cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.p2m22
title: Data from: Temporal patterns of genetic variation in a salmon population undergoing rapid change in migration timing

description: Though genetic diversity is necessary for population persistence in
 rapidly changing environments, little is known about how climate-warming
 influences patterns of intra-population genetic variation. For a pink
 salmon population experiencing increasing temperatures, we used temporal
 genetic data (microsatellite = 1993, 2001, 2009; allozyme = 1979, 1981,
 1983) to quantify the genetic effective population size (Ne) and genetic
 divergence due to differences in migration timing and to estimate whether
 these quantities have changed over time. We predicted that temporal trends
 toward earlier migration timing and a corresponding loss of phenotypic
 variation would decrease genetic divergence based on migration timing and
 Ne. We observed significant genetic divergence based on migration timing
 and genetic heterogeneity between early- and late-migrating fish. There
 was also some evidence for divergent selection between early- and
 late-migrating fish at circadian rhythm genes, but results varied over
 time. Estimates of Ne from multiple methods were large (&gt;1200) and
 Ne/Nc generally exceeded 0.2. Despite shifts in migration timing and loss
 of phenotypic variation, there was no evidence for changes in
 within-population genetic divergence or Ne over the course of this study.
 These results suggest that in instances of population stability, genetic
 diversity may be resistant to climate-induced changes in migration timing.
description: Data_For_Kovachetal2013_EvolAppsThis file contains the data used in "Temporal patterns of genetic variation in a salmon population undergoing rapid change in migration timing". The data are organized based on the methods used to analyze them and year. The first three sheets are the data used for estimating the effective population size - the files are in ONeSAMP format. The next three files are the data sets used to test for autocorrelation (GENALEX) and population structure (STRUCTURE) - the files are in GENALEX format. The next sheet "Allozymes" contains the raw allele frequency data that were used to calculate G"st between early and late migrating fish in 1979-1983. Each row is a different locus, the first column is the number of genotypes for each locus, and the next several columns are the observed allele frequencies at that locus. The next three sheets are the data files used to calculate G"st for the microsatellite data from 1993, 2001, 2009. The final file contain the data that were used to test for genetic homogeneity between the different quartiles of the migration timing distribution.
DOI: 10.5061/dryad.j0k05
title: Data from: Return of the ghosts of dispersal past: historical spread and contemporary gene flow in the blue sea star Linckia laevigata

description: Marine animals inhabiting the Indian and Pacific oceans have some of the
 most extensive species ranges in the world, sometimes spanning over half
 the globe. These Indo-Pacific species present a challenge for study with
 both geographic scope and sampling density as limiting factors. Here, we
 augment and aggregate phylogeographic sampling of the iconic blue sea
 star, Linckia laevigata Linnaeus, 1758, and present one of the most
 geographically comprehensive genetic studies of any Indo-Pacific species
 to date, sequencing 392 base pairs of mitochondrial COI from 791
 individuals from 38 locations spanning over 14,000 km. We first use a
 permutation based multiple-regression approach to simultaneously evaluate
 the relative influence of historical and contemporary gene flow together
 with putative barriers to dispersal. We then use a discrete diffusion
 model of phylogeography to infer the historical migration and colonization
 routes most likely used by L. laevigata across the Indo-Pacific. We show
 that estimates of genetic structure have a stronger correlation to
 geographic distances than to “oceanographic” distances from a biophysical
 model of larval dispersal, reminding us that population genetic estimates
 of gene flow and genetic structure are often shaped by historical
 processes. While the diffusion model was equivocal about the location of
 the mitochondrial most recent common ancestor (MRCA), we show that gene
 flow has generally proceeded in a step-wise manner across the Indian and
 Pacific oceans. We do not find support for previously described barriers
 at the Sunda Shelf and within Cenderwasih Bay. Rather, the strongest
 genetic disjunction is found to the east of Cenderwasih Bay along northern
 New Guinea. These results underscore the importance of comprehensive
 range-wide sampling in marine phylogeography.
description: Data and Analysis Files
 from Crandall et al. 2014DryadSubmission.zip
DOI: 10.5281/zenodo.16965892
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Jules Dumont d'Urville, http://www.wikidata.org/entity/Q204735. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q204735
DOI: 10.5281/zenodo.18381728
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Jules Dumont d'Urville, http://www.wikidata.org/entity/Q204735. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q204735
DOI: 10.5061/dryad.tv41g
title: Data from: Microelastic mapping of the rat dentate gyrus

