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424 results for “population differentiation”
Data from: Population genomic evidence reveals subtle patterns of differentiation in the trophically polymorphic Cuatro Ciénegas cichlid, Herichthys minckleyi
In recent decades, an increased understanding of molecular ecology has led to a reinterpretation of the role of gene flow during the evolution of reproductive isolation and biological novelty. For example, even in the face of ongoing gene flow strong selection may maintain divergent polymorphisms, or gene flow may introduce novel biological diversity via hybridization and introgression from a divergent species. Herein, we elucidate the evolutionary history and genomic basis of a trophically polymorphic trait in a species of cichlid fish, Herichthys minckleyi. We explored genetic variation at three hierarchical levels; between H. minckleyi (n=69) and a closely related species H. cyanoguttatus (n=10), between
Low levels of genetic differentiation with isolation by geography and environment in populations of Drosophila melanogaster from across China
<p>The fruit fly <i>Drosophila</i> <i>melanogaster</i> is a model species in evolutionary studies. However, the population processes of this species in East Asia are poorly studied, even though this area was one of the first regions colonized outside of its native distribution range. Here we examined the population genetic structure of <i>D.</i> <i>melanogaster</i> across China. There were 14 mitochondrial haplotypes with ten unique ones out of 23 known from around the globe. Pairwise F<sub>ST</sub> values estimated from 15 novel microsatellites ranged from 0 to 0.11, with geographically isolated populations showing the highest level of genetic uniqueness. STRUCTURE analysis identified high levels of admixture at both the individual and population levels. Mantel tests indicated a strong association between genetic distance and geographical distance as well as environmental distance. Full RDA analysis showed that independent effects of environmental conditions and geography accounted for 62.10% and 31.58% of the total explained genetic variance, respectively. When geographic variables were constrained in a partial RDA analysis, three environmental variables of bio2 (mean diurnal air temperature range), bio13 (precipitation of the wettest month), and bio15 (precipitation seasonality) were correlated with genetic distance. Our study suggests that a high level of gene flow, geographical isolation, and environmental factors have together shaped the population genetic structure of <i>D.</i> <i>melanogaster</i> after its introduction into China.</p>
Data from: Curation: heat stress responses and population genetics of the kelp Laminaria digitata (Phaeophyceae) across latitudes reveal differentiation among North Atlantic populations
<p>We aim to understand the thermal plasticity of a coastal foundation species across its latitudinal distribution by assessing physiological responses to high temperature stress in the kelp <i>Laminaria digitata</i> in combination with population genetic characteristics. We <a>hypothesize</a> that Arctic and cold-temperate populations are less heat resilient than warm-temperate populations. Using meristems of natural <i>L. digitata</i> populations from six locations ranging between Kongsfjorden, Spitsbergen (79°N), and Quiberon, France (47°N), we performed a common-garden heat stress experiment applying 15°C to 23°C over eight days. We assessed growth, quantum yield, carbon and nitrogen storage, and xanthophyll pigment contents as response traits. Population connectivity and genetic diversity were analysed with microsatellite markers to relate heat resilience to genetic features and phylogeography. Microsatellite genotyping revealed all sampled populations to be genetically distinct, underlying strong hierarchical structuring between and within southern and northern clades. Genetic diversity was lowest in the isolated population of the North Sea island of Helgoland and highest in Roscoff in the English Channel. Results from the heat stress experiment suggest that the upper temperature limit of <i>L. digitata</i> is nearly identical across its distribution range, but subtle differences we<a>re </a>revealed for the two populations currently at their warm limits. They respectively <a>show</a> a significant advantage in growth at 19°C and 21°C (Quiberon) and a lack of stress responses in photosynthetic quantum yield and xanthophyll pigments at 23°C (Helgoland). In addition, quantum yield indicated the highest heat sensitivity in <i>L. digitata</i> from the northernmost population in Spitsbergen. All together, these results support the hypothesis of moderate local differentiation across <i>L. digitata</i>'s European distribution, whereas effects are likely too weak to ameliorate the species' capacity to withstand ocean warming and marine heatwaves at the southern range edge.</p>
Data from: Continental-level population differentiation and environmental adaptation in the mushroom Suillus brevipes
Recent advancements in sequencing technology allowed researchers to better address the patterns and mechanisms involved in microbial environmental adaptation at large spatial scales. Here we investigated the genomic basis of adaptation to climate at the continental scale in Suillus brevipes, an ectomycorrhizal fungus symbiotically associated with the roots of pine trees. We used genomic data from 55 individuals in seven locations across North America to perform genome scans to detect signatures of positive selection and assess whether temperature and precipitation were associated with genetic differentiation. We found that S. brevipes exhibited overall strong population differentiation, with potential admixture in Canadian populations. This species also displayed genomic signatures of positive selection as well as genomic sites significantly associated with distinct climatic regimes and abiotic environmental parameters. These genomic regions included genes involved in transmembrane transport of substances and helicase activity potentially involved in cold stress response. Our study sheds light on large-scale environmental adaptation in fungi by identifying putative adaptive genes and providing a framework to further investigate the genetic basis of fungal adaptation.
