Origin of agouPhylogenetic Characterizationti-melanistic polymorphism in wild black rats (Rattus rattus) inferred from Mc1r gene sequences

Zoological Science

Volumn 28, Issue 8, 2011, Pages 560-567

  Kambe, Yoshikazu ^a   Tanikawa, Tsutomu ^b   Matsumoto, Yasuharu ^c   Tomozawa, Morihiko ^a,e   Aplin, Ken P ^d   Suzuki, Hitoshi ^a  

^a HOKKAIDO UNIVERSITY   (Japan)

^b Lkari Corporation   (Japan)

^c Kobe 652 0866   (Japan)

^d CSIRO   (Australia)

^e KEIO UNIVERSITY   (Japan)

Author keywords

coat color variation; Mc1r; melanism; R. tanezumi; Rattus rattus

Indexed keywords

AGOUTI; RATTUS; RATTUS RATTUS; VERTEBRATA;

AGOUTI PROTEIN; ASIP PROTEIN, RAT; MELANOCORTIN 1 RECEPTOR; PIGMENT;

ANIMAL; ARTICLE; GENETIC POLYMORPHISM; GENETICS; METABOLISM; PHYSIOLOGY; PIGMENTATION; RAT; SPECIES DIFFERENCE; WILD ANIMAL;

AGOUTI SIGNALING PROTEIN; ANIMALS; ANIMALS, WILD; PIGMENTATION; PIGMENTS, BIOLOGICAL; POLYMORPHISM, GENETIC; RATS; RECEPTOR, MELANOCORTIN, TYPE 1; SPECIES SPECIFICITY;

EID: 79961046966     PISSN: 02890003     EISSN: None     Source Type: Journal    
DOI: 10.2108/zsj.28.560     Document Type: Article

References (62)

