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Precision and accuracy of F ST estimates with sequencing and experimental errors. Our estimator ^ F pool ST was computed from Pool-seq data over all demes and loci without error, with sequencing error (occurring at rate m e ¼ 0:001), and with experimental error (e ¼ 0:5). Each boxplot represents the distribution of multilocus F ST estimates across 50 independent replicates of the ms simulations. We used two migration rates, corresponding to (A and B) F ST ¼ 0:05 or (C and D) F ST ¼ 0:20: The size of each pool was either fixed to (A and C) 10 or to (B and D) 100. For Poolseq data, we show the results for different coverages (203, 503, and 1003). In each graph, the dashed line indicates the simulated value of F ST . Exp., experimental; Seq., sequencing.
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The advent of high throughput sequencing and genotyping technologies enables the comparison of patterns of polymorphisms at a very large number of markers. While the characterization of genetic structure from individual sequencing data remains expensive for many non-model species, it has been shown that sequencing pools of individual DNAs (Pool-seq...
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... to sequencing and experimental errors Figure 5 shows that sequencing errors cause a negligible negative bias for ^ F pool ST estimates. Filtering (using an MRC of 4) improves estimation slightly, but only at high coverage (Fig- ure 6B). ...
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... must be noted, however, that filtering increases the bias in the absence of sequencing error, especially at low coverage ( Figure 6A). With experimental error, i.e., when individuals do not contribute evenly to the final set of reads, we observed a positive bias for ^ F pool ST estimates ( Figure 5). We note that the bias decreases as the size of the pools increases. ...
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... studies use a large range of methods, which aim at characterizing fine-scaled population structure (see, e.g., Fischer et al. Figure 6 Precision and accuracy of F ST estimates with and without filtering. Our estimator ^ F pool ST was computed from Pool-seq data over all demes and loci (A) without error, (B) with sequencing error, and (C) with experimental error (see the legend of Figure 5 for further details). For each case, we computed F ST without filtering (no MRC) and with filtering (using a MRC = 4). ...
Citations
... The mpileup file was then converted to sync format by PoPoolation2 version 1201 (Kofler et al., 2011). 8.03 million (M) SNPs were detected on this sync file using R/poolfstat package v2.0.0 (Hivert et al., 2018) and the following parameters: coverage per pool between 10 and 50. In parallel, nucleotidic diversity (n) was computed using PoPoolation2 Variancesliding.pl ...
In the last few years, the bed bug Cimex lectularius has been an increasing problem worldwide, mainly due to the development of insecticide resistance to pyrethroids. The characterization of resistance alleles is a prerequisite to improve surveillance and resistance management. To identify genomic variants associated with pyrethroid resistance in Cimex lectularius, we compared the genetic composition of two recent and resistant populations with that of two ancient‐susceptible strains using a genome‐wide pool‐seq design. We identified a large 6 Mb “superlocus” showing particularly high genetic differentiation and association with the resistance phenotype. This superlocus contained several clustered resistance genes and was also characterized by a high density of structural variants (inversions, duplications). The possibility that this superlocus constitutes a resistance “supergene” that evolved after the clustering of alleles adapted to insecticide and after reduction in recombination is discussed.
... We anticipated the microbial community structure to vary within a single representative pool because these samples are naturally fermented. Nucleotide differences and the neutrality test were used to interpret the pooled sample using statistics, and the results clearly showed that there was little polymorphism and variation within the pooled sample, indicating that samples from the same origin have very little diversity differences (Hivert et al., 2018). Negative FST values are also unequivocal proof that there are more alleles than necessary in a single pooled sample, which is truly more than one sample (de Meeûs, 2018). ...