Data from: Does sex-biased dispersal account for the lack of geographic and host-associated differentiation in introduced populations of an aphid parasitoid?
Host recognition and use in female parasitoids strongly relies on host fidelity, a plastic behavior which can significantly restrict the host preferences of parasitoids, thus reducing the gene flow between parasitoid populations attacking different insect hosts. However, the effect of migrant males on the genetic differentiation of populations has been frequently ignored in parasitoids, despite its known impact on gene flow between populations. Hence, we studied the extent of gene flow mediated by female and male parasitoids by assessing sibship relationships among parasitoids within and between populations, and its impact on geographic and host-associated differentiation in the aphid parasitoid Aphidius ervi. We report evidences of a high gene flow among parasitoid populations on different aphid hosts and geographic locations. The high gene flow among parasitoid populations was found to be largely male mediated, suggested by significant differences in the distribution of full-sib and paternal half-sib dyads of parasitoid populations.
Data from: A novel approach to wildlife transcriptomics provides evidence of disease-mediated differential expression and changes to the microbiome of amphibian populations
Ranaviruses are responsible for a lethal, emerging infectious disease in amphibians and threaten their populations throughout the world. Despite this, little is known about how amphibian populations respond to ranaviral infection. In the United Kingdom, ranaviruses impact the common frog (Rana temporaria). Extensive public engagement in the study of ranaviruses in the UK has led to the formation of a unique system of field sites containing frog populations of known ranaviral disease history. Within this unique natural field system, we used RNA sequencing (RNA-Seq) to compare the gene expression profiles of R. temporaria populations with a history of ranaviral disease and those without. We have applied a RNA read filtering protocol that incorporates Bloom filters, previously used in clinical settings, to limit the potential for contamination that comes with the use of RNA-Seq in non-laboratory systems. We have identified a suite of 407 transcripts that are differentially expressed between populations of different ranaviral disease history. This suite contains genes with functions related to immunity, development, protein transport and olfactory reception amongst others. A large proportion of potential non-coding RNA transcripts present in our differentially expressed set provides first evidence of a possible role for long non-coding RNA (lncRNA) in amphibian response to viruses. Our read-filtering approach also removed significantly more bacterial reads from libraries generated from postitive disease history populations. Subsequent analysis revealed these bacterial read sets to represent distinct communities of bacterial species, which is suggestive of an interaction between ranavirus and the host microbiome in the wild.
Data from: Isolation by distance and isolation by environment contribute to population differentiation in Protea repens (Proteaceae L.), a widespread South African species
PREMISE OF THE STUDY: The Cape Floristic Region (CFR) of South Africa is renowned for its botanical diversity, but the evolutionary origins of this diversity remain controversial. Both neutral and adaptive processes have been implicated in driving diversification, but population-level studies of plants in the CFR are rare. Here, we investigate the limits to gene flow and potential environmental drivers of selection in Protea repens L. (Proteaceae L.), a widespread CFR species. METHODS: We sampled 19 populations across the range of P. repens and used genotyping by sequencing to identify 2066 polymorphic loci in 663 individuals. We used a Bayesian FST outlier analysis to identify single-nucleotide polymorphisms (SNPs) marking genomic regions that may be under selection; we used those SNPs to identify potential drivers of selection and excluded them from analyses of gene flow and genetic structure. RESULTS: A pattern of isolation by distance suggested limited gene flow between nearby populations. The populations of P. repens fell naturally into two or three groupings, which corresponded to an east-west split. Differences in rainfall seasonality contributed to diversification in highly divergent loci, as do barriers to gene flow that have been identified in other species. CONCLUSIONS: The strong pattern of isolation by distance is in contrast to the findings in the only other widespread species in the CFR that has been similarly studied, while the effects of rainfall seasonality are consistent with well-known patterns. Assessing the generality of these results will require investigations of other CFR species.
