CytochromebPhylogeny of North American Hares and Jackrabbits (Lepus,Lagomorpha) and the Effects of Saturation in Outgroup Taxa

Molecular Phylogenetics and Evolution

Volumn 11, Issue 2, 1999, Pages 213-221

  Halanych, Kenneth M ^a   Demboski, John R ^b,c   Van Vuuren, Bettine Jansen ^a   Klein, David R ^b   Cook, Joseph A ^b,c  

^a UNIVERSITY OF PRETORIA   (South Africa)

^b UNIVERSITY OF ALASKA FAIRBANKS   (United States)

^c UNIVERSITY OF ALASKA MUSEUM   (United States)

Author keywords

cytochromeb; jackrabbit; Lagomorpha; Lepus; hare; phylogeny; rooting; saturation

Indexed keywords

CYTOCHROME B;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; GENETICS; LAGOMORPH; MOLECULAR EVOLUTION; NORTH AMERICA; PHYLOGENY; SPECIES DIFFERENCE;

ANIMALS; CYTOCHROME B GROUP; EVOLUTION, MOLECULAR; LAGOMORPHA; MODELS, BIOLOGICAL; NORTH AMERICA; PHYLOGENY; SPECIES SPECIFICITY;

EID: 0033087736     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1006/mpev.1998.0581     Document Type: Article

References (58)

