Selection, Recombination and Demographic History in <i>Drosophila miranda</i>

Bachtrog, Doris; Andolfatto, Peter

doi:10.1534/genetics.106.062760

Cited by 75 publications

(65 citation statements)

References 91 publications

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“…There is thus no evidence in either species for an elevation of the effective population size of the X chromosome above three-quarters of the autosomal value, in contrast to what was proposed previously on the basis of smaller data sets (Yi et al 2003;Bartolomé et al 2005) and that has been found in the Zimbabwe population of D. melanogaster (Andolfatto 2001;Hutter et al 2007), but is in agreement with the results of Bachtrog and Andolfatto (2006) for D. miranda. Mean synonymous diversity is much higher for D. pseudoobscura than for D. miranda, with a D. pseudoobscura/D.…”

Section: Resultssupporting

confidence: 54%

Estimating the Parameters of Selection on Nonsynonymous Mutations inDrosophila pseudoobscuraandD. miranda

2010

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We present the results of surveys of diversity in sets of .40 X-linked and autosomal loci in samples from natural populations of Drosophila miranda and D. pseudoobscura, together with their sequence divergence from D. affinis. Mean silent site diversity in D. miranda is approximately one-quarter of that in D. pseudoobscura; mean X-linked silent diversity is about three-quarters of that for the autosomes in both species. Estimates of the distribution of selection coefficients against heterozygous, deleterious nonsynonymous mutations from two different methods suggest a wide distribution, with coefficients of variation greater than one, and with the average segregating amino acid mutation being subject to only very weak selection. Only a small fraction of new amino acid mutations behave as effectively neutral, however. A large fraction of amino acid differences between D. pseudoobscura and D. affinis appear to have been fixed by positive natural selection, using three different methods of estimation; estimates between D. miranda and D. affinis are more equivocal. Sources of bias in the estimates, especially those arising from selection on synonymous mutations and from the choice of genes, are discussed and corrections for these applied. Overall, the results show that both purifying selection and positive selection on nonsynonymous mutations are pervasive.

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Section: Resultssupporting

confidence: 54%

Estimating the Parameters of Selection on Nonsynonymous Mutations inDrosophila pseudoobscuraandD. miranda

2010

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“…In contrast, short introns and third codon positions show the highest level of nucleotide variability, while UTR sequences, intergenic regions, and long introns show intermediate levels of polymorphism. These relative levels of polymorphism across functional categories of site are broadly consistent with previous reports from a variety of Drosophila species including D. miranda (Bachtrog and Andolfatto 2006), D. simulans (Begun et al 2007;Haddrill et al 2008), and D. melanogaster (Andolfatto 2005;Parsch et al 2010;Zeng and Charlesworth 2010).…”

Section: Polymorphism and Divergencesupporting

confidence: 90%

Inferences of Demography and Selection in an African Population of Drosophila melanogaster

