Relaxed Selection During a Recent Human Expansion

Peischl, Stephan; Dupanloup, Isabelle; Foucal, Adrien; Jomphe, Michèle; Bruat, Vanessa; Grenier, Jean; Gouy, Alexandre; Gilbert, Kimberly J.; Gbeha, Elias; Bosshard, Lars; Hip-Ki, Elodie; Agbessi, Mawussé; Hodgkinson, Alan; Vézina, Hélène; Awadalla, Philip; Excoffier, Laurent

doi:10.1534/genetics.117.300551

Cited by 55 publications

(38 citation statements)

References 57 publications

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“…The genetic patterns that result from range expansion, however, have wide‐ranging implications in biology. For example, given the importance of ongoing climate‐driven range shifts in species distributions (Chen, Hill, Ohlemüller, Roy, & Thomas, ), it will be important to understand genetic diversity and fitness in expanding populations (Bosshard et al, ; Pauls, Nowak, Bálint, & Pfenninger, ; Peischl et al, ). Similarly, the effect of changing geographic distribution on genetic diversity and its structure is an integral component of the field of biogeography (Waters, Fraser, & Hewitt, ) and an important aspect of the global ecological problem of invasive species (Bock et al, ).…”

Section: Introductionmentioning

confidence: 99%

Loss of genetic diversity, recovery and allele surfing in a colonizing parasite, Geomydoecus aurei

Demastes

Hafner

et al. 2019

Molecular Ecology

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Understanding the genetic consequences of changes in species distributions has wide‐ranging implications for predicting future outcomes of climate change, for protecting threatened or endangered populations and for understanding the history that has led to current genetic patterns within species. Herein, we examine the genetic consequences of range expansion over a 25‐year period in a parasite (Geomydoecus aurei) that is in the process of expanding its geographic range via invasion of a novel host. By sampling the genetics of 1,935 G. aurei lice taken from 64 host individuals collected over this time period using 12 microsatellite markers, we test hypotheses concerning linear spatial expansion, genetic recovery time and allele surfing. We find evidence of decreasing allelic richness (AR) with increasing distance from the source population, supporting a linear, stepping stone model of spatial expansion that emphasizes the effects of repeated bottleneck events during colonization. We provide evidence of post‐bottleneck genetic recovery, with average AR of infrapopulations increasing about 30% over the 225‐generation span of time observed directly in this study. Our estimates of recovery rate suggest, however, that recovery has plateaued and that this population may not reach genetic diversity levels of the source population without further immigration from the source population. Finally, we employ a grid‐based sampling scheme in the region of ongoing population expansion and provide empirical evidence for the power of allele surfing to impart genetic structure on a population, even under conditions of selective neutrality and in a place that lacks strong barriers to gene flow.

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Section: Introductionmentioning

confidence: 99%

Loss of genetic diversity, recovery and allele surfing in a colonizing parasite, Geomydoecus aurei

Demastes

Hafner

et al. 2019

Molecular Ecology

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“…In fact, most mutations affecting fitness are deleterious (Keightley & Lynch, ) and, excluding those with severe/lethal effects, mildly deleterious mutations are expected to accumulate and ultimately impact wild populations (mutation load; Kimura, Maruyama, & Crow, ). Therefore, understanding the mechanisms underlying the accumulation of deleterious mutations is of great interest and has led to studies testing the effects of mating systems, demography, domestication, recombination rate, and other genomic features on deleterious mutation trajectories (Bosshard et al., ; Charlesworth, ; Chen, Glémin, & Lascoux, ; Laenen et al., ; Peischl et al., ; Renaut & Rieseberg, ; Zhang, Zhou, Bawa, Suren, & Holliday, ; Zhou, Massonnet, Sanjak, Cantu, & Gaut, 2017). Systems in which genetic drift prevails over natural selection (e.g.…”

Section: Introductionmentioning

confidence: 99%

Impact of supplementation on deleterious mutation distribution in an exploited salmonid

