Multilocus phylogenetics of a rapid radiation in the genus thomomys (Rodentia: Geomyidae)

Systematic Biology

Volumn 57, Issue 2, 2008, Pages 294-310

  Belfiore, Natalia M ^a   Liu, Liang ^b   Moritz, Craig ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b HARVARD UNIVERSITY   (United States)

Author keywords

Gene tree; Importance sampling; Incomplete lineage sorting; Multilocus phylogeny; Pocket gopher; Species tree; Thomomys Geomyidae

Indexed keywords

GEOMYIDAE; RODENTIA; THOMOMYS;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; DEMOGRAPHY; GENETICS; GOPHER; NORTH AMERICA; PHYLOGENY; SPECIES DIFFERENTIATION;

ANIMALS; DEMOGRAPHY; GENETIC SPECIATION; GOPHERS; MODELS, GENETIC; NORTH AMERICA; PHYLOGENY;

EID: 52149099649     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1080/10635150802044011     Document Type: Article

References (87)

1. Alvarez-Castaneda, S. T., and J. L. Patton. 2004. Geographic genetic architecture of pocket gopher (Thomomys bottae) populations in Baja California, Mexico. Mol. Ecol. 13:2287-2301. (Pubitemid 38946418)
2. Avise, J. C., and K. Wollenberg. 1997. Phylogenetics and the origin of species. Proc. Nat. Acad. Sci. USA 94:7748-7755. (Pubitemid 27343721)
3. Ballard, J. W. O., and D. M. Rand. 2005. The population biology of mitochondrial DNA and its phylogenetic implications. Annu. Rev. Ecol. Evol. Syst. 36:621-642. (Pubitemid 43068873)
4. Beltrán, M., C. D. Jiggins, V. Bull, M. Linares, J. Mallet,W. O. McMillan, and E. Bermingham. 2002. Phylogenetic discordance at the species boundary: Comparative gene genealogies among rapidly radiating Heliconius butterflies. Mol. Biol. Evol. 19:2176-2190. (Pubitemid 35440452)
5. Bush, G. L., S. M. Case, A. C.Wilson, and J. L. Patton. 1977. Rapid speciation and chromosomal evolution in mammals. Proc. Natl. Acad. Sci. USA 74:3942-3946. (Pubitemid 8193540)
6. Chang, J.T. 1996. Full reconstruction ofMarkovmodels on evolutionary trees: Identifiability and consistency. Math. Biosci. 137:51-73. (Pubitemid 26307662)
7. Dalquest, W. W. 1983. Mammals of the Coffee Ranch local fauna Hemphillian of Texas. Texas Memorial Museum, University of Texas at Austin.
8. Daly, J. C., and J. L. Patton. 1990. Dispersal, gene flow, and allelic diversity between local populations of Thomomys bottae pocket gophers in the Coastal Ranges of California. Evolution 44:1283-1294.
9. Davis,W. B. 1937. Variations in Townsend pocket gophers. J. Mammal. 18:145-158.
10. Davis,W. B. 1938. Relation of size of pocket gophers to soil and altitude. J. Mammal. 19:338-342.
11. Degnan, J. H., and N. A. Rosenberg. 2006. Discordance of species trees with their most likely gene trees. PLoS Genet. 2:0762-0768.
12. Degnan, J. H., and L. A. Salter. 2005. Gene tree distributions under the coalescent process. Evolution 59:24-37. (Pubitemid 40181296)
13. Dolman, G., and C. Moritz. 2006. A multilocus perspective on refugial isolation and divergence in rainforest skinks (Carlia). Evolution 60:573-582. (Pubitemid 44804542)
14. Drummond, A. J., and A. Rambaut. 2003. BEAST v1.0, Available from http://evolve.zoo.ox.ac.uk/beast/.
15. Drummond, A. J., S. Y. W. Ho, M. J. Phillips, and A. Rambaut. 2006. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4:e88.
16. 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. (Pubitemid 32113816)
17. Edwards, S. V., L. Liu, and D. K. Pearl. 2007. High resolution species trees without concatenation. Proc. Natl. Acad. Sci. USA 104:5936- 5941. (Pubitemid 47175637)
18. Felsenstein, J. 2004. Coalescents and species trees. Pages 488-495, Inferring phylogenies. Sinauer Associates, Sunderland, Massachusetts.
19. Gatesy, J., and R. H. Baker. 2005. Hidden likelihood support in genomic data: can forty-five wrongs make a right? syst. Biol. 54:483-492. (Pubitemid 41040446)
20. Getz, L. L. 1957. Color variation in pocket gophers, Thomomys. J.Mammal. 38:523-526.
21. Goodman, S. N. 1999. Toward evidence-based medical statistics. 2. The Bayes Factor. Ann. Intern. Med. 130:1005-1013. (Pubitemid 29283992)
