When non-coding is non-neutral: The role of CHD1 gene polymorphism in sexing, in phylogenetics and as a correlate of fitness in birds

Ibis

Volumn 152, Issue 2, 2010, Pages 223-225

  Benedict, Lauryn ^a   Bowie, Rauri C K ^a   Fuchs, Jerome ^a,b   Macmanes, Matthew ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CAPE TOWN   (South Africa)

Author keywords

[No Author keywords available]

Indexed keywords

AVES;

EID: 77952533401     PISSN: 00191019     EISSN: 1474919X     Source Type: Journal    
DOI: 10.1111/j.1474-919X.2010.01015.x     Document Type: Note

References (36)

1. Backström N, Fagerber S, Ellegren H. Genomics of natural bird populations: a gene-based set of reference markers evenly spread across the avian genome. Mol. Ecol. 2008, 17:964-980.
2. Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D. Ultraconserved elements in the human genome. Science 2004, 304:1321-1325.
3. Bowie RCK, Fjeldså J, Kiure J. Multilocus molecular DNA variation in Winifred's Warbler Scepomycter winifredae suggests cryptic speciation and the existence of a threatened species in the Rubeho-Ukaguru Mountains of Tanzania. Ibis 2009, 151:709-719.
4. Carling MD, Brumfield RT. Haldane's rule in an avian system: using cline theory and divergence population genetics to test for differential introgression of mitochondrial, autosomal, and sex-linked loci across the Passerina bunting hybrid zone. Evolution 2008, 62:2600-2615.
5. Chapman JR, Nakagawa S, Coltman DW, Slate J, Sheldon BC. A quantitative review of heterozygosity-fitness correlations in animal populations. Mol. Ecol. 2009, 18:2746-2765.
6. Dawson DA, Darby S, Hunter FM, Krupta AP, Jones IL, Burke T. A critique of avain CHD-based molecular sexing protocols illustrated by a Z-chromosome polymorphism detected in auklets. Mol. Ecol. Notes 2001, 1:201-204.
7. Edwards SV, Dillon M. Hitchhiking and recombination in birds: evidence from Mhc-linked and unlinked loci in Red-winged Blackbirds (Agelaius phoeniceus). Genet. Res. 2004, 84:175-192.
8. Ellegren H. The avian genome uncovered. Trends Ecol. Evol. 2005, 20:180-186.
9. Excoffier L, Heckel G. Computer programs for population genetics data analysis: a survival guide. Nat. Rev. Genet. 2006, 7:745-758.
10. Fu YX. New statistical tests of neutrality for DNA samples from a population. Genetics 1996, 143:557-570.
11. Garcia-Moreno J, Mindell DP. Rooting a phylogeny with homologous genes on opposite sex chromosomes (gametologs): a case study using avian CHD. Mol. Biol. Evol. 2000, 17:1826-1832.
12. Griffiths R, Double MC, Orr K, Dawson RJG. A DNA test to sex most birds. Mol. Ecol. 1998, 7:1071-1075.
13. Hackett SJ, Kimball RT, Reddy S, Bowie RCK, Braun EL, Braun MJ, Chojnowski JL, Cox WA, Han K-L, Harshman J, Huddleton CJ, Marks BD, Miglia KJ, Moore WA, Sheldon FH, Steadman DW, Witt CC, Yuri T. A phylogenomic study of birds reveals their evolutionary history. Science 2008, 320:1763-1768.
14. Haldane JBS. Sex ratio and unisexual sterility in animal hybrids. J. Genet. 1922, 12:101-109.
15. Hillier LW. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 2004, 432:695-716.
16. Hudson RR, Kreitman M, Aguadé M. A test of neutral molecular evolution based on nucleotide data. Genetics 1987, 116:153-159.
17. Jennings WB, Edwards SV. Speciational history of Australian Grass Finches (Poephila) inferred from 30 gene trees. Evolution 2005, 59:2033-2047.
18. Kim SY, Pritchard JK. Adaptive evolution of conserved noncoding elements in mammals. PLoS Genet. 2007, 3:1572-1586.
19. Kimball RT, Braun EL, Barker FK, Bowie RCK, Braun MJ, Chojnowski JL, Hackett SJ, Han K, Harshman J, Heimer-Torres V, Holznagel W, Huddleston CJ, Marks BD, Miglia KJ, Moore WS, Reddy S, Sheldon FH, Smith JV, Witt CC, Yuri T. A well-tested set of primers to amplify regions spread across the avian genome. Mol. Phylogenet. Evol. 2009, 50:654-660.
20. Lee PLM, Brain PF, Forman DW, Bradbury RB, Griffiths R. Sex and death: CHD1Z associated with high mortality in Moorhens. Evolution 2002, 56:2548-2553.
21. McDonald JH, Kreitman M. Apaptive protein evoluation at the Adh locus in Drosophila. Nature 1991, 351:652-654.
22. Mullen LM, Vignieri SN, Gore JA, Hoekstra H. Adaptive basis of geographic variation: genetic, phenotypic and environmental differences among beach mouse populations. Proc. R. Soc. Lond. B 2009, 276:3809-3818.
23. Nielsen R. Molecular signatures of natural selection. Annu. Rev. Genet. 2005, 39:197-218.
24. Nielsen R, Beaumont MA. Statistical inferences in phylogeography. Mol. Ecol. 2009, 18:1034-1047.
25. Penn DJ, Potts WK. The evolution of mating preferences and major histocompatibility complex genes. Am. Nat. 1999, 153:145-164.
26. Peters JL, McCracken KG, Zhuravlev YN, Lu Y, Wilson RE, Johnson KP, Omland KE. Phylogenetics of wigeons and allies (Anatidae: Anas): the importance of sampling multiple loci and multiple individuals. Mol. Phylogenet. Evol. 2005, 35:209-224.
27. Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 2010, 20:110-121.
28. Rosenblum EB, Römpler H, Schöneberg T, Hoekstra HE. Molecular and functional basis of phenotypic convergence in white lizards at white sands. Proc. Natl Acad. Sci. USA 2010, 107:2113-2117.
29. Sæther SA, Sætre G, Borge T, Wiley C, Svedin N, Andersson G, Veen T, Haavie J, Servedio MR, Bureš S, Král M, Hjernquist MB, Gustafsson L, Träff J, Qvarnström A. Sex chromosome-linked species recognition and evolution of reproductive isolation in flycatchers. Science 2007, 318:95-97.
30. Schroeder J, Lourenço PM, Hooijmeijer JCEW, Both C, Piersma T. A possible case of contemporary selection leading to a decrease in sexual plumage dimorphism in a grassland-breeding shorebird. Behav. Ecol. 2009, 20:797-807.
31. Schroeder J, Kentie R, van der Velde M, Hooijmeijer JCEW, Both C, Haddrath O, Baker AJ, Piersma T. Linking intronic polymorphism on the CHD1-Z gene with fitness correlates in Black-tailed Godwits Limosa l. limosa. Ibis 2010, 152:368-377.
32. Stinchcombe JR, Hoekstra HE. Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits. Heredity 2008, 100:158-170.
33. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 1989, 123:585-595.
34. Uy JAC, Moyle RG, Filardi CE, Cheviron ZA. Difference in plumage color used in species recognition between incipient species is linked to a single amino acid substitution in the Melanocortin-1 Receptor. Am. Nat. 2009, 174:244-254.
35. Yang Z. Computational Molecular Evoluation 2006, Oxford, Oxford University Press
36. Zelano B, Edwards SV. An Mhc component to kin recognition and mate choice in birds: predictions, progress, and prospects. Am. Nat. 2002, 160:225-237.