scholarly journals High homozygosity of inversions in sunflower species largely averts accumulation of deleterious mutations

2022 ◽  
Author(s):  
Kaichi Huang ◽  
Kate L Ostevik ◽  
Cassandra Elphinstone ◽  
Marco Todesco ◽  
Natalia Bercovich ◽  
...  
Keyword(s):  
Stop Codon ◽  
Element Abundance ◽  
Adaptive Divergence ◽  
Phenotypic Traits ◽  
Sequence Evolution ◽  
Deleterious Mutations ◽  
Recombination Rates ◽  
Recombination Suppression ◽  
Geographic Structure ◽  
Divergence With Gene Flow

Recombination is critical both for accelerating adaptation and for the purging of deleterious mutations. Chromosomal inversions can act as recombination modifiers that suppress local recombination and, thus, are predicted to accumulate such mutations. In this study, we investigated patterns of recombination, transposable element abundance and coding sequence evolution across the genomes of 1,445 individuals from three sunflower species, as well as within nine inversions segregating within species. We also analyzed the effects of inversion genotypes on 87 phenotypic traits to test for overdominance. We found significant negative correlations of long terminal repeat retrotransposon abundance and deleterious mutations with recombination rates across the genome in all three species. However, we failed to detect an increase in these features in the inversions, except for a modest increase in the proportion of stop codon mutations in several very large or rare inversions. Moreover, there was little evidence of phenotypic overdominance in inversion heterozygotes, consistent with observations of minimal deleterious load. On the other hand, significantly greater load was observed for inversions in populations polymorphic for a given inversion compared to populations monomorphic for one of the arrangements, suggesting that the local state of inversion polymorphism affects deleterious load. These seemingly contradictory results can be explained by the geographic structuring and consequent excess homozygosity of inversions in wild sunflowers. Inversions contributing to local adaptation often exhibit geographic structure; such inversions represent ideal recombination modifiers, acting to facilitate adaptive divergence with gene flow, while largely averting the accumulation of deleterious mutations due to recombination suppression.

scholarly journals Recessive deleterious variation has a limited impact on signals of adaptive introgression in human populations

2020 ◽  
Author(s):  
Xinjun Zhang ◽  
Bernard Kim ◽  
Kirk E. Lohmueller ◽  
Emilia Huerta-Sánchez
Keyword(s):  
False Positive ◽  
False Positive Rate ◽  
Genomic Variation ◽  
Human Populations ◽  
Deleterious Mutations ◽  
Modern Humans ◽  
Recombination Rates ◽  
Limited Impact ◽  
Adaptive Mutations ◽  
Adaptive Introgression

AbstractAdmixture with archaic hominins has altered the landscape of genomic variation in modern human populations. Several gene regions have been previously identified as candidates of adaptive introgression (AI) that facilitated human adaptation to specific environments. However, simulation-based studies have suggested that population genetics processes other than adaptive mutations, such as heterosis from recessive deleterious variants private to populations before admixture, can also lead to patterns in genomic data that resemble adaptive introgression. The extent to which the presence of deleterious variants affect the false-positive rate and the power of current methods to detect AI has not been fully assessed. Here, we used extensive simulations to show that recessive deleterious mutations can increase the false positive rates of tests for AI compared to models without deleterious variants. We further examined candidates of AI in modern humans identified from previous studies and show that, although deleterious variants may hinder the performance of AI detection in modern humans, most signals remained robust when deleterious variants are included in the null model. While deleterious variants may have a limited impact on detecting signals of adaptive introgression in humans, we found that at least two AI candidate genes, HYAL2 and HLA, are particularly susceptible to high false positive rates due to the recessive deleterious mutations. By quantifying parameters that affect heterosis, we show that the high false positives are largely attributed to the high exon densities together with low recombination rates in the genomic regions, which can further be exaggerated by the population growth in recent human evolution. Although the combination of such parameters is rare in the human genome, caution is still warranted in other species with different genomic composition and demographic histories.

