cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1771
title: Data from: A cryptic invasion within an invasion and widespread introgression in the European water frog complex: consequences of uncontrolled commercial trade and weak international legislation

description: In western Europe many pond owners introduce amphibians for ornamental
 purposes. Although indigenous amphibians are legally protected in most
 European countries, retailers are circumventing national and international
 legislation by selling exotic non-protected sibling species. We
 investigated to what extent non-native species of the European water frog
 complex (genus Pelophylax) have become established in Belgium, using
 morphological, mitochondrial and nuclear genetic markers. A survey of 87
 sampling sites showed the presence of non-native water frogs at 47
 locations, mostly Marsh frogs (P. ridibundus). Surprisingly, at least 19%
 of all these locations also harboured individuals with mitochondrial
 haplotypes characteristic of Anatolian water frogs (P. cf. bedriagae).
 Nuclear genotyping indicated widespread hybridisation and introgression
 between P. ridibundus and P. cf. bedriagae. In addition, water frogs of
 Turkish origin obtained through a licensed retailer, also contained P.
 ridibundus and P. cf. bedriagae, with identical haplotypes to the wild
 Belgian populations. Although P. ridibundus might have invaded Belgium by
 natural range expansion from neighbouring countries, our results suggest
 that its invasion was at least partly enhanced by commercial trade, with
 origins as far as the Middle East. Also the invasion and rapid spread of
 Anatolian lineages, masked by their high morphological similarity to P.
 ridibundus, is likely the result of unregulated commercial trade. We
 expect that Anatolian frogs will further invade the exotic as well as the
 native range of P. ridibundus and other Pelophylax species elsewhere in
 western and central Europe, with risks of large-scale hybridisation and
 introgression.
description: InvasionNoteND1SequinGenbank.txtSequence information of the samples included in the paper
DOI: 10.5061/dryad.q45n7
title: Data from: Highly contrasted responses of Mediterranean octocorals to climate change along a depth gradient

description: Climate change has a strong impact on marine ecosystems, including
 temperate species. Analysing the diversity of thermotolerance levels
 within species along with their genetic structure enables a better
 understanding of their potential response to climate change. We performed
 this integrative study on the Mediterranean octocoral Eunicella cavolini,
 with samples from different depths and by means of a common garden
 experiment. This species does not host photosynthetic Symbiodinium,
 enabling us to focus on the cnidarian response. We compared the
 thermotolerance of individuals from 20 m and 40 m depths from the same
 site and with replicates from the same colony. On the basis of an
 innovative statistical analysis of necrosis kinetics and risk, we
 demonstrated the occurrence of a very different response between depths at
 this local scale, with lower thermotolerance of deep individuals. Strongly
 thermotolerant individuals were observed at 20 m with necrosis appearing
 at higher temperatures than observed in situ. On the basis of nine
 microsatellite loci, we showed that these marked thermotolerance
 differences occur within a single population. This suggests the importance
 of acclimatization processes in adaptation to these different depths. In
 addition, differences between replicates demonstrated the occurrence of a
 variability of response between fragments from the same colony with the
 possibility of an interaction with a tank effect. Our results provide a
 basis for studying adaptation and acclimatization in Mediterranean
 octocorals in a heterogeneous environment.
description: Raw necrosis
 dataThis file gives the
 detailed data of the evolution of necrosis through timeNecrosis data Pivotto et
 al.xlsxmicrosatellites
 genotypes Pivotto et alMicrosatellite
 genotypes
DOI: 10.5061/dryad.vm125vv
title: Data from: Spatial heterogeneity in plant-soil feedbacks alters competitive interactions between two grassland plant species

