Find research datasets worth reusing

opencc-zeroJan 2020View details →

Data and code from: Phenotypic memory drives population growth and extinction risk in a noisy environment

Random environmental fluctuations pose major threats to wild populations. As patterns of environmental noise are themselves altered by global change, there is growing need to identify general mechanisms underlying their effects on population dynamics. This notably requires understanding and predicting population responses to the color of environmental noise, i.e. its temporal autocorrelation pattern. Here, we show experimentally that environmental autocorrelation has a large influence on population dynamics and extinction rates, which can be predicted accurately provided that a memory of past environment is accounted for. We exposed near to 1000 lines of the microalgae Dunaliella salina to randomly fluctuating salinity, with autocorrelation ranging from negative to highly positive. We found lower population growth, and twice as many extinctions, under lower autocorrelation. These responses closely matched predictions based on a tolerance curve with environmental memory, showing that non-genetic inheritance can be a major driver of population dynamics in randomly fluctuating environments.

opencc-zeroDec 2016View details →

Data from: Combining niche-shift and population genetic analyses predicts rapid phenotypic evolution during invasion

Rapid evolution of non-native species can facilitate invasion success, but recent reviews indicate that such microevolution rarely yields expansion of the climatic niche in the introduced habitats. However, because some invasions originate from a geographically restricted portion of the native species range and its climatic niche, it is possible that the frequency, direction and magnitude of phenotypic evolution during invasion has been underestimated. We explored the utility of niche-shift analyses in the red seaweed Gracilaria vermiculophylla, which expanded from the northeastern coastline of Japan to North America, Europe and northwestern Africa within the last 100 years. A genetically-informed climatic niche shift analysis indicates that native source populations occur in colder and highly seasonal habitats, while most non-native populations typically occur in warmer, less seasonal habitats. This climatic niche expansion predicts that non-native populations evolved greater tolerance for elevated heat conditions relative to native source populations. We assayed 935 field-collected and 325 common-garden thalli from 40 locations and as predicted, non-native populations had greater tolerance for ecologically-relevant extreme heat (40ºC) than did Japanese source populations. Non-native populations also had greater tolerance for cold and low-salinity stresses relative to source populations. The importance of local adaptation to warm temperatures during invasion was reinforced by evolution of parallel clines: populations from warmer, lower-latitude estuaries had greater heat tolerance than did populations from colder, higher-latitude estuaries in both Japan and eastern North America. We conclude that rapid evolution plays an important role in facilitating the invasion success of this and perhaps other non-native marine species. Genetically-informed ecological niche analyses readily generate clear predictions of phenotypic shifts during invasions, and may help to resolve debate over the frequency of niche conservatism versus rapid adaptation during invasion.

opencc-zeroMar 2020View details →

Data from: How "simple" methodological decisions affect interpretation of population structure based on reduced representation library DNA sequencing: a case study using the lake whitefish

Reduced representation (RRL) sequencing approaches (e.g., RADSeq, genotyping by sequencing) require decisions about how much to invest in genome coverage and sequencing depth (library quality), as well as choices of values for adjustable bioinformatics parameters. To empirically explore the importance of these "simple" decisions, we generated two independent sequencing libraries for the same 142 individual lake whitefish (Coregonus clupeaformis) using a nextRAD RRL approach: (1) A small number of loci and low sequencing depth (library A); and (2) more loci and higher sequencing depth (library B). The fish were selected from populations with different levels of expected genetic subdivision. Each library was analyzed using the STACKS pipeline followed by three types of population structure assessment (FST, DAPC and ADMIXTURE) with iterative increases in the stringency of sequencing depth and missing data requirements, as well as more specific a priori population maps. Library B was always able to resolve strong population differentiation in all three types of assessment regardless of the selected parameters. In contrast, library A produced more variable results; increasing the minimum sequencing depth threshold (-m) resulted in a reduced number of retained loci, and therefore lost resolution at high -m values for FST and ADMIXTURE, but not DAPC. FST and DAPC were robust to varying the population map and increasing the stringency of missing data requirements. In contrast, ADMIXTURE was unable to resolve strong population differentiation when increasing these same parameters in library A. Similarly, when examining fine scale population subdivision, library B was robust to changing parameters but library A lost resolution depending on the parameter set. We used library B to examine actual subdivision in our study populations. All three types of analysis found complete subdivision among populations in Lake Huron, ON and Dore Lake, SK, Canada using 10,640 SNP loci. Weak population subdivision was detected in Lake Huron with fish from sites in the north-west, Search Bay, North Point and Hammond Bay, showing slight differentiation. Overall, we show that apparently simple decisions about library quality and bioinformatics parameters can have potentially important impacts on the interpretation of population subdivision. Although costly, the early investment in a high-quality library and more conservative stringency settings on STACKS parameters lead to a final dataset that was more consistent and robust when examining both weak and strong population differentiation.