Data from: Serotonin differentially affects morph-specific behavior in divergent populations of a horned beetle
Associations between animal weapons and corresponding aggressive behaviors are among the most characteristic features of species, yet at the same time their co-expression is itself often strongly dependent on context, such as male condition or population ecology. Yet the mechanisms that modulate associations between aggression, morphology, and biological context remain poorly understood. The biogenic amine serotonin has been shown to regulate a wide range of aggressive and morph-specific behaviors in diverse insect species. However, the extent to which serotonin may coordinate the expression of behavior with morphology across biological contexts remains unclear. In this study, we pharmacologically increased serotonin biosynthesis in males of the polyphenic beetle, Onthophagus taurus, and assessed how this manipulation affects both aggressive and non-aggressive behaviors in alternative fighter and sneaker morphs, as well as in males derived from rapidly diverging populations characterized by disparate levels of competition for mates. We find (i) that enhancing serotonin biosynthesis increases most measures of aggressive behaviors, but influences only a subset of non-aggressive behaviors, (ii) that similar serotonin-mediated behavioral changes manifest in both morphs within populations more often than just a single morph, and (iii) that males derived from populations subject to disparate levels of competition for mates have diverged in their behavioral responsiveness to serotonin up-regulation. Collectively, our study suggests that serotonin signaling plays a critical role in the regulation of male behavior and its evolution, including in the context of rapid, short term population divergence.
Data from: Gene duplication, population genomics and species-level differentiation within a tropical mountain shrub
Gene duplication leads to paralogy, which complicates the de novo assembly of genotyping-by-sequencing (GBS) data. The issue of paralogous genes is exacerbated in plants, because they are particularly prone to gene duplication events. Paralogs are normally filtered from GBS data before undertaking population genomics or phylogenetic analyses. However, gene duplication plays an important role in the functional diversification of genes and it can also lead to the formation of postzygotic barriers. Using populations and closely related species of a tropical mountain shrub, we examine: (1) the genomic differentiation produced by putative orthologs, and (2) the distribution of recent gene duplication among lineages and geography. We find high differentiation among populations from isolated mountain peaks and species-level differentiation within what is morphologically described as a single species. The inferred distribution of paralogs among populations is congruent with taxonomy and shows that GBS could be used to examine recent gene duplication as a source of genomic differentiation of non-model species.
Data from: Complex selection on a regulator of social cognition: evidence of balancing selection, regulatory interactions and population differentiation in the prairie vole Avpr1a locus
Adaptive variation in social behavior depends upon standing genetic variation, but we know little about how evolutionary forces shape genetic diversity relevant to brain and behavior. In prairie voles (Microtus ochrogaster), variants at the Avpr1a locus predict expression of the vasopressin 1a receptor in the retrosplenial cortex (RSC), a brain region that mediates spatial and contextual memory; cortical V1aR abundance in turn predicts diversity in space-use and sexual fidelity in the field. To examine the potential contributions of adaptive and neutral forces to variation at the Avpr1a locus, we explore sequence diversity at the Avpr1a locus and throughout the genome in two populations of wild prairie voles. First, we refine results demonstrating balancing selection at the locus by comparing the frequency spectrum of variants at the locus to a random sample of the genome. Next, we find that the four SNPs that predict high V1aR expression in the RSC are in stronger linkage disequilibrium than expected by chance despite high recombination among intervening variants, suggesting that epistatic selection maintains their association despite recombination. Analysis of population structure and a haplotype network for two populations revealed that this excessive LD was unlikely to be due to admixture alone. Furthermore, the two populations differed considerably in the region shown to be a regulator of V1aR expression despite the extremely low levels of genome-wide genetic differentiation. Together, our data suggest that complex selection on Avpr1a locus favors specific combinations of regulatory polymorphisms, maintains the resulting alleles at populations-specific frequencies, and may contribute to unique patterns of spatial cognition and sexual fidelity among populations.
