Habitat variability correlates with duplicate content of drosophila genomes

Molecular Biology and Evolution

Volumn 29, Issue 10, 2012, Pages 3169-3179

  Makino, Takashi ^a   Kawata, Masakado ^a  

^a TOHOKU UNIVERSITY   (Japan)

Author keywords

adaptation; duplicated genes; evolvability; habitat distributions; habitat diversity

Indexed keywords

ARTICLE; BIODIVERSITY; CLIMATE; CORRELATION ANALYSIS; DROSOPHILA; DROSOPHILA MELANOGASTER; DROSOPHILA SIMULANS; EVOLUTIONARY ADAPTATION; GENE CLUSTER; GENE DUPLICATION; GENETIC DATABASE; GENETIC VARIABILITY; GENOME ANALYSIS; HABITAT; NONHUMAN; PHYLOGENY; SEQUENCE ANALYSIS; SPECIES DIVERSITY;

ANIMALS; CLIMATE; DROSOPHILA; ECOSYSTEM; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENES, DUPLICATE; GENES, INSECT; GENETIC VARIATION; GENOME, INSECT; GEOGRAPHY; POPULATION DENSITY; SPECIES SPECIFICITY;

EID: 84866953056     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/mss133     Document Type: Article

References (44)

1. Ashburner M, Thompson J, Carson HL. 1982. The genetics and biology of Drosophila, Vol. 3b. San Diego (CA): Academic Press.
2. Bosco G, Campbell P, Leiva-Neto JT, Markow TA. 2007. Analysis of Drosophila species genome size and satellite DNA content reveals significant differences among strains as well as between species. Genetics 177:1277-1290. (Pubitemid 350277032)
3. Bridle JR, Vines TH. 2007. Limits to evolution at range margins: when and why does adaptation fail? Trends Ecol Evol. 22:140-147. (Pubitemid 46273823)
4. Clark AG, EisenMB, Smith DR, et al. (417 co-authors). 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218. (Pubitemid 351972300)
5. Dean EJ, Davis JC, Davis RW, Petrov DA. 2008. Pervasive and persistent redundancy among duplicated genes in yeast. PLoS Genet. 4: e1000113.
6. Dong D, Yuan Z, Zhang Z. 2011. Evidences for increased expression variation of duplicate genes in budding yeast: from cis-to trans-regulation effects. Nucleic Acids Res. 39:837-847.
7. Felsenstein J. 1985. Phylogenies and the comparative method. Am Nat. 125:1-15.
8. Ha M, Kim ED, Chen ZJ. 2009. Duplicate genes increase expression diversity in closely related species and allopolyploids. Proc Natl Acad Sci USA. 106:2295-2300.
9. Hartman JL 4th, Garvik B, Hartwell L. 2001. Principles for the buffering of genetic variation. Science 291:1001-1004.
10. Heger A, Ponting CP. 2007. Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes. Genome Res. 17: 1837-1849. (Pubitemid 351360007)
11. Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A. 2005. Very high resolution interpolated climate surfaces for global land areas. Int J Climatol. 25:1965-1978. (Pubitemid 43013915)
12. Hoffmann AA. 2010. A genetic perspective on insect climate specialists. Austr J Entomol. 49:93-103.
13. Hoffmann AA, Willi Y. 2008. Detecting genetic responses to environmental change. Nat Rev Genet. 9:421-432. (Pubitemid 351693974)
14. Kellermann V, van Heerwaarden B, Sgro CM, Hoffmann AA. 2009. Fundamental evolutionary limits in ecological traits drive Drosophila species distributions. Science 325:1244-1246.
15. Kirkpatrick M, Barton NH. 1997. Evolution of a species' range. Am Nat. 150:1-23. (Pubitemid 27413925)
16. Kliebenstein DJ. 2008. A role for gene duplication and natural variation of gene expression in the evolution of metabolism. PLoS One. 3: e1838.
17. Kliman RM, Andolfatto P, Coyne JA, Depaulis F, Kreitman M, Berry AJ, McCarter J, Wakeley J, Hey J. 2000. The population genetics of the origin and divergence of the Drosophila simulans complex species. Genetics 156:1913-1931. (Pubitemid 32001252)
