Find research datasets worth reusing

opencc-zeroJul 2022View details →

Data From: Population-specific responses in eastern oysters exposed to low salinity in the northern Gulf of Mexico

Eastern oysters, Crassostrea virginica, are facing rapid environmental changes in the northern Gulf of Mexico and can respond to these changes via plasticity or evolution. Plastic responses can immediately buffer against environmental changes, although this buffering may impact the organism's ability to evolve in subsequent generations. While plasticity and evolution are not mutually exclusive, the relative contribution and interaction between them remain unclear. In this study, we investigate the roles of plastic and evolved responses to low salinity in C. virginica using a common garden experiment with four populations exposed to two salinities. We use three transcriptomic analyses (edgeR, PERMANOVA, and WGCNA) combined with physiology data to identify the effect of genotype (population), environment (salinity), and genotype-by-environment interaction on both whole organism and molecular phenotypes. We demonstrate that variation in gene expression is mainly driven by population, with relatively small changes in response to salinity. In contrast, the morphology and physiology data reveal that salinity has a larger influence on oyster performance than the population of origin. All analyses lacked signatures of genotype-by-environment interaction, and in contrast to previous studies, we find no evidence for population-specific responses to low salinity. However, individuals from the highest salinity estuary displayed highly divergent gene expression from other populations, which could potentially drive population-specific responses to other stressors. Our findings suggest that C. virginica largely rely on plasticity in physiology to buffer the effects of low salinity, but that these changes in physiology do not rely on large persistent changes in gene expression.

opencc-by-4.0Jun 2022View details →

Data and code for "Changing allometric relationships among fossil and Recent populations in two colonial species"

MEPS.plus.xlsx (dataset from Di Martino & Liow 2021) Microporella_allometry_22.03.2022.xlsx (Sheet 1: Measurement data; Sheet 2: Fossil sample metadata; Sheet 3: Recent samples metadata) allo.10.R (code)

opencc-by-4.0Jul 2022View details →

Data Release: Population properties and multimessenger prospects of neutron star-black hole mergers following GWTC-3

Neutron star-black hole (NSBH) mergers detected in gravitational waves have the potential to shed light on supernova physics, the dense matter equation of state, and the astrophysical processes that power their potential electromagnetic counterparts. We use the population of four candidate NSBH events detected in gravitational waves so far with a false alarm rate  ≤1 yr−1 to constrain the mass and spin distributions and multimessenger prospects of these systems. We find that the black holes in NSBHs are both less massive and more slowly spinning than those in black hole binaries. We also find evidence for a mass gap between the most massive neutron stars and least massive black holes in NSBHs at 98.6% credibility. We consider both a Gaussian and a power-law pairing function for the distribution of the mass ratio between the neutron star and black hole masses but find no statistical preference between the two. Using an approach driven by gravitational-wave data rather than binary simulations, we find that fewer than 14% of NSBH mergers detectable in gravitational waves will have an electromagnetic counterpart. Finally, we propose a method for the multimessenger analysis of NSBH mergers based on the nondetection of an electromagnetic counterpart and conclude that, even in the most optimistic case, the constraints on the neutron star equation of state that can be obtained with multimessenger NSBH detections are not competitive with those from gravitational-wave measurements of tides in binary neutron star mergers and radio and X-ray pulsar observations.

opencc-by-4.0May 2022View details →

Data to accompany the publication "Combined biophysical and genetic modelling approaches reveal complementary information about population connectivity of New Zealand green-lipped mussels"

Data to accompany the publication "Combined biophysical and genetic modelling approaches reveal complementary information about population connectivity of New Zealand green-lipped mussels".  migrationmatrix14.txt contains the particle tracking matrix, with the total number of particles that migrated from row i to column j (out of a total of 2217864 particles released per population). mussel_microsat_Genepop.txt contains the microsatellite data for each population in Genepop format.

opencc-zeroAug 2022View details →

Data for Contrasting life-history responses to climate variability in eastern and western North Pacific sardine populations

Massive populations of sardines inhabit both the western and eastern boundaries of the world's subtropical ocean basins, supporting both commercial fisheries and populations of marine predators. Sardine populations in western and eastern boundary current systems have responded oppositely to decadal scale anomalies in ocean temperature, but the mechanism for differing variability has remained unclear. Here, based on otolith microstructure and high-resolution stable isotope analyses, we show that habitat temperature, early life growth rates, energy expenditure, metabolically optimal temperature and, most importantly, the relationship between growth rate and temperature were remarkably different between the two subpopulations in the western and eastern North Pacific. Varying metabolic response to environmental changes partly explain the contrasting growth responses. Consistent differences in the life-history traits are observed between subpopulations in the western and eastern boundary current systems around South Africa. These growth and survival characteristics can facilitate the contrasting responses of sardine populations to climate change.

