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171 results for “environmental association”

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dryad36/100

Hierarchical multi-grain models improve descriptions of species' environmental associations, distribution, and abundance

The characterization of species' environmental niches and spatial distribution predictions based on them are now central to much of ecology and conservation, but implicitly requires decisions about the appropriate spatial scale (i.e. grain) of analysis. Ecological theory and empirical evidence suggest that range-resident species respond to their environment at two characteristic, hierarchical spatial grains: (i) response grain, the (relatively fine) grain at which an individual uses environmental resources, and (ii) occupancy grain, the (relatively coarse) grain equivalent to a typical home range. We use a multi-grain (MG) occupancy model, aided by fine-grain remotely sensed imagery, to simultaneously estimate species-environment associations at both grains, conduct grain optimization to measure response grain, and apply this analysis framework to an example species: a medium-sized bird (Tockus deckeni) in a heterogeneous East African landscape. Based on home range analysis of movement data, we calculate an occupancy grain of 1km for T. deckeni. Using a grain optimization procedure across 32 grains from 10m to 500m, we identify 60m as the most strongly supported response grain for a suite of environmental variables, slightly coarser than opportunistic behavioral observations would have suggested. Validation confirms that the accuracy of the optimized MG occupancy model substantially exceeds that of equivalent single-grain (SG) occupancy models. We further use a simulation approach to assess the potential impacts of accounting for the multi-scale structure of species' environmental requirements on estimates of population size. We find that the more strongly supported MG approach consistently predicts a minimum population sizes in the study landscape that is much lower than that provided by the SG model. This suggests that SG approaches commonly used in conservation applications could lead to overly optimistic abundance and population estimates and that the MG approach may be more appropriate for supporting species conservation goals. More generally, we conclude that multi-grain approaches of the sort presented, and increasingly enabled by growing high-resolution remotely sensed data, hold great promise for offering a more mechanistic framework for assessing the appropriate grain(s) for population monitoring and management and enable more reliable estimates of abundances and species' distributions.

opencc-zeroJan 2020View details →

dryad36/100

Data from: Putative climate adaptation in American pikas (Ochotona princeps) is associated with copy number variation across environmental gradients

Improved understanding of the genetic basis of adaptation to climate change is necessary for maintaining global biodiversity moving forward. Studies to date have largely focused on sequence variation, yet there is growing evidence that suggests that changes in genome structure may be an even more significant source of adaptive potential. The American pika (Ochotona princeps) is an alpine specialist that shows some evidence of adaptation to climate along elevational gradients, but previous work has been limited to single nucleotide polymorphism (SNP)-based analyses within a fraction of the species range. Here, we investigated the role of copy number variation underlying patterns of local adaptation in the American pika using genome-wide data previously collected across the entire species range. We identified 37-193 putative copy number variants (CNVs) associated with environmental variation (temperature, precipitation, solar radiation) within each of the six major American pika lineages, with patterns of divergence largely following elevational and latitudinal gradients. Genes associated (n=158) with independent annotations across lineages, variables, and/or CNVs had functions related to mitochondrial structure/function, immune response, hypoxia, olfaction, and DNA repair, some of which have been previously linked to putative high elevation and/or climate adaptation that may serve as important targets in future studies.

opencc-zeroDec 2023View details →

zenodo36/100

Massaciuccoli Lake basin in Tuscany, Italy. Datasets of 75 environmental, geomorphologic, and socio-economic variables associated from remote past to remote future

Collection of 148 datasets representing 75 environmental, geomorphologic, and socio-economic variables associated with the Massaciuccoli Lake basin in Tuscany, Italy.  The data cover five temporal snapshots: remote past (1950-1980), recent past (1981-2015), present (2016.2024), near future (2050 under RCP4.5 and 8.5), and remote future (2100 under RCP4.5 and 8.5) Raster data have been harmonised and resampled at 0.0005° (~50 m) resolution. Vector data have been aligned and cut over the basin boundaries. A QGIS project using the WGS84 EPSG:4326 projection is included in the ZIP file.  A metadata file (in MS Excel format) reports data content descriptions, the primary sources, their FAIRness levels, and the direct links to the primary sources when available.  The dataset numbers are aligned to the table Id-column entries.

opencc-by-4.0Dec 2023View details →

dryad36/100

Data from: Spatiotemporal incidence of Zika and associated environmental drivers for the 2015-2016 epidemic in Colombia

Despite a long history of mosquito-borne virus epidemics in the Americas, the impact of the Zika virus (ZIKV) epidemic of 2015-2016 was unexpected. The need for scientifically informed decision-making is driving research to understand the emergence and spread of ZIKV. To support that research, we assembled a data set of key covariates for modeling ZIKV transmission dynamics in Colombia, where ZIKV transmission was widespread and the government made incidence data publically available. On a weekly basis between January 1, 2014 and October 1, 2016 at three administrative levels, we collated spatiotemporal Zika incidence data, nine environmental variables, and demographic data into a single downloadable database. These new datasets and those we identified, processed, and assembled at comparable spatial and temporal resolutions will save future researchers considerable time and effort in performing these data processing steps, enabling them to focus instead on extracting epidemiological insights from this important data set. Similar approaches could prove useful for filling data gaps to enable epidemiological analyses of future disease emergence events.

