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1,068 results for “demographic”
Population structure and demographic history of the gastropod Thaisella chocolata (Duclos, 1832) from the Southeast Pacific inferred from mitochondrial DNA analyses
<p>The present-day population structure of a species reflects the combination of oceanographic currents, life-history traits, and historical events. However, little is known about the mechanisms that have shaped the gene lineage distribution of marine species inhabiting the Southeast Pacific. Here we provide a comprehensive phylogeographical study of a species distributed along the Southeast Pacific coastal region by analyzing the endemic gastropod Thaisella chocolata (Duclos, 1832). Sequencing of mitochondrial cytochrome c oxidase subunit 1 (CO1) and 16S rRNA revealed strikingly high haplotypic nucleotide and genetic diversity but a lack of significant population differentiation within the survey area. In addition, a star-shaped phylogeny and significantly negative Tajima's D and Fu's Fs tests of neutrality suggested historical occurrence of rapid demographic expansion. Mismatch distributions and Bayesian inference analyses also confirmed T. chocolata to have undergone two ancestral demographic expansions. Calculations suggested that these expansions began in the lower and middle Pleistocene epoch, likely due to continental shelf development and climatic conditions. These findings could help establish a genetic baseline for T. chocolata as the first step toward sustainable spatial management of this species, as well as understand this species' response to future climate change.</p>
Bumble bee demographic data for functional linear models
<p>1. Behavior and organization of social groups is thought to be vital to the functioning of societies, yet the contributions of various roles within social groups towards population growth and dynamics have been difficult to quantify. A common approach to quantifying these role-based contributions is evaluating the number of individuals conducting certain roles, which ignores how behavior might scale up to effects at the population-level. Manipulative experiments are another common approach to determine population-level effects, but they often ignore potential feedbacks associated with these various roles.<br> 2. Here, we evaluate the effects of worker size distribution in bumblebee colonies on worker production in 24 observational colonies across three environments, using functional linear models. Functional linear models are an underused correlative technique that has been used to assess lag effects of environmental drivers on plant performance. We demonstrate potential applications of this technique for exploring high-dimensional ecological systems, such as the contributions of individuals with different traits to colony dynamics.<br> 3. We found that more larger workers had mostly positive effects and more smaller workers had negative effects on worker production. Most of these effects were only detected under low or fluctuating resource environments suggesting that the advantage of colonies with larger-bodied workers becomes more apparent under stressful conditions.<br> 4. We also demonstrate the wider ecological application of functional linear models. We highlight the advantages and limitations when considering these models, and how they are a valuable complement to many of these performance-based and manipulative experiments.</p>
Genomic divergence, local adaptation, and complex demographic history may inform management of a popular sportfish species complex
<p>We investigated genomic divergence, interspecific and intraspecific diversity and population structure, local directional selection, and complex demographic history in a popular freshwater species complex in the Central Interior Highlands, North America. Specifically, we assessed differentiation between the Neosho Bass (<em>Micropterus velox</em>) and Smallmouth Bass (<em>M. dolomieu</em>) where their ranges are parapatric in this ecoregion. We scanned the genome for signatures of local direction and mapped divergence at selected SNPs at the population level. Additionally, we identified stream populations with extensive admixture, and we used a model-testing framework to investigate complex demographic histories between the two species.</p> <p>Raw ddRADseq .fastq sequence files, along with intermediate processing files, finalized VCF files, a data summary report, and other data information, are given in the "smb_ddRAD_rawdata.tar file. Metadata, including sample_id, species designation, and stream population, are given in the "metadata.xlsx" file.</p>
Data from: Are genetic variation and demographic performance linked?
