The genetic background effect on domesticated species: A mouse evolutionary perspective

TheScientificWorldJournal

Volumn 11, Issue , 2011, Pages 429-436

  Reuveni, Eli ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY EMBL   (Italy)

Author keywords

Domesticated species; Evolution; Genotype phenotype map; Laboratory mouse strains; Natural selection; Population genetics; Speciation; Wild species

Indexed keywords

DOMESTIC ANIMAL; EVOLUTION; GENETICS; GENOTYPE; LABORATORY TEST; MEDICAL TECHNOLOGY; MOLECULAR EVOLUTION; MOUSE STRAIN; NONHUMAN; PHENOTYPE; PUBLISHING; SHORT SURVEY;

ANIMALS; BIOLOGICAL EVOLUTION; GENETIC VARIATION; GENETICS, POPULATION; GENOTYPE; MICE; PHENOTYPE;

MAMMALIA;

EID: 79952365137     PISSN: None     EISSN: 1537744X     Source Type: Journal    
DOI: 10.1100/tsw.2011.32     Document Type: Short Survey

References (61)

1. Grubb, S.C., Maddatu, T.P., Bult, C.J., and Bogue, M.A. (2009) Mouse phenome database. Nucleic Acids Res. 37, D720-730.
2. Peirce, J.L., Derr, R., Shendure, J., Kolata, T., and Silver, L.M. (1998) A major influence of sex-specific loci on alcohol preference in C57Bl/6 and DBA/2 inbred mice. Mamm. Genome 9, 942-948. (Pubitemid 29030893)
3. Zhang, Y., Proenca, R., Maffei, M., Barone, M., Leopold, L., and Friedman, J.M. (1994) Positional cloning of the mouse obese gene and its human homologue. Nature 372, 425-432. (Pubitemid 24365442)
4. Cryan, J.F. and Holmes, A. (2005) The ascent of mouse: advances in modelling human depression and anxiety. Nat. Rev. Drug Discov. 4, 775-790. (Pubitemid 43090498)
5. Brown, S.D., Hancock, J.M., and Gates, H. (2006) Understanding mammalian genetic systems: the challenge of phenotyping in the mouse. PLoS Genet. 2, e118.
6. Rosenthal, N. and Brown, S. (2007) The mouse ascending: perspectives for human-disease models. Nat. Cell Biol. 9, 993-999. (Pubitemid 47338136)
7. Friedel, R.H., Seisenberger, C., Kaloff, C., and Wurst, W. (2007) EUCOMM--the European conditional mouse mutagenesis program. Brief. Funct. Genomic. Proteomic. 6, 180-185. (Pubitemid 351863874)
8. Collins, F.S., Rossant, J., and Wurst, W. (2007) A mouse for all reasons. Cell 128, 9-13.
9. Guenet, J.L. and Bonhomme, F. (2003) Wild mice: an ever-increasing contribution to a popular mammalian model. Trends Genet. 19, 24-31.
10. Beck, J.A., Lloyd, S., Hafezparast, M., Lennon-Pierce, M., Eppig, J.T., Festing, M.F., and Fisher, E.M. (2000) Genealogies of mouse inbred strains. Nat. Genet. 24, 23-25. (Pubitemid 30041415)
11. Bonhomme, F., Guenet, J.-L, Dod, B., Moriwaki, K., and Bulfield, G. (1987) The polyphyletic origin of laboratory inbred mice and their rate of evolution. Biol. J. Linnean Soc. 30, 51-58.
12. Boursot, P., Auffray, J.C., Brittondavidian, J., and Bonhomme, F. (1993) The evolution of house mice. Annu. Rev. Ecol. Syst. 24, 119-152.
13. Suzuki, H., Shimada, T., Terashima, M., Tsuchiya, K., and Aplin, K. (2004) Temporal, spatial, and ecological modes of evolution of Eurasian Mus based on mitochondrial and nuclear gene sequences. Mol. Phylogenet. Evol. 33, 626-646. (Pubitemid 39444505)
14. Boursot, P., Din, W., Anand, R., Darviche, D., Dod, B., VonDeimling, F., Talwar, G., and Bonhomme, F. (1996) Origin and radiation of the house mouse: mitochondrial DNA phylogeny. J. Evol. Biol. 9, 391-415.
15. Abe, K., Noguchi, H., Tagawa, K., Yuzuriha, M., Toyoda, A., Kojima, T., Ezawa, K., Saitou, N., Hattori, M., Sakaki, Y., Moriwaki, K., and Shiroishi, T. (2004) Contribution of Asian mouse subspecies Mus musculus molossinus to genomic constitution of strain C57BL/6J, as defined by BAC-end sequence-SNP analysis. Genome Res. 14, 2439-2447. (Pubitemid 40012227)
16. Paigen, K. (2003) One hundred years of mouse genetics: an intellectual history. II. The molecular revolution (1981- 2002). Genetics 163, 1227-1235.
17. Morse, H.C. (1978) Origins of Inbred Mice. Academic Press, New York.