Body mass, temperature, and pathogen intensity differentially affect critical thermal maxima and their population-level variation in a solitary bee
<p>Climate change presents a major threat to species distribution and persistence. Understanding what abiotic or biotic factors influence the thermal tolerances of natural populations is critical to assessing their vulnerability under rapidly changing thermal regimes. This study evaluates how body mass, local climate, and pathogen intensity influence heat tolerance and its population-level variation (SD) among individuals of the solitary bee <em>Xenoglossa pruinosa</em>. We assess the sex-specific relationships between these factors and heat tolerance given the differences in size between sexes and the ground-nesting behavior of the females. We collected <em>X. pruinosa</em> individuals from fourteen sites across Pennsylvania, USA that varied in mean temperature, precipitation, and soil texture. We measured the critical thermal maxima (CT<sub>max</sub>) of <em>X. pruinosa</em> individuals as our proxy for heat tolerance, and used quantitative PCR to determine relative intensities of three parasite groups—trypanosomes, <em>Spiroplasma apis</em> (mollicute bacteria), and <em>Vairimorpha apis</em> (microsporidian). While there was no difference in CT<sub>max</sub> between the sexes, we found that CT<sub>max</sub> increased significantly with body mass, and that this relationship was stronger for males than for females. Air temperature, precipitation, and soil texture did not predict mean CT<sub>max</sub> for either sex. However, population-level variation in CT<sub>max</sub> was strongly and negatively correlated with air temperature, which suggests that temperature is acting as an environmental filter. Of the parasites screened, only trypanosome intensity correlated with heat tolerance. Specifically, trypanosome intensity negatively correlated with the CT<sub>max</sub> of female <em>X. pruinosa</em> but not males. Our results highlight the importance of considering size, sex, and infection status when evaluating thermal tolerance traits. Importantly, this study reveals the need to evaluate trends in the variation of heat tolerance within and between populations, and consider implications of reduced variation in heat tolerance for the persistence of ectotherms in future climate conditions. </p>
Data from: genetic evidence of differential dispersal pattern in Asiatic wild dog: comparing populations with different pack size and tiger densities
<p><span>Dispersal is a multi-causal, crucial life-history event in shaping the genetic and behavioral structure of mammals. We assessed the dispersal pattern of dholes aka Asiatic wild dog (<em>Cuon alpinus</em>), a social monogamous mammal at two tiger reserves of Maharashtra with different degrees of pack size and competition with tigers i.e. Tadoba-Andhari (TATR, smaller pack size, higher tiger density) and Nawegaon-Nagzira (NNTR, larger pack size, lower tiger density). We used the microsatellite data of 174 individual genotypes (98 males and 67 females) to assess the dispersal pattern of dholes from two populations with varying pack size, tiger density, and landscape connectivity using gene flow as a proxy. We compared the population structure, pairwise F statistics, assignment index, and relatedness across a spatial scale. Overall, the results suggested a difference in sex-bias dispersal pattern for the two sub-populations, exhibiting significant results for female-biased dispersal in the TATR population with a smaller pack size and higher tiger density. Our study highlights the variability in sex-biased dispersal patterns in two different populations which could be the consequence of different variables such as pack size, tiger density, and geographical scale. The study warrants further quantitative investigation including several factors including individual behavior, pack composition, pack size, tiger density, etc. In the present Anthropocene era, determining the sex bias in dispersal patterns for a short-range, pack-living carnivore will help in devising an effective conservation management plan for their long-term survival.</span></p>
SINGER-inferred targets for exceptional population differentiation in coalescence times in African populations in 1000 Genomes Project