<p>Quantifying the empirical relationships between genetic variation and population viability is important from both basic biological and applied conservation perspectives, yet few populations have been monitored with both long-term demographic and population genetics approaches. Here, we present eight years of historical demographic data from five populations of <em>Boechera fecunda </em>(Brassicaceae), a rare, self-compatible perennial plant endemic to Montana, USA, and use integral projection models to estimate the stochastic population growth rate (λ<sub>S</sub>) and extinction risk of each population. We combine these demographic estimates with previously published metrics of genetic variation in the same populations to test whether genetic diversity within populations is linked to demographic performance. Our results show that in this predominantly inbred species, genetics and demography are not strongly correlated, suggesting that more inbred populations are not necessarily less viable or at higher extinction risk than more genetically diverse populations. Interestingly, however, a contemporary re-census revealed that, among these populations, genetic rather than demographic parameters were better predictors of current population density, with populations harboring greater genetic diversity maintaining denser populations at present. In the absence of evidence for inbreeding depression decreasing population viability in this species, we recommend conservation of distinct, potentially locally adapted populations of <em>B. fecunda </em>rather than alternatives such as translocations or reintroductions.</p>
Replication data for: Demographic declines and responses of breeding bird populations to human footprint in the Athabasca Oil Sands Region, Alberta, Canada
<p class="MsoNormal">This data package includes data files and an R script to reproduce results reported in the paper "Demographic declines and responses of breeding bird populations to human footprint in the Athabasca Oil Sands Region, Alberta, Canada". Analyses include hierarchical multispecies models applied to data from 31 bird species at 38 Monitoring Avian Productivity and Survivorship (MAPS) stations to assess 10-year (2011–2020) demographic trends and responses to energy sector disturbance (human footprint proportion) in the Athabasca oil sands region of Alberta, Canada. Adult captures, productivity, and residency probability all declined over the study period, and adult apparent survival probability also tended to decline. Trends in adult captures, productivity, and survival were all more negative at stations with larger increases in disturbance over the study period. Species associated with early seral stages were more commonly captured at more disturbed stations, while species typical of mature forests were more commonly captured at less disturbed stations. Productivity was positively correlated with disturbance within 5 km of stations after controlling for disturbance within 1 km of stations. Adult apparent survival showed relatively little response to disturbance; stresses experienced beyond the breeding grounds likely play a larger role in influencing survival. Residency probability was negatively related to disturbance within 1-km scale of stations and could reflect processes affecting the ability of birds to establish or maintain territories in disturbed landscapes.</p>
The niche through time: Considering phenology and demographic stages in plant distribution models
<p>Species distribution models (SDMs) are widely used to infer species-environment relationships, predict spatial distributions, and characterise species' environmental niches. While the importance of space and spatial scales is widely acknowledged in SDM applications, temporal components of the niche are rarely addressed. We discuss how phenology and demographic stages affect model inference in plant SDMs. Ignoring conspicuousness and timing of phenological stages may bias niche estimates through increased observer bias, while ignoring stand age may bias niche estimates through temporal mismatches with environmental variables, especially during times of rapid global warming. We present different methods to consider phenology and demographic stages in plant SDMs, including the selection of causal, spatiotemporally explicit predictors, and the calibration of stage-specific SDMs. Based on a case study with citizen science data, we illustrate how spatiotemporal SDMs provide deeper insights on the coincidence of range and phenological shifts under climate change. The proliferation of digitally available biodiversity and citizen science data increasingly allows considering time explicitly in SDMs. This offers a more mechanistic understanding of plant distributions, and more robust predictions under global change, especially if the reporting of phenological stages and age is facilitated and promoted by relevant data portals.</p>
