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Competing selective sweeps

竞争选择性扫描

基本信息

批准号：
209410416
负责人：
Professor Dr. Martin Hutzenthaler
金额：
--
依托单位：
Mathematisches Institut
依托单位国家：
德国
项目类别：
Research Units
财政年份：
2011
资助国家：
德国
起止时间：
2010-12-31 至 2015-12-31
项目状态：
已结题

来源：
https://gepris.dfg.de/gepris/projekt/209410416?language=en
关键词：
Competing selective sweeps

项目摘要

The fixation of a positively selected allele reduces linked neutral sequence diversity, an effect known as a “selective sweep”. The literature on recurrent selective sweeps has so far mainly focused on the non-overlapping case where at most a single beneficial allele sweeps to fixation at any time. In this project, we study competing selective sweeps where further beneficial mutations arise at different recombining loci during the time-course of the first selective sweep. For example, such a scenario is realistic for a structured population with low migration rates or with previously isolated demes (subpopulations). Recombination events can then bring beneficial alleles to the same genetic background. If such recombination events happen more than once, we expect that competing selective sweeps leave the following distinct genetic footprint: Between selected loci, there is a strong haplotype structure; outside the selected loci, there is a severe reduction of genetic diversity, similar to the case of a single selective sweep. We analyze and apply this model of competing selective sweeps in three steps: (1) The genealogy at a neutral locus, linked to the beneficial alleles, can be studied using the ancestral selection graph. Using this genealogical picture we will quantify the genetic footprint. (2) Using simulation techniques based on the recently developed software MSMS and its proposed extension, we establish and analyze the distinct genetic footprint of competing sweeps in panmictic and structured populations. In particular, we explore possible sources of a strong haplotype structure. (3) In collaboration with empirical groups of the research unit, we scan for the signature of competing sweeps in SNP data of Drosophila melanogaster and in SNP data of Solanum chilense and Solanum peruvianum.

正选择等位基因的固定减少了连锁的中性序列多样性，这种效应被称为“选择性扫描”。迄今为止，关于反复选择性扫描的文献主要集中在非重叠的情况下，即在任何时候最多只有一个有益的等位基因扫描到固定。在这个项目中，我们研究了竞争性选择性扫描，在第一次选择性扫描的时间过程中，在不同的重组位点出现进一步的有益突变。例如，对于移徙率低的结构化人口或以前与世隔绝的部落（亚人口）来说，这种设想是现实的。然后，突变事件可以将有益的等位基因带到相同的遗传背景中。如果这样的重组事件发生不止一次，我们预计竞争性选择性扫描会留下以下不同的遗传足迹：在选择的基因座之间，有一个强大的单倍型结构;在选择的基因座之外，遗传多样性严重减少，类似于单一选择性扫描的情况。我们分三步分析和应用这种竞争性选择扫描模型：（1）与有益等位基因连锁的中性位点的系谱可以使用祖先选择图来研究。利用这张系谱图，我们将量化遗传足迹。(2)使用模拟技术的基础上，最近开发的软件MSMS及其建议的扩展，我们建立和分析不同的遗传足迹的竞争扫描panmictic和结构化的人口。特别是，我们探讨了一个强大的单倍型结构的可能来源。(3)与研究单位的经验小组合作，我们扫描了果蝇SNP数据和智利茄和秘鲁茄SNP数据中竞争性扫描的签名。