cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tk05d
title: Data from: Song sparrows Melospiza melodia have a home-field advantage in defending against sympatric malarial parasites

description: Hosts and parasites interact on both evolutionary and ecological
 timescales. The outcome of these interactions, specifically whether hosts
 are more resistant to their local parasites (sympatric) than to parasites
 from another location (allopatric), is likely to affect the spread of
 infectious disease and the fitness consequences of host dispersal. We
 conducted a cross-infection experiment to determine whether song sparrows
 (Melospiza melodia) have an advantage in dealing with sympatric parasites.
 We captured birds from two breeding sites 437 km apart, and inoculated
 them with avian malaria (Plasmodium spp.) cultured either from their
 capture site or from the other site. Infection risk was lower for birds
 exposed to sympatric than to allopatric Plasmodium lineages, suggesting
 that song sparrows may have a home-field advantage in defending against
 local parasite strains. This pattern was more pronounced at one capture
 site than at the other, consistent with mosaic models of host–parasite
 interactions. Home-field advantage may arise from evolutionary processes,
 whereby host populations become adapted to their local parasites, and/or
 from ecological interactions, whereby host individuals develop resistance
 to the local parasites through previous immune exposure. Our findings
 suggest that greater susceptibility to novel parasites may represent a
 fitness consequence of natal dispersal.
description: Dryad_Sarquis_MacShack_InfectivityDataOutcome and severity of infections for 24 song sparrows experimentally inoculated with Plasmodium. Spreadsheet includes sex, capture date and location, and previous infection status for these birds plus 8 others used in the experiment as donors, amplifiers and controls. Parasite loads expressed as # parasites per 10,000 erythrocytes.
DOI: 10.5061/dryad.8m9t1
title: Data from: A redescription and phylogenetic analysis based on new material of the fossil newts Taricha oligocenica Van Frank, 1955 and Taricha lindoei Naylor, 1979 (Amphibia, Salamandridae) from the Oligocene of Oregon.

description: Complete body fossils of salamanders are relatively rare, but provide
 critical information on the evolutionary roots of extant urodele clades.
 We describe new specimens of the fossil salamandrids Taricha oligocenica
 Van Frank, 1955, and Taricha lindoei Naylor, 1979, from the Oligocene
 Mehama and John Day Formations of Oregon that illustrate aspects of
 skeletal morphology previously unseen in these taxa, and contribute to our
 understanding of population-level variation. Morphological analysis of
 these specimens supports the classification of T. oligocenica and T.
 lindoei as two different species, distinct from extant Taricha.
 Parsimony-based, heuristic analysis of phylogeny using 108 morphological
 characters for 40 taxa yields different results from a phylogenetic
 analysis that excludes four taxa known only via vertebrae. Our smaller
 analysis generally agrees with molecular phylogenies of the family
 Salamandridae, but with poorer resolution for molgin newts, especially
 between Taricha and Notophthalmus. The analysis including all taxa
 produced polytomies mostly related to complications from several fossil
 taxa. The presence or absence of dorsally expanded, sculptured neural
 spine tables on trunk vertebrae, an important character in past
 descriptions of fossil salamandrids, appears to be either homoplastic
 within the Salamandridae, or requires an expansion of characters or
 character states. T. oligocenica and T. lindoei are separate species of an
 at least 33 million-year-old clade, but their relationships with each
 other and extant North American salamandrids remain unclear with current
 levels of morphological data. Salamandrid research requires additional
 morphological data, particularly for the vertebrae and ribs, to better
 resolve salamandrid evolutionary history through morphological characters.
description: JJJ_SSBH_Supplement_new_character_descriptionsDescription of characters used for the phylogenetic analyses in the study.JJJ_SSBH_Supplement2_MATRIXCharacter matrix for the phylogenetic analyses in the study.
DOI: 10.15468/dl.et5j2f
title: Occurrence Download

description: A dataset containing 134281 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Fungi",
 "Country is Japan",
 "HasCoordinate is true"
 ]
}

 The dataset includes 134281 records from 174 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001003-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.58791
title: Data from: Retinal capillary rarefaction in patients with type 2 diabetes mellitus

