Evidence of Site-Specific and Male-Biased Germline Mutation Rate in a Wild Songbird
Zhang, Hongkai LU ; Lundberg, Max LU ; Tarka, Maja LU ; Hasselquist, Dennis LU and Hansson, Bengt LU
(2023)
In Genome Biology and Evolution
15(11).
- Abstract
Germline mutations are the ultimate source of genetic variation and the raw material for organismal evolution. Despite their significance, the frequency and genomic locations of mutations, as well as potential sex bias, are yet to be widely investigated in most species. To address these gaps, we conducted whole-genome sequencing of 12 great reed warblers (Acrocephalus arundinaceus) in a pedigree spanning 3 generations to identify single-nucleotide de novo mutations (DNMs) and estimate the germline mutation rate. We detected 82 DNMs within the pedigree, primarily enriched at CpG sites but otherwise randomly located along the chromosomes. Furthermore, we observed a pronounced sex bias in DNM occurrence, with male warblers exhibiting three... (More)
Germline mutations are the ultimate source of genetic variation and the raw material for organismal evolution. Despite their significance, the frequency and genomic locations of mutations, as well as potential sex bias, are yet to be widely investigated in most species. To address these gaps, we conducted whole-genome sequencing of 12 great reed warblers (Acrocephalus arundinaceus) in a pedigree spanning 3 generations to identify single-nucleotide de novo mutations (DNMs) and estimate the germline mutation rate. We detected 82 DNMs within the pedigree, primarily enriched at CpG sites but otherwise randomly located along the chromosomes. Furthermore, we observed a pronounced sex bias in DNM occurrence, with male warblers exhibiting three times more mutations than females. After correction for false negatives and adjusting for callable sites, we obtained a mutation rate of 7.16 × 10−9 mutations per site per generation (m/s/g) for the autosomes and 5.10 × 10−9 m/s/g for the Z chromosome. To demonstrate the utility of species-specific mutation rates, we applied our autosomal mutation rate in models reconstructing the demographic history of the great reed warbler. We uncovered signs of drastic population size reductions predating the last glacial period (LGP) and reduced gene flow between western and eastern populations during the LGP. In conclusion, our results provide one of the few direct estimates of the mutation rate in wild songbirds and evidence for male-driven mutations in accordance with theoretical expectations.
(Less)
- author
- Zhang, Hongkai
LU
; Lundberg, Max
LU
; Tarka, Maja
LU
; Hasselquist, Dennis
LU
and Hansson, Bengt
LU
- organization
-
- Molecular Ecology and Evolution Lab (research group)
- MEMEG
- CAnMove - Centre for Animal Movement Research (research group)
- Speciation, Adaptation and Coevolution (research group)
- Life History and Functional Ecology (research group)
- Genetics of Sex Differences (research group)
- BECC: Biodiversity and Ecosystem services in a Changing Climate
- publishing date
- 2023-11-01
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- bird, CpG sites, de novo mutation, demographic history, sex bias
- in
- Genome Biology and Evolution
- volume
- 15
- issue
- 11
- article number
- evad180
- publisher
- Oxford University Press
- external identifiers
-
- pmid:37793164
- scopus:85176508239
- ISSN
- 1759-6653
- DOI
- 10.1093/gbe/evad180
- language
- English
- LU publication?
- yes
- id
- 6dc6ce85-519e-4c2a-845c-a898fc375dec
- date added to LUP
- 2023-12-28 14:49:34
- date last changed
- 2024-04-26 21:49:41
@article{6dc6ce85-519e-4c2a-845c-a898fc375dec,
abstract = {{<p>Germline mutations are the ultimate source of genetic variation and the raw material for organismal evolution. Despite their significance, the frequency and genomic locations of mutations, as well as potential sex bias, are yet to be widely investigated in most species. To address these gaps, we conducted whole-genome sequencing of 12 great reed warblers (Acrocephalus arundinaceus) in a pedigree spanning 3 generations to identify single-nucleotide de novo mutations (DNMs) and estimate the germline mutation rate. We detected 82 DNMs within the pedigree, primarily enriched at CpG sites but otherwise randomly located along the chromosomes. Furthermore, we observed a pronounced sex bias in DNM occurrence, with male warblers exhibiting three times more mutations than females. After correction for false negatives and adjusting for callable sites, we obtained a mutation rate of 7.16 × 10<sup>−9</sup> mutations per site per generation (m/s/g) for the autosomes and 5.10 × 10<sup>−9</sup> m/s/g for the Z chromosome. To demonstrate the utility of species-specific mutation rates, we applied our autosomal mutation rate in models reconstructing the demographic history of the great reed warbler. We uncovered signs of drastic population size reductions predating the last glacial period (LGP) and reduced gene flow between western and eastern populations during the LGP. In conclusion, our results provide one of the few direct estimates of the mutation rate in wild songbirds and evidence for male-driven mutations in accordance with theoretical expectations.</p>}},
author = {{Zhang, Hongkai and Lundberg, Max and Tarka, Maja and Hasselquist, Dennis and Hansson, Bengt}},
issn = {{1759-6653}},
keywords = {{bird; CpG sites; de novo mutation; demographic history; sex bias}},
language = {{eng}},
month = {{11}},
number = {{11}},
publisher = {{Oxford University Press}},
series = {{Genome Biology and Evolution}},
title = {{Evidence of Site-Specific and Male-Biased Germline Mutation Rate in a Wild Songbird}},
url = {{http://dx.doi.org/10.1093/gbe/evad180}},
doi = {{10.1093/gbe/evad180}},
volume = {{15}},
year = {{2023}},
}