The structured coalescent in the context of gene copy number variation

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Title:Main Title: The structured coalescent in the context of gene copy number variation
Description:Abstract: The Structured Coalescent was introduced to describe the coalescent process in spatially subdivided populations with migration. Here, we re-interpret migration routes of individuals in the original model as "migration routes" of single genes in tandemly arranged gene arrays. A gene copy may change its position within the array via unequal recombination. Hence, in a coalescent framework, two copies sampled from two chromosomes may coalesce only if they are at exactly homologous positions. Otherwise, one or multiple recombination events have to occur before they can coalesce, thereby increasing mean coalescence time and expected genetic diversity among the copies in a gene array. We explicitly calculate the transition probabilities on these routes backward in time. We simulate the structured coalescent with migration and coalescence rates informed by the unequal recombination process of gene copies. With this novel interpretation of population structure models we determine coalescence times and expected genetic diversity in samples of orthologous and paralogous copies from a gene family. As a case study, we discuss the site frequency spectrum of a small gene family in the two scenarios of high and of no gene copy number variation among individuals. These examples underline the significance of our model, since standard test-statistics may lead to misinterpretations when analyzing sequence data of multi-copy genes due to their different expected genetic diversity.
Identifier:https://doi.org/10.1016/j.tpb.2023.08.001 (DOI)
Citation Advice:Otto, M., & Wiehe, T. (2023). The structured coalescent in the context of gene copy number variation. Theoretical population biology, 154, 67–78. Advance online publication. https://doi.org/10.1016/j.tpb.2023.08.001
Responsible Party
Creators:Moritz Otto (Author), Thomas Wiehe (Author)
Funding Reference:Deutsche Forschungsgemeinschaft (DFG): CRC 1211: Earth - Evolution at the Dry Limit
Publisher:Theoretical Population Biology
Publication Year:2023
Topic
CRC1211 Topic:Biology
Related Subproject:B6
Subject:Keyword: Population Genetics
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Filename:1-s2.0-S0040580923000564-main.pdf
Data Type:Text - Article
File Size:1.2 MB
Dates:Issued: 30.08.2023
Submitted: 28.02.2023
Mime Type:application/pdf
Data Format:PDF
Language:English
Status:Completed
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Download Permission:Free
General Access and Use Conditions:According to the CRC1211DB data policy agreement.
Access Limitations:According to the CRC1211DB data policy agreement.
Licence:None
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Publication Status:Published
Review Status:Peer reviewed
Publication Type:Article
Article Type:Journal
Source:ScienceDirect
Number of Pages:12 (67 - 78)
Metadata Details
Metadata Creator:Moritz Otto
Metadata Created:22.11.2023
Metadata Last Updated:22.11.2023
Subproject:B6
Funding Phase:2
Metadata Language:English
Metadata Version:V50
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