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732 results for “population variation”
Linking spatial variations in life-history traits to environmental conditions across American black bear populations
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Detection and analysis of complex structural variation in human genomes across populations and in brains of donors with psychiatric disorders
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To rise to temperature: Variation in temperature effects within and among populations
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Mesoscale variation in fish populations in two small Appalachian streams (fish population data) at the Coweeta Hydrologic Laboratory in 1996
We examined the reach-scale distributions of three fish species to determine which biotic and abiotic factors are influential in the fishes distributions.
Mesoscale variation in fish populations in two small Appalachian streams (light data) at the Coweeta Hydrologic Laboratory in 1996
We examined the reach-scale distribution of macroinvertebrates to determine if photosynthetically active radiation (PAR) is influential in the distribution of the macroinvertebrates and macroinvertebrate functional feeding groups.
Data from: Candidate gene SNP variation in floodplain populations of pedunculate oak (Quercus robur L.) near the species' southern range margin: weak differentiation yet distinct associations with water availability
<p>Populations residing near species' low-latitude range margins (LLM) often occur in warmer and drier environments than those in the core range. Thus, their genetic composition could be shaped by climatic drivers that differ from those occurring at higher latitudes, resulting in potentially adaptive variants of conservation value. Such variants could facilitate the adaptation of populations from other portions of the geographic range to similar future conditions anticipated under ongoing climate change. However, very few studies have assessed standing genetic variation at potentially adaptive loci in natural LLM populations. We investigated standing genetic variation at SNPs located within 117 candidate genes and its links to putative climatic selection pressures across 19 pedunculate oak (Quercus robur L.) populations distributed along a regional climatic gradient near the species' southern range margin in southeastern Europe. These populations are restricted to floodplain forests along large lowland rivers, whose hydric regime is undergoing significant shifts under modern rapid climate change. The populations showed very weak geographic structure, suggesting extensive genetic connectivity and gene flow or shared ancestry. We identified eight (6.2%) positive FST-outlier loci, and genotype-environment association analyses revealed consistent associations between SNP allele frequencies and several climatic variables linked to water availability. A total of 61 associations involving 37 SNPs (28.5%) from 35 annotated genes provided important insights into putative functional mechanisms in our system. Our findings provide empirical support for the role of LLM populations as sources of potentially adaptive variation that could enhance species' resilience to climate change-related pressures.</p>
Data for: Coevolution fails to maintain genetic variation in a host-parasite model with constant finite population size
<p>Coevolutionary negative frequency-dependent selection has been hypothesized to maintain genetic variation in host and parasites. <br> Despite the extensive literature pertaining to host-parasite coevolution, the dynamics of genetic variation has not been examined in a matching-alleles model (MAM) with a finite population size relative to the expectation under neutral genetic drift alone. The dynamics of the MA coevolution in an infinite population, in fact, suggests that genetic variation in these coevolving populations behaves neutrally. By comparing host heterozygosity to the expectation in a single-species model of neutral genetic drift we find that while this is also largely true in finite populations two additional phenomena arise. First, reciprocal natural selection acting on stochastic perturbations in host and pathogen allele frequencies results in a slight increase or decrease in genetic variation depending on the parameter conditions. Second, following the fixation of an allele in the parasite, selection in the MAM becomes directional, which then rapidly erodes genetic variation in the host. Hence, rather than maintain it, we find that, on average, matching-alleles coevolution depletes genetic variation.</p>
Migration trajectories of the diamondback moth Plutella xylostella in China inferred from population genomic variation
<p><span class="fontstyle01"><span><b>BACKGROUND</b></span></span><span class="fontstyle01"><span><b>:</b></span></span></p> <p><span class="fontstyle01"><span>The diamondback moth (DBM),</span></span><span class="fontstyle01"><span><i> Plutella xylostella</i></span></span><span class="fontstyle01"><span> (Lepidoptera: Plutellidae),</span></span><span class="fontstyle01"><span><i> </i></span></span><span class="fontstyle01"><span>is a notorious pest of cruciferous plants. In temperate areas, annual populations of DBM originate from adult migrants. However, the source populations and migration trajectories of immigrants remain unclear. Here, we investigated migration trajectories of DBM in China with genome-wide single nucleotide polymorphisms (SNPs) genotyped using double-digest RAD (ddRAD) sequencing. We first analyzed patterns of spatial and temporal genetic structure among southern source and northern recipient populations, then inferred migration trajectories into northern regions using discriminant analysis of principal components (DAPC), assignment tests and spatial kinship patterns.</span></span></p> <p><span class="fontstyle01"><span><b>RESULTS:</b></span></span></p> <p><span class="fontstyle01"><span>Temporal</span></span><span class="fontstyle01"><span><b> </b></span></span><span class="fontstyle01"><span>genetic differentiation among populations was low, indicating sources of </span></span><span class="fontstyle01"><span>recipient </span></span><span class="fontstyle01"><span>populations and migration trajectories are stable.