Maximum Likelihood Implementation of an Isolation-with-Migration Model for Three Species
Maximum Likelihood Implementation of an Isolation-with-Migration Model for Three Species
复制标题
三个物种的隔离与迁移模型的最大似然实现
DOI：
10.1093/sysbio/syw063
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发表时间：
2017-05-01
影响因子：
6.5
通讯作者：
Yang, Ziheng
中科院分区：
文献类型：
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作者：
Dalquen, Daniel A.;Zhu, Tianqi;Yang, Ziheng
我们开发了一种使用基因组序列数据估算物种之间迁移率的最大可能性（ML）方法。物种树用于适应三个物种之间的系统发育关系，从而可以在两个姐妹物种之间迁移，而第三种则被用作群体外部。 Markov链的融合式迁移谱系过程的表征用于分析每个基因座的迁移历史，而高斯正交正交被用来在每个家谱树上的聚结时整合。这是我们早期实施三个物种的对称分离模型的对称分离模型的扩展，以适应每个基因座的两个或三个序列的任意基因座，并允许不对称的迁移速率。我们的实施可以容纳数万个基因座，这使得分析基因组规模数据集以测试基因流程是可行的。我们计算单个基因座基因树的后验概率，以鉴定由于基因流而可能已在物种之间转移的基因组区域。我们进行了一项仿真研究，以检查两个小组内物种和模型参数（例如迁移速率）的ML估计值之间基因流量的统计特性。发现包含来自第三个群体外种物种的数据可显着增加测试的功能和参数估计的精度。我们从果蝇果蝇中编译并分析了几个基因组数据集。我们的分析表明，没有从D. melanogaster到D. simulans的迁移，也没有大量的基因流从D. simulans到D. melanogaster，其速度与每代0.02个移民个体相似。我们讨论了多物种合并模型对物种树估计的实用性，这是宗谱分类和迁移不完全的。
We develop a maximum likelihood (ML) method for estimating migration rates between species using genomic sequence data. A species tree is used to accommodate the phylogenetic relationships among three species, allowing for migration between the two sister species, while the third species is used as an out-group. A Markov chain characterization of the genealogical process of coalescenceandmigration is used to integrate out the migration histories at each locus analytically, whereas Gaussian quadrature is used to integrate over the coalescent times on each genealogical tree numerically. This is an extension of our early implementation of the symmetrical isolation-with-migration model for three species to accommodate arbitrary loci with two or three sequences per locus and to allow asymmetrical migration rates. Our implementation can accommodate tens of thousands of loci, making it feasible to analyze genome-scale data sets to test for gene flow. We calculate the posterior probabilities of gene trees at individual loci to identify genomic regions that are likely to have been transferred between species due to gene flow. We conduct a simulation study to examine the statistical properties of the likelihood ratio test for gene flow between the two in-group species and of the ML estimates of model parameters such as the migration rate. Inclusion of data from a third out-group species is found to increase dramatically the power of the test and the precision of parameter estimation. We compiled and analyzed several genomic data sets from the Drosophila fruit flies. Our analyses suggest no migration from D. melanogaster to D. simulans, and a significant amount of gene flow from D. simulans to D. melanogaster, at the rate of similar to 0.02 migrant individuals per generation. We discuss the utility of the multispecies coalescent model for species tree estimation, accounting for incomplete lineage sorting and migration.