Evidence from a house finch (haemorhous mexicanus) spleen transcriptome for adaptive evolution and biased gene conversion in passerine birds

Molecular Biology and Evolution

Volumn 30, Issue 5, 2013, Pages 1046-1050

  Backström, Niclas ^a,b   Zhang, Qu ^a   Edwards, Scott V ^a  

^a HARVARD UNIVERSITY   (United States)

^b UPPSALA UNIVERSITY   (Sweden)

Author keywords

biased gene conversion; dN dS; effective population size; house finch; positive selection; transcriptome

Indexed keywords

TRANSCRIPTOME;

ARTICLE; BIRD; CHICKEN; CODON; DNA BASE COMPOSITION; ECOLOGY; EVOLUTIONARY RATE; FINCH; GENE CONVERSION; GENE FUNCTION; HAEMORHOUS MEXICANUS; LIPID METABOLISM; NATURAL SELECTION; NERVE CELL DIFFERENTIATION; NONHUMAN; PASSERINE BIRD; SEXUAL SELECTION; SPLEEN; TAENIOPYGIA GUTTATA;

ANIMALS; EVOLUTION, MOLECULAR; FINCHES; SPLEEN; TRANSCRIPTOME;

AVES; CARPODACUS MEXICANUS; GALLIFORMES; PASSERIFORMES; TAENIOPYGIA GUTTATA;

EID: 84876544645     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/mst033     Document Type: Article

References (43)