description: Purpose: In diabetes mellitus type 2, capillary rarefaction plays a
 pivotal role in the pathogenesis of end-organ damage. We investigated
 retinal capillary density in patients with early disease. Methods: This
 cross-sectional study compares retinal capillary rarefaction determined by
 intercapillary distance (ICD) and capillary area (CapA), measured
 non-invasively and in vivo by scanning laser Doppler flowmetry, in 73
 patients with type 2 diabetes, 55 healthy controls and 134 individuals
 with hypertension stage 1 or 2. Results: In diabetic patients, ICD was
 greater (23.2±5.5 vs 20.2±4.2, p = 0.013) and CapA smaller (1592±595 vs
 1821±652, p = 0.019) than in healthy controls after adjustment for
 differences in cardiovascular risk factors between the groups. Compared to
 hypertensive patients, diabetic individuals showed no difference in ICD
 (23.1±5.8, p = 0.781) and CapA (1556±649, p = 0.768). Conclusion: In the
 early stage of diabetes type 2, patients showed capillary rarefaction
 compared to healthy individuals.
description: PlosOne_beb
DOI: 10.5061/dryad.77c9n6b
title: Data from: Local mate competition modifies the costs of mating in a mostly monandrous parasitoid wasp

description: The costs and benefits of mating are frequently measured in order to
 understand why females mate multiply. However, to separate the factors
 that initiate the evolution of polyandry (from monandry) from the factors
 that maintain it, we must ascertain how the environment changes the
 economics of mating. Here we show how context-dependent costs of mating
 can lead to the evolution of polyandry in a species that is monandrous in
 the wild, the parasitoid wasp Nasonia vitripennis. We have previously
 shown that when females have insufficient time between mating and
 ovipositing, they appear unable to process sperm effectively and end up
 overproducing sons (i.e. laying unfertilised eggs, since Nasonia is in
 haplodiploid). This overproduction of sons is costly due to selection on
 sex allocation in this species. Although N. vitripennis is monandrous in
 the wild, polyandry evolves under laboratory culture despite this sex
 allocation cost. In this study we show why: when groups of females
 oviposit together, as in laboratory culture, selection on sex allocation
 via Local Mate Competition (LMC) is reduced, increasing the reproductive
 value of sons. This relaxes the fitness cost of male production.
 Overproduction of sons still occurs, but it is penalised less than when
 females oviposit alone, under high LMC conditions, as they typically do in
 the field. Our results highlight how the costs and benefits of mating can
 vary under different ecologically relevant conditions, in this case the
 spatio-temporal distribution of resources and competitors, promoting the
 evolution of polyandry from monandry, and vice versa.
description: Boulton et
 al_varLMC_Nov.18Data for experiment 1
 (sheet 1) and 2 (sheet 2) and simulated data used to prepare figure
 2.
DOI: 10.5061/dryad.th15b
title: Data from: Meta-analysis indicates that oxidative stress is both a constraint on and a cost of growth

description: Oxidative stress (OS) as a proximate mechanism for life-history trade-offs
 is widespread in the literature. One such resource allocation trade-off
 involves growth rate, and theory suggests that OS might act as both a
 constraint on and a cost of growth, yet studies investigating this have
 produced conflicting results. Here, we use meta-analysis to investigate
 whether increased OS levels impact on growth (OS as a constraint on
 growth) and whether greater growth rates can increase OS (OS as a cost of
 growth). The role of OS as a constraint on growth was supported by the
 meta-analysis. Greater OS, in terms of either increased damage or reduced
 levels of antioxidants, was associated with reduced growth although the
 effect depended on the experimental manipulation used. Our results also
 support an oxidative cost of growth, at least in terms of increased
 oxidative damage, although faster growth was not associated with a change
 in antioxidant levels. These findings that OS can act as a constraint on
 growth support theoretical links between OS and animal life histories and
 provide evidence for a growth–self-maintenance trade-off. Furthermore, the
 apparent oxidative costs of growth imply individuals cannot alter this
 trade-off when faced with enhanced growth. We offer a starting platform
 for future research and recommend the use of oxidative damage biomarkers
 in nonlethal tissue to investigate the growth–OS relationship further.
description: Data for
 constraint-MAData for conducting the
 constraint-MA investigating the effects of OS on growth. Hedges' g
 values (the response variable denoting whether groups of the same species
 that had been found to differ in OS levels also had significantly
 different growth rates) and their variances are given, as well as
 moderator details and sample size.SSmith
 Eco&Evol_constraint-MA_data.xlsxData for cost-MAData for conducting the cost-MA investigating the effects of growth on OS. Hedges' g values (the response variable indicating if there was a significant difference in OS between two groups of the same species that had been found to differ phenotypically in growth rate) and their variances are given, as well as moderator details and sample size.SSmith Eco&Evol_cost-MA_data.xlsx
DOI: 10.5061/dryad.7sn14
title: Data from: Parasitism in early life: environmental conditions shape intra-brood variation in responses to infection