opencc-zeroSep 2022View details →

Epidendrum radicans - genetic data of 4 regional populations

Colonization is a fundamental ecological process that is important for the persistence of species, particularly when a changing environment necessitates range shifts. Vacant habitats available for colonization often arise from landscape disturbance. Colonization and population expansion processes can be inferred by examining the levels and spatial distribution of genetic variation of plant populations with known disturbance histories. Samples (N = 690) of the terrestrial orchid, Epidendrum radicans, were collected from five lava flow sites on the slopes of Volcán Arenal in Costa Rica that last experienced major eruptions in 1968 and 1992. Individuals were also sampled (N = 188) from four regional populations. Samples were characterized using 15 nuclear genetic markers and analyzed using population genetics statistics. Genetic diversity within sites was moderate (He = 0.092 – 0.192). Contrary to expectation, diversity tended to be lower on the older lava flows (0.131 versus 0.172) which may reflect their more sheltered topography that restricted pollen/seed immigration, and/or greater intra- and interspecific competition. Genetic diversity measures indicate that the lava flows were colonized by numerous individuals that likely originated from multiple sources while spatial genetic structure (SGS) statistics indicate that most recruitment in the study sites subsequent to colonization resulted from in situ reproduction and localized seed deposition. Younger sites had significantly greater SGS over larger distances which reflects fewer reproductive events, and less spatial and temporal overlap of seed shadows relative to the older sites. Clones were also generally larger on the older sites (≤ 8m versus ≤ 3m).

opencc-zeroSep 2022View details →

Raw RADseq data for: Population genomics analysis with RAD, reprised: Stacks 2

Restriction enzymes have been one of the primary tools in the population genetics toolkit for 50 years, being coupled with each new generation of technology to provide a more detailed view into the genetics of natural populations. Restriction site-Associated DNA protocols, which joined enzymes with short-read sequencing technology, have democratized the field of population genomics, providing a means to assay the underlying alleles in scores of populations. More than 10 years on, the technique has been widely applied across the tree of life and served as the basis for many different analysis techniques. Here, we provide a detailed protocol to conduct a RAD analysis from experimental design to de novo analysis—including parameter optimization—as well as reference-based analysis, all in Stacks version 2, which is designed to work with paired-end reads to assemble RAD loci up to 1000 nucleotides in length. The protocol focuses on major points of friction in the molecular approaches and downstream analysis, with special attention given to validating experimental analyses. Finally, the protocol provides several points of departure for further analysis.

opencc-zeroSep 2022View details →

Epidendrum radicans – x, y coordinates and genetic data of individuals within 5 focal populations

Colonization is a fundamental ecological process that is important for the persistence of species, particularly when a changing environment necessitates range shifts. Vacant habitats available for colonization often arise from landscape disturbance. Colonization and population expansion processes can be inferred by examining the levels and spatial distribution of genetic variation of plant populations with known disturbance histories. Samples (N = 690) of the terrestrial orchid, Epidendrum radicans, were collected from five lava flow sites on the slopes of Volcán Arenal in Costa Rica that last experienced major eruptions in 1968 and 1992. Individuals were also sampled (N = 188) from four regional populations. Samples were characterized using 15 nuclear genetic markers and analyzed using population genetics statistics. Genetic diversity within sites was moderate (He = 0.092–0.192). Contrary to expectation, diversity tended to be lower on the older lava flows (0.131 versus 0.172) which may reflect their more sheltered topography that restricted pollen/seed immigration, and/or greater intra- and interspecific competition. Genetic diversity measures indicate that the lava flows were colonized by numerous individuals that likely originated from multiple sources while spatial genetic structure (SGS) statistics indicate that most recruitment in the study sites subsequent to colonization resulted from in situ reproduction and localized seed deposition. Younger sites had significantly greater SGS over larger distances which reflects fewer reproductive events, and less spatial and temporal overlap of seed shadows relative to the older sites. Clones were also generally larger on the older sites (≤ 8m versus ≤ 3m).

