scholarly journals Genomics of a killifish from the Seychelles islands supports transoceanic island colonization and reveals relaxed selection of developmental genes

2020 ◽  
Author(s):  
Rongfeng Cui ◽  
Alexandra M Tyers ◽  
Zahabiya Juzar Malubhoy ◽  
Sadie Wisotsky ◽  
Stefano Valdesalici ◽  
...  
Keyword(s):  
Purifying Selection ◽  
Deleterious Mutations ◽  
Effective Population ◽  
Relaxed Selection ◽  
Annual Killifish ◽  
Tectonic Events ◽  
Genome Wide ◽  
Seychelles Islands ◽  
Slightly Deleterious Mutations ◽  
Selection Of

AbstractHow freshwater fish colonize remote islands remains an evolutionary puzzle. Tectonic drift and trans-oceanic dispersal models have been proposed as possible alternative mechanisms. Integrating dating of known tectonic events with population genetics and experimental test of salinity tolerance in the Seychelles islands golden panchax (Pachypanchax playfairii), we found support for trans-oceanic dispersal being the most likely scenario. At the macroevolutionary scale, the non-annual killifish golden panchax shows stronger genome-wide purifying selection compared to annual killifishes from continental Africa. Reconstructing past demographies in isolated golden panchax populations provides support for decline in effective population size, which could have allowed slightly deleterious mutations to segregate in the population. Unlike annual killifishes, where relaxed selection preferentially targets aging-related genes, relaxation of purifying selection in golden panchax affects genes involved in developmental processes, including fgf10.

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 Purifying Selection in Corvids Is Less Efficient on Islands

2019 ◽  
Vol 37 (2) ◽  
pp. 469-474 ◽  
Author(s):  
Verena E Kutschera ◽  
Jelmer W Poelstra ◽  
Fidel Botero-Castro ◽  
Nicolas Dussex ◽  
Neil J Gemmell ◽  
...  
Keyword(s):  
Purifying Selection ◽  
Life History Strategies ◽  
Whole Genome Sequencing Data ◽  
Small Populations ◽  
Deleterious Mutations ◽  
Mutation Load ◽  
Sequencing Data ◽  
Effective Population ◽  
Extinction Rates ◽  
Island Species

Abstract Theory predicts that deleterious mutations accumulate more readily in small populations. As a consequence, mutation load is expected to be elevated in species where life-history strategies and geographic or historical contingencies reduce the number of reproducing individuals. Yet, few studies have empirically tested this prediction using genome-wide data in a comparative framework. We collected whole-genome sequencing data for 147 individuals across seven crow species (Corvus spp.). For each species, we estimated the distribution of fitness effects of deleterious mutations and compared it with proxies of the effective population size Ne. Island species with comparatively smaller geographic range sizes had a significantly increased mutation load. These results support the view that small populations have an elevated risk of mutational meltdown, which may contribute to the higher extinction rates observed in island species.

scholarly journals Intra-Species Differences in Population Size shape Life History and Genome Evolution

2019 ◽  
Author(s):  
David Willemsen ◽  
Rongfeng Cui ◽  
Martin Reichard ◽  
Dario Riccardo Valenzano
Keyword(s):  
Life History ◽  
Population Size ◽  
Genetic Drift ◽  
Sex Chromosome ◽  
Purifying Selection ◽  
Life History Trait ◽  
Deleterious Mutations ◽  
Effective Population ◽  
Annual Life Cycle ◽  
Evolutionary Forces

