cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18382829
title: Processed data and code used in the paper
DOI: 10.5061/dryad.2t965
title: Data from: Demographic history influences spatial patterns of genetic diversity in recently expanded coyote (Canis latrans) populations

description: Human-mediated range expansions have increased in recent decades and
 represent unique opportunities to evaluate genetic outcomes of
 establishing peripheral populations across broad expansion fronts. Over
 the past century, coyotes (Canis latrans) have undergone a pervasive range
 expansion and now inhabit every state in the continental United States.
 Coyote expansion into eastern North America was facilitated by
 anthropogenic landscape changes and followed two broad expansion fronts.
 The northern expansion extended through the Great Lakes region and
 southern Canada, where hybridization with remnant wolf populations was
 common. The southern and more recent expansion front occurred
 approximately 40 years later and across territory where gray wolves have
 been historically absent and remnant red wolves were extirpated in the
 1970s. We conducted a genetic survey at 10 microsatellite loci of 482
 coyotes originating from 11 eastern U.S. states to address how divergent
 demographic histories influence geographic patterns of genetic diversity.
 We found that population structure corresponded to a north-south divide,
 which is consistent with the two known expansion routes. Additionally, we
 observed extremely high genetic diversity, which is atypical of recently
 expanded populations and is likely the result of multiple complex
 demographic processes, in addition to hybridization with other Canis
 species. Finally, we considered the transition of allele frequencies
 across geographic space and suggest the mid-Atlantic states of North
 Carolina and Virginia as an emerging contact zone between these two
 distinct coyote expansion fronts.
description: HDY-17-OR0230R_GenotypesGenotypes at 10 microsatellite loci for 482 coyotes. Sampling locations (state & county) and sampling year (if known), are also provided.HDY-17-OR0230R_Data_for_dryad.xlsx
DOI: 10.15468/dl.ykvqx8
title: Occurrence Download

description: A dataset containing 2634 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((105 20,170 20,170 70,105 70,105 20))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Spiraea salicifolia"
 ]
}

 The dataset includes 2634 records from 87 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000906-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.pq387
title: Data from: A reanalysis of relationships among Calypsoinae (Orchidaceae: Epidendroideae): floral and vegetative evolution and the placement of Yoania

description: Calypsoinae are a small, largely temperate subtribe that are diverse with
 respect to trophic strategy (many species have an unusual winter leaf and
 several are leafless) and pollinium stalk morphology. Here we sought to
 re-evaluate the placement of Yoania and recently proposed genera and to
 examine trophic strategy, pollinium stalk type, and geographic
 distribution in a phylogenetic context. We analyzed ITS and matK sequences
 from all accepted genera using maximum likelihood and parsimony on
 individual and combined data sets. The only supported disagreement among
 trees was between the combined ML and parsimony analyses for the placement
 of Dactylostalix and Ephippianthus; the trees from one analysis reflected
 the nuclear pattern, while the other resembled the plastid pattern. A
 group of genera related to Calypso and a group related to Corallorhiza
 were resolved. Yoania is closely related to Calypso; the recently proposed
 Yunorchis is a species of Yoania, while Didiciea is part of Tipularia.
 Examining leaf morphology on the tree revealed two originations of the
 winter leaf morphology and four losses of leaves (and shifts to
 mycoheterotrophy). Pollinium stalks evolved in three directions, two of
 which resulted in epidermally-derived stalks (tegulae) and one that
 comprises the entire rostellum (a hamulus). Biogeographic analysis
 suggests a New World origin for the subtribe, with two major shifts to the
 Old World and one shift back to the New World.
description: calyps_ITS&matK_May2016ITS and matK sequence data in Phylip format
DOI: 10.5061/dryad.74cj2
title: Data from: Metabolic programming mediated by an essential fatty acid alters body composition and survival skills of a marine fish

