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opencc-zeroOct 2023View details →

Data for: Environmental complexity mitigates the demographic impact of sexual selection

Sexual selection and the evolution of costly mating strategies can negatively impact population demography and adaptive potential. While laboratory studies have documented outcomes stemming from these processes, theory suggests that the demographic impact of sexual selection is contingent on the environment and therefore may have been overestimated in simple laboratory settings. Here we find support for this claim. We exposed copies of beetle lines, previously evolved with or without sexual selection, to a 10-generation heatwave while maintaining half of them in a simple environment and the other half in a complex environment. Populations with an evolutionary history of sexual selection maintained larger sizes and more stable growth rates in complex (relative to simple) environments, an effect not seen in populations that evolved without sexual selection. These results have implications for evolutionary forecasting and suggest that the demographic impact of sexual selection in natural populations might be lower than predicted.

opencc-by-4.0Apr 2022View details →

Mark loss can strongly bias estimates of demographic rates in multi-state models: a case study with simulated and empirical datasets

This archive contains the empirical data analysed in the paper 'Mark loss can strongly bias estimates of demographic rates in multi-state models: a case study with simulated and empirical datasets' by Touzalin et al. (https://doi.org/10.24072/pci.ecology.100416).  The dataset is provided as a .Rdata file ('TLoss_GMdata.Rdata'), and full description of the content is provided in the file 'Readme_TLdata.csv'. All additional details are available in the main text (https://doi.org/10.24072/pci.ecology.100416) or in the supporting information (https://doi.org/10.5281/zenodo.10204538).

opencc-zeroNov 2023View details →

Data from: Ability of seedlings to survive heat and drought portends future demographic challenges for five southwestern US conifers

Climate change and disturbance are altering forests and the rates and locations of tree regeneration. We examined seedling survival of five southwestern United States (US) conifer species found in warmer and drier woodlands (Pinus edulis, P. ponderosa) and cooler and wetter subalpine forests (Pseudotsuga menziesii, Abies concolor, and Picea engelmanii) under hot and dry conditions in incubators. We constructed models that explained 53% to 76% of the species-specific survival variability, then applied these to recent climate (1980-2019) and projected climate (1980-2099) for the southwestern US. We found that lower elevations within species' range would have low survival under projected climate and that range contraction would be greatest for species that currently occupy warm-dry conditions. These results demonstrate that empirically derived physiological limitations can be used to identify where species composition or vegetation type change are likely to occur in the southwest US.

opencc-zeroApr 2024View details →

Extending Grime's CSR model to predict plant demographic responses across resource availability gradients: evidence from the Patagonian steppes

Sexual reproduction, growth, and survival are crucial demographic strategies for plant population viability. Here, we propose a conceptual model predicting demographic responses of species based on their ecological strategy and the heterogeneity of environmental conditions within a biogeographical unit and then applied it to a case study from a 5-degree latitudinal gradient in the Patagonian steppes. We also aim to disentangle genetic from environmental effects on demographic responses. We performed in-situ and common garden experiments with two species from six local populations of the Occidental Phytogeographical District of the Patagonian steppes. Species differ in key ecological traits, and thus fit into Grime´s model for evolutionary strategies in plants: one as competitive species and the other as stress-tolerant species. We calculated population growth rate (λ) and performed elasticity analyses to compare the contribution of each demographic strategy to population fitness between species and among local populations distributed along 600 km latitudinal gradient with differences in mean annual precipitation (MAP). We highlight four results. First, the competitive species change from sexual reproduction to growth as MAP increases. Second, the stress-tolerant species relied on growth and survival along the MAP gradient. Third, interannual variation in resource availability modulated demographic responses for both strategies. Fourth, based on the comparison of the in-situ and common garden experiments, we submit that demographic responses were genetically driven. Our study shows that demographic responses can be roughly predicted by the ecological strategy across environmental gradients. We show that differences arise not only between species, but also were genetically driven differences within species among local populations. Scaling up plant-level responses to population-level dynamics allows for a process-based understanding of current and future biogeographical species organization. Furthermore, conservation and restoration efforts should be guided by demographic strategies underlying population viability.

FIG. 5. Correlation between the spatial distribution index and population density. A 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. 5. Correlation between the spatial distribution index and population density. A. For Brephulopsis cylindrica and Xeropicta derbentina at 160 plots for three years. B. For Harmozica ravergiensis in nine sites×20 plots for two years. РИС. 5. Корреляция меЖду индексом пространственного распределения и плотностью популяции. А. Для Brephulopsis cylindrica и Xeropicta derbentina на 160 плоЩадках За три года. В. Для Harmozica ravergiensis на девяти участках по 20 плоЩадок За два года.

