nearctic Beringia. Journal of Mammalogy, 85, 601 610.
16. Excoffier, L., Laval, G. Schneider, S. (2005) Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 1, 47 50.
17. Findley, J. S. (1969) Biogeography of southwestern boreal and desert mammals. Contributions in mammalogy (ed. by J. K. Jones pp 113 128. University of Kansas Miscellaneous Publications of the Museum of Natural History No. 51, Lawrence, KS.
18. Fu, Y.-X. (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147, 915 925.
19. Gannon, W. L., Sikes, R. S. 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.
20. Goodwin, H. T. Reynolds, R. E. (1989) Late Quaternary Sciuridae from low elevations in the Mojave Desert, California. Southwestern Naturalist, 34, 506 512.
21. Gustafson, J. R. (1993) A status review of the Mohave ground squirrel (Spermophilus mohavensis). Nongame Bird and Mammal Report, 93-99, State of California. Department of Fish and Game, Sacramento, CA.
22. Hafner, D. J. (1981) Evolution and historical zoogeography of antelope ground squirrels, genus Ammospermophilus (Rodentia: Sciuridae). PhD Thesis, University of New Mexico, Albuquerque, NM.
23. Hafner, D. J. (1992) Speciation and persistence of a contact zone in Mojave Desert ground squirrels, subgenus Xerospermophilus. Journal of Mammalogy, 73, 770 778.
24. Hafner, D. J. (1998) Spermophilus mohavensis Merriam 1889. Mohave ground squirrel. North American rodents: status survey and conservation action plan (ed. by D. J. Hafner, E. Yensen G. L. Kirkland Jr. pp. 47 49. IUCN/SSC Rodent Specialist Group, IUCN, Cambridge, UK.
25. Hafner, D. J. Riddle, B. R. (1997) Biogeography of Baja California Peninsular Desert mammals. Life among the muses: papers in honor of James S. Findley (ed. by T. L. Yates, W. L. Gannon D. E. Wilson pp 39 65. Special Publication No. 3, Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM.
26. Hafner, D. J. Riddle, B. R. (2005) Mammalian phylogeography and evolutionary history of northern Mexico's deserts. Biodiversity, ecosystems, and conservation in northern Mexico (ed. by G. Ceballos, J. L. Catron R. S. Felger pp. 225 245. Oxford University Press, New York.
27. Hafner, D. J. Riddle, B. R. (in press) Boundaries and barriers of North American warm deserts: an evolutionary perspective. Palaeogeography and palaeobiogeography: biodiversity in space and time (ed. by P. Upchurch, A. McGowan C. Slater). National Institute for Environmental Science, Cambridge, UK.
28. Hafner, D. J. Yates, T. L. (1983) Systematic status of the Mojave ground squirrel, Spermophilus mohavensis (subgenus Xerospermophilus). Journal of Mammalogy, 64, 397 404.
29. Hall, E. R. (1981) The mammals of North America. John Wiley and Sons, Inc., New York.
30. Harris, J. H. Leitner, P. (2004) Home-range size and use of space by adult Mohave ground squirrels, Spermophilus mohavensis. Journal of Mammalogy, 85, 517 523.
31. Harris, J. H. Leitner, P. (2005) Long-distance movements of juvenile Mohave ground squirrels, Spermophilus mohavensis. Southwestern Naturalist, 50, 188 196.
32. Harrison, R. G., Bogdanowicz, S. M., Hoffman, R. S., Yensen, E. Sherman, P. W. (2003) Phylogeny and evolutionary history of the ground squirrels (Rodentia: Marmotinae). Journal of Mammalian Evolution, 10, 249 275.
33. Helgen, K. M., Cole, F. R., Helgen, L. E. Wilson, D. E. (2009) Generic revision in the Holarctic ground squirrel genus Spermophilus. Journal of Mammalogy, 90, 270 305.
34. Henikoff, S. Henikoff, J. G. (1992) Amino acid substitution matrices from protein blocks. Proceedings of the National Academy of Sciences USA, 89, 10915 10919.
35. Hubbard, J. P. (1974) Avian evolution in the aridlands of North America. Living Bird, 12, 155 196.
36. Huelsenbeck, J. P. Ronquist, F. R. (2001) MrBayes: Bayesian inference for phylogeny. Biometrics, 17, 754 756.
37. Hunter, K. L., Betancourt, J. L., Riddle, B. R., Van Devender, T. R., Cole, K. L. Spaulding, W. G. (2001) Ploidy race distributions since the Last Glacial Maximum in the North American desert shrub, Larrea tridentata. Global Ecology and Biogeography, 10, 521 533.
