The causes of mitochondrial DNA gene tree paraphyly in birds

McKay, Bailey D.; Zink, Robert M.

doi:10.1016/j.ympev.2009.08.024

Cited by 168 publications

(145 citation statements)

References 26 publications

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“…This is a large figure, especially when combined with the number of systems with discordance documented in the last two decades (Table 1), the suggestive cases requiring further confirmation (Table S3, Supporting information) and those likely caused by incomplete lineage sorting not included in our survey (e.g. McKay & Zink 2010). This suggests that discordance between the mitochondrial and nuclear genomes is a prevalent and important phenomenon.…”

Section: Prevalence Of Mito-nuclear Discordancementioning

confidence: 74%

“…While some authors suggest that taxonomy may not be the ideal guide for studies of mtDNA paraphyly (i.e. Rheindt & Edwards 2011), McKay & Zink (2010 reported that approximately 14% of 856 avian species examined showed evidence of paraphyly and that imperfect taxonomy was the most prevalent explanation for the discordances (55.7% of cases) as compared to incomplete lineage sorting (15.6%) or introgression (5.7%), although in many cases, they suggest that the latter two processes could not be distinguished (21.3%;McKay & Zink 2010).…”

Section: Box 1 Previous Treatments Of Mitochondrial Discordance and mentioning

confidence: 99%

“…Distinguishing between incomplete lineage sorting and these other types of discordance can be difficult (McKay & Zink 2010). One important distinction, however, is that discordance that arises from incomplete lineage sorting is not expected to leave any predictable biogeographic pattern (Fig.…”

Section: Introductionmentioning

confidence: 99%

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The biogeography of mitochondrial and nuclear discordance in animals

2012

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Combining nuclear (nuDNA) and mitochondrial DNA (mtDNA) markers has improved the power of molecular data to test phylogenetic and phylogeographic hypotheses and has highlighted the limitations of studies using only mtDNA markers. In fact, in the past decade, many conflicting geographic patterns between mitochondrial and nuclear genetic markers have been identified (i.e. mito-nuclear discordance). Our goals in this synthesis are to: (i) review known cases of mito-nuclear discordance in animal systems, (ii) to summarize the biogeographic patterns in each instance and (iii) to identify common drivers of discordance in various groups. In total, we identified 126 cases in animal systems with strong evidence of discordance between the biogeographic patterns obtained from mitochondrial DNA and those observed in the nuclear genome. In most cases, these patterns are attributed to adaptive introgression of mtDNA, demographic disparities and sex-biased asymmetries, with some studies also implicating hybrid zone movement, human introductions and Wolbachia infection in insects. We also discuss situations where divergent mtDNA clades seem to have arisen in the absence of geographic isolation. For those cases where foreign mtDNA haplotypes are found deep within the range of a second taxon, data suggest that those mtDNA haplotypes are more likely to be at a high frequency and are commonly driven by sex-biased asymmetries and ⁄ or adaptive introgression. In addition, we discuss the problems with inferring the processes causing discordance from biogeographic patterns that are common in many studies. In many cases, authors presented more than one explanation for discordant patterns in a given system, which indicates that likely more data are required. Ideally, to resolve this issue, we see important future work shifting focus from documenting the prevalence of mito-nuclear discordance towards testing hypotheses regarding the drivers of discordance. Indeed, there is great potential for certain cases of mitochondrial introgression to become important natural systems within which to test the effect of different mitochondrial genotypes on whole-animal phenotypes.

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Section: Prevalence Of Mito-nuclear Discordancementioning

confidence: 74%

Section: Box 1 Previous Treatments Of Mitochondrial Discordance and mentioning

confidence: 99%

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The biogeography of mitochondrial and nuclear discordance in animals

2012

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“…Accumulating multilocus studies have shown that when mtDNA is under selection, adding this marker will gain a more comprehensive phylogeographic picture. Lastly, a few persuasive exceptions should not discount the fact that mtDNA often reveals geographically and taxonomically important patterns, especially among recently isolated taxa (Zink and Barrowclough, 2008;McKay and Zink, 2010).…”

Section: Resultsmentioning

confidence: 99%

Distinguishing the effects of selection from demographic history in the genetic variation of two sister passerines based on mitochondrial–nuclear comparison

Hung

Zink

2014

Heredity

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Determining the mechanisms responsible for the distribution of genetic diversity in natural populations has occupied a central role in molecular evolution. Our study was motivated by the unprecedented observation that a widespread Eurasian flycatcher, Ficedula albicilla, exhibited no variation at the mitochondrial DNA (mtDNA) ND2 gene in 75 individuals sampled over a 5000-km distance. In contrast, its sister species, F. parva, had low but considerably higher levels of mtDNA variation. We assessed whether natural selection or demographic factors could explain the absence of mtDNA variation in F. albicilla. Eighteen nuclear genes were sequenced to estimate the two species' phylogeographic histories, and for comparison to the mtDNA data. Multilocus coalescence analyses suggested that F. albicilla experienced a population expansion perhaps following a population bottleneck. Simulations based on this demographic history, however, did not replicate the extremely low level of mtDNA variation. Historical range changes based on ecological niche models also failed to explain the observed mtDNA patterns. Neutrality tests (DHEW and ML-HKA) suggested a non-neutral pattern in the mtDNA of F. albicilla. We found a transmembrane-skewed distribution of nonsynonymous substitutions between the two species, three of which caused functional change; the results implied that positive selection could have targeted mtDNA. Several lines of evidence support selection rather than demographic history as the main force influencing the patterns of mtDNA variation. Despite the influence of natural selection, many of the phylogeographic inferences derived from mtDNA were robust, including species limits and a high level of gene flow among populations within species.

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“…Given the documented role of anole dewlaps in species recognition and presumably reproductive isolation (e.g., Losos, 1985;Macedonia and Stamps, 1994;Sigmund, 1983), these results may indicate that D. philopunctata is still in its very first stages of speciation. A vast number of studies have documented paraphyly among animal species that are phenotypically and often ecologically distinct (e.g., Brown and Twomey, 2009;Johnson et al, 2005;McKay and Zink, 2010;Omland et al, 2000), including anoles (Thorpe and Stenson, 2003). From the perspective of allele coalescence, the speciation process inherently starts with paraphyly in gene genealogies, and the probability of achieving reciprocal monophyly increases with time since population divergence (Knowles and Carstens, 2007).…”

Section: Genetic and Phenotypic Divergence Between D Punctata And Dmentioning

confidence: 99%