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opencc-zeroJan 2023View details →

Data for: The climatic variability hypothesis and trade–offs in thermal performance in coastal and inland populations of Mimulus guttatus

Ecologists and evolutionary biologists have long predicted that organisms in more climatically variable environments should be adapted to handle a wider range of conditions. This intuitive idea, known as the Climatic Variability Hypothesis, has gained mixed support from empirical studies. We tested the Climatic Variability Hypothesis in a novel system by comparing the thermal breadth of coastal and inland populations of Mimulus guttatus. To quantify thermal breadth, we performed a thermal performance experiment and built performance curves. Using these performance curves, we also evaluated evidence for a breadth–performance trade–off and the Hotter–is–Better hypothesis. We did not find support for the Climatic Variability Hypothesis; coastal and inland populations did not differ in thermal breadth. However, we found evidence for a breadth performance trade–off and the Hotter–is–Better hypothesis. Surprisingly, the two most inland populations differed the most in the thermal performance traits we evaluated. Our results highlight the importance of explicitly measuring thermal performance to test explanations of species distribution patterns and the need to examine alternative mechanisms by which organisms occupy different climatic regimes.

opencc-zeroJan 2023View details →

Data from: Microbial population dynamics decouple growth response from environmental nutrient concentration

To explore the diversity of microbial growth responses, we have compiled 247 measurements of half-saturation concentrations K and maximum growth rates gmax from previously-published studies (see Methods). The data includes a wide range of resources, including sources of carbon, nitrogen, phosphorus, metals, and vitamins, with phosphate, glucose, and nitrate having the largest number of measurements due to their emphasis in marine and laboratory systems. Organisms include prokaryotes and eukaryotes as well as autotrophs and heterotrophs. This data has been analyzed in a companion research article. For data plots and a discussion of results, please refer to: <div class="csl-bib-body"> <div class="csl-entry">Fink, Justus Wilhelm, Noelle A. Held, and Michael Manhart. "Microbial Population Dynamics Decouple Growth Response from Environmental Nutrient Concentration." Proceedings of the National Academy of Sciences 120, no. 2 (January 10, 2023). <a href="https://doi.org/10.1073/pnas.2207295120">https://doi.org/10.1073/pnas.2207295120</a>.</div> </div>

opencc-zeroJan 2023View details →

A big data–model integration approach for predicting epizootics and population recovery in a keystone species

Infectious diseases pose a significant threat to global health and biodiversity. Yet, predicting the spatiotemporal dynamics of wildlife epizootics remains challenging. Disease outbreaks result from complex non-linear interactions among a large collection of variables that rarely adhere to the assumptions of parametric regression modeling. We adopted a non-parametric machine learning approach to model wildlife epizootics and population recovery, using the disease system of colonial black-tailed prairie dogs (BTPD, Cynomys ludovicianus) and sylvatic plague as an example. We synthesized colony data between 2001–2020 from eight USDA Forest Service National Grasslands across the range of BTPD in central North America. We then modeled extinctions due to plague and colony recovery of BTPD in relation to complex interactions among climate, topoedaphic variables, colony characteristics, and disease history. Extinctions due to plague occurred more frequently when BTPD colonies were spatially clustered, in closer proximity to colonies decimated by plague during the previous year, following cooler than average temperatures the previous summer, and when wetter winter/springs were preceded by drier summer/falls. Rigorous cross-validations and spatial predictions indicated that our final models predicted plague outbreaks and colony recovery in BTPD with high accuracy (e.g., AUC generally > 0.80). Thus, these spatially-explicit models can reliably predict the spatial and temporal dynamics of wildlife epizootics and subsequent population recovery in a highly complex host-pathogen system. Our models can be used to support strategic management planning (e.g., plague mitigation) to optimize benefits of this keystone species to associated wildlife communities and ecosystem functioning. This optimization can reduce conflicts among different landowners and resource managers, as well as economic losses to the ranching industry. More broadly, our big data–model integration approach provides a general framework for spatially-explicit forecasting of disease-induced population fluctuations, for use in natural resource management decision-making.