18. Frazer, K.A., Eskin, E., Kang, H.M., Bogue, M.A., Hinds, D.A., Beilharz, E.J., Gupta, R.V., Montgomery, J., Morenzoni, M.M., Nilsen, G.B., Pethiyagoda, C.L., Stuve, L.L., Johnson, F.M., Daly, M.J., Wade, C.M., and Cox, D.R. (2007) A sequence-based variation map of 8.27 million SNPs in inbred mouse strains. Nature 448, 1050-1053. (Pubitemid 47345584)
19. Wade, C.M. and Daly, M.J. (2005) Genetic variation in laboratory mice. Nat. Genet. 37, 1175-1180. (Pubitemid 41568696)
20. Wade, C.M., Kulbokas, E.J., 3rd, Kirby, A.W., Zody, M.C., Mullikin, J.C., Lander, E.S., Lindblad-Toh, K., and Daly, M.J. (2002) The mosaic structure of variation in the laboratory mouse genome. Nature 420, 574-578. (Pubitemid 35477050)
21. Yang, H., Bell, T.A., Churchill, G.A., and Pardo-Manuel de Villena, F. (2007) On the subspecific origin of the laboratory mouse. Nat. Genet. 39, 1100-1107. (Pubitemid 47340646)
22. Payseur, B.A., Krenz, J.G., and Nachman, M.W. (2004) Differential patterns of introgression across the X chromosome in a hybrid zone between two species of house mice. Evolution 58, 2064-2078. (Pubitemid 39348506)
23. Payseur, B.A. and Hoekstra, H.E. (2005) Signatures of reproductive isolation in patterns of single nucleotide diversity across inbred strains of mice. Genetics 171, 1905-1916.
24. Hunt, W.G. and Selander, R.K. (1973) Biochemical genetics of hybridisation in European house mice. Heredity 31, 11-33.
25. Harr, B. (2006) Genomic islands of differentiation between house mouse subspecies. Genome Res. 16, 730-737.
26. Imhof, M. and Schlotterer, C. (2001) Fitness effects of advantageous mutations in evolving Escherichia coli populations. Proc. Natl. Acad. Sci. U. S. A. 98, 1113-1117. (Pubitemid 32121195)
27. Wyckoff, G.J., Malcom, C.M., Vallender, E.J., and Lahn, B.T. (2005) A highly unexpected strong correlation between fixation probability of nonsynonymous mutations and mutation rate. Trends Genet. 21, 381-385. (Pubitemid 40835722)
28. Yang, Z. (2002) Inference of selection from multiple species alignments. Curr. Opin. Genet. Dev. 12, 688-694.
29. Balbi, K.J. and Feil, E.J. (2007) The rise and fall of deleterious mutation. Res. Microbiol. 158, 779-786. (Pubitemid 350235178)
30. Miyata, T. and Yasunaga, T. (1980) Molecular evolution of mRNA: a method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its applications. J. Mol. Evol. 16, 23-26.
31. Rocha, E.P., Smith, J.M., Hurst, L.D., Holden, M.T., Cooper, J.E., Smith, N.H., and Feil, E.J. (2006) Comparisons of dN/dS are time dependent for closely related bacterial genomes. J. Theor. Biol. 239, 226-235.
32. Goldman, N. and Yang, Z. (1994) A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11, 725-736.
33. Nielsen, R. and Yang, Z. (2003) Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA. Mol. Biol. Evol. 20, 1231-1239. (Pubitemid 36961241)
34. Kryazhimskiy, S. and Plotkin, J.B. (2008) The population genetics of dN/dS. PLoS Genet. 4, e1000304.
35. Vallender, E.J. and Lahn, B.T. (2007) Uncovering the mutation-fixation correlation in short lineages. BMC Evol. Biol. 7, 168.
36. Salcedo, T., Geraldes, A., and Nachman, M.W. (2007) Nucleotide variation in wild and inbred mice. Genetics 177, 2277-2291.
37. Reuveni, E., Birney, E., and Gross, C.T. (2010) The consequence of natural selection on genetic variation in the mouse. Genomics 95, 196-202.
38. Ideraabdullah, F.Y., de la Casa-Esperon, E., Bell, T.A., Detwiler, D.A., Magnuson, T., Sapienza, C., and de Villena, F.P. (2004) Genetic and haplotype diversity among wild-derived mouse inbred strains. Genome Res. 14, 1880-1887. (Pubitemid 39386501)
39. Hancock, J.F. (2005) Contributions of domesticated plant studies to our understanding of plant evolution. Ann. Bot. 96, 953-963.
40. Purugganan, M.D. and Fuller, D.Q. (2009) The nature of selection during plant domestication. Nature 457, 843-848.