FIG. 4 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. 4. Boxplots for estimating the density of different age classes in the Xeropicta derbentina population in warm months of 2017, 2019, and 2020 for 160 test plots. Adult snails are represented by red boxes; juvenile snails are represented by blue boxes. РИС. 4. Боксплоты для оценок плотности раЗличных воЗрастных классов в популяции Xeropicta derbentina в раЗные теплые месяцы 2017, 2019 и 2020 гг. для 160 пробных плоЩадок. ВЗрослые особи покаЗаны красным цветом, ювенильные особи покаЗаны голубым цветом.

FIG. 3 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. 3. Boxplots for estimating the density of different age classes in the Brephulopsis cylindrica population in warm months of 2017, 2019, and 2020 for 160 test plots. Adult snails are represented by red boxes; juvenile snails are represented by blue boxes. РИС. 3. Боксплоты для оценок плотности раЗличных воЗрастных классов в популяции Brephulopsis cylindrica в раЗные теплые месяцы 2017, 2019 и 2020 гг. для 160 пробных плоЩадок. ВЗрослые особи покаЗаны красным цветом, ювенильные особи покаЗаны голубым цветом.

FIG. 2 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. 2. Scheme of plots in a regular grid. A. Study site. B. Brephulopsis cylindrica and Xeropicta derbentina in the field. C. Scheme of plots in a regular grid. РИС. 2. Регулярная сетка плоЩадок. A. РасполоЖение исследуемого участка. B. Brephulopsis cylindrica и Xeropicta derbentina в месте обитания. C. Схема регулярной сетки плоЩадок.

opencc-by-4.0Nov 2021View details →

Demographic history and natural selection shape patterns of deleterious mutation load and barriers to introgression across Populus genome

Abbreviation of species names in each folder: Palb, P. alba; Pade, P. adenopoda; Pdav, P. davidiana; Ptra, P. tremula; Ptrs, P. tremuloides; Prot, P. rotundifolia; Pqio,P. qiongdaoensis. 1. FST Relative divergence (FST) for pairwise species comparisons was calculated for all sites with 100 Kbp non-overlapping windows.  2. dxy Absolute divergence (dxy) was calculated for all sites with 100 Kbp non-overlapping windows.  3. Nucleotide diversity Nucleotide diversity (π) was calculated for all sites with 100 Kbp non-overlapping windows.  4. Derived allele frequency The derived frequencies of 4 different functional categories. Each folder contains seven Populus resluts 5. Derived_allele_statistics The statistics of homozygous and  heterozygous derived alleles for loss of function, deleterious, tolerated and synonymous variants for each individual. The last two individuals in each file are outgroups  6. dsuite-dinvestigate The outputs of 10 trios using program Dinvestigate from Dsuite. The sliding window is 50 SNPs, and the step is 20 SNPs. 7. Recombination rate The result of population-scaled recombination rate was calculated by LDhat v2.2. 8. Volcanofinder Genome-wide scans of introgression sweeps within each species was implemented using VolcanFinder v.1.0 with the Model over 10 Kbp non-overlapping windows. 9. ihh12 phased SNPs were used to computed ihh12 by selscan v1.3.0.  10 populus162.phased.recode.vcf.gz SNPs were phased with Beagle v.4.1 for the 162 non-hybrid individuals. 11 populus227.snp.rm_indel.para_filter.biallelic.GQ30.max_miss20.bed.recode.vcf.gz  The vcf of 227 Populus samples.

opencc-zeroNov 2021View details →

Phylogenomics, introgression, and demographic history of South American true toads (Rhinella)

The effects of genetic introgression on species boundaries and how they affect species' integrity and persistence over evolutionary time have received increased attention. The increasing availability of genomic data has revealed contrasting patterns of gene flow across genomic regions, which impose challenges to inferences of evolutionary relationships and of patterns of genetic admixture across lineages. By characterizing patterns of variation across thousands of genomic loci in a widespread complex of true toads (Rhinella), we assess the true extent of genetic introgression across species thought to hybridize to extreme degrees based on natural history observations and multi-locus analyses. Comprehensive geographic sampling of five large-ranged Neotropical taxa revealed multiple distinct evolutionary lineages that span large geographic areas and, at times, distinct biomes. The inferred major clades and genetic clusters largely correspond to currently recognized taxa; however, we also found evidence of cryptic diversity within taxa. While previous phylogenetic studies revealed extensive mito-nuclear discordance, our genetic clustering analyses uncovered several admixed individuals within major genetic groups. Accordingly, historical demographic analyses supported that the evolutionary history of these toads involved cross-taxon gene flow both at ancient and recent times. Lastly, ABBA-BABA tests revealed widespread allele sharing across species boundaries, a pattern that can be confidently attributed to genetic introgression as opposed to incomplete lineage sorting. These results confirm previous assertions that the evolutionary history of Rhinella was characterized by various levels of hybridization even across environmentally heterogeneous regions, posing exciting questions about what factors prevent complete fusion of diverging yet highly interdependent evolutionary lineages.

