A molecular supermatrix of the rabbits and hares (Leporidae) allows for the identification of five intercontinental exchanges during the Miocene

Systematic Biology

Volumn 53, Issue 3, 2004, Pages 433-447

  Matthee, Conrad A ^a   Jansen Van Vuuren, Bettine ^a   Bell, Diana ^b   Robinson, Terence J ^a  

^a STELLENBOSCH UNIVERSITY   (South Africa)

^b UNIVERSITY OF EAST ANGLIA   (United Kingdom)

Author keywords

Evolution; Lagomorpha; Mammalia; Nuclear DNA; Phylogeny; Systematics

Indexed keywords

MITOCHONDRIAL DNA; NUCLEAR PROTEIN; PRIMER DNA;

ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; COMPARATIVE STUDY; DEMOGRAPHY; DNA SEQUENCE; GENETICS; GEOGRAPHY; GEOLOGY; LAGOMORPH; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; POPULATION DYNAMICS; SEQUENCE ALIGNMENT; STATISTICAL MODEL;

ANIMALS; BASE SEQUENCE; BAYES THEOREM; DEMOGRAPHY; DNA PRIMERS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GEOGRAPHY; GEOLOGY; LAGOMORPHA; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; NUCLEAR PROTEINS; PHYLOGENY; POPULATION DYNAMICS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

INSERTION SEQUENCES; LAGOMORPHA; LEPORIDAE; LEPUS; MAMMALIA; ORYCTOLAGUS CUNICULUS;

EID: 3242703950     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/10635150490445715     Document Type: Article

References (76)