Moiya pansung, mileye amileye, moiya koshak, and midukeye are naturally fermented bamboo shoot foods of Tripura. The present study aimed to reveal the whole microbial community structure of naturally fermented moiya pangsung, mileye amileye, moiya koshak, and midukeye along with the prediction of microbial functional profiles by shotgun metagenomic sequence analysis. The metataxonomic profile of moiya pangsung, mileye amileye, moiya koshak, and midukeye samples showed different domains, viz., bacteria (97.70%) followed by the virus (0.76%), unclassified (0.09%), eukaryotes (1.46%) and archaea (0.05%). Overall, 49 phyla, 409 families, 841 genera, and 1,799 species were found in all the fermented bamboo shoot samples collected from different places of Tripura. Firmicutes was the most abundant phylum (89.28%) followed by Proteobacteria (5.13%), Bacteroidetes (4.38%), Actinobacteria (1.02%), and Fusobacteria (0.17%). Lactiplantibacillus plantarum was the most abundant species in moiya pangsung, mileye amileye, moiya koshak, and midukeye followed by Lactococcus lactis, Levilactobacillus brevis, Leuconostoc mesenteroides, Weissella paramesenteroides, Leuconostoc kimchii, Pediococcus pentosaceus, Leuconostoc gasicomitatum, and Lacticaseibacillus casei. A few phyla of fungus were found, viz., Ascomycota, Basidiomycota, and Glomeromycota, where Ascomycota was present in high abundance. Functional analysis of moiya pangsung, mileye amileye, moiya koshak, and midukeye metagenome revealed the genes for the synthesis and metabolism of a wide range of bioactive compounds including, various essential amino acids, and conjugated amino acids. The abundance profile and predictive analysis of fermented bamboo shoots revealed a huge plethora of essential microorganisms and KEGG analysis revealed genes for amino acid metabolism, pectin degradation, lipid metabolism, and many other essential pathways that can be essential for the improvement of nutritional and sensory qualities of the fermented bamboo shoot products.
KEYWORDS: fermented bamboo shoot, meloncana baccifera, shotgun metagenomics, microbial community analysis, functional gene analysis.
... We used allele frequency estimates from the control pools of the DBF, RFF, GPO, and BBM populations to test for population differentiation using global F ST values calculated with the R package poolfstat [v. 2.1.1 (Hivert et al., 2018)]. We also estimated F ST for each SNP to identify regions of the genome that were enriched for SNPs that contribute to population differentiation. ...
Introduction: Heavy metal pollutants can have long lasting negative impacts on ecosystem health and can shape the evolution of species. The persistent and ubiquitous nature of heavy metal pollution provides an opportunity to characterize the genetic mechanisms that contribute to metal resistance in natural populations.
Methods: We examined variation in resistance to copper, a common heavy metal contaminant, using wild collections of the model organism Drosophila melanogaster . Flies were collected from multiple sites that varied in copper contamination risk. We characterized phenotypic variation in copper resistance within and among populations using bulked segregant analysis to identify regions of the genome that contribute to copper resistance.
Results and Discussion: Copper resistance varied among wild populations with a clear correspondence between resistance level and historical exposure to copper. We identified 288 SNPs distributed across the genome associated with copper resistance. Many SNPs had population-specific effects, but some had consistent effects on copper resistance in all populations. Significant SNPs map to several novel candidate genes involved in refolding disrupted proteins, energy production, and mitochondrial function. We also identified one SNP with consistent effects on copper resistance in all populations near CG11825 , a gene involved in copper homeostasis and copper resistance. We compared the genetic signatures of copper resistance in the wild-derived populations to genetic control of copper resistance in the Drosophila Synthetic Population Resource (DSPR) and the Drosophila Genetic Reference Panel (DGRP), two copper-naïve laboratory populations. In addition to CG11825 , which was identified as a candidate gene in the wild-derived populations and previously in the DSPR, there was modest overlap of copper-associated SNPs between the wild-derived populations and laboratory populations. Thirty-one SNPs associated with copper resistance in wild-derived populations fell within regions of the genome that were associated with copper resistance in the DSPR in a prior study. Collectively, our results demonstrate that the genetic control of copper resistance is highly polygenic, and that several loci can be clearly linked to genes involved in heavy metal toxicity response. The mixture of parallel and population-specific SNPs points to a complex interplay between genetic background and the selection regime that modifies the effects of genetic variation on copper resistance.
... Moreover, unequal contributions of genetic material per individual in a pooled sample can create allele frequency bias and thus, downstream summary statistic (e.g. F ST ) bias if sample sizes are small (Schlötterer et al., 2014;Hivert et al., 2018). Haplotype construction and inferences using linkage disequilibrium are also hindered with short-read pooled data (Schlötterer et al., 2014). ...
Next generation sequencing technologies have facilitated a shift from a few targeted loci in population genetic studies to whole genome approaches. Here, we review the types of questions and inferences regarding the population biology and evolution of parasitic helminths being addressed within the field of population genomics. Topics include parabiome, hybridization, population structure, loci under selection and linkage mapping. We highlight various advances, and note the current trends in the field, particularly a focus on human-related parasites despite the inherent biodiversity of helminth species. We conclude by advocating for a broader application of population genomics to reflect the taxonomic and life history breadth displayed by helminth parasites. As such, our basic knowledge about helminth population biology and evolution would be enhanced while the diversity of helminths in itself would facilitate population genomic comparative studies to address broader ecological and evolutionary concepts.
