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Footprints of adaptive evolution revealed by whole Z chromosomes haplotypes in flycatchers.

ABSTRACT: Detecting positive selection using genomic data is critical to understanding the role of adaptive evolution. Of particular interest in this context is sex chromosomes since they are thought to play a special role in local adaptation and speciation. We sought to circumvent the challenges associated with statistical phasing when using haplotype-based statistics in sweep scans by benefitting from that whole chromosome haplotypes of the sex chromosomes can be obtained by resequencing of individuals of the hemizygous sex. We analyzed whole Z chromosome haplotypes from 100 females from several populations of four black and white flycatcher species (in birds, females are ZW and males ZZ). Based on integrated haplotype score (iHS) and number of segregating sites by length (nSL) statistics, we found strong and frequent haplotype structure in several regions of the Z chromosome in each species. Most of these sweep signals were population-specific, with essentially no evidence for regions under selection shared among species. Some completed sweeps were revealed by the cross-population extended haplotype homozygosity (XP-EHH) statistic. Importantly, by using statistically phased Z chromosome data from resequencing of males, we failed to recover the signals of selection detected in analyses based on whole chromosome haplotypes from females; instead, what likely represent false signals of selection were frequently seen. This highlights the power issues in statistical phasing and cautions against conclusions from selection scans using such data. The detection of frequent selective sweeps on the avian Z chromosome supports a large role of sex chromosomes in adaptive evolution.

SUBMITTER: Nadachowska-Brzyska K

PROVIDER: S-EPMC6852393 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature

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Footprints of adaptive evolution revealed by whole Z chromosomes haplotypes in flycatchers.

Nadachowska-Brzyska Krystyna K Burri Reto R Ellegren Hans H

Molecular ecology 20190529 9

Detecting positive selection using genomic data is critical to understanding the role of adaptive evolution. Of particular interest in this context is sex chromosomes since they are thought to play a special role in local adaptation and speciation. We sought to circumvent the challenges associated with statistical phasing when using haplotype-based statistics in sweep scans by benefitting from that whole chromosome haplotypes of the sex chromosomes can be obtained by resequencing of individuals ...[more]

PMID: 30653779

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Project description:BACKGROUND:Climatic factors play an important role in determining species distributions and phenotypic variation of populations over geographic space. Since domestic sheep is managed under low intensive systems animals could have retained some genome adaptive footprints. The gene encoding the Hsp90? has been extensively studied in sheep and some polymorphisms located at its promoter have been associates with differences in the transcription rate of the gene depending on climatic conditions. In this work the relationships among the distribution and frequencies of 11 polymorphisms of the ovine HSP90AA1 gene promoter in 31 sheep breeds and the climatic and geographic variables prevailing in their regions of origin have been studied. Also the promoter sequence has been characterized in 9 species of the Caprinae subfamily. RESULTS:Correlations among several climatic variables and allele frequencies of the polymorphisms of the HSP90AA1 gene promoter linked with differences in the transcription activity of the gene under heat stress conditions have been assessed. A group of breeds reared in semi dry climates have high frequencies of the insertion allele of the g.667-668insC associated with the heat stress response. Other group of breeds native to semi arid conditions showed very low frequencies of this same allele. However, in some cases, this previous correlation has not been achieved, revealing the high levels of gene flow among populations occurred following domestication. The Bayesian Test of Beaumont and Balding identified two outlier loci, the g.522A?>?G and g.703_704del(2)A candidates to balancing and directional selection, respectively. Polymorphisms detected in O. aries are also present in several species of the Caprinae subfamily being C. hircus, O. musimon and O. moschatus those sharing the highest number of them with O. aries. CONCLUSIONS:Despite domestication, sheep breeds showed some genetic footprints related to climatic variables. Adaptation of breeds to heat climates can suppose a selective advantage to cope with global warming caused by climatic change. Polymorphisms of the HSP90AA1 gene detected in the Ovis aries species are also present in wild species from the Caprinae subfamily, indicating a great antiquity of these mutations and its importance in the adaptation of species to past climatic conditions existing in its native environments.

Dataset Information

Footprints of adaptive evolution revealed by whole Z chromosomes haplotypes in flycatchers.

Publications

Footprints of adaptive evolution revealed by whole Z chromosomes haplotypes in flycatchers.

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