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5,538 results for “Population data”
Partnerships with TNCs to Better Serve the Transportation Disadvantaged Populations Data Repository
<p>Data repository for the STRIDE project A2 "Changing Access to Public Transportation and the Potential for Increased Travel," Thrust 2---Access for Transportation Disadvantaged Populations. </p>
Visualization of Demographic Data for 20 Most Populous U.S. Cities
<p>The main objective of this project is to use data visualizations to compare different demographic and community data for the 20 most populous U.S. cities. The data was obtained from the American Community Survey (ACS) and FBI crime data. The analysis is broken into a general demographic overview, a detailed crime breakdown, and a detailed income breakdown. These visualizations allow users to filter and select data to gain key insights into each city in the analysis.</p>
Data from: Spatio-temporal trends in richness and persistence of bacterial communities in decline-phase water vole populations
<p><strong>ABSTRACT</strong><br> Understanding the driving forces that control vole population dynamics requires identifying bacterial parasites hosted by the voles and describing their dynamics at the community level. To this end, we used high-throughput DNA sequencing to identify bacterial parasites in cyclic populations of montane water voles that exhibited a population outbreak and decline in 2014-2018. An unexpectedly large number of 155 Operational Taxonomic Units (OTUs) representing at least 13 genera in 11 families was detected. Individual bacterial richness was higher during declines, and vole body condition was lower. Richness as estimated by Chao2 at the local population scale did not exhibit clear seasonal or cycle phase-related patterns, but at the vole meta-population scale, exhibited seasonal and phase-related patterns. Moreover, bacterial OTUs that were detected in the low density phase were geographically widespread and detected earlier in the outbreak; some were associated with each other. Our results demonstrate the complexity of bacterial community patterns with regard to host density variations, and indicate that investigations about how parasites interact with host populations must be conducted at several temporal and spatial scales: multiple times per year over multiple years, and at both local and long-distance dispersal scales for the host(s) under consideration.</p> <p><strong>FILE DESCRIPTION:</strong></p> <p><strong>Trapping, physical, and demographic data for the 1376 <em>Arvicola terrestris</em> included in sequencing runs 1 to 8</strong></p> <p>This XLSX file contains the following information concerning the 1376 animals included in the eight sequencing runs: location, session numbering, animal_id, trap_name, capture_date, species, sex (1=male, 2=female), weight (g), length_body (mm), length_tail (mm, testes (0=abdominal, 1=scrotal), testes_length (mm), testes_width (mm), nipples (0=small, 1=lactating), vagina (0=not perforate, 1=perforate), pub_symph (0=closed, 1=open), uterus_scars (#), embryos(#), lens_weight (g), lens_weight2 (g) and sequencing labels</p> <p>File name: Animal_details.xlsx</p> <p> </p> <p><strong>Information concerning the <em>Arvicola terrestris</em> samples and the positive and negative controls multiplexed in the 16Sv4 MiSeq sequencing runs 1 to 8</strong></p> <p>This XLSX file contains the Run IDs, Sample IDs, Sample types, Dates & Site names, DNA extraction kit, PCR IDs, PCR replicate numbers, numbers of reads before and after filtering and the fastq file names for the 6615 PCR products multiplexed in the eight different Illumina MiSeq runs.</p> <p>File name: Sample_and_sequencing_informations.xlsx</p> <p> </p> <p><strong>MiSeq raw sequences of the 16Sv4 rRNA gene from <em>Arvicola terrestris</em> samples (Run1)</strong></p> <p>This ZIP file contains the Run1 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each <em>Arvicola terrestris</em> sample using the MiSeq platform. The 1570 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx.</p> <p>File name: MiSeq_Reads_16S_Arvicola_terrestris_Run1.zip</p> <p> </p> <p><strong>MiSeq raw sequences of the 16Sv4 rRNA gene from <em>Arvicola terrestris</em> samples (Run2)</strong></p> <p>This ZIP file contains the Run2 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each <em>Arvicola terrestris</em> sample using the MiSeq platform. The 1668 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx.</p> <p>File name: MiSeq_Reads_16S_Arvicola_terrestris_Run2.zip</p> <p> </p> <p><strong>MiSeq raw sequences of the 16Sv4 rRNA gene from <em>Arvicola terrestris</em> samples (Run3)</strong></p> <p>This ZIP file contains the Run3 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each <em>Arvicola terrestris</em> sample using the MiSeq platform. The 1646 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx.