Complex population history affects admixture analyses in nine‐spined sticklebacks

Feng, Xueyun; Merilä, Juha; Löytynoja, Ari

doi:10.1111/mec.16651

Cited by 18 publications

(78 citation statements)

References 97 publications

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“…Since selection is less effective in fixing (or removing) introgressed variation in the genomes of smaller populations, differences in effective population sizes can lead to a strong variation in admixture proportions among populations ( Sankararaman et al 2014 ). Population size may thus be particularly relevant for unequal introgression between the recipient and donor population in Pungitius sticklebacks, since these populations are known to be small in general ( Merilä 2013 ; Bae and Suk 2015 ; Kemppainen et al 2021 ; Feng et al 2022 ). In this study, the recipient populations (e.g., P. sinensis and P. kaibarae from the Japanese archipelago) have much smaller population sizes than the donor populations (e.g., P. pungitius from the Japanese archipelago; supplementary fig.…”

Section: Discussionmentioning

confidence: 99%

“…DNA extraction, library construction, and sequencing strategy for WGS and RAD-seq are given in detail in Wang et al (2022) and Guo et al (2019) . Published WGS and RAD-seq data for an additional 109 Pungitius individuals and six individuals of three outgroup species from earlier studies ( Guo et al 2019 ; Yamasaki et al 2020 ; Feng et al 2022 ; Wang et al 2022 ) were retrieved from GenBank ( supplementary table S1, Supplementary Material online). Raw sequencing read quality assessment and filtering for each sample was done using FastQC and FastX toolkits, respectively.…”

Section: Methodsmentioning

confidence: 99%

“…This seems plausible, given that introgression has been increasingly recognized as a critically important source of genetic variation in adaptation and diversification ( Hedrick 2013 ; Arnold and Kunte 2017 ; Suarez-Gonzalez et al 2018 ; Burgarella et al 2019 ; Taylor and Larson 2019 ; Edelman and Mallet 2021 ). However, little is known about the genomic footprints of historical gene flow and its impact on the diversification of Pungitius sticklebacks ( Yamasaki et al 2020 ; Feng et al 2022 ).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Prevalent Introgression Underlies Convergent Evolution in the Diversification ofPungitiusSticklebacks

Wang

Cheng

et al. 2023

Molecular Biology and Evolution

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New mutations and standing genetic variations contribute significantly to repeated phenotypic evolution in sticklebacks. However, less is known about the role of introgression in this process. We analysed taxonomically and geographically comprehensive genomic data from Pungitius sticklebacks to decipher the extent of introgression and its consequences for the diversification of this genus. Our results demonstrate that introgression is more prevalent than suggested by earlier studies. Although gene flow was generally bidirectional, it was often asymmetric and left unequal genomic signatures in hybridizing species, which might, at least partly, be due to biased hybridization and/or population size differences. In several cases, introgression of variants from one species to another was accompanied by transitions of pelvic and/or lateral plate structures – important diagnostic traits in Pungitius systematics – and frequently left signatures of adaptation in the core gene regulatory networks of armor trait development. This finding suggests that introgression has been an important source of genetic variation and enabled phenotypic convergence among Pungitius sticklebacks. The results highlight the importance of introgression of genetic variation as a source of adaptive variation underlying key ecological and taxonomic traits. Taken together, our study indicates that introgression-driven convergence likely explains the longstanding challenges in resolving the taxonomy and systematics of this small but phenotypically highly diverse group of fish.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Prevalent Introgression Underlies Convergent Evolution in the Diversification ofPungitiusSticklebacks

Wang

Cheng

et al. 2023

Molecular Biology and Evolution

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“…The dates of three nodes that most studies have focused on (i.e. A = divergence of P. pungitius and G. aculeatus; B = the MRCA for all P. pungitius lineages; C = divergence of eastern and western European lineages of P. pungitius; Guo et al 2019;Feng et al 2022) were shared and supported in both topological scenarios (fig. 4 and supplementary fig.…”

Section: Divergence Time Estimation With Dnm Ratesmentioning

confidence: 99%

“…The nine-spined stickleback (Pungitius pungitius) is a small teleost fish which has recently been subject to many population genomic, demographic and phylogenetic investigations (e.g. Guo et al 2019;Natri et al 2019;Varandhajan et al 2019;Yamasaki et al 2020;Fang et al 2021;Kemppainen et al 2021;Wang Y et al 2022;Feng et al 2022;Kivikoski et al 2023), meaning that there is a community of researchers that would benefit from access to DNM rates in this species. This is because mutation rate estimates are key scaling parameters in many population genetic, demographic and phylogenetic inferences (e.g.…”

Section: Introductionmentioning

confidence: 99%

De novomutation rates in sticklebacks

Zhang

Reid

Sands

et al. 2023

Preprint

Self Cite

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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 is the expected level of genetic diversity 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 (mu) in two marine populations of the nine-spined stickleback (Pungitius pungitius) with the aid of several 2- and 3-generational family pedigrees, deep (> 50x) whole genome re-sequencing and a high-quality reference genome. After stringent filtering, we discovered 295 germline mutations from 106 offspring translating to mu = 4.64 x 10 to the -9 and mu = 4.08 x 10 to the -9 per base, per generation, in the two populations, respectively. Twenty percent of the mutations were shared by full-sibs showing that the level of parental mosaicism was relatively high. Since the estimated mu was 3.2 times smaller than the commonly used substitution rate, recalibration with mu led to substantial increase in estimated divergence times between different stickleback species. Our estimates of de novo mutation rate should provide a useful resource for research focused on fish population genetics and that of sticklebacks in particular.

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Sex chromosome turnover in hybridizing stickleback lineages

Yi,

Wang,

Reid

et al. 2024

Evolution Letters

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Recent discoveries of sex chromosome diversity across the tree of life have challenged the canonical model of conserved sex chromosome evolution and evoked new theories on labile sex chromosomes that maintain less differentiation and undergo frequent turnover. However, theories of labile sex chromosome evolution lack direct empirical support due to the paucity of case studies demonstrating ongoing sex chromosome turnover in nature. Two divergent lineages (viz. WL & EL) of nine-spined sticklebacks (Pungitius pungitius) with different sex chromosomes (linkage group [LG] 12 in the EL, unknown in the WL) hybridize in a natural secondary contact zone in the Baltic Sea, providing an opportunity to study ongoing turnover between coexisting sex chromosomes. In this study, we first identify an 80 kbp genomic region on LG3 as the sex-determining region (SDR) using whole-genome resequencing data of family crosses of a WL population. We then verify this region as the SDR in most other WL populations and demonstrate a potentially ongoing sex chromosome turnover in admixed marine populations where the evolutionarily younger and homomorphic LG3 sex chromosome replaces the older and heteromorphic LG12 sex chromosome. The results provide a rare glimpse of sex chromosome turnover in the wild and indicate the possible existence of additional yet undiscovered sex chromosome diversity in Pungitius sticklebacks.

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Complex population history affects admixture analyses in nine‐spined sticklebacks

Cited by 18 publications

References 97 publications

Prevalent Introgression Underlies Convergent Evolution in the Diversification ofPungitiusSticklebacks

Prevalent Introgression Underlies Convergent Evolution in the Diversification ofPungitiusSticklebacks

De novomutation rates in sticklebacks

Sex chromosome turnover in hybridizing stickleback lineages

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