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Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population

Viluma, Agnese and Flagstad, Oystein and Åkesson, Mikael and Wikenros, Camilla and Sand, Håkan and Wabakken, Petter and Ellegren, Hans (2022). Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population. Genome Research. 32 :3 , 449-458
[Research article]

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Abstract

Genetic drift can dramatically change allele frequencies in small populations and lead to reduced levels of genetic diversity, including loss of segregating variants. However, there is a shortage of quantitative studies of how genetic diversity changes over time in natural populations, especially on genome-wide scales. Here, we analyzed whole-genome sequences from 76 wolves of a highly inbred Scandinavian population, founded by only one female and two males, sampled over a period of 30 yr. We obtained chromosome-level haplotypes of all three founders and found that 10%-24% of their diploid genomes had become lost after about 20 yr of inbreeding (which approximately corresponds to five generations). Lost haplotypes spanned large genomic regions, as expected from the amount of recombination during this limited time period. Altogether, 160,000 SNP alleles became lost from the population, which may include adaptive variants as well as wild-type alleles masking recessively deleterious alleles. Although not sampled, we could indirectly infer that the two male founders had megabase-sized runs of homozygosity and that all three founders showed significant haplotype sharing, meaning that there were on average only 4.2 unique haplotypes in the six copies of each autosome that the founders brought into the population. This violates the assumption of unrelated founder haplotypes often made in conservation and management of endangered species. Our study provides a novel view of how whole-genome resequencing of temporally stratified samples can be used to visualize and directly quantify the consequences of genetic drift in a small inbred population.

Authors/Creators:Viluma, Agnese and Flagstad, Oystein and Åkesson, Mikael and Wikenros, Camilla and Sand, Håkan and Wabakken, Petter and Ellegren, Hans
Title:Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population
Series Name/Journal:Genome Research
Year of publishing :2022
Volume:32
Number:3
Page range:449-458
Number of Pages:10
Publisher:COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
ISSN:1088-9051
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution-Noncommercial 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) > Genetics (medical genetics to be 30107 and agricultural genetics to be 40402)
URN:NBN:urn:nbn:se:slu:epsilon-p-116946
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-116946
Additional ID:
Type of IDID
DOI10.1101/gr.276070.121
Web of Science (WoS)000764610400005
ID Code:27766
Faculty:S - Faculty of Forest Sciences
Department:(NL, NJ) > Dept. of Ecology
(S) > Dept. of Ecology
Deposited By: SLUpub Connector
Deposited On:12 May 2022 07:59
Metadata Last Modified:13 May 2022 22:39

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