Data for: Perishing rich, expanding poor: Demography and population genetic patterns in two congeneric butterflies

In human-altered landscapes, specialist butterflies typically form spatially restricted populations, genetically differentiated due to dispersal restrictions. Generalists, in contrast, display minimum differentiation but high genetic diversity. While local-level actions suffice to conserve specialists and landscape-level actions are necessary for generalists, minimum information exists regarding conservation of species with intermediate features. We targeted two congeneric butterflies, the recently re-expanding Argynnis adippe and the strongly declining A. niobe, co-occurring in the pastoral landscape of the Carpathian Mountains, Czech Republic. We integrated species distribution models, mark-recapture, and microsatellite analysis to compare their habitat requirements, adult demography, dispersal, and genetic patterns, and expanded the genetic analysis across the Carpathian Arc and beyond to delimit spatial conservation units. In two mountain valleys, both species formed interconnected populations numbering thousands of individuals. Mobility patterns suggested the populations' interconnection across the Czech Carpathians. Genetic diversity was extremely poor in the non-threatened A. adippe and moderate in the declining A. niobe. No population differentiation was detected within the Czech Carpathians (ca 1500 km2). Low genetic diversity and no differentiation was preserved in A. adippe across East Central Europe, whereas in A. niobe, populations from Serbia were differentiated from the Carpathian Arc + Alps. The high adult mobility linked to low differentiation probably reflect the distribution of larval resources, historically widespread but sparse and currently declining for A. niobe (grazing-disturbed grounds), while currently increasing for A. adippe (abandonment scrub, disturbed woodlands). Units as large as entire mountain systems define population boundaries, and hence conservation management units, for both species.

openDec 2022View details →

Data from: Population recovery and occurrence of the endemic Rhine sculpin (Cottus rhenanus)

Two datasets belonging to the paper "Population recovery and occurrence of the endemic Rhine sculpin (Cottus rhenanus)" published in Knowledge and Management of Aquatic Ecosystems, are provided here. Since little was known about the occurrence, densities and habitat use of C. rhenanus, this study was conducted. The study area was located in the River Geul and tributaries, in the south of the Netherlands. The first dataset "WFD 2005-2010-2015 fish data.csv" contains data of fish in transects sampled as part of ecological status assessments of water systems according to the EU Water Framework Directive. Average 300-metre transects in upstream direction in one run using handheld backpack electrofishing equipment. The second dataset "Habitat characterization Cottus rhenanus 2014.csv" contains data of the Rhine sculpin (and other encountered fish species) in relation to its habitat. The data were collected in the same way as described above. In addition, we estimated the relative abundance of each sediment type (bed substratum) per transect, which yielded the ordinal categories: 0%, <5%, 5-10%, 11-25%, 26-50%, 51-75%, and 76-100%. Distinguished sediment types were silt (mud/sludge), sand, fine granule (0.1-20 mm), pebble (21-65 mm), cobble (66-200 mm), and boulder (>200 mm). Furthermore, we estimated the percentage area of large structures (e.g., woody debris) and riffles. Finally, we measured stream width (m) and depth (cm). This was done by recording width with a tape measure and depth with a measuring rod at five (beginning, middle, end and two representatives in between) locations in a transect. The mean values were recorded as stream width and depth. The included coordinates refer to the start and end of a transect. The coordinate system used here concerns Amersfoort RD (EPSG: 28992).  Abstract The Rhine sculpin (Cottus rhenanus) is a benthic rheophilic fish species that is endemic to tributaries of the rivers Rhine and Meuse in North-western Europe. Little is known about its occurrence and individuals density in relation to habitat characteristics. A core population of C. rhenanus occurs in the River Geul in the Netherlands. Since the late 19th century, this river was heavily polluted by communal and industrial wastewater, causing a strong population decline. As the core population of C. rhenanus is recovering, the status, distribution, and habitat use should be studied to facilitate recovery in other locations. Cottus rhenanus density of individuals significantly increased over the period 2005-2015 and it became one of the most abundant fish species in assemblages. Negative relationships were observed between C. rhenanus densities and a high abundance of boulders (> 200 mm), large structures such as woody debris, and water depth. The population increase and recolonization of C. rhenanus coincided with water quality improvement, which suggests that this fish species can be used to assess small streams ecosystem integrity. The recent range expansion of the Ponto-Caspian round goby (Neogobius melanostomus) poses a high risk of negative effects on C. rhenanus populations via food and shelter competition. Further water quality improvement, habitat conservation, and prevention of the spread of invasive gobies could favour C. rhenanus populations within their natural range.