Data and analysis from: Body mass, temperature, and depth shape the maximum intrinsic rate of population increase in sharks and rays

An important challenge in ecology is to understand variation in species' maximum intrinsic rate of population increase, 𝑟𝑚𝑎𝑥, not least because 𝑟𝑚𝑎𝑥 underpins our understanding of the limits of fishing, recovery potential, and ultimately extinction risk. Across many vertebrate species, terrestrial and aquatic, body mass and environmental temperature are important correlates of 𝑟𝑚𝑎𝑥. In sharks and rays, specifically, 𝑟𝑚𝑎𝑥 is known be lower in larger species, but also in deep-sea ones. We use an information-theoretic approach that accounts for phylogenetic relatedness to evaluate the relative importance of body mass, temperature and depth on 𝑟𝑚𝑎𝑥. We show that both temperature and depth have separate effects on shark and ray 𝑟𝑚𝑎𝑥 estimates, such that species living in deeper waters have lower 𝑟𝑚𝑎𝑥. Furthermore, temperature also correlates with changes in the mass scaling coefficient, suggesting that as body size increases, decreases in 𝑟𝑚𝑎𝑥 are much steeper for species in warmer waters. These findings suggest that there are (as-yet understood) depth-related processes that limit the maximum rate at which populations can grow in deep sea sharks and rays. While the deep ocean is associated with colder temperatures, other factors that are independent of temperature, such as food availability and physiological constraints, may influence the low 𝑟𝑚𝑎𝑥 observed in deep sea sharks and rays. Our study lays the foundation for predicting the intrinsic limit of fishing, recovery potential, and extinction risk species based on easily accessible environmental information such as temperature and depth, particularly for data-poor species. This repository contains the data and a minimum working example of the model-fitting process used for the article "Body mass, temperature, and depth shape productivity in sharks and rays", which is currently in press at Ecology and Evolution.

Data from: Identification of a minority population of LMO2+ breast cancer cells that integrate into the vasculature and initiate metastasis.

Metastasis is responsible for the majority of breast cancer-related deaths, however, identifying the cellular determinants of metastasis has remained challenging. Here, we identified a minority population of immature THY1+/VEGFA+ tumor epithelial cells in human breast tumor biopsies that display angiogenic features and are marked by the expression of the oncogene, LMO2. Higher abundance of LMO2+ basal cells correlated with tumor endothelial content and predicted poor distant recurrence-free survival in patients. Using MMTV-PyMT/Lmo2CreERT2 mice, we demonstrated that Lmo2 lineage-traced cells integrate into the vasculature and have a higher propensity to metastasize. LMO2 knockdown in human breast tumors reduced lung metastasis by impairing intravasation, leading to a reduced frequency of circulating tumor cells. Mechanistically, we find that LMO2 binds to STAT3 and is required for STAT3 activation by TNFα and IL6. Collectively, our study identifies a population of metastasis-initiating cells with angiogenic features and establishes the LMO2-STAT3 signaling axis as a therapeutic target in breast cancer metastasis.

Data from: Local adaptation in shell shape traits of a brooding chiton with strong population genomic differentiation

Comparing divergence in quantitative traits and neutral molecular markers, such as QST–FST comparisons, provides a means to distinguish between natural selection and genetic drift as causes of population differentiation in complex polygenic traits. Onithochiton neglectus (Rochebrune, 1881) is a morphologically variable chiton endemic to New Zealand, with populations distributed over a broad latitudinal environmental gradient. In this species, the morphological variants cluster into two geographically separated shell shape groups, and the phenotypic variation in shell shape has been hypothesised to be adaptive. Here, we assessed this hypothesis by comparing neutral genomic differentiation between populations (FST) with an index of phenotypic differentiation (PST). We used 7,562 putatively neutral single nucleotide polymorphisms (SNPs) across 15 populations and three clades of O. neglectus throughout New Zealand to infer FST. PST was calculated from 18 shell shape traits and gave highly variable estimates across populations, clades and shape groups. By systematically comparing PST with FST, we identified evidence of local adaptation in a number of the O. neglectus shell shape traits. This supports the hypothesis that shell shape could be an adaptive trait, potentially correlated with the ability to live and raft in kelp holdfasts.

Data and R computer code from: Summer elk calf survival in a partially migratory population

These data and computer code (written in R, https://www.r-project.org) were created to statistically evaluate a suite of intrinsic and extrinsic risk factors related to calf elk and their mothers' body condition and age. Specifically, known-fate data were collected from 94 elk calves monitored from 2013-2016 in a partially migratory elk (Cervus canadensis) population in Alberta, Canada. Along with adult female data on pregnancy status, age, and body condition, we created a time-to-event dataset that allowed us to analyze calf mortality risk in a time-to-event approach. We also estimated pooled survivorship and cause-specific mortality, as well as stratifying these metrics by migration tactic (resident vs. eastern migrant). Cox proportional hazards models were used to evaluate calf mortality risk in terms of forage biomass (kg/ha), bear predation risk (from an RSF), and other factors that varied between migration tactics. We tested for differences in a number of maternal reproductive parameters (e.g., pregnancy status) and for calf explanatory variables between migrant and resident elk segments. We also use cumulative incidence functions to estimate cause-specific mortality in this multiple carnivore system. Ultimately, we hope that this work helps wildlife managers anticipate how elk calf survival and partial migration dynamics are affected by grizzly bear predation, and our study builds on a long-term partial migration study at the Ya Ha Tinda Ranch in Alberta, Canada.

