DILS: Demographic inferences with linked selection by using ABC
DILS: Demographic inferences with linked selection by using ABC
复制标题
DOI：
10.1111/1755-0998.13323
复制
发表时间：
2021-02-03
影响因子：
7.7
通讯作者：
Roux, Camille
中科院分区：
文献类型：
--
作者：
Fraiesse, Christelle;Popovic, Iva;Roux, Camille
我们提出了DILS，一个可部署的统计分析平台，用于使用近似贝叶斯计算框架从人口基因组数据中进行人口统计推断。DILS将单种群或双种群数据集作为输入（多基因座fasta序列），并以分层方式进行三种类型的分析，鉴定：（a）研究基因流动和群体大小变化对遗传模式多态性和趋异性的重要性的最佳人口统计学模型，（B）确定有效大小Ne和迁移率N的最佳基因组模型，m是不均匀分布沿着基因组（意味着连锁选择）和（c）基因组区域中的基因座与基因流动的障碍最相关。DILS的目标之一是促进物种形成基因组学方面的合作研究，也可通过网络界面获得。在这里，我们通过模拟显示DILS的性能和局限性，并最终将该方法应用于由28对贻贝种群/物种组成的发散连续体上的已发表数据。
We present DILS, a deployable statistical analysis platform for conducting demographic inferences with linked selection from population genomic data using an Approximate Bayesian Computation framework. DILS takes as input single-population or two-population data sets (multilocus fasta sequences) and performs three types of analyses in a hierarchical manner, identifying: (a) the best demographic model to study the importance of gene flow and population size change on the genetic patterns of polymorphism and divergence, (b) the best genomic model to determine whether the effective size Ne and migration rate N, m are heterogeneously distributed along the genome (implying linked selection) and (c) loci in genomic regions most associated with barriers to gene flow. Also available via a Web interface, an objective of DILS is to facilitate collaborative research in speciation genomics. Here, we show the performance and limitations of DILS by using simulations and finally apply the method to published data on a divergence continuum composed by 28 pairs of Mytilus mussel populations/species.