Estimation of species divergence times in presence of cross-species gene flow.
Estimation of species divergence times in presence of cross-species gene flow.
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DOI：
10.1093/sysbio/syad015
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发表时间：
2023-08-07
影响因子：
6.5
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中科院分区：
文献类型：
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跨物种的渗入可以对物种差异事件的系统生成重建产生重大影响。在这里，我们使用仿真来展示即使少量渗入的存在如何在分析中忽略基因流程时偏向差异时间估计。利用多种聚合（MSC）模型下的分析方法的进步，我们证明，可以避免使用大型系统基因组数据集来考虑不完整的谱系分类和渗入，可以避免此问题。多种含量 - 钙化 - 触发感（MSCI）模型能够准确估计差异时间和祖先有效的人口大小，即使每种物种只有一个单个二倍体个体。在三种不同的情况下，我们表征了对差异时间估计中偏见的一些普遍期望：1）姊妹物种之间的渗入，2）非姐姐物种之间的渗入，和3）未从未采样（即幽灵）外群的渗入。我们还在分离移民（IM）模型下进行了模拟，发现尽管连续基因流量很高，但假设发作基因流动流动流动流动的MSCI模型仍能够准确估计物种差异时间。我们估计了两个已发表的经验数据集的MSC和MSCI模型下的差异时间，并具有先前的渗入证据，其中一个来自Baobabs（Adansonia）的372个目标 - 富含目标 - 一个来自Baobabs的目标 - 含量 - 来自1000个转录组基因座中的另一个来自番茄14种。经验分析不仅证实了我们从模拟中的发现，表明MSCI模型可以可靠地估计差异时间，而且还表明，MSC下的差异时间估计可以强大，可以在经验数据集中具有广泛的分类单元采样。 [分歧时间；基因流；杂交；渗入； MSCI模型；多人合并]
Cross-species introgression can have significant impacts on phylogenomic reconstruction of species divergence events. Here, we used simulations to show how the presence of even a small amount of introgression can bias divergence time estimates when gene flow is ignored in the analysis. Using advances in analytical methods under the multispecies coalescent (MSC) model, we demonstrate that by accounting for incomplete lineage sorting and introgression using large phylogenomic data sets this problem can be avoided. The multispecies-coalescent-with-introgression (MSci) model is capable of accurately estimating both divergence times and ancestral effective population sizes, even when only a single diploid individual per species is sampled. We characterize some general expectations for biases in divergence time estimation under three different scenarios: 1) introgression between sister species, 2) introgression between non-sister species, and 3) introgression from an unsampled (i.e., ghost) outgroup lineage. We also conducted simulations under the isolation-with-migration (IM) model and found that the MSci model assuming episodic gene flow was able to accurately estimate species divergence times despite high levels of continuous gene flow. We estimated divergence times under the MSC and MSci models from two published empirical datasets with previous evidence of introgression, one of 372 target-enrichment loci from baobabs (Adansonia), and another of 1000 transcriptome loci from 14 species of the tomato relative, Jaltomata. The empirical analyses not only confirm our findings from simulations, demonstrating that the MSci model can reliably estimate divergence times but also show that divergence time estimation under the MSC can be robust to the presence of small amounts of introgression in empirical datasets with extensive taxon sampling. [divergence time; gene flow; hybridization; introgression; MSci model; multispecies coalescent]
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影响因子：
4.5
作者：
Gutenkunst RN;Hernandez RD;Williamson SH;Bustamante CD
通讯作者：
Bustamante CD
影响因子：
1.9
作者：
BAUM, DA
通讯作者：
BAUM, DA
DOI：
10.1098/rstb.2016.0098
发表时间：
2016-07-19
期刊：
Philosophical transactions of the Royal Society of London. Series B, Biological sciences
影响因子：
--
作者：
De Baets K;Antonelli A;Donoghue PC
通讯作者：
Donoghue PC
影响因子：
6.5
作者：
Blischak, Paul D.;Chifman, Julia;Kubatko, Laura S.
通讯作者：
Kubatko, Laura S.
影响因子：
6.5
作者：
Breinholt, Jesse W.;Earl, Chandra;Kawahara, Akito Y.
通讯作者：
Kawahara, Akito Y.