Coding sequence polymorphism in avian mitochondrial genomes reflects population histories

Molecular Ecology

Volumn 16, Issue 7, 2007, Pages 1369-1376

  Hughes, Austin L ^a   Hughes, Mary Ann K ^a  

^a UNIVERSITY OF SOUTH CAROLINA   (United States)

Author keywords

Nearctic migrant birds; Nearly neutral theory; Population bottleneck; Population effects of glaciation; Slightly deleterious mutations

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; BIRD; COMPARATIVE STUDY; DNA SEQUENCE; GENETIC POLYMORPHISM; GENETIC SELECTION; GENETICS; GEOGRAPHY; POPULATION DYNAMICS; POPULATION GENETICS; SPECIES DIFFERENCE;

ANIMALS; BIRDS; DNA, MITOCHONDRIAL; GENETICS, POPULATION; GEOGRAPHY; MODELS, GENETIC; POLYMORPHISM, GENETIC; POPULATION DYNAMICS; SELECTION (GENETICS); SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

AVES;

EID: 33947507808     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2007.03242.x     Document Type: Article

References (59)

1. Alvarez-Buylla ER, García-Burrios C, Lara-Moreno Martínez-Ramos M (1996) Demographic and genetic models in conservation biology: applications and perspectives for tropical rain forest tree species. Annual Review of Ecology and Systematics, 27, 387-421.
2. Askins RA, Lynch F, Greenberg R (1990) Population declines in migratory birds in eastern North America. Current Ornithology, 7, 1-57.
3. Avise JC, Ball RM, Arnold J (1988) Current versus historical population sizes in vertebrate species with high gene flow: a comparison based on mitochondrial DNA lineages and inbreeding theory for neutral mutations. Molecular Biology and Evolution, 5, 331-344.
4. Ballard JWO, Whitlock MC (2004) The incomplete natural history of mitochondria. Molecular Ecology, 13, 729-744.
5. Barron EJ (1984) Ancient climates: investigation with climate models. Reports of Progress in Physics, 47, 1563-1599.
6. Bazin E, Glémin S, Galtier N (2006) Population size does not influence mitochondrial genetic diversity in animals. Science, 312, 570-572.
7. Berthold P (1991) Orientation in birds: spatiotemporal programmes and genetics of orientation. EXS, 60, 86-105.
8. Berthold P, Pulido F (1994) Heritability of migratory activity in a natural bird population. Proceedings of the Royal Society of London. Series B, Biological Sciences, 257, 311-315.
9. Bucklin A, Wiebe PH (1998) Low mitochondrial diversity and small effective population sizes of the copepods Calanus finmarchicus and Nannocalanus minor: possible impact of climatic variation during recent glaciation. Journal of Heredity, 8, 383-392.
10. Charlesworth B (1992) New genes sweep clean. Nature, 356, 475-476.
11. Estoup A, Clegg M (2003) Bayesian inferences on the recent island colonization history by the bird Zosterops lateralis. Molecular Ecology, 12, 657-674.
12. Fay JC, Wu C-I (1999) A human population bottleneck can account for the discordance between patterns of mitochondrial versus nuclear DNA variation. Molecular Biology and Evolution, 16, 1003-1005.
13. Felsenstein J (1985) Phylogenies and the comparative method. American Naturalist, 125, 1-15.
14. Fuerst PA, Chakraborty R, Nei M (1977) Statistical studies on protein polymorphism in natural populations. I. Distribution of single-locus heterozygosity. Genetics, 86, 455-483.
15. Hewitt GM (2004) The structure of biodiversity - insights from molecular phylogeography. Frontiers in Zoology, 2004, I: 4.
16. Hughes AL (2004) A statistical analysis of factors associated with historical extinction and current endangerment of non-passerine birds. Wilson Bulletin, 116, 330-336.
17. Hughes AL (2005) Evidence for abundant slightly deleterious polymorphisms in bacterial populations. Genetics, 169, 533-538.
18. Hughes AL, Packer B, Welch R, Bergen AW, Chanock SJ, Yeager M (2003) Widespread purifying selection at polymorphic sites in human protein-coding loci. Proceedings of the National Academy of Sciences, USA, 100, 15754-15757.
19. Hughes AL, Packer B, Welch R, Bergen AW, Chanock SJ, Yeager M (2005) Effects of natural selection on inter-population divergence at polymorphic sites in human protein-coding loci. Genetics, 170, 1181-1187.
20. Hughes AL, Hughes MA, Friedman R (2006) Variable intensity of purifying selection on cytotoxic T-lymphocyte epitopes in hepatitis C virus. Virus Research, (in press).
21. Kastner TP, Goñi MA (2003) Constancy in the vegetation of the Amazon Basin during the Late Pleistocene: evidence from the organic matter composition of Amazon deep sea fan sediments. Geology, 31, 291-294.
22. Kimura M (1977) Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution. Nature, 267, 275-276.
23. Kimura M (1983) The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge, UK.
24. Kimura M, Ohta T (1974) On some principles governing molecular evolution. Proceedings of the National Academy of Sciences, USA, 71, 2848-2852.
25. Kuhner MK, Yamato J, Felsenstein J (1998) Maximum likelihood estimation of population growth rates based on the coalescent. Genetics, 149, 429-434.
26. Kumar S, Tamura K, Jakobsen IB, Nei M (2001) mega 2: molecular evolutionary genetics analysis software. Bioinformatics, 17, 1244-1245.