1. Axelsson E, Ellegren H. 2009. Quantification of adaptive evolution of genes expressed in avian brain and the population size effect on the efficacy of selection. Mol Biol Evol. 26: 1073-1079.
2. Axelsson E, Hultin-Rosenberg L, BrandströmM, ZwahlénM, ClaytonDF, Ellegren H. 2008. Natural selection in avian protein-coding genes expressed in brain. Mol Ecol. 17: 3008-3017. (Pubitemid 351793532)
3. Backström N, Shipilina D, Blom MPK, Edwards SV. 2013. Cis-regulatory sequence variation and association with Mycoplasma load in natural populations of the house finch (Carpodacus mexicanus). Ecol Evol., doi: 10.1002/ece3.484.
4. Berglund J, Pollard KS,Webster MT. 2009. Hotspots of biased nucleotide substitutions in human genes. PLoS Biol. 7: e1000026.
5. Bonneaud C, Balenger SL, Russell AF, Zhang J, Hill GE, Edwards SV. 2011. Rapid evolution of disease resistance is accompanied by functional changes in gene expression in a wild bird. Proc Natl Acad Sci USA. 108: 7866-7871.
6. Bonneaud C, Balenger SL, Zhang J, Edwards SV, Hill GE. 2012. Innate immunity and the evolution of resistance to an emerging infectious disease in a wild bird. Mol Ecol. 21: 2628-2639.
7. Bonneaud C, Burnside J, Edwards SV. 2008. High-speed developments in avian genomics. Bioscience 58: 587-595.
8. Boussau B, Gouy M. 2006. Efficient likelihood computations with nonreversible models of evolution. Syst Biol. 55: 756-768.
9. Butler PJ, Woakes AJ. 1990. The physiology of bird flights. In: Gwinner E, editor. Bird migration. New York: Springer. p. 300-318.
10. Clutton-Brock TH, Sheldon BC. 2010. Individuals and populations: the role of long-term, individual-based studies in ecology and evolutionary biology. Trends Ecol Evol. 25: 562-573.
11. de Magalhaes JP, Costa J. 2009. A database of vertebrate longevity records and their relation to other life-history traits. J Evol Biol. 22: 1770-1774.
12. Dunning JB Jr. 2008. CRC handbook of avian body masses. Boca Raton (FL): CRC Press.
13. Eyre-Walker A, Keightley PD. 2007. The distribution of fitness effects of new mutations. Nat Rev Genet. 8: 610-618. (Pubitemid 47077280)
14. Fidler AE, van Oers K, Drent PJ, Kuhn S, Mueller JC, Kempenaers B. 2007. Drd4 gene polymorphisms are associated with personality variation in a passerine bird. Proc Biol Sci. 274: 1685-1691. (Pubitemid 47356118)
15. Fitzpatrick JW. 1988. Why so many passerine birds? A response to Raikow. Syst Zool. 37: 66-76.
16. Fujita MK, Edwards SV, Ponting CP. 2011. The Anolis lizard genome: an amniote genome without isochores. Genome Biol Evol. 3: 974-984.
17. Galtier N, Gouy M. 1998. Inferring pattern and process: maximumlikelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis. Mol Biol Evol. 15: 871-879. (Pubitemid 28321885)
18. George RD, McVicker G, Diederich R, Ng SB, MacKenzie AP, Swanson WJ, Shendure J, Thomas JH. 2011. Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection. Genome Res. 21: 1686-1694.
19. Hedges SB, Kumar S. 2009. The timetree of life. New York: Oxford University Press.
20. ICGSC. 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695-716.
21. Jenni-Eiermann S, Jenni L. 1991. Metabolic responses to flight and fasting in night-migrating passerines. J Comp Physiol B. 161: 465-474.
22. Kochmer JP, Wagner RH. 1988. Why are there so many kinds of Passerine birds? Because they are small. A reply to Raikow. Syst Zool. 37: 68-69.
23. Kosakovsky Pond SL, Murrell B, Fourment M, Frost SD, Delport W, Scheffler K. 2011. A random effects branch-site model for detecting episodic diversifying selection. Mol Biol Evol. 28: 3033-3043.
24. Kosiol C, Vinar T, da Fonseca RR, Hubisz MJ, Bustamante CD, Nielsen R, Siepel A. 2008. Patterns of positive selection in six mammalian genomes. PLoS Genet. 4: e1000144.
25. Kumar S, Filipski AJ, Battistuzzi FU, Kosakovsky Pond SL, Tamura K. 2012. Statistics and truth in phylogenomics. Mol Biol Evol. 29: 457-472.
26. Künstner A, Wolf JBW, Backström N, et al. (13 co-authors). 2010. Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 11 bird species. Mol Ecol. 19: 266-276.
27. Lartillot N. Phylogenetic patterns of GC-biased gene conversion in placental mammals and the evolutionary dynamics of recombination landscapes. Mol Biol Evol., Advance Access published October 18, 2012, doi: 10.1093/molbev/mss239.
28. Lundgren BO, Kiessling K-H. 1986. Catabolic enzyme activities in the pectoralis muscle of premigratory and migratory juvenile reed warblers Acrocephalus scirpaceus (Herin.). Oecologia 68: 529-532.
29. Lynch M. 2007. The origins of genome architecture. Sunderland (MA): Sinauer Associates.
30. Marais G. 2003. Biased gene conversion: implications for genome and sex evolution. Trends Genet. 19: 330-338. (Pubitemid 36694616)
31. Mindell DP, Knight A, Baer CF, Hiuddleston J. 1996. Slow rates of molecular evolution in birds and the metabolic rate and body temperature hypotheses. Mol Biol Evol. 13: 422-426.
32. Mueller JC, Pulido F, Kempenaers B. 2011. Identification of a gene associated with avian migratory behaviour. Proc Roy Soc B. 278: 2848-2856.
33. Nabholz B, Kunstner A, Wang R, Jarvis ED, Ellegren H. 2011. Dynamic evolution of base composition: causes and consequences in avian phylogenomics. Mol Biol Evol. 28: 2197-2210.
34. Nam K, Mugal C, Nabholz B, et al. (12 co-authors). 2010. Molecular evolution of genes in avian genomes. Genome Biol. 11: R68.
35. Ohta T. 1992. The nearly neutral theory of molecular evolution. Annu Rev Ecol Evol Syst. 23: 263-286. (Pubitemid 24412250)
36. Peterson MP, Whittaker DJ, Ambreth S, et al. (12 co-authors). 2012. De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis)-genomic tools for an ecological model system. BMC Genomics 13: 305.
37. Romiguier J, Ranwez V, Douzery EJ, Galtier N. 2010. Contrasting GC-content dynamics across 33 mammalian genomes: relationship with life-history traits and chromosome sizes. Genome Res. 20: 1001-1009.
38. Rubin CJ, Megens HJ, Martinez Barrio A, et al. (14 co-authors). 2012. Strong signatures of selection in the domestic pig genome. Proc Natl Acad Sci USA. 109: 19529-19536.
39. Sætre GP, Sæther SA. 2010. Ecology and genetics of speciation in Ficedula flycatchers. Mol Ecol. 19: 1091-1106.
40. Santure AW, Gratten J, Mossman JA, Sheldon BC, Slate J. 2011. Characterisation of the transcriptome of a wild great tit Parus major population by next generation sequencing. BMC Genomics 12: 283.
41. Wang Z, Gerstein M, Snyder M. 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 10: 57-63.
42. Welch JJ, Bininda-Emonds ORP, Bromham L. 2008. Correlates of substitution rate variation in mammalian protein-coding sequences. BMC Evol Biol. 8: e53.
43. White EP, Ernest SKM, Kerkhoff AJ, Enquist BJ. 2007. Relationships between body size and abundance in ecology. Trends Ecol Evol. 22: 323-330. (Pubitemid 46734519)