1. Anderson TM, vonHoldt BM, Candille SI, Musiani M, Greco C, Stahler DR, et al. (2009) Molecular and evolutionary history of melanism in North American gray wolves. Science 323: 1339-1343
2. Aplin KP, Chesser T, Have JT (2003a) Evolutionary biology of the genus Rattus: Profile of an archetypal rodent pest. In "Rats, Mice and People: Rodent Biology and Management" Ed by GR Singleton, LA Hinds, J Krebs, DM Spratt, ACIAR Monograph 96, Australian Centre for International Agricultural Research, Canberra, pp 487-498
3. Aplin KP, Brown PB, Jacob J, Krebs CJ, Singleton GR (2003b) Field methods for rodent studies in Asia and the Indo-Pacific. ACIAR Monograph No. 100, Australian Centre for International Agricultural Research, Canberra
4. Aplin KP, Suzuki H, Chinen AA, Chesser RT, ten Have J, Donnellan SC, et al. (2011) Multiple geographic origins of commensalism and complex dispersal history of Black Rats. PLoS One (in press)
5. Armitage PL (1994) Unwelcome companions: Ancient rats reviewed. Antiquity 68: 231-240
6. Barsh GS (1996) The genetics of pigmentation: From fancy genes to complex traits. Trends Genet 12: 299-305 (Pubitemid 26258355)
7. Candille SI, Kaelin CB, Cattanach BM, Yu B, Thompson DA, Nix MA, et al. (2007) A defensin mutation causes black coat color in domestic dogs. Science 318: 1418-1423 (Pubitemid 350208947)
8. Cavagna P, Stone G, Stanyon R (2002) Black rat (Rattus rattus) genomic variability characterized by chromosome painting. Mamm Genome 13: 157-163 (Pubitemid 34185315)
9. Chinen AA, Suzuki H, Aplin KP, Tsuchiya K, Suzuki S (2005) Preliminary genetic characterization of two lineages of black rats (Rattus rattus sensu lato) in Japan, with evidence for introgression at several localities. Genes Genet Syst 80: 367-375 (Pubitemid 43015758)
10. Clement M, Posada D, Crandall KA (2000) TCS: A computer program to estimate gene genealogies. Mol Ecol 9: 1657-1659
11. De l'Isle A (1865) De rexistence d'une race nègre chez le rat, ou de l'identité spécifique du Mus rattus et du Mus alexandrinus. Ann Sci Nat Ser V, Zoologie et Palieontologie 4: 173-222
12. Eizirik E, Yuhki N, Johnson WE, Menotti-Raymond M, Hannah SS, O'Brien SJ (2003) Molecular genetics and evolution of melanism in the cat family. Curr Biol 13: 448-453 (Pubitemid 36280466)
13. Feldman HW (1926) Unit character inheritance of color in the Black Rat, Mus rattus L. Genetics 11: 456-465
14. Filatov DA (2002) ProSeq: A software for preparation and evolutionary analysis of DNA sequence datasets. Mol Ecol Notes 2: 621-624 (Pubitemid 35436767)
15. Goldman N, Yang Z (1994) A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol 11: 725-736
16. Green MC (1981) Catalog of mutant genes and polymorphic loci. In "Genetic Variants and Strains of the Laboratory Mouse" Ed by MC Green, Gustav Fischer Verlag Stuttgart, New York, pp 8- 278
17. Hinton MAC (1918) Scientific results from the mammal survey, No. 18, Report on the house rats of India, Burma, Ceylon. J Bombay Nat Hist Soc 25: 59-88, 384-416
18. Hinton MAC (1919) The zoology of rats and mice, with special reference to the question of the future control of the rat population. J Roy Soc Promot Health 40: 44-52
19. Hoekstra HE, Krenz JG, Nachman MW (2005) Local adaptation in the rock pocket mouse (Chaetodipus intermedius): Natural selection and phylogenetic history of populations. Heredity 94: 217-228 (Pubitemid 40198965)
20. Hoekstra HE, Hirschmann RJ, Bundey RA, Insel PA, Crossland JP (2006) A single amino acid contributes to adaptive beach mouse color pattern. Science 313: 101-104 (Pubitemid 44051263)
21. Hoekstra HE, Price T (2004) Parallel evolution is in the genes. Science 303: 1779-1780
22. Hosoda T, Sato JJ, Shimada T, Campbell KL, Suzuki H (2005) Independent non-frameshift deletions in the MC1R gene are not associated with melanistic coat coloration in three mustelid lineages. J Hered 96: 607-613 (Pubitemid 41442794)
23. Hudson RR, Kaplan NL (1985) Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111: 147-164 (Pubitemid 16248827)
24. Huson DH, Bryant D (2006) Appllication of phylogenetic network in evolutionary studies. Mol Biol Evol 23: 254-267 (Pubitemid 43100040)
25. Jackson IJ (1994) Molecular and developmental genetics of Mouse coat color. Annu Rev Genet 28: 189-217
26. Kerje S, Lind J, Schutz K, Jensen P, Andersson L (2003) Melanocortin 1-receptor (MC1R) mutations are associated with plumage color in chicken. Anim Genet 34: 241-248 (Pubitemid 36946719)
27. Kijas JMH, Wales R, Törnsten A, Chardon P, Möller M, Andersson L (1998) Melanocortin receptor 1 (MC1R) mutations and coat color in pigs. Genetics150: 1177-1185 (Pubitemid 28510045)
28. Klungland H, Våge DI, Gomez-Raya L, Adalsteinsson S, Lein S (1995) The role of melanocyte-stimulating hormone (MSH) receptor in bovine coast color determination. Mamm Genome 6: 636-639
29. Lecompte E, Aplin KP, Denys C, Catzeflis F, Chades M, Chevret P (2008) Phylogeny and biogeography of African Murinae based on mitochondrial and nuclear gene sequences, with a new tribal classification of the subfamily. BMC Evol Biol 8: 199
30. Librado P, Rozas J (2009) DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452