27. Leonard JA, Wayne RK, Cooper A (2000) Population genetics of Ice Age brown bears. Proceedings of the National Academy of Sciences, USA, 97, 1651-1654.
28. Lessa EP, Cook JA, Patton JL (2003) Genetic footprints of demographic expansion in North America, but not Amazonia, during the Late Quaternary. Proceedings of the National Academy of Sciences, USA, 100, 10331-10334.
29. Li W-H (1993) Unbiased estimates of the rates of synonymous and nonsynonymous substitution. Journal of Molecular Evolution, 36, 96-99.
30. Lowe L (2006) Quantifying the genomic decay paradox due to Muller's ratchet in human mitochondrial DNA. Genetical Research, 87, 133-159.
31. Martin PR, McKay JK (2004) Latitudinal variation in genetic divergence of populations and the potential for future speciation. Evolution, 58, 938-945.
32. Maynard Smith J, Haigh J (1974) The hitch-hiking effect of a favorable gene. Genetical Research, 23, 23-35.
33. McCusker MR, Parkinson E, Taylor EB (2000) Mitochondrial DNA variation in rainbow trout (Onchorhynchus mykiss) across its native range: testing biogeographical hypotheses and their relevance to conservation. Molecular Ecology, 9, 2089-2108.
34. McLean RG (2006) West Nile virus in North American birds. Ornithological Monographs, 60, 44-64.
35. Miller HC, Lambert DM (2004) Genetic drift outweighs balancing selection in shaping post-bottleneck major histocompatibility complex variation in New Zealand robins (Petroicidae). Molecular Ecology, 13, 3709-3721.
36. Nei M (1987) Molecular Evolutionary Genetics. Columbia University Press, New York.
37. Nei M, Kumar S (2000) Molecular Evolution and Phylogenetics. Oxford University Press, New York.
38. Nei M, Maruyama T, Chakraborty R (1975) The bottleneck effect and genetic variability in populations. Evolution, 29, 1-10.
39. Nielsen R, Weinreich DM (1999) The age of nonsynonymous and synonymous mutations in animal mtDNA and implications for the mildly-deleterious theory. Genetics, 153, 497-506.
40. O'Brien S (1994) A role for molecular genetics in biological conservation. Proceedings of the National Academy of Sciences, USA, 91, 5748-5755.
41. Ohta T (1976) Role of very slightly deleterious mutations in molecular evolution and polymorphism. Theoretical Population Biology, 10, 254-275.
42. Ohta T (2002) Near-neutrality in evolution of genes and gene regulation. Proceedings of the National Academy of Sciences, USA, 99, 6134-16137.
43. Pimm SL, Askins RA (1995) Forest losses predict bird extinctions in eastern North America. Proceedings of the National Academy of Sciences, USA, 92, 9343-9347.
44. Pulido F, Berthold P, Mohr G, Querner U (2001) Heritability of the timing of autumn migration in a natural bird population. Proceedings of the Royal Society of London. Series B, Biological Sciences, 268, 953-959.
45. Pulido F, Berthold P, van Noordwijk AJ (1996) Frequency of migrants and migrant activity are genetically correlated in a bird population: evolutionary implications. Proceedings of the National Academy of Sciences, USA, 93, 14642-14647.
46. Ruiz-Pesini E, Mishmar D, Brandon M, Procaccio V, Wallace DC (2004) Effects of purifying and adaptive selection on regional variation in human mtDNA. Science, 303, 223-226.
47. Schaeffer SW (2002) Molecular population genetics of sequence length diversity in the Adh region of Drosophila pseudoobscura. Genetical Research, 80, 163-175.
48. Sibley CG, Monroe BL (1990) Distribution and Taxonomy of Birds of the World. Yale University Press, New Haven, Connecticut.
49. Stattersfield AJ, Crosby MJ, Long AJ, Wege DC (1998) Endemic Bird Areas of the World: Priorities for Biodiversity Conservation. BirdLife International, Cambridge, UK.
50. Steadman DW (2005) The paleoecology and fossil history of migratory landbirds. In: Birds of Two Worlds: the Ecology and Evolution of Migration (eds Greenberg R, Marra PP), pp. 5-17. Johns Hopkins University Press, Baltimore, Maryland.
51. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 125, 585-595.
52. Takata N, Nei M (1990) Allelic genealogy under overdominant and frequency-dependent selection and polymorphism of major histocompatibility complex loci. Genetics, 124, 967-978.
53. Templeton AR (1994) Biodiversity at the molecular genetic level: experiences from disparate macrooorganisms. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 345, 59-64.
54. Thompson JD, Higgins DG, Gibson T (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22, 4673-4680.
55. Van der Meulen KM, Pensaert MB, Nauuwynck HJ (2005) West Nile virus in the vertebrate world. Archives of Virology, 150, 637-657.
56. Wakeley J (2000) The effects of subdivision on the genetic divergence of populations and species. Evolution, 54, 1092-1101.
57. Weinreich DM, Rand DM (2000) Contrasting patterns of non-neutral evolution in proteins encoded in nuclear and mitochondrial genomes. Genetics, 156, 385-399.
58. Williams TC, Webb TH III (1996) Neotropical bird migration during the Ice Ages: orientation and ecology. Auk, 113, 105-118.
59. Zhang J, Rosenberg HF, Nei M (1998) Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proceedings of the National Academy of Sciences, USA, 98, 3708-3713.