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Estimating uncertainty in divergence times among three-spined stickleback clades using the multispecies coalescent


Fang, Bohao; Merilä, Juha; Matschiner, Michael; Momigliano, Paolo (2020). Estimating uncertainty in divergence times among three-spined stickleback clades using the multispecies coalescent. Molecular Phylogenetics and Evolution, 142:106646.

Abstract

Incomplete lineage sorting (ILS) can lead to biased divergence time estimates. To explore if and how ILS has influenced the results of a recent worldwide phylogeny of three-spined sticklebacks (Gasterosteus aculeatus), we estimated divergence times among major clades by applying both a concatenation approach and the multispecies coalescent (MSC) model to single-nucleotide polymorphisms. To further test the influence of different calibration strategies, we applied different calibrations to the root and to younger nodes in addition to the ones used in the previous study. Both the updated calibrations and the application of the MSC model influenced divergence time estimates, sometimes significantly. The new divergence time estimates were more ancient than in the previous study for older nodes, whereas the estimates of younger nodes were not strongly affected by the re-analyses. However, since the applied MSC method employs a simple substitution model and cannot account for changes in population size, we suggest that different analytical approaches and calibration strategies should be used in order to explore uncertainty in divergence time estimates. This study provides a valuable reference timeline for the ages of worldwide three-spined stickleback populations and emphasizes the need to embrace, rather than obscure, uncertainties around divergence time estimates.

Abstract

Incomplete lineage sorting (ILS) can lead to biased divergence time estimates. To explore if and how ILS has influenced the results of a recent worldwide phylogeny of three-spined sticklebacks (Gasterosteus aculeatus), we estimated divergence times among major clades by applying both a concatenation approach and the multispecies coalescent (MSC) model to single-nucleotide polymorphisms. To further test the influence of different calibration strategies, we applied different calibrations to the root and to younger nodes in addition to the ones used in the previous study. Both the updated calibrations and the application of the MSC model influenced divergence time estimates, sometimes significantly. The new divergence time estimates were more ancient than in the previous study for older nodes, whereas the estimates of younger nodes were not strongly affected by the re-analyses. However, since the applied MSC method employs a simple substitution model and cannot account for changes in population size, we suggest that different analytical approaches and calibration strategies should be used in order to explore uncertainty in divergence time estimates. This study provides a valuable reference timeline for the ages of worldwide three-spined stickleback populations and emphasizes the need to embrace, rather than obscure, uncertainties around divergence time estimates.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Paleontological Institute and Museum
Dewey Decimal Classification:560 Fossils & prehistoric life
Uncontrolled Keywords:Genetics, Ecology, Evolution, Behavior and Systematics, Molecular Biology
Language:English
Date:1 January 2020
Deposited On:08 Nov 2019 15:42
Last Modified:29 Feb 2020 08:10
Publisher:Elsevier
ISSN:1055-7903
OA Status:Green
Publisher DOI:https://doi.org/10.1016/j.ympev.2019.106646
Official URL:https://www.sciencedirect.com/science/article/pii/S1055790319300983

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