Department of Evolutionary Biology, University of Uppsala, Uppsala, Sweden.
Department of Population Ecology, Friedrich Schiller University Jena, Jena, Germany.
Mol Ecol. 2019 May;28(9):2290-2304. doi: 10.1111/mec.15021. Epub 2019 May 29.
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.
利用基因组数据检测正选择对于理解适应性进化的作用至关重要。在这方面，性染色体尤其引人注目，因为它们被认为在局部适应和物种形成中发挥特殊作用。我们试图通过利用性染色体整条染色体单倍型来规避基于单倍型统计数据在扫描中进行统计相位时所面临的挑战，这些单倍型可以通过对杂合性别个体进行重测序获得。我们分析了来自四个黑白色雀科鸟类物种的 100 个雌性个体的整条 Z 染色体单倍型（在鸟类中，雌性为 ZW，雄性为 ZZ）。基于综合单倍型得分（iHS）和按长度分离的核苷酸数（nSL）统计，我们在每个物种的 Z 染色体的几个区域发现了强烈而频繁的单倍型结构。这些扫描信号大多数是种群特异性的，基本上没有证据表明存在物种间共享的选择区域。一些跨越种群的扩展单倍型纯合性（XP-EHH）统计数据揭示了完成的扫描信号。重要的是，通过使用来自雄性重测序的统计相位 Z 染色体数据，我们未能恢复基于雌性整个染色体单倍型分析中检测到的选择信号；相反，经常看到的可能是虚假的选择信号。这凸显了统计相位中的功率问题，并警告人们不要根据此类数据进行选择扫描的结论。在鸟类 Z 染色体上频繁发生的选择扫描检测结果支持性染色体在适应性进化中发挥重要作用。
