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2,445 results for “Genetics: population”
FIGURE 1 in Population genetics of the endangered catfish Pseudoplatystoma magdaleniatum (Siluriformes: Pimelodidae) based on species-specific microsatellite loci
FIGURE 1 | Sampling sites of Pseudoplatystoma magdaleniatum in the Magdalena-Cauca basin.
Seasonality and inter-annual stability in the population genetic structure of Batrachospermum gelatinosum (Rhodophyta)
<p>Data used for Shainker-Connelly et al. in biorxiv: https://www.biorxiv.org/content/10.1101/2024.09.20.614195v1</p>
Data from: Local prey community composition and genetic distance predict venom divergence among populations of the northern Pacific rattlesnake (Crotalus oreganus)
Identifying the environmental correlates of divergence in functional traits between populations can provide insights into the evolutionary mechanisms that generate local adaptation. Here, we assess patterns of population differentiation in expressed venom proteins in Northern Pacific rattlesnakes (Crotalus oreganus) from 13 locations across California. We evaluate the relative importance of major biotic (prey species community composition), abiotic (temperature, precipitation, and elevation) and genetic factors (genetic distance based on RADseq loci) as correlates of population divergence in venom phenotypes. We found that over half of the variation in venom composition is associated with among-population differentiation for genetic and environmental variables, and that this variation occurred along axes defining previously observed functional trade-offs between venom proteins that have neurotoxic, myotoxic and hemorrhagic effects. Surprisingly, genetic differentiation among populations was the best predictor of venom divergence, accounting for 46% of overall variation, whereas differences in prey community composition and abiotic factors explained smaller amounts of variation (23% and 19%, respectively). The association between genetic differentiation and venom composition could be due to an isolation by distance effect or, more likely it may reflect an isolation-by-environment effect where selection against recent migrants is strong, producing a correlation between neutral genetic differentiation and venom differentiation. Our findings suggest that even coarse estimates of prey community composition can be useful in understanding the selection pressures acting on patterns of venom protein expression. Additionally, our results suggest that factors other than adaptation to spatial variation in prey need to be considered when explaining population divergence in venom.
Data from: RAD sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference
Restriction site-associated DNA sequencing (RADseq) provides researchers with the ability to record genetic polymorphism across thousands of loci for non-model organisms, potentially revolutionising the field of molecular ecology. However, as with other genotyping methods, RADseq is prone to a number of sources of error that may have consequential effects for population genetic inferences, and these have received only limited attention in terms of the estimation and reporting of genotyping error rates. Here we use individual sample replicates, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome. We then use sample replicates to (1) optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci, and; (2) quantify error rates for loci, alleles and SNPs. As an empirical example we use a double digest RAD dataset of a non-model plant species, Berberis alpina, collected from high altitude mountains in Mexico.