AbstractThe evolutionary forces shaping life history trait divergence within species are largely unknown. Killifish (oviparous Cyprinodontiformes) evolved an annual life cycle as an exceptional adaptation to life in arid savannah environments characterized by seasonal water availability. The turquoise killifish (Nothobranchius furzeri) is the shortest-lived vertebrate known to science and displays differences in lifespan among wild populations, representing an ideal natural experiment in the evolution and diversification of life history. Here, by combining genome sequencing and population genetics, we investigate the evolutionary forces shaping lifespan among turquoise killifish populations. We generate an improved reference assembly for the turquoise killifish genome, trace the evolutionary origin of the sex chromosome, and identify genes under strong positive and purifying selection, as well as those evolving neutrally. We find that the shortest-lived turquoise killifish populations, which dwell in fragmented and isolated habitats at the outer margin of the geographical range of the species, are characterized by small effective population size and accumulate throughout the genome several small to large-effect deleterious mutations due to genetic drift. The genes most affected by drift in the shortest-lived turquoise killifish populations are involved in the WNT signalling pathway, neurodegenerative disorders, cancer and the mTOR pathway. As the populations under stronger genetic drift are the shortest-lived ones, we propose that limited population size due to habitat fragmentation and repeated population bottlenecks, by causing the genome-wide accumulation of deleterious mutations, cumulatively contribute to the short adult lifespan in turquoise killifish populations.

scholarly journals A Conservative Test of Genetic Drift in the Endosymbiotic Bacterium Buchnera: Slightly Deleterious Mutations in the Chaperonin groEL

Genetics ◽  
2003 ◽  
Vol 165 (4) ◽  
pp. 1651-1660
Author(s):  
Joshua T Herbeck ◽  
Daniel J Funk ◽  
Patrick H Degnan ◽  
Jennifer J Wernegreen
Keyword(s):  
Genetic Drift ◽  
Balancing Selection ◽  
Purifying Selection ◽  
Nonsynonymous Substitution ◽  
Maximum Likelihood Estimates ◽  
Sequence Evolution ◽  
Endosymbiotic Bacterium ◽  
Deleterious Mutations ◽  
Synonymous Polymorphism ◽  
Slightly Deleterious Mutations

Abstract The obligate endosymbiotic bacterium Buchnera aphidicola shows elevated rates of sequence evolution compared to free-living relatives, particularly at nonsynonymous sites. Because Buchnera experiences population bottlenecks during transmission to the offspring of its aphid host, it is hypothesized that genetic drift and the accumulation of slightly deleterious mutations can explain this rate increase. Recent studies of intraspecific variation in Buchnera reveal patterns consistent with this hypothesis. In this study, we examine inter- and intraspecific nucleotide variation in groEL, a highly conserved chaperonin gene that is constitutively overexpressed in Buchnera. Maximum-likelihood estimates of nonsynonymous substitution rates across Buchnera species are strikingly low at groEL compared to other loci. Despite this evidence for strong purifying selection on groEL, our intraspecific analysis of this gene documents reduced synonymous polymorphism, elevated nonsynonymous polymorphism, and an excess of rare alleles relative to the neutral expectation, as found in recent studies of other Buchnera loci. Comparisons with Escherichia coli generally show patterns predicted by their differences in Ne. The sum of these observations is not expected under relaxed or balancing selection, selective sweeps, or increased mutation rate. Rather, they further support the hypothesis that drift is an important force driving accelerated protein evolution in this obligate mutualist.

scholarly journals Patterns of polymorphism, selection and linkage disequilibrium in the subgenomes of the allopolyploid Arabidopsis kamchatica

2018 ◽  
Author(s):  
Timothy Paape ◽  
Roman V. Briskine ◽  
Heidi E.L Lischer ◽  
Gwyneth Halstead-Nussloch ◽  
Rie Shimizu-Inatsugi ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Association Studies ◽  
Diploid Species ◽  
Purifying Selection ◽  
Metal Hyperaccumulation ◽  
Effective Population ◽  
Genome Wide ◽  
Evolutionary Trajectories ◽  
Neutrality Tests ◽  
Arabidopsis Kamchatica

AbstractAlthough genome duplication is widespread in wild and crop plants, little is known about genome-wide selection due to the complexity of polyploid genomes. In allopolyploid species, the patterns of purifying selection and adaptive substitutions would be affected by masking owing to duplicated genes or ‘homeologs’ as well as by effective population size. We resequenced 25 distribution-wide accessions of the allotetraploid Arabidopsis kamchatica, which has a relatively small genome size (450 Mb) derived from the diploid species A. halleri and A. lyrata. The level of nucleotide polymorphism and linkage disequilibrium decay were comparable to A. thaliana, indicating the feasibility of association studies. A reduction in purifying selection compared with parental species was observed. Interestingly, the proportion of adaptive substitutions (α) was significantly positive in contrast to the majority of plant species. A recurrent pattern observed in both frequency and divergence-based neutrality tests is that the genome-wide distributions of both subgenomes were similar, but the correlation between homeologous pairs was low. This may increase the opportunity of different evolutionary trajectories such as in the HMA4 gene involved in heavy metal hyperaccumulation.