description: The lineage commitment of many cultured stem cells, including adult neural
 stem cells (NSCs), is strongly sensitive to the stiffness of the
 underlying extracellular matrix. However, it remains unclear how well the
 stiffness ranges explored in culture align with the microscale stiffness
 values stem cells actually encounter within their endogenous tissue
 niches. To address this question in the context of hippocampal NSCs, we
 used atomic force microscopy to spatially map the microscale elastic
 modulus (E) of specific anatomical substructures within living slices of
 rat dentate gyrus in which NSCs reside during lineage commitment in vivo.
 We measured depth-dependent apparent E-values at locations across the
 hilus (H), subgranular zone (SGZ) and granule cell layer (GCL) and found a
 two- to threefold increase in stiffness at 500 nm indentation from the H
 (49 ± 7 Pa) and SGZ (58 ± 8 Pa) to the GCL (115 ± 18 Pa), a fold change in
 stiffness we have previously found functionally relevant in culture.
 Additionally, E exhibits nonlinearity with depth, increasing significantly
 for indentations larger than 1 µm and most pronounced in the GCL. The
 methodological advances implemented for these measurements allow the
 quantification of the elastic properties of hippocampal NSC niche at
 unprecedented spatial resolution.
description: ESM 1 - AFM
 DataContains calculated
 Young's moduli from brains assayed in this study. Each sheet
 represents a different brain. From each brain, 5 slices were taken
 (labeled a-e). Within each slice, up to 8 locations were assayed (-1 to
 7), where 0 is the GCL and 6 is the hilus. At each location, force curves
 were fitted for indentation depths up to 3000 microns (pre500-i3000). And
 for each indentation, five force curves were taken and averaged (0-4).
 Overall averages are located in the final sheet.
DOI: 10.5061/dryad.58g12
title: Data from: Challenging the conceptual framework of maintenance hosts for influenza A viruses in wild birds

description: 1.The conceptual framework considering Anseriformes and Charadriiformes as
 the main maintenance hosts for influenza A viruses (IAV) in wild birds has
 shaped IAV research and surveillance over the last decades. 2.We challenge
 this framework by reviewing the worldwide surveillance data on
 non-Anseriformes and non-Charadriiformes (NANC) species, generally
 considered as playing little role in IAV maintenance, available in
 literature and online data bases (close to 200 sources). 3.Globally, we
 found an IAV infection rate of 1.51% (95% CI, 1.44%–1.59%) for c.101 000
 birds tested from NANC species. If Anseriformes have, as expected, a
 higher infection rate than any other bird orders, eight bird orders have
 an infection rate higher or close to the Charadriiformes infection rate,
 challenging the status of Charadriiformes. 4.We interpret the attention
 paid in favour of Charadriiformes by an extrapolation bias from data
 collected in hotspots of IAV infection in Charadriiformes (e.g. Delaware
 Bay, USA). 5.The growing data on IAV in wild birds worldwide, summarised
 here, supports two non-exclusive hypotheses: (i) the quality of the
 diagnostic tools and techniques used explain the patterns observed; (ii)
 IAV maintenance is determined by complex multi-host systems composed of
 multiple bird species, dependent on the ecosystem and its bird diversity
 and composition. 6.Synthesis and applications. Our results have two main
 implications. First, new research and surveillance should be designed in
 order to understand influenza A viruses ecology in wild birds across the
 world, along with appropriate diagnostic tools and new hypotheses and
 dedicated protocols. This should be done in line with our new conceptual
 framework that conveys less a priori than its predecessor. Secondly, our
 results call for more bridging between biological and epidemiological
 sciences in order to tackle disease ecology in multi-host systems.
description: AIV in Non-Anseriformes
 and Non-Charadriiformes wild birdsThis database displays
 up to the end of 2015 all data on the Non-Anseriformes and
 Non-Charadriiformes wild birds tested for Avian Influenza A by RT-PCR or
 Virus Isolation, based on a systematic literature
 review.JAE-ACaron-2016-00625.R1.xlsx
DOI: 10.5061/dryad.kk33f
title: Data from: Group augmentation, collective action, and territorial boundary patrols by male chimpanzees