Data from: The socially parasitic ant Polyergus mexicanus has host-associated genetic population structure and related neighboring nests
<p>The genetic structure of populations can be both a cause and a consequence of ecological interactions. For parasites, genetic structure may be a consequence of preferences for host species or of mating behavior. Conversely, genetic structure can determine where conspecific interactions among parasites lay on a spectrum from cooperation to conflict. We used microsatellite loci to characterize the genetic structure of a population of the socially parasitic dulotic (aka "slave-making") ant (<i>Polyergus mexicanus</i>), which is known for its host-specificity and conspecific aggression. First, we assessed whether the pattern of host species use by the parasite has influenced parasite population structure. We found that host species use was correlated with subpopulation structure, but this correlation was imperfect: some subpopulations used one host species exclusively, while others used several. Second, we examined the viscosity of the parasite population by measuring the relatedness of pairs of neighboring parasitic ant nests at varying distances from each other. Although natural history observations of local dispersal by queens suggested the potential for viscosity, there was no strong correlation between relatedness and distance between nests. However, 35% of nests had a closely related neighboring nest, indicating that kinship could potentially affect the nature of some interactions between nests of this social parasite. Our findings confirm that ecological forces like host species selection can shape the genetic structure of parasite populations, and that such genetic structure has the potential to influence parasite-parasite interactions in social parasites via inclusive fitness.</p>
Data from: Combining niche-shift and population genetic analyses predicts rapid phenotypic evolution during invasion
Rapid evolution of non-native species can facilitate invasion success, but recent reviews indicate that such microevolution rarely yields expansion of the climatic niche in the introduced habitats. However, because some invasions originate from a geographically restricted portion of the native species range and its climatic niche, it is possible that the frequency, direction and magnitude of phenotypic evolution during invasion has been underestimated. We explored the utility of niche-shift analyses in the red seaweed Gracilaria vermiculophylla, which expanded from the northeastern coastline of Japan to North America, Europe and northwestern Africa within the last 100 years. A genetically-informed climatic niche shift analysis indicates that native source populations occur in colder and highly seasonal habitats, while most non-native populations typically occur in warmer, less seasonal habitats. This climatic niche expansion predicts that non-native populations evolved greater tolerance for elevated heat conditions relative to native source populations. We assayed 935 field-collected and 325 common-garden thalli from 40 locations and as predicted, non-native populations had greater tolerance for ecologically-relevant extreme heat (40ºC) than did Japanese source populations. Non-native populations also had greater tolerance for cold and low-salinity stresses relative to source populations. The importance of local adaptation to warm temperatures during invasion was reinforced by evolution of parallel clines: populations from warmer, lower-latitude estuaries had greater heat tolerance than did populations from colder, higher-latitude estuaries in both Japan and eastern North America. We conclude that rapid evolution plays an important role in facilitating the invasion success of this and perhaps other non-native marine species. Genetically-informed ecological niche analyses readily generate clear predictions of phenotypic shifts during invasions, and may help to resolve debate over the frequency of niche conservatism versus rapid adaptation during invasion.
The genetic architecture of temperature adaptation is shaped by population ancestry and not by selection regime
<p class="western"><span>Understanding the genetic architecture of temperature adaptation is key for characterizing and predicting the effect of climate change on natural populations. One particularly promising approach is Evolve and Resequence (E&R), which combines advantages of experimental evolution such as time series, replicate populations and controlled environmental conditions, with whole genome sequencing. </span></p> <p class="western"><span>The recent analysis of replicate populations from two different </span><span><i>Drosophila simulans</i></span><span> founder populations, which were adapting to the same novel hot environment, uncovered very different architectures - either many selection targets with large heterogeneity among replicates or fewer selection targets with a consistent response among replicates. </span></p> <p class="western"><span>Here, we exposed the founder population from Portugal to a cold temperature regime. Although almost no selection targets were shared between the hot and cold selection regime, the adaptive architecture was similar: we identified a moderate number of targets under strong selection (19 selection targets, mean selection coefficient = 0.072) and very parallel responses in the cold evolved replicates. This similarity across different environments indicates that the adaptive architecture depends more on the ancestry of the founder population than the specific selection regime. These observations will have broad implications for the correct interpretation of the genomic responses to a changing climate in natural populations.</span></p> <p class="western"> </p>
