scholarly journals Genome evolution in bacteria isolated from million-year-old subseafloor sediments

2020 ◽  
Author(s):  
William D Orsi ◽  
Tobias Magritsch ◽  
Sergio Vargas ◽  
Omer K Coskun ◽  
Aurele Vuillemin ◽  
...  
Keyword(s):  
Homologous Recombination ◽  
Genome Evolution ◽  
Purifying Selection ◽  
Small Population ◽  
Genomic Evolution ◽  
Bacterial Strains ◽  
Physical Isolation ◽  
Genome Wide ◽  
Population Sizes

The nature and extent of genomic evolution in subseafloor microbial populations subsisting for millions of years below the seafloor is unknown. Subseafloor populations have ultra-slow metabolic rates that are hypothesized to restrict reproduction and, consequently, the spread of new traits. Our findings demonstrate that genomes of cultivated bacterial strains from the genus Thalassospira isolated from million-year-old abyssal sediment exhibit greatly reduced levels of homologous recombination, elevated numbers of pseudogenes, and genome-wide evidence of relaxed purifying selection. These substitutions and pseudogenes are fixed into the population, suggesting the genome evolution of these bacteria has been dominated by genetic drift, whereby under long-term physical isolation in small population sizes, and in the absence of homologous recombination, newly acquired mutations accumulate in the genomes of clonal populations over millions of years.

scholarly journals Long-term experimental evolution reveals purifying selection on piRNA-mediated control of transposable element expression

BMC Biology ◽  
2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Ulfar Bergthorsson ◽  
Caroline J. Sheeba ◽  
Anke Konrad ◽  
Tony Belicard ◽  
Toni Beltran ◽  
...  
Keyword(s):  
Natural Selection ◽  
Transcriptional Activation ◽  
Small Rnas ◽  
Active Regions ◽  
Purifying Selection ◽  
Ancestral Population ◽  
Sequence Context ◽  
C Elegans ◽  
Population Sizes

Abstract Background Transposable elements (TEs) are an almost universal constituent of eukaryotic genomes. In animals, Piwi-interacting small RNAs (piRNAs) and repressive chromatin often play crucial roles in preventing TE transcription and thus restricting TE activity. Nevertheless, TE content varies widely across eukaryotes and the dynamics of TE activity and TE silencing across evolutionary time is poorly understood. Results Here, we used experimentally evolved populations of C. elegans to study the dynamics of TE expression over 409 generations. The experimental populations were evolved at population sizes of 1, 10 and 100 individuals to manipulate the efficiency of natural selection versus genetic drift. We demonstrate increased TE expression relative to the ancestral population, with the largest increases occurring in the smallest populations. We show that the transcriptional activation of TEs within active regions of the genome is associated with failure of piRNA-mediated silencing, whilst desilenced TEs in repressed chromatin domains retain small RNAs. Additionally, we find that the sequence context of the surrounding region influences the propensity of TEs to lose silencing through failure of small RNA-mediated silencing. Conclusions Our results show that natural selection in C. elegans is responsible for maintaining low levels of TE expression, and provide new insights into the epigenomic features responsible.

scholarly journals Mutation load decreases with haplotype age in wild Soay sheep

2021 ◽  
Author(s):  
M.A. Stoffel ◽  
S.E. Johnston ◽  
J.G. Pilkington ◽  
J.M Pemberton
Keyword(s):  
Inbreeding Depression ◽  
Purifying Selection ◽  
Small Population ◽  
First Year ◽  
Mutation Load ◽  
Soay Sheep ◽  
Recessive Mutations ◽  
Deleterious Alleles ◽  
Lower Population

AbstractRuns of homozygosity (ROH) are pervasive in diploid genomes and expose the effects of deleterious recessive mutations, but how exactly these regions contribute to variation in fitness remains unclear. Here, we combined empirical analyses and simulations to explore the deleterious effects of ROH with varying genetic map lengths in wild Soay sheep. Using a long-term dataset of 4,592 individuals genotyped at 417K SNPs, we found that inbreeding depression increases with ROH length. A 1% genomic increase in long ROH (>12.5cM) reduced the odds of first-year survival by 12%, compared to only 7% for medium ROH (1.56-12.5cM), while short ROH (<1.56cM) had no effect on survival. We show by forward genetic simulations that this is predicted: compared with shorter ROH, long ROH will have higher densities of deleterious alleles, with larger average effects on fitness and lower population frequencies. Taken together, our results are consistent with the idea that the mutation load decreases in older haplotypes underlying shorter ROH, where purifying selection has had more time to purge deleterious mutations. Finally, our study demonstrates that strong inbreeding depression can persist despite ongoing purging in a historically small population.

scholarly journals Intrahost Selection Pressure Drives Equine Arteritis Virus Evolution during Persistent Infection in the Stallion Reproductive Tract

