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5,538 results for “Population data”
Data from: Mannose-binding lectin gene polymorphisms in the East Siberia and Russian Arctic populations
<p><b>Background:</b> Mannose-binding lectin (MBL) encoded by <i>MBL2</i> gene is a protein with the ability to form carbohydrate complexes with microbial wall promoting their subsequent elimination. Genetically determined levels of MBL can modify the risk and clinical characteristics of many infectious diseases. The frequency of <i>MBL2</i> genotypes exhibits significant population differences. The data on the distribution of <i>MBL2</i> genotypes among the aborigines of the Russian Arctic territories have not yet been published.</p> <p><b>Methods:</b> A total of 880 <a name="_Hlk41162363">specimens of </a><a name="_Hlk41162353">dried blood spots </a>of the newborns were genotyped. The newborns represented four populations: <a name="_Hlk28526418">Nenets, Dolgan-Nganasans</a>, Mixed <a name="_Hlk28526407">aboriginal population</a>, and Russians (<a name="_Hlk28526350">Caucasians</a>, Krasnoyarsk). Six polymorphisms of the <i>MBL2</i> gene were studied: rs11003125, rs7096206, rs7095891, rs5030737, rs1800450, and rs1800451.</p> <p><b>Results:</b> The frequency of the combined rare O allele (composed of the coding region variants rs5030737, rs1800450, and rs1800451) in the homozygous state was significantly higher in Russians: 10% vs 2% in Nenets and 1% in Dolgan-Nganosans (p<0.001 for Russians vs other populations). The frequency of the high-producing haplotype (HYPA) was 35.4% in the Russian newborns, in keeping with European populations (27-33%); 64% for Nenets and 56% for Dolgan-Nganasans, similar to the estimates obtained for Eskimos and North Amerinds (64-81%).</p> <p><b>Conclusion: </b>Our study results are in line with the hypothesis that human evolution has been moving in the direction of accumulation of the genotypes associated with low activity of the lectin complement activation pathway because of the prevalence of some intracellular infections such as tuberculosis, whereby low MBL activity may have a protective effect.</p>
Data from: Stage- and thermal-specific genetic architecture for preadult viability in natural populations of Drosophila melanogaster
Studying the processes affecting variation for preadult viability is essential to understand the evolutionary trajectories followed by natural populations. This task requires focusing on the complex nature of the phenotype-genotype relationship by taking into account usually neglected aspects of the phenotype and recognizing the modularity between different ontogenetic stages. Here we describe phenotypic variability for viability during the larval and pupal stages in lines derived from three natural populations of Drosophila melanogaster, as well as the variability for phenotypic plasticity and canalization at two different rearing temperatures. The observed phenotypic differences between populations can be attributed both to adaptation to environmental conditions and lack of gene flow between them. According to our results, different aspects of the phenotype (means, plasticity, canalization, plasticity of canalization) are affected by different genetic bases underlying changes in viability in a stage- and environment-specific manner. These findings explain the generalized maintenance of genetic variability for this fitness trait.
Data from: Friends and Family: a software program for identification of unrelated individuals from molecular marker data. And from: Genetic diversity, relatedness and inbreeding of ranched and fragmented Cape buffalo populations in southern Africa
The identification of related and unrelated individuals from molecular marker data is often difficult, particularly when no pedigree information is available and the data set is large. High levels of relatedness or inbreeding can influence genotype frequencies and thus genetic marker evaluation, as well as the accurate inference of hidden genetic structure. Identification of related and unrelated individuals is also important in breeding programmes, to inform decisions about breeding pairs and translocations. We present Friends and Family, a Windows executable program with a graphical user interface that identifies unrelated individuals from a pairwise relatedness matrix or table generated in programs such as COANCESTRY and GenAlEx. Friends and Family outputs a list of samples that are all unrelated to each other, based on a user-defined relatedness cut-off value. This unrelated data set can be used in downstream analyses, such as marker evaluation or inference of genetic structure. The results can be compared to that of the full data set to determine the effect related individuals have on the analyses. We demonstrate one of the applications of the program: how the removal of related individuals altered the Hardy-Weinberg equilibrium test outcome for microsatellite markers in an empirical data set. Friends and Family can be obtained from https://github.com/DeondeJager/Friends-and-Family.
