Identifying genetic signatures of selection in a non-model species, alpine gentian (Gentiana nivalis L.), using a landscape genetic approach

Bothwell, Helen M.; Bisbing, Sarah M.; Therkildsen, Nina Overgaard; Crawford, Lindsay A.; Alvarez, Nadir; Holderegger, Rolf; Manel, Stéphanie

doi:10.1007/s10592-012-0411-5

Cited by 33 publications

(27 citation statements)

References 58 publications

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“…; Bothwell et al. ). These and other climatic factors are likely to be intermingled with geographic area.…”

Section: Discussionmentioning

confidence: 98%

“…This would be the case if such an unmeasured, but relevant environmental factor was correlated with habitat types in the original sample tested by Buehler et al (2013), but uncorrelated with habitat types in the present study. Especially temperature and precipitation have been shown to be determinants of allele distribution in A. alpina and other alpine plants Poncet et al 2010;Bothwell et al 2013). These and other climatic factors are likely to be intermingled with geographic area.…”

Section: Potential Causes For the Failure Of Validationmentioning

confidence: 99%

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Validation of outlier loci through replication in independent data sets: a test on Arabis alpina

Buehler

Holderegger

Brodbeck

et al. 2014

Ecology and Evolution

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Outlier detection and environmental association analysis are common methods to search for loci or genomic regions exhibiting signals of adaptation to environmental factors. However, a validation of outlier loci and corresponding allele distribution models through functional molecular biology or transplant/common garden experiments is rarely carried out. Here, we employ another method for validation, namely testing outlier loci in specifically designed, independent data sets. Previously, an outlier locus associated with three different habitat types had been detected in Arabis alpina. For the independent validation data set, we sampled 30 populations occurring in these three habitat types across five biogeographic regions of the Swiss Alps. The allele distribution model found in the original study could not be validated in the independent test data set: The outlier locus was no longer indicative of habitat-mediated selection. We propose several potential causes of this failure of validation, of which unaccounted genetic structure and technical issues in the original data set used to detect the outlier locus were most probable. Thus, our study shows that validating outlier loci and allele distribution models in independent data sets is a helpful tool in ecological genomics which, in the case of positive validation, adds confidence to outlier loci and their association with environmental factors or, in the case of failure of validation, helps to explain inconsistencies.

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“…; Bothwell et al. ). These and other climatic factors are likely to be intermingled with geographic area.…”

Section: Discussionmentioning

confidence: 98%

Section: Potential Causes For the Failure Of Validationmentioning

confidence: 99%

Validation of outlier loci through replication in independent data sets: a test on Arabis alpina

Buehler

Holderegger

Brodbeck

et al. 2014

Ecology and Evolution

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“…In this context, changes in allele frequencies can be interpreted as being driven by divergent adaptation due to differences in local environments [19]. This strategy has successfully been applied to identify candidate loci correlated with a variety of environmental conditions [7], [8], [16]–[23].…”

Section: Introductionmentioning

confidence: 99%

Divergent Selection and Local Adaptation in Disjunct Populations of an Endangered Conifer, Keteleeria davidiana var. formosana (Pinaceae)

et al. 2013

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The present study investigated the genetic diversity, population structure, F ST outliers, and extent and pattern of linkage disequilibrium in five populations of Keteleeria davidiana var. formosana, which is listed as a critically endangered species by the Council of Agriculture, Taiwan. Twelve amplified fragment length polymorphism primer pairs generated a total of 465 markers, of which 83.74% on average were polymorphic across populations, with a mean Nei’s genetic diversity of 0.233 and a low level of genetic differentiation (approximately 6%) based on the total dataset. Linkage disequilibrium and HICKORY analyses suggested recent population bottlenecks and inbreeding in K. davidiana var. formosana. Both STRUCTURE and BAPS observed extensive admixture of individual genotypes among populations based on the total dataset in various clustering scenarios, which probably resulted from incomplete lineage sorting of ancestral variation rather than a high rate of recent gene flow. Our results based on outlier analysis revealed generally high levels of genetic differentiation and suggest that divergent selection arising from environmental variation has been driven by differences in temperature, precipitation, and humidity. Identification of ecologically associated outliers among environmentally disparate populations further support divergent selection and potential local adaptation.

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“…; Bothwell et al . ). On the other hand, our models did not account for postzygotic barriers to gene flow (Feldman et al .…”

Section: Discussionmentioning

confidence: 97%

Wheat alleles introgress into selfing wild relatives: empirical estimates from approximate Bayesian computation in Aegilops triuncialis

et al. 2014

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Extensive gene flow between wheat (Triticum sp.) and several wild relatives of the genus Aegilops has recently been detected despite notoriously high levels of selfing in these species. Here, we assess and model the spread of wheat alleles into natural populations of the barbed goatgrass (Aegilops triuncialis), a wild wheat relative prevailing in the Mediterranean flora. Our sampling, based on an extensive survey of 31 Ae. triuncialis populations collected along a 60 km × 20 km area in southern Spain (Grazalema Mountain chain, Andalousia, totalling 458 specimens), is completed with 33 wheat cultivars representative of the European domesticated pool. All specimens were genotyped with amplified fragment length polymorphism with the aim of estimating wheat admixture levels in Ae. triuncialis populations. This survey first confirmed extensive hybridization and backcrossing of wheat into the wild species. We then used explicit modelling of populations and approximate Bayesian computation to estimate the selfing rate of Ae. triuncialis along with the magnitude, the tempo and the geographical distance over which wheat alleles introgress into Ae. triuncialis populations. These simulations confirmed that extensive introgression of wheat alleles (2.7 × 10(-4) wheat immigrants for each Ae. triuncialis resident, at each generation) into Ae. triuncialis occurs despite a high selfing rate (Fis ≈ 1 and selfing rate = 97%). These results are discussed in the light of risks associated with the release of genetically modified wheat cultivars in Mediterranean agrosystems.

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Identifying genetic signatures of selection in a non-model species, alpine gentian (Gentiana nivalis L.), using a landscape genetic approach

Cited by 33 publications

References 58 publications

Validation of outlier loci through replication in independent data sets: a test on Arabis alpina

Validation of outlier loci through replication in independent data sets: a test on Arabis alpina

Divergent Selection and Local Adaptation in Disjunct Populations of an Endangered Conifer, Keteleeria davidiana var. formosana (Pinaceae)

Wheat alleles introgress into selfing wild relatives: empirical estimates from approximate Bayesian computation in Aegilops triuncialis

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