38. Hurtado, L. A., Erez, T., Castrezana, S. Markow, T. A. (2004) Contrasting population genetic patterns and evolutionary histories among sympatric Sonoran Desert cactophilic Drosophila. Molecular Ecology, 13, 1365 1375.
39. Ingle, J. C., Jr. (1974) Paleobathymetric history of Neogene marine sediments, northern Gulf of California. The geology of peninsular California (ed. by G. Gastil J. Lillegraven pp. 121 138. Guidebook 49 of the Pacific Section, American Association of Petroleum Geologists and Society of Economic Paleontologists and Mineralogists, Los Angeles, CA.
40. Jennings, M. R. Hayes, M. P. (1994) Amphibian and reptile species of special concern in California. California Department of Fish and Game, Rancho Cordova, CA. Available at: http://www.dfg.ca.gov/hcpb/info/herp-ssc.pdf.
41. Jezkova, T., Jaeger, J. R., Marshall, Z. L. Riddle, B. R. (2009) Pleistocene impacts on the phylogeography of the desert pocket mouse (Chaetodipus penicillatus). Journal of Mammalogy, 90, 306 320.
42. Jones, K. B. (1995) Phylogeography of the desert horned lizard (Phrynosoma platyrhinos) and the short-horned lizard (Phrynosoma douglassi): Patterns of divergence and diversity. PhD Thesis, University of Nevada, Las Vegas, NV.
43. Kuhner, M. K., Yamato, J. Felsenstein, J. (1998) Maximum likelihood estimation of population growth rates based on the coalescent. Genetics, 149, 429 434.
44. Lamb, T., Avise, J. C. Gibbons, J. W. (1989) Phylogeographic patterns in mitochondrial DNA of the desert tortoise (Xerobates agassizi), and evolutionary relationships among the North American gopher tortoises. Evolution, 43, 76 87.
45. Lancaster, N. Tchakerian, V. P. (2003) Late Quaternary eolian dynamics, Mojave Desert, California. Paleoenvironments and paleohydrology of the Mojave and southern Great Basin deserts (ed. by Y. Enzel, S. G. Wells N. Lancaster pp. 207 230. Geological Society of America Special Paper 368. Geological Society of America, Boulder, CO.
46. Larget, B. Simon, D. (1999) Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Molecular Biology and Evolution, 16, 750 759. (Pubitemid 29260829)
47. Lenz, L. W. (2007) Reassessment of Yucca brevifolia and recognition of Y. jaegariana as a distinct species. Aliso, 24, 97 104.
48. Lessa, E. P., Cook, J. A. Patton, J. L. (2003) Genetic footprints of demographic expansion in North America, but not Amazonia, during the late Quaternary. Proceedings of the National Academy of Sciences USA, 100, 10331 10334.
49. Lindell, J., Méndez-de la Cruz, F. R. Murphy, R. W. (2005) Deep genealogical history without population differentiation: discordance between mtDNA and allozyme divergence in the zebra-tailed lizard (Callisaurus draconoides). Molecular phylogenetics and Evolution, 36, 682 694.
50. Lindell, J., Ngo, A. Murphy, R. W. (2006) Deep genealogies and the mid-peninsular seaway of Baja California. Journal of Biogeography, 33, 1327 1331.
51. 2. Journal of Arid Environments, 46, 43 56.
52. Lucchitta, I. (1979) Late Cenozoic uplift of the southwestern Colorado Plateau and adjacent lower Colorado River region. Tectonophysics, 61, 63 95.
53. Mabey, D. R. (1960) Gravity survey of the western Mojave Desert, California. United States Geological Survey Professional Paper, 361-D, 51 73.
54. Maddison, D. R. Maddison, W. P. (2005) MacClade: analysis of phylogeny and character evolution. Sinauer, Sunderland, MA.
55. Martin, A. P. Wilcox, J. L. (2004) Evolutionary history of Ash Meadows pupfish (genus Cyprinodon) populations inferred using microsatellite markers. Conservation Genetics, 5, 1566 1621.
56. Mead, J. I., van Devender, T. R. Cole, K. L. (1983) Late Quaternary small mammals from Sonoran Desert packrat middens, Arizona and California. Journal of Mammalogy, 64, 173 180.
57. Morafka, D. J. (1974) A biogeographical analysis of the Chihuahuan Desert through its herpetofauna. PhD Thesis, University of Southern California, Los Angeles, CA.
