scholarly journals The Genetic cost of Neanderthal introgression

2015 ◽  
Author(s):  
Kelley Harris ◽  
Rasmus Nielsen

AbstractApproximately 2-4% of genetic material in human populations outside Africa is derived from Neanderthals who interbred with anatomically modern humans. Recent studies have shown that this Neanderthal DNA is depleted around functional genomic regions; this has been suggested to be a consequence of harmful epistatic interactions between human and Neanderthal alleles. However, using published estimates of Neanderthal inbreeding and the distribution of mutational fitness effects, we infer that Neanderthals had at least 40% lower fitness than humans on average; this increased load predicts the reduction in Neanderthal introgression around genes without the need to invoke epistasis. We also predict a residual Neanderthal mutational load in non-Africans, leading to a fitness reduction of at least 0.5%. This effect of Neanderthal admixture has been left out of previous debate on mutation load differences between Africans and non-Africans. We also show that if many deleterious mutations are recessive, the Neanderthal admixture fraction could increase over time due to the protective effect of Neanderthal haplotypes against deleterious alleles that arose recently in the human population. This might partially explain why so many organisms retain gene flow from other species and appear to derive adaptive benefits from introgression.

2018 ◽  
Author(s):  
E. Noël ◽  
E. Fruitet ◽  
D. Lelaurin ◽  
N. Bonel ◽  
A. Ségard ◽  
...  

AbstractTheory and empirical data showed that two processes can boost selection against deleterious mutations, thus facilitating the purging of the mutation load: inbreeding, by exposing recessive deleterious alleles to selection in homozygous form, and sexual selection, by enhancing the relative reproductive success of males with small mutation loads. These processes tend to be mutually exclusive because sexual selection is reduced under mating systems that promote inbreeding, such as self-fertilization in hermaphrodites. We estimated the relative efficiency of inbreeding and sexual selection at purging the genetic load, using 50 generations of experimental evolution, in a hermaphroditic snail (Physa acuta). To this end, we generated lines that were exposed to various intensities of inbreeding, sexual selection (on the male function) and nonsexual selection (on the female function). We measured how these regimes affected the mutation load, quantified through the survival of outcrossed and selfed juveniles. We found that juvenile survival strongly decreased in outbred lines with reduced male selection, but not when female selection was relaxed, showing that male-specific sexual selection does purge deleterious mutations. However, in lines exposed to inbreeding, where sexual selection was also relaxed, survival did not decrease, and even increased for self-fertilized juveniles, showing that purging through inbreeding can compensate for the absence of sexual selection. Our results point to the further question of whether a mixed strategy combining the advantages of both mechanisms of genetic purging could be evolutionary stable.


Genetics ◽  
1999 ◽  
Vol 153 (4) ◽  
pp. 1885-1898 ◽  
Author(s):  
John H Willis

Abstract The goal of this study is to provide information on the genetics of inbreeding depression in a primarily outcrossing population of Mimulus guttatus. Previous studies of this population indicate that there is tremendous inbreeding depression for nearly every fitness component and that almost all of this inbreeding depression is due to mildly deleterious alleles rather than recessive lethals or steriles. In this article I assayed the homozygous and heterozygous fitnesses of 184 highly inbred lines extracted from a natural population. Natural selection during the five generations of selfing involved in line formation essentially eliminated major deleterious alleles but was ineffective in purging alleles with minor fitness effects and did not appreciably diminish overall levels of inbreeding depression. Estimates of the average degree of dominance of these mildly deleterious alleles, obtained from the regression of heterozygous fitness on the sum of parental homozygous fitness, indicate that the detrimental alleles are partially recessive for most fitness traits, with h~∼0.15 for cumulative measures of fitness. The inbreeding load, B, for total fitness is ~1.0 in this experiment. These results are consistent with the hypothesis that spontaneous mildly deleterious mutations occur at a rate >0.1 mutation per genome per generation.


2010 ◽  
Vol 365 (1552) ◽  
pp. 2559-2569 ◽  
Author(s):  
N. H. Barton

The prevalence of recombination in eukaryotes poses one of the most puzzling questions in biology. The most compelling general explanation is that recombination facilitates selection by breaking down the negative associations generated by random drift (i.e. Hill–Robertson interference, HRI). I classify the effects of HRI owing to: deleterious mutation, balancing selection and selective sweeps on: neutral diversity, rates of adaptation and the mutation load. These effects are mediated primarily by the density of deleterious mutations and of selective sweeps. Sequence polymorphism and divergence suggest that these rates may be high enough to cause significant interference even in genomic regions of high recombination. However, neither seems able to generate enough variance in fitness to select strongly for high rates of recombination. It is plausible that spatial and temporal fluctuations in selection generate much more fitness variance, and hence selection for recombination, than can be explained by uniformly deleterious mutations or species-wide selective sweeps.


