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The Influence of Gene Flow on Species Tree Estimation: A Simulation Study

Leache, AD; Harris, RB; Rannala, B; Yang, Z; (2014) The Influence of Gene Flow on Species Tree Estimation: A Simulation Study. Systematic Biology , 63 (1) pp. 17-30. 10.1093/sysbio/syt049. Green open access

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Abstract

Gene flow among populations or species and incomplete lineage sorting (ILS) are two evolutionary processes responsible for generating gene tree discordance and therefore hindering species tree estimation. Numerous studies have evaluated the impacts of ILS on species tree inference, yet the ramifications of gene flow on species trees remain less studied. Here, we simulate and analyse multilocus sequence data generated with ILS and gene flow to quantify their impacts on species tree inference. We characterize species tree estimation errors under various models of gene flow, such as the isolation-migration model, the n-island model, and gene flow between non-sister species or involving ancestral species, and species boundaries crossed by a single gene copy (allelic introgression) or by a single migrant individual. These patterns of gene flow are explored on species trees of different sizes (4 vs. 10 species), at different time scales (shallow vs. deep), and with different migration rates. Species trees are estimated with the multispecies coalescent model using Bayesian methods (BEST and *BEAST) and with a summary statistic approach (MPEST) that facilitates phylogenomic-scale analysis. Even in cases where the topology of the species tree is estimated with high accuracy, we find that gene flow can result in overestimates of population sizes (species tree dilation) and underestimates of species divergence times (species tree compression). Signatures of migration events remain present in the distribution of coalescent times for gene trees, and with sufficient data it is possible to identify those loci that have crossed species boundaries. These results highlight the need for careful sampling design in phylogeographic and species delimitation studies as gene flow, introgression, or incorrect sample assignments can bias the estimation of the species tree topology and of parameter estimates such as population sizes and divergence times.

Type: Article
Title: The Influence of Gene Flow on Species Tree Estimation: A Simulation Study
Open access status: An open access version is available from UCL Discovery
DOI: 10.1093/sysbio/syt049
Publisher version: http://dx.doi.org/10.1093/sysbio/syt049
Language: English
Additional information: This is a pre-copyedited, author-produced PDF of an article accepted for publication in Systematic Biology following peer review. The version of record, Leache, AD; Harris, RB; Rannala, B; Yang, Z; (2014) The Influence of Gene Flow on Species Tree Estimation: A Simulation Study. Systematic Biology , 63 (1) pp. 17-30, is available online at: http://dx.doi.org/10.1093/sysbio/syt049
Keywords: BEAST; BEST; coalescence; compression; dilation; introgression; MPEST; migration; simulation
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/1473660
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