</p> <p>File name: MiSeq_Reads_16S_Arvicola_terrestris_Run3.zip</p> <p> </p> <p><strong>MiSeq raw sequences of the 16Sv4 rRNA gene from <em>Arvicola terrestris</em> samples (Run4)</strong></p> <p>This ZIP file contains the Run4 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each <em>Arvicola terrestris</em> sample using the MiSeq platform. The 1712 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx.</p> <p>File name: MiSeq_Reads_16S_Arvicola_terrestris_Run4.zip</p> <p> </p> <p><strong>MiSeq raw sequences of the 16Sv4 rRNA gene from <em>Arvicola terrestris</em> samples (Run5)</strong></p> <p>This ZIP file contains the Run5 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each <em>Arvicola terrestris</em> sample using the MiSeq platform. The 1680 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx.</p> <p>File name: MiSeq_Reads_16S_Arvicola_terrestris_Run5.zip</p> <p> </p> <p><strong>MiSeq raw sequences of the 16Sv4 rRNA gene from <em>Arvicola terrestris</em> samples (Run6)</strong></p> <p>This ZIP file contains the Run6 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each <em>Arvicola terrestris</em> sample using the MiSeq platform. The 1704 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx.</p> <p>File name: MiSeq_Reads_16S_Arvicola_terrestris_Run6.zip</p> <p> </p> <p><strong>MiSeq raw sequences of the 16Sv4 rRNA gene from <em>Arvicola terrestris</em> samples (Run7)</strong></p> <p>This ZIP file contains the Run7 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each <em>Arvicola terrestris</em> sample using the MiSeq platform. The 1620 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx.</p> <p>File name: MiSeq_Reads_16S_Arvicola_terrestris_Run7.zip</p> <p> </p> <p><strong>MiSeq raw sequences of the 16Sv4 rRNA gene from <em>Arvicola terrestris</em> samples (Run8)</strong></p> <p>This ZIP file contains the Run8 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each <em>Arvicola terrestris</em> sample using the MiSeq platform. The 1630 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx.</p> <p>File name: MiSeq_Reads_16S_Arvicola_terrestris_Run8.zip</p> <p> </p> <p><strong>Raw abundance table of the 16v4 rRNA gene from <em>Arvicola terrestris samples before data filtering (Run1 to 8)</em></strong></p> <p>This CSV file contains the number of reads for each distinct variant (OTU) and each of the 6615 PCR products, including the <em>Arvicola terrestris</em> samples and the controls, sequenced in the MiSeq runs 1 to 8 before the data filtering.</p> <p>File name: Read_abundance_table_before_filtering.csv</p> <p> </p> <p><strong>Abundance table of the 16v4 rRNA gene from <em>Arvicola terrestris</em> samples after data filtering (Run1 to 8)</strong></p> <p>This CSV file contains the number of reads for each distinct variant (OTU) and each <em>Arvicola terrestris</em> sample sequenced in the MiSeq runs 1 to 8 after the data filtering.</p> <p>File name: Read_abundance_table_after_filtering.csv</p>
Data from: Responses of activity rhythms to temperature cues evolve in Drosophila populations selected for divergent timing of eclosion
Even though the rhythm in adult emergence and rhythm in locomotor activity are two different rhythmic phenomena that occur at distinct life-stages of the fly life cycle, previous studies have hinted at similarities in certain aspects of the organisation of the circadian clock driving these two rhythms. For instance, the period gene plays an important regulatory role in both rhythms. In an earlier study, we have shown that selection on timing of adult emergence behaviour in populations of Drosophila melanogaster leads to the co-evolution of temperature sensitivity of circadian clocks driving eclosion. In this study, we were interested in asking if temperature sensitivity of the locomotor activity rhythm has evolved in our populations with divergent timing of adult emergence rhythm, with the goal of understanding the extent of similarity (or lack of it) in circadian organisation between the two rhythms. We found that in response to simulated jetlag with temperature cycles, late chronotypes (populations selected for predominant emergence during dusk) indeed re-entrain faster than early chronotypes (populations selected for predominant emergence during dawn) to 6-h phase-delays, thereby indicating enhanced sensitivity of the activity/rest clock to temperature cues in these stocks (entrainment is the synchronisation of internal rhythms to cyclic environmental time-cues). Additionally, we found that late chronotypes show higher plasticity of phases across regimes, day-to-day stability in phases and amplitude of entrainment, all indicative of enhanced temperature sensitive activity/rest rhythms. Our results highlight remarkably similar organisation principles between emergence and activity/rest rhythms.