description: How can collective action evolve when individuals benefit from cooperation
 regardless of whether they pay its participation costs? According to one
 influential perspective, collective action problems are common, especially
 when groups are large, but may be solved when individuals who have more to
 gain from the collective good or can produce it at low costs provide it to
 others as a byproduct. Several results from a 20-y study of one of the
 most striking examples of collective action in nonhuman animals,
 territorial boundary patrolling by male chimpanzees, are consistent with
 these ideas. Individuals were more likely to patrol when (i) they had more
 to gain because they had many offspring in the group; (ii) they incurred
 relatively low costs because of their high dominance rank and superior
 physical condition; and (iii) the group size was relatively small.
 However, several other findings were better explained by group
 augmentation theory, which proposes that individuals should bear the
 short-term costs of collective action even when they have little to gain
 immediately if such action leads to increases in group size and long-term
 increases in reproductive success. In support of this theory, (i)
 individual patrolling effort was higher and less variable than
 participation in intergroup aggression in other primate species; (ii)
 males often patrolled when they had no offspring or maternal relatives in
 the group; and (iii) the aggregate patrolling effort of the group did not
 decrease with group size. We propose that group augmentation theory
 deserves more consideration in research on collective action.
description: Patrol
 dataPatrol #: A unique
 identifier for each of 284 patrols. Date = Date each patrol occurred. Male
 = For each patrol, each male who was present in the community and &gt;=13
 years when the patrol ocurred is listed in his own row. Patrol
 participation = whether the male in that row participated in the patrol
 (1) or not (0). Age squared = the male's age in years at the time of
 the patrol, squared. Rank: the male's standardized dominance rank in
 the year the patrol occurred. Paternity success = at the time of the
 patrol, the sum of the relatedness values (0.5) to the male's
 offspring living in the community. Maternal relatedness = at the time of
 the patrol, the sum of the relatedness values to the male's close
 maternal relatives. See methods in supplementary info of original paper
 for details.
DOI: 10.5061/dryad.66k59
title: Data from: Anthropogenic and ecological drivers of amphibian disease (Ranavirosis)

description: Ranaviruses are causing mass amphibian die-offs in North America, Europe
 and Asia, and have been implicated in the decline of common frog (Rana
 temporaria) populations in the UK. Despite this, we have very little
 understanding of the environmental drivers of disease occurrence and
 prevalence. Using a long term (1992-2000) dataset of public reports of
 amphibian mortalities, we assess a set of potential predictors of the
 occurrence and prevalence of Ranavirus-consistent common frog mortality
 events in Britain. We reveal the influence of biotic and abiotic drivers
 of this disease, with many of these abiotic characteristics being
 anthropogenic. Whilst controlling for the geographic distribution of
 mortality events, disease prevalence increases with increasing frog
 population density, presence of fish and wild newts, increasing pond depth
 and the use of garden chemicals. The presence of an alternative host
 reduces prevalence, potentially indicating a dilution effect. Ranavirosis
 occurrence is associated with the presence of toads, an urban setting and
 the use of fish care products, providing insight into the causes of
 emergence of disease. Links between occurrence, prevalence, pond
 characteristics and garden management practices provides useful management
 implications for reducing the impacts of Ranavirus in the wild.
description: Frog Mortality Project
 dataset 1992-2000 (Froglife)This CSV data file
 contains amphibian mortality reports submitted by members of the public
 between 1992-2000 to the Frog Mortality Project, administered by Froglife.
 Those wishing to use this data should acknowledge Froglife (Charity number
 1093372). For more details please see the Read Me file. For any further
 queries with regards to this data or to request more recent data, please
 contact Froglife info@froglife.org.Dryad data 1992-2000
 FMP.csv
DOI: 10.5061/dryad.vr93sj5
title: Data from: Advancing restoration ecology: a new approach to predict time to recovery

