cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7910/dvn/6n0b0s
title: synaptic vesicle data Ena LOF

description: electron microscopy data for synaptic vesicle analysis in Ena mutants FP4mito, data generated by Elizabeth McNeill and Vivian Chou
DOI: 10.5281/zenodo.16870228
title: Asthma loupe browser

description: Asthma loupe browsercontrol from Healthy control tissue was obtained from the trachea of a non-smoker, as referenced in the previously published dataset GSE134174

Asthma biosy from Severe asthma airway tissue biopsies were collected from patients (n=5)
DOI: 10.5281/zenodo.16870229
title: Asthma loupe browser

description: Asthma loupe browsercontrol from Healthy control tissue was obtained from the trachea of a non-smoker, as referenced in the previously published dataset GSE134174

Asthma biosy from Severe asthma airway tissue biopsies were collected from patients (n=5)
DOI: 10.5061/dryad.mg1tb
title: Data from: Keeping pace with climate change: stage-structured moving-habitat models

description: Life cycles can limit the abilities of species to track changing climatic
 conditions. We combined age or stage structure and a moving-habitat model
 to explore the effects of life history on the persistence of populations
 in the presence of climate change. We studied four dissimilar plant
 species in moving patches and found that (1) population growth rates, (2)
 elasticities with respect to the survival (stasis and shrinkage)
 components of the projection matrix, and (3) the evenness of the
 elasticities with respect to the components of the projection matrix all
 decreased as we increased the translational speeds of the patches. In
 addition, the value of long-distance dispersal increased with patch speed
 for three of the four species. Our analyses confirm that rapid growth,
 high fecundity, and long-distance dispersal can benefit species in moving
 patches. Thus, species with long generation times and limited dispersal
 ability are especially vulnerable to habitat movement. Stage-structured
 moving-habitat models can easily incorporate spatial complexity and can
 help us predict the effects of shifting climatic conditions.
description: c_code.tarPlease see the ReadMe file for a full description of the code.
DOI: 10.5061/dryad.567v8
title: Data from: Application of a dense genetic map for assessment of genomic responses to selection and inbreeding in Heliothis virescens

description: Adaptation of pest species to laboratory conditions and selection for
 resistance to toxins in the laboratory are expected to cause inbreeding
 and genetic bottlenecks that reduce genetic variation. Heliothis
 virescens, a major cotton pest, has been colonized in the laboratory many
 times, and a few laboratory colonies have been selected for Bacillus
 thuringiensis (Bt) resistance. We developed 350-bp double-digest
 restriction-site associated DNA-sequencing (ddRAD-seq) molecular markers
 to examine and compare changes in genetic variation associated with
 laboratory adaptation, artificial selection and inbreeding in this
 nonmodel insect species. We found that allelic and nucleotide diversity
 declined dramatically in laboratory-reared H. virescens as compared with
 field-collected populations. The declines were primarily a result of the
 loss of low frequency alleles present in field-collected H. virescens. A
 further, albeit modest decline in genetic diversity was observed in a
 Bt-selected population. The greatest decline was seen in H. virescens that
 were sib-mated for 10 generations, in which more than 80% of loci were
 fixed for a single allele. To determine which regions of the genome were
 resistant to fixation in our sib-mated line, we generated a dense
 intraspecific linkage map containing three PCR-based and 659 ddRAD-seq
 markers. Markers that retained polymorphism were observed in small
 clusters spread over multiple linkage groups, but this clustering was not
 statistically significant. Overall, we have confirmed and extended the
 general expectations for reduced genetic diversity in laboratory colonies,
 provided tools for further genomic analyses and produced highly homozygous
 genomic DNA for future whole genome sequencing of H. virescens.
description: Hybrid_Parent_Marker_SequencesThis zipped folder contains multiple fasta files that contain molecular marker sequence data for the hybrid parent used in our mapping cross. Each fasta file contains the sequence data for all markers that grouped together on a single linkage group. Marker genotypes/sequences provided here were produced using Stacks version 1.09.Hybrid_Parent_Markers.fasta.tar.gzYHD2_Parent_Marker_SequencesThis zipped folder contains multiple fasta files that contain molecular marker sequence data for the YHD2 (Bt Resistant) parent used in our mapping cross. Each fasta file contains the sequence data for all markers that grouped together on a single linkage group. Marker genotypes/sequences provided here were produced using Stacks version 1.09.YHD2_Parent_Markers.fasta.tar.gzMarker_Position_FileThis file provides the Stacks catalog number of each marker along with its linkage group (Chr) number and position (pos; given in cM) within each linkage group. Markers 0, 1, and 2 represent the partial candidate gene sequences for ABCC2, HevCalp, and DesatI, respectively.all_lgs.csv
DOI: 10.5061/dryad.q75p2
title: Data from: Symbiodinium thermophilum sp. nov., a thermotolerant symbiotic alga prevalent in corals of the world’s hottest sea, the Persian/Arabian Gulf