58. Mulcahy, D. G., Spaulding, A. W., Mendelson, J. R., III. Brodie, E. D., 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.
59. Murphy, R. W., Trépanier, T. L. Morafka, D. J. (2006) Conservation genetics, evolution and distinct population segments of the Mojave fringe-toed lizard, Uma scoparia. Journal of Arid Environments, 67, 226 247.
60. Nason, J. D., Hamrick, J. L. Fleming, T. H. (2002) Historical vicariance and postglacial colonization effects on the evolution of genetic structure in Lophocereus, a Sonoran Desert columnar cactus. Evolution, 56, 2214 2226.
61. Norris, R. M. Webb, R. W. (1990) Geology of California, 2nd edn. John Wiley and Sons, New York.
62. Nunney, L. Elam, D. R. (1994) Estimating the effective population size of conserved populations. Conservation Biology, 8, 175 184.
63. Orr, R. T. (1960) An analysis of the Recent land mammals. Systematic Zoology, 9, 171 179.
64. Patton, J. L., Huckaby, D. G. Álvarez-Castañeda, S. T. (2007) The evolutionary history and a systematic revision of woodrats of the Neotoma lepida group. University of California Publications in Zoology, 135, 1 411.
65. Pellmyr, O. Segraves, K. A. (2003) Pollinator divergence within an obligate mutualism: Two yucca moth species (Lepidoptera; Prodoxidae: Tegeticula) on the Joshua tree (Yucca brevifolia; Agavaceae). Annals of the Entomological Society of America, 96, 716 722.
66. Pellmyr, O., Segraves, K. A., Althoff, D. M., Balcázar-Lara, M. Leebens-Mack, J. (2007) The phylogeny of yuccas. Molecular Phylogenetics and Evolution, 43, 493 501.
67. Posada, D. Crandall, K. A. (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics, 14, 817 818.
68. Rado, T. A. Rowlands, P. G. (1984) A small mammal survey and plant inventory of wetland habitats in Amargosa Canyon and Grimshaw Lake areas of critical environmental concern. Unpublished report, United States Department of the Interior, Bureau of Land Management, Barstow, CA.
69. Ray, N., Currat, M. Excoffier, L. (2003) Intra-deme molecular diversity in spatially expanding populations. Molecular Biology and Evolution, 20, 76 86.
70. Riddle, B. R. Hafner, D. J. (1999) Species as units of analysis in ecology and biogeography: time to take the blinders off. Global Ecology and Biogeography, 8, 433 441.
71. Riddle, B. R. Hafner, D. J. (2006) A step-wise approach to integrating phylogeographic and phylogenetic biogeographic perspectives on the history of a core North American warm desert biota. Journal of Arid Environments, 66, 435 461.
72. Riddle, B. R., Hafner, D. J., Alexander, L. F. Jaeger, J. R. (2000a) Cryptic vicariance in the historical assembly of a Baja California Peninsular Desert biota. Proceedings of the National Academy of Sciences USA, 97, 14438 14443.
73. Riddle, B. R., Hafner, D. J. Alexander, L. F. (2000b) Comparative phylogeography of Bailey's pocket mouse (Chaetodipus baileyi) and the Peromyscus eremicus species group: historical vicariance of the Baja California Peninsular Desert. Molecular Phylogenetics and Evolution, 17, 161 172.
74. Rodríguez, F., Oliver, J. L., Marin, A. Medina, J. R. (1990) The general stochastic model of nucleotide substitution. Journal of Theoretical Biology, 142, 485 501.
75. Rogers, A. R. Harpending, H. C. (1992) Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution, 9, 552 569.
76. Ronquist, F. Huelsenbeck, J. P. (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572 1574.
77. Savage, J. M. (1960) Evolution of a peninsular herptofauna. Systematic Zoology, 9, 184 212.
78. Schmidly, D. J., Wilkins, K. T. Derr, J. N. (1993) Biogeography. Biology of the Heteromyidae (ed. by H. H. Genoways J. H. Brown pp. 319 356. Special Publication No. 10, American Society of Mammalogists. Allen Press, Lawrence, KS.
79. Sharp, R. P. Glazner, A. F. (1997) Geology underfoot in Death Valley and Owens Valley. Mountain Press Publishing Company, Missoula, MT.
80. Shreve, F. (1942) The desert vegetation of North America. Botanical Review, 8, 195 246.
81. Simpson, G. G. (1960) Notes on the measurement of faunal resemblance. American Journal of Science, 258A, 300 311.
82. Sissom, W. D. Hendrixson, B. E. (2005) Scorpion biodiversity and patterns of endemism in northern Mexico. Biodiversity, ecosystems, and conservation in Northern Mexico (ed. by G. Ceballos, J. L. Catron R. S. Felger pp. 122 137. Oxford University Press, New York.