description: Metabolic programming occurs when variations in nutrition during a speciﬁc
 developmental window result in long-term metabolic effects. It has been
 studied almost exclusively in humans and other mammals but never in an
 ecological context. Here, we report metabolic programming and its
 functional consequences in a marine fish, red drum. We demonstrate that
 maternal provisioning of eggs with an essential fatty acid,
 docosahexaenoic acid (DHA), varies with DHA content of the maternal diet.
 When offspring are reared on a DHA-replete diet, whole-body DHA content of
 offspring depends upon the amount of DHA that was in the egg. We further
 demonstrate that whole-body DHA content is correlated with traits related
 to offspring fitness (escape responses, routine swimming, growth, and
 survival). DHA content of red drum eggs produced in nature is in the range
 where the effects of metabolic programming are most pronounced. Our
 findings indicate that during a brief developmental window DHA plays a
 role in establishing the pathways for its own uptake or storage, with
 protracted and possibly permanent effects on ecologically important
 survival skills of individuals and important implications for dynamics of
 populations and food webs.
description: Fuiman and Perez PRSB
 dataData file includes
 results from experiments 1, 2, and 3 plus complete fatty acid profiles for
 all samples of eggs, larval diets, and larvae. File contains notes to
 explain variables.
DOI: 10.5061/dryad.t3635
title: Data from: Environmental context and contaminant biotransport by Pacific salmon interact to mediate the bioaccumulation of contaminants by stream-resident fish

description: 1.The extent to which environmental context mediates the bioaccumulation
 of biotransported contaminants by stream-resident organisms is poorly
 understood. For example, it is unclear the extent to which contaminant
 type, instream characteristics, or resident fish identity interact to
 influence the uptake of contaminants deposited by Pacific salmon
 (Oncorhynchus spp.) during their spawning runs. 2.To address this
 uncertainty, we sampled four stream-resident fish species from 13
 watersheds of the Laurentian Great Lakes in locations with and without
 salmon runs across a gradient of instream and watershed characteristics.
 We determined the polychlorinated biphenyl (PCB) and mercury (Hg)
 concentration along with the stable isotope ratios for salmon and
 stream-resident fish. 3.We found that stream-resident fish PCB
 concentrations were higher in reaches with salmon and were positively
 related to δ15N. In contrast, resident fish Hg concentrations were similar
 or lower in reaches with salmon compared to reaches lacking salmon and
 either exhibited a negative or no relationship with δ15N. 4.Based upon
 AICc, resident fish exhibited species-specific PCB concentrations that
 were positively related to salmon PCB flux. Hg burdens exhibited an
 interaction between fish length and salmon Hg flux – as salmon Hg inputs
 increased, Hg levels decreased with increasing resident fish length.
 Because salmon eggs are enriched in PCBs but depleted in Hg, contaminant
 loads of resident fish appear to be driven by consumption of salmon eggs.
 We found no support for models that included the mediating influence of
 instream or watershed factors. 5.Synthesis and applications. Our results
 highlight that contaminants bioaccumulate differently depending on
 contaminant type, species identity, and the trophic pathway to
 contamination. Consequently, consideration of the recipient food web and
 route of exposure is critical to understanding the fate of biotransported
 contaminants in ecosystems. The transfer of contaminants by migratory
 organisms represents an understudied stressor in ecology. Effective
 management of biotransported contaminants will require the delineation of
 hotspots of biotransport and implementation of best management practices
 to reduce inputs of salmon-derived pollutants.
description: JAE_Gerig_Dryad_Data
DOI: 10.5061/dryad.m33cb
title: Data from: Demography of the upward-shifting temperate woody species of the Rhododendron pseudochrysanthum complex and ecologically relevant adaptive divergence in its trailing edge populations