18. Kottek M, Grieser J, Beck C, Rudolf B, Rubel F. 2006. World Map of the Köppen-Geiger climate classification updated. Meteorologische Zeitschrift 15:259-263. (Pubitemid 44027664)
19. Legendre P, Legendre L. 1998. Numerical ecology, 2nd English ed. Amsterdam: Elsevier.
20. Lynch M, Conery JS. 2000. The evolutionary fate and consequences of duplicate genes. Science 290:1151-1155.
21. Lynch M, Conery JS. 2003. The origins of genome complexity. Science 302:1401-1404. (Pubitemid 37452183)
22. LynchM, SungW,Morris K, et al. (11 co-authors). 2008. A genome-wide view of the spectrum of spontaneous mutations in yeast. Proc Natl Acad Sci USA. 105:9272-9277.
23. Margalef DR. 1958. Information theory in ecology. Gen Syst. 3:36-71.
24. Markow T, O'Grady P. 2006. Drosophila: A guide to species identification and use. San Diego (CA): Academic Press.
25. Markow TA, O'Grady PM. 2007. Drosophila biology in the genomic age. Genetics 177:1269-1276. (Pubitemid 350277031)
26. McBride CS. 2007. Rapid evolution of smell and taste receptor genes during host specialization in Drosophila sechellia. Proc Natl Acad Sci USA. 104:4996-5001. (Pubitemid 47186165)
27. McBride CS, Arguello JR, O'Meara BC. 2007. Five Drosophila genomes reveal nonneutral evolution and the signature of host specialization in the chemoreceptor superfamily. Genetics 177: 1395-1416. (Pubitemid 350277040)
28. Metzker ML. 2010. Sequencing technologies-the next generation. Nat Rev Genet. 11:31-46.
29. Mirol PM, Routtu J, Hoikkala A, Butlin RK. 2008. Signals of demographic expansion in Drosophila virilis. BMC Evol Biol. 8:59.
30. Nardon C, Deceliere G, Loevenbruck C, Weiss M, Vieira C, Biemont C. 2005. Is genome size influenced by colonization of new environments in dipteran species? Mol Ecol. 14:869-878. (Pubitemid 40346478)
31. Notredame C, Higgins DG, Heringa J. 2000. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol. 302: 205-217.
32. Ohno S. 1970. Evolution by gene duplication. New York: Springer.
33. Pagel M. 1999. Inferring the historical patterns of biological evolution. Nature 401:877-884.
34. Petit N, Barbadilla A. 2009. Selection efficiency and effective population size in Drosophila species. J Evol Biol. 22:515-526.
35. Piano F, Craddock EM, Kambysellis MP. 1997. Phylogeny of the island populations of the Hawaiian Drosophila grimshawi complex: evidence from combined data. Mol Phylogenet Evol. 7: 173-184. (Pubitemid 127345880)
36. Reed LK,Markow TA. 2004. Early events in speciation: polymorphism for hybrid male sterility in Drosophila. Proc Natl Acad Sci USA. 101: 9009-9012. (Pubitemid 38781601)
37. Root TL, Price JT, Hall KR, Schneider SH, Rosenzweig C, Pounds JA. 2003. Fingerprints of global warming on wild animals and plants. Nature 421:57-60. (Pubitemid 36077083)
38. Roy K, Hunt G, Jablonski D, Krug AZ, Valentine JW. 2009. A macroevolutionary perspective on species range limits. Proc Biol Sci. 276: 1485-1493.
39. Singh ND, Larracuente AM, Sackton TB, Clark AG. 2009. Comparative genomics on the Drosophila phylogenetic tree. Annu Rev Ecol Evol Systemat. 40:459-480.
40. Tajima F. 1993. Simple methods for testing the molecular evolutionary clock hypothesis. Genetics 135:599-607. (Pubitemid 23307610)
41. Tsuda ME, Kawata M. 2010. Evolution of gene regulatory networks by fluctuating selection and intrinsic constraints. PLoS Comput Biol. 6: e1000873.
42. Wilkins AS. 1997. Canalization: a molecular genetic perspective. Bioessays 19:257-262. (Pubitemid 27140650)
43. Yang Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci. 13:555-556. (Pubitemid 27480216)
44. Yang Z, Nielsen R. 2000. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models.Mol Biol Evol. 17:32-43. (Pubitemid 30056990)