Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands.
Carl von Ossietzky University, Oldenburg, Germany.
Mol Ecol Resour. 2022 Apr;22(3):908-926. doi: 10.1111/1755-0998.13519. Epub 2021 Oct 10.
After admixture, recombination breaks down genomic blocks of contiguous ancestry. The breakdown of these blocks forms a new "molecular clock" that ticks at a much faster rate than the mutation clock, enabling accurate dating of admixture events in the recent past. However, existing theory on the breakdown of these blocks, or the accumulation of delineations between blocks, so-called "junctions", has mostly been limited to using regularly spaced markers on phased data. Here, we present an extension to the theory of junctions using the ancestral recombination graph that describes the expected number of junctions for any distribution of markers along the genome. Furthermore, we provide a new framework to infer the time since admixture using unphased data. We demonstrate both the phased and unphased methods on simulated data and show that our new extensions have improved accuracy with respect to previous methods, especially for smaller population sizes and more ancient admixture times. Lastly, we demonstrate the applicability of our method on three empirical data sets, including labcrosses of yeast (Saccharomyces cerevisae) and two case studies of hybridization in swordtail fish and Populus trees.
混合后，重组会打破连续祖先的基因组块。这些块的打破形成了一个新的“分子钟”，其计时速度比突变钟快得多，从而能够准确确定最近发生的混合事件的时间。然而，关于这些块的打破或块之间的划分（所谓的“接头”）的积累的现有理论，主要局限于在分相数据上使用规则间隔的标记。在这里，我们使用描述基因组上任何标记分布的预期接头数量的祖先重组图来扩展接头理论。此外，我们提供了一个使用非分相数据推断混合后时间的新框架。我们在模拟数据上展示了分相和非分相方法，并表明我们的新扩展在精度上优于以前的方法，特别是对于较小的种群规模和更古老的混合时间。最后，我们在三个实证数据集上展示了我们的方法的适用性，包括酵母（酿酒酵母）的实验室杂交和剑尾鱼和杨树杂交的两个案例研究。