Data from: Effective population size in a partially clonal plant is not predicted by the number of genetic individuals

Estimating effective population size (Ne) is important for theoretical and practical applications in evolutionary biology and conservation. Nevertheless, estimates of Ne in organisms with complex life-history traits remain scarce because of the challenges associated with estimation methods. Partially clonal plants capable of both vegetative (clonal) growth and sexual reproduction are a common group of organisms for which the discrepancy between the apparent number of individuals (ramets) and the number of genetic individuals (genets) can be striking, and it is unclear how this discrepancy relates to Ne. In this study, we analysed two populations of the orchid Cypripedium calceolus to understand how the rate of clonal vs. sexual reproduction affected Ne. We genotyped >1,000 ramets at microsatellite and SNP loci, and estimated contemporary Ne with the linkage disequilibrium method, starting from the theoretical expectation that variance in reproductive success among individuals caused by clonal reproduction and by constraints on sexual reproduction would lower Ne. We considered factors potentially affecting our estimates, including different marker types and sampling strategies, and the influence of pseudoreplication in genomic datasets on Ne confidence intervals. The magnitude of Ne/Nramets and Ne/Ngenets ratios we provide may be used as reference points for other species with similar life-history traits. Our findings demonstrate that Ne in partially clonal plants cannot be predicted based on the number of genets generated by sexual reproduction, because demographic changes over time can strongly influence Ne. This is especially relevant in species of conservation concern, in which population declines may not be detected by only ascertaining the number of genets.

Data from: Demographic histories shape population genomics of the common coral grouper (Plectropomus leopardus)

Many coral reef fishes display remarkable genetic and phenotypic variation across their geographic ranges. Understanding how historical and contemporary processes have shaped these patterns remains a focal question in evolutionary biology since they reveal how diversity is generated and how it may respond to future environmental change. Here we compare the population genomics and demographic histories of a commercially and ecologically important coral reef fish, the common coral grouper (Plectropomus leopardus [Lacépède 1802]), across two adjoining regions (the Great Barrier Reef; GBR, and the Coral Sea, Australia) spanning approximately 14 degrees of latitude and 9 degrees of longitude. We analysed 4,548 single nucleotide polymorphism (SNP) markers across 11 sites and show that genetic connectivity between regions is low, despite their relative proximity (~ 100 km) and an absence of any obvious geographic barrier. Inferred demographic histories using 10,479 markers suggest that the Coral Sea population was founded by a small number of GBR individuals and that divergence occurred ~ 190 kya under a model of isolation with asymmetric migration. We detected population expansions in both regions, but estimates of contemporary effective population sizes were approximately 50 % smaller in Coral Sea sites, which also had lower genetic diversity. Our results suggest that P. leopardus in the Coral Sea have experienced a long period of isolation that precedes the recent glacial period (~ 10–120 kya) and may be vulnerable to localised disturbances due to their relative reliance on local larval replenishment. While it is difficult to determine the underlying events that led to the divergence of Coral Sea and GBR lineages, we show that even geographically proximate populations of a widely dispersed coral reef fish can have vastly different evolutionary histories.

opencc-by-4.0Nov 2022View details →

Source Data: No evidence for a common blood microbiome based on a population study of 9,770 healthy humans

Source data for manuscript titled: 'No evidence for a common blood microbiome based on a population study of 9,770 healthy humans' (https://www.biorxiv.org/content/10.1101/2022.07.29.502098v1)

opencc-by-4.0Feb 2023View details →

On the seed population of solar energetic particles in the inner heliosphere : simulation data