2019 ◽  
Vol 93 (12) ◽  
Author(s):  
Bora Nam ◽  
Zelalem Mekuria ◽  
Mariano Carossino ◽  
Ganwu Li ◽  
Ying Zheng ◽  
...  
Keyword(s):  
Persistent Infection ◽  
Viral Genome ◽  
Reproductive Tract ◽  
Purifying Selection ◽  
Buffy Coat ◽  
Equine Arteritis Virus ◽  
Nucleotide Substitutions ◽  
Genome Wide ◽  
Nasal Secretions

ABSTRACTEquine arteritis virus (EAV) is the causative agent of equine viral arteritis (EVA), a reproductive and respiratory disease of horses. Following natural infection, 10 to 70% of infected stallions can become carriers of EAV and continue to shed virus in the semen. In this study, sequential viruses isolated from nasal secretions, buffy coat cells, and semen of seven experimentally infected and two naturally infected EAV carrier stallions were deep sequenced to elucidate the intrahost microevolutionary process after a single transmission event. Analysis of variants from nasal secretions and buffy coat cells lacked extensive positive selection; however, characteristics of the mutant spectra were different in the two sample types. In contrast, the initial semen virus populations during acute infection have undergone a selective bottleneck, as reflected by the reduction in population size and diversifying selection at multiple sites in the viral genome. Furthermore, during persistent infection, extensive genome-wide purifying selection shaped variant diversity in the stallion reproductive tract. Overall, the nonstochastic nature of EAV evolution during persistent infection was driven by active intrahost selection pressure. Among the open reading frames within the viral genome, ORF3, ORF5, and the nsp2-coding region of ORF1a accumulated the majority of nucleotide substitutions during persistence, with ORF3 and ORF5 having the highest intrahost evolutionary rates. The findings presented here provide a novel insight into the evolutionary mechanisms of EAV and identified critical regions of the viral genome likely associated with the establishment and maintenance of persistent infection in the stallion reproductive tract.IMPORTANCEEAV can persist in the reproductive tract of infected stallions, and consequently, long-term carrier stallions constitute its sole natural reservoir. Previous studies demonstrated that the ampullae of the vas deferens are the primary site of viral persistence in the stallion reproductive tract and the persistence is associated with a significant inflammatory response that is unable to clear the infection. This is the first study that describes EAV full-length genomic evolution during acute and long-term persistent infection in the stallion reproductive tract using next-generation sequencing and contemporary sequence analysis techniques. The data provide novel insight into the intrahost evolution of EAV during acute and persistent infection and demonstrate that persistent infection is characterized by extensive genome-wide purifying selection and a nonstochastic evolutionary pattern mediated by intrahost selective pressure, with important nucleotide substitutions occurring in ORF1a (region encoding nsp2), ORF3, and ORF5.

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 A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Ursula Oggenfuss ◽  
Thomas Badet ◽  
Thomas Wicker ◽  
Fanny E Hartmann ◽  
Nikhil Kumar Singh ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Genome Evolution ◽  
Genome Size ◽  
Population Genomics ◽  
Demographic History ◽  
Large Population ◽  
Purifying Selection ◽  
Zymoseptoria Tritici ◽  
Genome Wide ◽  
Genome Size Evolution

Genome evolution is driven by the activity of transposable elements (TEs). The spread of TEs can have deleterious effects including the destabilization of genome integrity and expansions. However, the precise triggers of genome expansions remain poorly understood because genome size evolution is typically investigated only among deeply divergent lineages. Here, we use a large population genomics dataset of 284 individuals from populations across the globe of Zymoseptoria tritici, a major fungal wheat pathogen. We built a robust map of genome-wide TE insertions and deletions to track a total of 2456 polymorphic loci within the species. We show that purifying selection substantially depressed TE frequencies in most populations, but some rare TEs have recently risen in frequency and likely confer benefits. We found that specific TE families have undergone a substantial genome-wide expansion from the pathogen’s center of origin to more recently founded populations. The most dramatic increase in TE insertions occurred between a pair of North American populations collected in the same field at an interval of 25 years. We find that both genome-wide counts of TE insertions and genome size have increased with colonization bottlenecks. Hence, the demographic history likely played a major role in shaping genome evolution within the species. We show that both the activation of specific TEs and relaxed purifying selection underpin this incipient expansion of the genome. Our study establishes a model to recapitulate TE-driven genome evolution over deeper evolutionary timescales.

scholarly journals Strain population structure varies widely across bacterial species and predicts strain colonization in unrelated individuals

2020 ◽  
Author(s):  
Jeremiah J. Faith ◽  
Alice Chen-Liaw ◽  
Varun Aggarwala ◽  
Nadeem O. Kaakoush ◽  
Thomas J. Borody ◽  
...  
Keyword(s):  
Population Structure ◽  
Gut Microbiota ◽  
Population Size ◽  
Bacterial Species ◽  
Fecal Microbiota ◽  
Small Population ◽  
Bacterial Strains ◽  
Bacterial Genomes ◽  
Population Sizes ◽  
Microbial Strain

SummaryThe population structure of strains within a bacterial species is poorly defined, despite the functional importance of strain variation in the human gut microbiota on health. Here we analyzed >1000 sequenced bacterial strains from the fecal microbiota of 47 individuals from two countries and combined them with >150,000 bacterial genomes from NCBI to quantify the strain population size of different bacterial species, as well as the frequency of finding the same strain colonized in unrelated individuals who had no opportunities for direct microbial strain transmission. Strain population sizes ranged from tens to over one-hundred thousand per species. Prevalent strains in common gut microbiota species with small population sizes were the most likely to be harbored in two or more unrelated individuals. The finite strain population size of certain species creates the opportunity to comprehensively sequence the entirety of these species’ prevalent strains and associate their presence in different individuals with health outcomes.

