Molecular genetics of Rhabdomys pumilio subspecies boundaries: MtDNA phylogeography and karyotypic analysis by fluorescence in situ hybridization

Molecular Phylogenetics and Evolution

Volumn 28, Issue 3, 2003, Pages 564-575

  Rambau, Ramugondo V ^a   Robinson, Terence J ^a   Stanyon, Roscoe ^b  

^a STELLENBOSCH UNIVERSITY   (South Africa)

^b NATIONAL CANCER INSTITUTE   (United States)

Author keywords

Cytochrome b; Fluorescence in situ hybridization; Phylogeography; Rhabdomys pumilio

Indexed keywords

MURIDAE; RHABDOMYS DILECTUS; RHABDOMYS PUMILIO;

EID: 0344099435     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1055-7903(03)00058-7     Document Type: Article

References (89)

1. Applied Biosystems, 1994. Sequence Navigator DNA and Protein sequence comparison Software, Perkin-Elmer, Forster City, CA.
2. Arctander, P., 1995. Comparison of a mitochondrial gene and a corresponding nuclear pseudogene. Proc. R. Soc. Lond. B 262, 13-19.
3. Avery, D.M., 1991. Late quaternary incidence of some micromammalian species in Natal. Durban Mus. Novit. 16, 1-11.
4. Avise, J.C., Aquadro, C.F., 1982. A comparative summary of genetic distances in the vertebrates. Evol. Biol. 15, 151-184.
5. Avise, J.C., 1994. Molecular Markers, Natural History, and Evolution. Chapman Hall, New York.
6. Barome, P-O., Lymberakis, P., Monnerot, M., Gautun, J-C., 2001. Cytochrome b sequences reveal Acomys minous (Rodentia, Muridae) paraphyly and answer the question about the ancestral karyotype of Acomys dimidiatus. Mol. Phylogenet. Evol. 18 (1), 37-46.
7. Bonnefille, R., 1985. Evolution of the continental vegetation: the palaeobotanical record from East Africa. S. Afr. J. Sci. 81, 267-270.
8. Bradley, R.D., Tiemann-Boege, I., Kilpatrick, C.W., Schmidly, D.J., 2000. Taxonomic status of Peromyscus boylii sacarensis: inferences from DNA sequences of the mitochondrial cytochrome b gene. J. Mammal. 81 (3), 875-884.
9. Bradley, R.D., Baker, R.J., 2001. A test of the genetic species concept: cytochrome b sequences and mammals. J. Mammal. 82 (4), 960-973.
10. Britton-Davidian, J., Catalan, J., Granjon, L., Duplantier, J-M., 1995. Chromosomal phylogeny and evolution in the genus Mastomys (Mammalia, Rodentia). J. Mammal. 76 (1), 248-262.
11. Bush, G.L., Case, S.M., Wilson, A.C., Patton, J.L., 1977. Rapid speciation and chromosomal evolution in mammals. Proc. Natl. Acad. Sci. USA 74 (9), 3942-3946.
12. Chimimba, CT., 2001. Infraspecific morphometric variation in Aethomys namaquensis (Rodentia: Muridae) from southern Africa. J. Zool., Lond. 253, 191-210.
13. Christian, D.P., 1977. Physiological correlates of demographic patterns in three sympatric Namib desert rodents. Phys. Zool. 52, 329-339.
14. Christian, D.P., 1979. Comparative demography of three Namib desert rodents: responses to the provision of supplementary water. J. Mammal. 60 (4), 679-690.
15. Churchfield, S., 1985. Diets of two syntopic mammals in the Inyanga National Park Zimbabwe. S. Afr. J. Zool. 20 (2), 65-67.
16. De Graaff, G., 1961. A short survey of investigations of fossil rodents in African deposits. S. Afr. J. Sci. 57, 191-196.
17. De Graaff, G., 1981. The Rodents of Southern Africa. Butterworths, Durban.
18. Denys, C., Jaeger, J-J., 1986. A biostratigraphic problem: the case of the East African Plio-Pleistocene rodent faunas. Modern. Geol. 10, 215-233.
19. Ducroz, J-F., Volobouev, V., Granjon, L., 1998. A molecular perspective on the systematics and evolution of the genus Arvicanthis (Rodentia, Muridae): inferences from complete cytochrome b gene sequences. Mol. Phylogenet. Evol. 10 (1), 104-117.