Data from: Risk of extinction of a unique skate population due to predation by a recovering marine mammal
Benefitting from reduced harvesting and an end to culling, many marine mammals are now recovering from past overexploitation. These recoveries represent important conservation successes but present a serious conservation problem when the recovering mammals are predators of species of conservation concern. Here we examine the role of predation by recovering grey seals (Halichoerus grypus) in the near-extinction of a unique skate population in the southern Gulf of St. Lawrence (sGSL) in Atlantic Canada. Winter skate (Leucoraja ocellata) in the sGSL are distinct from winter skate elsewhere and may represent an endemic species. Their adult abundance has declined by 98% since 1980 and these skates are now detectable in only a small fraction of their former range. Population modelling indicates that the ongoing collapse of this population is due to increases in the natural mortality of adults. Based on model projections this population would be extinct by mid-century if its current rate of productivity were to persist. A second population model incorporated predation by grey seals. Model estimates of skate consumption by seals were consistent with historical and recent estimates of the contribution of skates to grey seal diets. The estimated consumption accounted for the increases in the natural mortality of adult skates. A Type III functional response for grey seals preying on winter skate emerged from the model results. This indicates that, when skate abundance is very low, grey seals are expected to switch to alternate prey, resulting in declines in the mortality of skates due to predation. Consequently, contrary to projections at current productivity, winter skate are expected to be trapped at very low abundance in a "predator pit" instead of declining to extinction. Nonetheless, extinction risk would remain very high at the very small population size in the predator pit. Our results emphasize the need for an ecosystem-based approach to the management of living resources in this ecosystem.
Data from: Mining the stable quantitative trait loci for agronomic traits in wheat (Triticum aestivum L.) based on an introgression line population
<p><span><span><b>Background</b>: Human demand for wheat will continue to increase together with the continuous global population growth. Agronomic traits in wheat are susceptible to environmental conditions. Therefore, in breeding practice, priority is given to QTLs of agronomic traits that can be stably detected across multiple environments and over many years.</span></span></p> <p><span><span><b>Results: </b>In this study, QTL analysis was conducted for eight agronomic traits using an introgression line population across eight environments (drought stressed and well-watered) for five years. In total, 44 additive QTLs for the above agronomic traits were detected on 15 chromosomes. Among these, <i>qPH-6A</i>, <i>qHD-1A</i>, <i>qSL-2A</i>, <i>qHD-2D</i> and<i> qSL-6A</i> were detected across seven, six, five, five and four environments, respectively. The means in the phenotypic variation explained by these five QTLs were 12.26%, 9.51%, 7.77%, 7.23%, and 8.49%, respectively. </span></span></p> <p><b>Conclusions: </b>We identified five stable QTLs, which includes <i>qPH-6A</i>, <i>qHD-1A</i>, <i>qSL-2A</i>, <i>qHD-2D</i> and<i> qSL-6A</i>. They play a critical role in wheat agronomic traits. One of the dwarf genes<i> Rht14</i>, <i>Rht16</i>, <i>Rht18</i> and <i>Rht25</i> on chromosome 6A might be the candidate gene for <i>qPH-6A</i>. The <i>qHD-1A</i> and <i>qHD-2D</i> were novel stable QTLs for heading date and they differed from known vernalization genes, photoperiod genes and earliness per se genes.</p>
Data from: Population-specific effect of Wolbachia on the cost of fungal infection in spider mites
<p>Many studies have revealed the ability of the endosymbiotic bacterium <i>Wolbachia </i>to protect its arthropod hosts against diverse pathogens. However, as <i>Wolbachia </i>may also increase the susceptibility of its host to infection, predicting the outcome of a particular <i>Wolbachia</i>-host-pathogen interaction remains elusive. Yet, understanding such interactions and their eco-evolutionary consequences is crucial for disease and pest control strategies. Moreover, how natural <i>Wolbachia </i>infections affectartificially introduced pathogens for biocontrol has never been studied. <i>Tetranychus urticae </i>spider mites are herbivorous crop pests, causing severe damage on numerous economically important crops. Due to the rapid evolution of pesticide resistance, biological control strategies using entomopathogenic fungi are being developed. However, although spider mites are infected with various <i>Wolbachia </i>strains worldwide, whether this endosymbiont protects them from fungi is as yet unknown. Here, we compared the survival of two populations, treated with antibiotics or naturally harbouring different <i>Wolbachia </i>strains, after exposure to the fungal biocontrol agents <i>Metarhizium brunneum </i>and <i>Beauveria bassiana</i>. To control for