description: Trailing edge populations of upward migrating species induced by
 postglacial climatic warming can be evolutionarily significant in the face
 of global warming. We tested for population size changes between lower-
 and higher-elevation populations located in the same mountainous regions
 of the upward-shifting temperate woody species of the Rhododendron
 pseudochrysanthum complex in Taiwan. We also tested whether natural
 selection evoked adaptive divergence in trailing edge populations of this
 species complex. We genotyped 26 expressed sequence tag-simple sequence
 repeat (EST-SSR) loci of 185 individuals from nine populations of the R.
 pseudochrysanthum complex including Rhododendron rubropunctatum,
 Rhododendron hyperythrum, Rhododendron morii, and R. pseudochrysanthum. R.
 rubropunctatum populations in the R. pseudochrysanthum complex possessed
 the lowest estimates of genetic diversity and effective population size.
 Higher-elevation R. pseudochrysanthum populations had lower effective
 population sizes than lower-elevation R. morii populations in Hohuanshan
 and Tahsueshan, as revealed by estimates using both MIGRATE-N and
 approximate Bayesian computation (ABC). R. rubropunctatum populations
 diverged significantly from populations of other members of the R.
 pseudochrysanthum complex. An outlier potentially under positive selection
 specific to R. rubropunctatum populations was identified and strongly
 associated with ecologically relevant environmental variables. Postglacial
 climatic warming has a significant influence on population isolation in
 the R. pseudochrysanthum complex. The results indicate adaptive evolution
 in the trailing edge populations, i.e., R. rubropunctatum populations of
 the upward shifting R. pseudochrysanthum complex.
description: Rhododendron
 pseudochrysanthum cmplex_26lociMicrosatellite data
 format: microsatellite analalyzer. RTG: Rhododendron rubropunctatum
 population Tsaigongkeng; RTK: R. rubropunctatum population Tsankuanliao;
 PTH: R. pseudochrysanthum population Tashueshan; PHH: R. pseudochrysanthum
 population Hohuanshan; PLL: R. pseudochrysanthum population Lulinshan;
 MAL: R. morii population Alishan; MTH: R. morii population Tashueshan;
 MHH: R. morii population Hohuanshan; HNH: R. hyperythrum population
 Nanhutashan
DOI: 10.5061/dryad.6c33h
title: Data from: Contemporary and historic factors influence differently genetic differentiation and diversity in a tropical palm

description: Population genetics theory predicts loss in genetic variability because of
 drift and inbreeding in isolated plant populations; however, it has been
 argued that long-distance pollination and seed dispersal may be able to
 maintain gene flow, even in highly fragmented landscapes. We tested how
 historical effective population size, historical migration and
 contemporary landscape structure, such as forest cover, patch isolation
 and matrix resistance, affect genetic variability and differentiation of
 seedlings in a tropical palm (Euterpe edulis) in a human-modified
 rainforest. We sampled 16 sites within five landscapes in the Brazilian
 Atlantic forest and assessed genetic variability and differentiation using
 eight microsatellite loci. Using a model selection approach, none of the
 covariates explained the variation observed in inbreeding coefficients
 among populations. The variation in genetic diversity among sites was best
 explained by historical effective population size. Allelic richness was
 best explained by historical effective population size and matrix
 resistance, whereas genetic differentiation was explained by matrix
 resistance. Coalescence analysis revealed high historical migration
 between sites within landscapes and constant historical population sizes,
 showing that the genetic differentiation is most likely due to recent
 changes caused by habitat loss and fragmentation. Overall, recent
 landscape changes have a greater influence on among-population genetic
 variation than historical gene flow process. As immediate restoration
 actions in landscapes with low forest amount, the development of more
 permeable matrices to allow the movement of pollinators and seed
 dispersers may be an effective strategy to maintain microevolutionary
 processes.
description: Microsatellite genotype
 for Euterpe edulisMicrosatellite genotype
 for Euterpe edulisData.xls
DOI: 10.5061/dryad.45ds3
title: Data from: Effect of H. pylori infection on cytokine profiles and oxidative balance in subjects with chronic alcohol ingestion