Data from: Protection status, human disturbance, snow cover and trapping drive density of a declining wolverine population in the Canadian Rocky Mountains

Protected areas are important in species conservation, but high rates of human-caused mortality outside their borders and increasing popularity for recreation can negatively affect wildlife populations. We quantified wolverine (Gulo gulo) population trends from 2011 to 2020 in >14 000 km2 protected and non-protected habitat in southwestern Canada. We conducted wolverine and multi-species surveys using non-invasive DNA and remote camera-based methods. We developed Bayesian integrated models combining spatial capture-recapture data of marked and unmarked individuals with occupancy data. Wolverine density and occupancy declined by 39 percent, with an annual population growth rate of 0.925. Density within protected areas was 3 times higher than outside and declined between 2011 (3.6 wolverines/1000 km2) and 2020 (2.1 wolverines/1000 km2). Wolverine density and detection probability increased with snow cover and decreased near development. Detection probability also decreased with human recreational activity. The annual harvest rate of 13% was above the maximum sustainable rate. We conclude that humans negatively affected the population through direct mortality, sub-lethal effects and habitat impacts. Our study exemplifies the need to monitor population trends for species at risk – within and between protected areas - as steep declines can occur unnoticed if key conservation concerns are not identified and addressed.

Data: Applying stochastic and Bayesian integral projection modeling to amphibian population viability analysis

Integral projection models (IPMs) can estimate the population dynamics of species for which both discrete life stages and continuous variables influence demographic rates. Stochastic IPMs for imperiled species, in turn, can facilitate population viability analyses (PVAs) to guide conservation decision-making. Biphasic amphibians are globally distributed, often highly imperiled, and ecologically well-suited to the IPM approach. Herein, we present the first stochastic size- and stage-structured IPM for a biphasic amphibian, the U.S. federally threatened California tiger salamander (Ambystoma californiense; CTS). This Bayesian model reveals that CTS population dynamics show the greatest elasticity to changes in juvenile and metamorph growth and that populations are likely to experience rapid growth at low density. We integrated this IPM with climatic drivers of CTS demography to develop a PVA and examined CTS extinction risk under the primary threats of habitat loss and climate change. The PVA indicates that long-term viability is possible with surprisingly high (20–50%) terrestrial mortality, but simultaneously identified likely minimum terrestrial buffer requirements of 600–1000 m while accounting for numerous parameter uncertainties through the Bayesian framework. These analyses underscore the value of stochastic and Bayesian IPMs for understanding both climate-dependent taxa and those with cryptic life histories (e.g., biphasic amphibians) in service of ecological discovery and biodiversity conservation. In addition to providing guidance for CTS recovery, the contributed IPM and PVA supply a framework for applying these tools to investigations of ecologically-similar species.

opencc-by-4.0Oct 2022View details →

Data for Survival probabilities of atmospheric particles: comparison based on theory, cluster population simulations, and observations in Beijing

Data for Survival probabilities of atmospheric particles: comparison based on theory, cluster population simulations, and observations in Beijing (https://doi.org/10.5194/acp-2022-484) Contact Santeri Tuovinen (santeri.tuovinen@helsinki.fi) for more details.

opencc-by-4.0May 2024View details →

Data for publication: A pipeline for in-depth analysis of DNA virus populations by profiling the low abundant virus variants and partial genomic components

Raw and processed sequence data from Oxford Nanopore and BGI short read sequencing platforms used in the publication: "A pipeline for in-depth analysis of DNA virus populations by profiling the low abundant virus variants and partial genomic components".

