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Biases in Demographic Modeling Affect Our Understanding of Recent Divergence

Momigliano, Paolo and Florin, Ann-Britt and Merila, Juha (2021). Biases in Demographic Modeling Affect Our Understanding of Recent Divergence. Molecular Biology and Evolution. 38 , 2967-2985
[Research article]

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Abstract

Testing among competing demographic models of divergence has become an important component of evolutionary research in model and non-model organisms. However, the effect of unaccounted demographic events on model choice and parameter estimation remains largely unexplored. Using extensive simulations, we demonstrate that under realistic divergence scenarios, failure to account for population size (N-e) changes in daughter and ancestral populations leads to strong biases in divergence time estimates as well as model choice. We illustrate these issues reconstructing the recent demographic history of North Sea and Baltic Sea turbots (Scophthalmus maximus) by testing 16 isolation with migration (IM) and 16 secondary contact (SC) scenarios, modeling changes in N-e as well as the effects of linked selection and barrier loci. Failure to account for changes in N-e resulted in selecting SC models with long periods of strict isolation and divergence times preceding the formation of the Baltic Sea. In contrast, models accounting for N-e changes suggest recent (<6 kya) divergence with constant gene flow. We further show how interpreting genomic landscapes of differentiation can help discerning among competing models. For example, in the turbot data, islands of differentiation show signatures of recent selective sweeps, rather than old divergence resisting secondary introgression. The results have broad implications for the study of population divergence by highlighting the potential effects of unmodeled changes in N-e on demographic inference. Tested models should aim at representing realistic divergence scenarios for the target taxa, and extreme caution should always be exercised when interpreting results of demographic modeling.

Authors/Creators:Momigliano, Paolo and Florin, Ann-Britt and Merila, Juha
Title:Biases in Demographic Modeling Affect Our Understanding of Recent Divergence
Series Name/Journal:Molecular Biology and Evolution
Year of publishing :2021
Volume:38
Page range:2967-2985
Number of Pages:19
Publisher:OXFORD UNIV PRESS
ISSN:0737-4038
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Evolutionary Biology
Keywords:demographic modeling, allele frequency spectrum, secondary contact, isolation with migration
URN:NBN:urn:nbn:se:slu:epsilon-p-113184
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-113184
Additional ID:
Type of IDID
DOI10.1093/molbev/msab047
Web of Science (WoS)000671060500022
ID Code:25096
Faculty:NJ - Fakulteten för naturresurser och jordbruksvetenskap
Department:(NL, NJ) > Department of Aquatic Resources
Deposited By: SLUpub Connector
Deposited On:30 Aug 2021 11:25
Metadata Last Modified:30 Aug 2021 11:31

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