<p>This repo saves the gene targets which shows the signal of population differentiation in coalescence times in African populations in 1000 Genomes Project. </p> <p>Here are the detailed explanations for the header of the files:</p> <p>chrom The chromosome where the genomic window is located (e.g., chr1, chrX).<br>window_start The 0-based start position of the genomic window being analyzed.<br>window_end The 1-based end position of the genomic window (exclusive).<br>score Ratio between the overall diversity and the population specific diversity, in the genomic window.<br>transcript_chrom The chromosome where the transcript is located.<br>transcript_start The 0-based start position of the transcript.<br>transcript_end The 1-based end position of the transcript (exclusive).<br>transcript_id The unique identifier for the transcript (e.g., Ensembl or RefSeq ID).<br>strand The strand of the transcript: "+" for forward, "-" for reverse.<br>coding_start The start position of the coding region of the transcript (if applicable).<br>coding_end The end position of the coding region of the transcript (if applicable).<br>RGB The RGB color used for visualization in genome browsers (format: R,G,B).<br>block_count The number of exons in the transcript.<br>block_sizes Comma-separated list of exon lengths (in base pairs).<br>block_starts Comma-separated list of exon start positions relative to transcript_start.</p>
Population differentiation and intraspecific genetic admixture in two Eucryptorrhynchus weevils (Coleoptera: Curculionidae) across northern China
<p><span>Inreasing damage of pests in agriculture and forestry can arise both as a consequence of changes in local species and through the introduction of alien species. In this study, we used population genetics approaches to examine population processes of two pests of the tree-of-heaven trunk weevil (TTW), <em>Eucryptorrhynchus brandti</em> (Harold) and the tree-of-heaven root weevil (TRW), <em>E. scrobiculatus</em> (Motschulsky) on the tree-of-heaven across their native range of China. We analyzed the population genetics of the two weevils based on ten highly polymorphic microsatellite markers. Population genetic diversity analysis showed strong population differentiation among populations of each species, with FST ranges from 0.0197 to 0.6650 and from -0.0724 to 0.6845, respectively. Populations from the same geographical areas can be divided into different genetic clusters, and the same genetic cluster contained populations from different geographical populations, pointing to dispersal of the weevils possibly being human-mediated. Redundancy analysis showed that the independent effects of environment and geography could account for 93.94% and 29.70% of the explained genetic variance in TTW, and 41.90% and 55.73% of the explained genetic variance in TRW, respectively, indicating possible impacts of local climates on population genetic differentiation. Our study helps to uncover population genetic processes of these local pest species with relevance to control methods.</span></p>
IIb-RAD-seq coupled with random forest classification indicates regional population structuring and sex-specific differentiation in salmon lice (Lepeophtheirus salmonis)
<p><span>The aquaculture industry has been dealing with salmon lice problems forming serious threats to salmonid farming. Several treatment approaches have been used to control the parasite. Treatment effectiveness must be optimized, and the systematic genetic differences between sub-populations must be studied to monitor louse species and enhance targeted control measures. We have used IIb-RAD sequencing in tandem with a random forest classification algorithm to detect the regional genetic structure of the Norwegian salmon lice and identify important markers for sex differentiation of this species. We identified 19428 single nucleotide polymorphisms (SNPs) from 95 individuals of salmon lice. These SNPs, however, were not able to distinguish differential structure of lice populations. Using the random forest algorithm, we selected 91 SNPs important for geographical classification and 14 SNPs important for sex classification. The geographically important SNP data substantially improved the genetic understanding of the population structure and classified regional demographic clusters along the Norwegian coast. </span><span>We also uncovered SNP markers that could help determine the sex of the salmon louse. </span><span>A large portion of the SNPs identified to be under directional selection were also ranked highly important by random forest. According to our findings, there is a regional population structure of salmon lice associated with the geographical location along the Norwegian coastline.</span></p>
Fig. 3 in Genetic Differentiation Of Ukrainian Populations Of Eusomus Ovulum (Coleoptera, Curculionidae): Evidence Of Multiple Hybrid Speciation
Fig. 3. Polyclonal structure of studied Eusomus ovlulum samples inUkraine.
Fig. 2 in Genetic Differentiation Of Ukrainian Populations Of Eusomus Ovulum (Coleoptera, Curculionidae): Evidence Of Multiple Hybrid Speciation
Fig. 2. The electrophoretic spectra of the esterases in the Eusomus ovulum specimens.
