Find research datasets worth reusing

opencc-by-nc-4.0Oct 2016View details →

Comparing Machine Learning Classifiers and Linear/Logistic Regression to Explore the Relationship between Hand Dimensions and Demographic Characteristics

----------------------------------------------------------------------------------------------------------------- Data for "Comparing Machine Learning Classifiers and Linear/Logistic Regression to Explore the Relationship between Hand Dimensions and Demographic Characteristics" (PLOSONE) Oscar Miguel-Hurtado1, Richard Guest1, Sarah V. Stevenage2,Greg J. Neil2,Sue Black3 <ul> <li>1 School of Engineering and Digital Arts, University of Kent, Canterbury, UK</li> <li>2 Department of Psychology, University of Southampton, Southampton, UK</li> <li>3 Centre for Anatomy and Human Identification, University of Dundee, Dundee, UK</li> </ul> ----------------------------------------------------------------------------------------------------------------- For more information please contact: O.Miguel-Hurtado-98@kent.ac.uk (Oscar Miguel) ----------------------------------------------------------------------------------------------------------------- The zip contains right and left hand geometry images from 112 participants. The images were captured using a Nikon D200 SLR camera (format: jpg, size: 3504x2336 pixels), with both the palm of the hand and camera facing downwards. Participants placed each hand on an acetate sheet with a series of positioning pegs. ----------------------------------------------------------------------------------------------------------------- The excel contains a series of length measurements (based on the underlying skeleton of the hand) manually extracted (see Figure 1 for details) along with demographic information from the participants: sex (male or female), height (in cm), weight (in kg) and foot size (in UK sizes).

opencc-zeroNov 2023View details →

Data from: Investigating the spatial, demographic, and genetic structures of Cylicodiscus gabunensis Harms, a light-demanding African timber species

Most Central African rainforest canopies consist of light-demanding tree species that hold high commercial value but also suffer locally from regeneration deficits, raising concerns about the sustainability of logging. Regeneration is influenced by factors such as past perturbations (including human activity), mating systems, and seed/pollen dispersal processes that impact demographic, spatial, and genetic structures within populations. To gain a better understanding of these interactions, we studied the spatial distribution and trunk diameter structure of Cylicodiscus gabunensis (Fabaceae) - a wind-dispersed, insect-pollinated, timber species - in three plots ranging from 400 to 839 ha situated in various environmental contexts (e.g. forest types and elephant densities) across Central Africa. We also genotyped adults and juveniles using microsatellite markers to analyze the spatial genetic structure of each population and infer the selfing rate, seed and pollen dispersal capacities and selection gradients using the 'neighborhood model'. The selfing rate was low (3 – 4 %), and seed dispersal distances (ds = 184 m) were much shorter than pollen dispersal distances (dp > 2 km). The three populations displayed contrasted spatial, demographic and genetic structures. One population showed no spatial aggregation or genetic structure, and a multimodal diameter structure indicating pulses of regeneration events. Two populations showed strong spatial aggregation and genetic structures. One exhibited a unimodal diameter structure indicating one ancient pulse of regeneration, while the other displayed a 'reverse J-shaped' diameter structure, typical of ongoing regeneration. In the latter, reproductive success appeared leptokurtic, three mother trees accounting for over 90 % of the regeneration and no tree below the minimum cutting diameter implemented by logging companies had offspring. The idiosyncratic nature of population characteristics observed in C. gabunensis suggests that, for sustainable management, a nuanced approach is needed. This involves protecting productive seed trees in areas where natural regeneration is occurring and actively supporting regeneration in areas exhibiting deficits, especially in contexts with low elephant densities.

opencc-zeroNov 2023View details →

Genetic diversity, genetic differentiation and demographic history of Cryptomeria (Cupressaceae), a Tertiary relict plant in East Asia based on RAD sequencing