description: 1. The effects of plants on soil vary greatly between plant species and in
 mixed plant communities this can lead to spatial variation in plant-soil
 feedback (PSF) effects. Such spatial effects are thought to influence
 plant species coexistence, but the empirical evidence for this hypothesis
 is limited. 2. Here, we investigate how spatial heterogeneity in PSFs
 influences plant growth and competition. The experiment was carried out
 with high and low nutrient soils to examine how these effects depend on
 soil fertility. We collected soil from field plots planted for three years
 with monocultures of Anthoxanthum odoratum and Centaurea jacea and tested
 the performance of the two species in a greenhouse experiment in
 heterogeneous soils consisting of patches of “own” and “foreign” soils and
 in soils where the “own” and “foreign” soils were mixed homogeneously. In
 the test phase, plants were grown in monocultures and in 1:1 mixtures in
 live or sterilized soils. 3. Overall, A. odoratum in monocultures produced
 less aboveground biomass in heterogeneous soils than in homogeneous soils.
 Centaurea jacea produced less belowground biomass in live heterogeneous
 soils than in live homogeneous soils, but there was no difference between
 sterile heterogeneous and homogeneous soils. The belowground biomass per
 patch varied more in pots with live heterogeneous soils than in pots with
 live homogeneous soils for both plant species, but there was no difference
 between pots with sterile heterogeneous and homogeneous soils. In pots
 with plant mixtures, the difference in aboveground biomass between the two
 competing species tended to be smaller in heterogeneous than in
 homogeneous soils. In pots with heterogeneous soils, both plant species
 grown in mixtures produced more aboveground biomass in “foreign” soil
 patches than in “own” soil patches. The responses of plants to
 heterogeneous PSFs were not different between low and high nutrient soils.
 4. Our results show that spatially heterogeneous PSFs can influence plant
 performance and competition via reducing the growth inequality between the
 two competing species by allowing selective growth in foreign soil
 patches, independent of initial soil nutrient availability. Such effect
 may slow down exclusion processes and thus promote the coexistence of
 competing species at the local scale in mixed plant communities.
description: Aboveground biomass in
 homogeneous soil and heterogeneous soilAboveground biomass in
 homogeneous and heterogeneous
 soils.csvRoot biomass in
 homogeneous and heterogeneous soilsAboveground biomass in
 different patches within heterogeneous soilAboveground biomass in
 pure soilsRoot biomass in pure
 soils
DOI: 10.5061/dryad.7b37k
title: Data from: Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men

description: There is growing interest in understanding how diet affects the intestinal
 microbiota, including its possible associations with systemic diseases
 such as metabolic syndrome. Here we report a comprehensive and deep
 microbiota analysis of fourteen obese males consuming fully controlled
 diets supplemented with resistant starch (RS) or non-starch
 polysaccharides (NSP), and a weight-loss diet (WL). We analyzed the
 composition, diversity and dynamics of the faecal microbiota on each
 dietary regime by phylogenetic microarray and quantitative PCR analysis.
 Additionally, we analyzed faecal short chain fatty acids (SCFA) as a proxy
 of colonic fermentation, and indices of insulin sensitivity from blood
 samples. The diet explained around 10% of the total variance in microbiota
 composition, which was substantially less than the inter-individual
 variance. Yet, each of the study diets induced clear and distinct changes
 in the microbiota. Multiple Ruminococcaceae phylotypes increased on the RS
 diet, whereas mostly Lachnospiraceae phylotypes increased on the NSP diet.
 Bifidobacteria decreased significantly on the WL diet. The RS diet
 decreased significantly diversity of the microbiota. The total 16S rRNA
 gene signal estimated by qPCR correlated positively with the three major
 SCFAs, while the amount of propionate specifically correlated with the
 Bacteroidetes. The dietary responsiveness of the individual’s microbiota
 varied substantially and associated inversely with its diversity,
 suggesting that individuals can be stratified into responders and
 non-responders based on the features of their intestinal microbiota.
description: HITChip microarray
 dataThe file contains
 phylogenetic microarray signal intensities for 130 intestinal genus-like
 bacterial groups (≥ 90% sequence similarity in the 16S rRNA gene) derived
 from the 55 faecal samples analysed during four different diets, for
 details see Supplementary Figure S1 in the article. The sample ID
 indicates volunteer number followed by a letter code for dietary regime as
 well as number of days passed from beginning of the trial. More
 information about the phylogenetic design of the HITChip can be found at
 http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.01900.x/full.
 The data were extracted with using min-max normalisation (Bolstad et al.
 2003, Bioinformatics 19:185) and log-transformed.ISMEJ_Salonen_HITChip
 L2_Dryad.txt
DOI: 10.5061/dryad.pm8p741
title: Data from: Does prey encounter and nutrient content affect prey selection in wolf spiders inhabiting Bt cotton fields?

