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

Bohao Fang, Juha Merilä, Michael Matschiner, Paolo Momigliano

Research output: Contribution to journalArticleScientificpeer-review

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 study of 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, given 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.
Original languageEnglish
JournalMolecular Phylogenetics and Evolution
Volume142
ISSN1055-7903
DOIs
Publication statusPublished - Jan 2020
MoE publication typeA1 Journal article-refereed

Fields of Science

  • multispecies coalescent
  • Gasterosteus
  • phylogenomics
  • RAD-seq
  • SNP
  • threespine stickleback
  • 1181 Ecology, evolutionary biology
  • 1182 Biochemistry, cell and molecular biology

Cite this

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title = "Estimating uncertainty in divergence times among three-spined stickleback clades using the multispecies coalescent",
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 study of 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, given 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.",
keywords = "multispecies coalescent, Gasterosteus, phylogenomics, RAD-seq, SNP, threespine stickleback, 1181 Ecology, evolutionary biology, 1182 Biochemistry, cell and molecular biology",
author = "Bohao Fang and Juha Meril{\"a} and Michael Matschiner and Paolo Momigliano",
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language = "English",
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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.

In: Molecular Phylogenetics and Evolution, Vol. 142, 01.2020.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

T1 - Estimating uncertainty in divergence times among three-spined stickleback clades using the multispecies coalescent

AU - Fang, Bohao

AU - Merilä, Juha

AU - Matschiner, Michael

AU - Momigliano, Paolo

PY - 2020/1

Y1 - 2020/1

N2 - Incomplete lineage sorting (ILS) can lead to biased divergence time estimates. To explore if and how ILS has influenced the results of a recent study of 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, given 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.

AB - Incomplete lineage sorting (ILS) can lead to biased divergence time estimates. To explore if and how ILS has influenced the results of a recent study of 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, given 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.

KW - multispecies coalescent

KW - Gasterosteus

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