2015 ◽  
Vol 113 (4) ◽  
pp. E440-E449 ◽  
Author(s):  
Brenna M. Henn ◽  
Laura R. Botigué ◽  
Stephan Peischl ◽  
Isabelle Dupanloup ◽  
Mikhail Lipatov ◽  
...  

The Out-of-Africa (OOA) dispersal ∼50,000 y ago is characterized by a series of founder events as modern humans expanded into multiple continents. Population genetics theory predicts an increase of mutational load in populations undergoing serial founder effects during range expansions. To test this hypothesis, we have sequenced full genomes and high-coverage exomes from seven geographically divergent human populations from Namibia, Congo, Algeria, Pakistan, Cambodia, Siberia, and Mexico. We find that individual genomes vary modestly in the overall number of predicted deleterious alleles. We show via spatially explicit simulations that the observed distribution of deleterious allele frequencies is consistent with the OOA dispersal, particularly under a model where deleterious mutations are recessive. We conclude that there is a strong signal of purifying selection at conserved genomic positions within Africa, but that many predicted deleterious mutations have evolved as if they were neutral during the expansion out of Africa. Under a model where selection is inversely related to dominance, we show that OOA populations are likely to have a higher mutation load due to increased allele frequencies of nearly neutral variants that are recessive or partially recessive.


2020 ◽  
Author(s):  
Daniel Shaw ◽  
Samuel Miravet-Verde ◽  
Carlos Pinero ◽  
Luis Serrano ◽  
Maria Lluch-Senar

AbstractThe removal of unwanted genetic material is a key aspect in many synthetic biology efforts, and often requires preliminary knowledge of which genomic regions are dispensable. Typically, these efforts are guided by transposon mutagenesis studies, coupled to deep-sequencing (TnSeq) to identify insertion points and gene essentiality. However, epistatic interactions can cause unforeseen changes in essentiality after the deletion of a gene, leading to the redundancy of these essentiality maps. Here, we present LoxTnSeq, a new methodology to generate and catalogue libraries of genome reduction mutants. LoxTnSeq combines random integration of lox sites by transposon mutagenesis, and the generation of mutants via cre recombinase, catalogued via deep-sequencing. When LoxTnSeq was applied to the naturally genome reduced bacterium Mycoplasma pneumoniae, we obtained a mutant pool containing 285 unique deletions. These deletions spanned from >50 bp to 28 Kb, which represent 21% of the total genome. LoxTnSeq also highlighted large regions of non-essential genes that could be removed simultaneously, and other non-essential regions that could not, providing a guide for future genome reductions.


2019 ◽  
Author(s):  
Hannes Becher ◽  
Benjamin C. Jackson ◽  
Brian Charlesworth

SUMMARYSurveys of DNA sequence variation have shown that the level of genetic variability in a genomic region is often strongly positively correlated with its rate of crossing over (CO) [1–3]. This pattern is caused by selection acting on linked sites, which reduces genetic variability and can also cause the frequency distribution of segregating variants to contain more rare variants than expected without selection (skew). These effects of selection may involve the spread of beneficial mutations (selective sweeps, SSWs), the elimination of deleterious mutations (background selection, BGS) or both together, and are expected to be stronger with lower rates of crossing over [1–3]. However, in a recent study of human populations, the skew was reduced in the lowest CO regions compared with regions with somewhat higher CO rates [4]. A similar pattern is seen in the population genomic studies of Drosophila simulans described here. We propose an explanation for this paradoxical observation, and validate it using computer simulations. This explanation is based on the finding that partially recessive, linked deleterious mutations can increase rather than reduce neutral variability when the product of the effective population size (Ne) and the selection coefficient against homozygous carriers of mutations (s) is ≤ 1, i.e. there is associative overdominance (AOD) rather than BGS [5]. We show that AOD can operate in a genomic region with a low rate of CO, opening up a new perspective on how selection affects patterns of variability at linked sites.


2015 ◽  
Author(s):  
Brenna M. Henn ◽  
Laura R Botigue ◽  
Stephan Peischl ◽  
Isabelle Dupanloup ◽  
Mikhail Lipatov ◽  
...  