The Main Sequence Evolution of Inhomogeneous Stars

1982 ◽  
Vol 4 (4) ◽  
pp. 396-400 ◽  
Author(s):  
J. Lattanzio
Keyword(s):  
Gravitational Collapse ◽  
Heavy Element ◽  
Main Sequence ◽  
Element Abundance ◽  
Sequence Evolution ◽  
Interstellar Gas ◽  
Convective Mixing ◽  
The Core ◽  
Gas Cloud

Duley (1974) has shown that, at the temperatures usually associated with interstellar gas clouds, we would expect CNO grains to be present. During gravitational collapse these grains migrate to the centre of the gas cloud, leading to an enhancement of the heavy-element abundance in the core (Prentice 1976, 1978). It was Krautschneider (1977) who verified such a scenario, by considering the dynamical collapse of gas and grain clouds. If such an initial radial abundance inhomogeneity existed, Prentice (1976a) showed that this configuration may well survive the later convective mixing phase and thus approach the zero-age main-sequence (ZAMS) with a small (-v 3% by mass) metal enhanced core.

scholarly journals Genome-wide patterns of divergence during speciation: the lake whitefish case study

2012 ◽  
Vol 367 (1587) ◽  
pp. 354-363 ◽  
Author(s):  
S. Renaut ◽  
N. Maillet ◽  
E. Normandeau ◽  
C. Sauvage ◽  
N. Derome ◽  
...  
Keyword(s):  
Reproductive Isolation ◽  
Genomic Islands ◽  
Next Generation Sequencing Data ◽  
Adaptive Divergence ◽  
Phenotypic Traits ◽  
Lake Whitefish ◽  
Sequencing Data ◽  
Species Pairs ◽  
Selective Forces ◽  
Genomic Regions

The nature, size and distribution of the genomic regions underlying divergence and promoting reproductive isolation remain largely unknown. Here, we summarize ongoing efforts using young (12 000 yr BP) species pairs of lake whitefish ( Coregonus clupeaformis ) to expand our understanding of the initial genomic patterns of divergence observed during speciation. Our results confirmed the predictions that: (i) on average, phenotypic quantitative trait loci (pQTL) show higher F ST values and are more likely to be outliers (and therefore candidates for being targets of divergent selection) than non-pQTL markers; (ii) large islands of divergence rather than small independent regions under selection characterize the early stages of adaptive divergence of lake whitefish; and (iii) there is a general trend towards an increase in terms of numbers and size of genomic regions of divergence from the least (East L.) to the most differentiated species pair (Cliff L.). This is consistent with previous estimates of reproductive isolation between these species pairs being driven by the same selective forces responsible for environment specialization. Altogether, dwarf and normal whitefish species pairs represent a continuum of both morphological and genomic differentiation contributing to ecological speciation. Admittedly, much progress is still required to more finely map and circumscribe genomic islands of speciation. This will be achieved through the use of next generation sequencing data but also through a better quantification of phenotypic traits moulded by selection as organisms adapt to new environmental conditions.

scholarly journals A comparison of methodological approaches to the study of young sex chromosomes: A case study in Poecilia

2021 ◽  
Author(s):  
Iulia Darolti ◽  
Pedro Almeida ◽  
Alison E Wright ◽  
Judith E Mank
Keyword(s):  
Sex Chromosomes ◽  
Reference Genome ◽  
Sex Chromosome ◽  
De Novo ◽  
Sequence Similarity ◽  
Sequence Evolution ◽  
Structural Variations ◽  
Recombination Suppression ◽  
Custom Made ◽  
Methodological Approaches

