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, EGFR）是一类必需基因，在整个动物界的发育进程中发挥着多样的多效性功能。本研究针对来自3个黑腹果蝇（Drosophila melanogaster）种群的250个等位基因样本，对覆盖其完整编码区的10.9 千碱基对（kilobase pair, kb）序列以及6.4 千碱基对（kilobase pair, kb）潜在调控区域的序列多样性展开分析，结果表明不同群体遗传作用力在该基因座上的作用强度存在异质性。共检测到238个独立的常见单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点与20个插入缺失（insertion-deletion, indel）多态性位点；其中仅6个常见错义突变影响了超过1475个氨基酸残基，其中4个位于较短的可变第一外显子中。序列多样性在第2内含子的一段2 千碱基对（kilobase pair, kb）区域内达到最低值，与拟暗果蝇（Drosophila simulans）和伪暗果蝇（Drosophila pseudoobscura）相比，该区域同样呈现高度保守性。大多数位点周边500 碱基对（base pair, bp）范围内，连锁不平衡（Linkage disequilibrium, LD）即衰减至背景水平，因此单倍型通常仅包含至多5个多态性位点。来自北卡罗来纳州与加利福尼亚州的两个北美样本，在少量单核苷酸多态性位点的等位基因频率上存在分化；而肯尼亚样本不仅分化程度更高，多态性也更为丰富。本研究还探讨了样本量对推断群体结构、不均一重组以及弱选择在塑造该基因座核苷酸变异模式中所发挥作用的影响。