Genetic structure and distribution patterns of modern floras are strongly affected by climatic change and geographical isolation. In the present study, we applied restriction-site-associated DNA sequencing (RAD-seq) to analyze the genetic structure and to simulate the demographic history of two extant Cryptomeria species in Japan (C. japonica) and Southeastern China (C. japonica var. sinensis). Thirteen natural populations representing the entire species distributed in East Asia were collected from Japan and China. At the species level, the genetic diversity of Cryptomeria was moderate (Ho = 0.217, He = 0.203) with a significant genetic differentiation among populations (85.30%, P < 0.001), especially between Japan and China lineages (FST = 0.147). Except for the Lushan (LS) population in China, all populations were clustered into two lineages (Japanese and Chinese), which was consistent with their geographical distribution. Approximate Bayesian computations (ABC) model indicated that the current two geographical lineages diverged from a common ancestral lineage and that their divergence time was about 0.417 ~ 0.139 million years ago (Mya). Geographical isolation, climate change in the Quaternary, and human disturbance played important roles in genetic variation and distribution patterns of Cryptomeria in East Asia. Our results shed light on the speciation processes of Cryptomeria and provide a reference for the conservation of this species.

opencc-zeroDec 2023View details →

High quality genomes produced from single MinION flow cells clarify polyploid and demographic histories of critically endangered Fraxinus (ash) species

With populations of threatened and endangered species declining worldwide, efforts are being made to generate high-quality genomic records of these species before they are lost forever. Here, we demonstrate that data from single Oxford Nanopore Technologies (ONT) MinION flow cells can, even in the absence of highly accurate short DNA-read polishing, produce high-quality de novo plant genome assemblies adequate for downstream analyses, such as synteny and ploidy evaluations, paleodemographic analyses, and phylogenomics. This study focuses on three North American ash tree species in the genus Fraxinus (Oleaceae) that were recently added to the International Union for Conservation of Nature (IUCN) Red List as critically endangered. Our results support a whole genome triplication at the base of the Oleaceae as well as a subsequent whole genome duplication shared by Syringa, Osmanthus, Olea, and Fraxinus. Finally, we demonstrate the use of ONT long-read sequencing data to reveal patterns in demographic history.

opencc-by-4.0Dec 2023View details →

Supporting Data for "Local exposure misclassification in national models: relationships with urban infrastructure and demographics"

Overview: This dataset accompanies the recent publication "Local exposure misclassification in national models: relationships with urban infrastructure and demographics" (DOI: 10.1038/s41370-023-00624-z). It provides essential data for replicating and extending the analysis conducted in the study. The script for the analysis is available at https://github.com/SEChambliss-AQ/LD-analysis. The dataset consists of four key files. Files Included: <ol> <li> Gridded OSM and GSV Data (gridded_OSM_GSV.RDS): <ul> <li>This R object offers a 100mx100m grid covering select neighborhoods in the San Francisco Bay Area.</li> <li>Each grid cell includes average air pollution levels (Ultrafine Particle Count in thousand count per cubic meter; Nitrogen Dioxide in ppb) from mobile monitoring.</li> <li>The file also provides normalized z-scores of local density of urban infrastructure related to air pollutants based on OpenStreetMap (OSM) data.</li> <li>Further details can be found in the associated publication.</li> </ul> </li> <li> BartMachine Outputs (bartMachine R objects.zip): <ul> <li>A collection of R object outputs from the bartMachine package, an R-Java Bayesian Additive Regression Trees implementation.</li> <li>These objects, which can be regenerated using the provided script, are included to reduce computational requirements for future analyses.</li> <li>The script for generating these outputs is available at the above <a href="https://github.com/SEChambliss-AQ/LD-analysis">GitHub Repository</a>.</li> </ul> </li> <li> NO2 Predictions (CACES_criteria.csv): <ul> <li>Land Use Regression (LUR) data for Nitrogen Dioxide, provided by the Center for Air, Climate, and Energy Solutions.</li> <li>Methodologies for integrating these data with the gridded dataset are described in the publication and script.</li> </ul> </li> <li> UFP Predictions (CACES_UFP.csv): <ul> <li>Similar to the NO2 dataset, this file contains LUR data for Ultrafine Particle predictions.</li> <li>Methods for data integration are detailed in the publication and available script.</li> </ul> </li> </ol> Usage: These files are intended for researchers and analysts aiming to replicate or build upon the study's findings. They provide a source of data for exploring the complex interplay between air pollution, urban infrastructure, and demographic factors in urban environments. For detailed methodology and analysis, refer to the original publication and the accompanying GitHub repository.