Fig. 1 in Genetic Differentiation Of Ukrainian Populations Of Eusomus Ovulum (Coleoptera, Curculionidae): Evidence Of Multiple Hybrid Speciation
Fig. 1. Geographic localization of Eusomus ovulum samples.
Genetic diversity and differentiation of populations of Anthyllis vulneraria along elevational and latitudinal gradients
<p>The abundant centre model (ACM) predicts that the suitability of environmental conditions for a species decreases from the centre of its distribution towards its range periphery and consequently its populations will become scarcer, smaller and more isolated, resulting in lower genetic diversity and increased differentiation. However, little is known about whether genetic diversity shows similar patterns along elevational and latitudinal gradients with similar changes in important environmental conditions. Using microsatellite markers we studied the genetic diversity and structure of 20 populations each of <em>Anthyllis vulneraria </em>along elevational gradients in the Alps from the valleys to the elevational limit (2500 m), and along a latitudinal gradient (2500 km) from Central Europe to the range margin in northern Scandinavia. Both types of gradients corresponded to a 11.5 °C difference in mean annual temperature. Genetic diversity strongly declined and differentiation increased with latitude in line with the predictions of the ACM. However, as population size did not decline with latitude and genetic diversity was not related to population size in <em>A. vulneraria</em>, this pattern is not likely to be due to less favourable conditions in the North, but due to serial founder effects during the post-glacial recolonization process. Genetic diversity was not related to elevation, but we found significant isolation by distance along both gradients, although the elevational gradient was shorter by orders of magnitude. Subarctic populations differed genetically from alpine populations indicating that the northern populations did not originate from high elevational Alpine ones. Our results support the notion that postglacial latitudinal colonization over large distances resulted in a larger loss of genetic diversity than elevational range shifts. The lack of genetic diversity in subarctic populations may threaten their long-term persistence in the face of climate change, whereas alpine populations could benefit from gene flow from low-elevation populations.</p>
Pollinator data from: Pollinator movement activity influences genetic diversity and differentiation of spatially isolated populations of clonal forest herbs
<p>In agricultural landscapes, forest herbs live in small, spatially isolated forest patches. For their long-term survival, their populations depend on animals as genetic linkers that provide pollen- or seed-mediated gene flow among different forest patches. However, whether insect pollinators serve as genetic linkers among spatially isolated forest herb populations in agricultural landscapes remains to be shown. Here, we used population genetic methods to analyze: (A) the genetic diversity and genetic differentiation of populations of two common, slow-colonizing temperate forest herb species (<em>Polygonatum</em> <em>multiflorum</em> (L.) All. and <em>Anemone</em> <em>nemorosa</em> L.) in spatially isolated populations within three agricultural landscapes in Germany and Sweden and (B) the movement activity of their most relevant associated pollinator species, i.e., the bumblebee <em>Bombus</em> <em>pascuorum</em> (Scopoli, 1763) and the hoverfly <em>Melanostoma</em> <em>scalare</em> (Fabricus, 1794), respectively, which differ in their mobility. We tested whether the indicated pollinator movement activity affected the genetic diversity and genetic differentiation of the forest herb populations. Bumblebee movement indicators that solely indicated movement activity between the forest patches affected both genetic diversity and genetic differentiation of the associated forest herb <em>P</em>. <em>multiflorum</em> in a way that can be explained by pollen-mediated gene flow among the forest herb populations. In contrast, movement indicators reflecting the total movement activity at a forest patch (including within-forest patch movement activity) showed unexpected effects for both plant-pollinator pairs that might be explained by accelerated genetic drift due to enhanced sexual reproduction. Our integrated approach revealed that bumblebees serve as genetic linkers of associated forest herb populations, even if they are more than 2 km apart from each other. No such evidence was found for the forest-associated hoverfly species which showed significant genetic differentiation among forest patches itself. Our approach also indicated that a higher within-forest patch movement activity of both pollinator species might enhance sexual recruitment and thus diminishes the temporal buffer that clonal growth provides against habitat fragmentation effects.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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