description: Different amounts of ingested alcohol can have distinct effects on the
 human body. However, there is limited research on chronic alcohol
 consumption with Helicobacter pylori infection. We sought to investigate
 the relationship between the cytokine profile, oxidative balance and H.
 pylori infection in subjects with chronic alcohol consumption. A total of
 142 subjects were divided into three groups: 59 subjects with chronic
 alcohol ingestion and H. pylori infection (group A); 53 subjects with
 chronic alcohol ingestion without H. pylori infection (group B); and 30
 control subjects (group C). The serum levels of CagA, interleukin (IL)-10,
 E-selectin, TNF-α, malondialdehyde (MDA) and superoxide dismutase (SOD)
 activity were measured by enzyme-linked immunosorbent assay (ELISA). We
 found that the ages and serum H. pylori CagA levels among the three
 groups, as well as both the mean drinking age and the mean daily alcohol
 consumption between groups A and B, were matched and comparable. Comparing
 the BMIs among the three groups, the BMI differences were found to be
 statistically significant (F=3.921, P&lt;0.05). Compared with group C,
 the BMIs in groups A and B were significantly higher (P&lt;0.001 and
 P&lt;0.01, respectively); however, the BMI differences between group A
 and group B were not statistically significant (P&gt;0.05).
 Additionally, no differences in the serum CagA levels were found in
 comparisons among the groups (all P&gt;0.05). The serum IL-10 and
 E-selectin levels in group A were significantly lower than those in group
 B (serum IL-10: P&lt;0.05; E-selectin: P&lt;0.05). The serum IL-10
 in group A was significantly higher than that in group C (P&lt;0.01);
 the serum E-selectin levels in group A did not significantly differ
 compared with those in group C (P&gt;0.05). Furthermore, the serum
 IL-10 and E-selectin levels in group B were significantly higher than
 those in group C (serum IL-10: P&lt;0.001; E-selectin: P&lt;0.05);
 however, the serum TNF-α levels did not differ among groups (all
 P&gt;0.05). Although the serum levels of MDA and SOD in groups A and B
 were slightly lower than those in group C, there were no significant
 differences among groups (all P&gt;0.05). In conclusion, we believe
 that H. pylori infection might cause a significant inhibition of certain
 cytokine profiles in subjects with chronic alcohol ingestion. Moreover,
 chronically ingested alcohol may exert an adjusted inflammatory effect,
 but there was no association between H. pylori infection, chronic alcohol
 consumption and oxidative balance.
description: Effect of H. pylori
 Infection on Cytokine Profiles and Oxidative Balance in Subjects with
 Chronic Alcohol Ingestion
DOI: 10.5061/dryad.6dh6g
title: Data from: Constraining the role of early land plants in Early Palaeozoic weathering and global cooling

description: How the colonization of terrestrial environments by early land plants over
 400 Ma influenced rock weathering, the biogeochemical cycling of carbon
 and phosphorus, and climate in the Palaeozoic is uncertain. Here we show
 experimentally that mineral weathering by liverworts—an extant lineage of
 early land plants—partnering arbuscular mycorrhizal (AM) fungi, like those
 in 410 Ma-old early land plant fossils, amplified calcium weathering from
 basalt grains threefold to sevenfold, relative to plant-free controls.
 Phosphate weathering by mycorrhizal liverworts was amplified 9–13-fold
 over plant-free controls, compared with fivefold to sevenfold
 amplification by liverworts lacking fungal symbionts. Etching and
 trenching of phyllosilicate minerals increased with AM fungal network size
 and atmospheric CO2 concentration. Integration of grain-scale weathering
 rates over the depths of liverwort rhizoids and mycelia (0.1 m), or tree
 roots and mycelia (0.75 m), indicate early land plants with shallow
 anchorage systems were probably at least 10-fold less effective at
 enhancing the total weathering flux than later-evolving trees. This work
 challenges the suggestion that early land plants significantly enhanced
 total weathering and land-to-ocean fluxes of calcium and phosphorus, which
 have been proposed as a trigger for transient dramatic atmospheric CO2
 sequestration and glaciations in the Ordovician.
description: Quirk_early_land_plant_weathering_PRSB_DataThe data file is an Excel document consisting of 11 worksheets numbered (1) – (11). The data supporting the paper are brought together from two separate controlled-environment experiments and from various literature sources. The experimental data come from the new experiments with liverworts conducted for this study, and from an earlier experiment with trees under comparable environmental and experimental conditions reported previously by Quirk et al. 2014 (Biology letters, 10, DOI: 10.1098/rsbl.2014.0375). The data are also drawn from literature sources used to calculate and compare rates of weathering by lichens and mosses. The worksheets are ordered to correspond with the order that results are presented in the elements of each figure of the main paper. The underpinning data and calculations or conversions used to obtain and compare the results are presented in the relevant worksheets, with calculation steps clearly shown. Numbers in parenthesis in the column headings of worksheet (3), which corresponds to figure 3a, refer to the corresponding numbered worksheets containing the separate datasets (individual box-plot bars) used to construct the figure panel.
DOI: 10.5061/dryad.ck2d2
title: Data from: What can aquatic gastropods tell us about phenotypic plasticity? A review and meta-analysis

