Paraphyly, polyphyly, and the nature of species boundaries in pocket gophers (genus thomomys)

Systematic Biology

Volumn 43, Issue 1, 1994, Pages 11-26

  Patton, James L ^a   Smith, Margaret F ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Allozymes; Globin sequence; Mtdna sequence; Paraphyly; Pocket gophers; Polyphyly; Species concepts; Thomomys

Indexed keywords

GEOMYIDAE; THOMOMYS; THOMOMYS BOTTAE; THOMOMYS TOWNSENDII;

EID: 12044256661     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/43.1.11     Document Type: Article

References (61)

1. Anderson, S. 1966. Taxonomy of gophers, especially Thomomys, in Chihuahua. Syst. Zool. 15:189-198.
2. Avise, J. C. 1989. Gene trees and organismal histories: A phylogenetic approach to population biology. Evolution 43:1192-1208.
3. Avise, J. C, J. Arnold, R. M. Ball, E. Bermingham, T. Lamb, J. E. Neigel, C. A. Reed, and N. C. Saunders. 1987. Intraspecific phylogeography: The mitochondrial bridge between population genetics and systematics. Annu. Rev. Ecol. Syst. 18:489-522.
4. Avise, J. C, J. E. Neigel, and J. Arnold. 1984. Demographic influences on mitochondrial DNA lineage survivorship in animal populations. J. Mol. Evol. 20:99-105.
5. Baum, D. 1992. Phylogenetic species concepts. Trends Ecol. Evol. 7:1-2.
6. Bibb, M. J., R. A. Van Ehen, C. T. Wright, M. W. Walberg, and D. A. Clayton. 1981. Sequence and gene organization of mouse mitochondrial DNA. Cell 26:167-180.
7. Birky, C. W„ Jr. 1989. Evolution and population genetics of organelle genes: Mechanisms and models. Pages 112-134 in Evolution at the molecular level (R. K. Selander, A. G. Clark, and T. S. Whittam, eds.). Sinauer, Sunderland, Massachusetts.
8. Cabot, E. L., and A. T. Beckenbach. 1989. Simultaneous editing of multiple nucleic acid and protein sequences with ESEE. Comput. Appl. Biosci. 5:233-234.
9. Cavalli-Sforza, L. L., and A. W. F. Edwards. 1967. Phylogenetic analysis: Models and estimation procedures. Evolution 21:550-570.
10. Cracraft, J. 1983. Species concepts and speciation analysis. Pages 159-187 in Current ornithology, Volume 1 (R. F. Johnston, ed.). Plenum, New York.
11. Cracraft, J. 1989. Speciation and its ontogeny: The empirical consequences of alternative species concepts for understanding patterns and processes of differentiation. Pages 28-57 in Speciation and its consequences (D. Otte and J. A. Endler, eds.). Sinauer, Sunderland, Massachusetts.
12. Davis, J. L., and P. S. Manos. 1991. Isozyme variation and species delimitation in the Puccinellia nut-talliana complex (Poaceae): An application of the phylogenetic species concept. Syst. Bot. 16:431-445.
13. Davis, W. B. 1937. Variations in Townsend pocket gophers. J. Mammal. 18:145-158.
14. DE Queiroz, K. 1992. Phylogenetic relationships and rates of allozyme evolution among the lineages of sceloporine sand lizards. Biol. J. Linn. Soc. 45:333-362.
15. DE Queiroz, K., and M. J. Donoghue. 1988. Phylogenetic systematics and the species problem. Cla-distics 4:317-338.
16. de Queiroz, K., and M. J. Donoghue. 1990a. Phylogenetic systematics or Nelson's version of cladis-tics? Cladistics 6:61-75.
17. de Queiroz, K., and M. J. Donoghue. 1990b. Phylogenetic systematics and species revisited. Cladistics 6:83-90.
18. Donoghue, M. J. 1985. A critique of the biological species concept and recommendations for a phylogenetic alternative. Bryologist 88:172-181.