1. Adkins R. M., Honeycutt R. L. Evolution of the primate cytochromec. J. Mol. Evol. 38:1994;215-231.
2. Angermann R. The taxonomy of Old WorldLepus. Acta Zool. Fennica. 174:1983;17-21.
3. Azzaroli Puccetti M. L., Corti M., Scanzani A., Civitelli M. V., Cappana E. Karyotypes of two endemic species of hare from Ethiopia,Lepus habessinicusL. starckiL. europaeus. Mammalia. 60:1996;223-230.
4. Baker A. J., Eger J. L., Peterson R. L., Manning T. H. Geographic variation and taxonomy of arctic hares. Acta Zool. Fennica. 174:1983;45-48.
5. Chapman J. A., Flux J. E. C. Introduction and overview of the Lagomorphs. Rabbits, Hares and Pikas, Status Survey and Conservation Action Plan. 1990;IUCN, Gland. p. 1-6.
6. Corbet G. B. Relationships and origins of European lagomorphs. Mammal Rev. 16:1986;105-110.
7. Corbet G. B., Hill J. E. A World List of Mammalian Species. 1980;Comstock, London.
8. Dannelid E. The genusSorex. Mammal Rev. 21:1991;1-20.
9. Dawson M. R. Later Tertiary Leporidae of North America. Univ. Kans. Paleontol. Contrib. Vertebrata. 1958;1-75.
10. Dawson M. R. Evolution of the modern lagomorphs. Myers K., MacInnes C. D. Proceedings of the World Lagomorph Conference. 1981;1-8 Univ. of Guelph Press, Guelph.
11. Dragoo J. W., Bradley R. D., Honeycutt R. L., Templeton J. W. Phylogenetic relationships among the skunks: A molecular perspective. J. Mammal. Evol. 1:1993;255-267.
12. Felsenstein, J. 1993, PHYLIP (phylogeny inference package), Department of Genetics, Univ. of Washington, Seattle, Washington.
13. Flux J. E. C. Introduction to taxonomic problems in hares. Acta Zool. Fennica. 174:1983;7-10.
14. Flux J. E. C., Angermann R. The hares and jackrabbits. Chapman J. A., Flux J. E. C. Rabbits, Hares and Pikas, Status Survey and Conservation Action Plan. 1990;61-94 IUCN, Gland.
15. Flux J. E., Flux M. M. Taxonomy and distribution of East African hares. Acta Zool. Fennica. 174:1983;41-43.
16. González F. X., Cervantes F. A. Karyotype of the white-sided jackrabbit (Lepus callotis. Southwest. Nat. 41:1996;93-95.
17. Graybeal A. The phylogenetic utility of cytochromeb: Mol. Phylogenet. Evol. 2:1993;256-269.
18. Groves P., Shields G. Phylogenetics of the Caprinae based on cytochromeb. Mol. Phylogenet. Evol. 5:1996;467-476.
19. Gureev A. A. Zaitzeobrazniye (Lagomorpha). Fauna SSSR. 3:1964.
20. Halanych K. M. Testing hypotheses of chaetognath origins: Long branches revealed by 18S rDNA. Syst. Biol. 45:1996;223-246.
21. Halanych K. M., Robinson T. J. Phylogenetic relationships of cottontails (Sylvilagus, Mol. Phylogenet. Evol. 7:1997;294-302.
22. Halanych K. M., Robinson T. J. The utility of cytochromeb. J. Mol. Evol. 48:1999;369-379.
23. Hendy M. D., Penny D. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38:1989;297-309.
24. Hibbard C. The origin of the P3 pattern ofSylvilagus, Caprolagus, Oryctolagus,Lepus. J. Mammal. 44:1963;1-15.
25. Hillis D. M., Huelsenbeck J. P. Signal, noise, and reliability in molecular phylogenetic analysis. J. Hered. 83:1992;189-195.
26. Hillis D. M., Larson A., Davis S. K., Zimmer E. A. Nucleic Acids III: Sequencing. Hillis D. M., Moritz C. Molecular Systematics. 1990;318-370 Sinauer, Sunderland.
27. Hoffmann R. S. Order Lagomorpha. Wilson D. E., Reeder D. M. Mammal Species of the World: A Taxonomic and Geographic Reference. 1993;807-827 Smithsonian Inst. Press, Washington.
28. Irwin D. M., Árnason U. Cytochromeb. J. Mammal. Evol. 2:1994;37-55.
29. Irwin D. M., Kocher T. D., Wilson A. C. Evolution of the cytochromeb. J. Mol. Evol. 32:1991;128-144.
30. Jin L., Nei M. Relative efficiencies of the maximum-parsimony and distance-matrix methods of phylogeny construction for restriction data. Mol. Biol. Evol. 8:1991;356-365.
31. Kishino H., Hasegawa M. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J. Mol. Evol. 29:1989;170-179.
32. Kocher T. D., Thomas W. K., Meyer W. K., Edwards S. V., Pääbo S., Villablanca F. X., Wilson A. C. Dynamics of mitochondrial DNA evolution in animals: Amplification and sequencing with conserved primers. Proc. Natl. Acad. Sci. USA. 86:1989;6196-6200.
33. Kusukawa N., Uemori T., Asada K., Kato I. Rapid and reliable protocol for direct sequencing of material amplified by the polymerase chain reaction. Biotechniques. 9:1990;66-72.
34. Lessa E., Cook J. A. The molecular phylogenetics of tuco-tucos (genusCtenomys, Mol. Phylogenet. Evol. 9:1998;88-99.
35. Maddison D. R., Ruvolo M., Swofford D. L. Geographic origins of human mitochondrial DNA: Phylogenetic evidence from control region sequences. Syst. Biol. 41:1992;111-124.
36. Maddison, W. P. Maddison, D. R. 1992, MacClade: Analysis of phylogeny and character evolution, version 3, Sinauer, Sunderland, Massachusetts.
37. Maniatis T., Fritsch E. F., Sambrook J. Molecular Cloning. A Laboratory Manual. 1982;Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
38. Matthee C. A., Robinson T. J. Molecular phylogeny of the springhare,Pedetes capensis, Mol. Biol. Evol. 14:1997;20-29.
39. Meyer A. Shortcomings of the cytochromeb. TREE. 9:1994;378-380.
40. Miller S. A., Dykes D. D., Polesky H. F. A simple salting procedure for extracting DNA from human nucleated cells. Nucleic Acids Res. 16:1988;215.
41. Miyamoto M. M., Boyle S. M. The potential importance of mitochondrial DNA sequence data to eutherian mammal phylogeny. Fernholm B., Bremer K., Jörnvall H. The Hierarchy of Life. 1989;437-450 Elsevier, Amsterdam.
42. Muse S. V., Gaut B. S. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol. Biol. Evol. 11:1994;715-724.
43. Nelson E. W. The rabbits of North America. North Am. Fauna. 29:1909;1-314.
44. Olsen G. J., Matsuda H., Hagstrom R., Overbeek R. fastDNAml: A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput. Appl. Biosci. 10:1994;41-48.
45. Pääbo S., Wilson A. C. Polymerase chain reaction reveals cloning artifacts. Nature. 334:1988;387-388.
46. Palumbi S. R. Nucleic acids II: The polymerase chain reaction. Hillis D. M., Mortiz C., Mable B. K. Molecular Systematics. 1996;205-248 Sinauer, Sunderland.
47. Pérez-Suárez G., Palacios F., Boursot P. Speciation and paraphyly in western Mediterranean hares (Lepus castroviejoi, L.europaeus, L. grantensis,L. capensis. Biochem. Genet. 32:1994;423-436.
48. Reig O. A. Karyotypic repatterning as one triggering factor in cases of explosive speciation. Fontevilla A. Evolutionary Biology of Transient Unstable Populations. 1989;246-289 Springer-Verlag, Berlin.
49. Robinson T. J., Osterhoff D. R. Protein variation and its systematic implications for the South African Leporidae (Mammalia: Lagomorpha). Animal Blood Groups Biochem. Genet. 14:1983;139-149.
50. Robinson T. J., Elder F. F. B., Chapman J. A. Karyotype conservatism in the genusLepus. Can. J. Genet. Cytol. 25:1983;540-544.
51. Smith M. F., Patton J. L. The diversification of South American murid rodents: Evidence from mitochondrial DNA sequence data for the akodontine tribe. Biol. J. Linn. Soc. 50:1993;149-177.
52. Sudman P. D., Hafner M. S. Phylogenetic relationships among Middle American Pocket Gophers (GenusOrthogeomys. Mol. Phylogenet. Evol. 1:1992;17-25.
53. Sullivan J., Holsinger K. E., Simon C. Among-site rate variation and phylogenetic analysis of 12S rRNA in Sigmodontine rodents. Mol. Biol. Evol. 12:1995;988-1001.
54. Swofford, D. L. 1993, PAUP: Phylogenetic analysis using parsimony, Illinois Natural History Survey, Champaign, IL.
55. Thompson J. D., Higgins D. G., Gibson T. J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:1994;4673-4680.
56. Thulin C.-G., Jaarola M., Tegelström H. The occurrence of mountain hare mitochondrial DNA in wild brown hares. Mol. Ecol. 6:1997;463-467.
57. Walsh P. S., Metzger D. A., Higuchi R. Chelex 100 as a medium for simple extraction of DNA from PCR-based typing from forensic material. Biotechniques. 19:1991;506-513.
58. Wheeler W. C. Nucleic acid sequence phylogeny and random outgroups. Cladistics. 6:1990;363-368.