opencc-by-4.0Feb 2022View details →

Hybrid gridded demographic data for the world, 1950-2020 0.25˚ resolution

This is a hybrid gridded dataset of demographic data for the world, given as 5-year population bands at a 0.25 degree grid resolution. This dataset combines the NASA SEDAC Gridded Population of the World version 4 (GPWv4) with the ISIMIP Histsoc gridded population data and the United Nations World Population Program (WPP) demographic modelling data. Demographic fractions are given for the time period covered by the UN WPP model (1950-2050) while demographic totals are given for the time period covered by the combination of GPWv4 and Histsoc (1950-2020). More detailed can be found on the page of <a href="https://doi.org/10.5281/zenodo.3768003">the original version</a> (https://doi.org/10.5281/zenodo.3768003). This release increases the resolution to 0.25˚ and is explicitly designed to match with the grid definition of the ERA5 climate reanalysis dataset. For pre-2000 population data, the ISIMIP Histsoc data was upscaled from it's native 0.5˚ resolution.

opencc-zeroJun 2022View details →

Metabolic and demographic data from the LTEE

These data are the metabolic data and demographic data underlying the paper, "Long-term experimental evolution decouples size and production costs in Escherichia coli".

opencc-zeroJun 2022View details →

Joint analysis of microsatellites and flanking sequences enlightens complex demographic history of interspecific gene flow and vicariance in rear-edge oak populations

Inference of recent population divergence requires fast evolving markers and necessitates to differentiate shared genetic variation caused by ancestral polymorphism and gene flow. Theoretical research shows that the use of compound marker systems integrating linked polymorphisms with different mutational dynamics, such as a microsatellite and its flanking sequences, can improve estimation of population structure and inference of demographic history, especially in the case of complex population dynamics. However, empirical application in natural populations has so far been limited by lack of suitable methods for data collection. A solution comes from the development of sequence-based microsatellite genotyping which we used to study molecular variation at 36 sequenced nuclear microsatellites in seven Quercus canariensis and four Q. faginea rear-edge populations across Algeria. We aim to decipher their taxonomic relationship, past evolutionary history and recent demographic trajectory. First, we compare the estimation of population genetics parameters and simulation-based inference of demographic history from microsatellite sequence alone, flanking sequence alone or the combination of linked microsatellite and flanking sequence variation. Second, we apply random forest approximate Bayesian computation to identify which of these sequence types is most informative. Whereas analysing microsatellite variation alone indicates recent interspecific gene flow, additional information gained by integrating nucleotide variation in flanking sequences, by reducing homoplasy, suggests ancient interspecific gene flow followed by drift in isolation instead. The weight of each polymorphism in the inference also demonstrates the value of linked variations with contrasted mutation dynamic to improve estimation of both demographic and mutational parameters.

opencc-zeroJun 2022View details →

Data for the manuscript: Demographic basis of spatially structured fluctuations in a threespine stickleback metapopulation

Uncovering the demographic basis of population fluctuations is a central goal of population biology. This is particularly challenging for spatially structured populations, which require disentangling synchrony in demographic rates from coupling via immigration. In this study, we fit a stage-structured metapopulation model to a 29-year times series of threespine stickleback abundance in the heterogeneous and productive Lake Myvatn, Iceland. The lake comprises two basins (North and South) connected by a channel through which the stickleback disperse. The model includes time-varying demographic rates, allowing us to assess the potential contributions of recruitment and survival, spatial coupling via immigration, and demographic transience to the population's large fluctuations in abundance. Our analyses indicate that recruitment was only modestly synchronized between the two basins, whereas survival probabilities of adults were more strongly synchronized, contributing to cyclic fluctuations in the lake-wide population size with a period of approximately six years. The analyses further show that the two basins are coupled through immigration, with the North Basin subsidizing the South Basin and playing a dominant role in driving the lake-wide dynamics. Our results show that cyclic fluctuations of a metapopulation can be explained in terms of the combined effects of synchronized demographic rates and spatial coupling.

opencc-by-4.0Jun 2022View details →

A dataset of anonymised hospitalised COVID-19 patient data: outcomes, demographics and biomarker measurements for two New York hospitals