1. Allard, M. W., and R. L. Honeycutt. 1992. Nucleotide sequence variation in the mitochondrial 12S rRNA gene and the polyphyly of African mole-rats (Rodentia: Bathyergidae). Mol. Biol. Evol. 9:27-40.
2. Angerman, R., J. E. C. Flux, J. A. Chapman, and A. T. Smit. 1990. Lagomorph Classification. Pages 7-13 in Rabbits, hares and pikas: Status conservation action plan (J. A. Chapman and J. E. C. Flux, eds.). International Union for Conservation of Nature and Natural Resources, Gland, Switzerland.
3. Baker, R. H., and R. DeSalle. 1997. Multiple sources of character information and the phylogeny of Hawaiian drosophilids. Syst. Biol. 46:654-673.
4. Bollback, J. P. 2002. Bayesian model adequacy and choice in phylogenetics. Mol. Biol. Evol. 19:1171-1180.
5. Buckley, T. R. 2002. Model misspecification and probabilistic tests of topology: Evidence from empirical data sets. Syst. Biol. 51:509-523.
6. Buckley, T. R., P. Arensburger, C. Simon, and G. K. Chambers. 2002. Combined data, Bayesian phylogenetics, and the origin of the New Zealand cicada genera. Syst. Biol. 51:4-18.
7. Buckley, T. R., C. Simon, and G. K. Chambers. 2001. Exploring among-site rate variation models in a maximum likelihood framework using empirical data: Effects of model assumptions on estimates of topology, branch lengths, and bootstrap support. Syst. Biol. 50:67-86.
8. Can, D. N., A. V. Abramov, A. N. Tikhonov, and A. O. Averianov. 2001. Annamite striped rabbit Nesolagus timminsi in Vietnam. Acta Theriol. 46:437-440.
9. Chapman, J. A., and G. Ceballos. 1990. The Cottontails. Pages 95-110 in Rabbits, hares and pikas: Status conservation action plan (J. A. Chapman and J. E. C. Flux, eds.). International Union for Conservation of Nature and Natural Resources, Gland, Switzerland.
10. Chapman, J. A., K. L. Cramer, N. J. Dippenaar, and T. J. Robinson. 1992. Systematics and biogeography of the New England cotton-tail, Sylvilagus transitionalis (Bangs, 1895), with the description of a new species from the Appalachian Mountains. Proc. Biol. Soc. Washington 105:841-866.
11. Chapman, J. A., and J. E. C. Flux. 1990. Introduction and overview of the Lagomorpha. Pages 1-6 in Rabbits, hares and pikas: Status conservation action plan (J. A. Chapman and J. E. C. Flux, eds.). International Union for Conservation of Nature and Natural Resources, Gland, Switzerland.
12. Cognato, A. I., and A. P. Vogler. 2001. Exploring data interaction and nucleotide alignment in a multiple gene analysis of Ips (Coleoptera: Scolytinae). Syst. Biol. 50:758-780.
13. Corbet, G. B. 1983. A review of classification in the family Leporidae. Acta Zool. Fennica 174:11-15.
14. Dawson, M. 1958. Later Tertiary Leporidae of North America. Univ. Kansas Paleont. Contr., Vertebrate 6:1-75.
15. Dawson, M. R. 1981. Evolution of modern leporids. Pages 1-8 in Proceedings of the World Lagomorph Conference (K. Myers and C. D. MacInnes, eds.). University of Guelph Press, Ontario.
16. Diersing, V. E. 1984. Lagomorphs. Pages 241-254 in Orders and Families of recent mammals of the world (S. Anderson and J. Knox Jones Jr., eds.). John Wiley and Sons, New York.
17. Dowton, M., and A. D. Austin. 2002. Increased congruence does not necessarily indicate increased phylogenetic accuracy-the behavior of the incongruence length difference test in mixed-model analyses. Syst. Biol. 51:19-31.
18. Ellerman, J. R., and T. C. S. Morrison-Scott. 1951. Checklist of palearctic and Indian mammals 1758-1946. British Museum (Natural History), London.
19. Farris, J. S., M. Kallersjo, A. G. Kluge, and C. Bult. 1995. Constructing a significance test for incongruence. Syst. Biol. 44:570-572.
20. Flux, J. E. C., and R. Angermann. 1990. The hares and jackrabbits. Pages 61-94 in Rabbits, hares and pikas: Status conservation action plan (J. A. Chapman and J. E. C. Flux, eds.). International Union for Conservation of Nature and Natural Resources, Gland, Switzerland.
21. Frey, J. K., R. D. Fisher, and L. A. Ruedas. 1997. Identification and restriction of the type locality of the Manzano Mountains cottontail, Sylvilagus cognatus Nelson, 1907 (Mammalia: Lagomorpha: Leporidae). Proc. Biol. Soc. Washington 110:329-331.
22. Gatesy, J., G. Amato, E. Vrba, G. Schaller, and R. DeSalle. 1997. A cladistic analysis of mitochondrial ribosomal DNA from the Bovidae. Mol. Phylogenet. Evol. 7:303-319.
23. Gatesy, J., C. Matthee, R. DeSalle, and C. Hayashi. 2002. Resolution of a supertree/supermatrix paradox. Syst. Biol. 51:652-664.