potential effects of the bacterial community of spider mites, we also compared the susceptibility of two populations naturally uninfected by <i>Wolbachia</i>, treated with antibiotics or not. In one population, <i>Wolbachia</i>-infected mites had a better survival than uninfected ones in absence of fungi but not in their presence, whereas in the other population <i>Wolbachia </i>increased the mortality induced by <i>B. bassiana</i>. In one naturally <i>Wolbachia</i>-uninfected populations, the antibiotic treatment increased the susceptibility of spider mites to <i>M. brunneum</i>, but it had no effect in the other treatments. These results suggest that natural <i>Wolbachia </i>infections may not hamper and may even improve the success of biological control using entomopathogenic fungi. However, they also draw caution on the generalization of such effects, given the complexity of within-host pathogens interaction and the potential eco-evolutionary consequences of the use of biocontrol agents for <i>Wolbachia</i>-host associations.</p>
Data from: The geographic mosaic of arms race coevolution is closely matched to prey population structure
<p>Reciprocal adaptation is the hallmark of arms race coevolution. Local coadaptation between natural enemies should generate a geographic mosaic pattern where both species have roughly matched abilities across their shared range. However, mosaic variation in ecologically relevant traits can also arise from processes unrelated to reciprocal selection, such as population structure or local environmental conditions. We tested whether these alternative processes can account for trait variation in the geographic mosaic of arms race coevolution between resistant garter snakes (<i>Thamnophis sirtalis</i>) and toxic newts (<i>Taricha granulosa</i>). We found that predator resistance and prey toxin levels are functionally matched in co-occurring populations, suggesting that mosaic variation in the armaments of both species results from the local pressures of reciprocal selection. By the same token, phenotypic and genetic variation in snake resistance deviates from neutral expectations of population genetic differentiation, showing a clear signature of adaptation to local toxin levels in newts. Contrastingly, newt toxin levels are best predicted by genetic differentiation among newt populations, and to a lesser extent, by the local environment and snake resistance. Exaggerated armaments suggest that coevolution occurs in certain hotspots, but prey population structure seems to be of particular influence on local phenotypic variation in both species throughout the geographic mosaic. Our results imply that processes other than reciprocal selection, like historical biogeography and environmental pressures, represent an important source of variation in the geographic mosaic of coevolution. Such a pattern supports the role of "trait remixing" in the geographic mosaic theory, the process by which non-adaptive forces dictate spatial variation in the interactions among species.</p>
Data from: Phenotypic, ecological and genomic variation in common bully (Gobiomorphus cotidianus) populations along depth gradients in New Zealand's Southern Great Lakes
<p>Depth gradients in lakes are often key drivers of population divergence and speciation in fishes. New Zealand has many deep lakes but no known profundal specialist fishes or cases of intralacustrine speciation. We sampled a native benthic fish, the common bully, from 5–90 m depth in four South Island lakes, to test for morphological, ecological, or genetic differentiation associated with depth. Deeper fish consistently had narrower bodies, while other morphological traits showed variable relationships with depth. Carbon and nitrogen stable isotope values of fish increased with depth, largely tracking isotopic trends with depth of benthic invertebrate prey. Genotyping-by-sequencing showed some genome-wide differentiation between two of the lakes, but no evidence for within-lake genetic structuring along depth gradients. These results indicate that individual bullies associate with shallower or deeper habitats within their lifetimes, but we found no evidence of progress toward genetic divergence within lakes. The apparent lack of intralacustrine genetic divergence in New Zealand's fishes may be explained by a combination of environmental factors and constraints intrinsic to its marine-derived freshwater fish fauna.</p>
Data from: Patterns of genomic divergence and signals of selection in sympatric and allopatric northeastern Pacific and Sea of Cortez populations of the sargo (Anisotremus davidsonii) and longjaw mudsucker (Gillichthys mirabilis)