description: Coral reefs are in rapid decline on a global scale due to human activities
 and a changing climate. Shallow water reefs depend on the obligatory
 symbiosis between the habitat forming coral host and its algal symbiont
 from the genus Symbiodinium (zooxanthellae). This association is highly
 sensitive to thermal perturbations and temperatures as little as 1°C above
 the average summer maxima can cause the breakdown of this symbiosis,
 termed coral bleaching. Predicting the capacity of corals to survive the
 expected increase in seawater temperatures depends strongly on our
 understanding of the thermal tolerance of the symbiotic algae. Here we use
 molecular phylogenetic analysis of four genetic markers to describe
 Symbiodinium thermophilum, sp. nov. from the Persian/Arabian Gulf, a
 thermally tolerant coral symbiont. Phylogenetic inference using the
 non-coding region of the chloroplast psbA gene resolves S. thermophilum as
 a monophyletic lineage with large genetic distances from any other ITS2 C3
 type found outside the Gulf. Through the characterisation of Symbiodinium
 associations of 6 species (5 genera) of Gulf corals, we demonstrate that
 S. thermophilum is the prevalent symbiont all year round in the
 world's hottest sea, the southern Persian/Arabian Gulf.
description: Multiple sequence
 alignment of psba(ncr) DNA sequences from Symbiodinium thermophilum and
 closely related Symbiodinium spp.This file is a multiple
 sequence alignment of partial chloroplast psbA non coding region genes
 from Symbiodinium thermophilum and other closely related species of
 Symbiodinium. It is in a FASTA format. The first 22 Symbiodinium sequences
 were obtained from algae within Porites spp. corals from the
 Persian/Arabian gulf. The host identity, specific collection location and
 host species for each sample are detailed in the supplementary materials
 of the associated paper. The alignment was implemented using ClustalW but
 heavily modified manually. Reference sequences are included in the
 alignment. These are available in Genbank as detailed in the associated
 paper.Dryad
 Submission alignment.fas
DOI: 10.5061/dryad.41131ns8
title: Data from: Interactions between soil habitat and geographic range location affect plant fitness

