Sciurid phylogeny and the paraphyly of Holarctic ground squirrels (Spermophilus)

Molecular Phylogenetics and Evolution

Volumn 31, Issue 3, 2004, Pages 1015-1030

  Herron, Matthew D ^a   Castoe, Todd A ^a   Parkinson, Christopher L ^a  

^a UNIVERSITY OF CENTRAL FLORIDA   (United States)

Author keywords

Bayesian phylogeny; Cytochrome b; Marmotini; Sciuridae; Spermophilus; Squirrels; Taxonomy

Indexed keywords

AMMOSPERMOPHILUS; CANIS FAMILIARIS; CYNOMYS; MAMMALIA; MARMOTA; MICROSCIURUS; MICROSCIURUS FLAVIVENTER; PETAURISTINAE; SCIURIDAE; SCIURILLUS; SCIURILLUS PUSILLUS; SCIURUS; SPERMOPHILUS; UNDETERMINED SCIURIDAE 'CHIPMUNKS';

EID: 2442617184     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ympev.2003.09.015     Document Type: Article

References (75)

1. Adkins, R.M., Gelke, E.L., Rowe, D., Honeycutt, R.L., 2001. Molecular phylogeny and divergence time estimates for major rodent groups: evidence from multiple genes. Mol. Biol. Evol. 18, 777-791.
2. Anthony, H.E., Tate, G.H.H., 1935. Notes on South American Mammalia-No. I. Sciurillus. Am. Mus. Novit. 780, 1-13.
3. Arbogast, B.S., Browne, R.A., Weigl, P.D., 2001. Evolutionary genetics and Pleistocene biogeography of North American tree squirrels (Tamiaschirus). J. Mamm. 82, 302-319.
4. Ball, S.S., Roth, V.L., 1995. Jaw muscles of New World squirrels. J. Morphol. 224, 265-291.
5. Black, C.C., 1963. A review of the North American Tertiary Sciuridae. Bull. Mus. Comp. Zool. 130, 109-248.
6. Black, C.C., 1972. Holarctic evolution and dispersal of squirrels (Rodentia: Sciuridae). Evol. Biol. 6, 305-322.
7. Bryant, M.D., 1945. Phylogeny of nearctic sciuridae. Am. Midl. Nat. 33, 257-390.
8. DeBry, R.W., Sagel, R.M., 2001. Phylogeny of Rodentia (Mammalia) inferred from the nuclear-encoded gene IRBP. Mol. Phylogenet. Evol. 19, 290-301.
9. Ellerman, J.R., Hayman, R.W., Holt, G.W.C., 1940. The Families and Genera of Living Rodents. Trustees of the British Museum, London, England.
10. Ellis, L.S., Maxson, L.R., 1979. Evolution of the chipmunk genera Eutamias and Tamias. J. Mamm. 60, 331-334.
11. Ellis, L.S., Maxson, L.R., 1980. Albumin evolution within New World squirrels (Sciuridae). Am. Midl. Nat. 104, 57-62.
12. Engesser, B., 1979. Relationships of some insectivores and rodents from the Miocene of North America and Europe. Bull. Carnegie Mus. Nat. Hist. 14, 1-45.
13. Felsenstein, J., 1968. Statistical Inference and the Estimation of Phylogenies. University of Chicago, Chicago.
14. Forsyth Major, C.J., 1893. On some Miocene squirrels, with remarks on the dentition and classification of the Sciurinae. Proc. Zool. Soc. Lond., 179-215.
15. Griffiths, C.S., 1997. Correlation of functional domains and rates of nucleotide substitution in cytochrome b. Mol. Phylogenet. Evol. 7, 352-365.
16. Hafner, D.J., 1984. Evolutionary relationships of the Nearctic Sciuridae. In: Murie, J., Michener, G. (Eds.), The Biology of Ground- Dwelling Squirrels: Annual Cycles, Behavioral Ecology, and Sociality. University of Nebraska Press, Lincoln, pp. 3-23.
17. Hafner, M., Barkley, L., Chupasko, J., 1994. Evolutionary genetics of New World tree squirrels (tribe Sciurini). J. Mamm. 75, 102-109.
18. Hall, E.R., 1981. The Mammals of North America. Wiley, New York.
19. Hall, E.R., Kelson, K.R., 1959. The Mammals of North America. The Ronald Press Company, New York.
20. Hight, M.E., Goodman, M., Prychodko, W., 1974. Immunological studies of the Sciuridae. Syst. Zool. 23, 12-25.
21. Hoffmann, R.S., Anderson, C.G., Thorington Jr., R.W., Heaney, L.R., 1993. Family Sciuridae. In: Wilson, D.E., Reeder, D.M. (Eds.), Mammal Species of the World: A Taxonomic and Geographic Reference. Smithsonian Institution Press, Washington, DC, pp. 419-466.
22. Howell, N., 1989. Evolutionary conservation of protein regions in the proton-motive cytochrome b and their possible roles in redox catalysis. J. Mol. Evol. 29, 157-169.
23. Huchon, D., Catzeflis, F.M., Douzery, E.J., 1999. Molecular evolution of the nuclear von Willebrand factor gene in mammals and the phylogeny of rodents. Mol. Biol. Evol. 16, 577-589.