<p><span><span>Studying how isolation can impact population divergence and adaptation in co-distributed species can bring us closer to understanding how landscapes affect biodiversity. The Sargo, </span><i><span>Anisotremus davidsonii </span></i><span>(Haemulidae), and the Longjaw mudsucker, </span><i><span>Gillichthys mirabilis </span></i><span>(Gobiidae), offer a notable framework to study such mechanisms as their Pacific populations cross phylogeographic breaks at Point Conception, California, USA, and Punta Eugenia, Mexico, and are separated to those in the Sea of Cortez by the Baja California peninsula. Here, thousands of loci are genotyped from 48 Sargos and 73 mudsuckers using RADseq to characterize overall genomic divergence, and search for common patterns of putatively neutral and non-neutral structure based on outlier loci among populations with hypothesized different levels of isolation.</span></span><span> </span><span><span>We further search for parallels between population divergence and the total proportion of outliers, outlier </span></span><span><span>F</span><sub><span>ST</span></sub></span><span><span> distribution, and </span></span><span><span>the proportion of outliers matching coding regions in GenBank. This dataset consists of demultiplexed sequence data from Sbf1 single digest RADseq analysis of poulations of both fish species throughout their distributions. </span></span></p>
Data from: Hidden genetic variance contributes to increase the short-term adaptive potential of selfing populations
Standing genetic variation is considered a major contributor to the adaptive potential of species. The low heritable genetic variation observed in self-fertilising populations has led to the hypothesis that species with this mating system would be less likely to adapt. However, a non-negligible amount of cryptic genetic variation for polygenic traits, accumulated through negative linkage disequilibrium, could prove to be an important source of standing variation in self-fertilising species. To test this hypothesis we simulated populations under stabilizing selection subjected to an environmental change. We demonstrate that, when the mutation rate is high (but realistic), selfing populations are better able to store genetic variance than outcrossing populations through genetic associations, notably due to the reduced effective recombination rate associated with predominant selfing. Following an environmental shift, this diversity can be partially remobilized, which increases the additive variance and adaptive potential of predominantly (but not completely) selfing populations. In such conditions, despite initially lower observed genetic variance, selfing populations adapt as readily as outcrossing ones within a few generations. For low mutation rates, purifying selection impedes the storage of diversity through genetic associations, in which case, as previously predicted, the lower genetic variance of selfing populations results in lower adaptability compared to their outcrossing counterparts. The population size and the mutation rate are the main parameters to consider, as they are the best predictors of the amount of stored diversity in selfing populations. Our results and their impact on our knowledge of adaptation under high selfing rates are discussed.
Data from: Characterizing population and individual migration patterns among native and restored bighorn sheep (Ovis canadensis)
Migration evolved as a behavior to enhance fitness through exploiting spatially and temporally variable resources and avoiding predation or other threats. Globally, landscape alterations have resulted in declines to migratory populations across taxa. Given the long time periods over which migrations evolved in native systems, it is unlikely restored populations embody the same migratory complexity that existed before population reductions or regional extirpation. 2. We used GPS location data collected from 209 female bighorn sheep (Ovis canadensis) to characterize population and individual migration patterns along elevational and geographic continuums for 18 populations of bighorn sheep with different management histories (i.e., restored, augmented, and native) across the western United States. 3. Individuals with resident behaviors were present in all management histories. Elevational migrations were the most common population-level migratory behavior. There were notable differences in the degree of individual variation within a population across the three management histories. Relative to native populations, restored and augmented populations had less variation among individuals with respect to elevational and geographic migration distances. Differences in migratory behavior were most pronounced for geographic distances, where the majority of native populations had a range of variation that was 2 to 4 times greater than restored or augmented populations. 4. Synthesis and applications. Migrations within native populations include a variety of patterns that translocation efforts have not been able to fully recreate within restored and augmented populations. Theoretical and empirical research has highlighted the benefits of migratory diversity in promoting resilience and population stability. Limited migratory diversity may serve as an additional factor limiting demographic performance and range expansion. We suggest preserving native systems with intact migratory portfolios and a more nuanced approach to restoration and augmentation in which source populations are identified based on a suite of criteria that includes matching migratory patterns of source populations with local landscape attributes.
