Neotomine-peromyscine rodent systematics based on combined analyses of nuclear and mitochondrial DNA sequences

Molecular Phylogenetics and Evolution

Volumn 40, Issue 1, 2006, Pages 251-258

  Reeder, Serena A ^a   Carroll, Darin S ^a   Edwards, Cody W ^b   Kilpatrick, C William ^c   Bradley, Robert D ^a  

^a TEXAS TECH UNIVERSITY   (United States)

^b GEORGE MASON UNIVERSITY   (United States)

^c UNIVERSITY OF VERMONT   (United States)

Author keywords

Combined data; Neotominae; Neotomine; Peromyscine; Rodent systematics; Sigmodontinae

Indexed keywords

CYTOCHROME B; FIBRINOGEN; MITOCHONDRIAL DNA; PHOSPHOPROTEIN; SCLEROPROTEIN;

ANIMAL; ARTICLE; CELL NUCLEUS; CLASSIFICATION; GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; RODENT;

ANIMALS; BASE SEQUENCE; CELL NUCLEUS; CYTOCHROMES B; DNA, MITOCHONDRIAL; EXTRACELLULAR MATRIX PROTEINS; FIBRINOGEN; PHOSPHOPROTEINS; PHYLOGENY; RODENTIA;

OCHROTOMYS; RODENTIA;

EID: 33745131435     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2006.03.016     Document Type: Article

References (41)