Studies of sex chromosome systems at early stages of divergence are key to understanding the initial process and underlying causes of recombination suppression. However, identifying signatures of divergence in homomorphic sex chromosomes can be challenging due to high levels of sequence similarity between the X and the Y. Variations in methodological precision and underlying data can make all the difference between detecting subtle divergence patterns or missing them entirely. Recent efforts to test for X-Y sequence differentiation in the guppy have led to contradictory results. Here we apply different analytical methodologies to the same dataset to test for the accuracy of different approaches in identifying patterns of sex chromosome divergence in the guppy. Our comparative analysis reveals that the most substantial source of variation in the results of the different analyses lies in the reference genome used. Analyses using custom-made de novo genome assemblies for the focal species successfully recover a signal of divergence across different methodological approaches. By contrast, using the distantly related Xiphophorus reference genome results in variable patterns, due to both sequence evolution and structural variations on the sex chromosomes between the guppy and Xiphophorus. Changes in mapping and filtering parameters can additionally introduce noise and obscure the signal. Our results illustrate how analytical differences can alter perceived results and we highlight best practices for the study of nascent sex chromosomes.

scholarly journals Transition from background selection to associative overdominance promotes diversity in regions of low recombination

2019 ◽  
Author(s):  
Kimberly J. Gilbert ◽  
Fanny Pouyet ◽  
Laurent Excoffier ◽  
Stephan Peischl
Keyword(s):  
Genetic Diversity ◽  
Balancing Selection ◽  
Purifying Selection ◽  
Heterozygote Advantage ◽  
Background Selection ◽  
Deleterious Mutations ◽  
Recombination Rates ◽  
Locus Model ◽  
Genome Wide ◽  
Linked Selection

SummaryLinked selection is a major driver of genetic diversity. Selection against deleterious mutations removes linked neutral diversity (background selection, BGS, Charlesworth et al. 1993), creating a positive correlation between recombination rates and genetic diversity. Purifying selection against recessive variants, however, can also lead to associative overdominance (AOD, Ohta 1971, Zhao & Charlesworth, 2016), due to an apparent heterozygote advantage at linked neutral loci that opposes the loss of neutral diversity by BGS. Zhao & Charlesworth (2016) identified the conditions when AOD should dominate over BGS in a single-locus model and suggested that the effect of AOD could become stronger if multiple linked deleterious variants co-segregate. We present a model describing how and under which conditions multi-locus dynamics can amplify the effects of AOD. We derive the conditions for a transition from BGS to AOD due to pseudo-overdominance (Ohta & Kimura 1970), i.e. a form of balancing selection that maintains complementary deleterious haplotypes that mask the effect of recessive deleterious mutations. Simulations confirm these findings and show that multi-locus AOD can increase diversity in low recombination regions much more strongly than previously appreciated. While BGS is known to drive genome-wide diversity in humans (Pouyet et al. 2018), the observation of a resurgence of genetic diversity in regions of very low recombination is indicative of AOD. We identify 21 such regions in the human genome showing clear signals of multi-locus AOD. Our results demonstrate that AOD may play an important role in the evolution of low recombination regions of many species.

scholarly journals Faster-X adaptive differentiation under divergence-with-gene-flow in diploids and haplodiploids

2021 ◽  
Author(s):  
Emily E. Bendall ◽  
Robin Bagley ◽  
Catherine R. Linnen ◽  
Vitor C. Sousa
Keyword(s):  
Gene Flow ◽  
Meta Analysis ◽  
Stochastic Simulations ◽  
Adaptive Divergence ◽  
Effective Population ◽  
Isolation With Migration ◽  
Demographic Modeling ◽  
Novel Approach ◽  
Divergence With Gene Flow ◽  
Adaptive Differentiation