Figures and simulation data of the paper titled 'On the seed population of solar energetic particles in the inner heliosphere', which is submitted to the Journal of Geophysical Research: Space Physics.  The simulation data consist of all the output from the EUHFORIA model and the PARADISE model that was used in the paper. The abstract of the paper is: Particles measured in large gradual solar energetic particle (SEP) events are believed to be predominantly accelerated at shocks driven by coronal mass ejections (CMEs).  Ion charge state and composition analyses suggest that the origin of the seed particle population for the mechanisms of particle acceleration at CME-driven shocks is not the bulk solar wind thermal material, but rather a suprathermal population present in the solar wind. This suprathermal population could result from remnant material accelerated in prior solar flares and/or preceding CME-driven shocks. In this work, we examine the distribution of this suprathermal particle population in the inner heliosphere by combining a magnetohydrodynamic (MHD) simulation of the solar wind and a Monte-Carlo simulation of particle acceleration and transport. Assuming that the seed particles are uniformly distributed near the Sun by solar flares of various magnitudes, we study the longitudinal distribution of the seed population at multiple heliocentric distances. We consider a non-uniform background solar wind, consisting of fast and slow streams that lead to compression and rarefaction regions within the solar wind. Our simulation shows that the seed population at a particular location (e.g., 1 au) is strongly modulated by the underlying solar wind configuration. Corotating interaction regions (CIRs) and merged interactions regions (MIRs) can strongly alter the energy spectra of the seed particle populations. In addition, cross-field diffusion plays an important role in mitigating strong  variations of the seed population in both space and energy.

Data for: Sex-biased infections scale to population impacts for an emerging wildlife disease

Demographic factors are fundamental in shaping infectious disease dynamics. Aspects of populations that create structure, like age and sex, can affect patterns of transmission, infection intensity and population outcomes. However, studies rarely link these processes from individual to population-scale effects. Moreover, the mechanisms underlying demographic differences in disease are frequently unclear. Here, we explore sex-biased infections for a multi-host fungal disease of bats, white-nose syndrome, and link disease-associated mortality between sexes, the distortion of sex ratios, and the potential mechanisms underlying sex differences in infection. We collected data on host traits, infection intensity, and survival of five bat species at 42 sites across seven years. We found females were more infected than males for all five species. Females also had lower apparent survival over winter and accounted for a smaller proportion of populations over time. Notably, female-biased infections were evident by early hibernation and likely driven by sex-based differences in autumn mating behavior. Male bats were more active during autumn which likely reduced replication of the cool-growing fungus. Higher disease impacts in female bats may have cascading effects on bat populations beyond the hibernation season by limiting recruitment and increasing the risk of Allee effects.

opencc-zeroFeb 2022View details →

Data on range-wide breeding habitat use of the critically endangered Yellow-breasted Bunting Emberiza aureola after population collapse

The population of the Yellow-breasted Bunting Emberiza aureola, a formerly widely distributed and abundant songbird of northern Eurasia, suffered a catastrophic decline and a strong range contraction between 1980 and 2013. There is evidence that the decline was driven by illegal trapping during migration, but potential contributions of other factors to the decline, such as land-use change, have not yet been evaluated. Before effects of land-use change can be evaluated, a basic understanding of the ecological requirements of the species is needed. We therefore compared habitat use in ten remaining breeding regions across the range, from European Russia to Japan and the Russian Far East. We also assessed large-scale variation in habitat parameters across the breeding range. We found large variation in habitat use, within and between populations. Differences were related to the cover and height of trees and shrubs at Yellow-breasted Bunting territories. In many regions, Yellow-breasted Buntings occupied early successional stages, including anthropogenic habitats characterized by mowing, grazing or fire regimes. We found that the probability of presence can be best predicted with the cover of shrubs, herbs and grasses. Highest probabilities were found at shrub cover values of 40 to 70 %. Differences in habitat use along a longitudinal gradient were small, but we found strong differences across latitudes, possibly related to habitat availability. We conclude that the remaining Yellow-breasted Bunting populations are not limited to specific habitat types. Our results provide important baseline information to model the range-wide distribution of this critically endangered species and to guide targeted conservation measures.

