cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ns23j
title: Data from: Spatial and temporal patterns of genetic variation in the widespread antitropical deep-sea coral Paragorgia arborea

description: Numerous deep-sea species have apparent widespread and discontinuous
 distributions. Many of these are important foundation species, structuring
 hard-bottom benthic ecosystems. Theoretically, differences in the genetic
 composition of their populations vary geographically and with depth.
 Previous studies have examined the genetic diversity of some of these taxa
 in a regional context, suggesting that genetic differentiation does not
 occur at scales of discrete features such as seamounts or canyons, but at
 larger scales (e.g. ocean basins). However, to date, few studies have
 evaluated such diversity throughout the known distribution of a putative
 deep-sea species. We utilized sequences from seven mitochondrial gene
 regions and nuclear genetic variants of the deep-sea coral Paragorgia
 arborea in a phylogeographic context to examine the global patterns of
 genetic variation and their possible correlation with the spatial
 variables of geographic position and depth. We also examined the
 compatibility of this morphospecies with the genealogical-phylospecies
 concept by examining specimens collected worldwide. We show that the
 morphospecies P. arborea can be defined as a genealogical-phylospecies, in
 contrast to the hypothesis that P. arborea represents a cryptic species
 complex. Genetic variation is correlated with geographic location at the
 basin-scale level, but not with depth. Additionally, we present a
 phylogeographic hypothesis in which P. arborea originates from the North
 Pacific, followed by colonization of the southern hemisphere prior to
 migration to the North Atlantic. This hypothesis is consistent with the
 latest ocean circulation model for the Miocene.
description: ParboreaMtHaplotypes_16S_COI_ND3_ND2_MSH1_ND6_intParagorgia arborea mt haplotypes. Concatenated genes 16S_COI_ND3_ND2_MSH1_ND6ParboreaITS2Haplotypes
DOI: 10.5061/dryad.7f32h
title: Data from: Experimental evolution reveals differences between phenotypic and evolutionary responses to population density

description: Group living can select for increased immunity, given the heightened risk
 of parasite transmission. Yet, it also may select for increased male
 reproductive investment, given the elevated risk of female multiple
 mating. Trade-offs between immunity and reproduction are well documented.
 Phenotypically, population density mediates both reproductive investment
 and immune function in the Indian meal moth, Plodia interpunctella.
 However, the evolutionary response of populations to these traits is
 unknown. We created two replicated populations of P. interpunctella,
 reared and mated for 14 generations under high or low population
 densities. These population densities cause plastic responses in immunity
 and reproduction: at higher numbers, both sexes invest more in one index
 of immunity (phenoloxidase (PO) activity) and males invest more in sperm.
 Interestingly, our data revealed divergence in PO and reproduction in a
 different direction to previously reported phenotypic responses. Males
 evolving at low population densities transferred more sperm and both males
 and females displayed higher PO than individuals at high population
 densities. These positively correlated responses to selection suggest no
 apparent evolutionary trade-off between immunity and reproduction. We
 speculate that the reduced PO activity and sperm investment when evolving
 under high population density may be due to the reduced population fitness
 predicted under increased sexual conflict and/or to trade-offs between
 pre- and post-copulatory traits.
description: Data for
 dryadEvolutionary responses
 of Plodia interpunctella in sperm production, immunity, development,
 mating frequency and longevity in response to being reared at high (HD) or
 low (LD) population densities.
DOI: 10.5061/dryad.pm885
title: Data from: Persistent organic pollution in a high-Arctic top predator: sex-dependent thresholds in adult survival

description: In long-lived species, any negative effect of pollution on adult survival
 may pose serious hazards to breeding populations. In the present study we
 measured concentrations of various organochlorines (OCs: PCB and
 organochlorine pesticides) in the blood of a large number of adult
 glaucous gulls (Larus hyperboreus) breeding on Bjørnøya (Bear Island) in
 the Norwegian Arctic, and modelled their local survival using
 capture–recapture analysis. Survival was negatively associated with
 concentrations of OCs in the blood. The effect of OCs was nonlinear and
 evident only among birds with the highest concentrations (the uppermost
 deciles of contamination). The threshold for depressed survival differed
 between the sexes, with females being more sensitive to contamination. For
 birds with lower OC concentration, survival was very high, i.e. at the
 upper range of survival rates reported from glaucous and other large gull
 species in other, presumably less contaminated populations. We propose two
 non-exclusive explanations. Firstly, at some threshold of OC
 concentration, parents (especially males) may abandon reproduction to
 maximise their own survival. Secondly, high contamination of OC may
 eliminate the most sensitive individuals from the population (especially
 among females), inducing a strong selection towards high-quality and less
 sensitive phenotypes.
description: Individual
 dataRaw data used in
 analyses: individual capture histories, biometry and contamination levels
 of glaucous gulls on Bjørnøyainput.csvPopulation viability analysesMethods, data and results of population viability analysis of glaucous gulls on BjørnøyaPVA.pdf
DOI: 10.5061/dryad.14hp7
title: Data from: Edge effects and beta diversity in ground and canopy beetle communities of fragmented subtropical forest