22. Hafner, M. S., J. W. Demastes, D. J. Hafner, T. A. Spradling, P. D. Sudman, and S. A. Nadler. 1998. Age and movement of a hybrid zone: Implications for dispersal distance in pocket gophers and their chewing lice. Evolution 52:278-282. (Pubitemid 28195169)
23. Hafner,M. S., J. C. Hafner, J. L. Patton, and M. F. Smith. 1987. Macrogeographic patterns of the genetic differentiation in the pocket gopher Thomomys umbrinus. Syst. Zool. 36:18-34.
24. Hasegawa, M., H. Kishino, and T. Yano. 1985. Dating of the human ape splitting by a molecular clock of mitochondrial-DNA. J. Mol. Evol. 22:160-174. (Pubitemid 16227864)
25. Hey, J., and C. A. Machado. 2003. The study of structured populations - New hope for a difficult and divided science. Nat. Rev. Genet. 4:535- 543. (Pubitemid 36781344)
26. Hey, J. and R. Nielsen. 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)
27. Hey, J.,andR. Nielsen. 2007. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc. Nat. Acad. Sci. USA 104:2785-2790. (Pubitemid 46327957)
28. Huelsenbeck, J. P., and B. Rannala. 2004. Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Syst. Biol. 53:904-913. (Pubitemid 40141314)
29. Korth, W. W. 1994. Geomyidae. Pages 199-212 in The Tertiary record of rodents in North America. Topics in geobiology, volume 12 (F. G. Stehli and D. S. Jones, series eds.). Springer, New York.
30. Korth, W. W., and D. S. Chaney. 1999. A new subfamily of Geomyoid rodents (Mammalia) and a possible origin of Geomyidae. J. Paleo. 73:1191-1200.
31. Kubatko, L. S., and J. H. Degnan. 2007. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst. Biol. 56:17- 24.
32. Lanave, C., G. Preparata, C. Sacone, and G. Serio. 1984. A new method for calculating evolutionary substitution rates. J. Mol. Evol. 20:86-93. (Pubitemid 14116237)
33. Lee, M. S. Y., and A. F. Hugall. 2006. Model type, implicit data weighting, and model averaging in phylogenetics. Mol. Phylogenet. Evol. 38:846-857.
34. Lemmon, A. R., and E. C. Moriarty. 2004. The importance of proper model assumption in Bayesian phylogenetics. Syst. Biol. 53:265- 277. (Pubitemid 38611183)
35. Lindsay, E., Y. Mou, W. Downs, J. Pederson, T. S. Kelly, C. Henry, and J. Trexler. 2002. Recognition of the Hemphillian/Blancan boundary in Nevada. J. Vert. Paleo. 22:429-442. (Pubitemid 35016471)
36. Liu, L., S. V. Edwards, N. M. Belfiore, R. T. Brumfield, and D. K. Pearl. (2008). Estimating species trees using multiple-allele data. Evolution (in press).
37. Liu, L., and D. K. Pearl. 2007. Species trees from gene trees: Reconstuction Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst. Biol. 56:504-514.
38. Maddison,W. P. 1997. Gene trees in species trees. Syst. Biol. 46:523-536.
39. Maddison,W. P., and L. L. Knowles. 2006. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 55:21-30.
40. Nei, M. 1987. Molecular evolutionary genetics. Columbia University Press, New York.
41. Neigel, J. E., and J. C. Avise. 1986. Phylogenetic relationships of mitochondrial DNA under various demographic models of speciation. Pages 515-534 in Evolutionary processes and theory (E. Nevo and S. Karlin, eds.). Academic Press, New York.
42. Nevo, E., Y. J. Kim, C. R. Shaw, and C. S. Thaeler. 1974. Genetic variation, selection and speciation in Thomomys talpoides pocket gophers. Evolution 28:1-23.
43. Nylander, J. A. A. 2004. MrModelTest v2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University. 24 instead of 56 models of nucleotide substitution. Pamilo, P., and M. Nei. 1988. Relationships between gene trees and species trees. Mol. Biol. Evol. 5:568-583.
44. Patterson, B. D., G. Ceballos, W. Sechrest, M. F. Tognelli, T. Brooks, L. Luna, P. Ortega, I. Salazar, and B. E. Young. 2005. Digital distribution. Maps of the mammals of theWestern Hemisphere, version 2.0. NatureServe, Arlington, Virginia.
45. Patton, J. L. 1972. Patterns of geographic variation in karyotype in the pocket gopher. Thomomys bottae (Eydoux and Gervais). Evolution 26:574-586.