Genetic diversity and population structure from a Peruvian nucleus cattle herd using SNP data

New-generation sequencing technologies, among them SNP chips for massive genotyping, have proven to be useful for the effective management of genetic resources. Also, developing nucleus herds is an effective method for genetic improvement work. To date, molecular studies in Peruvian cattle are still in their infancy. To close this gap, we here employed two SNP panels (BovineHD and Bovine100K) to determine for the first time the Peruvian nucleus herd's genetic diversity and population structure that belong to INIA. This nucleus comprises Brahman (N=16), Braunvieh (N=14), Gyr (N=11), and Fleckvieh (N=22) breeds. Additionally, samples from a locally adapted creole cattle, the Arequipa Fighting Bull (AFB, N=12), were incorporated into the study. The genetic diversity indices in all breeds showed a high proportion of polymorphic SNPs, varying from 69.37% in Gyr to 80.81% in Braunvieh. Also, Braunvieh possessed the highest observed heterozygosity (0.53±0.17), while Brahman possessed the lowest (0.44±0.10), indicating that the former is more diverse compared to the other cattle breed groups. According to the molecular variance analysis, 83.92% of the variance occurs within individuals, whereas 16.0% occurs between populations. The pairwise FST estimates between breeds showed values that ranged from 0.054 (Braunvieh vs AFB) to 0.266 (Brahman vs AFB). Pairwise Reynold's distance showed a pattern similar to the one obtained with the FST statistics, with values ranging from 0.058 to 0.309. A dendrogram was constructed using the Neighbor-Joining clustering algorithm, and similar to the principal coordinate analysis, three groups were identified. Results showed a clear separation between Bos indicus (Brahman and Gyr) and B. taurus breeds (Braunvieh and Fleckvieh). For Fleckvieh and Braunvieh, there were two subgroups each one of them grouping with the AFB group. Similar results were obtained with ADMIXTURE analysis with K= 3 as the most optimal number for the inferred genetic structure of the populations. The results from the current study would contribute to the appropriate management avoiding loss of genetic variability in these breeds and to future improvements for this nucleus. Additional work is needed to speed up the breeding process in the Peruvian cattle system.

Data for: Breeding honey bees (Apis mellifera L.) for low and high Varroa destructor population growth: gene expression of bees performing grooming behavior

Background Social organisms, including honey bees (Apis mellifera L.), have defense mechanisms to control the multiplication and transmission of parasites and pathogens within their colonies. Self-grooming, a mechanism of behavioral immunity, seems to contribute to restraining the population growth of the ectoparasitic mite Varroa destructor in honey bee colonies. Because V. destructor is the most damaging parasite of honey bees, breeding them for resistance against the mite is a high priority of the beekeeping industry. We conducted a bidirectional breeding program to select honey bee colonies with low and high varroa population growth (LVG and HVG, respectively). Having high and low lines of bees allowed the study of genetic mechanisms underlying self-grooming behavior between the extreme genotypes. Worker bees were classified into two categories: 'light groomers' and 'intense groomers'. The brains of bees from the different categories (LVG-intense, LVG-light, HVG-intense, and HVG-light) were used for gene expression and viral quantification analyses. Results Differentially expressed genes (DEGs) associated with the LVG and HVG lines were identified, including four odorant-binding proteins and a gustatory receptor. A functional enrichment analysis showed 19 enriched pathways from a list of 219 down-regulated DEGs in HVG bees, including the Kyoto Encyclopedia of Genes and Genomes (KEGG) term of oxidative phosphorylation. Additionally, bees from the HVG line showed higher levels of Apis rhabdovirus 1 and 2, Varroa destructor virus -1 (VDV-1), and Deformed wing virus-A (DWV-A) compared to bees of the LVG line. Conclusions The difference in expression of odorant-binding protein genes and a gustatory receptor between bee lines suggests a possible link between them and the perception of irritants to trigger rapid self-grooming instances that require the activation of energy metabolic pathways. Therefore, our results provide new insights into the molecular mechanisms involved in honey bee grooming behavior. Differences in viral levels in the brains of LVG and HVG bees showed the importance of investigating the pathogenicity and potential impacts of neurotropic viruses on behavioral immunity. The results of this study advance the understanding of a trait used for selective breeding, self-grooming, and the potential of using genomic-assisted selection to improve breeding programs.