description: 1. Species composition is a vital attribute of any ecosystem. Accordingly,
 ecological restoration often has the original, or ‘natural’, species
 composition as its target. However, we still lack adequate methods for
 predicting the expected time to compositional recovery in restoration
 studies. 2. We describe and explore a new, ordination regression-based
 approach (ORBA) for predicting time to recovery that allows both linear
 and asymptotic (logarithmic) relationships of compositional change with
 time. The approach uses distances between restored plots and reference
 plots along the successional gradient, represented by a vector in
 ordination space, to predict time to recovery. Thus, the approach rests on
 three requirements: (1) the general form of the relationship between
 compositional change and time must be known; (2) a sufficiently strong
 successional gradient must be present and adequately represented in a
 species compositional data set; and (3) a restoration target must be
 specified. We tested the approach using data from a boreal old-growth
 forest that was followed for 18 years after experimental disturbance. Data
 from the first nine years after disturbance were used to develop models,
 the subsequent nine years for validation. 3. Rates of compositional
 recovery in the example data set followed the general pattern of decrease
 with time since disturbance. Accordingly, linear models were too
 optimistic about the time to recovery whereas the asymptotic models
 provided more precise predictions. 4. Synthesis and applications. Our
 results demonstrate that the new approach opens for reliable prediction of
 recovery rates and time to recovery using species compositional data.
 Moreover, it allows us to assess whether recovery proceeds in the desired
 direction and to quantitatively compare restoration speed, and hence
 effectiveness, between alternative management options.
description: Rydgren&al_rawdtaRydgren&al_OrdinationResultsThe DCA (four axes) and GNMDS (3-dimensional solution) ordination results of the species compositional data from the 1031 plots. These data were collected in 80 permanently marked plots (8 plots in each of 10 blocks) in a boreal forest in SE Norway over the years 1993-2003, 2005, and 2011.Nine plots were devoid of species in 1994, The plots were experimentally disturbed before after 1993. The treatments were: T1 (removal of vegetation), T2 (removal of vegetation and the litter layer), T3 (removal of vegetation, the litter, and the mor soil layers), T4 and T5 (removal of vegetation, organic, and bleached soil layers; with T4 bordering intact vegetation on two sides, whereas T5 had a minimum distance of 0.5 m to intact vegetation). Three of the plots in each block served as controls (C).Rydgren&al_AppendixS1_Rcode Fig1Rydgren&al_dtafig1aData belonging to the R-script named: Rydgren&al_AppendixS1_Rcode Fig1.RRydgren&al_dtafig1bData belonging to the R-script named: Rydgren&al_AppendixS1_Rcode Fig1.R
DOI: 10.5061/dryad.6m5k3
title: Data from: Why does inbreeding reduce male paternity? Effects on sexually selected traits