Data from: eDNA concentration, population size structure, and mark-recapture data
<p>Organism abundance is a critical parameter in ecology, but its estimation is often challenging. Approaches utilizing eDNA to indirectly estimate abundance have recently generated substantial interest. However, preliminary correlations observed between eDNA concentration and abundance in nature are typically moderate in strength with significant unexplained variation. Here we apply a novel approach to integrate allometric scaling coefficients into models of eDNA concentration and organism abundance. We hypothesize that eDNA particle production scales non-linearly with mass, with scaling coefficients < 1. Wild populations often exhibit substantial variation in individual body size distributions; we therefore predict that the distribution of mass across individuals within a population will influence population-level eDNA production rates. To test our hypothesis, we collected standardized body size distribution and mark-recapture abundance data using whole-lake experiments involving nine populations of brook trout. We correlated eDNA concentration with three metrics of abundance: density (individuals/ha), biomass (kg/ha), and allometrically scaled mass (ASM) (∑(individual mass<sup>0.73</sup>)/ha). Density and biomass were both significantly positively correlated with eDNA concentration (adj. r<sup>2</sup> = 0.59 and 0.63, respectively), but ASM exhibited improved model fit (adj. r<sup>2</sup> = 0.78). We also demonstrate how estimates of ASM derived from eDNA samples in 'unknown' systems can be converted to biomass or density estimates with additional size structure data. Future experiments should empirically validate allometric scaling coefficients for eDNA production, particularly where substantial intraspecific size distribution variation exists. Incorporating allometric scaling may improve predictive models to the extent that eDNA concentration may become a reliable indicator of abundance in nature.</p>
Data from: Temporal variation in spatial genetic structure during population outbreaks: distinguishing among different potential drivers of spatial synchrony
Spatial synchrony is a common characteristic of spatio-temporal population dynamics across many taxa. While it is known that both dispersal and spatially autocorrelated environmental variation (i.e., the Moran effect) can synchronize populations, the relative contributions of each, and how they interact, is generally unknown. Distinguishing these mechanisms and their effects on synchrony can help us to better understand spatial population dynamics, design conservation and management strategies, and predict climate change impacts. Population genetic data can be used to tease apart these two processes as the spatio-temporal genetic patterns they create are expected to be different. A challenge, however, is that genetic data are often collected at a single point in time, which may introduce context-specific bias. Spatio-temporal sampling strategies can be used to reduce bias and to improve our characterization of the drivers of spatial synchrony. Using spatio-temporal analyses of genotypic data, our objective was to identify the relative support for these two mechanisms to the spatial synchrony in population dynamics of the irruptive forest insect pest, the spruce budworm (Choristoneura fumiferana), in Quebec (Canada). AMOVA, cluster analysis, isolation by distance and sPCA were used to characterize spatio-temporal genomic variation using 1370 SBW larvae sampled over four years (2012-2015) and genotyped at 3,562 SNP loci. We found evidence of overall weak spatial genetic structure that decreased from 2012 to 2015 and a genetic diversity homogenization among the sites. We also found genetic evidence of a long-distance dispersal event over > 140 km. These results indicate that dispersal is the key mechanism involved in driving population synchrony of the outbreak. Early intervention management strategies that aim to control source populations have the potential to be effective through limiting dispersal. However, the timing of such interventions relative to outbreak progression is likely to influence their probability of success.
Data from: Phylogenetic and functional distinctiveness explain alien plant population responses to competition
Several invasion hypotheses predict a positive association between phylogenetic and functional distinctiveness of aliens and their performance, leading to the idea that distinct aliens compete less with their resident communities. However, synthetic pattern relationships between distinctiveness and alien performance and direct tests of competition as the driving mechanism have not been forthcoming. This is likely because different patterns are observed at different spatial grains, because functional trait and phylogenetic information are often incomplete, and due to the need for competition experiments that measure demographic responses across a variety of alien species that vary in their distinctiveness. We conduct a competitor removal experiment and parameterize matrix population and integral projection models for 14 alien plant species. More novel aliens compete less strongly with co-occurring species in their community, but these results dissipate at a larger spatial grain of investigation. Further, we find that functional traits used in conjunction with phylogeny improve our ability to explain competitive responses. Our investigation shows that competition is an important mechanism underlying the differential success of alien species.