46. Patton, J. L. 1985. Population structure and the genetics of speciation in pocket gophers, genus Thomomys. Acta Zool. Fennica 170:109- 114.
47. Patton, J. L. 1990. Geomyid evolution: The historical, selective, and random basis for divergence patterns within and among species. Pages 49-69. in Evolution of subterranean mammals at the organismal and molecular levels (E. Nevo and O. A. Reig, eds.). Wiley-Liss, New York.
48. Patton, J. L. 1993. Hybridization and hybrid zones in pocket gophers (Rodentia, Geomyidae). Pages 290-308 in Hybrid zones and the evolutionary process (R. G. Harrison, ed.). Oxford University Press,New York.
49. Patton, J. L. 2005. Family Geomyidae. Pages 859-870 inMammalspecies of the world: A taxonomic and geographic reference, 3rd edition (D. E. Wilson and D. M. Reeder, eds.). The Johns Hopkins University Press, Baltimore, Maryland.
50. Patton, J. L., R. K. Selander, and M. H. Smith. 1972. Genic variation in hybridizing populations of gophers (genus Thomomys). Syst. Zool. 21:263-270.
51. Patton, J. L., and S.W. Sherwood. 1982. Genome evolution in pocket gophers (genus Thomomys) I. Heterochromatin variation and speciation potential. Chromosoma 85:149-162. (Pubitemid 12029944)
52. Patton, J. L., and M. F. Smith. 1981. Molecular evolution in Thomomys: Phyletic systematics, paraphyly, and rates of evolution. J. Mammal. 62:493-500.
53. Patton, J. L., and M. F. Smith. 1989. Population structure and the genetic and morphologic divergence among pocket gopher species (genus Thomomys). Pages 284-304 in Speciation and its consequences (D. Otte and J. A. Endler, eds.). Sinauer Associates, Sunderland, Massachusetts.
54. Patton, J. L., and M. F. Smith. 1990. The evolutionary dynamics of the pocket gopher Thomomys bottae, with emphasis on California populations. Univ. Calif. Publ. Zool. 123:1-161.
55. Patton, J. L., and M. F. Smith. 1994. Paraphyly, polyphyly, and the nature of species boundaries in pocket gophers (genus Thomomys). Syst. Biol. 43:11-26. (Pubitemid 24979621)
56. Patton, J. L., M. F. Smith, R. D. Price, and R. A. Hellenthal. 1984. Genetics of hybridization between the pocket gophers Thomomys bottae and Thomomys townsendii in northeastern California. Great Basin Naturalist 44:431-440.
57. Philippe, H., F. Delsuc, H. Brinkmann, and N. Lartillot. 2005. Phylogenomics. Annu. Rev. Ecol. Evol. Syst. 36:541-562. (Pubitemid 43068870)
58. Posada, D., and K. A. Crandall. 1998. ModelTest: Testing the model of DNA substitution. Bioinformatics 14:817-818. (Pubitemid 28552116)
59. Reid, F. A. 2006. Peterson field guide to mammals of North America, 4th edition. Houghton Mifflin.
60. Rogers, J. S. 2001.Maximumlikelihood estimation of phylogenetic trees is consistent when substitution rates vary according to the invariable sites plus gamma distribution. Syst. Biol. 50:713-722.
61. Rogers, M. A. 1991a. Evolutionary differentiation within the Northern Great Basin pocket gopher Thomomys townsendii, I. Morphological variation. Great Basin Naturalist 51:109-126.
62. Rogers, M. A. 1991b. Evolutionary differentiation within the Northern Great Basin pocket gopher Thomomys townsendii, II. Genetic variation and biogeographic consequences. Great Basin Naturalist 51:127-152.
63. Rokas, A., B. L.Williams, N. King, and S. B. Carroll. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425:798-804. (Pubitemid 37355944)
64. Ronquist, F., and J. P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572- 1574. (Pubitemid 37038874)
65. Rosenberg, N. A. 2002. The probability of topological concordance of gene trees and species trees. Theor. Popul. Biol. 61:225- 247. (Pubitemid 38042804)
66. Rosenberg, N. A. 2003. The shapes of neutral gene genealogies in two species: Probabilities of monophyly, paraphyly, and polyphyly in a coalescent model. Evolution 57:1465-1477. (Pubitemid 36953636)
67. Rosenberg, N. A., and M. Nordberg. 2002. Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nat. Rev. Genet. 3:380-390. (Pubitemid 34506719)
68. Sherwood, S. W., and J. L. Patton. 1982. Genome evolution in pocket gophers genus Thomomys 2. Variation in cellularDNAcontent. Chromosoma 85:163-180.