24. Huchon, D., Catzeflis, F.M., Douzery, E.J., 2000. Variance of molecular datings, evolution of rodents and the phylogenetic affinities between Ctenodactylidae and Hystricognathi. Proc. R. Soc. Lond. B Biol. Sci. 267, 393-402.
25. Huelsenbeck, J.P., Crandall, K.A., 1997. Phylogeny estimation and hypothesis testing using maximum likelihood. Annu. Rev. Ecol. Syst. 28, 437-466.
26. Huelsenbeck, J.P., Ronquist, P., 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755.
27. Huelsenbeck, J.P., Larget, B., Miller, R.E., Ronquist, F., 2002. Potential applications and pitfalls of bayesian inference of phylogeny. Syst. Biol. 51, 672-688.
28. Irwin, D., Kocher, T., Wilson, A., 1991. Evolution of the cytochrome b gene in mammals. J. Mol. Evol. 32, 37-55.
29. James, G.T., 1963. Paleontology and nonmarine stratigraphy of the Cuyama Valley Badlands, California. Part I. Geology, faunal interpretations, and systematic descriptions of Chiroptera, Insectivora, and Rodentia. Univ. Calif. Publ. Geol. Sci. 45, 1-171.
30. Jameson Jr., E.W., 1999. Host-ectoparasite relationships among North American chipmunks. Acta Theriol. 44, 225-231.
31. Kimura, M., 1986. The role of compensatory neutral mutations in molecular evolution. J. Genet. 64, 7-19.
32. Krajewski, C., King, D.G., 1996. Molecular divergence and phylogeny: rates and patterns of cytochrome b evolution in cranes. Mol. Biol. Evol. 13, 21-30.
33. Lavocat, R., Parent, J.-P., 1985. Phylogenetic analysis of middle-ear features in fossil and living rodents. In: Luckett, W.P., Hartenberger, J.-L. (Eds.), Evolutionary Relationships Among Rodents: A Multidisciplinary Analysis. Plenum Press, New York, pp. 333-354.
34. Layne, J.N., 1952. The os genitale of the red squirrel, Tamiasciurus. J. Mamm. 33, 457-459.
35. Levenson, H., Hoffman, R.S., Nadler, C.F., Deutsch, L., Freeman, S.D., 1985. Systematics of the Holarctic chipmunks (Tamias). J. Mamm. 66, 219-242.
36. McKenna, M.C., Bell, S.K., 1997. Classification of Mammals Above the Species Level. Columbia University Press, New York.
37. Mein, P., 1970. Les sciuropteres (Mammalia, Rodentia) Neogenes d'Europe occidentale. Geobios 3, 7-77.
38. Mercer, J.M., Roth, V.L., 2003. The effects of Cenozoic global change on squirrel phylogeny. Science 299, 1568-1572.
39. Montgelard, C., Bentz, S., Tirard, C., Verneau, O., Catzeflis, P.M., 2002. Molecular systematics of Sciurognathi (Rodentia): the mitochondrial cytochrome b and 12S rRNA genes support the Anomaluroidea (Pedetidae and Anomaluridae). Mol. Phylogenet. Evol. 22, 220-233.
40. Moore, J.C., 1959. Relationships among the living squirrels of the Sciurinae. Bull. Am. Mus. Nat. Hist. 118, 159-206.
41. Moore, J.C., 1961. Geographic variation in some reproductive characteristics of diurnal squirrels. Bull. Am. Mus. Nat. Hist. 122, 1-32.
42. Mossman, H.W., Lawlah, J.W., Bradley, J.A., 1932. The male reproductive tract of the Sciuridae. Am. J. Anat. 51, 89-155.
43. Nadler, C.F., 1964. Contributions of chromosomal analysis to the systematics of North American chipmunks. Am. Midl. Nat. 72, 298-312.
44. Nadler, C.F., Hoffmann, R.S., Lay, D.M., 1969. Chromosomes of the Asian chipmunk Eutamias sibiricus Laxmann (Rodentia: Sciuridae). Experientia 25, 868-869.
45. Nadler, C.F., Hoffmann, R.S., Pizzimenti, J.J., 1971. Chromosomes and serum proteins of prairie dogs and a model of Cynomys evolution. J. Mamm. 52, 545-555.
46. Nadler, C.F., Hoffmann, R.S., Honacki, J.H., Pozin, D., 1977. Chromosomal evolution in chipmunks, with special emphasis on A and B karyotypes of the subgenus Neotamias. Am. Midl. Nat. 98, 343-353.
47. Nedbal, M.A., Honeycutt, R.L., Schlitter, D.A., 1996. Higher-level systematics of rodents (Mammalia: Rodentia): Evidence from the mitochondrial 12S rRNA gene. J. Mamm. Evol. 3, 201-237.
48. Nicholas, K.B., Nicholas Jr., H.B., 1997. Genedoc: a tool for editing and annotating multiple sequence alignments. Distributed by the authors.
49. Nielsen, R., 1997. Site-by-site estimation of the rate of substitution and the correlation of rates in mitochondrial DNA. Syst. Biol. 46, 346-353.