scholarly journals Not out of the woods yet: signatures of the prolonged negative genetic consequences of a population bottleneck in a rapidly re-expanding wader, the black-faced spoonbill Platalea minor

2021 ◽  
Author(s):  
Shou-Hsien Li ◽  
Yang Liu ◽  
Chia-Fen Yeh ◽  
Yuchen Fu ◽  
Carol K. L. Yeung ◽  
...  
Keyword(s):  
Conservation Status ◽  
Genetic Effect ◽  
Purifying Selection ◽  
Population Bottleneck ◽  
Population Recovery ◽  
Effective Population ◽  
Demographic Dynamics ◽  
Genome Wide ◽  
The Last Glacial

The long-term persistence of a population which has suffered a bottleneck partly depends on how historical demographic dynamics impacted its genetic diversity and the accumulation of deleterious mutations. Here we provide genomic evidence for the detrimental genetic effect of a recent population bottleneck in the endangered black-faced spoonbill (Platalea minor) even after its rapid population recovery. Our population genomic data suggest that the bird’s effective population size, N, had been relatively stable (7,500-9,000) since the end of the last glacial maximum; however, a recent brief yet severe bottleneck (N= 20) around the 1940s wiped out more than 99% of its historical N in roughly three generations. By comparing it with its sister species, the royal spoonbill (P. regia) whose conservation status is of lesser concern, we found that despite a more than 15-fold population recovery since 1988, genetic drift has led to higher levels of inbreeding (7.4 times more runs of homozygosity longer than 100 Kb) in the black-faced spoonbill than in the royal spoonbill genome. Although the two spoonbills have similar levels of genome-wide nucleotide diversity and heterozygosity, because of relaxed purifying selection, individual black-faced spoonbills carry 3% more nonsynonymous substitutions than royal spoonbills each of which is 7% more deleterious. Our results imply that the persistence of a threatened species cannot be inferred from a recovery in its population. They also highlight the necessity of continually using genomic indices to monitor its genetic health and employing all possible measures to assure its long-term persistence in the ever-changing environment.

scholarly journals Relaxed selection during a recent human expansion

2016 ◽  
Author(s):  
S. Peischl ◽  
I. Dupanloup ◽  
A. Foucal ◽  
M. Jomphe ◽  
V. Bruat ◽  
...  
Keyword(s):  
Wave Front ◽  
Rare Variants ◽  
Genetic Diseases ◽  
Low Frequency ◽  
Purifying Selection ◽  
Genomic Diversity ◽  
Human Populations ◽  
Deleterious Mutations ◽  
Relaxed Selection ◽  
French Canadians

AbstractHumans have colonized the planet through a series of range expansions, which deeply impacted genetic diversity in newly settled areas and potentially increased the frequency of deleterious mutations on expanding wave fronts. To test this prediction, we studied the genomic diversity of French Canadians who colonized Quebec in the 17th century. We used historical information and records from ∼4000 ascending genealogies to select individuals whose ancestors lived mostly on the colonizing wave front and individuals whose ancestors remained in the core of the settlement. Comparison of exomic diversity reveals that i) both new and low frequency variants are significantly more deleterious in front than in core individuals, ii) equally deleterious mutations are at higher frequencies in front individuals, and iii) front individuals are two times more likely to be homozygous for rare very deleterious mutations present in Europeans. These differences have emerged in the past 6-9 generations and cannot be explained by differential inbreeding, but are consistent with relaxed selection on the wave front. Modeling the evolution of rare variants allowed us to estimate their associated selection coefficients as well as front and core effective sizes. Even though range expansions had a limited impact on the overall fitness of French Canadians, they could explain the higher prevalence of recessive genetic diseases in recently settled regions. Since we show that modern human populations are experiencing differential strength of purifying selection, similar processes might have happened throughout human history, contributing to a higher mutation load in populations that have undergone spatial expansions.