AbstractEmpirical data from diverse taxa indicate that the hemizygous portions of the genome (X/Z chromosomes) evolve more rapidly than their diploid counterparts. Faster-X theory predicts increased rates of adaptive substitutions between isolated species, yet little is known about species experiencing gene flow. Here we investigate how hemizygosity impacts genome-wide patterns of differentiation during adaptive divergence with gene flow, combining simulations under isolation-with-migration models, a meta-analysis of autosomes and sex-chromosomes from diverse taxa, and analysis of haplodiploid species. First, using deterministic and stochastic simulations, we show that elevated differentiation at hemizygous loci occurs when there is gene flow, irrespective of dominance. This faster-X adaptive differentiation stems from more efficient selection resulting in reduced probability of losing the beneficial allele, greater migration-selection threshold, greater allele frequency differences at equilibrium, and a faster time to equilibrium. Second, by simulating neutral variation linked to selected loci, we show that faster-X differentiation affects linked variation due to reduced opportunities for recombination between locally adaptive and maladaptive immigrant haplotypes. Third, after correcting for expected differences in effective population size, we find that most taxon pairs (24 out of 28) exhibit faster-X differentiation in the meta-analysis. Finally, using a novel approach combining demographic modeling and simulations, we found evidence for faster-X differentiation in haplodiploid pine-feeding hymenopteran species adapted to different host plants. Together, our results indicate that divergent selection with gene flow can lead to higher differentiation at selected and linked variation in hemizygous loci (i.e., faster-X adaptive differentiation), both in X/Z-chromosomes and haplodiploid species.

scholarly journals Multivariate distributions of behavioural, morphological, and ontogenetic traits in hybrids bring new insights into the divergence of sympatric Arctic charr morphs

2020 ◽  
Author(s):  
Quentin J.B. Horta-Lacueva ◽  
Sigurður S. Snorrason ◽  
Michael B. Morrissey ◽  
Camille A. Leblanc ◽  
Kalina H. Kapralova
Keyword(s):  
Salvelinus Alpinus ◽  
Arctic Charr ◽  
Common Garden ◽  
Covariance Structures ◽  
Adaptive Divergence ◽  
Phenotypic Traits ◽  
Phenotypic Variance ◽  
Multivariate Distributions ◽  
Phenotypic Novelty ◽  
Trait Covariance

AbstractStudying the development of fitness related traits in hybrids from populations diverging in sympatry is a fundamental approach to understand the processes of speciation. However, such traits are often affected by covariance structures that complicate the comprehension of these processes, especially because the interactive relationships between traits of different nature (e.g. morphology, behaviour, life-history) remain largely unknown in this context. In a common garden setup, we conducted an extensive examination of phenotypic traits suspected to be involved in the divergence of two recently evolved morphs of Arctic charr (Salvelinus alpinus), and investigated the consequences of potential patterns of trait covariance on the phenotype of their hybrids. We observed differences among morphs in overall phenotypic variance and in trait correlations. Phenotypic contrainsts also tended to be reduced in the hybrids, which corroborates the narrative of hybridization facilitating adaptive divergence by relaxing trait covariance. However, the hybrids were associated with reduced phenotypic variance at different scales (i.e. at the scale of the entire P matrix and in different parts of the multivariate space), and we identified stronger correlations between several ontogenetic and morphological traits in the hybrids than in both morphs. These findings suggest a limited potential for hybridization to generate phenotypic novelty, and emphasise the need for multivariate approaches conciliating ontogenetic, morphological and behavioural processes to study the processes of adaptive divergence and speciation.

scholarly journals Deleterious mutation accumulation and the long-term fate of chromosomal inversions

PLoS Genetics ◽  
2021 ◽  
Vol 17 (3) ◽  
pp. e1009411
Author(s):  
Emma L. Berdan ◽  
Alexandre Blanckaert ◽  
Roger K. Butlin ◽  
Claudia Bank
Keyword(s):  
Adaptive Evolution ◽  
Simulation Study ◽  
Feedback Loop ◽  
Deleterious Mutation ◽  
Adaptive Divergence ◽  
Deleterious Mutations ◽  
Dynamic Features ◽  
Chromosomal Inversions

