Drosophila simulans LD results from PLINK for Chromosome X

Abstract: Heritable phenotypic variation in natural populations exceeds the levels predicted under mutation-selection balance where purifying selection removes variation. Balancing selection, inefficient or weak selection, polygenic adaptation, and non-equilibrium populations are all possible explanations for excess variation. Yet, available genomic data indicate an abundance of directional selection. One potential explanation is that fleeting directional selection drives beneficial mutations to high frequency in rapid waves resulting in many intermediate frequency haplotypes. This hypothesis is supported by the genomic data from a panel of 170 D. simulans genotypes established from a single stable population which show evidence for an abundance of incomplete soft sweeps. Demography, admixture, and balancing selection cannot entirely explain the patterns in these data, while transient selective sweeps can account for all the patterns of variation observed in this population. One interpretation is that constant environmental shifts rapidly change the optimal phenotype within Drosophila populations, leaving a signature of adaptive responses.

Material type: Text files of pairwise linkage disequilibrium (LD) calculations from Plink (v). 

Larger Body of Work: Pervasive incomplete selective sweeps in D. simulans account for excess variation.

Related publications and datasets: Drosophila simulans VCF, LD results from chromosomes 2L, 2R,  3R, 3L, and 4.

摘要：自然种群中的可遗传表型变异超出了纯化选择清除变异的突变-选择平衡模型下的预测水平。平衡选择、选择效率低下或选择作用微弱、多基因适应以及非平衡种群，均为该过剩变异的潜在解释。然而现有基因组数据却显示存在大量定向选择。一种可能的解释是：短暂的定向选择以快速的选择浪潮推动有益突变达到高频率，进而形成大量中等频率单倍型。该假说得到了来自170个拟果蝇（Drosophila simulans）基因型的基因组数据支持——这些基因型源自单个稳定种群，其数据显示存在大量不完全选择性软清扫的特征。种群动态、群体混合与平衡选择均无法完全解释该数据集的变异模式，而瞬时选择性清扫则可以解释该种群中观测到的全部变异模式。一种解读是：持续的环境变化快速改变了果蝇种群内的最优表型，留下了适应性响应的分子印记。
材料类型：来自PLINK（v）的成对连锁不平衡（linkage disequilibrium, LD）计算结果文本文件。
整体研究成果：拟果蝇中广泛存在的不完全选择性软清扫可解释过剩变异。
相关出版物与数据集：拟果蝇变异识别格式（Variant Call Format, VCF）数据集，以及2L、2R、3R、3L与4号染色体的连锁不平衡分析结果。