description: Populations are often found on different habitats at different geographic
 locations. This habitat shift may be due to biased dispersal,
 physiological tolerances or biotic interactions. To explore how fitness of
 the native plant Chamaecrista fasciculata depends on habitat within, at
 and beyond its range edge, we planted seeds from five populations in two
 soil substrates at these geographic locations. We found that with reduced
 competition, lifetime fitness was always greater or equivalent in one
 habitat type, loam soils, though early-season survival was greater on sand
 soils. At the range edge, natural populations are typically found on sand
 soil habitats, which are also less competitive environments. Early-season
 survival and fitness differed among source populations, and when
 transplanted beyond the range edge, range edge populations had greater
 fitness than interior populations. Our results indicate that even when the
 optimal soil substrate for a species does not change with geographic range
 location, the realized niche of a species may be restricted to sub-optimal
 habitats at the range edge because of the combined effects of differences
 in abiotic and biotic effects (e.g. competitors) between substrates.
description: Field
 dataLife history data for
 seed from five source populations (AFT - Afton State Park, Afton, MN; GCD
 - Grey Cloud Dunes Scientific and Natural Area, Cottage Grove, MN; CRA -
 Conard Environmental Research Area, Grinnell College, Kellogg, IA; KZA -
 Konza Prairie Biological Station, Manhattan, KS; CUI - Cuivre River State
 Park, Troy, MO) planted at one sand and one loam site in each of three
 regions: the range interior in Iowa, range edge in Minnesota, and beyond
 the range edge in Minnesota. The sites are: CRA: Conard Environmental
 Research Area, Grinnell College, Kellogg, IA (interior-loam); MAR: Iowa
 River Conservation Area, Marshalltown, IA (interior-sand); SCW: St. Croix
 Watershed Research Station, Marine-on-St. Croix, MN (edge-loam) NOTE: this
 site was planted later than the others due to replanting after planting at
 a first site (UM ag fields) failed; CC: Cedar Creek Ecosystem Science
 Reserve, Univ. of Minnesota, East Bethel, MN (edge-sand); KEN: Kensington
 Runestone Park, Kensington, MN (beyond-loam); IDA: Lake Ida, 3223 Sahara
 LN NW (property of Sheila Stanton), Alexandria, MN (beyond-sand). Data
 collected include early-season survival, which includes both germination
 and survival for the first two weeks, about 3-4 weeks after planting.
 About eight weeks after planing, I collected data on mid-season survival,
 reproductive stage, height, leaf number, and collected the top-most fully
 expanded leaf to calculate SLA. At the end of the growing season, I
 recorded height, branch number and collected a subsample of ~10% of the
 seedpods on a plant.CfE2_data.csvanalysis scriptR script for data analysis using CfE2_data.csvJSG_Chamaecrista_PLoSONE_analysis.r
DOI: 10.5061/dryad.64jk6
title: Data from: What seeds tell us about birds: a multi-year analysis of acorn woodpecker foraging movements

description: Background: Foraging movements of animals shape their efficiency in
 finding food and their exposure to the environment while doing so. Our
 goal was to test the optimal foraging theory prediction that territorial
 acorn woodpeckers (Melanerpes formicivorus) should forage closer to their
 'central place' in years of high resource availability and
 further afield when resources are less available. We used genetic data on
 acorns stored in caching sites (granaries) and adult trees for two oak
 species (Quercus lobata and Quercus agrifolia) to track acorn movements
 across oak savanna habitat in central California. We also compared the
 patterns of trees these territorial bird groups foraged upon, examining
 the effective numbers of source trees represented within single granaries
 (alpha), the effective number of granaries (beta), the diversity across
 all granaries (gamma), and the overlap (omega) in source trees among
 different granaries, both within and across years. Results: In line with
 optimal foraging theory predictions, most bird groups foraged shorter
 distances in years with higher acorn abundance, although we found some
 exceptionally long distance foraging movements in high acorn crop years.
 The alpha-diversity values were significantly higher for Quercus lobata,
 but not for Quercus agrifolia, in years of high acorn production. We also
 found that different woodpecker family groups visited almost completely
 non-overlapping sets of source trees, and each particular group visited
 largely the same set of source trees from year to year, indicating strong
 territorial site fidelity. Conclusions: Acorn woodpeckers forage in a
 pattern consistent with optimal foraging theory, with a few fascinating
 exceptions of long distance movement. The number of trees they visit
 increases in years of high acorn availability, but the extra trees visited
 are mostly local. The territorial social behavior of the birds also
 restricts their movement patterns to a minimally overlapping subsets of
 trees, but the median movement distance appears to be shaped more by the
 availability of trees with acorns than by rigid territorial boundaries.
description: Thompson_DataDryad_Genotypes_Q.lobata_Q.agrifoliaMulti-locus genotypes for adults and pericarps from two years, of two oak species (sheet 1 is Quercus lobata, sheet 2 is Quercus agrifolia). Locations in decimal degrees follow the genotypes of adults on each sheet.
DOI: 10.5061/dryad.5d781
title: Data from: The role of feeding morphology and competition in governing the diet breadth of sympatric stomatopod crustaceans