19. Felsenstein, J. 1989. PHYLIP—Phylogeny inference package, version 3.4. Cladistics 5:164-166.
20. Frost, D. R and D. M. Hillis. 1990. Species in concept and practice: Herpetological applications. Herpetologica 46:87-104.
21. Frost, D. R., A. G. Kluge, and D. M. Hillis. 1992. Species in contemporary herpetology: Comments on phylogenetic inference and taxonomy. Herpe-tol. Rev. 23:46-54.
22. Hafner, M. S., J. C. Hafner, J. L. Patton, and M. F. Smith. 1987. Macrogeographic patterns of genetic differentiation in the pocket gopher Thomomys um-brinus. Syst. Zool. 36:18-34.
23. Harrison, R. G. 1991. Molecular changes at speciation. Annu. Rev. Ecol. Syst. 22:281-308.
24. Heaney, L. R„ and R. M. Timm. 1985. Morphology, genetics, and ecology of pocket gophers (genus Geo-mys) in a narrow hybrid zone. Biol. J. Linn. Soc. 25: 301-317.
25. Hillis, D. M. 1991. Discriminating between phylogenetic signal and random noise in DNA se-quences. Pages 278-294 in Phylogenetic analysis of DNA sequences (M. M. Miyamoto and J. Cracraft, eds.). Oxford Univ. Press, New York.
26. Hillis, D. M., and J. P. Huelsenbeck. 1992. Signal, noise, and reliability in molecular phylogenetic analyses. J. Hered. 83:189-195.
27. Kishino, H„ and M. Hasegawa. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J. Mol. Evol. 29:170-179.
28. Lansman, R. A., R. O. Shade, J. F. Shapira, and J. C. Avise. 1981. The use of restriction endonucleases to measure mitochondrial DNA sequence relatedness in natural populations. III. Techniques and potential application. J. Mol. Evol. 17:214-226.
29. Lessa, E. P. 1992. Rapid surveying of DNA sequence variation in natural populations. Mol. Biol. Evol. 9:323-330.
30. Lessa, E. P., and J. L. Patton. 1989. Structural constraints, recurrent shapes, and allometry in pocket gophers (genus Thomomys). Biol. J. Linn. Soc. 36: 349-363.
31. Maniatis, T„ E. F. Fritsch, and J. Sambrook. 1982. Molecular cloning. A laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.
32. McKitrick, M. C, and R. M. Zink. 1988. Species concepts in ornithology. Condor 90:1-14.
33. 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 (S. Karlin and E. Nevo, eds.). Academic Press, New York.
34. Nixon, K. C, and Q. D. Wheeler. 1990. An amplification of the phylogenetic species concept. Cla-distics 6:211-223.
35. Nixon, K. C, and Q. D. Wheeler. 1992. Extinction and the origin of species. Pages 119-143 in Extinction and phylogeny (M. J. Novacek and Q. D. Wheeler, eds.). Columbia Univ. Press, New York.
36. Pamilo, P., and M. Nei. 1988. Relationships between gene trees and species trees. Mol. Biol. Evol. 5:568-583.
37. Patton, J. L. 1990. Geomyid evolution: The historical, selective, and random basis for divergence patterns within and among populations. Pages 49-69 in Evolution of subterranean mammals at the or-ganismal and molecular levels (E. Nevo and O. A. Reig, eds.). Alan R. Liss, New York.
38. 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 Univ. Press, New York.
39. Patton, J. L., and R. E. Dingman. 1968. Chromosomal studies of pocket gophers, genus Thomomys. I. The specific status of Thomomys umbrinus (Richardson) in Arizona. J. Mammal. 49:1-13.
40. Patton, J. L., J. C. Hafner, M. S. Hafner, and M. F. Smith. 1979. Hybrid zones in Thomomys bottae pocket gophers: Genetic, phenetic, and ecologic concordance patterns. Evolution 33:860-876.
