Natural distributions of mitochondrial sequence diversity support new null hypotheses

Evolution

Volumn 64, Issue 4, 2010, Pages 1136-1142

  Wares, John P ^a  

^a University of Georgia ^*  (United States)

Author keywords

Cytochrome oxidase I; Demography; Metazoans; Neutrality; Selection; Tajima's D

Indexed keywords

CYTOCHROME; DATA SET; DEMOGRAPHY; EMPIRICAL ANALYSIS; META-ANALYSIS; METAZOAN; MITOCHONDRIAL DNA; POPULATION GENETICS; SELECTION; TAXONOMY;

ANIMALIA; METAZOA;

CYTOCHROME C OXIDASE; MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; GENETIC VARIABILITY; GENETICS; META ANALYSIS; MOLECULAR EVOLUTION;

ANIMALS; DNA, MITOCHONDRIAL; ELECTRON TRANSPORT COMPLEX IV; EVOLUTION, MOLECULAR; GENETIC VARIATION;

EID: 77954978722     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/j.1558-5646.2009.00870.x     Document Type: Article

References (45)

1. Arunyawat U, Stephan W, Städler T. Using multilocus sequence data to assess population structure, natural selection, and linkage disequilibrium in wild tomatoes. Mol. Biol. Evol. 2007, 24:2310-2322.
2. Avise J C. Phylogeography 2000, Harvard Univ. Press, Cambridge, MA
3. Avise J C, Arnold J, Ball R M, Bermingham E, Lamb T, Neigel J E, Reeb C A, Saunders N C. Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Ann. Rev. Ecol. Syst. 1987, 18:489-522.
4. Bazin E, Duret L, Penel S, Galtier N. Polymorphix, a sequence polymorphism database. Nucleic Acids Res. 2005, 33:D481-D484.
5. Bazin E, Glémin S, Galtier N. Population size does not influence mitochondrial genetic diversity in animals. Science 2006, 312:570-572.
6. Cariello N F, Swenberg J A, Skopek T R. Fidelity of Thermococcus litoralis DNA polymerase (vent) in PCR determined by denaturing gradient gel electrophoresis. Nucleic Acids Res. 1991, 19:4193-4198.
7. Dowling D K, Friberg U, Lindell J. Evolutionary implications of non-neutral mitochondrial genetic variation. Trends Ecol. Evol. 2008, 23:546-554.
8. Ellegren H. Is genetic diversity really higher in large populations?. J. Biol. 2009, 8:41.
9. Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Marine Biol. Biotechnol. 1994, 3:294-299.
10. Foltz D W, Hrincevich A W, Rocha-Olivares A. Apparent selection intensity for the cytochrome oxidase subunit I gene varies with mode of reproduction in echinoderms. Genetica 2004, 122:115-125.
11. Fu Y X. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 1997, 147:915-925.
12. Haddrill P R, Bachtrog D, Andolfatto P. Positive and negative selection on noncoding DNA in Drosophila simulans. Mol. Biol. Evol. 2008, 25:1825-1834.
13. Hahn M W. Toward a selection theory of molecular evolution. Evolution 2008, 62:255-265.
14. Hebert P D N, Ratnasingham S, deWaard J R. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Philos. Trans. R Soc. Lond. B 2003, 270S:1-4.
15. Hickerson M J, Stahl E, Lessios H. Test for simultaneous divergence using approximate Bayesian computation. Evolution 2006, 60:2435-2453.
16. Huelsenbeck J P, Rannala B. Phylogenetic methods come of age: testing hypotheses in an evolutionary context. Science 1997, 276:227-232.
17. Ingman M, Gyllensten U. Rate variation between mitochondrial domains and adaptive evolution in humans. Hum. Mol. Genet. 2007, 16:2281-2287.
18. Luikart G, England P R, Tallmon D, Jordan S, Taberlet P. The power and promise of population genomics: from genotyping to genome typing. Nat. Rev. Genet. 2003, 4:981-994.
19. Meiklejohn C D, Montooth K L, Rand D M. Positive and negative selection on the mitochondrial genome. Trends Genet. 2007, 23:259-263.