description: Wolf spiders are abundant and voracious predators at the soil-plant
 interface in cotton crops. Among other prey, they attack late-instar
 larvae of the cotton bollworm Helicoverpa spp., an economically important
 pest. Consequently, wolf spiders in transgenic Bt cotton could provide
 significant biological control of Bt-resistant Helicoverpa larvae that
 descend to the soil to pupate. The predator-prey interactions between wolf
 spiders and Helicoverpa could, however, be constrained by the presence of
 alternative prey and intraguild predators. This study used laboratory
 enclosures to analyse the effect of alternative prey on predatory
 selection of the wolf spider Tasmanicosa leuckartii Thorell. The prey
 included another wolf spider Hogna crispipes Koch (potential intraguild
 predator), the ground cricket Teleogryllus commodus Walker (minor pest),
 and Helicoverpa armigera larvae (major pest). We tested if encounter
 rates, prey vulnerability, and prey nutritional content influenced the
 likelihood that a prey was attacked. In three-way food webs, Tasmanicosa
 encountered and attacked Teleogryllus and Helicoverpa in similar
 frequencies. However, in the presence of a competing intraguild predator
 and potential prey (Hogna) in a four-way food web, Tasmanicosa did not
 always attack Teleogryllus at first encounter, but still attacked
 Helicoverpa at each encounter. Helicoverpa (protein-poor) and Hogna
 (protein-rich) were consumed by Tasmanicosa in similar proportions,
 suggesting that Tasmanicosa might benefit from nutrient balance as an
 outcome of diverse prey in this food web. As Teleogryllus (protein rich)
 escapes quicker than Helicoverpa and Hogna, Hogna may be an easier
 protein-rich option than Teleogryllus. Field surveys showed that while
 Teleogryllus was the most common prey, wolf spiders feed on diverse insect
 taxa, as well as other spiders. That Tasmanicosa readily attacked
 Helicoverpa larvae in the presence of alternative prey is an encouraging
 result that supports the potential of Tasmanicosa predation to assist in
 the control of Bt-resistant Helicoverpa larvae and thereby inhibit the
 proliferation and spread of resistance.
description: 3_way 4_way food
 websDescribes
 characteristics of animals and encounter and predation outcomes in 3-way
 and 4-way food websLipid and protein
 analysis dataRaw data on the analysis
 of protein and lipid contents of arthropods in this food
 webLipid
 and protein analysis raw
 data.xlsxPrey of wolf spiders in
 cotton fieldsField observations of
 spider predation in cotton fields
DOI: 10.5061/dryad.61c6n05
title: Data from: Of poisons and parasites: the defensive role of tetrodotoxin against infections in newts