description: Parasites play key ecological and evolutionary roles through the costs
 they impose on their host. In wild populations, the effect of parasitism
 is likely to vary considerably with environmental conditions, which may
 affect the availability of resources to hosts for defense. However, the
 interaction between parasitism and prevailing conditions is rarely
 quantified. In addition to environmental variation acting on hosts,
 individuals are likely to vary in their response to parasitism, and the
 combined effect of both may increase heterogeneity in host responses.
 Offspring hierarchies, established by parents in response to uncertain
 rearing conditions, may be an important source of variation between
 individuals. Here, we use experimental antiparasite treatment across 5
 years of variable conditions to test how annual population productivity (a
 proxy for environmental conditions) and parasitism interact to affect
 growth and survival of different brood members in juvenile European shags
 (Phalacrocorax aristotelis). In control broods, last-hatched chicks had
 more plastic growth rates, growing faster in more productive years. Older
 siblings grew at a similar rate in all years. Treatment removed the effect
 of environment on last-hatched chicks, such that all siblings in treated
 broods grew at a similar rate across environmental conditions. There were
 no differences in nematode burden between years or siblings, suggesting
 that variation in responses arose from intrinsic differences between
 chicks. Whole-brood growth rate was not affected by treatment, indicating
 that within-brood differences were driven by a change in resource
 allocation between siblings rather than a change in overall parental
 provisioning. We show that gastrointestinal parasites can be a key
 component of offspring's developmental environment. Our results also
 demonstrate the value of considering prevailing conditions for our
 understanding of parasite effects on host life-history traits.
 Establishing how environmental conditions shape responses to parasitism is
 important as environmental variability is predicted to increase.
description: Chick Growth
 RatesGrowth rates of all
 individual chicks in the experiment with all explanatory variables tested,
 including treatment, productivity, rank, sex, nest etc.ChickGrowthRates.csvBrood Growth RatesGrowth rates of the brood as a whole (i.e. sum of all siblings) with all explanatory variables tested.BroodGrowthRates.csvFECsCounts of nematode eggs in faeces of chicks in three of our experimental years with all explanatory variables tested.
DOI: 10.5061/dryad.rc2mp
title: Data from: Promise and challenge of DNA barcoding in Venus slipper (Paphiopedilum)

description: Orchidaceae are one of the largest families of flowering plants, with over
 27,000 species described and all orchids are listed in CITES. Moreover,
 the seedlings of orchid species from the same genus are similar. The
 objective of DNA barcoding is rapid, accurate, and automated species
 identification, which may be used to identify illegally traded endangered
 species from vegetative specimens of Paphiopedilum (Venus slipper), a
 flagship group for plant conservation with high ornamental and commercial
 values. Here, we selected eight chloroplast barcodes and nrITS to evaluate
 their suitability in Venus slippers. The results indicate that all tested
 barcodes had no barcoding gap and the core plant barcodes showed low
 resolution for the identification of Venus slippers (18.86%). Of the
 single-locus barcodes, nrITS is the most efficient for the species
 identification of the genus (52.27%), whereas matK + atpF-atpH is the most
 efficient multi-locus combination (28.97%). Therefore, we recommend the
 combination of matK + atpF-atpH + ITS as a barcode for Venus slippers.
 Furthermore, there is an upper limit of resolution of the candidate
 barcodes, and only half of the taxa with multiple samples were identified
 successfully. The low efficiency of these candidate barcodes in Venus
 slippers may be caused by relatively recent speciation, the upper limit of
 the barcodes, and/or the sampling density. Although the discriminatory
 power is relatively low, DNA barcoding may be a promising tool to identify
 species involved in illegal trade, which has broad applications and is
 valuable for orchid conservation.
description: Alignment of the
 sequences
DOI: 10.5061/dryad.380g2
title: Data from: Is saltmarsh restoration success constrained by matching natural environments or altered succession? a test using niche models

