Selection, recombination and demographic history in Drosophila miranda
Selection, recombination and demographic history in Drosophila miranda
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DOI：
10.1534/genetics.106.062760
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发表时间：
2006-12-01
期刊：
影响因子：
3.3
通讯作者：
Andolfatto, Peter
中科院分区：
文献类型：
--
作者：
Bachtrog, Doris;Andolfatto, Peter
一个物种的选择、重组和人口统计学历史都可能对全基因组变异模式产生深远的影响。为了评估这些力量在果蝇米兰达基因组中的影响，我们研究了分散在基因组中的62个位点的多态性和趋异模式。根据D.黑腹果蝇，我们发现，非编码DNA一般比同义位点进化得更慢，非编码DNA的多态性频率的分布是显着偏向罕见的变异相对于同义位点，长内含子进化显着慢于短内含子或同义位点。这些观察结果表明，大多数非编码DNA在功能上受到限制，并在纯化选择下进化。然而，与D.黑腹果蝇物种组，我们发现很少有证据表明适应性进化作用于编码或非编码序列在D。米兰达连锁不平衡（LD）水平在D.米兰达与D.黑腹动物，但在染色体之间差异很大。这些模式表明常染色体上的重组率显著较低，可能是由于存在多态性常染色体倒位和/或染色体大小差异。所有的染色体显示出显着偏离标准的中性模型，包括太多的异质性同义位点多态性相对于基因座之间的分歧和普遍过剩的罕见的同义多态性。这些偏离中性的均衡预期的背景下，人口和选择的非均衡模型进行了讨论。
Selection, recombination, and the demographic history of a species can all have profound effects on genomewide patterns of variability. To assess the impact of these forces in the genome of Drosophila miranda, we examine polymorphism and divergence patterns at 62 loci scattered across the genome. In accordance with recent findings in D. melanogaster, we find that noncoding DNA generally evolves more slowly than synonymous sites, that the distribution of polymorphism frequencies in noncoding DNA is significantly skewed toward rare variants relative to synonymous sites, and that long introns evolve significantly slower than short introns or synonymous sites. These observations suggest that most noncoding DNA is functionally constrained and evolving under purifying selection. However, in contrast to findings in the D. melanogaster species group, we find little evidence of adaptive evolution acting on either coding or noncoding sequences in D. miranda. Levels of linkage disequilibrium (LD) in D. miranda are comparable to those observed in D. melanogaster., but vary considerably among chromosomes. These patterns suggest a significantly lower rate of recombination on autosomes, possibly due to the presence of polymorphic autosomal inversions and/or differences in chromosome sizes. All chromosomes show significant departures from the standard neutral model, including too much heterogeneity in synonymous site polymorphism relative to divergence among loci and a general excess of rare synonymous polymorphisms. These departures from neutral equilibrium expectations are discussed in the context of nonequilibrium models of demography and selection.