Demographics and song repertoire sizes of cirl bunting populations

In order to improve conservation outcomes translocation or reintroduction of individuals may be necessary. When song learning birds are translocated, changes in the cultural diversity of song repertoires, or abnormal vocalisations, in the new population can be a problem. We monitored song production over 8 years in a reintroduced population of the cirl bunting (Emberiza cirlus). Chicks were removed from nests in Devon, UK, between 2006-2011, translocated at six days old to be hand-reared and released in Cornwall, UK. Recordings at the release site in 2011 showed a significantly reduced population repertoire and individuals sang abnormal song types compared to the source populations in Devon. However, recordings in 2019, showed population song repertoire had reached the level of source populations of similar size, and song types were species typical. Our study shows that species can recover from a cultural bottleneck and suggests that, for some song learning birds, if translocation of nestlings is necessary it may not lead to long-term problems for communication and thus population persistence. For future translocations of nestlings, we recommend that efforts are made to provide tutoring to enable song learning. This may be achieved by providing recordings but may also include providing adult song tutors. In addition, playback of 'normal' songs to translocated populations may aid in development of species typical song repertoires, although care must be taken that this is not disturbing the reintroduced birds.

Data from: Same places, same stories? Genomics reveals similar structuring and demographic patterns for four Pocillopora coral species in the southwestern Indian Ocean

Aim Efficiently protecting species requires knowing their ecological, life history and reproductive traits. This is particularly decisive for scleractinian corals, key components of coral reefs, which are experiencing critical declines. Yet their connectivity remains insufficiently documented. Here, we focused on four distinct species of the coral genus Pocillopora found in diverse habitats of the southwestern Indian Ocean and presenting various reproductive strategies. We aimed to understand whether these traits affect species connectivity. Location Archipelagos and islands of the southwestern Indian Ocean. Taxon Pocillopora spp. Methods We used target-capture to collect single-nucleotide polymorphisms (SNPs) from over a thousand colonies sampled across nine localities. From the ca. 1,400 SNPs retained per species, Bayesian clustering methods, networks and demographic inferences were applied to first infer the population genetic structure and connectivity of each species, then the demographic history of each population. Results All four Pocillopora species exhibited almost the same genetic structuring pattern, reflecting the sampled ecoregions (Madagascar and surrounding islands vs. Mascarene Islands). However, the genetic differentiation was stronger ( FST about 10 times higher) for P. acuta, the species inhabiting more enclosed habitats, such as lagoons and shallow waters, and reproducing mainly asexually. Similarly, all populations, except those from P. acuta, showed a signature of population expansion ca. 100,000 years ago, following the penultimate glacial period. Main conclusions These results indicate reduced gene flow between Madagascar and the Mascarenes, probably linked to currents, suggesting distinct connectivity networks that should be considered independently when setting up conservation plans. In addition, shared demographic histories reflect that populations from these species have probably met the same environmental constraints and reacted similarly, something that should be considered in light of the ongoing rapid climate change.

Supplementary material from: Alpine extremophytes in evolutionary turmoil: Complex diversification patterns and demographic responses of a Halophilic grass in a Central Asian biodiversity hotspot

Diversification and demographic responses are key processes shaping species evolutionary history. Yet we still lack a full understanding of ecological mechanisms that shape genetic diversity at different spatial scales upon rapid environmental changes. In this study, we examined genetic differentiation in an extremophilic grass Puccinellia pamirica and factors affecting its population dynamics among the occupied hypersaline alpine wetlands on the arid Pamir Plateau in Central Asia. Using genomic data, we found evidence of fine-scale population structure and gene flow among the localities established across the high-elevation plateau as well as fingerprints of historical demographic expansion. We showed that an increase in the effective population size could coincide with the Last Glacial Period, which was followed by the species demographic decline during the Holocene. Geographic distance plays a vital role in shaping the spatial genetic structure of P. pamirica alongside with isolation-by-environment and habitat fragmentation. Our results highlight a complex history of divergence and gene flow in this species-poor alpine region during the Late Quaternary. We demonstrate that regional climate specificity and a shortage of nonclimate data largely impede predictions of future range changes of the alpine extremophile using ecological niche modeling. This study emphasizes the importance of fine-scale environmental heterogeneity for population dynamics and species distribution shifts.

