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A haplotype method detects diverse scenarios of local adaptation from genomic sequence variation.

ABSTRACT: Identifying genomic targets of population-specific positive selection is a major goal in several areas of basic and applied biology. However, it is unclear how often such selection should act on new mutations versus standing genetic variation or recurrent mutation, and furthermore, favoured alleles may either become fixed or remain variable in the population. Very few population genetic statistics are sensitive to all of these modes of selection. Here, we introduce and evaluate the Comparative Haplotype Identity statistic (?MD ), which assesses whether pairwise haplotype sharing at a locus in one population is unusually large compared with another population, relative to genomewide trends. Using simulations that emulate human and Drosophila genetic variation, we find that ?MD is sensitive to a wide range of selection scenarios, and for some very challenging cases (e.g. partial soft sweeps), it outperforms other two-population statistics. We also find that, as with FST , our haplotype approach has the ability to detect surprisingly ancient selective sweeps. Particularly for the scenarios resembling human variation, we find that ?MD outperforms other frequency- and haplotype-based statistics for soft and/or partial selective sweeps. Applying ?MD and other between-population statistics to published population genomic data from D. melanogaster, we find both shared and unique genes and functional categories identified by each statistic. The broad utility and computational simplicity of ?MD will make it an especially valuable tool in the search for genes targeted by local adaptation.

SUBMITTER: Lange JD

PROVIDER: S-EPMC4931985 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature

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A haplotype method detects diverse scenarios of local adaptation from genomic sequence variation.

Lange Jeremy D JD Pool John E JE

Molecular ecology 20160606 13

Identifying genomic targets of population-specific positive selection is a major goal in several areas of basic and applied biology. However, it is unclear how often such selection should act on new mutations versus standing genetic variation or recurrent mutation, and furthermore, favoured alleles may either become fixed or remain variable in the population. Very few population genetic statistics are sensitive to all of these modes of selection. Here, we introduce and evaluate the Comparative H ...[more]

PMID: 27135633

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Project description:BackgroundThe management of farm animal genetic resources and the adaptation of animals to climate change will probably have major effects on the long-term sustainability of the livestock sector. Genomic data harbour useful relevant information that needs to be harnessed for effectively managing genetic resources. In this paper, we report the genome characterization of the highly productive Mediterranean Chios dairy sheep and focus on genetic diversity measures related with local adaptation and selection and the genetic architecture of animal resilience to weather fluctuations as a novel adaptative trait linked to climate change.ResultsWe detected runs of homozygosity (ROH) and heterozygosity (ROHet) that revealed multiple highly homozygous and heterozygous hotspots across the Chios sheep genome. A particularly highly homozygous region was identified on chromosome 13 as a candidate of directional genetic selection associated with milk traits, which includes annotated genes that were previously shown to be linked to local adaptation to harsh environmental conditions. Favourable heterozygosity related with a potentially protective role against livestock diseases and enhanced overall fitness was revealed in heterozygous-rich regions on sheep chromosomes 3, 10, 13 and 19. Furthermore, genomic analyses were conducted on sheep resilience phenotypes that display changes in milk production in response to weather variation. Sheep resilience to heat stress was a significantly heritable trait (h2 = 0.26) and genetically antagonistic to milk production. Genome-wide association and regional heritability mapping analyses revealed novel genomic markers and regions on chromosome 5 that were significantly associated with sheep resilience to climate change. Subsequently, an annotation analysis detected a set of genes on chromosome 5 that were associated with olfactory receptor complexes that could participate in heat stress mitigation through changes in respiration rate and respiratory evaporation. Other genes were grouped in previously reported biological processes relevant to livestock heat dissipation, including stress and immune response.ConclusionsOur results may contribute to the optimal management of sheep genetic resources and inform modern selective breeding programmes that aim at mitigating future environmental challenges towards sustainable farming, while better balancing animal adaptation and productivity. Our results are directly relevant to the studied breed and the respective environmental conditions; however, the methodology may be extended to other livestock species of interest.

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A haplotype method detects diverse scenarios of local adaptation from genomic sequence variation.

Publications

A haplotype method detects diverse scenarios of local adaptation from genomic sequence variation.

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