... The NJ tree and PCA were run with a minimum coverage requirement of 10×. Pairwise F ST values among pairs of populations were calculated using the poolfstat r package (Hivert et al., 2018) with the full data set. ...
Distribution of ecotypic variation in natural populations is influenced by neutral and adaptive evolutionary forces that are challenging to disentangle. This study provides a high-resolution portrait of genomic variation in Chinook salmon (Oncorhynchus tshawytscha) with emphasis on a region of major effect for ecotypic variation in migration timing. With a filtered dataset of ~13 million SNPs from low coverage whole genome resequencing of 53 populations (3,566 barcoded individuals), we contrasted patterns of genomic structure within and among major lineages and examined the extent of a selective sweep at a major effect region underlying migration timing (GREB1L/ROCK1). Neutral variation provided support for fine scale structure of populations, while allele frequency variation in GREB1L/ROCK1 was highly correlated with mean return timing for early and late migrating populations within each of the lineages (r2 between 0.58-0.95; P < 0.001). However, the extent of selection within the genomic region controlling migration timing was much narrower in one lineage (interior stream-type) compared to the other two major lineages which corresponded to the breadth of phenotypic variation in migration timing observed among lineages. Evidence of a duplicated block within GREB1L/ROCK1 may be responsible for reduced recombination in this portion of the genome and contributes to phenotypic variation within and across lineages. Lastly, SNP positions across GREB1L/ROCK1 were assessed for their utility in discriminating migration timing among lineages, and we recommend multiple markers nearest the duplication to provide highest accuracy in conservation applications such as those that aim to protect early migrating Chinook salmon. These results highlight the need to investigate variation throughout the genome and the effects of structural variants on ecologically relevant phenotypic variation in natural species.
... This method is comparatively less costly than individual-level genotyping owing to reduced library preparation costs, though data at the individual level is lost. Nevertheless, it is possible to measure robust and unbiased genetic differentiation among populations with poolseq if enough individuals are sampled (Hivert et al. 2018). The first draft of theZ. ...
A global decline in seagrass populations has led to renewed calls for their conservation as important providers of biogenic and foraging habitat, shoreline stabilisation, and carbon storage. Eelgrass (Zostera marina) occupies the largest geographic range among seagrass species spanning a commensurately broad spectrum of environmental conditions. However, relatively little is known about their fine-scale genetic structure and broad-scale genomic signatures of environmental adaptation, and in Canada, eelgrass is considered a single phylogroup despite occurring across three oceans. We used a pooled whole-genome re-sequencing approach to characterise population structure, gene flow, and adaptation of 23 eelgrass populations ranging from the Northeast United States, to Atlantic, subarctic, and Pacific Canada. We identified over 500,000 SNPs, which when mapped to a chromosome-level genome assembly revealed six broad clades of eelgrass across the study area, with pairwise FST ranging from 0 among neighbouring populations to 0.54 between Pacific and Atlantic coasts. Genetic diversity was highest in the Pacific and lowest in the Arctic, consistent with colonisation of the Arctic and Atlantic oceans from the Pacific. Using redundancy analyses and two climate change projection scenarios, we found that subarctic populations are more vulnerable to climate change through genomic offset predictions. Conservation planning in Canada should ensure that representative populations from each identified clade are included within a national network so that latent genetic diversity is protected, and gene flow is maintained. Northern populations, in particular, may require stronger protective measures given their susceptibility to change climate.
... This method is comparatively less costly than individual-level genotyping owing to reduced library preparation costs, though data at the individual level is lost. Nevertheless, it is possible to measure robust and unbiased genetic differentiation among populations with poolseq if enough individuals are sampled (Hivert et al. 2018). The first draft of theZ. ...
A global decline in seagrass populations has led to renewed calls for their conservation as important providers of biogenic and foraging habitat, shoreline stabilisation, and carbon storage. Eelgrass (Zostera marina) occupies the largest geographic range among seagrass species spanning a commensurately broad spectrum of environmental conditions. However, relatively little is known about their fine-scale genetic structure and broad-scale genomic signatures of environmental adaptation, and in Canada, eelgrass is considered a single phylogroup despite occurring across three oceans. We used a pooled whole-genome re-sequencing approach to characterise population structure, gene flow, and adaptation of 23 eelgrass populations ranging from the Northeast United States, to Atlantic, subarctic, and Pacific Canada. We identified over 500,000 SNPs, which when mapped to a chromosome-level genome assembly revealed six broad clades of eelgrass across the study area, with pairwise FST ranging from 0 among neighbouring populations to 0.54 between Pacific and Atlantic coasts. Genetic diversity was highest in the Pacific and lowest in the Arctic, consistent with colonisation of the Arctic and Atlantic oceans from the Pacific. Using redundancy analyses and two climate change projection scenarios, we found that subarctic populations are more vulnerable to climate change through genomic offset predictions. Conservation planning in Canada should ensure that representative populations from each identified clade are included within a national network so that latent genetic diversity is protected, and gene flow is maintained. Northern populations, in particular, may require stronger protective measures given their susceptibility to change climate.