</span></span><span class="fontstyle01"><span> Spatial genetic structure indicated three genetic clusters in the southern source populations. Assignment tests linked northern populations to the Sichuan cluster, and central-eastern populations to the South and Yunnan clusters, indicating that Sichuan populations are sources of northern immigrants and South and Yunnan populations are sources of central-eastern populations. First-order (full-sib) and second-order (half-sib) kin pairs were always found within populations, but about 35-40% of third-order (cousin) pairs were found in different populations. Closely related individuals in different populations were in about 35-40% of cases found at distances of 900 to 1500 km, while some were separated by over 2000 km.</span></span></p> <p><span class="fontstyle01"><span><b>CONCLUSION:</b></span></span></p> <p><span class="fontstyle01"><span>This study unravels seasonal migration patterns in the DBM. We demonstrate how careful sampling and population genomic analyses can be combined to help understand cryptic migration patterns in insects.</span></span></p>
Data from: Genomic variation, population history and within-archipelago adaptation between island bird populations
<p>Oceanic island archipelagos provide excellent models to understand evolutionary processes. Colonisation events and gene flow can interact with selection to shape genetic variation at different spatial scales. Landscape-scale variation in biotic and abiotic factors may drive fine-scale selection within islands, while long-term evolutionary processes may drive divergence between distantly related populations. Here, we examine patterns of population history and selection between recently diverged populations of the Berthelot's pipit (Anthus berthelotii), a passerine endemic to three North Atlantic archipelagos. First we use demographic trees and f3 statistics to show that genome-wide divergence across the species range is largely shaped by colonisation and bottlenecks, with evidence of very weak gene flow between populations. Then, using a genome scan approach, we identify signatures of divergent selection within-archipelagos at SNPs in genes potentially associated with craniofacial development and DNA repair. We did not detect within-archipelago selection at the same SNPs as were detected previously at broader spatial scales between archipelagos, but did identify signatures of selection at loci associated with similar biological functions. These findings suggest that similar ecological factors may repeatedly drive selection between recently separated populations, as well as at broad spatial scales across varied landscapes. </p>
Data from: Genetic wealth, population health: major histocompatibility complex variation in captive and wild ring-tailed lemurs (Lemur catta)
Across species, diversity at the major histocompatibility complex (MHC) is critical to individual disease resistance and, hence, to population health; however, MHC diversity can be reduced in small, fragmented, or isolated populations. Given the need for comparative studies of functional genetic diversity, we investigated whether MHC diversity differs between populations which are open, that is experiencing gene flow, versus populations which are closed, that is isolated from other populations. Using the endangered ring-tailed lemur (Lemur catta) as a model, we compared two populations under long-term study: a relatively "open," wild population (n = 180) derived from Bezà Mahafaly Special Reserve, Madagascar (2003–2013) and a "closed," captive population (n = 121) derived from the Duke Lemur Center (DLC, 1980–2013) and from the Indianapolis and Cincinnati Zoos (2012). For all animals, we assessed MHC-DRB diversity and, across populations, we compared the number of unique MHC-DRB alleles and their distributions. Wild individuals possessed more MHC-DRB alleles than did captive individuals, and overall, the wild population had more unique MHC-DRB alleles that were more evenly distributed than did the captive population. Despite management efforts to maintain or increase genetic diversity in the DLC population, MHC diversity remained static from 1980 to 2010. Since 2010, however, captive-breeding efforts resulted in the MHC diversity of offspring increasing to a level commensurate with that found in wild individuals. Therefore, loss of genetic diversity in lemurs, owing to small founder populations or reduced gene flow, can be mitigated by managed breeding efforts. Quantifying MHC diversity within individuals and between populations is the necessary first step to identifying potential improvements to captive management and conservation plans.
Data from: Population variation, environmental gradients, and the evolutionary ecology of plant defense against herbivory
A central tenet of plant defense theory is that adaptation to the abiotic environment sets the template for defense strategies, imposing a tradeoff between plant growth and defense. Yet, this tradeoff, commonly found among species occupying divergent resource environments, may not occur across populations of single species. We hypothesized that more favorable climates and higher levels of herbivory would lead to increases in growth and defense across plant populations. We evaluated whether plant growth and defense traits co-varied across 18 populations of showy milkweed (Asclepias speciosa) inhabiting an east-west climate gradient, spanning 25° of longitude. A suite of traits impacting defense (e.g., latex, cardenolides), growth (e.g., size), or both (e.g., SLA, trichomes) were measured in natural populations and in a common garden, allowing us to evaluate plastic and genetically based variation in these traits. In natural populations, herbivore pressure increased towards warmer sites with longer growing seasons. Growth and defense traits showed strong clinal patterns and were positively correlated. In a common garden, clines with climatic origin were only recapitulated for defense traits. Correlations between growth and defense traits were also weaker and more negative in the common garden compared to the natural populations. Thus, our data suggest that climatically favorable sites likely facilitate the evolution of greater defense at minimal costs to growth, likely because of increased resource acquisition.
