Estimation of species divergence times in presence of cross-species gene flow

Tiley，George P.1; Flouri，Tomáš2; Jiao，Xiyun2,3; Poelstra，Jelmer W.1; Xu，Bo4; Zhu，Tianqi5,6; Rannala，Bruce7; Yoder，Anne D.1; Yang，Ziheng2

2023-07-01

10.1093/sysbio/syad015

Systematic Biology   Impact Factor & Quartile

1063-5157

1076-836X

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.

SCI

English

Others

Biotechnology and Biological Sciences Research Council[BB/N000609/1];Biotechnology and Biological Sciences Research Council[BB/P006493/1];Biotechnology and Biological Sciences Research Council[BB/T003502/1];

WOS:000978139700001

ENVIRONMENT/ECOLOGY

2-s2.0-85159472603

Scopus

1.Department of Biology,Duke University,Durham,United States
2.Department of Genetics,Evolution and Environment,University College London,London,United Kingdom
3.Department of Statistics and Data Science,China Southern University of Science and Technology,Shenzhen,Guangdong,China
4.Beijing Institute of Genomics,Chinese Academy of Sciences,Beijing,100101,China
5.National Center for Mathematics and Interdisciplinary Sciences,Academy of Mathematics and Systems Science,Chinese Academy of Sciences,China
6.Key Laboratory of Random Complex Structures and Data Science,Academy of Mathematics and Systems Science,Chinese Academy of Sciences,China
7.Department of Evolution and Ecology,University of California,Davis,Davis,United States

Tiley，George P.,Flouri，Tomáš,Jiao，Xiyun,et al. Estimation of species divergence times in presence of cross-species gene flow[J]. Systematic Biology,2023,72(4):820-836.

Tiley，George P..,Flouri，Tomáš.,Jiao，Xiyun.,Poelstra，Jelmer W..,Xu，Bo.,...&Yang，Ziheng.(2023).Estimation of species divergence times in presence of cross-species gene flow.Systematic Biology,72(4),820-836.

Tiley，George P.,et al."Estimation of species divergence times in presence of cross-species gene flow".Systematic Biology 72.4(2023):820-836.