Quantitative trait locus mapping reveals an independent genetic basis for joint divergence in leaf function, life-history, and floral traits between scarlet monkeyflower (Mimulus cardinalis) populations
<p><b>PREMISE </b></p> <p>Across taxa, vegetative and floral traits that vary along a fast-slow life-history axis are often correlated with leaf functional traits arrayed along the leaf economics spectrum, suggesting a constrained set of adaptive trait combinations. Such broad-scale convergence may arise from genetic constraints imposed by pleiotropy (or tight linkage) within species, or from natural selection alone. Understanding the genetic basis of trait syndromes and their components is key to distinguishing these alternatives and predicting evolution in novel environments.</p> <p><b>METHODS </b></p> <p>We used a line-cross approach and quantitative trait locus (QTL) mapping to characterize the genetic basis of twenty leaf functional/physiological, life history, and floral traits in hybrids between annualized and perennial populations of scarlet monkeyflower (<i>Mimulus cardinalis</i>).</p> <p><b>RESULTS </b></p> <p>We mapped both single and multi-trait QTLs for life history, leaf function and reproductive traits, but found no evidence of genetic co-ordination across categories. A major QTL for three leaf functional traits (thickness, photosynthetic rate, and stomatal resistance) suggests that a simple shift in leaf anatomy may be key to adaptation to seasonally dry habitats.</p> <p><b>CONCLUSIONS </b></p> <p>Our results suggest that the co-ordination of resource-acquisitive leaf physiological traits with a fast life history and more selfing mating system results from environmental selection rather than functional or genetic constraint. Independent assortment of distinct trait modules, as well as a simple genetic basis to leaf physiological traits associated with drought escape, may facilitate adaptation to changing climates. </p>
Population genetic assessment of newly discovered, extremely small populations of Xanthocyparis Vietnamensis from southwestern China
<p><i>Xanthocyparis vietnamensis</i> is an endangered species that is currently restricted to karst montane areas in southwestern China and Vietnam. This rare conifer was first recorded in 2002 from northern Vietnam and then in 2013 from Guangxi, China, yet little is known about its genetic diversity and population structure. We developed expressed sequence tag microsatellite markers (EST-SSR) for <i>X. vietnamensis</i>. Illumina HiSeq data were used to reconstruct the transcriptome of this species by de novo assembly. Based on this transcriptome, 20 SSR markers were designed and successfully amplified, and no loci with excessive null allele was detected. These polymorphic loci were then employed to access the genetic diversity and population structure of <i>X. vietnamensis</i>. As well, they could be useful in promoting sustainable forest management strategies for this species in the vulnerable karst ecosystem.</p>
Genetic disruption of synthesis pathways of Arabidopsis secondary metabolites dramatically affects root-associated nematode populations directly and via modulation of microbial communities
<p>Dataset of nematode, fungal and bacterial sequence reads of Arabidopsis roots. Dataset of fungal and bacterial sequence reads of Arabidopsis microbial suspension. DNA concentration of Arabidopsis root microbial suspension. Meloidogyne incognita J2 invasion into tomato roots. qPCR dataset of Meloidogyne hapla infection pressure into Arabidopsis roots. </p>
Genetic variation for upper thermal tolerance diminishes within and between populations with increasing acclimation temperature in Atlantic salmon
<p>Populations may counteract lasting temperature changes or recurrent extremes through plasticity or adaptation. However, it remains underexplored how outbreeding, either naturally, unintentionally, or facilitated, may modify a local response potential and whether genotype-by-environment interactions or between-trait correlations can restrict this potential. We quantified population differences and outbreeding effects, within-population genetic variation, and plasticity of these, for thermal performance proxy traits using 32 pedigreed wild, domesticated, and wild-domesticated Atlantic salmon families reared under common-garden conditions. Following exposure to ambient cold (11.6°C) or ~4- and ~8-degree warmer summer temperatures, populations differed notably for body length and critical thermal maximum (CT<sub>max</sub>) and for thermal plasticity of length, condition, and CT<sub>max</sub>, but not for haematocrit. Line-cross analysis suggested mostly additive and some dominant outbreeding effects on means and solely additive outbreeding effects on plasticity. Heritability was detected for all traits. However, with increasing acclimation temperature, differences in CT<sub>max</sub> between populations and CT<sub>max</sub> heritability diminished, and CT<sub>max</sub> breeding values re-ranked. Furthermore, CT<sub>max</sub> and body size were negatively correlated at the genetic and phenotypic levels, and there was indirect evidence for a positive correlation between growth potential and thermal performance breadth for growth. Thus, population differences (including those between wild and domesticated populations) in thermal performance and plasticity may present a genetic resource in addition to the within-population genetic variance to facilitate, or impede, thermal adaptation. However, unfavourable genotype-by-environment interactions and negative between-trait correlations may generally hamper joint evolution in response to increase in average temperature and temporary extremes.</p>
Fig. 1 in Low Genetic Variability In The Recovering Urban Banded Leaf Monkey Population Of Singapore
Fig. 1. Distribution of Presbytis femoralis.
