Ji, Jiayi;
Roberts, Thomas;
Flouri, Tomas;
Yang, Ziheng;
(2025)
Inference of Cross‑Species Gene Flow Using Genomic Data Depends
on the Methods: Case Study of Gene Flow in Drosophila.
Systematic Biology
10.1093/sysbio/syaf019.
(In press).
Preview |
Text
Yang_syaf019.pdf Download (2MB) | Preview |
Abstract
Analysis of genomic data in the past two decades has highlighted the prevalence of introgression as an important evolutionary force in both plants and animals. The genus Drosophila has received much attention recently, with an analysis of genomic sequence data revealing widespread introgression across the species phylogeny for the genus. However, the methods used in the study are based on data summaries for species triplets and are unable to infer gene flow between sister lineages or to identify the direction of gene flow. Hence, we reanalyze a subset of the data using the Bayesian program bpp, which is a full-likelihood implementation of the multispecies coalescent model and can provide more powerful inference of gene flow between species, including its direction, timing, and strength. While our analysis supports the presence of gene flow in the species group, the results differ from the previous study: we infer gene flow between sister lineages undetected previously whereas most gene-flow events inferred in the previous study are rejected in our tests. To verify our conclusions, we performed simulations to examine the properties of Bayesian and summary methods. Bpp was found to have high power to detect gene flow, high accuracy in estimated rates of gene flow, and robustness under misspecification of the mode of gene flow. In contrast, summary methods had low power and produced biased estimates of introgression probability. Our results highlight an urgent need for improving the statistical properties of summary methods and the computational efficiency of likelihood methods for inferring gene flow using genomic sequence data.
| Type: | Article |
|---|---|
| Title: | Inference of Cross‑Species Gene Flow Using Genomic Data Depends on the Methods: Case Study of Gene Flow in Drosophila |
| Location: | England |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1093/sysbio/syaf019 |
| Publisher version: | https://doi.org/10.1093/sysbio/syaf019 |
| Language: | English |
| Additional information: | © The Author(s) 2025. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. https://doi.org/10.1093/sysbio/syaf019 |
| Keywords: | Science & Technology, Life Sciences & Biomedicine, Evolutionary Biology, <sc>bpp</sc>, Drosophila, introgression, migration, multispecies coalescent, MSC-I, MSC-M, DIVERGENCE TIME, TREE ESTIMATION, SEQUENCE DATA, INTROGRESSION |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10211260 |
Archive Staff Only
 |
View Item |