description: Competition for food drives divergence and specialization in feeding
 morphology. Stomatopod crustaceans have two kinds of highly specialized
 feeding appendages: either elongate spear-like appendages (spearers) used
 to ambush soft-bodied evasive prey or hammer-like appendages (smashers)
 that produce extremely high forces used both to break hard-shelled prey
 and to capture evasive prey. To evaluate associations between appendage
 type and feeding ecology, the diet of two small smasher and spearer
 species (size range: 21–27 mm) that co-occur were compared. Stable isotope
 analysis and the Bayesian mixing model MixSIAR were used to estimate the
 proportional contributions of prey types to the diet. Both species had
 relatively wide diets that included hard-shelled and soft-bodied prey,
 albeit in different proportions; the smasher consumed a greater proportion
 of hard-shelled prey, and the spearer consumed mostly soft-bodied prey.
 Appendage kinematics in stomatopods is known to scale linearly across
 species. These two small species may produce similar kinematics allowing
 them both to capture evasive prey and hammer hard-shelled prey, thereby
 widening their diets. Yet, the spearer species is more highly adept at
 capturing evasive prey, indicating that small spearers are stronger
 competitors for soft-bodied prey. These findings suggest that a
 smasher's ability to access hard prey reduced competition for soft
 prey, and therefore conferred an important benefit favouring the evolution
 of the impressive smashing strike.
description: Data.FileData files and R scripts for analyses associated with M. deVries Biology Letters submission entitled “The role of feeding morphology and competition in governing the diet breadth of sympatric stomatopod crustaceans.”
DOI: 10.5061/dryad.h7m5f83
title: Data from: Spring weather conditions influence breeding phenology and reproductive success in sympatric bat populations.

description: 1. Climate is known to influence breeding phenology and reproductive
 success in temperate zone bats, but long-term population level studies and
 interspecific comparisons are rare. 2. Investigating the extent to which
 intrinsic (i.e. age), and extrinsic (i.e. spring weather conditions),
 factors influence such key demographic parameters as the proportion of
 females becoming pregnant, or completing lactation, each breeding season,
 is vital to understanding of bat population ecology and life-history
 traits. 3. Using data from twelve breeding seasons (2006 - 2017),
 encompassing the reproductive histories of 623 Myotis daubentonii and 436
 M. nattereri adult females, we compare rates of recruitment to the
 breeding population, and show that these species differ in their relative
 sensitivity to environmental conditions and climatic variation, affecting
 annual reproductive success at the population level. 4. We demonstrate
 that i) Spring weather conditions influence breeding phenology, with warm,
 dry and calm conditions leading to earlier parturition dates and advanced
 juvenile development, whilst cold, wet and windy weather delays birth
 timing and juvenile growth, ii) Reproductive rates in first-year females
 are influenced by spring weather conditions in that breeding season and in
 the preceding breeding season when each cohort was born. Pregnancy and
 lactation rates were both higher when favourable spring foraging
 conditions were more prevalent, iii) Reproductive success increases with
 age in both species, but at different rates, iv) Reproductive rates were
 consistently higher, and showed less inter-annual variation, in
 second-year and older M. daubentonii (mean 91.55% ± 0.05 SD) than M.
 nattereri (mean 72.74% ± 0.15 SD), v) Estimates of reproductive success at
 the population level were highly correlated with the size of the juvenile
 cohort recorded each breeding season. 5. Improving understanding of the
 influence of environmental conditions, especially extreme climatic
 fluctuations, and the identification of critical periods (i.e. spring for
 reproductive female bats in temperate zones), which have disproportionate
 and lasting impacts on breeding phenology and reproductive success at a
 population level, is critical for improving predictions of the likely
 impact of climate change on bat populations.
description: Linton_DM_Macdonald_DW_J_Animal_Ecology_2018Data Archive includes R code (.R file) and data (.txt files) to replicate model outputs and reproduce figures from the article.
DOI: 10.13140/rg.2.2.18025.56162
title: ANSYS - Convergence of Nonlinear Solution
DOI: 10.5061/dryad.261553q
title: Data from: Experimental demonstration of the impact of hard and soft selection regimes on polymorphism maintenance in spatially heterogeneous environments

