Detecting inbreeding depression in structured populations.
Details
Serval ID
serval:BIB_FDC1D721148F
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Detecting inbreeding depression in structured populations.
Journal
Proceedings of the National Academy of Sciences of the United States of America
ISSN
1091-6490 (Electronic)
ISSN-L
0027-8424
Publication state
Published
Issued date
07/05/2024
Peer-reviewed
Oui
Volume
121
Number
19
Pages
e2315780121
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: ppublish
Publication Status: ppublish
Abstract
Measuring inbreeding and its consequences on fitness is central for many areas in biology including human genetics and the conservation of endangered species. However, there is no consensus on the best method, neither for quantification of inbreeding itself nor for the model to estimate its effect on specific traits. We simulated traits based on simulated genomes from a large pedigree and empirical whole-genome sequences of human data from populations with various sizes and structures (from the 1,000 Genomes project). We compare the ability of various inbreeding coefficients ([Formula: see text]) to quantify the strength of inbreeding depression: allele-sharing, two versions of the correlation of uniting gametes which differ in the weight they attribute to each locus and two identical-by-descent segments-based estimators. We also compare two models: the standard linear model and a linear mixed model (LMM) including a genetic relatedness matrix (GRM) as random effect to account for the nonindependence of observations. We find LMMs give better results in scenarios with population or family structure. Within the LMM, we compare three different GRMs and show that in homogeneous populations, there is little difference among the different [Formula: see text] and GRM for inbreeding depression quantification. However, as soon as a strong population or family structure is present, the strength of inbreeding depression can be most efficiently estimated only if i) the phenotypes are regressed on [Formula: see text] based on a weighted version of the correlation of uniting gametes, giving more weight to common alleles and ii) with the GRM obtained from an allele-sharing relatedness estimator.
Keywords
Humans, Inbreeding Depression, Models, Genetic, Pedigree, Genetics, Population/methods, Inbreeding, Alleles, inbreeding, inbreeding depression, population structure
Pubmed
Web of science
Open Access
Yes
Funding(s)
Swiss National Science Foundation / 31003A_179358
Create date
01/05/2024 15:38
Last modification date
13/07/2024 7:09