opencc-zeroDec 2018View details →

Data from: Heterosis is common and inbreeding depression absent in natural populations of Arabidopsis thaliana

The importance of genetic drift in shaping patterns of adaptive genetic variation in nature is poorly known. Genetic drift should drive partially recessive deleterious mutations to high frequency, and inter‐population crosses may therefore exhibit heterosis (increased fitness relative to intra‐population crosses). Low genetic diversity and greater genetic distance between populations should increase the magnitude of heterosis. Moreover, drift and selection should remove strongly deleterious recessive alleles from individual populations, resulting in reduced inbreeding depression. To estimate heterosis, we crossed 90 independent line pairs of Arabidopsis thaliana from 15 pairs of natural populations sampled across Fennoscandia, and crossed an additional 41 line pairs from a subset of 4 of these populations to estimate inbreeding depression. We measured lifetime fitness of crosses relative to parents in a large outdoor common garden (8448 plants in total) in central Sweden. To examine the effects of genetic diversity and genetic distance on heterosis, we genotyped parental lines for 869 SNPs. Overall, genetic variation within populations was low (median expected heterozygosity = 0.02), and genetic differentiation was high (median FST = 0.82). Crosses between 10 of 15 population pairs exhibited significant heterosis, with magnitudes of heterosis as high as 117%. We found no significant inbreeding depression, suggesting that the observed heterosis is due to fixation of mildly deleterious alleles within populations. Widespread and substantial heterosis indicates an important role for drift in shaping genetic variation, but there was no significant relationship between fitness of crosses relative to parents and genetic diversity or genetic distance between populations.

opencc-zeroJul 2021View details →

Data from: Exploring genomic variation associated with drought stress in Picea mariana populations

Predicted increases in drought and heat stress will likely induce shifts in species bioclimatic envelopes. Genetic variants adapted to water limitation may prove pivotal for species response under scenarios of increasing drought. In this study, we aimed to explore this hypothesis by investigating genetic variation in 16 populations of black spruce (Picea mariana) in relation to climate variables in Alaska. A total of 520 single nucleotide polymorphisms (SNPs) were genotyped for 158 trees sampled from areas of contrasting climate regimes. We used multivariate and univariate genotype-by-environment approaches along with available gene annotations to investigate the relationship between climate and genetic variation among sampled populations. Nine SNPs were identified as having a significant association with climate, of which five were related to drought stress response. Outlier SNPs with respect to the overall environment were significantly overrepresented for several biological functions relevant for coping with variable hydric regimes, including osmotic stress response. This genomic imprint is consistent with local adaptation of black spruce to drought stress. These results suggest that natural selection acting on standing variation prompts local adaptation in forest stands facing water limitation. Improved understanding of possible adaptive responses could inform our projections about future forest dynamics and help prioritize populations that harbor valuable genetic diversity for conservation.

opencc-by-4.0Sep 2021View details →

Raw data for the article: A commentary on "Simultaneous versus staged resection for synchronous colorectal liver metastases: A population-based cohort study". Importance of avoiding any other additional risk in selected patients with synchronous colorectal liver metastases

We read with great interest the article of Dr. Bogach and Colleagues, in which they have evaluated trends of resection for synchronous colorectal cancer liver metastases (CRLM) and associated patient outcomes with a retrospective cohort study from 2006 to 2015 in the province of Ontario, Canada.