opencc-by-4.0Mar 2023View details →

QGIS Data for Canadian Population, PM2.5, Nighttime lights.

This is the dataset for the QGIS analysis for Canadian Population, PM2.5, Nighttime lights.

Data for: Cytogeography of naturalized Solidago canadensis populations in Europe

Autopolyploidization has driven the successful invasion of Solidago canadensis in East Asia. However, it was believed that only diploid S. canadensis invaded Europe, whereas polyploids never did. In this study, we aim to investigate whether polyploidy S. canadensis invaded Europe and compare the ecological niche differentiation pattern driven by ploidy in Asia and Europe and North America.Here, molecular identification (combination of ribosomal ITS and psbA-trnH intergenic spacer), ploidy level, and morphological traits of ten S. canadensis populations collected in Europe were compared with previously identified S. canadensis populations from other continents and S. altissima populations. Furthermore, the ploidy-driven geographical differentiation pattern of S. canadensis in different continents was investigated. Results showed that all ten European populations were identified as S. canadensis with five diploid and five hexaploid populations. Significant differences in morphological traits existed among diploids and polyploids (tetraploids and hexaploids), rather than between polyploids from different introduced ranges and between S. altissima and polyploidy S. canadensis populations. The invasive hexaploids and diploids had few differences in latitudinal distributions in Europe which was similar to the native range but absolutely different from a distinct climate-niche differentiation in Asia. This may be attributed to the bigger difference in climate between Asia and Europe and North America.The above morphological and molecular evidences proved the invasion of polyploid S. canadensis in Europe and suggest that S. altissima may be merged into a complex of S. canadensis species. Our study may be concluded that geographical and ecological niche differentiation of an invasive plant driven by ploidy depends on the degree of difference in the environmental factors between the introduced range and the native range, which provides new insight into the invasive mechanism.

Data from: Differential gene expression and mitonuclear incompatibilities in fast- and slow-developing inter-population Tigriopus californicus hybrids

Mitochondrial functions are intimately reliant on proteins and RNAs encoded in both the nuclear and mitochondrial genomes, leading to inter-genomic coevolution within taxa. Hybridization can break apart coevolved mitonuclear genotypes, resulting in decreased mitochondrial performance and reduced fitness. This hybrid breakdown is an important component of outbreeding depression and early-stage reproductive isolation. However, the mechanisms contributing to mitonuclear interactions remain poorly resolved. Here we scored variation in developmental rate (a proxy for fitness) among reciprocal F2 inter-population hybrids of the intertidal copepod Tigriopus californicus, and used RNA sequencing to assess differences in gene expression between fast- and slow-developing hybrids. In total, differences in expression associated with developmental rate were detected for 2,925 genes, whereas only 135 genes were differentially expressed as a result of differences in mitochondrial genotype. Up-regulated expression in fast developers was enriched for genes involved in chitin-based cuticle development, oxidation-reduction processes, hydrogen peroxide catabolic processes, and mitochondrial respiratory chain complex I. In contrast, up-regulation in slow developers was enriched for DNA replication, cell division, DNA damage, and DNA repair. Eighty-four nuclear-encoded mitochondrial genes were differentially expressed between fast- and slow-developing copepods, including twelve subunits of the electron transport system (ETS) which all had higher expression in fast developers than in slow developers. Nine of these genes were subunits of ETS complex I. Our results emphasize the major roles that mitonuclear interactions within the ETS, particularly in complex I, play in hybrid breakdown, and resolve strong candidate genes for involvement in mitonuclear interactions.

