De Novo Mutation Rates in Sticklebacks

Chaowei Zhang; Kerry Reid; Arthur F. Sands; Antoine Fraimout; Mikkel Heide Schierup; Juha Merilä

doi:10.1093/molbev/msad192

De Novo Mutation Rates in Sticklebacks

Chaowei Zhang^*, Kerry Reid, Arthur F. Sands, Antoine Fraimout, Mikkel Heide Schierup, Juha Merilä^*

^*Corresponding author for this work

Department of Molecular Biology and Genetics - Bioinformatics Research Centre (BiRC)

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

3 Citations (Scopus)

Abstract

Mutation rate is a fundamental parameter in population genetics. Apart from being an important scaling parameter for demographic and phylogenetic inference, it allows one to understand at what rate new genetic diversity is generated and what the expected level of genetic diversity is in a population at equilibrium. However, except for well-established model organisms, accurate estimates of de novo mutation rates are available for a very limited number of organisms from the wild. We estimated mutation rates (µ) in two marine populations of the nine-spined stickleback (Pungitius pungitius) with the aid of several 2- and 3-generational family pedigrees, deep (>50×) whole-genome resequences and a high-quality reference genome. After stringent filtering, we discovered 308 germline mutations in 106 offspring translating to µ = 4.83 × 10-9 and µ = 4.29 × 10-9 per base per generation in the two populations, respectively. Up to 20% of the mutations were shared by full-sibs showing that the level of parental mosaicism was relatively high. Since the estimated µ was 3.1 times smaller than the commonly used substitution rate, recalibration with µ led to substantial increase in estimated divergence times between different stickleback species. Our estimates of the de novo mutation rate should provide a useful resource for research focused on fish population genetics and that of sticklebacks in particular.

Original language	English
Article number	msad192
Journal	Molecular Biology and Evolution
Volume	40
Issue	9
ISSN	0737-4038
DOIs	https://doi.org/10.1093/molbev/msad192
Publication status	Published - Sept 2023

Keywords

divergence time
genetic diversity
germline mutation rate
mutation rate
ninespine stickleback

Access to Document

10.1093/molbev/msad192Licence: CC BY

Cite this

@article{0546f4ad36a540cbac7151ed1e4300b7,

title = "De Novo Mutation Rates in Sticklebacks",

abstract = "Mutation rate is a fundamental parameter in population genetics. Apart from being an important scaling parameter for demographic and phylogenetic inference, it allows one to understand at what rate new genetic diversity is generated and what the expected level of genetic diversity is in a population at equilibrium. However, except for well-established model organisms, accurate estimates of de novo mutation rates are available for a very limited number of organisms from the wild. We estimated mutation rates (µ) in two marine populations of the nine-spined stickleback (Pungitius pungitius) with the aid of several 2- and 3-generational family pedigrees, deep (>50×) whole-genome resequences and a high-quality reference genome. After stringent filtering, we discovered 308 germline mutations in 106 offspring translating to µ = 4.83 × 10-9 and µ = 4.29 × 10-9 per base per generation in the two populations, respectively. Up to 20% of the mutations were shared by full-sibs showing that the level of parental mosaicism was relatively high. Since the estimated µ was 3.1 times smaller than the commonly used substitution rate, recalibration with µ led to substantial increase in estimated divergence times between different stickleback species. Our estimates of the de novo mutation rate should provide a useful resource for research focused on fish population genetics and that of sticklebacks in particular.",

keywords = "divergence time, genetic diversity, germline mutation rate, mutation rate, ninespine stickleback",

author = "Chaowei Zhang and Kerry Reid and Sands, {Arthur F.} and Antoine Fraimout and Schierup, {Mikkel Heide} and Juha Meril{\"a}",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.",

year = "2023",

month = sep,

doi = "10.1093/molbev/msad192",

language = "English",

volume = "40",

journal = "Molecular Biology and Evolution",

issn = "0737-4038",

publisher = "Oxford University Press",

number = "9",

}

TY - JOUR

T1 - De Novo Mutation Rates in Sticklebacks

AU - Zhang, Chaowei

AU - Reid, Kerry

AU - Sands, Arthur F.

AU - Fraimout, Antoine

AU - Schierup, Mikkel Heide

AU - Merilä, Juha

N1 - Publisher Copyright: © The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.

PY - 2023/9

Y1 - 2023/9

N2 - Mutation rate is a fundamental parameter in population genetics. Apart from being an important scaling parameter for demographic and phylogenetic inference, it allows one to understand at what rate new genetic diversity is generated and what the expected level of genetic diversity is in a population at equilibrium. However, except for well-established model organisms, accurate estimates of de novo mutation rates are available for a very limited number of organisms from the wild. We estimated mutation rates (µ) in two marine populations of the nine-spined stickleback (Pungitius pungitius) with the aid of several 2- and 3-generational family pedigrees, deep (>50×) whole-genome resequences and a high-quality reference genome. After stringent filtering, we discovered 308 germline mutations in 106 offspring translating to µ = 4.83 × 10-9 and µ = 4.29 × 10-9 per base per generation in the two populations, respectively. Up to 20% of the mutations were shared by full-sibs showing that the level of parental mosaicism was relatively high. Since the estimated µ was 3.1 times smaller than the commonly used substitution rate, recalibration with µ led to substantial increase in estimated divergence times between different stickleback species. Our estimates of the de novo mutation rate should provide a useful resource for research focused on fish population genetics and that of sticklebacks in particular.

AB - Mutation rate is a fundamental parameter in population genetics. Apart from being an important scaling parameter for demographic and phylogenetic inference, it allows one to understand at what rate new genetic diversity is generated and what the expected level of genetic diversity is in a population at equilibrium. However, except for well-established model organisms, accurate estimates of de novo mutation rates are available for a very limited number of organisms from the wild. We estimated mutation rates (µ) in two marine populations of the nine-spined stickleback (Pungitius pungitius) with the aid of several 2- and 3-generational family pedigrees, deep (>50×) whole-genome resequences and a high-quality reference genome. After stringent filtering, we discovered 308 germline mutations in 106 offspring translating to µ = 4.83 × 10-9 and µ = 4.29 × 10-9 per base per generation in the two populations, respectively. Up to 20% of the mutations were shared by full-sibs showing that the level of parental mosaicism was relatively high. Since the estimated µ was 3.1 times smaller than the commonly used substitution rate, recalibration with µ led to substantial increase in estimated divergence times between different stickleback species. Our estimates of the de novo mutation rate should provide a useful resource for research focused on fish population genetics and that of sticklebacks in particular.

KW - divergence time

KW - genetic diversity

KW - germline mutation rate

KW - mutation rate

KW - ninespine stickleback

UR - http://www.scopus.com/inward/record.url?scp=85171601285&partnerID=8YFLogxK

U2 - 10.1093/molbev/msad192

DO - 10.1093/molbev/msad192

M3 - Journal article

C2 - 37648662

AN - SCOPUS:85171601285

SN - 0737-4038

VL - 40

JO - Molecular Biology and Evolution

JF - Molecular Biology and Evolution

IS - 9

M1 - msad192

ER -

De Novo Mutation Rates in Sticklebacks

Abstract

Keywords

Access to Document

Other files and links

Fingerprint

Cite this