Demographic feedbacks during evolutionary rescue can slow or speed adaptive evolution

Populations declining toward extinction can persist via genetic adaptation in a process called evolutionary rescue. Predicting evolutionary rescue has applications ranging from conservation biology to medicine, but requires understanding and integrating the multiple effects of a stressful environmental change on population processes. Here we derive a simple expression for how generation time, a key determinant of the rate of evolution, varies with population size during evolutionary rescue. Change in generation time is quantitatively predicted by comparing how intraspecific competition and the source of maladaptation each affect the rates of births and deaths in the population. Depending on the difference between two parameters quantifying these effects, the model predicts that populations may experience substantial changes in their rate of adaptation in both positive and negative directions, or adapt consistently despite severe stress. These predictions were then tested by comparison to the results of individual-based simulations of evolutionary rescue, which validated that the tolerable rate of environmental change varied considerably as described by analytical results. We discuss how these results inform efforts to understand wildlife disease and adaptation to climate change, evolution in managed populations, and treatment resistance in pathogens.

opencc-zeroMar 2024View details →

The genomes of Hercules beetles reveal putative adaptive loci and distinct demographic histories in pristine North American forests

Beetles, despite their remarkable biodiversity and a long history of research, remain lacking in reference genomes annotated with structural variations of loci of adaptive significance. We sequenced and assembled high-quality chromosome-level genomes of four Hercules beetles which exhibit divergence in male horn size and shape, and body coloration. The four Hercules beetle genomes were assembled to 11 pseudo-chromosomes, where the three genomes assembled using Nanopore data (Dynastes grantii, D. hyllus, and D. tityus) were mapped to the genome assembled using PacBio + Hi-C data (D. maya). We demonstrated a striking similarity in genome structure among the four species. This conservative genome structure may be attributed to our use of the D. maya assembly as the reference; however, it is worth noting that such a conservative genome structure is a recurring phenomenon among scarab beetles. We further identified homologs of nine and three candidate-gene families that may be associated with the evolution of horn structure and body coloration, respectively. Structural variations in Scr and Ebony2 were detected and discussed for their putative impacts on generating morphological diversity in beetles. We also reconstructed the demographic histories of the four Hercules beetles using heterozygosity information from the diploid genomes. We found that the demographic histories of the beetles closely recapitulated historical changes in suitable forest habitats driven by climate shifts.

opencc-by-4.0Apr 2021View details →

AWESOME Demographic and Socio-economic Scenarios

In this record, scenarios for population and economic drivers are provided, expected to impact the agricultural sector for countries in the Mediterranean and adjacent regions relevant for the AWESOME models according to the Shared Socio-economic Pathways (SSP) guidelines for the horizon 2020-2100. These scenarios were designed, modelled and generated during the the first deliverable of AWESOME WP2, named D2.1 - Demographic Scenarios. Population scenarios are based on a probabilistic approach employing the Bayesian hierarchical population model proposed by Raftery et al., appropriately modified to fit within the SSP scenarios, while the economic drivers scenarios are provided in terms of the global macroeconomic MaGE model. Information concerning the methodology adopted for the scenario generation, the nature and format of the produced data as well as a small but representative sample of the produced projections are presented in the relevant report. This record contains: - The deliverable's report where the model considerations for generating both population (probabilistic) and economic scenarios under the SSP setting are presented. - The propabilistic scenarios output for population under the SSP framework for the aggregate Mediterannean region and at national level for each country in the region (rda files in the compresed folders) (the country list is contained in the report). - The generated economic drivers scenarios output under the SSP framework for the aggregate Mediterannean region and at national level for each country in the region (xls file). - Description of the data (txt file)

opencc-zeroMar 2024View details →

Nitrogen dioxide exposure, health outcomes, and associated demographic disparities due to gas and propane combustion by US stoves