... The mpileup file was then converted to sync format by PoPoolation2 version 1201 (Kofler et al., 2011). 8.03 million (M) SNPs were detected on this sync file using R/poolfstat package v2.0.0 (Hivert et al., 2018) and the following parameters: coverage per pool between 10 and 50. ...
In the last few years, the bed bug Cimex lectularius has been an increasing problem worldwide, mainly due to the development of insecticide resistance to pyrethroids. The characterization of resistance alleles is a prerequisite to improve surveillance and resistance management. To identify genomic variants associated with pyrethroid resistance in Cimex lectularius, we compared the genetic composition of two recent and resistant populations with that of two ancient-susceptible strains using a genome-wide pool-seq design. We identified a large 6 Mb "superlocus" showing particularly high genetic differentiation and association with the resistance phenotype. This superlocus contained several clustered resistance genes, and was also characterized by a high density of structural variants (inversions, duplications). The possibility that this superlocus constitute a resistance "supergene" that evolved after the clustering of alleles adapted to insecticide and after reduction in recombination is discussed.
... This method is comparatively less costly than individual-level genotyping owing to reduced library preparation costs, though data at the individual level is lost. Nevertheless, it is possible to measure robust and unbiased genetic differentiation among populations with poolseq if enough individuals are sampled (Hivert et al. 2018). The first draft of theZ. ...
A global decline in seagrass populations has led to renewed calls for their conservation as important providers of biogenic and foraging habitat, shoreline stabilisation, and carbon storage. Eelgrass (Zostera marina) occupies the largest geographic range among seagrass species spanning a commensurately broad spectrum of environmental conditions. However, relatively little is known about their fine-scale genetic structure and broad-scale genomic signatures of environmental adaptation, and in Canada, eelgrass is considered a single phylogroup despite occurring across three oceans. We used a pooled whole-genome re-sequencing approach to characterise population structure, gene flow, and adaptation of 23 eelgrass populations ranging from the Northeast United States, to Atlantic, subarctic, and Pacific Canada. We identified over 500,000 SNPs, which when mapped to a chromosome-level genome assembly revealed six broad clades of eelgrass across the study area, with pairwise FST ranging from 0 among neighbouring populations to 0.54 between Pacific and Atlantic coasts. Genetic diversity was highest in the Pacific and lowest in the Arctic, consistent with colonisation of the Arctic and Atlantic oceans from the Pacific. Using redundancy analyses and two climate change projection scenarios, we found that subarctic populations are more vulnerable to climate change through genomic offset predictions. Conservation planning in Canada should ensure that representative populations from each identified clade are included within a national network so that latent genetic diversity is protected, and gene flow is maintained. Northern populations, in particular, may require stronger protective measures given their susceptibility to change climate.
... 86 It is statistically challenging to derive correct estimates of genetic differentiation by analyzing sequencing data from a DNA pool instead of individual genotypes. 87 Therefore, we extracted genome regions with the top 1% of F ST values rather than the absolute value of F ST and identified strongly selected genes according to the positions of these genome regions. ...
After being exposed to environmental stimuli during early developmental stages, some organisms may gain or weaken physiological regulating abilities, which would have long-lasting effects on their performance. Environmental hypoxia events can have significant effects on marine organisms, but for breeding programs and other practical applications, it is important to further explore the long-term physiological effects of early hypoxia exposure in economically significant species. In this study, the Pacific abalone Haliotis discus hannai was exposed to moderate hypoxia (∼4 mg/L) from zygote to trochophora, and the assessments of hypoxia tolerance were conducted on the grow-out stage. The results revealed that juvenile abalones exposed to hypoxia at the early development stages were more hypoxia-tolerant but with slower weight growth, a phenomenon called the trade-off between growth and survival. These phenotypic effects driven by the hypoxia exposure were explained by strong selection of genes involved in signal transduction, autophagy, apoptosis, and hormone regulation. Moreover, long non-coding RNA regulation plays an important role modulating carry-over effects by controlling DNA replication and repair, signal transduction, myocardial activity, and hormone regulation. This study revealed that the ability to create favorable phenotypic differentiation through genetic selection and/or epigenetic regulation is important for the survival and development of aquatic animals in the face of rapidly changing environmental conditions.