41. Trut, L., Oskina, I., and Kharlamova, A. (2009) Animal evolution during domestication: the domesticated fox as a model. Bioessays 31, 349-360.
42. Liti, G., Carter, D.M., Moses, A.M., Warringer, J., Parts, L., James, S.A., Davey, R.P., Roberts, I.N., Burt, A., Koufopanou, V., Tsai, I.J., Bergman, C.M., Bensasson, D., O'Kelly, M.J., van Oudenaarden, A., Barton, D.B., Bailes, E., Nguyen, A.N., Jones, M., Quail, M.A., Goodhead, I., Sims, S., Smith, F., Blomberg, A., Durbin, R., and Louis, E.J. (2009) Population genomics of domestic and wild yeasts. Nature 458, 337-341.
43. Lippman, Z.B. and Zamir, D. (2007) Heterosis: revisiting the magic. Trends Genet. 23, 60-66. (Pubitemid 46161217)
44. Orr, H.A. (1995) The population genetics of speciation: the evolution of hybrid incompatibilities. Genetics 139, 1805-1813.
45. Dobzhansky, T. (1937) Genetics and the Origin of Species. Columbia University Press, New York.
46. Presgraves, D.C. (2010) The molecular evolutionary basis of species formation. Nat. Rev. Genet. 11, 175-180.
47. Forejt, J. and Ivanyi, P. (1974) Genetic studies on male sterility of hybrids between laboratory and wild mice (Mus musculus L.). Genet. Res. 24, 189-206.
48. Mihola, O., Trachtulec, Z., Vlcek, C., Schimenti, J.C., and Forejt, J. (2009) A mouse speciation gene encodes a meiotic histone H3 methyltransferase. Science 323, 373-375.
49. Orr, H.A. and Presgraves, D.C. (2000) Speciation by postzygotic isolation: forces, genes and molecules. Bioessays 22, 1085-1094. (Pubitemid 32010518)
50. Mallet, J. (2006) What does Drosophila genetics tell us about speciation? Trends Ecol. Evol. 21, 386-393.
51. Lee, H.Y., Chou, J.Y., Cheong, L., Chang, N.H., Yang, S.Y., and Leu, J.Y. (2008) Incompatibility of nuclear and mitochondrial genomes causes hybrid sterility between two yeast species. Cell 135, 1065-1073.
52. Phadnis, N. and Orr, H.A. (2009) A single gene causes both male sterility and segregation distortion in Drosophila hybrids. Science 323, 376-379.
53. Long, Y., Zhao, L., Niu, B., Su, J., Wu, H., Chen, Y., Zhang, Q., Guo, J., Zhuang, C., Mei, M., Xia, J., Wang, L., and Liu, Y.G. (2008) Hybrid male sterility in rice controlled by interaction between divergent alleles of two adjacent genes. Proc. Natl. Acad. Sci. U. S. A. 105, 18871-18876.
54. Shendure, J. and Ji, H. (2008) Next-generation DNA sequencing. Nat. Biotechnol. 26, 1135-1145.
55. Li, R., Li, Y., Fang, X., Yang, H., Wang, J., and Kristiansen, K. (2009) SNP detection for massively parallel whole-genome resequencing. Genome Res. 19, 1124-1132.
56. Adams, D.J., Dermitzakis, E.T., Cox, T., Smith, J., Davies, R., Banerjee, R., Bonfield, J., Mullikin, J.C., Chung, Y.J., Rogers, J., and Bradley, A. (2005) Complex haplotypes, copy number polymorphisms and coding variation in two recently divergent mouse strains. Nat. Genet. 37, 532-536. (Pubitemid 40617283)
57. Lee, S., Seo, C.H., Lim, B., Yang, J.O., Oh, J., Kim, M., Lee, B., and Kang, C. (2010) Accurate quantification of transcriptome from RNA-Seq data by effective length normalization. Nucleic Acids Res. [Epub ahead of print].
58. Wu, Z.J., Meyer, C.A., Choudhury, S., Shipitsin, M., Maruyama, R., Bessarabova, M., Nikolskaya, T., Sukumar, S., Schwartzman, A., Liu, J.S., Polyak, K., and Liu, X.S. (2010) Gene expression profiling of human breast tissue samples using SAGE-Seq. Genome Res. 20, 1730-1739.
59. Laird, P.W. (2010) Principles and challenges of genome-wide DNA methylation analysis. Nat. Rev. Genet. 11, 191-203.
60. Wang, E.T., Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., Kingsmore, S.F., Schroth, G.P., and Burge, C.B. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470-476. (Pubitemid 352759009)
61. Mott, R. and Flint, J. (2002) Simultaneous detection and fine mapping of quantitative trait loci in mice using heterogeneous stocks. Genetics 160, 1609-1618. (Pubitemid 34454382)