These datasets are for a cohort of n=1540 anonymised hospitalised COVID-19 patients, and the data provide information on outcomes (i.e. patient death or discharge), demographics and biomarker measurements for two New York hospitals: State University of New York (SUNY) Downstate Health Sciences University and Maimonides Medical Center. The file "demographics_both_hospitals.csv" contains the ultimate outcomes of hospitalisation (whether a patient was discharged or died), demographic information and known comorbidities for each of the patients. The file "dynamics_clean_both_hospitals.csv" contains cleaned dynamic biomarker measurements for the n=1233 patients where this information was available and the data passed our various checks (see https://doi.org/10.1101/2021.11.12.21266248 for information of these checks and the cleaning process). Patients can be matched to demographic data via the "id" column. Study approval and data collection Study approval was obtained from the State University of New York (SUNY) Downstate Health Sciences University Institutional Review Board (IRB\#1595271-1) and Maimonides Medical Center Institutional Review Board/Research Committee (IRB\#2020-05-07). A retrospective query was performed among the patients who were admitted to SUNY Downstate Medical Center and Maimonides Medical Center with COVID-19-related symptoms, which was subsequently confirmed by RT PCR, from the beginning of February 2020 until the end of May 2020. Stratified randomization was used to select at least 500 patients who were discharged and 500 patients who died due to the complications of COVID-19. Patient outcome was recorded as a binary choice of “discharged” versus “COVID-19 related mortality”. Patients whose outcome was unknown were excluded. Demographic, clinical history and laboratory data was extracted from the hospital’s electronic health records.

opencc-zeroJul 2022View details →

Data from: Non-native grazers affect physiological and demographic responses of Greater Sage-grouse

1. Non-native ungulate grazing has negatively impacted native species across the globe, leading to massive loss of biodiversity and ecosystem services. Despite their pervasiveness, interactions between non-native grazers and native species are not fully understood. We often observe declines in demography or survival of these native species, but lack understanding about the mechanisms underlying these declines. Physiological stress represents one mechanism of (mal)adaptation but data are sparse. 2. We investigated glucocorticoid levels in a native avian herbivore exposed to different intensities of non-native grazing in the cold desert Great Basin ecosystem, USA. We measured corticosterone, a glucocorticoid in feathers for a large sample (n = 280) of female Greater Sage-grouse (Centrocercus urophasianus) from three study areas in Northern Nevada and Southern Oregon with different grazing regimes of livestock and feral horses. 3. We found greater feral horse density was associated with higher corticosterone levels, and this effect was exacerbated by drought conditions. Livestock grazing produced similar results; however there was more model uncertainty about the livestock effect. Subsequent nesting success was lower with increased feather corticosterone, but corticosterone levels were not predictive of other vital rates. 4. Our results indicate a physiological response by sage-grouse to grazing pressure from non-native grazers. We found substantial among-individual variation in the strength of the response. These adverse effects were intensified during unfavorable weather events, highlighting the need to reevaluate management strategies in the face of climate change.

opencc-by-4.0Jul 2022View details →

SED templates for "Dwarf AGNs from Variability for the Origins of Seeds (DAVOS): Intermediate-mass black hole demographics from optical synoptic surveys"

FITS file containing the pre-computed grid of Done or Nemmen model SEDs. See Table 2 in the publication for details.

opencc-by-4.0Oct 2020View details →

The cost of self-promotion: Ecological and demographic implications of the mentor effect in natural Taraxacum populations

This data accompanies the pending publication "The cost of self-promotion: Ecological and demographic implications of the mentor effect in natural Taraxacum populations" by Lynn et al. The work is also published under Austin Lynn's PhD Dissertation, which is under embargo until 2022.

opencc-zeroAug 2022View details →

Data from: Density-dependence produces spurious relationships among demographic parameters in a harvested species

1. Harvest of wild organisms is an important component of human culture, economy, and recreation, but can also put species at risk of extinction. Decisions that guide successful management actions therefore rely on the ability of researchers to link changes in demographic processes to the anthropogenic actions or environmental changes that underlie variation in demographic parameters. 2. Ecologists often use population models or maximum sustained yield curves to estimate the impacts of harvest on wildlife and fish populations. Applications of these models usually focus exclusively on the impact of harvest and often fail to consider adequately other potential, often collinear, mechanistic drivers of the observed relationships between harvest and demographic rates. In this study, we used an integrated population model and long-term data (1973-2016) to examine the relationships among hunting and natural mortality, the number of hunters, habitat conditions, and population size of blue-winged teal (Spatula discors), an abundant North American dabbling duck with a relatively fast-paced life history strategy. 3. Over the last two and a half decades of the study, teal abundance tripled, hunting mortality probability increased slightly (< 0.02), and natural mortality probability increased substantially (> 0.1) at greater population densities. We demonstrate strong density-dependent effects on natural mortality and fecundity as population density increased, indicative of compensatory harvest mortality and compensatory natality. Critically, an analysis that only assessed the relationship between survival and hunting mortality would spuriously indicate depensatory hunting mortality due to multicollinearity between abundance, natural mortality, and hunting mortality. 4. Our findings demonstrate that models that only consider the direct effect of hunting on survival or natural mortality can fail to accurately assess the mechanistic impact of hunting on population dynamics due to multicollinearity among demographic drivers. This multicollinearity limits inference and may have strong impacts on applied management actions globally.