Ferchaud

Laporte

Perrier

et al. 2018

Evolutionary Applications

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Deleterious mutations have important implications for the evolutionary trajectories of populations. While several studies recently investigated the dynamics of deleterious mutations in wild populations, no study has yet explored the fate of deleterious mutations in a context of populations managed by supplementation. Here, based on a dataset of nine wild and 15 supplemented Lake Trout populations genotyped at 4,982 single nucleotide polymorphisms (SNP)s by means of genotype by sequencing (GBS), we explored the effect of supplementation on the frequency of putatively deleterious variants. Three main findings are consequential for the management of fish populations. First, an increase in neutral genetic diversity in stocked populations compared with unstocked ones was observed. Second, putatively deleterious mutations were more likely to be found in unstocked than in stocked populations, suggesting a lower efficiency to purge deleterious mutations in unstocked lakes. Third, a population currently used as a major source for supplementation is characterized by several fixed putatively deleterious alleles. Therefore, other source populations with lower abundance of putatively deleterious mutations should be favored as sources of supplementation. We discuss management implications of our results, especially pertaining to the joint identification of neutral and deleterious mutations that could help refining the choice of source and sink populations for supplementation in order to maximize their evolutionary potential and to limit their mutation load.

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“…Although most new mutations are likely deleterious [1], their importance in patterning phenotypic variation is controversial and not well understood [2]. Empirical work suggests that, although the long-term burden of deleterious variants is relatively insensitive to demography [3], population bottlenecks and expansion may lead to an increased abundance of deleterious alleles over shorter time scales such as those associated with domestication [4], postglacial colonization [5] or recent human migration [6]. Even when the impacts on total load are minimal, demographic change may have important consequences for the contribution of deleterious variants to phenotypic variation [3,[7][8][9].…”

Section: Introductionmentioning

confidence: 99%

Incomplete Dominance of Deleterious Alleles Contributes Substantially to Trait Variation and Heterosis in Maize

Yang

Mezmouk

Baumgarten

et al. 2016

Preprint

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Deleterious alleles have long been proposed to play an important role in patterning phenotypic variation and are central to commonly held ideas explaining the hybrid vigor observed in the offspring of a cross between two inbred parents. We test these ideas using evolutionary measures of sequence conservation to ask whether incorporating information about putatively deleterious alleles can inform genomic selection (GS) models and improve phenotypic prediction. We measured a number of agronomic traits in both the inbred parents and hybrids of an elite maize partial diallel population and re-sequenced the parents of the population. Inbred elite maize lines vary for more than 350,000 putatively deleterious sites, but show a lower burden of such sites than a comparable set of traditional landraces. Our modeling reveals widespread evidence for incomplete dominance at these loci, and supports theoretical models that more damaging variants are usually more recessive. We identify haplotype blocks using an identity-by-decent (IBD) analysis and perform genomic prediction analyses in which we weigh blocks on the basis of complementation for segregating putatively deleterious variants. Cross-validation results show that incorporating sequence conservation in genomic selection improves prediction accuracy for grain yield and other fitness-related traits as well as heterosis for those traits. Our results provide empirical support for an important role for incomplete dominance of deleterious alleles in explaining heterosis and demonstrate the utility of incorporating functional annotation in phenotypic prediction and plant breeding. Author summaryA key long-term goal of biology is understanding the genetic basis of phenotypic variation. Although most new mutations are likely disadvantageous, their prevalence and importance in explaining patterns of phenotypic variation is controversial and not well understood. In this study we combine whole genome-sequencing and field evaluation of a maize mapping population to investigate the contribution of deleterious mutations to phenotype. We show that a priori prediction of deleterious alleles correlates well with effect sizes for grain yield and that variants predicted to be more damaging are on average more recessive. We develop a simple model allowing for variation in the heterozygous effects of deleterious mutations and demonstrate its improved ability to predict both phenotypes and hybrid vigor. Our results help reconcile alternative explanations for hybrid vigor and highlight the use of leveraging evolutionary history to facilitate breeding for crop improvement.

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Relaxed Selection During a Recent Human Expansion

Cited by 55 publications

References 57 publications

Loss of genetic diversity, recovery and allele surfing in a colonizing parasite, Geomydoecus aurei

Loss of genetic diversity, recovery and allele surfing in a colonizing parasite, Geomydoecus aurei

Impact of supplementation on deleterious mutation distribution in an exploited salmonid

Incomplete Dominance of Deleterious Alleles Contributes Substantially to Trait Variation and Heterosis in Maize

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