description: There have been few attempts to synthesise the growing body of literature
 on phenotypic plasticity to reveal patterns and generalities about the
 extent and magnitude of plastic responses. Here, we conduct a review and
 meta-analysis of published literature on phenotypic plasticity in aquatic
 (marine and freshwater) gastropods, a common system for studying
 plasticity. We identified 96 studies, using pre-determined search terms,
 published between 1985 and November 2013. The literature was dominated by
 studies of predator-induced shell form, snail growth rates and life
 history parameters of a few model taxa, accounting for 67% of all studies
 reviewed. Meta-analyses indicated average plastic responses in shell
 thickness, shell shape, and growth and fecundity of freshwater species was
 at least three times larger than in marine species. Within marine
 gastropods, species with planktonic development had similar average
 plastic responses to species with benthic development. We discuss these
 findings in the context of the role of costs and limits of phenotypic
 plasticity and environmental heterogeneity as important constraints on the
 evolution of plasticity. We also consider potential publication biases and
 discuss areas for future research, indicating well-studied areas and
 important knowledge gaps.
description: Aquatic gastropod
 phenotypic plasticity dataData source and raw data
 used in the calculation and comparison of phenotypic plasticity in aquatic
 gastropodsMaster
 sheet_MarineFW_ToMW.csv
DOI: 10.5061/dryad.5459n
title: Data from: Parental optimism versus parental pessimism in plants: how common should we expect pollen limitation to be?

description: Many organisms exhibit parental optimism, producing more of the initial
 stages of offspring (e.g., eggs, embryos) than they can usually mature.
 For plants, parental optimism may be linked to the risk of seed production
 being limited by pollen receipt (pollen limitation). Here we elaborate a
 stochastic model of pollen limitation developed by Haig and Westoby (1988)
 and Burd (2008) and link it with published data on the magnitudes of
 prepollination costs versus postpollination costs of seed production in 80
 plant species. We demonstrate that parental optimism should be expected
 when prepollination costs of seed production are small relative to
 postpollination costs. This was observed for most (62 of 80) of the plant
 taxa surveyed. Under parental optimism, plants overinvest in securing
 fertilized ovules, and consequently pollen limitation is predicted to be
 uncommon. However, for a sizable minority of plant species (18 of 80),
 prepollination costs approach or exceed postpollination costs. For these
 species, parental pessimism is instead optimal. Parents initiate fewer
 zygotes than they can usually mature, and pollen limitation is predicted
 to be severe. Because the relative magnitudes of prepollination and
 postpollination costs vary by more than 1,000-fold across plant taxa,
 parental outlook (optimism vs. pessimism) and levels of pollen limitation
 are predicted to vary widely.
description: Comparative data on
 pre-pollination costs of seed productionThis data file
 summarizes data extracted from the published literature on the fraction of
 the total costs of seed production that is incurred pre-pollination. The
 table includes four columns: (1) plant species (and flower gender for
 plants that have both female and bisexual flowers); (2) plant group
 (gymnosperm vs. wind-pollinated angiosperm vs. animal-pollinated
 angiosperm; (3) the observed proportion of total investment in seed
 production associated with pre-pollination costs; and (4) the literature
 citation. The full references are given below the
 table.Table
 for Dryad.docx