24. Gatesy, J., M. Milinkovitch, V. Waddell, and M. Stanhope. 1999. Stability of cladistic relationships between Cetacea and higher-level artiodactyl taxa. Syst. Biol. 48:6-20.
25. Gissi, C., A. Gullberg, and U. Arnason. 1998 The complete mitochondrial DNA sequence of the rabbit, Oryctolagus cuniculus. Genomics 50:161-169.
26. Halanych, K. M., and T. J. Robinson. 1997. Phylogenetic relationships of cottontails (Sylvilagus, Lagomorpha): Congruence of 12S rDNA and cytogenetic data. Mol. Phylogenet. Evol. 7:294-302.
27. Halanych, K. M., and T. J. Robinson. 1999. Multiple substitutions affect the phylogenetic utility of cytochrome b and 12S rDNA data: Examining a rapid radiation in leporid (Lagomorpha) evolution. J. Mol. Evol. 48:369-379.
28. Halanych, K. M., J. R. Demboski, B. Jansen van Vuuren, D. R. Klein, and J. A. Cook. 1999. Cytochrome b phylogeny of North American hares and jackrabbits (Lepus, Lagomorpha) and the effects of saturation in outgroup taxa. Mol. Phylogenet. Evol. 11:213-221.
29. 3 pattern of Sylvilagus, Caprolagus, Oryctolagus and Lepus. J. Mammal. 44:1-15.
30. Hillis, D. M., B. K. Mable, A. Larson, S. K. Davis, and E. A. Zimmer. 1996. Nucleic acids IV: Sequencing and cloning. Pages 321-381 in Molecular systematics, 2nd ed. (D. M. Hillis, C. Moritz, and B. K. Mable, eds.). Sinauer Associates, Sunderland, MA.
31. Hillis, D. M., D. D. Pollock, J. A. McGuire, and D. J. Zwickl. 2003. Is sparse taxon sampling a problem for phylogenetic inference? Syst. Biol. 52:124-126.
32. Huelsenbeck, J. P. 2002. Testing a covariotide model of DNA substitution. Mol. Biol. Evol. 19:698-707.
33. Huelsenbeck, J. P., and F. Ronquist. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755.
34. Irwin, D. M., T. D. Kocher, and A. C. Wilson. 1991. Evolution of the cytochrome b gene of mammals. J. Mol. Evol. 32:128-144.
35. Källersjö, M., V. A. Albert, and J. S. Farris. 1999. Homoplasy increases phylogenetic structure. Cladistics 15:91-93.
36. Kelsey, C. R., K. A. Crandall, and A. F. voevodin. 1999. Different models, different trees: The geographic origin of PTLV-I. Mol. Phylogenet. Evol. 13:336-347.
37. Kishino, H., J. L. Thorne, and W. J. Bruno. 2001. Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol. Biol. Evol. 18:352-361.
38. Kocher, T. D., W. K. Thomas, A. Meyer, S. V. Edwards, S. Pääbo, F. X. Villablanca, and A. C. Wilson. 1989. Dynamics of mitochondrial DNA evolution in animals: Amplification and sequencing with conserved primers. Proc. Natl. Acad. Sci. U. S. A. 86:6196-6200.
39. Kummel, B. 1970. History of the earth: An introduction to historical geology. W. H. Freeman and Company, San Francisco.
40. Matthee, C. A., J. D. Burzlaff, J. F. Taylor, and S. K. Davis. 2001. Mining the mammalian genome for artiodactyl systematics. Syst. Biol. 50:367-390.
41. Matthee, C. A., and S. K. Davis. 2001. Molecular insights into the evolution of the family Bovidae: A nuclear DNA perspective. Mol. Biol. Evol. 18:1220-1230.
42. Matthee, C. A., and T. J. Robinson. 1996. Mitochondrial DNA differentiation among geographical populations of Pronolagus rupestris, Smith's red rock rabbit (Mammalia: Lagomorpha). Heredity 76:514-523.
43. Matthee, C. A., and T. J. Robinson. 1999. Cytochrome b phylogeny of the family bovidae: Resolution within the alcelaphini, antilopini, neotragini, and tragelaphini. Mol. Phylogenet. Evol. 12:31-46.
44. Meng, J., A. R. Wyss, M. R. Dawson, and Z. Renjie. 1994. Primitive fossil rodent from Inner Mongolia and its implications for mammalian phylogeny. Nature 370:134-136.
45. Morrone, J. J., and J. V. Crisci. 1995. Historical biogeography: Introduction to methods. Ann. Rev. Ecol. Syst. 26:373-401.
46. Murphy, W. J., E. Eizirik, W. E. Johnson, Y. P. Zhang, O. A. Ryder, and S. J. O'Brien. 2001. Molecular phylogenetics and the origins of placental mammals. Nature 409:614-618.
47. Murrell, A., N. J. Campbell, and S. C. Barker. 2001. A total-evidence phylogeny of ticks provides insights into the evolution of life cycles and biogeography. Mol. Phylogenet. Evol. 21:244-258.
48. Nowak, R. M. 1999. Walker's mammals of the world, 6th ed. John Hopkins University Press, Baltimore.
49. Pääbo, S., and A. C. Wilson. 1988. Polymerase chain reaction reveals cloning artifacts. Nature 334:387-388.
50. Pollock, D. D., D. J. Zwickl, J. A. McGuire, and D. M. Hillis. 2002. Increased taxon sampling is advantageous for phylogenetic inference. Syst. Biol. 51:664-671.