The Out-of-Africa (OOA) dispersal ~50,000 years ago is characterized by a series of founder events as modern humans expanded into multiple continents. Population genetics theory predicts an increase of mutational load in populations undergoing serial founder effects during range expansions. To test this hypothesis, we have sequenced full genomes and high-coverage exomes from 7 geographically divergent human populations from Namibia, Congo, Algeria, Pakistan, Cambodia, Siberia and Mexico. We find that individual genomes vary modestly in the overall number of predicted deleterious alleles. We show via spatially explicit simulations that the observed distribution of deleterious allele frequencies is consistent with the OOA dispersal, particularly under a model where deleterious mutations are recessive. We conclude that there is a strong signal of purifying selection at conserved genomic positions within Africa, but that many predicted deleterious mutations have evolved as if they were neutral during the expansion out of Africa. Under a model where selection is inversely related to dominance, we show that OOA populations are likely to have a higher mutation load due to increased allele frequencies of nearly neutral variants that are recessive or partially recessive.


2020 ◽  
Author(s):  
Karl Grieshop ◽  
Paul L. Maurizio ◽  
Göran Arnqvist ◽  
David Berger

AbstractTheory predicts that the ability of selection and recombination to purge mutation load is enhanced if selection against deleterious genetic variants operates more strongly in males than females. However, direct empirical support for this tenet is limited, perhaps because traditional quantitative genetic approaches allow dominance and intermediate-frequency polymorphisms to obscure the effects of rare and partially recessive deleterious alleles that make up the main part of a population’s mutation load. Here, we exposed the mutation load of a population of Callosobruchus maculatus seed beetles via successive generations of inbreeding, and quantified its effects by measuring heterosis – the increase in fitness upon the masking of deleterious alleles by heterozygosity – in a fully factorial sex-specific diallel cross among 16 inbred strains. Competitive lifetime reproductive success (i.e. fitness) was measured in male and female outcrossed F1s as well as inbred parental ‘selfs’, and we estimated the 4×4 male-female inbred-outbred genetic covariance matrix (G) for fitness using Bayesian Markov chain Monte Carlo simulations of a custom-made general linear mixed effects model. We found that heterosis estimated in males and females was highly correlated among strains, and that heterosis was strongly negatively correlated to strains’ outcrossed breeding values for male fitness, but not female fitness. This suggests that the additive genetic variation for fitness in the males, but not females, of this population reflect the amount of (partially) recessive deleterious alleles segregating at mutation-selection balance, and that the population’s mutation load therefore has greater potential to be purged via selection in males. These findings contribute to our understanding of the prevalence of sexual reproduction in nature and the maintenance of genetic variation in fitness-related traits.Impact statementA mainstay evolutionary question has been: why do the large majority of eukaryotic species reproduce sexually if such females must spend half of their reproductive effort producing sons, which produce no offspring themselves? In principle, a lineage of a mutant asexual female that simply clones herself into daughters would grow at twice the rate of her sexual competitors (all else equal). What prevents this from being the predominant mode of reproduction throughout eukaryotes? One category of hypotheses regards the role of males in facilitating the purging of deleterious mutations from the population’s genome since very strong selection in males, unlike females, can occur in many species without direct consequence to population offspring numbers. Due to the inherent difficulties of detecting selection on segregating genetic variation, empirical evidence for this theory is limited to indirect evidence from manipulative experiments and experimental evolution studies. Here we demonstrate that the standing deleterious allelic variation in a population of the seed beetle, Callosobruchus maculatus, is selected against strongly in males but not females. Using a fully factorial diallel cross among 16 inbred strains, we measured the degree to which fitness in the outbred offspring of those crosses improved relative to their inbred parents. This measure is known as heterosis and offers an estimate of the relative number of deleterious alleles carried among strains. We then analyzed the relationship between strains’ heterosis values and their sex-specific additive genetic breeding values for fitness, revealing the extent to which those segregating deleterious alleles are selected against in males and females. We found that strains heterosis values were strongly correlated with male fitness, but not female fitness. This demonstrates that the population’s deleterious mutations can be efficiently selected against (i.e. purged) via selection in males. This process would offer a benefit to sexual reproduction that may outweigh its costs, and therefore yields insight to the prevalence of sex in nature.


Genetics ◽  
1996 ◽  
Vol 142 (3) ◽  
pp. 1053-1060
Author(s):  
Joel R Peck

Abstract This study presents a mathematical model that allows for some offspring to be dispersed at random, while others stay close to their mothers. A single genetic locus is assumed to control fertility, and this locus is subject to the occurrence of deleterious mutations. It is shown that, at equilibrium, the frequency of deleterious mutations in the population is inversely related to the rate of dispersal. This is because dispersal of offspring leads to enhanced competition among adults. The results also show that sexual reproduction can lead to a decrease in the equilibrium frequency of deleterious mutations. The reason for this relationship is that sex involves the dispersal of genetic material, and thus, like the dispersal of offspring, sex enhances competition among adults. The model is described using the example of a hermaphroditic plant population. However, the results should apply to animal populations as well.


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