20. Ducroz, J-F., Granjon, L., Lombard, M., Volobouev, V., 1999. Comparative chromosome analysis (R-and C-bands) of two South African murid species, Lemniscomys rosalia and Rhabdomys pumilio (Rodentia, Murinae). Cytogenetic Cell Genet. 87, 69-74.
21. Ducroz, J-F., Volobouev, V., Granjon, L., 2001. An assessment of the systematics of Arvicanthine rodents using mitochondrial DNA sequences: evolutionary and biogeographical implications. J. Mammal. Evol. 8 (3), 173-206.
22. Ellerman, J.R., 1941. The Families and Genera of Living Rodents. British Museum, London.
23. Fedorov, V.B., Stenseth, N.C., 2001. Glacial survival of the Norwegian lemming (Lemmus lemmus) in Scandinavia: inference from mitochondrial DNA variation. Proc. R. Soc. Lond. 268, 809-814.
24. Feldhamer, G.A., Drickamer, L.C., Vessey, S.H., Merritt, J.F., 1999. Mammalogy: Adaptation, Diversity, and Ecology. McGraw-Hill, Boston.
25. Felsenstein, J., 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
26. Ferguson, J.W.H., 2002. On the use of genetic divergence for identifying species. Biol. J. Linn. Soc. 75, 509-516.
27. Geise, L., Smith, M.F., Patton, J.L., 2001. Diversification in the genus Akodon (Rodentia: Sigmodontinae) in southeastern South America: mitochondrial DNA sequence analysis. J. Mammal. 82 (1), 92-101.
28. Gillespie, J.H., 1986. Variability of evolutionary rates of DNA. Genetics 113, 1077-1091.
29. Graphodatsky, A.S., Yang, F., O'Brien, P.C.M., Perelman, P., Milne, B.S., Serdukova, N., Kawada, S-I., Ferguson-Smith, M.A., 2001. Phylogenetic implications of the 38 putative ancestral chromosome segments for four canid species. Cytogenet. Cell Genet. 92, 243-247.
30. Halanych, K.M., Demboski, J.R., Jansen van Vuuren, B., Klein, D.R., Cook, J., 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.
31. Harris, D., Rogers, D.S., Sullivan, J., 2000. Phylogeography of Peromyscus furvus (Rodentia; Muridae) based on cytochrome b sequence data. Mol. Ecol. 9, 2129-2135.
32. Harrison, J.A., Allan, D.G., Underhill, L.G., Herremans, M., Tree, A.J., Parker, V., Brown, C.J., 1997. The Atlas of Southern African Birds. BirdLife South Africa, Johannesburg.
33. Irwin, D.M., Kocher, T.D., Wilson, A.C., 1991. Evolution of cytochrome b gene of mammals. J. Mol. Evol. 32, 128-144.
34. Jacobs, L.L., Pilbeam, D., 1980. Of mice and men: fossil based divergence dates and molecular "clocks". J. Hum. Evol. 9, 551-555.
35. Johns, G.C., Avise, J.C., 1998. A comparative summary of genetic distances in the vertebrate from the mitochondrial cytochrome b gene. Mol. Biol. Evol. 15 (11), 1481-1490.
36. Jolley, T.W., Honeycutt, R.L., Bradley, R.D., 2000. Phylogenetic relationships of pocket gophers (genus Geomys) based on the mitochondrial 12S rRNA gene. J. Mammal. 81 (4), 1025-1034.
37. King, M., 1993. Species Evolution: The Role of Chromosome Change. University Press, Cambridge.
38. Kingdon, J., 1974. East African Mammals: An Atlas of Evolution in Africa. Academic Press, London.
39. Kocher, T.D., Thomas, W.K., Meyer, A., Edwards, S.V., Paabo, S., Villablanca, F.X., Wilson, A.C., 1989. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc. Natl. Acad. Sci. 86, 6196-6200.
40. Lande, R., 1985. The fixation of chromosomal rearrangements in a subdivided population with local extinction and colonization. Heredity 54, 323-332.
41. Lin, C.C., Sasi, R., Fan, Y-S., Chen, Z-Q., 1991. New evidence for tandem chromosome fusions in the karyotypic evolution of Asian muntjacs. Chromosoma 101, 19-24.
42. Lindesay, J., 1998. Past climates of Southern Africa. In: Hobbs, J.E., Lindesay, J.A., Bridgman, H.A. (Eds.), Climates of the Southern Continent: Present, Past and Future. Wiley, New York, pp. 161-206, 5-61.