20. Mishmar D, Ruiz-Pesini E, Golik P, Macaulay V, Clark A G, Hosseini S, Brandon M, Easley K, Chen E, Brown M D. Natural selection shaped regional mtDNA variation in humans. Proc. Natl. Acad. Sci. USA 2003, 100:171-176.
21. Nabholz B, Glémin S, Galtier N. The erratic mitochondrial clock: variations of mutation rate, not population size, affect mtDNA diversity across birds and mammals. BMC Evol. Biol. 2009, 9:54.
22. Pfenninger M, Schwenk K. Cryptic animal species are homogeneously distributed among taxa and biogeographical regions. BMC Evol. Biol. 2007, 7:121.
23. Ramos-Onsins S E, Puerma E, Balañá-Alcaide D, Salguero D, Aguadé M. Multilocus analysis of variation using a large empirical data set: phenylpropanoid pathway genes in Arabidopsis thaliana. Mol. Ecol. 2008, 17:1211-1223.
24. Rand D M. The units of selection on mitochondrial DNA. Annu. Rev. Ecol. Syst. 2001, 32:415-448.
25. Rand D M, Kann L M. Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans. Mol. Biol. Evol. 1996, 13:735-748.
26. Roman J, Palumbi S R. Whales before whaling in the North Atlantic. Science 2003, 301:508-510.
27. Seo T, Kishino H, Thorne J L. Estimating absolute rates of synonymous and nonsynonymous nucleotide substitution in order to characterize natural selection and date species divergences. Mol. Biol. Evol. 2004, 21:1201-1213.
28. Shearer T L, Coffroth M A. Barcoding corals: limited by interspecific divergence, not intraspecific variation. Mol. Ecol. Res. 2008, 8:247-255.
29. Smith J M, Smith N H. Recombination in animal mitochondrial DNA. Mol. Biol. Evol. 2002, 19:2330-2332.
30. Städler T, Haubold B, Merino C, Stephan W, Pfaffelhuber P. The impact of sampling schemes on the site frequency spectrum in nonequilibrium subdivided populations. Genetics 2009, 182:205-216.
31. Stajich J E, Hahn M W. Disentangling the effects of demography and selection in human history. Mol. Biol. Evol. 2005, 22:63-73.
32. Swofford D. Phylogenetic analysis using parsimony (PAUP) v. 2002, 4.0b10
33. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 1989, 123:585-595.
34. Thornton K. libsequence: a C++ class library for evolutionary genetic analysis. Bioinformatics 2003, 19:2325-2327.
35. Thornton K. Recombination and the properties of Tajima's D in the context of approximate-likelihood calculation. Genetics 2005, 171:2143-2148.
36. Tindall K R, Kunkel T A. Fidelity of DNA synthesis by the Thermus aquaticus DNA polymerase. Biochemistry 1988, 27:6008-6013.
37. Vermeij G. Foreword: Molecules, Markers, and Mollusks. Molecular systematics and phylogeography of mollusks 2003, vii-x. Lydeard CLindberg D L. Pp.,eds., Smithsonian Books, WashingtonDC
38. Wakeley J. Coalescent theory: an introduction 2008, Roberts & Co, Greenwood Village, CO
39. Wakeley J, Takahashi T. Gene genealogies when the sample size exceeds the effective size of the population. Mol. Biol. Evol. 2003, 20:208-213.
40. Wares J P. Intraspecific variation and geographic isolation in Idotea balthica (Isopoda: Valvifera). J. Crustacean Biol. 2001, 21:1007-1013.
41. Wares J P, Cunningham C W. Diversification predates glaciation in Balanus glandula. Biol. Bull. 2005, 208:60-68.
42. Wares J P, Pringle J M. Drift by drift: effective population size is limited by advection. BMC Evol. Biol. 2008, 8:235.
43. Wayne M L, Simonsen K L. Statistical tests of neutrality in the age of weak selection. Trends Ecol. Evol. 1998, 13:236-240.
44. Willett C S, Burton R S. Environmental influences on epistatic interactions: viabilities of cytochrome c genotypes in interpopulation crosses. Evolution 2003, 57:2286-2292.
45. Zeng K, Fu Y-X, Shi S, Wu C-I. Statistical tests for detecting positive selection by utilizing high-frequency variants. Genetics 2006, 174:1431-1439.