Topology testing and demographic modeling illuminate a novel speciation pathway in the Greater Caribbean Sea following the formation of the Isthmus of Panama
<p>Recent genomic analyses have highlighted the prevalence of speciation with gene flow in many taxa and have underscored the importance of accounting for these reticulate evolutionary processes when constructing species trees and generating parameter estimates. This is especially important for deepening our understanding of speciation in the sea where fast-moving ocean currents, expanses of deep water, and periodic episodes of sea level rise and fall act as soft and temporary allopatric barriers that facilitate both divergence and secondary contact. Under these conditions, gene flow is not expected to cease completely while contemporary distributions are expected to differ from historical ones. Here we conduct range-wide sampling for Pederson's cleaner shrimp (<em>Ancylomenes</em> <em>pedersoni</em>), a species complex from the Greater Caribbean that contains three clearly delimited mitochondrial lineages with both allopatric and sympatric distributions. Using mtDNA barcodes and a genomic ddRADseq approach, we combine classic phylogenetic analyses with extensive topology testing and demographic modeling (10 site frequency replicates x 45 evolutionary models x 50 model simulations/replicate = 22,500 simulations) to test species boundaries and reconstruct the evolutionary history of what was expected to be a simple case study. Instead, our results indicate a history of allopatric divergence, secondary contact, introgression, and endemic hybrid speciation that we hypothesize was driven by the final closure of the Isthmus of Panama and the strengthening of the Gulf Stream Current ~3.5 million years ago. The history of this species complex recovered by model-based methods that allow reticulation differs from that recovered by standard phylogenetic analyses and is unexpected given contemporary distributions. The geologically and biologically meaningful insights gained by our model selection analyses illuminate what is likely a novel pathway of species formation not previously documented that resulted from one of the most biogeographically significant events in Earth's history.</p>
Survey data on the demographics, motivations, mental-health issues and regrets of r/RoastMe posters
<p>Dataset including the data analysed in the "r/RoastMe: Characterising Self-Requested Online Mocking" paper describing the demographics, motivations, mental-health issues and consequences of posting on the r/RoastMe subreddit.</p>
Genomic data provides new insights on the demographic history and the extent of recent material transfers in Norway spruce
<p>This dataset includes files and scripts used for the paper "Genomic data provides new insights on the demographic history and the extent of recent material transfers in Norway spruce". </p>
A Comprehensive Assessment of Demographic, Environmental and Host Genetic Associations with Gut Microbiome Diversity in Healthy Individuals (GWAS)
<p>GWAS summary statistics accompanying manuscript "A Comprehensive Assessment of Demographic, Environmental and Host Genetic Associations with Gut Microbiome Diversity in Healthy Individuals".</p>
Dataset (raw questionnaire data and variable importance results) supplementing the publication "Does Gender Really Matter? How Demographics and Site Characteristics Influence Behavior and Attitudes of German Small-Scale Private Forest Owners"
<p>The dataset contains</p> <ul> <li>a translation of the questionnaire,</li> <li>the questionnaire raw data, and</li> <li>the results of the variable importance analysis</li> </ul> <p>used in the publication "Does Gender Really Matter? How Demographics and Site Characteristics Influence Behavior and Attitudes of Small-Scale Private Forest Owners".</p>
Silva, Harder et al. Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history Data
<p>Dataset used in the "Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history" paper by Silva, Harder et al.</p> <p>This dataset includes Fasta files for Simulated dataset and VCF files for both Empirical and Simulated datasets.</p>
Anderson Police Department Arrestee Demographics 2022-2023
