Competing selective sweeps

正选择等位基因的固定减少了相关的中性序列多样性，这种效应被称为“选择性扫描”。到目前为止，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等位基因扫描到固定。在这个项目中，我们研究了竞争选择性扫描，在第一次选择性扫描的时间过程中，在不同的重组位点上出现了进一步的有益突变。例如，对于迁移率低的结构种群或以前孤立的群落（亚种群）来说，这种情况是现实的。然后，重组事件可以使有益的等位基因具有相同的遗传背景。如果这样的重组事件不止一次发生，我们预计竞争性选择性扫描会留下以下明显的遗传足迹：在所选位点之间，存在强大的单倍型结构；在被选择的位点之外，遗传多样性严重减少，类似于一次选择性清除的情况。我们分三个步骤分析和应用了这一竞争选择性扫描模型：(1)使用祖先选择图来研究与有益等位基因相关的中性位点的家谱。利用这张系谱图，我们将量化遗传足迹。(2)利用基于最新开发的软件MSMS及其扩展的模拟技术，我们建立并分析了在泛型和结构化群体中竞争横扫的不同遗传足迹。特别是，我们探索了强单倍型结构的可能来源。(3)与本单位实验组合作，在果蝇SNP数据、智利茄（Solanum chilense）和茄子（Solanum peruvianum） SNP数据中扫描竞争扫描的特征。

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.