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 from: The contribution of hybridization to range‐wide population genetic structure in a Pacific coastal dune plant
<p>Premise of the study: Interspecific hybridization can cause genetic structure across species ranges if the mating system and degree of sympatry/parapatry with close relatives varies geographically. The coastal dune endemic <em>Camissoniopsis cheiranthifolia</em> (Onagraceae) exhibits genetic subdivisions across its range, some of which are associated with shifts in mating system from outcrossing to selfing, while others are not. For instance, strong differentiation between large-flowered, self-incompatible (LF-SI) and large-flowered, self-compatible (LF-SC) populations occurs without much reduction in outcrossing or obvious barriers to gene flow. We hypothesized that LF-SI diverged from LF-SC via hybridization with the predominantly inland SI sister species <em>C. bistort</em>a.</p> <p>Methods: We analyzed spatial proximity using 1460 herbarium records, and genetic variation at 12 microsatellites assayed for 805 and 404 individuals from 32 <em>C. cheiranthifolia</em> and 18 <em>C. bistorta</em> populations, respectively. We also assayed nine chloroplast microsatellites for 124 and 111 individuals from 27 and 19 populations, respectively. </p> <p>Key results: Closer parapatry was associated with unexpectedly high genetic continuity between LF-SI <em>C. cheiranthifolia</em> and <em>C. bistorta</em>. LF-SI genotypes clustered with <em>C. bistorta</em> exclusive of other <em>C. cheiranthifolia</em> genotypes. Similarly, pairwise FST among SI <em>C. cheiranthifolia</em> and <em>C. bistorta</em>, adjusted for geographic proximity, was not higher between heterospecific than conspecific populations. </p> <p>Conclusions: The lack of genetic differentiation between LF-SI <em>C. cheiranthifolia</em> and <em>C. bistorta</em> populations, even those located away from the zone of parapatry, suggests that LF-SI <em>C. cheiranthifolia</em> instead of hybridizing with <em>C. bistorta</em> is rather an ecotype of <em>C. bistorta</em> that has adapted to coastal dune habitat independent of other lineages in <em>C. cheiranthifolia</em> proper.</p>
Data from: Environmental change, if unaccounted, prevents detection of cryptic evolution in a wild population
Detecting contemporary evolution requires demonstrating that genetic change has occurred. Mixed-effects models allow estimation of quantitative genetic parameters and are widely used to study evolution in wild populations. However, predictions of evolution based on these parameters frequently fail to match observations. Furthermore, such studies often lack an independent measure of evolutionary change against which to verify predictions. Here, we applied three commonly used quantitative genetic approaches to predict the evolution of size at maturity in a wild population of Trinidadian guppies. Crucially, we tested our predictions against evolutionary change observed in common garden experiments performed on samples from the same population. We show that standard quantitative genetic models underestimated or failed to detect the cryptic evolution of this trait as demonstrated by the common garden experiments. The models failed because: 1) size at maturity and fitness both decreased with increases in population density, 2) offspring experienced higher population densities than their parents, and 3) selection on size was strongest at high densities. When we accounted for environmental change, predictions better matched observations in the common garden experiments, although substantial uncertainty remained. Our results demonstrate that predictions of evolution are unreliable if environmental change is not appropriately captured in models.
Data from: Adaptive landscape genetics and malaria across divergent island bird populations
Environmental conditions play a major role in shaping the spatial distributions of pathogens, which in turn can drive local adaptation and divergence in host genetic diversity. Haemosporidians, such as plasmodium (malaria) are a strong selective force, impacting survival and fitness of hosts, with geographic distributions largely determined by habitat suitability for their insect vectors. Here, we have tested whether patterns of fine-scale local adaptation to malaria are replicated across discrete, ecologically differing island populations of Berthelot's pipits Anthus berthelotii. We sequenced TLR4, an innate immunity gene that is potentially under positive selection in <i>Berthelot's pipits</i>, and two SNPs previously identified as being associated with malaria infection in a genome-wide association study (GWAS) in Berthelot's pipits in the Canary Islands. We determined the environmental predictors of malaria infection, using these to estimate variation in malaria risk on Porto Santo, and found some congruence with previously identified environmental risk factors on Tenerife. We also found a negative association between malaria infection and a TLR4 variant in Tenerife. In contrast, one of the GWAS SNPs showed an association with malaria risk in Porto Santo, but in the opposite direction to that found in the Canary Islands GWAS. Together, these findings suggest that disease-driven local adaptation may be an important factor in shaping variation among island populations.