43. Maddison, W.P., Maddison, D.R., 1992. McClade: analysis of phylogeny and character evolution, version v3.04 Sinauer, Sutherland, MA.
44. Mahida, H., Campbell, G.K., Taylor, P.J., 1999. Genetic variation in Rhabdomys pumilio (Sparrman, 1784) - an allozyme study. S. Afr. J. Zool. 34 (3), 91-101.
45. Maniatis, T., Fritsch, E.F., Sambrook, J., 1982. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory, USA.
46. Martin, A.P., Palumbi, S.R., 1993. Body size, metabolic rate, generation time, and the molecular clock. Proc. Natl. Acad. Sci. USA 90, 4087-4091.
47. Mayr, E., 1963. Animal Species and Evolution. McGraw-Hill Press, New York.
48. Mayr, E., Ashlock, P.B., 1991. Principles of Systematic Biology. McGraw-Hill, New York.
49. Meester, J., Rautenbach, I.L., Dippenaar, N.J., Baker, C.M., 1986. Classification of southern African mammals. Transvaal Mus. Monogr. 5, 1-359.
50. Musser, G.G., 1987. The occurrence of Hydromys (Rodentia: Muridae) in early Pleistocene Siwalik strata in northern Pakistan and its bearing on biogeographic affinities between Indian and Northeastern African murine faunas. Am. Mus. Nov. 10024 (2883), 1-36.
51. Nevo, E., 1978. Genetic variation in natural populations: patterns and theory. Theoret. Pop. Biol. 13, 121-177.
52. Paabo, S., Wilson, A.C., 1988. Polymerase chain reaction reveals cloning artifacts. Nature 334, 387-388.
53. Patridge, T.C., Wood, B.A., de Menocal, P.B., 1995. The influence of global climatic change and regional uplift on large-mammalian evolution in east and southern Africa. In: Vrba, E.S., Denton, G.H., Partridge, T.C., Burckle, L.H. (Eds.), Paleoclimate and Evolution with Emphasis on Human Origins. Yale University Press, London, pp. 385-424.
54. Peppers, L.L., Bradley, R., 2000. Cryptic species in Sigmodon hispidus: evidence from DNA sequences. J. Mammal. 81 (2), 332-343.
55. Perrin, M.R., 1980. The feeding habits of two co-existing rodents, Rhabdomys pumilio (Sparrman, 1784) and Otomys irroratus (Brants, 1827). Acta Oecol. Gener, 1, 71-89.
56. Pillay, N., 2000a. Reproductive isolation in three populations of the striped mouse Rhabdomys pumilio: interpopulation breeding studies. Mammalia 64, 461-470.
57. Pillay, N., 2000b. Female preference and reproductive isolation in populations of the striped mouse Rhabdomys pumilio. Behaviour 137, 1431-1441.
58. Pocock, T.N., 1987. Plio-pleistocene fossil mammalian microfauna of southern Africa - A preliminary report including description of two new fossil muroid genera (Mammalia: Rodentia). Palaeont. Afr. 26 (7), 69-91.
59. Posada, D., Crandall, K.A., 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14 (9), 817-818.
60. Rambau, R.V., Elder, F.F.B., Robinson, T.J., 2001. Chromosome evolution in the vlei rat, Otomys irroratus (Muridae: Otomyinae): a compound chromosomal rearrangement separates two major cytogenetic groups. Cytogenet. Cell Genet. 93, 253-257.
61. Rambaut, A., Bromham, L., 1998. Estimating divergence dates from molecular sequences. Mol. Biol. Evol. 15, 442-448.
62. Riddle, B.R., Hafner, D.J., Alexander, L.F., 2000. Phylogeography and systematics of the Peromyscus eremicus species group and the historical biogeography of North American warm regional deserts. Mol. Phylogenet. Evol. 17 (2), 145-160.
63. Roberts, A., 1951. The Mammals of South Africa. The mammals of South Africa' Book Fund, Johannesburg.
64. Robinson, M., Gouy, M., Gautier, C., Mouchiroud, D., 1998. Sensitivity of the relative-rate test to taxonomic sampling. Mol. Biol. Evol. 15 (9), 1091-1098.
65. Robinson-Rechavi, M., Huchon, D., 2000. RRTree: Relative-Rate Tests between groups of sequences on a phylogenetic tree. Bioinformatics 16 (3), 296-297.
