Molecular phylogeny and evolution of sex-chromosomal genes and SINE sequences in the family mustelidae

Mammal Study

Volumn 35, Issue 1, 2010, Pages 17-30

  Yamada, Chiemi ^a   Masuda, Ryuichi ^a  

^a HOKKAIDO UNIVERSITY   (Japan)

Author keywords

Molecular evolution; Mustelidae; SINE; X chromosomal gene; Y chromosomal gene

Indexed keywords

LUTRA; MARTES; MELES; MUSTELA; MUSTELA ERMINEA; MUSTELIDAE;

EID: 77749251208     PISSN: 13434152     EISSN: 13486160     Source Type: Journal    
DOI: 10.3106/041.035.0102     Document Type: Article

References (54)

1. Abe, H. 1994. A Pictorial Guide to the Mammals of Japan. Tokai University Press, Tokyo, 195 pp. (in Japanese).
2. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D. J. 1997. Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Research 25: 3389-3402.
3. Anistoroaei, R., Farid, A., Benkel, B., Cirera, S. and Christensen, K. 2006. Isolation and characterization of 79 microsatellite markers from the American mink (Mustela vison). Animal Genetics 37: 185-188.
4. Carpenter, P., Dawson, D. A., Greig, C., Parham, A., Cheeseman, C. L. and Burke, T. 2003. Isolation of 39 polymorphic microsatellite loci and the development of a fluorescently labelled marker set for the Eurasian badger (Meles meles) (Carnivora: Mustelidae). Molecular Ecology Notes 3: 610-615.
5. Chang, B. H. J., Shimmin, L. C., Shyue, S. K., Hewett-Emmett, D. and Li, W. H. 1994. Weak male-driven molecular evolution in rodents. Proceedings of National Academy of Science USA 91: 827-831.
6. Charlesworth, B. 1991. The evolution of sex chromosomes. Science 251: 1030-1033.
7. Coltman, D. W. and Wright, J. M. 1994. Can SINEs: a family of tRNA of tRNA-derived retroposons specific to the family Canoidea. Nucleic Acids Research 22: 2726-2730.
8. Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39: 783-791.
9. Flynn, J. J., Finarelli, J. A., Zehr, S., Hsu, J. and Nedbal, M. A. 2005. Molecular phylogeny of the Carnivora (Mammalia): Assessing the impact of increased sampling on resolving enigmatic relationships. Systematic Biology 54: 317-337.
10. Foster, J. W., Brennan, F. E., Hampikian, G. K., Goodfellow, P. N., Sinclair, A. H., Lovell-Badge, R., Selwood, L., Renfree, M. B., Cooper, D. W. and Graves, J. A. 1992. Evolution of sex determination and the Y chromosome: SRY-related sequences in marsupials. Nature 359: 531-532.
11. Fulton, T. L. and Strobeck, C. 2006. Molecular phylogeny of the Arctoidea (Carnivora): effect of missing data on supertree and supermatrix analyses of multiple gene data sets. Molecular Phylogenetics and Evolution 41: 165-181.
12. Goodfellow, P. N. and Lovell-Badge, R. 1993. SRY and sex determination in mammals. Annual Review of Genetics 27: 71-92.
13. Graphodatsky, A. S., Yang, F., Perelman, P. L., O'Brien, P. C. M., Serdukova, N. A., Miline, B. S., Biltueva, L. S., Fu, B., Vorobieva, N. V., Kawada, S. I., Robinson, T. J. and Ferguson-Smith, M. A. 2002. Comparative molecular cytogenetic studies in the order Carnivora: mapping chromosomal rearrangements onto the phylogenetic tree. Cytogenetisc and Genome Research 96: 137-145.
14. Hasegawa, M., Kishino, H. and Yano, T. 1985. Dating of the humanape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 22: 160-174.
15. Hosoda, T., Suzuki, H., Iwasa, M. A., Hayashida, M., Watanabe, S., Tatara, M. and Tsuchiya, K. 1999. Genetic relationships within and between the Japanese marten Martes melampus and the sable M. zibellina, based on variation of mitochondrial DNA and nuclear ribosomal DNA. Mammal Study 24: 25-33.
16. Hosoda, T., Suzuki, H., Harada, M., Tsuchiya, K., Han, S. H., Zhang, Y. P., Kryukov, A. P. and Lin, L. K. 2000. Evolutionary trends of the mitochondrial lineage differentiation in species of genera Martes and Mustela. Genes and Genetic Systems 75: 259-267.