83. Smith, C. I., Godsoe, W. K. W., Tank, S., Yoder, J. B. Pellmyr, O. (2008) Distinguishing coevolution from covicariance in an obligate pollination mutualism: asynchronous divergence in Joshua tree and its pollinators. Evolution, 62, 2676 2687.
84. Smith, G. I. Street-Perrott, F. A. (1983) Pluvial lakes of the western United States. Late-Quaternary environments of the United States, Vol. 1 (ed. by H. E. Wright Jr. pp. 190 212. Longman Group Limited, London, UK.
85. Smith, G. I., Bischoff, J. L. Bradbury, J. P. (1997) Synthesis of the paleoclimatic record from Owens Lake core OL-92. An 800,000-year paleoclimatic record from Core OL-92, Owens Lake, southeast California (ed. by G. I. Smith J. L. Bischoff pp. 143 160. Geological Society of America Special Paper 317. Geological Society of America, Boulder, CO.
86. Smith, M. F. Patton, J. L. (1993) The diversification of South American murid rodents: evidence from mitochondrial DNA sequence data for the akodontine tribe. Biological Journal of the Linnean Society, 50, 149 177.
87. Spaulding, W. G., Kowler, P. A. Anderson, R. S. (1994) A late Quaternary paleoenvironmental record from the central Mojave Desert. Off limits in the Mojave Desert (ed. by R. Reynolds pp. 56 60. San Bernardino County Museum Association Special Publication, Redlands, CA.
88. Spencer, J. E. Pearthree, P. A. (2001) Headward erosion versus closed-basin spillover as alternative causes of Neogene capture of the ancestral Colorado River by the Gulf of California. The Colorado River: origin and evolution (ed. by R. A. Young E. E. Spamer pp. 215 219. Grand Canyon Association Monograph 12, Grand Canyon, AZ.
89. Spencer, J. E. Pearthree, P. A. (2005) Abrupt initiation of the Colorado River and initial incision of the Grand Canyon. Arizona Geology, 35, 1 4.
90. Stebbins, R. C. (1974a) Off-road vehicles and the fragile desert: part 1. The American Biology Teacher, 36, 203 208.
91. Stebbins, R. C. (1974b) Off-road vehicles and the fragile desert: part 2. The American Biology Teacher, 36, 294 304.
92. Thorne, R. F. (1986) A historical sketch of the vegetation of the Mojave and Colorado Deserts of the American Southwest. Annals of the Missouri Botanical Gardens, 73, 642 651.
93. Trépanier, T. L. Murphy, R. W. (2001) The Coachella Valley fringe-toed lizard (Uma inornata): genetic diversity and phylogenetic relationships of an endangered species. Molecular Phylogenetics and Evolution, 18, 327 334.
94. Van Devender, T. R. Spaulding, W. G. (1979) Development of vegetation and climate in the southwestern United States. Science, 204, 701 710.
95. Webb, R. H. Wilshire, H. G. (1983) Environmental effects of off-road vehicles: impacts and management in arid regions. Springer Verlag, New York.
96. Wells, P. V. (1977) Postglacial origin of the Chihuahuan Desert less than 11,500 years ago. Symposium on the Biological Resources of the Chihuahuan Desert Region (ed. by R. H. Wauer D. H. Riskind pp. 67 83. United States Department of the Interior, National Park Service Transactions and Proceedings Series No. 3, Washington, DC.
97. Wells, P. V. Berger, R. (1967) Late Pleistocene history of coniferous woodland in the Mohave Desert. Science, 155, 1640 1647.
98. Wells, P. V. Hunziker, J. H. (1976) Origin of the creosote bush (Larrea) deserts of southwestern North America. Annals of the Missouri Botanical Gardens, 63, 843 861.
99. Wells, S. G., Borwn, W. J., Enzel, Y., Anderson, R. Y. McFadden, L. D. (2003) Late Quaternary geology and paleohydrology of pluvial Lake Mojave, southern California. Paleoenvironments and paleohydrology of the Mojave and southern Great Basin deserts (ed. by Y. Enzel, S. G. Wells N. Lancaster pp. 79 114. Geological Society of America Special Paper 368. Geological Society of America, Boulder, CO.
100. Yang, Z. (1994) Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. Journal of Molecular Evolution, 39, 306 314.