opencc-zeroDec 2017View details →

dryad36/100

Environmentally associated variation in dispersal distance affects inbreeding risk in a stream salamander

Avoiding inbreeding is considered a key driver of dispersal evolution, and dispersal distances should be especially important in mediating inbreeding risk because the likelihood of mating with relatives decreases with dispersal distance. However, a lack of direct data on dispersal distances has limited empirical tests of this prediction, particularly in the context of the multiple selective forces that can influence dispersal. Using a headwater salamander system, we tested whether spatial variation in environmental conditions leads to differences in dispersal distances, resulting in spatial variation in the effect of dispersal on inbreeding risk. Using capture-recapture and population genomic data from 5 streams, we found that dispersal distances were greater in downstream reaches than upstream reaches. Inbreeding risk was lower for dispersers than non-dispersers in downstream reaches, but not in upstream reaches. Furthermore, stream reaches did not differ in spatial patterns of individual relatedness, indicating that variation in inbreeding risk was in fact due to differences in dispersal distances. These results demonstrate that environmentally associated variation in dispersal distances can cause the inbreeding consequences of dispersal to vary at fine spatial scales. They also show that selective pressures other than inbreeding avoidance maintain phenotypic variation in dispersal, underscoring the importance of addressing alternative hypotheses in dispersal research.

opencc-zeroJul 2022View details →

dryad36/100

Global analysis of environmental and socioeconomic factors associated with human burden of environmentally mediated pathogens

This repository contains four datasets that support repeatability of the analyses in the Sokolow et al. paper published in Lancet Planetary Health. Descriptions of the four datasets are included in the metadata document. This study found that 80% of pathogen species known to infect humans are environmentally mediated, causing about 40% of contemporary infectious-disease burden (global loss of 130 million years of healthy life annually). More than 91% of this environmentally-mediated disease burden occurs in tropical countries, and the poorest countries carry the highest burdens across all latitudes. There were weak associations between disease burden and biodiversity or agricultural land use at the global scale. In contrast, the proportion of people with rural poor livelihoods in a country was a strong proximate indicator of environmentally mediated infectious disease burden there. Political stability and wealth were associated with improved sanitation, better health care, and lower proportions of rural poverty, indirectly resulting in lower burdens of environmentally mediated infections."

opencc-zeroAug 2022View details →

zenodo36/100

A mule deer's movements in the summer of 2016 in Wyoming, USA, and a set of associated environmental layers

These are the data associated with the paper "Defining Null Expectations for Animal Site Fidelity" by Picardi et al. The file muledeer_summer2016.rds is a data frame containing GPS tracking data for one individual mule deer during the summer of 2016 in Wyoming, USA. The file env_stack_issa.tiff is a raster stack containing environmental layers for the landscape where the mule deer was located. The layers in the stack are, in order: distance to roads (meters), distance to streams, rivers, or water bodies (meters), elevation (meters), slope (degrees), aspect (), topographic position index, terrain ruggedness index, roughness, percent tree cover, and forage biomass.

opencc-by-4.0Sep 2022View details →

dryad36/100

Do large-scale associations in birds imply biotic interactions or environmental filtering?

Aim: There has been a wide interest in the effect of biotic interactions on species' occurrences and abundances at large spatial scales, coupled with a vast development of the statistical methods to study them. Still, the evidence whether the effects of within-trophic level biotic interactions (e.g. competition and heterospecific attraction) are discernible beyond local scales remains inconsistent. Here, we present a novel hypothesis-testing framework based on joint dynamic species distribution models (JDSDMs) and functional trait similarity to dissect between environmental filtering and biotic interactions. Location: France and Finland. Taxon: Birds. Methods: We estimated species-to-species associations within a trophic level, independent of the main environmental variables (mean temperature and total precipitation) for common species at large spatial scale with joint dynamic species distribution models (VAST). We created hypotheses based on species' functionality (morphological and/or diet dissimilarity) and habitat preferences about the sign and strength of the pairwise spatio-temporal associations to estimate the extent to which they result from biotic interactions (competition, heterospecific attraction) and/or environmental filtering. Results: Spatio-temporal associations were mostly positive (80%), followed by random (15%), and only 5% were negative. Negative spatio-temporal associations in different communities were due to a few species when they existed. The relationship between spatio-temporal association and functional dissimilarity among species was negative, which fulfills the predictions of both environmental filtering and heterospecific attraction. Main conclusions: We showed that processes leading to species aggregation (mixture between environmental filtering and heterospecific attraction) seem to dominate assembly rules, and we did not find evidence for competition. Altogether, hypothesis-testing framework based on joint dynamic species distribution models and functional trait similarity is beneficial in ecological interpretation of species-to-species associations from the long-term large-scale data.

opencc-zeroSep 2022View details →

dryad36/100

Data from: Associations between developmental stability, canalization and phenotypic plasticity in plants with temporally heterogeneous environmental experience