description: Clearing of dry forests globally creates edges between remnant forest and
 open anthropogenic habitats. We used flight intercept traps to evaluate
 how forest beetle communities are influenced by distance from such edges,
 together with vertical height, spatial location, and local vegetation
 structure, in an urbanising region (Brisbane, Australia). Species
 composition (but not total abundance or richness) differed greatly between
 ground and canopy. Species composition also varied strongly among sites at
 both ground and canopy levels, but almost all other significant effects
 occurred only at ground level, where: species richness declined from edge
 to interior; composition differed between positions near edges (&lt;10
 m) and interiors (&gt; 50 m); high local canopy cover was associated
 with greater total abundance and richness and differing composition; and
 greater distances to the city centre were associated with increased total
 abundances and altered composition. Analyses of individual indicator
 species associated with this variation enabled further biological
 interpretations. A global literature synthesis showed that most spatially
 well-replicated studies of edge effects on ground-level beetles within
 forest fragments have likewise found that positions within tens of metres
 from edges with open anthropogenic habitats had increased species richness
 and different compositions from forest interior sites, with fewer effects
 on abundance. Accordingly, negative edge effects will not prevent
 relatively small compact fragments (if &gt;10-20 ha) from supporting
 forest-like beetle communities, although indirect consequences of habitat
 degradation remain a threat. Retention of multiple spatially scattered
 forest areas will also be important in conserving forest-dependent
 beetles, given high levels of between-site diversity.
description: BeetleAndEnviroData.Stone.et.al.2017This data set contains abundance, species richness, composition and environmental data sampled in 80 flight intercept trap locations. This data was used for data analyses and any species sampled in less that two trap locations have been excluded.
DOI: 10.15468/dl.cwv64v
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mandragora turcomanica",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 9 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000949-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7bn0fr99
title: Data from: Testing the phylogenetic affinities of Southeast Asia’s rarest geckos: Flap-legged geckos (Luperosaurus), Flying geckos (Ptychozoon) and their relationship to the pan-Asian genus Gekko

description: Some of Southeast Asia’s most poorly known vertebrates include forest
 lizards that are rarely seen by field biologists. Arguably the most
 enigmatic of forest lizards from the Indo Australian archipelago are the
 Flap-legged Geckos and the Flying Geckos of the genera Luperosaurus and
 Ptychozoon. As new species have accumulated, several have been noted for
 their bizarre combination of morphological characteristics, seemingly
 intermediate between these genera and the pan-Asian gecko genus Gekko. We
 used the first multilocus phylogeny for these taxa and Bayesian tests of
 alternate topologies to evaluate their relationships, with particular
 attention to the phylogenetic placement of the morphologically
 intermediate taxa Ptychozoon rhacophorus, Luperosaurus iskandari, and L.
 gulat. Surprisingly, our results demonstrate that Luperosaurus is more
 closely related to Lepidodactylus and Pseudogekko than it is to Gekko but
 that some species currently classified as Luperosaurus are nested within
 Gekko. The Flying Gecko genus Ptychozoon is also nested within Gekko,
 suggesting higher-level taxonomic revision of the generic boundaries
 within Southeast Asian gekkonines is a priority for the immediate future.
description: Luperosaurus Alignment
 FileAlignment files used in
 phylogenetic analyses. The character sets are provided in brackets at the
 end of the file.Luperosaurus_Alignment.nexLuperosaurus_joloensis_PhosducinThere is only a single tissue that we know of for this rare species. The tissue was degraded, and although we exhaustively tried to get more sequence data, we were left with just a short piece of nuclear data for the Phosducin gene. The file is formatted as a FASTA file. Genbank's new policy is to not accept sequences below 200bp. We therefore wanted to make this short read available via Dryad.Bayesian Consensus TreeBrown.etal.BayesianConsensus.treLikelihood Consensus TreeBrown.etal.RAxML_Consensus.tre
DOI: 10.5061/dryad.h4t15
title: Data from: The good, the bad and the Ulva: the density dependent role of macroalgal subsidies in influencing diversity and trophic structure of an estuarine community