opencc-zeroSep 2021View details →

Data from: Decreased selectivity during mate choice in a small-sized population of a long-lived seabird

As biparental care is crucial for breeding success in Procellariiformes seabirds (i.e., albatrosses and petrels), these species are expected to be choosy during pair formation. However, the choice of partners is limited in small-sized populations, which might lead to random pairing. In Procellariiformes, the consequences of such limitations for mating strategies have been examined in a single species. Here, we studied mate choice in another Procellariiforme, Bulwer's petrel Bulweria bulwerii, in the Azores (ca 70 breeding pairs), where the species has suffered a dramatic population decline. We based our approach on both a 11-year demographic survey (capture-mark-recapture) and a genetic approach (microsatellites, n = 127 individuals). The genetic data suggest that this small population is not inbred and did not experience a genetic bottleneck. Moreover, pairing occurred randomly with respect to genetic relatedness, we detected no extrapair parentage (n = 35 offspring), and pair fecundity was unrelated to relatedness between partners. From our demographic survey, we detected no assortative mating with respect to body measurements and breeding experience and observed very few divorces, most of which were probably forced. This contrasts with the pattern previously observed in the much larger population from the Selvagens archipelago (assortative mating with respect to bill size and high divorce rate). We suggest that the Bulwer's petrels from the Azores pair with any available partner and retain it as long as possible despite the fact that reproductive performance did not improve with pair common experience, possibly to avoid skipping breeding years in case of divorce. We recommend determining whether decreased choosiness during mate choice also occurs in reduced populations of other Procellariiform species. This might have implications for the conservation of small threatened seabird populations.

opencc-zeroOct 2022View details →

Data for: Population genomic insights into invasion success in the polyphagous agricultural pest, Halyomorpha halys

Invasive species are increasingly threatening ecosystems and agriculture by rapidly expanding their range and adapting to environmental and human-imposed selective pressures. The genomic mechanisms that underlie such rapid changes remain unclear, especially for agriculturally important pests. Here, we use genome-wide polymorphisms derived from native, invasive, and intercepted samples and populations of the brown marmorated stink bug (BMSB), Halyomorpha halys, to gain insights into population genomics processes that have promoted the successful global invasion of this polyphagous pest. Our analysis demonstrated that BMSB exhibits spatial structure but admixture rates are high among introduced populations, resulting in similar levels of genomic diversity across native and introduced populations. These spatial genomic patterns suggest a complex invasion scenario, potentially with multiple bridgehead events, posing a challenge for accurately assigning BMSB incursions to their source using reduced-representation genomic data. By associating allele frequencies with the invasion status of BMSB populations, we found significantly differentiated SNPs located in close proximity to genes for insecticide resistance and olfaction. Comparing variations in allele frequencies among populations for outlier SNPs suggests that BMSB invasion success has likely evolved from standing genetic variation. In addition to being a major nuisance of households, BMSB has caused significant economic losses to agriculture in recent years and continues to expand its range. Despite no record of BMSB insecticide resistance to date, our results show high capacity for potential evolution of such characters, highlighting the need for future sustainable and targeted management strategies.

opencc-zeroOct 2022View details →

Data from: Resource availability affects seasonal trajectories of population-level learning

Environmental effects on learning are well known, such as cognition that is mediated by nutritional consumption. Less known is how seasonally variable environments affect phenological trajectories of learning. Here, we test the hypothesis that nutritional availability affects seasonal trajectories of population-level learning in species with developmentally plastic cognition. We test this in bumble bees (Apidae: Bombus), a clade of eusocial insects that produce individuals at different time points across their reproductive season and exhibit organ developmental plasticity in response to nutritional consumption. To accomplish this, we develop a theoretical model that simulates learning development across a reproductive season for a colony parameterized with observed life history data. Our model finds two qualitative seasonal trajectories of learning: (1) an increase in learning across the season and (2) no change in learning across the season. We also find these two qualitative trajectories revealed by empirical learning data; the proportion of workers successfully completing a learning test increases across a season for two bumble bee species (Bombus auricomus, Bombus pensylvanicus), but does not change for another three (Bombus bimaculatus, Bombus griseocollis, Bombus impatiens). This study supports the novel consideration that resources affect seasonal trajectories of population-level learning in species with developmentally plastic cognition.