Gas and propane stoves emit nitrogen dioxide (NO2) pollution indoors, but the exposures of different U.S. demographic groups are unknown. We estimate NO2 exposure and health consequences using emissions and concentration measurements from >100 homes, a room-specific indoor air quality model, epidemiological risk parameters, and statistical sampling of published housing characteristics and occupant behavior. Gas and propane stoves increase long-term NO2 exposure by an estimated 4.0 ppbv on average across the United States, 75% of the World Health Organization (WHO)'s exposure guideline. This increased exposure may cause approximately 50 thousand cases of current pediatric asthma from long-term NO2 exposure alone. Short-term NO2 exposure from typical gas stove use frequently exceeds both World Health Organization and U.S. EPA benchmarks. Residents of residences <800 ft2 in size incur 4 times more long-term NO2 exposure than residents of residences >3000 ft2 in size; American Indian/Alaska Native and Black and Hispanic/Latino households incur 60% and 20% more NO2 exposure, respectively, than the national average.

opencc-by-4.0Mar 2024View details →

Supplementary file for the manuscript entitled: Demographic and genetic impacts of powdery mildew in a young oak cohort

Barres et al 2023 Supplementary material-vf.pdf: supplementary material file for the related article

opencc-zeroDec 2023View details →

Data from: Tree demographic strategies largely overlap across succession in Neotropical wet and dry forest communities

Secondary tropical forests play an increasingly important role in carbon budgets and biodiversity conservation. Understanding successional trajectories is therefore imperative for guiding forest restoration and climate change mitigation efforts. Forest succession is driven by the demographic strategies – combinations of growth, mortality, and recruitment rates – of the tree species in the community. However, our understanding of demographic diversity in tropical tree species stems almost exclusively from old-growth forests. Here, we assembled demographic information from repeated forest inventories along chronosequences in two wet (Costa Rica, Panama) and two dry (Mexico) Neotropical forests to assess whether the ranges of demographic strategies present in a community shift across succession. We calculated demographic rates for >500 tree species while controlling for canopy status to compare demographic diversity (i.e. the ranges of demographic strategies) in early successional (0-30 years), late successional (30-120 years), and old-growth forests using two-dimensional hypervolumes of pairs of demographic rates. Ranges of demographic strategies largely overlapped across successional stages, and early successional stages already covered the full spectrum of demographic strategies found in old-growth forests. An exception was a group of species characterized by exceptionally high mortality rates that were confined to early successional stages in the two wet forests. The range of demographic strategies did not expand with succession. Our results suggest that studies of long-term forest monitoring plots in old-growth forests, from which most of our current understanding of demographic strategies of tropical tree species is derived, are surprisingly representative of demographic diversity in general, but do not replace the need for further studies in secondary forests.

opencc-by-4.0Jan 2022View details →

FIG. 1 in Demographic and spatial structure at the stage of expansion in the populations of some alien land snails in Belgorod city (Central Russian Upland)

FIG. 1. Map of study sites. РИС. 1. Карта раЗмеЩения исследуемых участков.

opencc-by-4.0Nov 2024View details →

Harmonized INSEE socio-demographic IRIS-level data and IRIS conversion file (2010-2020)

The smallest level of aggregation for sociodemographic data made publicly available by the French INSEE is the IRIS. Data is downloadable on INSEE websites but decomposed by type of variable and by year. I thus combined all datasets into a single homogenous dataset for practicality. It includes on the period 2010-2020 : <ul> <li>Population structure (age, gender...) data</li> <li>Economic occupation CSP data</li> <li>Available income data</li> <li>Family data</li> </ul> Since a sizeable amount of IRIS change each year, timewise comparisons are limited. I therefore created a conversion file. Each IRIS is expressed as a % combination of previous IRIS. This allows to track IRIS merge, IRIS split and border changes. Measurement errors linked to border overlap were detected when the overlap of 2 IRIS was less than 1 percent. The IRIS overlap without the measurement error is the variable _ajuste (pardon my French). This allows to express the IRIS of a year as the wieghted sum of the IRIS of any other given year. You will also find the codes I used to create each of the files included in this project on my github. The annotation may be lacking, it is currently being improved.