Data from: Variation in thermal traits describing sex determination and development in Western Australian sea turtle populations
<p>Both the development rate and sex of sea turtle embryos depend on incubation temperature, as all species are ectotherms and show temperature-dependent sex determination (TSD). Theory predicts that selection should act on populations to optimise developmental times and primary sex ratios. In this study, we use a consistent methodology to measure development rates and model the reaction norm that defines TSD in three populations of flatback turtles (<i>Natator depressus) </i>and two populations of green turtles (<i>Chelonia mydas</i><i>) </i>that nest in Western Australia. We show that development rates vary between and within species, likely reflecting adaptation to local beach microclimates. Similarly, the parameters that define the TSD reaction norm vary between the two species, and among <i>N. depressus</i> populations, with pivotal temperatures (T<sub>PIV</sub>) varying by 1.5 °C (29.6 – 31.1 °C), and the transitional ranges of temperatures (TRT) varying by 1.4 – 3.3 °C. In contrast, we found a similar T<sub>PIV</sub> for the two <i>C. mydas </i>populations, but a wider TRT at the northernmost tropical rookery. Our findings support the view that thermal parameters in geographically-separated populations of sea turtles are broadly similar, but the variation we describe will be highly relevant for predicting how populations will respond to climate change.</p>
Data from: Genetic population structure and variation at phenology-related loci in anadromous Arctic char (Salvelinus alpinus)
The Arctic will be especially affected by climate change, resulting in altered seasonal timing. Anadromous Arctic char (Salvelinus alpinus) is strongly influenced by sea surface temperature (SST) delimiting time periods available for foraging in the sea. Recent studies of salmonid species have shown variation at phenology-related loci associated with timing of migration and spawning. We contrasted genetic population structure at 53 SNPs versus four phenology-related loci among 15 anadromous Arctic char populations from Western Greenland and three outgroup populations. Among anadromous populations, the time period available for foraging at sea (> 2oC) ranges from a few weeks to several months, motivating two research questions: 1) Is population structure compatible with possibilities for evolutionary rescue of anadromous populations during climate change? 2) Does selection associated with latitude or SST regimes act on phenology-related loci? In Western Greenland, strong isolation-by-distance at SNPs was observed and spatial autocorrelation analysis showed genetic patch size up to 450 km, documenting contingency and gene flow among populations. Outlier tests provided no evidence for selection at phenology-related loci. However, in Western Greenland, mean allele length at OtsClock1b was positively associated with the time of year when SST first exceeded 2oC and negatively associated with duration of the period where SST exceeded 2oC. This is consistent with local adaptation for making full use of the time period available for foraging in the sea. Current adaptation may become maladaptive under climate change, but long-distance connectivity of anadromous populations could redistribute adaptive variation across populations and lead to evolutionary rescue.
Data from: Seasonal shifts in feeding patterns: individual and population realized specialization in a high Arctic fish
Species with a broad and flexible diet may be at an advantage in a rapidly changing environment such as in today's Arctic ecosystems. Polar cod (Boreogadus saida), an abundant and ecologically important circumpolar Arctic fish, is often described as a zooplankton generalist feeder, which suggests that it may cope successfully with changes in prey composition. This description is justified based on the relatively broad diet of polar cod across sites and seasons. In this case study, we used polar cod dietary data from fall and winter and from two distinct environments, dominated either by Arctic or Atlantic water masses in Svalbard. Our results point to the importance of time and space when drawing conclusions on dietary plasticity and degree of specialization. Polar cod diet differed significantly between fall and the winter and between Arctic and Atlantic domains. Polar cod from Arctic domains displayed a strong realized population specialization on T.libellua in fall, and the larger dietary niche width observed in the winter was the product of realized individual specialization, with increased feeding on fish prey. Overall, we did not observe a generalized feeding behavior. If dietary niche width is to inform conservation management, we argue it must be recognized that populations from a single species may adopt seasonally contrasting degrees of dietary specialization and that these populations may differ in their vulnerability to climate-induced changes in prey community composition.