1. Adkins R.M., Gelke E.L., Rowe D., and Honeycutt R.L. Molecular phylogeny and divergence time estimates for major rodent groups: evidence from multiple genes. Mol. Biol. Evol. 18 (2001) 777-791
2. Barrett M., Donoghue M.J., and Sober E. Against consensus. Syst. Zool. 40 (1991) 486-493
3. Bradley R.D., Edwards C.W., Carroll D.S., and Kilpatrick C.W. Phylogenetic relationships of neotomine-peromyscine rodents: based on DNA sequences from the mitochondrial cytochrome b gene. J. Mammal. 85 (2004) 389-395
4. Bremer K. Branch support and tree stability. Cladistics 10 (1994) 295-304
5. Bull J.J., Huelsenbeck J.P., Cunningham C.W., Swofford D.L., and Waddell P.J. Partitioning and combining data in phylogenetic analysis. Syst. Biol. 42 (1993) 384-397
6. Carleton M.D. Phylogenetic relationships in neotomine-peromyscine rodents (Muroidea) and a reappraisal of the dichotomy within New World Cricetinae. Misc. Publ. Mus. Zool. Univ. Mich. 157 (1980) 1-146
7. Carleton M.D. Systematics and evolution. In: Kirkland Jr. G.L., and Layne J.N. (Eds). Advances in the study of Peromyscus (1989), Tex. Tech. Univ. Press, Lubbock 7-142
8. Chippindale P.T., and Wiens J.J. Weighting, partitioning, and combining characters in phylogenetic analysis. Syst. Biol. 43 (1994) 278-287
9. Cunningham C.W. Can three incongruence tests predict when data should be combined?. Mol. Biol. Evol. 14 (1997) 733-740
10. De Queiroz A. For consensus (sometimes). Syst. Biol. 42 (1993) 368-372
11. Dowton M., and Austin A.D. Increased congruence does not necessarily indicate increased phylogenetic accuracy-the behavior of the incongruence length difference test in mixed-model analyses. Syst. Biol. 51 (2002) 19-31
12. Drovetski S.V. Molecular phylogeny of grouse: individual and combined performance of W-linked, autosomal, and mitochondrial loci. Syst. Biol. 51 (2002) 930-945
13. Edwards C.W., and Bradley R.D. Molecular systematics of the genus Neotoma. Mol. Phylogenet. Evol. 25 (2002) 489-500
14. Engel S.R., Hogan K.M., Taylor J.F., and Davis S.K. Molecular systematics and paleobiogeography of the South American Sigmodontine rodents. Mol. Biol. Evol. 15 (1998) 35-49
15. Engstrom M.D., and Bickham J.W. Chromosome banding and phylogenetics of the golden mouse, Ochrotomys nuttalli. Genetica 59 (1982) 119-126
16. Eriksson, T., 1997. Autodecay version 3.0.3. Botaniska Inst., Stockholm Univ., Stockholm, Sweden.
17. Farris J.S., Kallersjo M., Kluge A.G., and Bult C. Testing significance of incongruence. Cladistics 10 (1994) 315-319
18. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 (1985) 783-791
19. Flynn J.J., and Nedbal M.A. Phylogeny of the Carnivora (Mammalia): congruence vs incompatibility among multiple data sets. Mol. Phylogenet. Evol. 9 (1998) 414-426
20. Goldman E.A. Revision of the wood rats of the genus Neotoma. N. Am. Fauna 31 (1910) 1-124
21. Hooper E.T., and Musser G.G. The glans penis in Neotropical cricetines (family Muridae), with comments on classification of muroid rodents. Misc. Publ. Mus. Zool. Univ. Mich. 123 (1964) 1-57
22. Huelsenbeck J.P., Swofford D.L., Cunningham C.W., Bull J.J., and Waddell P.J. Is character weighting a panacea for the problem of data heterogeneity in phylogenetic analysis?. Syst. Biol. 43 (1994) 288-291
23. Huelsenbeck J.P., Bull J.J., and Cunningham C.W. Combining data in phylogenetic analysis. Trends Ecol. Evol. 11 (1996) 152-158
24. Huelsenbeck J.P., and Ronquist F. MrBayes: Bayesian inference for phylogeny. Biometrics 17 (2001) 754-756
25. Kluge A.G. A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst. Zool. 38 (1989) 7-25
26. Maddison, W.P., Maddison, D.R., 2000. MacClade, Version 4: Analysis of Phylogeny and Character Evolution, Sinauer, Sunderland, MA.
27. McKenna M.C., and Bell S.K. Classification of mammals above the species level (1997), Columbia University Press, NY
28. Mickevich M.F., and Farris J.S. The implications of congruence in Menidia. Syst. Zool. 30 (1981) 351-370
29. Musser G.M., and Carleton M.D. Family Muridae. In: Wilson D.E., and Reeder D.M. (Eds). Mammal species of the world: a taxonomic and geographic reference (1993), Smithsonian Institute, Washington 501-756
30. Musser G.M., and Carleton M.D. Superfamily Muroidea. In: Wilson D.E., and Reeder D.M. (Eds). Mammal species of the world: a taxonomic and geographic reference. third ed. (2005), The Johns Hopkins University Press, Baltimore, MD 894-1531
31. Pereira S.L., Baker A.J., and Wajntal A. Combined nuclear and mitochondrial DNA sequences resolve generic relationships within the Cracidae (Galliformes, Aves). Syst. Biol. 51 (2002) 946-958
32. Posada D., and Crandall K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
33. Reeder S.A., and Bradley R.D. Molecular systematics of neotomine-peromyscine rodents based on the dentin matrix protein 1 gene. J. Mammal. 85 (2004) 1194-1200
34. Reeder, S.A., Bradley, R.D., in press. Phylogenetic relationships of neotomine-peromyscine rodents inferred through DNA sequences from intron 7 of the beta fibrinogen gene. In: Kelt, D.A., Lessa, E., Patton, J.L., Salazar-Bravo, J.A. (Eds.), The quintessential naturalist: honoring the life and legacy of Oliver P. Pearson. University of California Publications in Zoology.
35. Shimodaira H., and Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16 (1999) 1114-1116
36. Smith M.F., and Patton J.L. Phylogenetic relationships and the radiation of sigmodontine rodents in South America: evidence from cytochrome b. J. Mammal. Evol. 6 (1999) 89-128
37. Sullivan J. Combining data with different distributions of among-site rate variation. Syst. Biol. 45 (1996) 375-380
38. Swofford, D.L., 2002. PAUP*: Phylogenetic Analysis Using Parsimony (*and other methods) version 4.0b10. Sinauer Associates, Sunderland, MA.
39. Tamura K., and Nei M. Model selection in the estimation of the number of nucleotide substitutions. Mol. Biol. Evol. 10 (1993) 512-526
40. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24 (1997) 4876
41. Yoder A.D., Irwin J.A., and Payseur B.A. Failure of the ILD to determine data combinability for slow loris phylogeny. Syst. Biol. 50 (2001) 408-424