17. Huang, W., Chang, B. H. J., Gu, X., Hewett-Emmett, D. and Li, W. H. 1997. Sex differences in mutation rate in higer primates estimated from AMG intron sequences. Journal of Molecular Evolution 44: 463-465.
18. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16: 111-120.
19. Koepfli, K. P. and Wayne, R. K. 1998. Phylogenetic relationships of otters (Carnivora: Mustelidae) based on mitochondrial cytochrome b sequences. Journal of Zoology London 246: 401-416.
20. Koepfli, K. P. and Wayne, R. K. 2003. Type I STS markers are more informative that cytochrome b in phylogenetic reconstruction of the Mustelidae (Mammalia: Carnivora). Systematic Biology 52: 571-593.
21. Koepfli, K. P., Deere, K. A., Slater, G. J., Begg, C., Begg, K., Grassman, L., Lucherini, M., Veron, G. and Wayne, R. K. 2008. Multigene phylogeny of the Mustelidae: Resolving relationships, tempo and biogeographic history of a mammalian adaptive radiation. BMC Biology 6: 10 (Doi:10.1186/1741-7007-6-10).
22. Kumar, S., Tamura, K. and Nei, M. 2004. MEGA 3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Briefings in Buoinformatics 5: 150-163.
23. Kurose, N., Masuda, R., Siriaroonrat, B. and Yoshida, M. C. 1999a. Intraspecific variation of mitochondrial cytochrome b gene sequences of the Japanese marten Martes melampus and the sable Martes zibellina (Mustelidae, Carnivora, Mammalia) in Japan. Zoological Science 16: 693-700.
24. Kurose, N., Masuda, R. and Yoshida, M. C. 1999b. Phylogeographic variation in two Mustelines, the least weasel Mustela nivalis and the ermine Mustela erminea of Japan, based on mitochondrial DNA control region sequences. Zoological Science 16: 971-977.
25. Kurose, N., Abramov, A. V. and Masuda, R. 2000. Intrageneric diversity of the cytochrome b gene and phylogeny of Eurasian species of the genus Mustela (Mustelidae, Carnivora). Zoological Science 17: 673-679.
26. Lavrentieva, M. V., Rivkin, M. I., Shilov, A. G., Kobetz, M. L., Rogozin, I. B. and Serov, O. L. 1991. B2-like repetitive sequence from the X chromosome of the American mink (Mustela vison). Mammalian Genome 1: 161-170.
27. Ledje, C. and Arnason, U. 1996. Phylogenetic analyses of complete cytochrome b genes of the order carnivora with particular emphasis on the caniformia. Journal of Molecular Evolution 42: 135-144.
28. Leib, S. R., McGuire, T. C. and Prieur, D. J. 2005. Comparison of the tyrosine aminotransferase cDNA and genomic DNA sequences of normal mink and mink affected with tyrosinemia type II. Journal of Heredity 96: 302-309.
29. López-Giráldez, F., Gómez-Moliner, B. J., Marmi, J. and Domingo-Roura, X. 2005. Genetic distinction of American and European mink (Mustela vison and M. lutreola) and European polecat (M. putorius) hair samples by detection of a species-specific SINE and a RFLP assay. Journal of Zoology, London 265: 405-410.
30. Marmi, J., Lopez-Giraldez, J. F. and Domingo-Roura, X. 2004. Phylogeny, evolutionary history and taxonomy of the Mustelidae based on sequences of the cytochrome b gene and a complex repetitive flanking region. Zoologica Scripta 33: 481-499.
31. Masuda, R. and Yoshida, M. C. 1994. A molecular phylogeny of the family Mustelidae (Mammalia, Carnivora), based on comparison of mitochondrial cytochrome b nucleotide sequences. Zoological Science 11: 605-612.
32. Mittwoch, U. 2006. Sex is a threshold dichotomy mimicking a single gene effect. Trends in Genetics 22: 96-100.
33. Moreira, M. A. 2002. SRY evolution in Cebidae (Platyrrhini: Primates). Journal of Molecular Evolution 55: 92-103.
34. Nakagome, S., Pecon-Slattery, J. and Masuda, R. 2008. Unequal rates of Y chromosome gene divergence during speciation of the family Ursidae. Molecular Biology and Evolution 25: 1344-1356.