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 Long-term experimental evolution reveals purifying selection on piRNA-mediated control of transposable element expression

2019 ◽  
Author(s):  
Ulfar Bergthorsson ◽  
Caroline J. Sheeba ◽  
Anke Konrad ◽  
Tony Belicard ◽  
Toni Beltran ◽  
...  
Keyword(s):  
Natural Selection ◽  
Transcriptional Activation ◽  
Small Rnas ◽  
Active Regions ◽  
Purifying Selection ◽  
Ancestral Population ◽  
Sequence Context ◽  
C Elegans ◽  
Population Sizes

AbstractTransposable elements (TEs) are an almost universal constituent of eukaryotic genomes. In animals, Piwi-interacting small RNAs (piRNAs) and repressive chromatin often play crucial roles in preventing TE transcription and thus restricting TE activity. Nevertheless, TE content varies widely across eukaryotes and the dynamics of TE activity and TE silencing across evolutionary time is poorly understood. Here we used experimentally evolved populations of C. elegans to study the dynamics of TE expression over 400 generations. The experimental populations were evolved at three different population sizes to manipulate the efficiency of natural selection versus genetic drift. We demonstrate increased TE expression relative to the ancestral population, with the largest increases occurring in the smallest populations. We show that the transcriptional activation of TEs within active regions of the genome is associated with failure of piRNA-mediated silencing, whilst desilenced TEs in repressed chromatin domains retain small RNAs. Additionally, we find that the sequence context of the surrounding region influences the propensity of TEs to lose silencing through failure of small RNA-mediated silencing. Together, our results show that natural selection in C. elegans is responsible for maintaining low levels of TE expression, and provide new insights into the epigenomic features responsible.

Demography and reproductive ecology of the Columbia spotted frog (Rana luteiventris) across the Palouse

2005 ◽  
Vol 83 (5) ◽  
pp. 702-711 ◽  
Author(s):  
Abbey B Davis ◽  
Paul A Verrell
Keyword(s):  
Population Size ◽  
Reproductive Ecology ◽  
Small Population ◽  
Effective Population ◽  
Small Population Size ◽  
Rana Luteiventris ◽  
Breeding Populations ◽  
The Status ◽  
Population Sizes

Here we report on the demography and reproductive ecology of the Columbia spotted frog (Rana luteiventris Thompson, 1913) breeding in ponds across the Palouse Bioregion of Washington and Idaho. Spotted frogs are unusual, if not unique, among temperate ranids in that males establish the oviposition site before females become active. Females laid at one or two communal sites in shallow water. Our breeding populations were small, never exceeding 50 adults counted, and most displayed male-biased sex ratios. We estimated effective population sizes (Ne) as ranges determined by extremes in male breeding success; these varied between 3.2 and 37.8. Even the latter falls below the minimum required for long-term population viability. Small population size may make spotted frogs vulnerable to genetic problems and environmental insults. Communal oviposition certainly renders a population's reproductive effort vulnerable to variation in hydroperiod, which we observed during the dry spring of 2004. In the absence of information on the degree of "connectedness" among our ponds as subunits of more resilient metapopulations, we suggest that small population size and communal oviposition likely render R. luteiventris vulnerable to anthropogenic disturbance. Furthermore, the status of R. luteiventris on the Palouse may be less secure than assumed currently.

scholarly journals Intra-species differences in population size shape life history and genome evolution

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
David Willemsen ◽  
Rongfeng Cui ◽  
Martin Reichard ◽  
Dario Riccardo Valenzano
Keyword(s):  
Life History ◽  
Population Size ◽  
Wnt Signaling Pathway ◽  
Purifying Selection ◽  
Small Population ◽  
Population Bottlenecks ◽  
Adult Lifespan ◽  
Evolutionary Forces ◽  
Reference Genome Assembly ◽  
Genome Wide

The evolutionary forces shaping life history divergence within species are largely unknown. Turquoise killifish display differences in lifespan among wild populations, representing an ideal natural experiment in evolution and diversification of life history. By combining genome sequencing and population genetics, we investigate the evolutionary forces shaping lifespan among wild turquoise killifish populations. We generate an improved reference genome assembly and identify genes under positive and purifying selection, as well as those evolving neutrally. Short-lived populations from the outer margin of the species range have small population size and accumulate deleterious mutations in genes significantly enriched in the WNT signaling pathway, neurodegeneration, cancer and the mTOR pathway. We propose that limited population size due to habitat fragmentation and repeated population bottlenecks, by increasing the genome-wide mutation load, exacerbates the effects of mutation accumulation and cumulatively contribute to the short adult lifespan.

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