Mutation load decreases with haplotype age in wild Soay sheep

Stoffel, Martin; Johnston, Susan E.; Pilkington, Jill G.; Pemberton, Josephine M.

doi:10.1101/2021.03.04.433700

Cited by 15 publications

(24 citation statements)

References 49 publications

(83 reference statements)

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“…What are the implications for the conservation of populations of killer whales and more broadly any species that will shift their range towards higher latitudes under current directional global warming? Our results largely agree with simulation results and the empirical findings (Kyriazis et al 2021;Stoffel et al 2021;van der Valk et al 2021), that over the long-term, selection can remove deleterious mutations from small populations. However, the lack of a parallel pattern in other high latitude killer whale populations illustrates the complexity of these dynamics.…”

Section: Resultssupporting

confidence: 92%

“…Whilst this process can increase deleterious recessive mutation load, it can also increase rates of purging of these same mutations by exposing variants to purifying selection once they are in homozygous genotypes (Kirkpatrick and Jarne 2000;Glemin 2003;Balick et al 2015;Hedrick and Garcia-Dorado 2016). Despite these theoretical expectations, there is limited empirical evidence for purging due to recent demographic bottlenecks in wild populations (but see Xue et al 2015;Robinson et al 2018;Grossen et al 2020;Stoffel et al 2021). Given that range shifts are a common response to ongoing global warming (Chen et al 2011), understanding how range expansions and shifts influence the fitness of natural populations at the range margins presents an increasingly important consideration for conservation (Gibson et al 2009).…”

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confidence: 99%

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Evidence of long-term purging of mutation load in killer whale genomes

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Gilbert

Gopalakrishnan

et al. 2021

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Genomes of high latitude killer whales harbour signatures of post-glacial founding and expansion. Here, we investigate whether reduced efficacy of selection increased mutation load in founder populations, or whether recessive deleterious mutations exposed to selection in homozygous genotypes were purged. Comparing the accumulation of synonymous and non-synonymous mutations across pairs of globally sampled genomes reveals that the most significant outliers are high latitude North Atlantic genomes, which have accumulated significantly fewer non-synonymous mutations than all other populations. Comparisons with the genome of a 7.5-Kyr-old North Atlantic killer whale, inferred to be closely related to the population directly ancestral to present-day Icelandic and Norwegian populations, calibrates the timing of the action of selection on non-synonymous mutations predominantly to the mid-late Holocene. Non-synonymous mutations purged in modern Norwegian killer whale genomes are found as globally shared standing variation in heterozygote genotypes more often than expected, suggesting overdominance. Taken together, our findings are consistent with purging of recessive non-synonymous mutations exposed to selection in founder-associated homozygous genotypes.

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Section: Resultssupporting

confidence: 92%

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confidence: 99%

Evidence of long-term purging of mutation load in killer whale genomes

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Gilbert

Gopalakrishnan

et al. 2021

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“…This is because in small populations with ongoing high levels of mating between relatives, it might be expected that purging has removed all but the most recent deleterious rare alleles (Caballero et al, 2017). The priority in these species of conservation concern is therefore to identify and assess individuals who are highly inbred due to very recent consanguinity, as these individuals are more likely to harbour two copies of recent deleterious rare alleles that have not yet been exposed to selection (Grossen et al, 2020; Stoffel et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

Genomic data of different resolutions reveal consistent inbreeding estimates but contrasting homozygosity landscapes for the threatened Aotearoa New Zealand hihi

et al. 2021

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Mating between close relatives may reduce fitness in offspring, an effect attributed to the unmasking of deleterious recessive mutations in regions of the genome that are rendered identical by descent (IBD;Bosse et al., 2019;Charlesworth & Charlesworth, 1987). Whilst inbreeding is generally undesirable, the stakes are especially high in at-risk species, for example where genetic diversity has been reduced by severe bottlenecks or habitat fragmentation (Maya-Garcia et al., 2017). For these reasons, estimation of the inbreeding coefficient (F) is commonly used in ecology, evolution and conservation biology where it may be employed as a proxy for adaptive potential

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“…2). Several recent studies have highlighted the severe fitness consequences of long ROH, which tend to be enriched for highly deleterious recessive alleles, whereas more intermediate-length ROH may be largely purged of such variation (20, 47–49). Although our results imply an elevated genetic load in the Isle Royale moose population (Fig.…”

Section: Discussionmentioning

confidence: 99%

Genomic underpinnings of population persistence in Isle Royale moose

Kyriazis

Beichman

Brzeski

et al. 2022

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Island ecosystems provide models to assess the impacts of isolation on population persistence. However, most studies of persistence have focused on a single species, without comparisons to other organisms they interact with in the ecosystem. The simple predator-prey system of moose and gray wolves on Isle Royale provides allows a direct contrast of genetic variation in a prey species with their natural predator. Wolves on Isle Royale exhibited signs of severe inbreeding depression, which nearly drove the population to extinction in 2019. In the relative absence of wolves, the moose population has thrived and exhibits no obvious signs of inbreeding depression despite being isolated for ~120 years and having low genetic diversity. Here, we examine the genomic underpinnings of population persistence in the Isle Royale moose population. We document high levels of inbreeding in the population, roughly as high as the wolf population at the time of its decline. However, inbreeding in the moose population manifests in the form of intermediate-length runs of homozygosity indicative of gradual inbreeding, contrasting with the severe recent inbreeding observed in the wolf population. Using simulations, we demonstrate that this more gradual inbreeding in the moose population has resulted in an estimated 50% purging of the inbreeding load, helping to explain the continued persistence of the population. However, we also document notable increases in genetic load, which could eventually threaten population viability over the long term. Finally, we document low diversity in mainland North American moose populations due to a severe founder event occurring near the end of the Holocene. Overall, our results demonstrate a complex relationship between inbreeding, genetic diversity, and population viability that highlights the importance of maintaining isolated populations at moderate size to avert extinction from genetic factors.

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Mutation load decreases with haplotype age in wild Soay sheep

Cited by 15 publications

References 49 publications

Evidence of long-term purging of mutation load in killer whale genomes

Evidence of long-term purging of mutation load in killer whale genomes

Genomic data of different resolutions reveal consistent inbreeding estimates but contrasting homozygosity landscapes for the threatened Aotearoa New Zealand hihi

Genomic underpinnings of population persistence in Isle Royale moose

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