We subjected eight plant species to a first round of alternating inundation and drought vs. constantly moderate water treatments and a second round of water conditions. Fluctuating asymmetry (FA), intra- and inter-individual variations (CVintra and CVinter), and plasticity in traits were measured and correlations between variables were calculated for each species. Early temporally heterogeneous experience decreased the leaf size of half of the species, but had complex effects on leaf fluctuating asymmetry (FA) and inter-individual variation (CVinter) in traits immediately or in late conditions, with little effects on intra-individual variation (CVintra). There were several positive correlations between FA and CVinter, while there were correlations between CVinter and plasticity in early treatments, but negative ones in late treatments.

opencc-zeroApr 2024View details →

dryad36/100

Environmentally acquired gut-associated bacteria are not critical for growth and survival in a solitary bee, Megachile rotundata

Social bees have been extensively studied for their gut microbial functions, but the significance of the gut microbiota in solitary bees remain less explored. Solitary bee, Megachile rotundata females provision their offspring with pollen from various plant species, harboring a diverse microbial community that colonizes larvae guts. The Apilactobacillus is the most abundant microbe, but evidence concerning the effects of Apilactobacillus and other provision microbes on growth and survival are lacking. We hypothesized that the presence of Apilactobacillus in abundance would enhance larval and prepupal development, weight, and survival, while the absence of intact microbial communities was expected to have a negative impact on bee fitness. We reared larvae on pollen provisions with naturally collected microbial communities (Natural pollen) or devoid of microbial communities (Sterile pollen). We also assessed the impact of introducing Apilactobacillus micheneri by adding it to both types of pollen provisions. Feeding larvae with sterile pollen + A. micheneri led to the highest mortality rate, followed by natural pollen + A. micheneri, and sterile pollen. Larval development was significantly delayed in groups fed with sterile pollen. Interestingly, larval and prepupal weights did not significantly differ across treatments compared to natural pollen-fed larvae. 16S rRNA gene sequencing found a dominance of Sodalis, when A. micheneri was introduced to natural pollen. The presence of Sodalis with abundant A. micheneri suggests potential crosstalk between both, shaping bee nutrition and health. Hence, this study highlights that the reliance on non-host specific environmental bacteria may not impact fitness of M. rotundata.

opencc-zeroJun 2024View details →

zenodo36/100

A Comprehensive Assessment of Demographic, Environmental and Host Genetic Associations with Gut Microbiome Diversity in Healthy Individuals (GWAS)

GWAS summary statistics accompanying manuscript  "A Comprehensive Assessment of Demographic, Environmental and Host Genetic Associations with Gut Microbiome Diversity in Healthy Individuals".

opencc-by-4.0Dec 2018View details →

dryad36/100

Data from: Genome-wide association studies across environmental and genetic contexts reveal complex genetic architecture of symbiotic extended phenotypes

A goal of modern biology is to develop the genotype-phenotype (G→P) map, a predictive understanding of how genomic information generates trait variation that forms the basis of both natural and managed communities. As microbiome research advances, however, it has become clear that many of these traits are symbiotic extended phenotypes, being governed by genetic variation encoded not only by the host's own genome, but also by the genomes of myriad cryptic symbionts. Building a reliable G→P map therefore requires accounting for the multitude of interacting genes and even genomes involved in symbiosis. Here we use naturally-occurring genetic variation in 191 strains of the model microbial symbiont Sinorhizobium meliloti paired with two genotypes of the host Medicago truncatula in four genome-wide association studies (GWAS) to determine the genomic architecture of a key symbiotic extended phenotype – partner quality, or the fitness benefit conferred to a host by a particular symbiont genotype, within and across environmental contexts and host genotypes. We define three novel categories of loci in rhizobium genomes that must be accounted for if we want to build a reliable G→P map of partner quality; namely, 1) loci whose identities depend on the environment, 2) those that depend on the host genotype with which rhizobia interact, and 3) universal loci that are likely important in all or most environments. IMPORTANCE: Given the rapid rise of research on how microbiomes can be harnessed to improve host health, understanding the contribution of microbial genetic variation to host phenotypic variation is pressing, and will better enable us to predict the evolution of (and select more precisely for) symbiotic extended phenotypes that impact host health. We uncover extensive context-dependency in both the identity and functions of symbiont loci that control host growth, which makes predicting the genes and pathways important for determining symbiotic outcomes under different conditions more challenging. Despite this context-dependency, we also resolve a core set of universal loci that are likely important in all or most environments, and thus, serve as excellent targets both for genetic engineering and future coevolutionary studies of symbiosis.

opencc-zeroOct 2021View details →

dryad36/100

Fine-scale environmentally associated spatial structure of Lumpfish ( Cyclopterus lumpus) across the Northwest Atlantic

Lumpfish, Cyclopterus lumpus, have historically been harvested throughout Atlantic Canada and are increasingly in demand as a solution to controlling sea lice in Atlantic salmon farms – a process which involves both the domestication and the transfer of lumpfish between geographic regions. Here, we have 70K SNP array data and whole genome re-sequencing data (WGS) for a variety of sample sites across the Northwest Atlantic.

opencc-zeroSep 2023View details →

dryad36/100