description: Predicting and managing contemporary adaption requires a proper
 understanding of the determinants of genetic variation. Spatial
 heterogeneity of the environment may stably maintain polymorphism when
 habitat contribution to the next generation can be considered independent
 of the degree of adaptation of local populations within habitats (i.e.,
 under soft selection). In contrast, when habitats contribute
 proportionally to the mean fitness of the populations they host (hard
 selection), polymorphism is not expected to be maintained by selection.
 Although mathematically established decades ago, this prediction had never
 been demonstrated experimentally. Here we provide an experimental test in
 which polymorphic populations of Escherichia coli growing in heterogeneous
 habitats were exposed to hard and soft selection regimes. As predicted by
 theory, polymorphism was preserved longer under soft selection.
 Complementary tests established that soft selection slowed fixation
 processes and could even protect polymorphism in the long term by
 providing a systematic advantage to rare genotypes.
description: Gallet-et-al-2018-RawData-1This data file contains all the flow cytometry data used to estimate cell concentrations, fitness measures etc.
DOI: 10.5061/dryad.4h4r4
title: Data from: Bonobos and chimpanzees exhibit human-like framing effects

description: Humans exhibit framing effects when making choices, appraising decisions
 involving losses differently from those involving gains. To directly test
 for the evolutionary origin of this bias, we examined decision-making in
 humans' closest living relatives: bonobos (Pan paniscus) and
 chimpanzees (Pan troglodytes). We presented the largest sample of
 non-humans to date (n = 40) with a simple task requiring minimal
 experience. Apes made choices between a ‘framed’ option that provided
 preferred food, and an alternative option that provided a constant amount
 of intermediately preferred food. In the gain condition, apes experienced
 a positive ‘gain’ event in which the framed option was initially presented
 as one piece of food but sometimes was augmented to two. In the loss
 condition, apes experienced a negative ‘loss' event in which they
 initially saw two pieces but sometimes received only one. Both conditions
 provided equal pay-offs, but apes chose the framed option more often in
 the positive ‘gain’ frame. Moreover, male apes were more susceptible to
 framing than were females. These results suggest that some human economic
 biases are shared through common descent with other apes and highlight the
 importance of comparative work in understanding the origins of individual
 differences in human choice.
description: Krupenye_etal_Framing_subjectsSubject means data from economic decision making studies with bonobos and chimpanzees in Krupenye, Rosati & Hare "Bonobos and chimpanzees exhibit human-like framing effects"Krupenye_etal_Framing_trialsTrial by trial data from economic decision making studies with bonobos and chimpanzees in Krupenye, Rosati & Hare "Bonobos and chimpanzees exhibit human-like framing effects"
DOI: 10.5061/dryad.95pp7
title: Data from: Variation in the strength of inbreeding depression across environments: effects of stress and density dependence

description: In what types of environments should we expect to find strong inbreeding
 depression? Previous studies indicate that inbreeding depression, δ, is
 positively correlated with the stressfulness of the environment in which
 it is measured. However, it remains unclear why stress, per se, should
 increase δ. To our knowledge, only “competitive stress” has a logical
 connection to δ. Through competition for resources, better quality
 (outbred) individuals make the environment worse for lower quality
 (inbred) individuals, accentuating the differences between them. For this
 reason, we expect inbreeding depression to be stronger in environments
 where the fitness of individuals is more sensitive to the presence of
 conspecifics (i.e., where fitness is more density dependent). Indeed, some
 studies suggest a role for competition within environments but this idea
 has not been tested in the context of understanding variation in δ across
 environments. Using Drosophila melanogaster, we estimated δ for viability
 in 22 different environments. These environments were simultaneously
 characterized for (i) stressfulness and (ii) density dependence. Though
 stress and density dependence are moderately correlated with each other,
 inbreeding depression is much more strongly correlated with density
 dependence. These results suggest that mean selection across the genome is
 stronger in environments where competition is intense, rather than in
 environments that are stressful for other reasons.
description: NumberOfFliesEmergingNumber of adult flies collected (i.e., surviving from egg to adulthood) in different assays.IDinMultEnv.xlsx