<p>This dataset contains demographic information on people arrested for violent and property crimes reported to the Anderson Police Department in Anderson, CA. The data includes information on the sex, race, and gender of arrestees. It covers violent crimes such as assault and robbery, as well as property crimes such as burglary and theft. Charges are listed by the CJIS IBR Offense Codes, not by statute. </p> <p>The dataset was provided by the Anderson Police Department in response to our Public Records Act request and covers the time period from Jan 1, 2022 through Dec 31, 2023. The data is presented in Microsoft Word Document format. Each row summarizes individual offenses. The demographic labels are grouped by column.</p>
Anderson Police Department Victim Demographics 2022-2023
<p>This dataset contains demographic information on victims of violent and property crimes reported to the Anderson Police Department in Anderson, CA. The data includes information on the sex and race of victims. It covers violent crimes such as assault and robbery, as well as property crimes such as burglary and theft.</p> <p>Charges are listed by the CJIS IBR Offense Codes, not by statute. The department did not have a report for the Victim age or race in 2023 due to changing report systems in May of 2023. The reports for 2022 contain only Victim Sex and Victim Race.</p> <p>The dataset was provided by the Anderson Police Department in response to our Public Records Act request and covers the time period from Jan 1, 2022 through Dec 31, 2023. The data is presented in Word format. Each row summarizes individual offenses. The demographic labels are grouped by column.</p>
Anderson Police Department Offender Demographics 2022-2023
<p>This dataset contains demographic information on offenders alleged to commit violent and property crimes reported to the Anderson Police Department in Anderson, CA. The data includes information on the sex, race, and gender of offenders. It covers violent crimes such as assault and robbery, as well as property crimes such as burglary and theft. Charges are listed by the CJIS IBR Offense Codes, not by statute. </p> <p>The dataset was provided by the Anderson Police Department in response to our Public Records Act request and covers the time period from Jan 1, 2022 through Dec 31, 2023. The data is presented in Word format. Each row summarizes individual offenses. The demographic labels are grouped by column.</p>
Demographic differentiation among pioneer tree species during old-field succession of a Neotropical rainforest
<p>Early pioneer species share life histories enabling them to colonize disturbed sites, but how much they differ demographically and how such differentiation determines pioneer species turnover during succession are still open questions. Here, we approached these issues by comparing the demography of dominant pioneer tree species during the old-field succession of tropical rainforest in Southeast Mexico.</p> <p>We assessed changes in population density, population structure, vital rates, and intrinsic population growth rate (r) of the pioneer species Trema micrantha, Cecropia peltata, and Trichospermum mexicanum during the first 35 years of succession. For this, we combined chronosequence and long-term (from 2000 to 2018) data from 14 old-fields with 0.5-35 years fallow age.</p> <p>Trema colonized and disappeared first during succession (< 15 years), followed by Cecropia (< 28) and Trichospermum (> 31). All species exhibited hump-shaped successional trajectories of population density and biomass with Trema reaching a peak first, followed by Cecropia and later Trichospermum. Species exhibited a fast reduction in r with fallow age, with Trema reaching negative growth rates (r < 0) in the third, Cecropia in the fourth, and Trichospermum in the seventh year of succession. Recruitment, growth, and mortality rates of seedlings and juveniles defined the period of population increase and the age of succession at which each species reached maximum density and biomass. The mortality rate in mature stages determined how long each species persisted during succession. An important variation in species replacement occurred among study sites. In some sites one species was abundant and the others were almost absent, while it was the opposite in other sites. We inferred that priority inhibitory effects operated among species during the field colonization.</p> <p>Synthesis: Although Trema, Cecropia, and Trichospermum are considered typical pioneer trees, these species differed importantly in their demographic attributes during succession. The speed at which r declined with age of succession indicated the moment at which each species reached its maximum density and species replacement sequence during succession. However, inter-specific priority inhibitory effects during field colonization may also be involved in the chance of colonization and replacement between species with similar regeneration strategies.</p>