50. Oshida, T., Masuda, R., 2000. Phylogeny and zoogeography of six squirrel species of the genus Sciurus (Mammalia, Rodentia), inferred from cytochrome b gene sequences. Zool. Sci. 17, 405-410.
51. Oshida, T., Masuda, R., Yoshida, M., 1996. Phylogenetic relationships among Japanese species of the family Sciuridae (Mammalia, Rodentia), inferred from nucleotide sequences of mitochondrial 12S ribosomal RNA genes. Zool. Sci. 13, 615-620.
52. Oshida, T., Lin, L.K., Masuda, R., Yoshida, M.C., 2000. Phylogenetic relationships among Asian species of Petaurista (Rodentia, Sciuridae), inferred from mitochondrial cytochrome b gene sequences. Zool. Sci. 17, 123-128.
53. Oshida, T., Yasuda, M., Endo, H., Hussein, N.A., Masuda, R., 2001. Molecular phylogeny of five squirrel species of the genus Callosciurus (Mammalia, Rodentia) inferred from cytochrome b gene sequences. Mammalia 65, 473-482.
54. Piaggio, A.J., Spicer, G.S., 2000. Molecular phylogeny of the chipmunk genus Tamias based on the mitochondrial cytochrome oxidase subunit II gene. J. Mamm. Evol. 7, 147-166.
55. Piaggio, A.J., Spicer, G.S., 2001. Molecular phylogeny of the chipmunks inferred from mitochondrial cytochrome b and cytochrome oxidase II gene sequences. Mol. Phylogenet. Evol. 20, 335-350.
56. Pocock, R.I., 1923. The classification of the Sciuridae. Proc. Zool. Soc. Lond. 1923, 209-246.
57. Posada, D., Crandall, K., 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14, 817-818.
58. Posada, D., Crandall, K.A., 2001. Selecting the best-fit model of nucleotide substitution. Syst. Biol. 50, 580-601.
59. Saiki, R., Gelfand, D.H., Stoeffl, S., Scharf, S., Higuchi, T., Horn, G., Mullis, K.B., Erlich, H., 1988, Primer-directed enzymatic amplification of DNA with thermostable DNA polymerase. Science 239, 487-491.
60. Sambrook, J., Russell, D.W., 2001. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
61. Schöniger, M., Von Haeseler, A., 1994. A stochastic model for the evolution of autocorrelated DNA sequences. Mol. Phylogenet. Evol. 3, 240-247.
62. Simpson, G.G., 1945. Principles of classification and a classification of mammals. Bull. Am. Mus. Nat. Hist. 85, 1-350.
63. Smith, A.B., 1994. Rooting molecular trees: problems and strategies. Biol. J. Linnean Soc. 51, 279-292.
64. Steppan, S.J., Akhverdyan, M.R., Lyapunove, E.A., Fraser, D.G., Vorontsov, N.N., Hoffmann, R.S., Braun, M.J., 1999. Molecular phylogeny of the marmots (Rodentia: Sciuridae): tests of evolutionary and biogeographic hypotheses. Syst. Biol. 48, 715-734.
65. Steppan, S.J., Storz, B.L., Hoffmann, R.S., in press. Nuclear DNA phylogeny of the squirrels (Mammalia: Rodentia) and the evolution of arboreality from c-myc and RAG1. Mol. Phylogenet. Evol.
66. Swofford, D.L., 2002. PAUP*. Phylogenetic Analysis Using Parsimony (* and Other Methods). Sinauer Associates, Sunderland, MA.
67. Tavaré, S., 1986. Some probabilistic and statistical problems in the analysis of DNA sequences. In: Miura, R.M. (Ed.), Some Mathematical Questions in Biology/DNA Sequence Analysis. American Mathematical Society, Providence, RI, pp. 57-86.
68. Thorington Jr., R.W., 1984. Flying squirrels are monophyletic. Science 225, 1048-1050.
69. Thorington Jr., R.W., Darrow, K., 1996. Jaw muscles of Old World squirrels. J. Morphol. 230, 145-165.
70. Wade, O., Gilbert, P.T., 1940. The baculum of some Sciuridae and its significance in determining relationships. J. Mamm. 21, 52-63.
71. Wahlert, J.H., 1985. Cranial foramina of rodents. In: Luckett, W.P., Hartenberger, J.-L. (Eds.), Evolutionary Relationships Among Rodents: A Multidisciplinary Analysis. Plenum Press, New York, pp. 311-332.
72. Wettstein, P.J., Strausbauch, M., Lamb, T., States, J., Chakraborty, R., Jin, L., Riblet, R., 1995. Phylogeny of six Sciurus aberti subspecies based on nucleotide sequences of cytochrome b. Mol. Phylogenet. Evol. 4, 150-162.
73. White, J.W., 1953. Genera and subgenera of chipmunks. Univ. Kansas Publ. Mus. Nat. Hist. 5, 543-561.
74. Yang, Z., 1993. Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 10, 1396-1401.
75. Yang, Z., 1995. A space-time process model for the evolution of DNA sequences. Genetics 139, 993-1005.