31. MacDougall-Shackleton EA, Blanchard L, Gibbs HL (2003) Unmelanized plumage patterns in old world leaf warblers do not correspond to sequence variation at melanocortin-1 receptor locus (MC1R). Mol Biol Evol 20: 1675-1681 (Pubitemid 41070830)
32. Marklund L, Moller MJ, Sandberg K, Anderson L (1996) A missense mutation in the gene for melanocyte-stimulating hormone receptor (MC1R) is associated with the chestnut coat color in horses. Mamm Genome 7: 895-899 (Pubitemid 126439172)
33. Marshall JT (1976) Family Muridae: Rats and mice. Privately printed by the Government Printing Office, Bangkok: 396-487
34. Morgan TH (1909) Breeding experiments with rats. Amer Naturalist 43: 182-185
35. Moriwaki K, Kato H, Imai H, Tsuchiya K, Yosida T (1975) Geographical distribution of twelve transferrin alleles in black rats of Asia and Oceania. Genetics 79: 295-304
36. Mouchiroud D, Gautier C, Bernardi G (1988) The compositional distribution of coding sequences and DNA molecules in humans and murids. J Mol Evol 27: 311-320
37. Mountjoy KG, Robbins LS, Nortrud MT, Cone RD (1992) The cloning of a family of genes that encode the melanocortin receptors. Science 257: 1248-1251
38. Mundy NI, Kelly J (2003) Evolution of a pigmentation gene, the melanocortin- 1 receptor, in primates. Am J Phys Anthropol 121: 67-80 (Pubitemid 36444017)
39. Musser GG, Carleton MD (2005) Family Muridae. In "Mammal Species of the World, 3rd edition" Ed by DE Wilson, DM Reeder, Smithsonian Institute Press, Washington and London
40. Nachman MW, Hoekstra HE, D'Agostino SL (2003) The genetic basis of adaptive melanism in pocket mice. Proc Natl Acad Sci USA 100: 5268-5273 (Pubitemid 36542694)
41. Newton JM, Wilkie AL, He L, Jordan SA, Metallinos DL, Holmes NG, et al. (2000) Melanocortin-1 receptor variation in the domestic dog. Mamm Genome 11: 24-30 (Pubitemid 30033463)
42. Nunome M, Ishimori C, Aplin KP, Tsuchiya K, Yonekawa H, Moriwaki K, et al. (2010) Detection of recombinant haplotypes in wild mice (Mus musculus) provides new insights into the origin of Japanese mice. Mol Ecol 19: 2474-2489
43. Ondrias JC (1966) The taxonomy and geographical distribution of the rodents of Greece. Saugetierkundliche Mitteilungen 14: 1-134
44. Patton JL, Yang SY, Myers P (1975) Genetic and morphological divergence among introduced rat populations (Rattus rattus) of the Galapagos archipelago, Ecuador. Syst Zool 24: 296-310
45. Pagès M, Chaval Y, Herbreteau V, Waengsothorn S, Cosson JF, Hugot JP, et al. (2010) Revisiting the taxonomy of the Rattini tribe: A phylogeny-based delimitation of species boundaries. BMC Evol Biol 10: 184
46. Robbins LS, Nadeau JH, Johnson KR, Kelly MA, Roselli-Rehfuss L, Baack E, et al. (1993) Pigmentation phenotypes of variant extension locus alleles result from point mutations that alter MSH receptor function. Cell 72: 827-834 (Pubitemid 23110225)
47. Robins JH, Hingston M, Matisoo-Smith E, Ross HA (2007) Identifying Rattus species using mitochondrial DNA. Mol Ecol Notes 7: Schwarz E, Schwarz HKA (1967) A monograph of the Rattus rattus group. Anal Esc Nac Cienc Biol Mex 14: 79-178
48. Searle AG (1968) Comparative of coat color in mammals. Logos Press. London p 308
49. Shimada T, Sato JJ, Aplin KP, Suzuki H (2009) Comparative analysis of evolutionary modes in Mc1r coat color gene in wild mice and mustelids. Gene Genet Syst 84: 225-231
50. Smith NGC, Eyre-Walker A (2002) The compositional evolution of the murid genome. J Mol Evol 55: 197-201 (Pubitemid 34734782)
51. Swofford DL (2001) PAUP* Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4 Sunderland MA: Sinauer Associates
52. Suzuki S, Yonekawa H, Tsuchiya K, Tsutamune T, Fujikawa K, Uchida Y (2001) Oceanian-type black rat (Rattus rattus) found in port Otaru of Hokkaido, Japan. Med Entomol Zool 52: 1-7
53. Tamate HB, Takeuchi T (1981) Induction of the shift in melanin synthesis in lethal yellow (Ay/a) mice in vitro. Dev Genet 2: 349-356 (Pubitemid 12188665)
54. Tchernov E (1996) Rodent faunas, chronostratigraphy and paleobiogeography of the southern Levant during the Quaternary. Acta Zool Cracov 39: 513-530
55. Theron E, Hawkins K, Bermingham E, Ricklefs RE, Mundy NI (2001) The molecular basis of an avian plumage polymorphism in the wild: A melanocortin-1-receptor point mutation is perfectly associated with the melanic plumage morph of the bananaquit, Coereba flaveola. Curr Biol 11: 550-557 (Pubitemid 32324757)
56. Tomich PQ (1968) Coat color in wild populations of the roof rat in Hawaii. J Mammal 49: 74-82
57. Tomich PQ, Kami HT (1966) Coat color inheritance of the roof rat in Hawaii. J Mammal 47: 423-431
58. Yalden DW (2003) Mammals in Britain - a historical perspective. British Wildlife 14: 243-251 (Pubitemid 36524607)
59. Yang Z (1997) PAML: A program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13: 555-556 (Pubitemid 27480216)
60. Yosida TH, Kato H, Tsuchiya K, Moriwaki K (1971) Karyotypes and serum transferrin patterns of hybrids between Asian and Oceanian Black Rats, Rattus rattus. Chromosoma 34: 40-50
61. Yosida TH, Sagai T (1975) Variation of C-bands in the chromosomes of several subspecies of Rattus rattus. Chromosoma 50: 283-300
62. Yosida TH (1980) Cytogenetics of the Black Rat: Karyotype Evolution and Species differentiation. University of Tokyo Press, Tokyo, p 256