Fig. 35 in Hybridization Among Western Whiptail Lizards (Cnemidophorus Tigris) In Southwestern New Mexico: Population Genetics, Morphology, And Ecology In Three Contact Zones
Fig. 35. Ventral views of the same lizards arranged in the same sequence as in figure 34.
Fig. 3. The contact region. Numbers designate collecting sites. Compare with figure 49 in Hybridization Among Western Whiptail Lizards (Cnemidophorus Tigris) In Southwestern New Mexico: Population Genetics, Morphology, And Ecology In Three Contact Zones
Fig. 3. The contact region. Numbers designate collecting sites. Compare with figure 49.
Figure 4 in Population genetic structure and demographic history of the Chinese endemic Mongoloniscus sinensis (Dollfus, 1901) (Isopoda: Oniscidea)
Figure 4. Pairwise mismatch distributions for six derived clades.
Figure 1 in Genetic diversity, population structure and demographic history of Dugesia japonica in Taihang Mountains
Figure 1. Geographical distribution of Dugesia japonica populations sampled in Taihang Mountains.
pgHMA: Application of the Heteroduplex mobility assay analysis in phylogenetics and population genetics
<p><span><span><span><span><span><span><span><span><span><span><span>The Heteroduplex mobility assay (HMA) has proven to be a robust tool for the detection of genetic variation. Here, we describe a simple and rapid application of the HMA by microfluidic capillary electrophoresis, for phylogenetics and population genetic analyses (pgHMA). We show how commonly applied techniques in phylogenetics and population genetics have equivalents with pgHMA: phylogenetic reconstruction with bootstrapping, skyline plots, and mismatch distribution analysis. We assess the performance and accuracy of pgHMA by comparing the results obtained against those obtained using standard methods of analyses applied to sequencing data. The resulting comparisons demonstrate that: (1) there is a significant linear relationship (R = 0.992) between heteroduplex mobility and genetic distance; (2) phylogenetic trees obtained by HMA and nucleotide sequences present nearly identical topologies; (3) clades with high pgHMA parametric bootstrap support also have high bootstrap support on nucleotide phylogenies; (4) skyline plots estimated from the UPGMA trees of HMA and Bayesian trees of nucleotide data reveal similar trends, especially for the median trend estimate of effective population size; and (5) optimized mismatch distributions of HMA are closely fitted to the mismatch distributions of nucleotide sequences. In summary, pgHMA is an easily-applied method for approximating phylogenetic diversity and population trends.</span></span></span></span></span></span></span></span></span></span></span></p>
Crossing design shapes patterns of genetic variation in synthetic recombinant populations of Saccharomyces cerevisiae
<p>"Synthetic recombinant" populations have emerged as a useful tool for dissecting the genetics of complex traits. They can be used to derive inbred lines for fine QTL mapping, or the populations themselves can be sampled for experimental evolution. In latter application, investigators generally value maximizing genetic variation in constructed populations. This is because in evolution experiments initiated from such populations, adaptation is primarily fueled by standing genetic variation. Despite this reality, little has been done to systematically evaluate how different methods of constructing synthetic populations shape initial patterns of variation. Here we seek to address this issue by comparing outcomes in synthetic recombinant <i>Saccharomyces cerevisiae</i> populations<i> </i>created using one of two strategies: pairwise crossing of isogenic strains or simple mixing of strains in equal proportion. We also explore the impact of the varying the number of parental strains. We find that more genetic variation is initially present and maintained when population construction includes a round of pairwise crossing. As perhaps expected, we also observe that increasing the number of parental strains typically increases genetic diversity. In summary, we suggest that when constructing populations for use in evolution experiments, simply mixing founder strains in equal proportion may limit the adaptive potential.</p>
Strong population genetic structure and cryptic diversity in the Florida bonneted bat (Eumops floridanus)