description: 1.Restored habitats, such as saltmarsh created through managed
 realignment, sometimes fail to meet targets for biological equivalence
 with natural reference sites. Understanding why this happens is important
 in order to improve restoration outcomes. 2.Elevation in the tidal frame
 and sediment redox potential are major controls on the distribution of
 saltmarsh plants. We use niche models to characterize ten species’
 responses to these, and test whether differences in species occurrence
 between restored and natural saltmarshes in the UK result from failure to
 recreate adequate environmental conditions. 3.Six species occurred less
 frequently in recently restored marshes than natural marshes. Failure of
 restored marshes to achieve the elevation and redox conditions of natural
 marshes partially explained the underrepresentation of five of these
 species, but did not explain patterns of occurrence on older (&gt; 50
 years) restored marshes. 4.For all species, an effect of marsh age
 remained after controlling for differences in environmental conditions.
 This could be due to differences in successional mechanism between
 restored and natural marshes. In recently restored marshes, high-marsh
 species occurred lower in the tidal frame and low-marsh species occurred
 at higher elevations than in natural marshes. This supports the hypothesis
 that competition is initially weaker in restored marshes, because of the
 availability of bare sediment across the whole tidal frame. Species that
 establish outside their normal realized niche, such as Atriplex
 portulacoides, may inhibit subsequent colonization of other species that
 occurred less frequently than expected on older restored marshes.
 5.Synthesis and applications. Niche models can be used to test whether
 abiotic differences between restored sites and their natural counterparts
 are responsible for discrepancies in species occurrence. In saltmarshes,
 simply replicating environmental conditions will not result in equivalent
 species occurrence.
description: Species occurrence and
 environmental data from Sullivan et al "Is saltmarsh restoration
 success constrained by matching natural environments or altered
 succession? A test using niche models"Quadrat data used in
 statistical analysis. Columns are quadrat ID, region (Essex, Norfolk or
 Humber), marsh age (MR = managed realignment, AR = accidental realignment,
 NAT = natural reference), redox potential (mV), relative tidal height,
 then the presence (1) or absence (0) of each study species. Species
 abbreviations are as used in the paper. Note that one site (FHOLME,
 quadrat IDs FHOLME 1 to FHOLME 50) was excluded from the final analysis as
 it was subject to historic grazing.Species and environmental data
 from Sullivan et al Is saltmarsh restoration success constrained by
 matching natural environments or altered
 succession.csv
DOI: 10.5061/dryad.cj421
title: Data from: A cost of being amicable in a hibernating marmot

description: Amicable social interactions can enhance fitness in many species, have
 negligible consequences for some, and reduce fitness in others. For
 yellow-bellied marmots (Marmota flaviventris), a facultatively social
 rodent species with demonstrable costs of social relationships during the
 active season, the effects of sociality on overwinter survival have yet to
 be fully investigated. Here, we explored how summer social interactions,
 quantified as social network attributes, influenced marmot survival during
 hibernation. Using social data collected from 2002 to 2012 on free-living
 yellow-bellied marmots, we calculated 8 social network measures
 (in-degree, out-degree, in-closeness, out-closeness, in-strength,
 out-strength, embeddedness, and clustering coefficient) for both
 affiliative and agonistic interactions. We performed a principal component
 analysis (PCA) to reduce those attributes to 3 affiliative (connectedness,
 strength, and clustering) and 4 agonistic (submissiveness, bullying,
 strength, and clustering) components. Then, we fitted a generalized linear
 mixed model to explain variation in overwinter survival as a function of
 these social components, along with body mass, sex, age, weather
 conditions, hibernation group size, and hibernation group composition. We
 found that individuals with stronger amicable relationships were more
 likely to die during hibernation. This suggests that social relationships,
 even affiliative ones, need not be beneficial; for yellow-bellied marmots,
 they can even be fatal.
description: READMEYangetal_beheco_2016_owsurvival_BYangetal_beheco_2016_glmm
DOI: 10.5061/dryad.dg124q0
title: Data from: Differential effects of climate warming on reproduction and functional responses on insects in the fourth trophic level

description: 1. Understanding effects of Anthropogenic Global Warming (AGW) on species
 interactions is essential for predicting community responses to climate
 change. However, while effects of AGW on resource-consumer interactions at
 the first- and second trophic level have been well studied, little is
 known about effects on interactions at higher trophic levels at the
 terminal end of food chains (e.g. in the third and fourth trophic levels).
 2. Here, we examined the effects of temperature variability by simulating
 heatwaves on functional responses of two species at the fourth trophic
 level (hyperparasitoids) that parasitize host species at the third trophic
 level (parasitoid cocoons). 3. We found that host cocoons developed faster
 under simulated heatwave conditions, decreasing the temporal window of
 susceptibility of the host cocoons to parasitism by the two
 hyperparasitoids, and consequently parasitism declined with temperature.
 However the effects of a simulated heatwave markedly differed among the
 two hyperparasitoid species; temperature and host quality had a much
 stronger effect on early reproduction in the less fecund hyperparasitoid
 Gelis agilis, than in the more fecund species Acrolyta nens. 4. Our
 results suggest that exposure to heatwaves, which are expected to increase
 in frequency, will affect the ability of species at higher trophic levels
 to exploit transient resources whose suitability is temperature-dependent.
 In turn, the observed effects of AGW on the functional responses of the
 hyperparasitoids may disrupt trophic interactions and have profound impact
 on population dynamics and ecological processes.
description: A.
 nensThe file contain data on
 reproduction for Acolyta nensG.
 agilisThe file contain data on
 reproduction for Gelis agilisC.
 glomerataThe file contain data
 for Cotesia glomerataLongevityThe file contain data for longevity of two hyperparasitoids