The effects of climate and demographic history in shaping genomic variation across populations of the Desert Horned Lizard (Phrynosoma platyrhinos)
<p>Species often experience spatial <span class="NormalTextRun SCXW235808685 BCX2">environmental </span><span class="NormalTextRun SCXW235808685 BCX2">heterogeneity </span><span class="NormalTextRun SCXW235808685 BCX2">across their range</span><span class="NormalTextRun SCXW235808685 BCX2">, </span><span class="NormalTextRun SCXW235808685 BCX2">and </span><span class="NormalTextRun SCXW235808685 BCX2">populations </span><span class="NormalTextRun SCXW235808685 BCX2">may exhibit </span><span class="NormalTextRun SCXW235808685 BCX2">signatures </span><span class="NormalTextRun SCXW235808685 BCX2">of adaptation to local environmental </span><span class="NormalTextRun SCXW235808685 BCX2">characteristics.</span><span class="NormalTextRun SCXW235808685 BCX2"> Other population</span><span class="NormalTextRun SCXW235808685 BCX2"> genetic</span><span class="NormalTextRun SCXW235808685 BCX2"> processes, </span><span class="NormalTextRun SCXW235808685 BCX2">such as </span><span class="NormalTextRun SCXW235808685 BCX2">migration and genetic drift, </span><span class="NormalTextRun SCXW235808685 BCX2">can </span><span class="NormalTextRun SCXW235808685 BCX2">impede the effect</span><span class="NormalTextRun SCXW235808685 BCX2">s</span><span class="NormalTextRun SCXW235808685 BCX2"> of </span><span class="NormalTextRun SCXW235808685 BCX2">local adaptation</span><span class="NormalTextRun SCXW235808685 BCX2">. Genetic drift </span><span class="NormalTextRun SCXW235808685 BCX2">in particular </span><span class="NormalTextRun SCXW235808685 BCX2">can have a pronounced effect on population genetic structure during large-scale geographic expansions, where a series of founder effects lead</span><span class="NormalTextRun SCXW235808685 BCX2">s</span><span class="NormalTextRun SCXW235808685 BCX2"> to decreases in genetic variation in the direction of the expansion. </span><span class="NormalTextRun SCXW235808685 BCX2">Here </span><span class="NormalTextRun SCXW235808685 BCX2">we explore the </span><span class="NormalTextRun SCXW235808685 BCX2">genetic diversity</span><span class="NormalTextRun SCXW235808685 BCX2"> of a desert lizard that occupies a wide range of environmental conditions and that has experienced post-glacial expansion northwards along two colonization routes. </span><span class="NormalTextRun SCXW235808685 BCX2">Based on our analyses of a large SNP dataset, we find evidence </span><span class="NormalTextRun SCXW235808685 BCX2">that both </span><span class="NormalTextRun SCXW235808685 BCX2">climate and demographic history</span><span class="NormalTextRun SCXW235808685 BCX2"> </span><span class="NormalTextRun SCXW235808685 BCX2">have </span><span class="NormalTextRun SCXW235808685 BCX2">shape</span><span class="NormalTextRun SCXW235808685 BCX2">d</span><span class="NormalTextRun SCXW235808685 BCX2"> the </span><span class="NormalTextRun SCXW235808685 BCX2">genetic</span><span class="NormalTextRun SCXW235808685 BCX2"> structure of</span><span class="NormalTextRun SCXW235808685 BCX2"> populations. </span><span class="NormalTextRun SCXW235808685 BCX2">P</span><span class="NormalTextRun SCXW235808685 BCX2">ronounced genetic differentiation</span><span class="NormalTextRun SCXW235808685 BCX2"> was evident </span><span class="NormalTextRun SCXW235808685 BCX2">between populations occupying cold versus hot desert</span><span class="NormalTextRun SCXW235808685 BCX2">s</span><span class="NormalTextRun SCXW235808685 BCX2">,</span><span class="NormalTextRun SCXW235808685 BCX2"> and </span><span class="NormalTextRun SCXW235808685 BCX2">we </span><span class="NormalTextRun SCXW235808685 BCX2">detected numerous loci </span><span class="NormalTextRun SCXW235808685 BCX2">with </span><span class="NormalTextRun SCXW235808685 BCX2">significant association</span><span class="NormalTextRun SCXW235808685 BCX2">s</span><span class="NormalTextRun SCXW235808685 BCX2"> with climate. The genetic signal of founder effect</span><span class="NormalTextRun SCXW235808685 BCX2">s</span><span class="NormalTextRun SCXW235808685 BCX2">, however, is still present in the genomes of the recently expanded populations</span><span class="NormalTextRun SCXW235808685 BCX2">, </span><span class="NormalTextRun SCXW235808685 BCX2">which</span><span class="NormalTextRun SCXW235808685 BCX2"> comprise subsets of genetic variation found in the southern populations, and </span><span class="NormalTextRun SCXW235808685 BCX2">we found substantial evidence that </span><span class="NormalTextRun SCXW235808685 BCX2">genetic diversity of lizards differs along the two colonization routes.</span></p>