<p>Knowledge of genetic structure is essential for the long-term management and conservation of endangered species. We report the results from a genetic examination of the federally endangered Florida bonneted bat (<i>Eumops floridanus</i>) sampled from its range in southern Florida, USA. Bonneted bats are primarily found in four regions separated by approximately 100 to 250 kms, including three western natural areas (BW, PC, and CC) and one urban population on the east coast [Miami-Dade County (MD)]. We used 22 microsatellite loci and cytochrome <i>b</i> sequences to assess the extent of connectivity and levels of genetic diversity. Regional populations were highly differentiated (<i>F</i><sub>ST</sub> = 0.178) and model-based and multivariate analyses showed that MD was the most distinct among pairwise comparisons. Regional populations are small (i.e., <i>N<sub>e</sub></i><sub> </sub>< 100) but demographically stable. Estimates of contemporary migration and historic gene flow suggest that regional populations do not frequently exchange migrants, but simulations suggest that the divergence among western regions is likely a result of recent genetic drift rather than long-term isolation. Significantly, mitochondrial DNA revealed that haplotypes from MD were similar or shared with those recognized as <i>Eumops ferox</i> from Cuba and Jamaica, and divergent (1.5%) from the remainder of bonneted bats in Florida. Our data support the management of each of the four populations as distinct population segments, and that BW, PC and CC combined are on an independent evolutionary trajectory from bats in MD. Critically, bonneted bats in Florida appear to harbor cryptic diversity that will require a reassessment of their taxonomy.</p>
Population genetics under the Massenerhebung effect: the influence of topography on the demography of Acer morrisonense (Sapindaceae)
<p><span>Aim: </span><span><span>The Massenerhebung effect (Mass elevation effect) refers to heat or wind-driven altitudinal distribution patterns of temperature-dependent parameters among massifs with narrower range and lower elevation around peripheral and isolated mountains compared to core and continuous ones. Although common in ecology, this effect is rarely discussed in population genetics. Here, we use genetic markers to reveal population genetic patterns and also test the mountain- and sky-barrier hypotheses relevant to the Massenerhebung distribution pattern of <i>Acer morrisonense</i> in Taiwan's rugged topography and varied local climates.</span></span></p> <p><span>Location: </span><span><span>The alpine and cloud forest of Taiwan. </span></span></p> <p><span>Taxon: </span><span><i>Acer morrisonense </i>Hayata</span></p> <p><span>Methods: </span><span><span>Two chloroplast DNA (cpDNA) fragments and 17 <span>expressed sequence tag-simple sequence repeat (</span>EST-SSR) loci respectively from 200 and 286 individuals were used to elucidate the phylogeographic pattern of pollen and seed dispersal of <i>A. morrisonense</i>. These data were combined with ecological niche modeling (ENM) to infer distribution range shifts and refugia. We also correlated the genetic-divergence indices with spatial factors to clarify latitudinal and altitudinal effects on genetic diversity.</span></span></p> <p><span>Results: </span><span><span>The incongruent phylogeographic patterns of genetic distributions between nuclear and cpDNA markers indicate unhindered pollen flow but spatially constrained seed dispersal. Taken together with ENM, the genetic pattern further reflects historical colonization from central-mountain refugia to edges since the Holocene. The Massenerhebung reduces the gene flow by the surrounding mountains and also causes lower genetic diversity compared to central alpine populations.</span></span></p> <p><span>Main conclusions</span>: This study is the first to reveal the influence of Massenerhebung effect on cpDNA genetic structure of montane trees and reflect the spatial trends of seed dispersal. This population genetic pattern can also be attributed to the demography-related range shifts with paleoclimate fluctuations under complex mountain topography, supporting the mountain-barrier hypothesis. The results have important implications for conserving the genetic diversity of species with a wide altitudinal distribution range.</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.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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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.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.