51. Posada, D., and K. A. Crandall. 1998. Modeltest: Testing the model of DNA substitution. Bioinformatics 14:817-818.
52. Posada, D., and K. A. Crandall. 2001. Selecting the best-fit model of nucleotide substitution. Syst. Biol. 50:580-601.
53. Robinson-Rechavi, M., and Huchon, D. 2000. RRTree: Relative-rate tests on a tree. Bioinformatics 16:296-297.
54. Robinson, T. J., F. F. B. Elder, and J. A. Chapman. 1984. Evolution of chromosomal variation in cottontails, genus Sylvilagus (Mammalia: Lagomorpha). 2. Sylvilagus audubonii, S. idahoensis, S. nuttalli and S. palastris. Cytogenet. Cell Genet. 38:282-289.
55. Robinson, T. J., F. Yang, and W. R. Harrison. 2002. Chromosome painting refines the history of genome evolution in hares and rabbits (order Lagomorpha). Cytogenet. Genome Res. 96:223-227.
56. Ronquist, F. 1997. Dispersal-vicariance analysis: A new approach to the quantification of historical biogeography. Syst. Biol. 46:195-203.
57. Ronquist, F., and J. P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
58. Springer, M. S., L. J. Hollar, and A. Burk. 1995. Compensatory substitutions and the evolution of the mitochondrial 12S rRNA gene in mammals. Mol. Biol. Evol. 12:1138-1150.
59. Springer, M. S., W. J. Murphy, E. Eizirik, and S. J. O'Brien. 2003. Placental mammal diversification and the Cretaceous-Tertiary boundary. Proc. Natl. Acad. Sci. U. S. A. 100:1056-1061.
60. Su, C., and M. Nei. 1999. Fifty-million year old polymorphism at an immunoglobulin variable region gene locus in the rabbit evolutionary lineage. Proc. Natl. Acad. Sci. U. S. A. 96:9710-9715.
61. Sullivan, J., and D. L. Swofford. 2001. Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution pattern are violated? Syst. Biol. 50:723-729.
62. Surridge, A. K., R. J. Timmins, G. M. Hewitt, and D. J. Bell. 1999. Striped rabbits in Southeast Asia. Nature 400:726.
63. Swofford, D. L. 2000. PAUP: Phylogenetic Analysis using Parsimony (and other methods). Version 4. Sinauer Associates, Sunderland, MA.
64. Thorne, J. L., and H. Kishino. 2002. Divergence time and evolutionary rate estimation with multilocus data. Syst. Biol. 51:689-702.
65. Thorne, J. L., H. Kishino, and I. S. Painter. 1998. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15:1647-1657.
66. Voorhies, M. R., and C. L. Timperley. 1997. A new Pronotolagus (Lagomorpha: Leporidae) and other leporids from the Valentine railway quarriesw (Barstovian, Nebraska), and the archaeolagine-leporine transition. J. Ver. Paleon. 17:725-737.
67. Waddell, P. J., Y. Cao, M. Hasegawa, and D. P. Mindell. 1999. Assessing the Cretaceous superordinal divergence times within birds and placental mammals by using whole mitochondrial protein sequences and an extended statistical framework. Syst. Biol. 48:119-137.
68. Whelan, S., P. Lio, and N. Goldman. 2001. Molecular phylogenetics: State-of-the-art methods for looking into the past. Trends Genet. 7:262-272.
69. White, J. A. 1991. North American Leporidae (Mammalia, Lagomorpha) from Late Miocene (Clarendonian) to late Pliocene (Blancan). J. Ver. Paleon. 1:67-89.
70. Whiteford, C. E. M. 1995. Molecular phylogeny of the genus Pronolagus (Mammalia: Lagomorpha) and the use of morphological and molecular characters in the delineation of P. rupestris. MSc Thesis, University of Pretoria.
71. Yamada, F., M. Takaki, and H. Suzuki. 2002. Molecular phylogeny of Japanese Leporidae, the Amami rabbit Pentalagus furnessi, the Japanese hare Lepus brachyurus, and the mountain hare Lepus timidus, inferred from mitochondrial DNA sequences. Genes Genet. Syst. 77:107-116.
72. Yang, Z. 1997. PAML: A program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555-556.
73. Yang, Z., and A. D. Yoder. 2003. Comparison of Likelihood and Bayesian methods for estimating divergence times using multiple gene loci and calibration points, with application to a radiation of cute-looking mouse lemus species. Syst. Biol. 52:1-12.
74. Yu, N., C. Zheng, Y. P. Zhang, and W. H. Li. 2000. Molecular systematics of pikas (genus Ochotona) inferred from mitochondrial DNA sequences. Mol. Phylogenet. Evol. 16:85-95.
75. Zachos, J., M. Pagani, L. Sloan, E. Thomas, and K. Billups. 2001. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292:686-693.
76. Zwickl, D. J., and D. M. Hillis. 2002. Increased taxon sampling greatly reduces phylogenetic error. Syst. Biol. 51:588-598.