Predation, functional response and demographic parameters of Orius albidipennis (Hemiptera:Anthocoridae) on Schizaphis graminum (Hemiptera:Aphididae): effect of host plant morphological attributes
<p>Plant attributes like leaf hairiness and trichome compactness diversely affect the biocontrol agents of phytophagous insect pests. In the current study, effect of physical plant features on life table characteristics and functional response of <em>Orius albidipennis </em>(Rueter) females feeding on <em>Schizaphis graminum </em>(Rondani) was investigated on two common wheat cultivars (Falat and Pishtaz) differing in leaf morphological features. The trichome density of wheat cultivars considerably influenced a broad spectrum of attributes related to the performance of <em>O. albidipennis</em>. The intrinsic rate of increase (<em>rm</em>) was significantly greater on Falat (0.09±0.006) than on Pishtaz (0.06±0.008) cultivar. Similarly, the net reproductive rate and finite rate of increase were greater on Falat (16.72±3.38 and 1.083±7.54) than on Pishtaz (8.08±2.04 and 1.067±9.49). Although <em>Orius </em>predators exhibited type III of functional response on both wheat cultivars, they had lesser searching efficiencies and higher handling times on Pishtaz than those on Falat cultivar. Moreover, the maximum attack rate (<em>T</em>/<em>Th</em>) was greater on Falat than on Pishtaz. Lesser maximum predation and greater handling time of the <em>Orius </em>predators on Pishtaz cultivar might be imputed to the significantly more condensed surface trichomes of its leaves than that of Falat leaves, which physically prevented movement of the <em>Orius </em>bugs and decreased prey encounter rate. Moreover, increase of trichome density negatively influenced on foraging behavior of the predatory bug. Females were also found to prefer wheat leaves with fewer trichomes as oviposition hosts. It seems that trichomes provided hinderance to the <em>orius </em>bug. To recapitulate, it could be stated that the efficiency of <em>O. albidipennis </em>in controlling <em>S. graminum </em>on wheat may be more beneficial in cultivars with lower trichome density.</p>
Data from: Genomic data and multi-species demographic modelling uncover past hybridization between currently allopatric freshwater species
<p>Evidence for ancient interspecific gene flow through hybridization has been reported in many animal and plant taxa based on genetic markers. The study of genomic patterns of closely related species with allopatric distributions allows the assessment of the relative importance of vicariant isolating events and past gene flow. Here, we investigated the role of gene flow in the evolutionary history of four closely related freshwater fish species with currently allopatric distributions in western Iberian rivers - Squalius carolitertii, S. pyrenaicus, S. torgalensis and S. aradensis - using a population genomics dataset of 23 562 SNPs from 48 individuals, obtained through genotyping by sequencing (GBS). We uncovered a species tree with two well differentiated clades: (i) S. carolitertii and S. pyrenaicus; and (ii) S. torgalensis and S. aradensis. By using D-statistics and demographic modelling based on the site frequency spectrum, comparing alternative demographic scenarios of hybrid origin, secondary contact and isolation, we found that the S. pyrenaicus North lineage is likely the result of an ancient hybridization event between S. carolitertii (contributing ~84%) and S. pyrenaicus South lineage (contributing ~16%), consistent with a hybrid speciation scenario. Furthermore, in the hybrid lineage we identify outlier loci potentially affected by selection favouring genes from each parental lineage at different genomic regions. Our results suggest that ancient hybridization can affect speciation and that freshwater fish species currently in allopatry are useful to study these processes.</p>
Figure 4 in Population genetic structure and demographic history of the Chinese endemic Mongoloniscus sinensis (Dollfus, 1901) (Isopoda: Oniscidea)
Figure 4. Pairwise mismatch distributions for six derived clades.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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