41. Patton, J. L., and M. F. Smith. 1981. Molecular evolution in Thomomys: Phyletic systematics, para-phyly, and rates of evolution. J. Mammal. 62:493-500.
42. 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, Sunderland, Massachusetts.
43. Patton, J. L., and M. F. Smith. 1990. Evolutionary dynamics of Thomomys bottae pocket gophers, with emphasis on California populations. Univ. Calif. Publ. Zool. 123:1-161.
44. Patton, J. L., and M. F. Smith. 1993. Molecular evidence for mating asymmetry and female choice in a pocket gopher hybrid zone (Thomomys). Mol. Ecol. 2:1-8.
45. 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 Nat. 44:431-440.
46. Rogers, J. S. 1972. Measures of genetic similarity and genetic distance. Univ. Texas Publ. Stud. Genet. vol VIII 7213:145-153.
47. Rogers, M. A. 1991a. Evolutionary differentiation within the northern Great Basin pocket gopher, Thomomys townsendii. I. Morphological variation. Great Basin Nat. 51:109-126.
48. ROGERS, M. A. 1991b. Evolutionary differentiation within the northern Great Basin pocket gopher, Thomomys townsendii. II. Genetic variation and biogeographic considerations. Great Basin Nat. 51:127-152.
49. Rohlf, F. J. 1992. NTSYS-pc, numerical taxonomy and multivariate analysis system, version 1.70. Exeter Software, Setauket, New York.
50. Saiki, R. K., T. L. Bugawan, G. T. Horn, K. B. Mullis, and H. A. Erlich. 1986. Analysis of enzymatically amplified beta-globin and HLA-DQalpha DNA with allele-specific oligonucleotide probes. Nature 324: 163-166.
51. Saiki, R. K, D. H. Gelfand, S. Stoffel, S. J. Scharf, R. Higughi, G. T. Horn, K. B. Mullis, and H. A. Erlich. 1988. Primer-directed enzymatic amplifications of DNA with thermostable DNA polymerase. Science 239:487-491.
52. Sanger, F., S. Kicklon, and A. R. Coulson. 1977. DNA sequencing with chain terminating inhibitors. Proc. Natl. Acad. Sei. USA 74:5463-5467.
53. Smith, M. F„ and J. L. Patton. 1991. Variation in mitochondrial cytochrome b sequence in natural populations of South American akodontine rodents (Muridae: Sigmodontinae). Mol. Biol. Evol. 8:85103.
54. Smith, M. F., W. K. Thomas, and J. L. Patton. 1992. Mitochondrial DNA-like sequence in the nuclear genome of an akodontine rodent. Mol. Biol. Evol. 9:204-215.
55. Sudman, P. D., J. R. Choate, and E. G. Zimmerman. 1987. Taxonomy of chromosomal races of Ceomys bursarius lutescens Merriam. J. Mammal. 68:526-543.
56. Swofford, D. 1991. PAUP: Phylogenetic analysis using parsimony, version 3.0s. Illinois Natural History Survey, Champaign.
57. Templeton, A. R. 1989. The meaning of species and speciation: A genetic perspective. Pages 3-27 in Speciation and its consequences (D. Otte and J. A. Endler, eds.). Sinauer, Sunderland, Massachusetts.
58. Thaeler, C. S., Jr. 1968. An analysis of three hybrid populations of pocket gophers (genus Thomomys). Evolution 22:543-555.
59. Thaeler, C. S., Jr. 1980. Chromosome numbers and systematic relations in the genus Thomomys (Ro-dentia: Geomyidae). J. Mammal. 61:414-422.
60. Wiley, E. O. 1981. Phylogenetics: The theory and practice of phylogenetic systematics. John Wiley & Sons, New York.
61. Wu, C.-I. 1991. Inferences of species phylogeny in relation to segregation of ancient polymorphisms. Genetics 127:429-435.