Data from: Detecting the population dynamics of an autosomal sex-ratio distorter transgene in malaria vector mosquitoes
<p>1. The development of genetically modified mosquitoes and their subsequent field release offers innovative and cost-effective approaches to reduce mosquito-borne diseases, such as malaria. A sex-distorting autosomal transgene has been developed recently in G3 mosquitoes, a lab strain of the malaria vector Anopheles gambiae s.l. The transgene expresses an endonuclease called I-PpoI during spermatogenesis, which selectively cleaves the X chromosome to result in ~95% male progeny. Following the World Health Organization Guidance Framework for the testing of genetically modified mosquitoes, we assessed the dynamics of this transgene in large cages using a joint experimental-modelling approach.</p> <p>2. We performed a four-month experiment in indoor large cages to study the population genetics of the transgene. The cages were set up to mimic a simple tropical environment with a diurnal light-cycle, constant temperature, and constant humidity. We allowed the generations to overlap to engender a stable age structure in the populations. We constructed a model to mimic the experiments, and used the experimental data to infer the key model parameters.</p> <p>3. We identified two fitness costs associated to the transgene. First, transgenic adult males have reduced fertility and, second, their female progeny have reduced pupal survival rates. Our results demonstrate that the transgene is likely to disappear in less than three years under our confined conditions. Model predictions suggest this will be true over a wide range of background population sizes and transgene introduction rates.</p> <p>4. Synthesis and applications: Our semi-field indoor cage experiments are in line with WHO guidance recommendations in regards to the development and testing of self-limiting technologies. Since the transgenic strain (Ag(PMB)1) has been considered for genetic vector control of malaria, our results are fundamentally important for determining expectations on the persistence of the transgene post-release. Our results provide a demonstration of the self-limiting nature of the transgene, and indicate that longevity will be further reduced by fitness costs that were not previously identified. Finally, our study has showcased an alternative and effective method for characterising the phenotypic expression of a transgene in an insect pest population.</p>
Data from: Low coverage genomic data resolve the population divergence and gene flow history of an Australian rain forest fig wasp
Population divergence and gene flow are key processes in evolution and ecology. Model-based analysis of genome-wide datasets allows discrimination between alternative scenarios for these processes even in non-model taxa. We used two complementary approaches (one based on the blockwise site frequency spectrum (bSFS), the second on the Pairwise Sequentially Markovian Coalescent (PSMC)) to infer the divergence history of a fig wasp, Pleistodontes nigriventris. Pleistodontes nigriventris and its fig tree mutualist Ficus watkinsiana are restricted to rain forest patches along the eastern coast of Australia, and are separated into northern and southern populations by two dry forest corridors (the Burdekin and St. Lawrence Gaps). We generated whole genome sequence data for two haploid males per population and used the bSFS approach to infer the timing of divergence between northern and southern populations of P. nigriventris, and to discriminate between alternative isolation with migration (IM) and instantaneous admixture (ADM) models of post divergence gene flow. Pleistodontes nigriventris has low genetic diversity (π = 0.0008), to our knowledge one of the lowest estimates reported for a sexually reproducing arthropod. We find strongest support for an ADM model in which the two populations diverged ca. 196kya in the late Pleistocene, with almost 25% of northern lineages introduced from the south during an admixture event ca. 57kya. This divergence history is highly concordant with individual population demographies inferred from each pair of haploid males using PSMC. Our analysis illustrates the inferences possible with genome-level data for small population samples of tiny, non-model organisms and adds to a growing body of knowledge on the population structure of Australian rain forest taxa.