description: 1. Classical research on animal toxicity has focused on the role of toxins
 in protection against predators, but recent studies suggest these same
 compounds can offer a powerful defense against parasites and infectious
 diseases. 2. Newts in the genus Taricha are brightly colored and contain
 the potent neurotoxin, tetrodotoxin (TTX), which is hypothesized to have
 evolved as a defense against vertebrate predators such as garter snakes.
 However, newt populations often vary dramatically in toxicity, which is
 only partially explained by predation pressure. 3. The primary aim of this
 study was to evaluate the relationships between individual-level TTX
 concentration and infection by parasites. By systematically assessing
 micro- and macroparasite infections among 345 adult newts (sympatric
 populations of Taricha granulosa and T. torosa), we detected 18 unique
 taxa of helminths, fungi, viruses, and protozoans. 4. For both newt
 species, per-host concentrations of TTX, which varied from undetectable to
 &gt;60 µg cm-2 skin, negatively predicted overall parasite richness as
 well as the likelihood of infection by the chytrid fungus,
 Batrachochytrium dendrobatidis, and ranavirus. No such effect was found on
 infection load among infected hosts. Despite commonly occurring at the
 same wetlands, T. torosa supported higher parasite richness and average
 infection load than T. granulosa. Host body size and sex (females &gt;
 males) tended to positively predict infection levels in both species. For
 hosts in which we quantified leukocyte profiles, total white blood cell
 count correlated positively with both parasite richness and total
 infection load. 5. By coupling data on host toxicity and infection by a
 broad range of micro- and macroparasites, these results suggest that –
 alongside its effects on predators – tetrodotoxin may help protect newts
 against parasitic infections, highlighting the importance of integrative
 research on animal chemistry, immunological defenses, and natural enemy
 ecology.
description: Johnson et al RAW
 DATAThis CVS file individual
 dissection data
DOI: 10.5061/dryad.763
title: Data from: Molecular phylogenetics of desmognathine salamanders (Caudata: Plethodontidae): a reevaluation of evolution in ecology, life history, and morphology

description: Phylogenetic relationships were reconstructed for salamanders of the
 plethodontid subfamily Desmognathinae to examine evolution of morphology,
 ecology, and life history. Mitochondrial DNA sequences encoding 12S and
 16S ribosomal RNA and the valine transfer RNA provided 259
 phylogenetically informative sites from approximately 1,200 nucleotide
 positions for 21 specimens representing 15 species and subspecies. These
 data were analyzed in conjunction with 13 morphological and reproductive
 characters to generate phylogenetic hypotheses. The directly developing
 terrestrial desmognathines Phaeognathus hubrichti and Desmognathus wrighti
 represent, respectively, the first and second phylogenetic branching
 events within the subfamily, and the remaining terrestrial lineage, D.
 aeneus, also branches near the base of the phylogenetic tree. These
 results challenge earlier hypotheses that within Desmognathus the small
 nonmetamorphosing species, D. aeneus and D. wrighti, represent the end of
 a graded phylogenetic decrease in size and decrease in use of aquatic
 habitats. In contrast to previous hypotheses, our results suggest that
 desmognathine evolution includes transformations in the direction of
 larger body sizes, lengthened larval periods, and greater use of aquatic
 habitats.
description: mtDNA Data
 SetmtDNACombined Data Setcombined
DOI: 10.5061/dryad.c983b
title: Data from: Developmental plasticity affects sexual size dimorphism in an anole lizard

description: While developmental plasticity has been shown to contribute to sexual size
 dimorphism (SSD) in laboratory studies, its role in shaping SSD variation
 in wild vertebrate populations is unclear. Here we use a field study and a
 laboratory experiment to show that resource availability influences the
 degree of SSD among insular populations of Anolis sagrei lizards in the
 Bahamas. Total amounts of food biomass explained variation in male, but
 not female, body size on six Bahamian islands, giving rise to significant
 differences in SSD. Laboratory experiments on a captive colony of A.
 sagrei confirmed that variation in SSD was mediated by the effects of prey
 biomass on developmental plasticity in males, but not females. Indeed,
 males grew faster and attained larger sizes as adults under high food
 treatments than under restricted diets, whereas adult females retained
 similar body sizes under both conditions. Our results indicate that the
 amount of food available can influence inter-sexual variation in body size
 within a vertebrate species. Sex-specific developmental plasticity may be
 favored if it allows individuals to take advantage of varying levels of
 food opportunities offered by different habitats, by reducing competition
 between the sexes. As such, plasticity in response to food availability
 may have played a role in the invasion success of A. sagrei. This study
 adds to our growing understanding of the effect of resource availability
 in shaping SSD in reptiles and lends further support to the
 condition-dependence hypothesis, according to which the larger sex should
 display greater plasticity in growth in response to environmental
 conditions.
description: Field and laboratory
 measurements of SVL in male and female A. sagreiField and laboratory
 measurements of snout-vent length (SVL) of male and female A. sagrei
 lizards. Field data: Adult males and adult females were captured on six
 Bahamian islands (Acklins, Andros, Grand Bahamas, Chub Cay, Pidgeon Cay
 and Staniel Cay). Laboratory data: feeding experiments of juvenile male
 and female A. sagrei raised under low or high food
 diets.FE-2015-00041.R1_Bonneaud et
 al.xlsx
DOI: 10.5061/dryad.gt875
title: Data from: The pitcher plant flesh fly exhibits a mixture of patchy and metapopulation attributes