35. Nagai, K. 2001. Molecular evolution of SRY and Sox gene. Gene 270: 161-169
36. Nowak, R. M. 2005. Walker's Carnivores of the World. Johns Hopkins University Press, Baltimore and London, 313 pp.
37. Obara, Y. 1985. G-Band Homology and C-Band Variation in the Japanese Mustelids, Mustela erminea nippon and M. sibirica itatsi. Genetica 68: 59-64.
38. Obara, Y. 1991. Evolution and karyotypes. In (M. Asahi and T. Kawamichi, eds.) Recent Mammalogy, pp. 23-44. Asahi Shoten, Tokyo (in Japanese).
39. Page, D. C., Mosher, R., Simpson, E. M., Fisher, E. M. C., Mardon, G., Pollack, J., McGillivray, B., de la Chapelle, A. and Brown, L. G. 1987. The sex-determining region of the human Y chromosome encodes a finger protein. Cell 51: 1091-1104.
40. Pecon-Slattery, J. and O'Brien, S. J. 1998. Patterns of Y and X chromosome DNA sequence divergence during the Felidae radiation. Genetics 148: 1245-1255.
41. Pecon-Slattery, J., Sanner-Wachter, L. and O'Brien, S. J. 2000a. Novel gene conversion between X-Y homologues located in the nonrecombining region of the Y chromosome in Felidae (Mammalia). Proceedings of National Academy of Science USA 97: 5307-5312.
42. Pecon-Slattery, J., Murphy, W. J. and O'Brien, J. 2000b. Patterns of diversity among SINE elements isolated from three Y-chromosome genes in Carnivores. Molecular Biology and Evolution 17: 825-829.
43. Pecon-Slattery, J., Wilkerson, A. J. P., Murphy, W. J. and O'Brien, S. J. 2004. Phylogenetic assessment of introns and SINEs within the Y chromosome using the cat family Felidae as a species tree. Molecular Biology and Evolution 21: 2299-2309.
44. Posada, D. and Crandall, K. A. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817-818.
45. Saitou, N. and Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4: 406-425.
46. Sato, J. J., Hosoda, T., Wolsan, M., Tsuchiya, K., Yamamoto, M. and Suzuki, H. 2003. Phylogenetic relationships and divergence times among mustelids (Mammalia: Carnivora) based on nucleotide sequences of the nuclear interphotoreceptor retinoid binding protein and mitochondrial cytochrome b genes. Zoological Science 20: 243-264.
47. Sato, J. J., Hosoda, T., Wolsan, M. and Suzuki, H. 2004. Molecular phylogeny of arctoids (Mammalia: Carnivora) with emphasis on phylogenetic and taxonomic positions of the ferret-badgers and skunks. Zoological Science 21: 111-118.
48. Sato, J. J., Wolsan, M., Suzuki, H., Hosoda, T., Yamaguchi, Y., Hiyama, K., Kobayashi, M. and Minami, S. 2006. Evidence from nuclear DNA sequences sheds light on the phylogenetic relationships of Pinnipedia: single origin with affinity to Musteloidea. Zoological Science 23: 125-146.
49. Swofford, D. L. 2002. PAUP * Phylogenetic Analysis Using Parsimony ( * and Other Methods). Version 4. Sinauer Associates, Sunderland.
50. Tosi, A. J., Morales, J. C. and Melnick, D. J. 2000. Comparison of Y chromosome and mtDNA phylogenies leads to unique inferences of macaque evolutionary history. Molecular Phylogenetics and Evolution 17: 133-144.
51. Vassetzky, N. S. and Kramerov, D. A. 2002. CAN-a pan-carnivore SINE family. Mammalian Genome 13: 50-57.
52. Wang, X., Zhang, J. and Zhang, Y. P. 2002. Erratic evolution of SRY in higher primates. Molecular Phylogenetics and Evolution 19: 582-584.
53. Yonezawa, T., Nikaido, M., Kohno, N., Fukumoto, Y., Okada, N. and Hasegawa, M. 2007. Molecular phylogenetic study on the origin and evolution of Mustelidae. Gene 396: 1-12.
54. Yu, L., Liu, J., Luan, P. T., Lee, H., Lee, M., Min, M. S., Ryder, O. A., Chemnick, L., Davis, H. and Zhang, Y. P. 2008. New insights into the evolution of intronic sequences of the fibrinogen gene and their application in reconstructing mustelid phylogeny. Zoological Science 25: 662-672