opencc-by-4.0Sep 2022View details →

Data - Attack of the clones: population genetics reveals clonality of Colletotrichum lupini, the causal agent of lupin anthracnose

Colletotrichum lupini, causing lupin anthracnose, is one of the worst pathogens to lupin cultivation worldwide. Understanding its population structure and evolutionary potential is crucial to design successful disease management strategies. The objective of this study was to employ population genetics to investigate the genetic diversity, evolutionary dynamics and molecular basis of host-speciation of this notorious lupin pathogen. A collection of globally representative C. lupini isolates was genotyped through triple digest restriction-site associated DNA sequencing (3D-RADseq), resulting in a dataset of unparalleled resolution. Phylogenetic and structural analysis could distinguish four (I – IV) independent lineages. The strong population structure, low recombination rate and slow linkage decay strongly indicate that C. lupini reproduces clonally. Different morphologies and virulence patterns on white and Andean lupin were observed between and within clonal lineages. Lineage II  isolates were shown to have a mini chromosome which was also partly present in lineage III and IV, but not in lineage I isolates. Variation in the presence of this mini-chromosome could indicate a function related to virulence or host-speciation. All four lineages were present in the South American Andes region, which is concluded to be the center of origin of this species. Only members of lineage II have been found outside South America since the 1990s, indicating it as the current pandemic population. As a seed-borne pathogen, C. lupini has mainly spread through infected but symptomless seeds, stressing the importance of phytosanitary measures to prevent future outbreaks of strains that are yet confined to South America.

Dataset Literature Review Digital Forensic and Forensic Anthropology Population Data

Data ini dipergunakan untuk membuat penelitian sesuai dengan Tinjauan Literatur dengan kata kunci "Digital Forensik dan Forensic Anthropology Population Data"

Dataset Literature Review Digital Forensic AND Forensic Anthropology Population Data

Data ini digunakan untuk membuat penelitian berdasarkan tinjauan literatur dengan kata kunci "digital forensic" dan "forensic anthropology population data"

opencc-zeroNov 2022View details →

Data from: Hedging at the rear edge: Intraspecific trait variability drives the trajectory of marginal populations in a widespread boreal tree species

Rear-edge populations at the warm margin of species distribution are small, isolated and face environmental conditions at the limit of species bioclimatic envelope. Intraspecific phenotypic variation contributing to the persistence of peripheral populations is expected to become increasingly important under future climate conditions in order to avoid local extirpation where range shifts lag behind climate change velocity. We investigated the putative role of intraspecific phenotypic variation for the maintenance of rear-edge populations of fire-prone jack pine (Pinus banksiana), an obligate pyriscent boreal species. We assessed whether variation in cone serotiny is associated with the population trajectory of marginal stands located south of the boreal biome, in the temperate forest where natural wildfires are infrequent and unpredictable. To this end, we estimated stand-scale serotiny, minimal age and tree size structure in 26 jack pine stands from the rear edge (n = 17 sites) and the core (n = 9 sites) of the species' range in eastern Canada. On average, rear-edge jack pine populations are less serotinous albeit more variably compared to range-core populations where serotiny is more uniformly high. Rear-edge stands are generally older and display reverse J-shape tree size structure indicative of a multi-aged demographic equilibrium, whereas range-core stands are younger and show a unimodal stand structure depicting a single aging cohort generally lacking interfire recruitment. Eco-evolutionary dynamics shifts from a dependency on wildfires in range-core populations to stands that can regenerate and persist without recurrent fires at the rear edge, where stand-scale serotiny reaches values below 85%. Synthesis: Unlike range-core populations, rear-edge jack pine populations can locally rely on a dual life-history strategy to ensure both steady recruitment during fire-free intervals and successful postfire regeneration. This capacity to cope with infrequent and unpredictable fire regime should increase the resilience and resistance of jack pine populations as global changes alter fire dynamics of the boreal forest. More generally, unique intraspecific phenotypic variation in rear-edge populations contributes to long-term species persistence in marginal environmental conditions that might scale up with global changes. The conservation of rear-edge populations and their genetic legacy appears crucial for the resilience of species.

