Determination of Mitochondrial Genetic Diversity in Mammals

Nabholz, Benoît; Mauffrey, Jean-François; Bazin, Éric; Galtier, Nicolas; Glémin, Sylvain

doi:10.1534/genetics.107.073346

Cited by 119 publications

(150 citation statements)

References 67 publications

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“…Previous work has found that selection on mtDNA makes it a poor indicator of population size (Bazin et al 2006;Nabholz et al 2009) or species history (Bensch et al 2006) or is uncorrelated with life history traits (Nabholz et al 2008), but other work suggests that selection is not strong enough to bias phylogenetic inference (Zink 2005). Our results that mtDNA was under weak positive selection differ from previous work showing purifying selection reduced mtDNA genetic variability (Bazin et al 2006;Stewart et al 2008), but evidence of positive selection on mtDNA is not a unique finding.…”

Section: Selection On Mtdnacontrasting

confidence: 88%

“…However, mtDNA and nuclear DNA can exhibit discordant phylogeographic patterns due to sex-biased dispersal (Peters et al 2012), introgression (Bryson et al 2010;Reid et al 2012), and/or incomplete lineage sorting (Ballard and Whitlock 2004). Further, the utility of mtDNA as a phylogenetic marker has been questioned because of evidence of selective sweeps causing mtDNA genetic diversity to be incongruent with species abundance estimates (Bazin et al 2006;Nabholz et al 2008Nabholz et al , 2009. Since phylogeographic studies often do not measure selection, the usage of PRF models to estimate divergence times, effective population sizes, and selection coefficients provides a means of incorporating the informativeness of mtDNA and at the same time assessing the strength of selection on mtDNA markers.…”

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confidence: 99%

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Robust Estimates of Divergence Times and Selection with a Poisson Random Field Model: A Case Study of Comparative Phylogeographic Data

Amei

Smith

2014

Genetics

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Mutation frequencies can be modeled as a Poisson random field (PRF) to estimate speciation times and the degree of selection on newly arisen mutations. This approach provides a quantitative theory for comparing intraspecific polymorphism with interspecific divergence in the presence of selection and can be used to estimate population genetic parameters. Although the original PRF model has been extended to more general biological settings to make statistical inference about selection and divergence among model organisms, it has not been incorporated into phylogeographic studies that focus on estimating population genetic parameters for nonmodel organisms. Here, we modified a recently developed time-dependent PRF model to independently estimate genetic parameters from a nuclear and mitochondrial DNA data set of 22 sister pairs of birds that have diverged across a biogeographic barrier. We found that species that inhabit humid habitats had more recent divergence times and larger effective population sizes than those that inhabit drier habitats, and divergence time estimated from the PRF model were similar to estimates from a coalescent species-tree approach. Selection coefficients were higher in sister pairs that inhabited drier habitats than in those in humid habitats, but overall the mitochondrial DNA was under weak selection. Our study indicates that PRF models are useful for estimating various population genetic parameters and serve as a framework for incorporating estimates of selection into comparative phylogeographic studies.A range of analytical approaches have been developed to estimate divergence times and effective population sizes from DNA data (Takahata et al. 1995;Yang 1997Yang , 2002Hickerson et al. 2003;Rannala and Yang 2003;Hey and Nielsen 2004;Heled and Drummond 2010). These types of models have been applied to an array of empirical systems and used to reconstruct population history (e.g., Jennings and Edwards 2005;Won and Hey 2005;Lee and Edwards 2008;Hurt et al. 2009;Hailer et al. 2012), but the extension of these analyses to incorporate selection has been limited. A potential means of including selection estimates into studies examining population or phylogeographic history is the implementation of approaches that compare polymorphic and fixed nucleotide patterns within and between species (Hudson et al. 1987). Using this method, McDonald and Kreitman (1991) proposed a statistical test for homogeneity of synonymous and nonsynonymous DNA mutations among closely related species and demonstrated that an excess of nonsynonymous differences among fruit fly species was the result of the fixation of beneficial mutations.The McDonald-Kreitman test was extended and incorporated into a quantitative model used to compare intraspecific polymorphism with interspecific divergence by modeling mutation frequencies as a Poisson random field (PRF) (Sawyer and Hartl 1992). The PRF models the number of synonymous and nonsynonymous fixed differences and polymorphic sites as independent Poisson random varia...

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Section: Selection On Mtdnacontrasting

confidence: 88%

mentioning

confidence: 99%

Robust Estimates of Divergence Times and Selection with a Poisson Random Field Model: A Case Study of Comparative Phylogeographic Data

Amei

Smith

2014

Genetics

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“…Conversely, Bazin et al (2006) reported a non-significantly negative correlation (Kendall t¼À0.14) between mtDNA sequence diversity and nuclear allozyme genetic diversity across eight major animal groups encompassing 1683 species, while finding a significant positive correlation between nuclear DNA diversity and allozyme diversity (t¼0.87) across the same groups. Subsequent analyses using the same data set revealed significant positive correlations between mtDNA and allozyme genetic diversity across eutherian mammalian orders (Mulligan et al, 2006) and within mammals (Nabholz et al, 2008b). Several other studies have also reported positive correlations between mtDNA diversity and population size or its surrogates (Table 1), but these have all involved data across a narrower taxonomic range than used by Bazin et al (2006).…”