Data from: Environmental variables associated with Nothophaeocryptopus gaeumannii population structure and Swiss needle cast severity in Western Oregon and Washington
The environment has a strong influence on the abundance and distribution of plant pathogenic organisms, and plays a major role in the causation of plant disease. Climatological factors may also alter the dynamics of the interactions between plant pathogens and their hosts. Nothophaeocryptopus (=Phaeocryptopus) gaeumannii, the causal agent of Swiss needle cast (SNC) of Douglas-fir, is endemic to western North America where it exists as two sympatric, reproductively isolated lineages. The abundance of this fungus and the severity of SNC are strongly influenced by climate. We used statistical and population genetic analyses to examine relationships between environment, pathogen population structure, and SNC severity. Although N. gaeumannii Lineage 2 in western Oregon and Washington was most abundant where SNC symptoms were most severe, we did not detect a significant relationship between Lineage 2 and disease severity. Warmer winter temperatures were inversely correlated with foliage retention (AFR) and positively correlated with the relative abundance of Lineage 2 (PL2). However when distance inland, which was strongly correlated with both AFR and PL2, was included in the model, there was no significant relationship between Lineage 2 and AFR. Spring/early summer dew point temperatures also were positively associated with total N. gaeumannii abundance (colonization index (CI)), and inversely correlated with AFR. Warmer summer mean temperatures were associated with lower CI and higher AFR. Our results suggest that the two lineages have overlapping environmental optima, but slightly different tolerance ranges. Lineage 2 was absent from more inland sites where winters are colder and summers are warm and dry, while Lineage 1 occurred at most sites across an environmental gradient suggesting broader environmental tolerance. These relationships suggest that climate influences the abundance and distribution of this ecologically important plant pathogen, and may have played a role in the evolutionary divergence of these two cryptic fungal lineages.
Data from: The upper thermal tolerance for a Texas population of the hairy maggot blow fly Chrysomya rufifacies Macquart (Diptera: Calliphoridae)
<p>The hairy maggot blow fly (<i>Chrysomya rufifacies</i>: Macquart) is an invasive necrophagous fly found throughout the continental United States. <i>Chrysomya</i> <i>rufifacies</i> is of medical/veterinary, forensic, and ecological importance due to its ability to cause myiasis, colonize human remains, and displace native Diptera. However, little is known about their upper thermal tolerance, which could be used to better predict their invasion potential.</p> <p>We investigated the upper thermal tolerance of <i>C. rufifacies </i>exposed to different temperatures (20 – 45°C), times (1 – 6 h), and nutrients (no food or water, water only, or a food-water mixture) for both sexes and two age ranges (young = 6-8, old = 9-11 days post pupal emergence).</p> <p>As temperature or duration increased, the probability of knockdown increased (0 – 100% at 20 and 45°C and from 41 – 75% at 1 and 6 h), while the probability of survival decreased (99 – 2% at 20 and 45°C and from 75 – 28% at 1 and 6 h). The availability of nutrients increased thermal tolerance at moderate temperatures (40 and 42°C). Female flies were more thermally tolerant than males (probability of knockdown = 49% vs 58%; probability of survival = 58 % vs 46%). Thermal tolerance did not differ by age.</p> <p>These data reveal details about the upper thermal tolerance for a single population of <i>C. rufifacies</i>, and suggest that environmental and organismal factors ought to be considered in order to make meaningful predictions about the invasion potential of <i>C. rufifacies </i>in North America.</p>
Data from: Genotyping-in-Thousands by sequencing reveals marked population structure in Western Rattlesnakes to inform conservation status
<p>Delineation of units below the species level is critical for prioritizing conservation actions for species at-risk. Genetic studies play an important role in characterizing patterns of population connectivity and diversity to inform the designation of conservation units, especially for populations that are geographically isolated. The northernmost range margin of Western Rattlesnakes (<em>Crotalus oreganus</em>) occurs in British Columbia, Canada, where it is federally classified as threatened and restricted to five geographic regions. In these areas, Western Rattlesnakes hibernate (den) communally, raising questions about connectivity within and between den complexes. At present, Western Rattlesnake conservation efforts are hindered by a complete lack of information on genetic structure and degree of isolation at multiple scales, from the den to the regional level. To fill this knowledge gap, we used Genotyping-in-Thousands by sequencing (GT-seq) to genotype an optimized panel of 362 single nucleotide polymorphisms (SNPs) from individual samples (n = 461) collected across the snake's distribution in western Canada and neighboring Washington (USA). Hierarchical STRUCTURE analyses found evidence for population structure within and among the five geographic regions in BC, as well as in Washington. Within these regions, 11 genetically distinct complexes of dens were identified, with some regions having multiple complexes. No significant pattern of isolation-by-distance and generally low levels of migration were detected among den complexes across regions. Additionally, snakes within dens generally were more related than those among den complexes within a region, indicating limited movement. Overall, our results suggest that the single, recognized designatable unit for Western Rattlesnakes in Canada should be re-assessed to proactively focus conservation efforts on preserving total genetic variation detected range wide. More broadly, our study demonstrates a novel application of GT-seq for investigating patterns of diversity in wild populations at multiple scales to better inform conservation management.</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.
International Brain Laboratory public data
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.