opencc-zeroNov 2022View details →

Data for: Ectoparasite population dynamics affected by host body size but not host density or water temperature in a 32-year long time series

Host density, host body size, and ambient temperature have all been positively associated with increases in parasite infection. However, the relative importance of these factors in shaping long-term parasite population dynamics in wild host populations is unknown due to the absence of long-term studies. Here, we examine long-term drivers of gill lice (Copepoda) infections in Arctic charr (Salmonidae) over 32 years. We predicted that host density and body size and water temperature would all positively affect parasite population size and population growth rate. Our results show that fish size was the main driver of gill lice infections in Arctic charr. In addition, Arctic charr became infected at smaller sizes and with more parasites in years of higher brown trout population size. Negative intraguild interactions between brown trout and Arctic charr appear to drive smaller Arctic charr to seek refuge in deeper areas of the lake, thus increasing infection risk. There was no effect of host density on the force of infection, and the relationship between Arctic charr density and parasite mean abundance was negative, possibly due to an encounter-dilution effect. The population densities of host and parasite fluctuated independently of one another. Water temperature had negligible effects on the temporal dynamics of the gill lice population. Understanding long-term drivers of parasite population dynamics is key for research and management. In fish farms, artificially high densities of hosts lead to vast increases in the transmission of parasitic copepods. However, in wild fish populations fluctuating at natural densities, the surface area available for copepodid attachment might be more important than the density of available hosts.

single-cell RNAseq data (data set 20) in the publication scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data

The present dataset (dataset20) was used as input to build scFASTCORMICS models. The files correspond to the clusters identified by Seurat in the single-cell data from breast cancer samples downloaded from the GEO website (GSE180286). see the protocol: scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data and github: https://github.com/sysbiolux/scFASTCORMICS For more information, version updates of the scFASTCORMICS.

single-cell RNAseq data (data set 18) in the publication scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data

The present dataset (dataset18) was used as input to build scFASTCORMICS models. The files correspond to the clusters identified by Seurat in the single-cell data from Liver cancer set 1 samples downloaded from the GEO website (GSE125449).  see the protocol: scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data and github: https://github.com/sysbiolux/scFASTCORMICS For more information, version updates of the scFASTCORMICS.

single-cell RNAseq data (data set 17) in the publication scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data

The present dataset (dataset17 was used as input to build scFASTCORMICS models. The files correspond to the clusters identified by Seurat in the single-cell data from PBMC metastatic MCC samples downloaded from the GEO website (GSE117988).  see the protocol: scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data and github: https://github.com/sysbiolux/scFASTCORMICS For more information, version updates of the scFASTCORMICS.

single-cell RNAseq data (data set 12) in the publication scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data

The present dataset (dataset12) was used as input to build scFASTCORMICS models. The files correspond to the clusters identified by Seurat in the single-cell data from pancreas donor10 downloaded from the GEO website  (GSE114297).    see the protocol: scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data and github: https://github.com/sysbiolux/scFASTCORMICS For more information, version updates of the scFASTCORMICS.

single-cell RNAseq data (data set 16) in the publication scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data

The present dataset (dataset16) was used as input to build scFASTCORMICS models. The files correspond to the clusters identified by Seurat in the single-cell data from CD4 T-cells in PACA samples downloaded from the GEO website (GSE156728).  see the protocol: scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data and github: https://github.com/sysbiolux/scFASTCORMICS For more information, version updates of the scFASTCORMICS.

single-cell RNAseq data (data set 11) in the publication scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data

The present dataset (dataset11) was used as input to build scFASTCORMICS models. The files correspond to the clusters identified by Seurat in the single-cell data from pancreas donor9 downloaded from the GEO website  (GSE114297).    see the protocol: scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data and github: https://github.com/sysbiolux/scFASTCORMICS For more information, version updates of the scFASTCORMICS.