Data from: Aridity exacerbates grazing-induced rangeland degradation: a population approach for dominant grasses
<p>1. The current human-induced intensification of grazing pressure and the increase of aridity as a result of climate alterations are unprecedented and have been identified as the main drivers that cause desertification in rangelands worldwide. In these ecosystems, human well-being mostly depends on plant species that provide forage for domestic herbivores. However, scarce evidence exists about the interaction between regional aridity level and human-induced disturbances as determinants of forage plant populations' structure and dynamics.</p> <p>2. We studied the effects of domestic grazing intensification on the population structure of dominant native grasses, in three rangeland sites located across a regional aridity gradient: a semi-desert (high-aridity site), a shrub-grass steppe (intermediate-aridity site) and a grass steppe (low-aridity site). We also studied the effect of two-year grazing exclusion on plant growth of a key native forage grass species common to the three sites.</p> <p>3. Grazing decreased total grass density and increased the frequency of small plants in all sites, particularly for forage species. However, the size of the grazing intensification effect was the greatest in the high-aridity site, where intensive grazing produced a ten-fold reduction of grass density. Moreover, plant recovery (growth) after grazing exclusion was lower as aridity increased.</p> <p>4. Synthesis and applications. Our study provides evidence of a negative synergistic effect of grazing pressure and aridity that may lead to the collapse of grass populations. Long-term grazing intensification degrades the population structure of grasses, particularly in high-aridity sites, where the forage provision is substantially reduced. These results refute the hypothesis that plant-traits of dominant species adapted to high-aridity allow them to resist herbivory. Besides, high-aridity delays plant recovery after defoliation (low resilience). The management of both the grazing pressure and the length of grazing-rest according to the ecological-site aridity are key aspects for maintaining the forage provision of rangelands. Monitoring plant populations' structure through time and space strengthens inferences about responses of forage species to ongoing changes in disturbance and stress regimes. This knowledge is complementary to regional and worldwide monitoring endeavors based on land cover, and it contributes to the robust design of sustainable management of global rangelands.</p>
Data from: Can dominance genetic variance be ignored in evolutionary quantitative genetic analyses of wild populations?
<p>Accurately estimating genetic variance components is important for studying evolution in the wild. Empirical work on domesticated and wild outbred populations suggests that dominance genetic variance represents a substantial part of genetic variance, and theoretical work predicts that ignoring dominance can inflate estimates of additive genetic variance. Whether this issue is pervasive in natural systems is unknown, because we lack estimates of dominance variance in wild populations obtained <i>in situ</i>. Here, we estimate dominance and additive genetic variance, maternal variance, and other sources of non-genetic variance in 8 traits measured in over 9000 wild nestlings linked through a genetically resolved pedigree. We find that dominance variance, when estimable, does not statistically differ from zero and represents a modest amount (2-36%) of genetic variance. Simulations show that 1) inferences of all variance components for an average trait are unbiased; 2) the power to detect dominance variance is low; 3) ignoring dominance can mildly inflate additive genetic variance and heritability estimates but such inflation becomes substantial when maternal effects are also ignored. These findings hence suggest that dominance is a small source of phenotypic variance in the wild and highlight the importance of proper model construction for accurately estimating evolutionary potential.</p>
Data from: One panel to rule them all: DArTcap genotyping for population structure, historical demography, and kinship analyses, and its application to a threatened shark
With recent advances in sequencing technology, genomic data are changing how important conservation management decisions are made. Applications such as Close-Kin Mark-Recapture demand large amounts of data to estimate population size and structure, and their full potential can only be realised through ongoing improvements in genotyping strategies. Here we introduce DArTcap, a cost-efficient method that combines DArTseq and sequence capture, and illustrate its use in a high resolution population analysis of Glyphis garricki, a rare, poorly known and threatened euryhaline shark. Clustering analyses and spatial distribution of kin pairs from four different regions across northern Australia and one in Papua New Guinea, representing its entire known range, revealed that each region hosts at least one distinct population. Further structuring is likely within Van Diemen Gulf, the region that included the most rivers sampled, suggesting additional population structuring would be found if other rivers were sampled. Coalescent analyses and spatially explicit modelling suggest that G. garricki experienced a recent range expansion during the opening of the Gulf of Carpentaria following the conclusion of the Last Glacial Maximum. The low migration rates between neighbouring populations of a species that is found only in restricted coastal and riverine habitats show the importance of managing each population separately, including careful monitoring of local and remote anthropogenic activities that may affect their environments. Overall we demonstrated how a carefully chosen SNP panel combined with DArTcap can provide highly accurate kinship inference and also support population structure and historical demography analyses, therefore maximising cost-effectiveness.
