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Journal article
A new method for ecologists to estimate heterozygote excess and deficit for multi‐locus gene families
Ecology and evolution, Vol.14(7), e11561
2024
Abstract
The fixation index, F IS , has been a staple measure to detect selection, or departures from random mating in populations. However, current Next Generation Sequencing (NGS) cannot easily estimate F IS , in multi‐locus gene families that contain multiple loci having similar or identical arrays of variant sequences of ≥1 kilobase (kb), which differ at multiple positions. In these families, high‐quality short‐read NGS data typically identify variants, but not the genomic location, which is required to calculate F IS (based on locus‐specific observed and expected heterozygosity). Thus, to assess assortative mating, or selection on heterozygotes, from NGS of multi‐locus gene families, we need a method that does not require knowledge of which variants are alleles at which locus in the genome. We developed such a method. Like F IS , our novel measure, 1 H IS , is based on the principle that positive assortative mating, or selection against heterozygotes, and some other processes reduce within‐individual variability relative to the population. We demonstrate high accuracy of 1 H IS on a wide range of simulated scenarios and two datasets from natural populations of penguins and dolphins. 1 H IS is important because multi‐locus gene families are often involved in assortative mating or selection on heterozygotes. 1 H IS is particularly useful for multi‐locus gene families, such as toll‐like receptors, the major histocompatibility complex in animals, homeobox genes in fungi and self‐incompatibility genes in plants.
Details
- Title
- A new method for ecologists to estimate heterozygote excess and deficit for multi‐locus gene families
- Authors/Creators
- Gabe D. O'Reilly - UNSW SydneyOliver Manlik - UNSW SydneySandra Vardeh - UNSW SydneyJennifer Sinclair - UNSW SydneyBelinda Cannell - Murdoch University, Centre for Sustainable Aquatic EcosystemsZachary P. Lawler - UNSW SydneyWilliam B. Sherwin - UNSW Sydney
- Publication Details
- Ecology and evolution, Vol.14(7), e11561
- Publisher
- John Wiley & Sons Ltd.
- Identifiers
- 991005687459107891
- Copyright
- © 2024 The Author(s).
- Murdoch Affiliation
- School of Environmental and Conservation Sciences
- Language
- English
- Resource Type
- Journal article
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- Citation topics
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- Web Of Science research areas
- Ecology
- Evolutionary Biology
- ESI research areas
- Environment/Ecology