opencc-by-4.0Sep 2024View details →

Resources for "BMF CP 91: Socio-demographic factors, illness experience, severity perception, and sensitivity to air quality index"

The current study is conducted to examine the following research questions: <ul> <li>What are the factors associated with the sensitivity towards the air quality rating index to reduce outdoor activities?</li> </ul>

opencc-zeroOct 2021View details →

Dispersal patterns in black howler monkeys (Alouatta pigra): Integrating multi-year demographic and molecular data

Dispersal is a fundamental process in the functioning of animal societies as it regulates the degree to which closely related individuals are spatially concentrated. A species' dispersal pattern can be complex as it emerges from individuals' decisions shaped by the cost-benefit tradeoffs associated with either remaining in the natal group or dispersing. Given the potential complexity, combining long-term demographic information with molecular data can provide important insights into dispersal patterns of a species. Based on a 15-year study that integrates multi-year demographic data on six groups with longitudinal and cross-sectional genetic sampling of 20 groups (N=169 individuals, N=21 polymorphic microsatellite loci), we describe the various dispersal strategies of male and female black howler monkeys (Alouatta pigra) inhabiting Palenque National Park, Mexico. Genetically confirmed dispersal events (N=21 of 59 males; N=6 of 65 females), together with spatial autocorrelation analyses revealed that the dispersal pattern of black howlers is bisexual with strong sex-biases in both dispersal rate (males disperse more often than females) and dispersal distance (females disperse farther than males). Observational and genetic data confirm that both males and females can successfully immigrate into established groups, as well as form new groups with other dispersing individuals. Additionally, both males and females may disperse singly, as well as in pairs, and both may also disperse secondarily. Overall, our findings suggest multiple dispersal trajectories for black howler males and females, and longer multi-year studies are needed to unravel which demographic, ecological, and social factors underlie individuals' decisions about whether to disperse and which dispersal options to take.

opencc-zeroNov 2021View details →

Data from: Phylogeographic and demographic patterns reveal congruent histories in seven Amazonian white-sand ecosystems birds

Aim: As the most biodiverse region of the world, the drivers of genetic diversity in Amazonia are still poorly understood. It has been debated that species on distinct ecosystems will show unique biogeographic histories tied to their habitats which in turn help understand landscape climatic history in Amazonia. We studied bird species associated with patchy Amazonian white-sand ecosystems (WSE) to evaluate the occurrence of shared patterns and its relationship to species habitat preferences and Amazonian environmental and landscape history. Location: Northern South America; Amazonia. Taxon: Passerine birds. Methods: We sequenced Ultra-conserved Elements (UCEs) from 177 samples of seven bird species associated with WSE that have overlapping ranges. We used the SNP matrices and sequence data to estimate genetic structure patterns and migration surfaces using 'conStruct' and eems, perform model-selection to obtain the most probable demographic histories on 'PipeMaster', and implement analyses of shared demography with ecoevolity. Results: Shallow genetic structure patterns varied among species with the Amazon river being the only barrier shared among them. Population structure dates to no more than 450,000 years ago. We identified 17 geographically structured populations from which nine showed signals of population size changes and eight of these occur in Northern Amazonia. Population expansion was inferred at two distinct times: ~100,000 years ago and ~50,000 years ago. The timing of co-expanding populations is consistent with differences in habitat preference, as species that prefer dense scrubby to forested vegetation expanded more recently compared to species that prefer open vegetation. Main conclusions: We show that WSE species responded in concert to past environmental and landscape changes. Past population expansions were likely driven by the genesis of new WSE patches and a return to wetter conditions after glacial periods. Pleistocene climatic cycles affected the distribution and dynamics of open vegetation habitats in Amazonia, especially in the Northern region, driving genetic diversity and demographic patterns of its associated biota.