69. Shotwell, J. A. 1967. Late Tertiary Geomyoid rodents of Oregon. Mus. Nat. Hist. Bull. No. 9. Univ. Oregon.
70. Slowinski, J. B., and R. D. M. Page. 1999. How should species phylogenies be inferred from sequence data? Syst. Biol. 48:814- 825. (Pubitemid 129490565)
71. Smith, M. F. 1998. Phylogenetic relationships and geographic structure in pocket gophers in the genus Thomomys. Mol. Phylogenet. Evol. 9:1-14. (Pubitemid 128350006)
72. Spradling, T. A., S. V. Brant, M. S. Hafner, and C. J. Dickerson. 2004. DNA data support a rapid radiation of pocket gopher genera (Rodentia: Geomyidae), J. Mammal. Evolution 11:105-125. (Pubitemid 39622797)
73. Steel, M., and F. A. Matsen. 2007. The Bayesian "star paradox" persists for long finite sequences. Mol. Biol. Evol. 24:1075-1079. (Pubitemid 46536719)
74. Steinberg, E. K., and J. L. Patton. 2000. Genetic structure and the geography of speciation in subterranean rodents: Opportunities and constraints for evolutionary diversification. Pages 301-331 in Life underground: The biology of subterranean rodents (E. A. Lacey, J. L. Patton, and G. N. Cameron, eds.). The University of Chicago Press, Chicago, Illinois.
75. Swofford, D. L. 2003. PAUP*: Phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Assoc., Sunderland, MA.
76. Takahata, N. 1989. Gene genealogy in three related populations: Consistency probability between gene and population trees. Genetics 122:957-966.
77. Tedford, R. H., L. B. Albright, A. D. Barnosky, I. Ferrusquia- Villafranca, R. M. Hunt, J. E. Storer, C. C. Swisher, M. R. Voorhies, S. D. Webb, and D. P. Whistler. 2004. Mammalian biochronology of the Arikareean through Hemphillian interval (late Oligocene through early Pliocene epochs). Pages 169-231 in Late Cretaceous and Cenozoic mammals of North America: Biostratigraphy and geochronology (M. O.Woodburne, ed.). Columbia University Press, New York.
78. Thaeler, C. S. 1968a. An analysis of the distribution of pocket gopher species in northeastern California (genus Thomomys), volume 86. University of California Publications in Zoology. University of California Press, Berkeley, California.
79. Thaeler, C. S. 1968b. Karyotypes of sixteen populations of the Thomomys talpoides complex of pocket gophers (Rodentia-Geomyidae). Chromosoma 25:172-183.
80. Thaeler, C. S. 1974. Four contacts between ranges of different chromosome forms of the Thomomys talpoides complex (Rodentia: Geomyidae). Syst. Biol. 23:343-354.
81. Thaeler, C. S. 1980. Chromosome numbers and systematic relations in the genus Thomomys (Rodentia: Geomyidae). J. Mammal. 61:414- 422.
82. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The ClustalX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24:4876-4882. (Pubitemid 28022245)
83. Webb, S. D., and N. D. Opdyke. 1995. Global climatic influence on Cenozoic land mammal faunas. Pages 184-208 in Effects of past global change on life. Board on Earth Science Research, Commission on Geosciences. Environmental Research Nature Research Council, National Academy Press,Washington, DC.
84. Wilgenbusch J. C., Warren D. L., and D. L. Swofford. 2004. AWTY: A system for graphical exploration ofMCMCconvergence in Bayesian phylogenetic inference. http://ceb.csit.fsu.edu/awty.
85. Wood, A. E. 1937. Parallel radiation among the Geomyoid rodents. J. Mammal. 18:171-176.
86. Woodburne, M. O., and C. C. Swisher, III. 1995. Land mammal highresolution geochronology, intercontinental overland dispersals, sea level, climate, and vicariance. Pages 335-364 in Geochronology, time-scales and global stratigraphic correlation: Framework for an historical geology (W. A. Berggren, D. V. Kent, and J. Hardenbol, eds.). Society of Stratigraphic Geology Special Publication, volume 54, Tulsa, OK. (Pubitemid 26480205)
87. Zwickl, D. J., and M. T. Holder. 2004. Model parameterization, prior distributions, and the general time-reversible model in Bayesian phylogenetics. Syst. Biol. 53:877-888. (Pubitemid 40141313)