Data from: Alongshore variation in barnacle populations is determined by surfzone hydrodynamics
Larvae in the coastal ocean are transported toward shore by a variety of mechanisms. Crossing the surf zone is the last step in a shoreward migration and surf zones may act as semipermeable barriers altering delivery of larvae to the shore. We related variation in the structure of intertidal barnacle populations to surfzone width (surfzone hydrodynamics proxy), wave height, alongshore wind stress (upwelling proxy), solar radiation, and latitude at 40 rocky intertidal sites from San Diego, California to the Olympic Peninsula, Washington. We measured daily settlement and weekly recruitment of barnacles at selected sites and related these measures to surfzone width. Chthamalus density varied inversely with that of Balanus, and the density of Balanus and new recruits was negatively related to solar radiation. Across the region, long-term mean wave height and an indicator of upwelling intensity and frequency did not explain variation in Balanus or new-recruit densities. Balanus and new-recruit densities, daily settlement and weekly recruitment were up to three orders of magnitude higher at sites with wide (> 50 m), more dissipative surf zones with bathymetric rip currents than at sites with narrow (< 50 m) more reflective surf zones. Thirty to 50% of the variability in Balanus and new-recruit densities was explained by surfzone width. We sampled a subset of sites < 5 km apart where coastal hydrodynamics such as upwelling should be very similar. At paired sites with similar surfzone widths, Balanus densities were not different. If surfzone widths at paired sites were dissimilar, Balanus densities, daily settlement and weekly recruitment were significantly higher at sites with the wider more dissipative surf zone. The primary drivers of surfzone hydrodynamics are the wave climate and the slope of the shore and these persist over time, and therefore site-specific stability in surfzone hydrodynamics should result in stable barnacle population characteristics. Variations in surfzone hydrodynamics appear to play a fundamental role in regulating barnacle populations along the open coast, which in turn may have consequences for the entire intertidal community.
Data from: Evaluating shell variation across different populations of a freshwater snail
The freshwater snail Potamopyrgus antipodarum has become a model system for studying invasion ecology, host–parasite coevolution, the maintenance of sexual reproduction and ecotoxicology. One understudied aspect of this snail is the variation in morphology within and among populations, which could provide insights into ecological differences across its native range. In this study of 17 New Zealand lake populations of P. antipodarum we used linear measurements and geometric morphometrics to compare several aspects of shell size and shape. We found that, except for those from Lake Te Anau, most lake populations of P. antipodarum differ slightly in shape, but differ significantly in size and in the presence of spines, where larger and spinier snails are found in deeper regions. These striking distinctions in size and shell armature, but not in shape, suggest that the various components of form are under different selective regimes. Snails from Lake Te Anau are different in both shape and size, implying that this population is diverging from the rest of the species in multiple ways, making it an interesting study population for further research.
Data from: Variation in population structure and dynamics of montane forest tree species in Ethiopia guide priorities for conservation and research
The greatest extent of Afromontane environments in the world is found in Ethiopia. These areas support exceptional biodiversity, but forest cover and ecological integrity have declined sharply in recent decades. Conservation and management efforts are hampered in part by an inadequate understanding of the basic ecology of major tree species. We investigated population structure and inferred population dynamics from size frequency distributions of 22 forest tree species encountered in montane forests of Ethiopia. We collected new empirical data from four sites in the Bale Mountains, where some of the country's most extensive and least disturbed forests remain, and conducted a systematic review and analysis of all such studies that reported population structure for one or more of these species in Ethiopia. Thirteen widespread montane tree species showed a reverse-J size distribution, indicating a relatively stable population structure. Six other species had size-frequency distributions that indicate episodic recruitment and/or removal of certain size classes. Specific causes of these patterns are uncertain: they may involve timber harvesting, herbivory, fire, or natural disturbances, but patterns were inconsistent and locality dependent. For three other tree species, existing data are inadequate for any interpretation of population structure and dynamics. A species of particular conservation concern that emerged from this analysis was Hagenia abyssinica, which was found in all areas to consist only of larger individuals with no recent recruitment. For management and conservation purposes, the species in most urgent need of new research are those with inadequate or inconsistent data, and H. abyssinica..