Data from: Genome-wide association mapping within a local Arabidopsis thaliana population more fully reveals the genetic architecture for defensive metabolite diversity

A paradoxical finding from genome-wide association studies (GWAS) in plants is that variation in metabolite profiles typically maps to a small number of loci, despite the complexity of underlying biosynthetic pathways. This discrepancy may partially arise from limitations presented by geographically diverse mapping panels. Properties of metabolic pathways that impede GWAS by diluting the additive effect of a causal variant, such as allelic and genic heterogeneity and epistasis, would be expected to increase in severity with the geographic range of the mapping panel. We hypothesized that a population from a single locality would reveal an expanded set of associated loci. We tested this in a French Arabidopsis thaliana population (< 1 km transect) by profiling and conducting GWAS for glucosinolates, a suite of defensive metabolites that have been studied in depth through functional and genetic mapping approaches. For two distinct classes of glucosinolates, we discovered more associations at biosynthetic loci than previous GWAS with continental-scale mapping panels. Candidate genes underlying novel associations were supported by concordance between their observed effects in the TOU-A population and previous functional genetic and biochemical characterization. Local populations complement geographically diverse mapping panels to reveal a more complete genetic architecture for metabolic traits.

Data from: Winter-moth populations are isolated on co-occurring tree species with contrasting budburst-phenology

Differences between neighbouring tree species in phenology could isolate populations of host-plant generalists that depend on matching the phenology of their host. We studied the relationship between the budburst phenology of two co-occurring tree species with early (hornbeams) and late (oaks) budburst, and the egg-hatching date of associated winter moths (Operophtera brumata) during two seasons (autumns starting in 2020 and 2021). A previous study in spring 2019 had found no winter moth larvae on the focal oaks, while we found them mainly on oaks with hornbeam neighbours in 2022. Congruently, adult winter moths were rarely encountered during the autumns of 2018 and 2019 and sparsely in 2020 and 2021, and then mainly near hornbeams.The vast majority of winter moths had early-hatching eggs when both hornbeams and oaks were present, matching the hornbeams rather than the oaks. Where hornbeam was absent in the neighbourhood, the few winter moths had late-hatching eggs.These results suggest that winter moth populations on hornbeam and oak are to some degree isolated from each other despite spatial proximity, so that recolonization of oaks by populations synchronized with budburst of hornbeam is slow. Therefore, trees would benefit from differing from their neighbours in budburst phenology with respect to herbivore damage.

Data from: Climate change and population persistence in a hibernating marsupial

Climate change has physiological consequences on organisms, ecosystems, and human societies, surpassing the pace of organismal adaptation. Hibernating mammals are particularly vulnerable as winter survival is determined by short-term physiological changes triggered by temperature. In these animals, winter temperatures cannot surpass certain threshold, above which hibernators arouse from torpor, increasing several fold their energy needs when food is unavailable. Here, we parameterized a numerical model predicting energy consumption in heterothermic species, and modeled winter survival at different climate change scenarios. As a model species, we used the arboreal marsupial monito del monte (genus Dromiciops) which is recognized as one of the few South America hibernators. We modeled four climate change scenarios (from optimistic to pessimistic), based on IPCC projections, predicting that northern and coastal populations (Dromiciops bozinovici) will decline because the minimum number of cold days needed to survive the winter will not be attained. These populations are also the most affected by habitat fragmentation and change in land use. Conversely, Andean and other highland populations at cooler environments, are predicted to persist and thrive. Given the widespread presence of hibernating mammals around the world, models based on simple physiological parameters such as this one, are becoming essential for predicting species responses to warming in the short term.

Data from: Longitudinal gut microbiome dynamics in relation to age and senescence in a wild animal population

In humans, gut microbiome (GM) differences are often correlated with, and sometimes causally implicated in, ageing. However, it is unclear how these findings translate in wild animal populations. Studies that investigate how GM dynamics change within individuals, and with declines in physiological condition, are needed to fully understand links between chronological age, senescence, and the GM, but have rarely been done. Here, we use longitudinal data collected from a closed population of Seychelles warblers (Acrocephalus sechellensis) to investigate how bacterial GM alpha diversity, composition, and stability are associated with host senescence. We hypothesised that GM diversity and composition will differ, and become more variable, in older adults, particularly in the terminal year prior to death, as the GM becomes increasingly dysregulated due to senescence. However, GM alpha diversity and composition remained largely invariable with respect to adult age and did not differ in an individual's terminal year. Furthermore, there was no evidence that the GM became more heterogenous in senescent age groups (individuals older than 6 years), or in the terminal year. Instead, environmental variables such as season, territory quality, and time of day, were the strongest predictors of GM variation in adult Seychelles warblers. These results contrast with studies on humans, captive animal populations, and some (but not all) studies on non-human primates, suggesting that GM deterioration may not be a universal hallmark of senescence in wild animal species. Further work is needed to disentangle the factors driving variation in GM-senescence relationships across different host taxa.