Data from: Nucleotide variation in the Egfr locus of Drosophila melanogaster

The Epidermal growth factor receptor is an essential gene with diverse pleiotropic roles in development throughout the animal kingdom. Analysis of sequence diversity in 10.9 kb covering the complete coding region and 6.4 kb of potential regulatory regions in a sample of 250 alleles from three populations of Drosophila melanogaster suggests that the intensity of different population genetic forces varies along the locus. A total of 238 independent common SNPs and 20 indel polymorphisms were detected, with just six common replacements affecting >1475 amino acids, four of which are in the short alternate first exon. Sequence diversity is lowest in a 2-kb portion of intron 2, which is also highly conserved in comparison with D. simulans and D. pseudoobscura. Linkage disequilibrium decays to background levels within 500 bp of most sites, so haplotypes are generally restricted to up to 5 polymorphisms. The two North American samples from North Carolina and California have diverged in allele frequency at a handful of individual SNPs, but a Kenyan sample is both more divergent and more polymorphic. The effect of sample size on inference of the roles of population structure, uneven recombination, and weak selection in patterning nucleotide variation in the locus is discussed.

表皮生长因子受体（Epidermal growth factor receptor）是一类至关重要的基因，在整个动物界的发育过程中发挥着多样的多效性作用。本研究对取自3个黑腹果蝇（Drosophila melanogaster）种群的250个等位基因，开展了覆盖其完整编码区的10.9 kb序列以及6.4 kb潜在调控区域的序列多样性分析，结果显示不同群体遗传作用力的强度在该基因座上存在差异。共检测到238个独立的常见单核苷酸多态性（Single Nucleotide Polymorphism, SNPs）以及20个插入缺失（Insertion-Deletion, indel）多态性位点；其中仅6个常见氨基酸替换变异影响了超过1475个氨基酸残基，其中4个位于较短的可变第一外显子中。在第2内含子的一段2 kb区域内，序列多样性最低；相较于拟果蝇（Drosophila simulans）和伪暗果蝇（Drosophila pseudoobscura），该区域同样具有高度的保守性。连锁不平衡（Linkage disequilibrium）在大多数位点的500 bp范围内即衰减至背景水平，因此单倍型（haplotype）通常仅包含至多5个多态性位点。取自北卡罗来纳州与加利福尼亚州的两个北美样本，在少数单核苷酸多态性位点上的等位基因频率存在分化；而肯尼亚样本则表现出更高的分化程度与多态性水平。本研究还探讨了样本量对推断群体结构、不均衡重组以及弱选择在塑造该基因座核苷酸变异模式中所起作用的影响。