scholarly journals Large Number of Replacement Polymorphisms in Rapidly Evolving Genes of Drosophila: Implications for Genome-Wide Surveys of DNA Polymorphism

Genetics ◽  
1999 ◽  
Vol 153 (4) ◽  
pp. 1717-1729 ◽  
Author(s):  
Karl J Schmid ◽  
Loredana Nigro ◽  
Charles F Aquadro ◽  
Diethard Tautz
Keyword(s):  
Recombination Rate ◽  
Current Knowledge ◽  
Purifying Selection ◽  
Neutral Evolution ◽  
Nucleotide Polymorphism ◽  
Effective Population ◽  
Nucleotide Substitutions ◽  
Large Numbers ◽  
Genome Wide ◽  
Population Sizes

AbstractWe present a survey of nucleotide polymorphism of three novel, rapidly evolving genes in populations of Drosophila melanogaster and D. simulans. Levels of silent polymorphism are comparable to other loci, but the number of replacement polymorphisms is higher than that in most other genes surveyed in D. melanogaster and D. simulans. Tests of neutrality fail to reject neutral evolution with one exception. This concerns a gene located in a region of high recombination rate in D. simulans and in a region of low recombination rate in D. melanogaster, due to an inversion. In the latter case it shows a very low number of polymorphisms, presumably due to selective sweeps in the region. Patterns of nucleotide polymorphism suggest that most substitutions are neutral or nearly neutral and that weak (positive and purifying) selection plays a significant role in the evolution of these genes. At all three loci, purifying selection of slightly deleterious replacement mutations appears to be more efficient in D. simulans than in D. melanogaster, presumably due to different effective population sizes. Our analysis suggests that current knowledge about genome-wide patterns of nucleotide polymorphism is far from complete with respect to the types and range of nucleotide substitutions and that further analysis of differences between local populations will be required to understand the forces more completely. We note that rapidly diverging and nearly neutrally evolving genes cannot be expected only in the genome of Drosophila, but are likely to occur in large numbers also in other organisms and that their function and evolution are little understood so far.

scholarly journals Genomic Consequences of Long-Term Population Decline in Brown Eared Pheasant

2020 ◽  
Vol 38 (1) ◽  
pp. 263-273
Author(s):  
Pengcheng Wang ◽  
John T Burley ◽  
Yang Liu ◽  
Jiang Chang ◽  
De Chen ◽  
...  
Keyword(s):  
Natural Selection ◽  
Population Size ◽  
Population Decline ◽  
Deleterious Mutations ◽  
Loss Of Function ◽  
Wild Populations ◽  
Effective Population ◽  
Isolated Populations ◽  
Genome Wide

Abstract Population genetic theory and empirical evidence indicate that deleterious alleles can be purged in small populations. However, this viewpoint remains controversial. It is unclear whether natural selection is powerful enough to purge deleterious mutations when wild populations continue to decline. Pheasants are terrestrial birds facing a long-term risk of extinction as a result of anthropogenic perturbations and exploitation. Nevertheless, there are scant genomics resources available for conservation management and planning. Here, we analyzed comparative population genomic data for the three extant isolated populations of Brown eared pheasant (Crossoptilon mantchuricum) in China. We showed that C. mantchuricum has low genome-wide diversity and a contracting effective population size because of persistent declines over the past 100,000 years. We compared genome-wide variation in C. mantchuricum with that of its closely related sister species, the Blue eared pheasant (C. auritum) for which the conservation concern is low. There were detrimental genetic consequences across all C. mantchuricum genomes including extended runs of homozygous sequences, slow rates of linkage disequilibrium decay, excessive loss-of-function mutations, and loss of adaptive genetic diversity at the major histocompatibility complex region. To the best of our knowledge, this study is the first to perform a comprehensive conservation genomic analysis on this threatened pheasant species. Moreover, we demonstrated that natural selection may not suffice to purge deleterious mutations in wild populations undergoing long-term decline. The findings of this study could facilitate conservation planning for threatened species and help recover their population size.

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