Data from: Transcriptomic plasticity of mesophotic corals among natural populations and transplants of Montastraea cavernosa in the Gulf of Mexico and Belize
<p>While physiological responses to low-light environments have been studied among corals on mesophotic coral ecosystems worldwide (MCEs; 30–150 m), the mechanisms behind acclimatization and adaptation to depth are not well understood for most coral species. Transcriptomic approaches based on RNA sequencing are useful tools for quantifying gene expression plasticity, particularly in slow-growing species such as scleractinian corals, and for identifying potential functional differences among conspecifics. A tag-based RNA-Seq (Tag-Seq) pipeline was applied to quantify transcriptional variation in natural populations of the scleractinian coral <i>Montastraea cavernosa</i> from mesophotic and shallower environments across five sites in Belize and the Gulf of Mexico: Carrie Bow Cay, West and East Flower Garden Banks, Pulley Ridge, and Dry Tortugas. Regional site location was a stronger driver of gene expression patterns than depth. However, mesophotic corals among all sites shared similar regulation of metabolic and cell growth functional pathways that may represent common physiological responses to environmental conditions at depth. Additionally, in a transplant experiment at West and East Flower Garden Banks, colonies transplanted from mesophotic to shallower habitats diverged from the control mesophotic group over time, indicating depth-regulated plasticity of gene expression. When the shallower depth zone experienced a bleaching event, bleaching severity did not differ significantly between transplants and shallow controls, but gene expression patterns indicated variable regulation of stress responses among depth treatments. Coupled observational and experimental studies of gene expression among mesophotic and shallower <i>M. cavernosa</i> provide insights into the ability of this depth-generalist coral species to persist under varying environmental conditions. </p>
Data from: Population genomic diversity and structure at the discontinuous southern range of the Great Gray Owl in North America
<p>Species' distributions are often discontinuous near the edge of the range where the environment may be more variable than the core of the range. Range discontinuity can reduce or cut off gene flow to small peripheral populations and lead to genetic drift and subsequent loss of genetic diversity. The southern extent of the Great Gray Owl ( Strixnebulosa) range in North America is discontinuous, unlike their northern core range across the boreal forests. We sampled owls from five different locations on the periphery of the range across the western US (Wyoming, Idaho, California, northern Oregon, and southern Oregon) to investigate genetic population structure and genetic diversity. Using a reduced-representation genomic sequencing approach to genotype 123 individuals at 4,817 single nucleotide polymorphic loci, we identified four genetically differentiated populations: California, southern Oregon, northern Oregon, and Wyoming and Idaho grouped together as a single Rocky Mountain population. The four genetically differentiated populations of Great Gray Owls identified in this study display high differentiation and low genetic variation, which is suggestive of long-term isolation and lack of connectivity, potentially caused by range discontinuity. The populations that lack habitat connectivity to the rest of the breeding range (i.e. those in California and Oregon) had lower genetic diversity than the Rocky Mountain population that is connected to the core of the range. These factors and other risks (such as disease and human-caused mortality) heighten susceptibility of these range-edge populations to future habitat and climate changes, genetic diversity erosion, and potential extinction vortex. For these reasons, protecting and monitoring this species on the southern edge of their range is vital.</p>
Data from: Population genomic evidence reveals subtle patterns of differentiation in the trophically polymorphic Cuatro Ciénegas cichlid, Herichthys minckleyi
In recent decades, an increased understanding of molecular ecology has led to a reinterpretation of the role of gene flow during the evolution of reproductive isolation and biological novelty. For example, even in the face of ongoing gene flow strong selection may maintain divergent polymorphisms, or gene flow may introduce novel biological diversity via hybridization and introgression from a divergent species. Herein, we elucidate the evolutionary history and genomic basis of a trophically polymorphic trait in a species of cichlid fish, Herichthys minckleyi. We explored genetic variation at three hierarchical levels; between H. minckleyi (n=69) and a closely related species H. cyanoguttatus (n=10), between
Data from: Divergence of seminal fluid gene expression and function among natural snail populations
Seminal fluid proteins (SFPs) can trigger drastic changes in mating partners, mediating post-mating sexual selection and associated sexual conflict. Also, cross-species comparisons have demonstrated that SFPs evolve rapidly and hint that post-mating sexual selection drives their rapid evolution. In principle, this pattern should be detectable within species as rapid among-population divergence in SFP expression and function. However, given the multiple other factors that could vary among populations, isolating divergence in SFP-mediated effects is not straightforward. Here we attempted to address this gap by combining the power of a common garden design with functional assays involving artificial injection of SFPs in the simultaneously hermaphroditic freshwater snail, Lymnaea stagnalis. We detected among-population divergence in SFP gene expression, suggesting that seminal fluid composition differs among four populations collected in western Europe. Furthermore, by artificially injecting seminal fluid extracted from these field-derived snails into standardized mating partners, we also detected among-population divergence in the strength of post-mating effects induced by seminal fluid. Both egg production and subsequent sperm transfer of partners differed depending on the population origin of seminal fluid, with the response in egg production seemingly closely corresponding to among-population divergence in SFP gene expression. Our results thus lend strong intraspecific support to the notion that SFP expression and function evolve rapidly, and confirm L. stagnalis as an amenable system for studying processes driving SFP evolution.