Contrasting patterns of sequence variation in steelhead populations reflect distinct evolutionary processes
<p>Multiple evolutionary processes influence genome‐wide allele frequencies and quantifying effects of genetic drift, and multiple forms of selection remain challenging in natural populations. Here, we investigate variation at major effect loci in contrast to patterns of neutral drift across a wide collection of steelhead (<em>Oncorhynchus mykiss</em>) populations that have declined in abundance due to anthropogenic impacts. Whole‐genome resequencing of 74 populations of steelhead revealed genome‐wide patterns (~8 million SNPs) consistent with expected neutral population structure. However, allelic variation at major effect loci associated with adult migration timing (chromosome 28: GREB1L/ROCK1) and age at maturity (chromosome 25: SIX6) reflected how selection has acted on phenotypic variation in contrast with neutral structure. Variation at major effect loci was influenced by evolutionary processes with differing signals between the strongly divergent Coastal and Inland lineages, while allele frequencies within and among populations within the Inland lineage have been driven by local natural selection as well as recent anthropogenic influences. Recent anthropogenic effects appeared to have influenced the frequency of major effect alleles including artificial selection for specific traits in hatchery stocks with subsequent gene flow into natural populations. Selection from environmental factors at various scales has also likely influenced variation for major effect alleles. These results reveal evolutionary mechanisms that influence allele frequencies at major effect loci that are critical for conservation of phenotypic traits and life history variation of this protected species.</p>
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>
Fig. 1. Tick species and the total monthly tick numbers collected during the 5 in Seasonal variations in ixodid tick populations on a commercial game farm in the Limpopo Province, South Africa
Fig. 1. Tick species and the total monthly tick numbers collected during the 5-year study period.
Population-level variation in parasite resistance due to differences in immune initiation and rate of response
<p>Closely related populations often differ in resistance to a given parasite, as measured by infection success or failure. Yet, the immunological mechanisms of these evolved differences are rarely specified. Does resistance evolve via changes to the host's ability to recognize that an infection exists, actuate an effective immune response, or attenuate that response? We tested whether each of these phases of the host response contributed to threespine sticklebacks' recently evolved resistance to their tapeworm <i>Schistocephalus solidus. </i>While marine stickleback and some susceptible lake fish permit fast-growing tapeworms, other lake populations are resistant and suppress tapeworm growth via a fibrosis response. We subjected lab-raised fish from three populations (susceptible marine 'ancestors', a susceptible lake population, a resistant lake population), to a novel immune challenge using an injection of: 1) a saline control, 2) alum, a generalized pro-inflammatory adjuvant that causes fibrosis, 3) a tapeworm protein extract, or 4) a combination of alum and tapeworm protein). With enough time, all three populations generated a robust fibrosis response to the alum treatments. Yet, only the resistant population exhibited a fibrosis response to the tapeworm protein alone. Thus, these populations differed in their ability to respond to the tapeworm protein but shared an intact fibrosis pathway. The resistant population also initiated fibrosis faster in response to alum, and was able to attenuate fibrosis, unlike the susceptible populations' slow but longer-lasting response to alum. As fibrosis has pathological side-effects that reduce fecundity, the faster recovery by the resistant population may reflect an adaptation to mitigate the costs of immunity. Broadly, our results confirm that parasite detection and immune initiation, activation speed, and immune attenuation simultaneously contribute to the evolution of parasite resistance and adaptations to infection in natural populations.</p>
The population genetics of adaptation through copy-number variation in a fungal plant pathogen
<p>Supplementary Tables S1-S8 for the manuscript "The population genetics of adaptation through copy-number variation in a fungal plant pathogen"</p>
Fruit-feeding butterfly populations respond to variation in adult food availability: evidence from longitudinal body mass and abundance data
<p>The degree to which variation in adult food availability affects the population dynamics of a species depends on its position on the capital-income breeding continuum. The long-lived butterflies that feed on fruits as adults constitute an example of Lepidoptera with a high degree of income breeding. For three species of fruit-feeding butterflies in Uganda, we assessed the contribution of the income to breeding in the wild, and the consequences of variation in fruit availability for body mass and population dynamics. We interpreted body mass loss within individuals as well as younger individuals having higher body mass than older ones as evidence for the depletion of capital reserves. Despite large sample sizes, we were able to show only modest body mass loss in one species, indicating that large-bodied fruit-feeding butterflies are functionally income breeders in the wild. Butterfly body mass was sensitive to environmental factors, although the responses to fruit availability and weather parameters were dominated by interactive effects. In all three species, periods of higher availability of fruit were followed by periods of higher adult abundance three to five months later, fitting the egg-to-adult time. Our results suggest that adult food is rapidly used for reproduction so that body mass remains stable and population size responds to adult food availability. For these income breeding species, the frequent periods of low adult food availability may select for extended adult longevity for the purpose of postponing reproduction to the onset of more favorable conditions. </p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.