description: We investigated the pattern of spatial genetic structure and the extent of
 gene flow in the pitcher plant flesh fly Fletcherimyia fletcheri, the
 largest member of the inquiline community of the purple pitcher plant
 Sarracenia purpurea. Using microsatellite loci, we tested the theoretical
 predictions of different hypothesized population models (patchy
 population, metapopulation or isolated populations) among 11 bogs in
 Algonquin Provincial Park (Canada). Our results revealed that the pitcher
 plant flesh fly exhibits a mixture of patchy and metapopulation
 characteristics. There is significant differentiation among bogs and
 limited gene flow at larger spatial scales, but local populations do not
 experience frequent local extinctions/recolonizations. Our findings
 suggest a strong dispersal ability and stable population sizes in F.
 fletcheri, providing novel insights into the ecology of this member of a
 unique ecological microcosm.
description: F. fletcheri
 microsatellite genotyping dataIndividuals (e.g.
 ff2009-DL-10A) genotyped at 10 microsatellite loci (e.g. FF72), with one
 allele per column for each locus. The year of collection is designated
 after ff (e.g. ff2009 for the collection year 2009), followed by the bog
 code (e.g. DL), followed by an unique plant number (e.g. 10), followed by
 a leaf number where multiple individuals from the same plant are collected
 (e.g. A). The list of bog codes is found in Table 2 of the main
 text.Rasic&Keyghobadi_Supl_TablesSupplemental Tables 1-3
DOI: 10.5061/dryad.q9g1348
title: Data from: Nickel exposure has complex transgenerational effects in a butterfly

description: Heavy metal pollution is a major problem in urban and industrial
 environments, and has a myriad of negative effects on animals. Quantifying
 the amount of population-level variation that exists for heavy metal
 tolerance and how plastic responses to heavy metals play out across
 generations are essential for understanding how animals respond to
 pollution. As an initial step towards studying transgenerational effects
 and population-level variation in concert, we brought cabbage white
 butterflies (Pieris rapae) from two populations – collected from St. Paul,
 Minnesota and Davis, California – into common conditions and fed them a
 diet dosed with nickel. To measure transgenerational effects, we reared a
 second generation in a fully factorial design, within each population, to
 achieve all combinations of parent and offspring exposure to nickel or
 control diets. Across both generations, we quantified survival and other
 fitness-related traits, including development time, body size, and egg
 size and number. We found both population differences and complex
 transgenerational effects, including a positive effect of nickel on
 survival and development time in one of the populations. Overall, nickel
 exposure was stressful in one population, mainly after two generations of
 exposure, and had neutral or slightly positive effects on the other. We
 found no evidence for costs of mismatch between parental and offspring
 environments. While the reasons for the differences observed between the
 two populations are unclear, the variation in nickel tolerance observed in
 this species suggests that some organisms may be less affected by low
 levels of heavy metal pollution in urban and industrial areas than
 expected.
description: All data from
 "Nickel exposure has complex transgenerational effects in a
 butterfly"Excel spreadsheet with
 description of traits measured across two generations.ICB 2018 data for
 dryad.xlsx