Data from: The evolution of parasite host range in heterogeneous host populations
<p>Theory on the evolution of niche width argues that resource heterogeneity selects for niche breadth. For parasites, this theory predicts that parasite populations will evolve, or maintain, broader host ranges when selected in genetically diverse host populations relative to homogeneous host populations. To test this prediction, we selected the bacterial parasite Serratia marcescens to kill Caenorhabditis elegans in populations that were genetically heterogeneous (50% mix of two experimental genotypes) or homogeneous (100% of either genotype). After 20 rounds of selection, we compared the host range of selected parasites by measuring parasite fitness (i.e. virulence, the selected fitness trait) on the two focal host genotypes and on a novel host genotype. As predicted, heterogeneous host populations selected for parasites with a broader host range: these parasite populations gained or maintained virulence on all host genotypes. This result contrasted with selection in homogeneous populations of one host genotype. Here, host range contracted, with parasite populations gaining virulence on the focal host genotype and losing virulence on the novel host genotype. This pattern was not, however, repeated with selection in homogeneous populations of the second host genotype: these parasite populations did not gain virulence on the focal host genotype, nor did they lose virulence on the novel host genotype. Our results indicate that host heterogeneity can maintain broader host ranges in parasite populations. Individual host genotypes, however, vary in the degree to which they select for specialization in parasite populations.</p>
Data from: Estimating fish population abundance by integrating quantitative data on environmental DNA and hydrodynamic modeling
<p>Molecular analysis of DNA left in the environment, known as environmental DNA (eDNA), has proven to be a powerful and cost-effective approach to infer occurrence of species. Nonetheless, relating measurements of eDNA concentration to population abundance remains difficult because detailed knowledge on the processes that govern spatial and temporal distribution of eDNA should be integrated to reconstruct the underlying distribution and abundance of a target species. In this study, we propose a general framework of abundance estimation for aquatic systems on the basis of spatially replicated measurements of eDNA. The proposed method explicitly accounts for production, transport, and degradation of eDNA by utilizing numerical hydrodynamic models that can simulate the distribution of eDNA concentrations within an aquatic area. It turns out that, under certain assumptions, population abundance can be estimated via a Bayesian inference of a generalized linear model. Application to a Japanese jack mackerel (<em>Trachurus japonicus</em>) population in Maizuru Bay revealed that the proposed method gives an estimate of population abundance comparable to that of a quantitative echo sounder method. Furthermore, the method successfully identified a source of exogenous input of eDNA (a fish market), which may render a quantitative application of eDNA difficult to interpret unless its effect is taken into account. These findings indicate the ability of eDNA to reliably reflect population abundance of aquatic macroorganisms; when the "ecology of eDNA" is adequately accounted for, population abundance can be quantified on the basis of measurements of eDNA concentration.</p>
Data from: Telomere attrition with age in a wild amphibian population
<p>Telomere shortening with age has been documented in many organisms, but few studies have reported telomere length measurements in amphibians, and no information is available for growth after metamorphosis, nor in wild populations. We provide both cross-sectional and longitudinal evidence of net telomere attrition with age in a wild amphibian population of natterjack toads (<em>Epidalea calamita</em>). Based on age-estimation by skeletochronology and qPCR telomere length measurements in the framework of an individual-based monitoring programme, we confirmed telomere attrition in recaptured males. Our results support that toads experience telomere attrition throughout<br> their ontogeny, and that most attrition occurs during the first 1–2 years.We did not find associations between telomere length and inbreeding or body condition. Our results on telomere length dynamics under natural conditions confirm telomere shortening with age in amphibians and provide quantification of wide telomere length variation within and among age-classes in a wild breeding population.</p>
ScienceDex guides
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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.