A pooling approach to detect signatures of selective sweeps in genome scans using microsatellites

Thomas, Meike; Möller, Friedrich; Wiehe, Thomas; Tautz, Diethard

doi:10.1111/j.1471-8286.2007.01697.x

Cited by 14 publications

(21 citation statements)

References 7 publications

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“…To reduce the genotyping effort, we employed a two-step procedure. In the first step, we used pools of DNA from 40 animals of each population and compared variability patterns for each locus, which allows us to retrieve the subset of loci with signs of population-specific loss of polymorphism (Thomas et al 2007). In the second step we typed these loci individually for $40 animals from the respective population pairs.…”

Section: Resultsmentioning

confidence: 99%

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Identification of Selective Sweeps in Closely Related Populations of the House Mouse Based on Microsatellite Scans

Teschke¹,

Mukabayire²,

Wiehe

et al. 2008

Genetics

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Genome scans of polymorphisms promise to provide insights into the patterns and frequencies of positive selection under natural conditions. The use of microsatellites as markers has the potential to focus on very recent events, since in contrast to SNPs, their high mutation rates should remove signatures of older events. We assess this concept here in a large-scale study. We have analyzed two population pairs of the house mouse, one pair of the subspecies Mus musculus domesticus and the other of M. m. musculus. A total of 915 microsatellite loci chosen to cover the whole genome were assessed in a prescreening procedure, followed by individual typing of candidate loci. Schlötterer's ratio statistics (lnRH) were applied to detect loci with significant deviations from patterns of neutral expectation. For eight loci from each population pair we have determined the size of the potential sweep window and applied a second statistical procedure (linked locus statistics). For the two population pairs, we find five and four significant sweep loci, respectively, with an average estimated window size of 120 kb. On the basis of the analysis of individual allele frequencies, it is possible to identify the most recent sweep, for which we estimate an onset of 400-600 years ago. Given the known population history for the French-German population pair, we infer that the average frequency of selective sweeps in these populations is higher than 1 in 100 generations across the whole genome. We discuss the implications for adaptation processes in natural populations.

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Section: Resultsmentioning

confidence: 99%

“…Genome screen: A total of 960 microsatellite loci were assessed, using the pooling approach described in Thomas et al (2007). The resulting patterns were visually inspected via pairwise comparisons between the populations within the two subspecies.…”

Section: Methodsmentioning

confidence: 99%

Identification of Selective Sweeps in Closely Related Populations of the House Mouse Based on Microsatellite Scans

Teschke¹,

Mukabayire²,

Wiehe

et al. 2008

Genetics

Self Cite

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show abstract

“…and 76 (34.9%) had Gene Ontology (GO) annotations which covered a wide range of functional genes based on GO terms (Appendix S5, Supporting information). By checking pooled samples as recommended by Thomas et al 21,. we discarded loci that were not likely to be under selection.…”

Section: Resultsmentioning

confidence: 99%

“…Populations were represented by five unique pool samples where DNA samples were normalized to 15 ng/μL from all individuals in a given population. Subsequently, we genotyped 218 microsatellite loci using the five population pools and an individual was randomly selected for comparison as each locus showed characteristic slippage patterns21. The fragment patterns were visually inspected by pairwise comparison between populations as recommended by Thomas et al 21.…”

Section: Methodsmentioning

confidence: 99%

Genetic signatures of natural selection in a model invasive ascidian

Lin

Chen

et al. 2017

Sci Rep

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Invasive species represent promising models to study species’ responses to rapidly changing environments. Although local adaptation frequently occurs during contemporary range expansion, the associated genetic signatures at both population and genomic levels remain largely unknown. Here, we use genome-wide gene-associated microsatellites to investigate genetic signatures of natural selection in a model invasive ascidian, Ciona robusta. Population genetic analyses of 150 individuals sampled in Korea, New Zealand, South Africa and Spain showed significant genetic differentiation among populations. Based on outlier tests, we found high incidence of signatures of directional selection at 19 loci. Hitchhiking mapping analyses identified 12 directional selective sweep regions, and all selective sweep windows on chromosomes were narrow (~8.9 kb). Further analyses indentified 132 candidate genes under selection. When we compared our genetic data and six crucial environmental variables, 16 putatively selected loci showed significant correlation with these environmental variables. This suggests that the local environmental conditions have left significant signatures of selection at both population and genomic levels. Finally, we identified “plastic” genomic regions and genes that are promising regions to investigate evolutionary responses to rapid environmental change in C. robusta.

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“…; Thomas et al . ; Teschke et al . ) and constitute DNA pools representing each of the three geographic regions (‘Contact’, ‘Close allopatry’ and ‘Distant allopatry’) by pooling DNA extracts of 32 individuals per geographic region (Table S1, Supporting infromation).…”

Section: Methodsmentioning

confidence: 99%

Seeking signatures of reinforcement at the genetic level: a hitchhiking mapping and candidate gene approach in the house mouse

et al. 2015

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Reinforcement is the process by which prezygotic isolation is strengthened as a response to selection against hybridisation. Most empirical support for reinforcement comes from the observation of its possible phenotypic signature: an accentuated degree of prezygotic isolation in the hybrid zone as compared to allopatry. Here, we implemented a novel approach to this question by seeking for the signature of reinforcement at the genetic level. In the house mouse, selection against hybrids and enhanced olfactory-based assortative mate preferences are observed in a hybrid zone between the two European subspecies Mus musculus musculus and M. m. domesticus, suggesting a possible recent reinforcement event. To test for the genetic signature of reinforcing selection and identify genes involved in sexual isolation, we adopted a hitchhiking mapping approach targeting genomic regions containing candidate genes for assortative mating in mice. We densely scanned these genomic regions in hybrid zone and allopatric samples using a large number of fast evolving microsatellite loci that allow the detection of recent selection events. We found a handful of loci showing the expected pattern of significant reduction of variability in populations close to the hybrid zone and showing assortative odour preference in mate choice experiments as compared to populations further away and displaying no such preference. These loci lie close to genes that we pinpoint as testable candidates for further investigation.

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A pooling approach to detect signatures of selective sweeps in genome scans using microsatellites

Cited by 14 publications

References 7 publications

Identification of Selective Sweeps in Closely Related Populations of the House Mouse Based on Microsatellite Scans

Identification of Selective Sweeps in Closely Related Populations of the House Mouse Based on Microsatellite Scans

Genetic signatures of natural selection in a model invasive ascidian

Seeking signatures of reinforcement at the genetic level: a hitchhiking mapping and candidate gene approach in the house mouse

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