66. Rourke, J., Wiens, D., 1977. Convergent floral evolution in South Africa and Australian Proteaceae and its possible bearing on pollution by non-flying mammals. Ann. Mo. Bot. Gdn 64, 1-17.
67. Rowe-Rowe, D.T., 1986. Stomach contents of small mammals from the Drakensberg, South Africa. S. Afr. J. Wildlife Res. 16, 32-35.
68. Saitou, N., Nei, M., 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
69. Schneider, S., Roessli, D., Excoffier, L., 2000. Arlequin: a software for population genetics data analysis. Ver. 2.0. Genetics and Biometry Laboratory, Department of Anthropology, University of Geneva.
70. Shi, L., Ye, Y., Duan, X., 1980. Comparative cytogenetic studies on the red muntjac, Chinese muntjac and their F1 hybrids. Cytogenet. Cell Genet. 26, 22-27.
71. Skinner, J.D., Smithers, H.N., 1990. The Mammals of the Southern African Subregion. University of Pretoria, Pretoria.
72. Smith, S., 1990. Cytosystematic evidence against monophyly of the Peromyscus boylii species group (Rodentia: Cricetidae). J. Mammal. 71 (4), 654-667.
73. Smith, M.F., Patton, J.L., 1993. The diversification of South American murid rodents: evidence from mitochondrial DNA sequence data for the Akodontine tribe. Biol. J. Linn. Soc. 50, 149-177.
74. Smith, M.F., Patton, J.L., 1999. Phylogenetic relationships and the radiation of Sigmodontine rodents in South America: evidence from cytochrome b. J. Mammal. Evol. 6 (2), 89-128.
75. Stanyon, R., Yang, F., Cavagna, P., O'Brien, P.C.M., Bagga, M., Ferguson-Smith, M.A., Wienberg, J., 1999. Reciprocal chromosome painting shows that genomic rearrangement between rat and mouse proceeds ten times faster than between humans and cats. Cytogenet. Cell Genet. 84, 150-155.
76. Stiemie, S., Nel, J.A.J., 1973. Nest-building behaviour in Aethomys chrysophilus, Praomys (mastomys) natalensis and Rhabdomys pumilio. Zool. Afr. 8 (1), 91-100.
77. Sullivan, J., Markert, J.A., Kilpatric, C.W., 1997. Phylogeography and molecular systematics of the Peromyscus aztecus species group (Rodentia: Muridae) inferred using parsimony and likelihood. Syst. Biol. 46 (3), 426-440.
78. Swofford, D.L., 1998. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4. Sinauer Associates, Sunderland, MA.
79. Taylor, P.J., 2000. Patterns of chromosomal variation in southern African rodents. J. Mammal 81, 317-331.
80. Thackeray. J.F., 1987. Late quaternary environmental changes inferred from small mammalian fauna, southern Africa. Climatic Change 10, 285-305.
81. Todd, N.B., 1970. Karyotypic fission and canid phylogeny. J. Theor. Biol. 26, 380-445.
82. Van Zinderen Bakker, E.M., 1986. African climates and palaeoenvironments since Messian times. S. Afr. J. Sci. 82, 70-71.
83. Vassart, M., Seguela, A., Hayes, H., 1995. Chromosomal evolution in Gazelles. J. Heredity 86, 216-227.
84. Walsh, J.M., 1982. Rate of accumulation of reproductive isolation by chromosome rearrangements. Am. Nat. 120 (4), 510-532.
85. Willan, K., Meester, J., 1987. Food deprivation in two African rodents, Mastomys natalensis and Rhabdomys pumilio. S. Afr. J. Zool. 22, 190-194.
86. Wilson, A.C., Bush, G.L., Case, S.M., King, M., 1975. Social structuring of mammalian populations and rate of chromosomal evolution. Proc. Natl. Acad. Sci. USA 72, 5061-5065.
87. Wurster, D.H., Benirschke, K., 1968. Comparative cytogenetic studies of the order Carnivora. Chromosoma 24, 336-382.
88. Yang, F., Carter, N.P., Shi, L., Ferguson-Smith, M.A., 1995. A comparative study of karyotypes of muntjacs by chromosome painting. Chromosoma 103, 642-652.
89. Yang, F., O'Brien, P.C.M., Wienberg, J., Neitzel, H., Lin, C.C., Ferguson-Smith, M.A., 1997. Chromosomal evolution of the Chinese muntjac (Muntiacus reevesi). Chromosoma 106, 37-43.