Chromosomal inversions contribute widely to adaptation and speciation, yet they present a unique evolutionary puzzle as both their allelic content and frequency evolve in a feedback loop. In this simulation study, we quantified the role of the allelic content in determining the long-term fate of the inversion. Recessive deleterious mutations accumulated on both arrangements with most of them being private to a given arrangement. This led to increasing overdominance, allowing for the maintenance of the inversion polymorphism and generating strong non-adaptive divergence between arrangements. The accumulation of mutations was mitigated by gene conversion but nevertheless led to the fitness decline of at least one homokaryotype under all considered conditions. Surprisingly, this fitness degradation could be permanently halted by the branching of an arrangement into multiple highly divergent haplotypes. Our results highlight the dynamic features of inversions by showing how the non-adaptive evolution of allelic content can play a major role in the fate of the inversion.

scholarly journals The causes of mutation accumulation in mitochondrial genomes

2009 ◽  
Vol 276 (1660) ◽  
pp. 1201-1209 ◽  
Author(s):  
Maurine Neiman ◽  
Douglas R Taylor
Keyword(s):  
Mutation Accumulation ◽  
High Rate ◽  
Mitochondrial Genomes ◽  
Sequence Evolution ◽  
Deleterious Mutations ◽  
Effective Population ◽  
Mitochondrial Mutation ◽  
Evolutionary Forces ◽  
Body Of Knowledge ◽  
Primary Determinant

A fundamental observation across eukaryotic taxa is that mitochondrial genomes have a higher load of deleterious mutations than nuclear genomes. Identifying the evolutionary forces that drive this difference is important to understanding the rates and patterns of sequence evolution, the efficacy of natural selection, the maintenance of sex and recombination and the mechanisms underlying human ageing and many diseases. Recent studies have implicated the presumed asexuality of mitochondrial genomes as responsible for their high mutational load. We review the current body of knowledge on mitochondrial mutation accumulation and recombination, and conclude that asexuality, per se , may not be the primary determinant of the high mutation load in mitochondrial DNA (mtDNA). Very little recombination is required to counter mutation accumulation, and recent evidence suggests that mitochondrial genomes do experience occasional recombination. Instead, a high rate of accumulation of mildly deleterious mutations in mtDNA may result from the small effective population size associated with effectively haploid inheritance. This type of transmission is nearly ubiquitous among mitochondrial genomes. We also describe an experimental framework using variation in mating system between closely related species to disentangle the root causes of mutation accumulation in mitochondrial genomes.

scholarly journals Coevolution between transposable elements and recombination

2017 ◽  
Vol 372 (1736) ◽  
pp. 20160458 ◽  
Author(s):  
Tyler V. Kent ◽  
Jasmina Uzunović ◽  
Stephen I. Wright
Keyword(s):  
Transposable Elements ◽  
Genome Structure ◽  
Rate Variation ◽  
Species Variation ◽  
Insertion Polymorphism ◽  
Recombination Rates ◽  
Recombination Suppression ◽  
Evolutionary Forces ◽  
Genomic Regions ◽  
Recombination Rate Variation

One of the most striking patterns of genome structure is the tight, typically negative, association between transposable elements (TEs) and meiotic recombination rates. While this is a highly recurring feature of eukaryotic genomes, the mechanisms driving correlations between TEs and recombination remain poorly understood, and distinguishing cause versus effect is challenging. Here, we review the evidence for a relation between TEs and recombination, and discuss the underlying evolutionary forces. Evidence to date suggests that overall TE densities correlate negatively with recombination, but the strength of this correlation varies across element types, and the pattern can be reversed. Results suggest that heterogeneity in the strength of selection against ectopic recombination and gene disruption can drive TE accumulation in regions of low recombination, but there is also strong evidence that the regulation of TEs can influence local recombination rates. We hypothesize that TE insertion polymorphism may be important in driving within-species variation in recombination rates in surrounding genomic regions. Furthermore, the interaction between TEs and recombination may create positive feedback, whereby TE accumulation in non-recombining regions contributes to the spread of recombination suppression. Further investigation of the coevolution between recombination and TEs has important implications for our understanding of the evolution of recombination rates and genome structure. This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’.

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