et al. 2013

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It remains a central problem in population genetics to infer the past action of natural selection, and these inferences pose a challenge because demographic events will also substantially affect patterns of polymorphism and divergence. Thus it is imperative to explicitly model the underlying demographic history of the population whenever making inferences about natural selection. In light of the considerable interest in adaptation in African populations of Drosophila melanogaster, which are considered ancestral to the species, we generated a large polymorphism data set representing 2.1 Mb from each of 20 individuals from a Ugandan population of D. melanogaster. In contrast to previous inferences of a simple population expansion in eastern Africa, our demographic modeling of this ancestral population reveals a strong signature of a population bottleneck followed by population expansion, which has significant implications for future demographic modeling of derived populations of this species. Taking this more complex underlying demographic history into account, we also estimate a mean X-linked region-wide rate of adaptation of 6 · 10 211 /site/generation and a mean selection coefficient of beneficial mutations of 0.0009. These inferences regarding the rate and strength of selection are largely consistent with most other estimates from D. melanogaster and indicate a relatively high rate of adaptation driven by weakly beneficial mutations.T HERE is considerable interest in understanding the nature and extent of adaptation in natural populations. Drosophila melanogaster has been the focus of many such studies and a variety of approaches to address this fundamental question have been developed with this system. These include divergence-based methods (e.g., Sattath et al. 2011), polymorphism-based approaches (e.g., Kim and Stephan 2002;Sabeti et al. 2002;Kim and Nielsen 2004;Li and Stephan 2006b;Jensen et al. 2008a), and approaches that use both polymorphism and divergence data (e.g., Fay et al. 2002;Welch 2006;Andolfatto 2007;Macpherson et al. 2007;Shapiro et al. 2007). In some cases, these methods aim to localize putative targets of selection (e.g., Harr et al. 2002;Glinka et al. 2003;Jensen et al. 2007a), while in others the ultimate goal is to generally characterize the average rate and strength of adaptation (Wiehe and Stephan 1993;Li and Stephan 2006a;Andolfatto 2007;Macpherson et al. 2007;Jensen et al. 2008a). These approaches have enjoyed much success, and it is becoming clear that the signatures of both recent and recurrent selection abound in the D. melanogaster genome (for review see Sella et al. 2009).However, demographic history will also leave its signature in the genome, which has the potential to confound inferences of natural selection. Indeed, to effectively investigate models of natural selection, which are of great general interest in evolutionary biology, one must take into account the underlying demographic history of a population. Consequently, understanding demographic history is integr...

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“…The male-specific region of the Y-chromosome is a mosaic of heterochromatic sequences and three classes of euchromatic sequences: X-transposed, X-degenerate and ampliconic (Skaletsky et al, 2003). The absence of recombination with the X-chromosome causes rapid degeneration by mutation, deletion and transposon invasion that accumulate through time due to the larger number of cell divisions required to produce male gametes, and due to inefficient repair (for example, Muller's ratchet) and inefficient selection (Charlesworth et al, 2005;Graves, 2006;Bachtrog and Andolfatto, 2006;Van Laere et al, 2008). The repetitive nature of the Y-chromosome has been hypothesised to be a mechanism for maintaining Y-chromosome genes in a non-recombining environment and may arise by a number of mechanisms, including sexual antagonism, genomic conflict and hemizygous exposure (Vallender and Lahn, 2004;Murphy et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

Multiple paternal origins of domestic cattle revealed by Y-specific interspersed multilocus microsatellites

et al. 2010

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In this study, we show how Y-specific interspersed multilocus microsatellites, which are loci that yield several amplified bands differing in size from the same male individual and PCR reaction, are a powerful source of information for tracing the history of cattle. Our results confirm the existence of three main groups of sires, which are separated by evolutionary time and clearly predate domestication. These three groups are consistent with the haplogroups previously identified by Göther-ström et al. (2005) using five Y-specific segregating sites: Y1 and Y2 in taurine (Bos taurus) cattle and Y3 in zebu (Bos indicus) cattle. The zebu cattle cluster clearly originates from a domestication process that was geographically and temporally separated from that of taurine clusters. Our analyses further suggest that: (i) introgression of wild sire genetic material into domesticated herds may have a significant role in the formation of modern cattle, including the formation of the Y1 haplogroup; (ii) a putative domestication event in Africa probably included local Y2-like wild sires; (iii) the West African zebu cattle Ychromosome may have partially originated from an ancient introgression of humped cattle into Africa; and (iv) the high genetic similarity among Asian zebu sires is consistent with a single domestication process.

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Selection, Recombination and Demographic History in Drosophila miranda

Cited by 75 publications

References 91 publications

Estimating the Parameters of Selection on Nonsynonymous Mutations inDrosophila pseudoobscuraandD. miranda

Estimating the Parameters of Selection on Nonsynonymous Mutations inDrosophila pseudoobscuraandD. miranda

Inferences of Demography and Selection in an African Population of Drosophila melanogaster

Multiple paternal origins of domestic cattle revealed by Y-specific interspersed multilocus microsatellites

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