Data for: SNPs detected in pool-seq data from resistant and susceptible Cimex lectularius populations

In the last few years, the bed bug Cimex lectularius has been an increasing problem world-wide, mainly due to the development of insecticide resistance to pyrethroids. The characterization of resistance alleles is a prerequisite to improve surveillance and resistance management. To identify genomic variants associated with pyrethroid resistance in Cimex lectularius, we compared the genetic composition of two recent and resistant populations with that of two ancientsusceptible strains using a genome-wide pool-seq design. We identified a large 6 Mb "superlocus" showing particularly high genetic differentiation and association with the resistance phenotype. This superlocus contained several clustered resistance genes, andwas also characterized by a high density of structural variants (inversions, duplications). The possibility that this superlocus constitute a resistance "supergene" that evolved after the clustering of alleles adapted to insecticide and after reduction in recombination is discussed.

opencc-by-4.0Apr 2023View details →

TARDIS configuration and emulator weights and training data for "1991T-Like Type Ia Supernovae as an Extension of the Normal Population"

This dataset contains two archives of data related to the paper "1991T-Like Type Ia Supernovae as an Extension of the Normal Population" The first dataset, <a href="https://zenodo.org/api/files/de696fe0-3280-44f2-8ef4-975b92fad260/TARDIS_Emulator_Config.tar.gz">TARDIS_Emulator_Config.tar.gz </a>, contains the atomic data used to run TARDIS and a template configuration file from which samples are generated including the flags for the physics implementation used. The second dataset, InferenceScripts.tar.gz, contains the trained probabilistic neural network, the training/validation data (Under NNData), and scripts used to train the model and load and evaluate the model.  Scripts that perform inference on spectra, as well as a folder of observed spectra (Under CorrectedSpectra), are included as well.  A conda environment yaml file is included to rebuild the Python environment required to run all of the scripts.  For questions please email John O'Brien.

opencc-zeroApr 2023View details →

Data from: Genetic mark-recapture analysis of winter faecal pellets allows estimation of population size in sage grouse Centrocercus urophasianus

Sex ratio, and the extent to which it varies over time, is an important factor in the demography, management, and conservation of wildlife populations. We estimated pre-breeding sex ratio of greater sage-grouse (Centrocercus urophasianus) in a peripheral, geographically isolated population in northwestern Colorado during two consecutive winters using closed-population, robust-design, multi-state, genetic mark-recapture models in program MARK (White and Burnham 1999). This data release includes the data files (.inp format) used in those models, as described in Shyvers et al. 2023. The data include capture histories and auxiliary data for individual greater sage-grouse collected during two study seasons: Season 1 (winter 2012-2013) and Season 2 (winter 2013-2014) and are readable using program MARK or notepad. Each data row includes the unique bird identification number (GMR-ID); the bird's encounter history for n= sampling occasions coded as a static state (M = male, F = female); the group ID; and a region covariate (0 = North, 1 = South). The data were adapted from those originally developed for Shyvers et al. 2020 and applied using Closed Robust Design Multi-state (CRDMS) Huggins' p and c w/state probabilities in program MARK to obtain estimates of Omega, enabling estimation of sex ratio with associated confidence intervals (see Shyvers et al. 2023). References: Shyvers, J.E., Walker, B.L., Oyler-McCance, S.J., Fike, J.A. and Noon, B.R. 2023. Genetic mark-recapture analysis reveals large annual variation in pre-breeding sex ratio of greater sage-grouse. Wildlife Biology (https://doi.org/10.1002/wlb3.01085) Shyvers, J.E., Walker, B.L., Oyler‐McCance, S.J., Fike, J.A. and Noon, B.R., 2020. Genetic mark-recapture analysis of winter faecal pellets allows estimation of population size in Sage Grouse Centrocercus urophasianus. Ibis, 162(3), pp.749-765. White, G. C., and K. P. Burnham. 1999. Program Mark: survival estimation from populations of marked animals. – Bird Study 46:120–139.