description: [No abstract entered]
description: Why does inbreeding
 reduce paternity? Effects on sexually selected traitsThis is the data
 associated with the manuscript "Why does inbreeding reduce paternity?
 Effects on sexually selected traits". The data file contains 5
 worksheets. The first "association data" contains data from
 experiment 1 of the associated paper looking at female association time
 with inbred and outbred males. The second third and fourth contain data
 associated with the second experiment of the associated paper looking at
 the affect of inbreeding status on male sperm traits. The fifth,
 "Paternity" contains the data from the third experiment in the
 associated paper looking at how inbreeding status affect share of
 paternity.Why does inbreeding reduce
 paternity_DATA FOR DRYAD.xlsx
DOI: 10.5061/dryad.r50k9
title: Data from: Phosphorus limitation enhances parasite impact: feedback effects at the population level

description: Background: Nutrient deficiency affects the growth and population dynamics
 of consumers. Endoparasites can be seen as consumers that drain carbon (C)
 or energy from their host while simultaneously competing for limiting
 resources such as phosphorus (P). Depending on the relative demands of the
 host and the parasite for the limiting nutrient, intensified resource
 competition under nutrient limitation can either reduce the parasite?s
 effect on the host or further reduce the fitness of the nutrient-limited
 host. So far, knowledge of how nutrient limitation affects parasite
 performance at the host population level and how this affects the host
 populations is limited. Results: We followed the population growth of
 Daphnia magna that were uninfected or experimentally infected with a
 microsporidian, Glugoides intestinalis. The Daphnia were fed either
 P-sufficient or P-limited algae. The P-limited diet decreased the
 population density and biomass compared with the populations fed with the
 P-sufficient algae. In the P-sufficient populations, infection with the
 parasite reduced the population density but not the biomass of Daphnia,
 while in the P-limited populations, both the density and biomass of
 Daphnia decreased toward the end of the 32?day experiment compared with
 the uninfected controls. The infected animals from the P-limited
 populations had higher parasite spore cluster counts, while, in a separate
 experiment, host diet quality did not affect the number of parasites in
 individually kept Daphnia. Conclusions: Because host diet quality did not
 affect parasite numbers at the individual level, we suggest that the
 higher parasite load in the P-limited populations is a result of feedback
 effects arising at the population level. Because of the density-dependent
 transmission of the parasite and the time lag between exposure and
 transmission, the lower host population density in the P-limited
 populations led to a higher spore:host ratio. This effect may have been
 further reinforced by decreases in filtration rates caused by crowding in
 the P-sufficient populations and/or increases in filtration rates as a
 response to poor food quality in the P-limited populations. The increases
 in exposure led to a higher parasite load and aggravated the negative
 effects of parasite infection at the population level.
description: Pulkkinen_et_al_raw_data
DOI: 10.5061/dryad.6sk71
title: Data from: Age-dependent female responses to a male ejaculate signal alter demographic opportunities for selection

description: A central tenet of evolutionary explanations for ageing is that the
 strength of selection wanes with age. However, data on age-specific
 expression and benefits of sexually selected traits are
 lacking—particularly for traits subject to sexual conflict. We addressed
 this by using as a model the responses of Drosophila melanogaster females
 of different ages to receipt of sex peptide (SP), a seminal fluid protein
 transferred with sperm during mating. SP can mediate sexual conflict,
 benefitting males while causing fitness costs in females. Virgin and mated
 females of all ages showed significantly reduced receptivity in response
 to SP. However, only young virgin females also showed increased egg
 laying; hence, there was a narrow demographic window of maximal responses
 to SP. Males gained significant ‘per mating’ fitness benefits only when
 mating with young females. The pattern completely reversed in matings with
 older females, where SP transfer was costly. The overall benefits of SP
 transfer (hence opportunity for selection) therefore reversed with female
 age. The data reveal a new example of demographic variation in the
 strength of selection, with convergence and conflicts of interest between
 males and ageing females occurring over different facets of responses to a
 sexually antagonistic trait.
description: Fricke et al combined
 raw dataContains all the raw
 data for this study. Data on virgin females, mated females and male
 fitness. Each section has a tab containing the metadata explaining the
 data in detail.