Section: Correlations Of Genetic Diversity With Population Size and Fmentioning

confidence: 79%

How closely does genetic diversity in finite populations conform to predictions of neutral theory? Large deficits in regions of low recombination

Frankham

2011

Heredity

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Levels of genetic diversity in finite populations are crucial in conservation and evolutionary biology. Genetic diversity is required for populations to evolve and its loss is related to inbreeding in random mating populations, and thus to reduced population fitness and increased extinction risk. Neutral theory is widely used to predict levels of genetic diversity. I review levels of genetic diversity in finite populations in relation to predictions of neutral theory. Positive associations between genetic diversity and population size, as predicted by neutral theory, are observed for microsatellites, allozymes, quantitative genetic variation and usually for mitochondrial DNA (mtDNA). However, there are frequently significant deviations from neutral theory owing to indirect selection at linked loci caused by balancing selection, selective sweeps and background selection. Substantially lower genetic diversity than predicted under neutrality was found for chromosomes with low recombination rates and high linkage disequilibrium (compared with 'normally' recombining chromosomes within species and adjusted for different copy numbers and mutation rates), including W (median 100% lower) and Y (89% lower) chromosomes, dot fourth chromosomes in Drosophila (94% lower) and mtDNA (67% lower). Further, microsatellite genetic and allelic diversity were lost at 12 and 33% faster rates than expected in populations adapting to captivity, owing to widespread selective sweeps. Overall, neither neutral theory nor most versions of the genetic draft hypothesis are compatible with all empirical results.

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“…They suggested that complete genetic linkage in mtDNA genomes and recurrent positive selection (Gillespie 2001) may underlie such patterns. However, within-taxa comparisons show positive correlations between mtDNA heterozygosity and nuclear genome variation in mammals (Mulligan et al 2006;Nabholz et al 2008) and other animals (Piganeau and Eyre-Walker 2009). Variation in mutation rates, adaptive evolution, and=or biased transmission may contribute to within-and between-taxa differences for mtDNA polymorphism.…”

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confidence: 99%

Weak Selection and Protein Evolution

2012

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The "nearly neutral" theory of molecular evolution proposes that many features of genomes arise from the interaction of three weak evolutionary forces: mutation, genetic drift, and natural selection acting at its limit of efficacy. Such forces generally have little impact on allele frequencies within populations from generation to generation but can have substantial effects on long-term evolution. The evolutionary dynamics of weakly selected mutations are highly sensitive to population size, and near neutrality was initially proposed as an adjustment to the neutral theory to account for general patterns in available protein and DNA variation data. Here, we review the motivation for the nearly neutral theory, discuss the structure of the model and its predictions, and evaluate current empirical support for interactions among weak evolutionary forces in protein evolution. Near neutrality may be a prevalent mode of evolution across a range of functional categories of mutations and taxa. However, multiple evolutionary mechanisms (including adaptive evolution, linked selection, changes in fitness-effect distributions, and weak selection) can often explain the same patterns of genome variation. Strong parameter sensitivity remains a limitation of the nearly neutral model, and we discuss concave fitness functions as a plausible underlying basis for weak selection.U NDER the neutral model, newly arising mutations fall into two major fitness classes: strongly deleterious and selectively neutral (Kimura 1968;King and Jukes 1969). The first class is well supported by mutation accumulation experiments (reviewed in Simmons and Crow 1977;Halligan and Keightley 2009) and early DNA sequence comparisons (Grunstein et al. 1976;Kafatos et al. 1977) and is shared among competing evolutionary models. The novel and controversial aspect of the neutral theory was the proposition that, among mutations that go to fixation, the vast majority are selectively neutral. Advantageous substitutions, although important in phenotypic evolution, are sufficiently rare at the molecular level that they need not be considered to adequately model the process. Under the neutral theory, within-and between-species variation sample two aspects of a process of origination by mutation and changes in gene frequency dominated by drift and, for some mutations, negative selection (Kimura and Ohta 1971a). In contrast, polymorphism and divergence may be "uncoupled" under selection models (Gillespie 1987). Protein polymorphism and the neutral model: invariance of heterozygosityClear predictions for levels of polymorphism within populations and divergence among species are appealing aspects of the neutral model. However, within a few years of its proposal, the notion of drift-dominated evolution was challenged by overall patterns of allozyme polymorphism and contrasts between DNA and protein divergence.Although evolutionary geneticists were generally surprised by the extent of naturally occurring variation revealed by allozyme gel electrophoresis in the 197...

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Determination of Mitochondrial Genetic Diversity in Mammals

Cited by 119 publications

References 67 publications

Robust Estimates of Divergence Times and Selection with a Poisson Random Field Model: A Case Study of Comparative Phylogeographic Data

Robust Estimates of Divergence Times and Selection with a Poisson Random Field Model: A Case Study of Comparative Phylogeographic Data

How closely does genetic diversity in finite populations conform to predictions of neutral theory? Large deficits in regions of low recombination

Weak Selection and Protein Evolution

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