description: Worldwide, ecological subsidies enhance ecosystem productivity and
 therefore trophic support for greater biodiversity of taxa. While studies
 in terrestrial and aquatic ecosystems demonstrate that the magnitude of
 subsidies into ecosystems differs widely, the thresholds where subsidies
 may switch from exerting positive to negative effects are poorly
 understood. In estuaries, eutrophication promotes drift macroalgae that
 deposit on the benthos, cover intertidal flats for months and serve as
 pressed resource subsidies for benthic consumers. We hypothesized there
 would be a critical threshold of macroalgal biomass where ecosystem-level
 effects would turn from positive to negative. We used manipulative field
 experiments varying macroalgal mat thickness (0.5, 1.5 and 4 cm) over
 eight weeks and quantified effects on macrofauna on a lagoon mudflat in
 California. We documented that plots with mat depths of 0.5 and 1.5 cm had
 higher diversity by supporting both surface feeding and burrowing
 detritivores. Non-metric multidimensional scaling showed that the benthic
 community diverged with mat depth over the course of the experiment. After
 eight weeks, surface deposit feeders were associated mainly with 0.5 cm
 macroalgal subsidies, whereas subsurface deposit feeding capitellids were
 closely linked with 4 cm mats. Depth profiles of pore water sulfide
 concentration collected from 4 cm mats were 7622 ± 5294 μM, mean ± s.e.,
 (mean of means across depth profiles), whereas 0.5 cm treatments resulted
 in sulfide concentrations that were 0.25% of the 4 cm treatments. This
 suggests that the mechanism of negative effects for elevated macroalgal
 subsidies was development of anoxic conditions promoting sulfide
 accumulation. Thus, our study was the first to find a critical threshold,
 or ecological tipping point, beyond which the effects of anthropogenically
 enhanced subsidies to estuarine mudflat communities switched from positive
 to negative and to describe the mechanism by which elevated subsides
 altered the abiotic environment and likely reduced ecosystem functioning.
description: Macrofauna for 2008
 caging experimentMacrofauna count and
 proportion data for the 2008 caging experimentC4InfaunabyWeek.xlsxPorewater sulfide Summer 2008Sulfide concentrations for porewaters collected during the summer 2008 caging experimentC4PeeperSulfide.xlsxPorewater iron Summer 2008Fe(III) concentrations from porewaters collected during the summer 2008 caging experimentC4PeeperFe.xls
DOI: 10.5061/dryad.82bg7
title: Data from: The contribution of phenotypic plasticity to the evolution of insecticide tolerance in amphibian populations

description: Understanding population responses to rapid environmental changes caused
 by anthropogenic activities, such as pesticides, is a research frontier.
 Genetic assimilation (GA), a process initiated by phenotypic plasticity,
 is one mechanism potentially influencing evolutionary responses to novel
 environments. While theoretical and laboratory research suggests that GA
 has the potential to influence evolutionary trajectories, few studies have
 assessed its role in the evolution of wild populations experiencing novel
 environments. Using the insecticide, carbaryl, and 15 wood frog
 populations distributed across an agricultural gradient, we tested whether
 GA contributed to the evolution of pesticide tolerance. First, we
 investigated the evidence for evolved tolerance to carbaryl and discovered
 that population-level patterns of tolerance were consistent with
 evolutionary responses to pesticides; wood frog populations living closer
 to agriculture were more tolerant than populations living far from
 agriculture. Next, we tested the potential role of GA in the evolution of
 pesticide tolerance by assessing whether patterns of tolerance were
 consistent with theoretical predictions. We found that populations close
 to agriculture displayed constitutive tolerance to carbaryl whereas
 populations far from agriculture had low naïve tolerance but high
 magnitudes of induced tolerance. These results suggest GA could play a
 role in evolutionary responses to novel environments in nature.
description: Time to death + Wood
 frog stage and massTime to death data +
 Wood frog stage and mass dataEVA-2014-170-OA.R2.xlsx
DOI: 10.5061/dryad.br47r
title: Data from: Landscape and environmental influences on Mycobacterium ulcerans distribution among aquatic sites in Ghana

description: Buruli ulcer, caused by Mycobacterium ulcerans, is highly endemic in West
 Africa. While the mode of transmission is unknown, many studies associate
 Buruli ulcer with different types of water exposure. We present results
 from the largest study to date to test for M. ulcerans in aquatic sites
 and identify environmental attributes associated with its presence.
 Environmental samples from 98 aquatic sites in the Greater Accra, Ashanti,
 and Volta regions of Ghana were tested for the presence of M. ulcerans DNA
 by polymerase chain reaction. The proportion of aquatic sites positive for
 M. ulcerans varied by region: Ashanti 66% (N = 39), Greater Accra 34% (N =
 29), and Volta 0% (N = 30). We explored the spatial distribution of M.
 ulcerans positive and negative water bodies and found no significant
 clusters. We also determined both highly localized water attributes and
 broad scale remotely sensed land cover and terrain environmental
 characteristics associated with M. ulcerans presence through logistic
 regression. Our results concur with published results regarding conditions
 suitable for M. ulcerans growth and associations with Buruli ulcer disease
 burden with regards to water characteristics and disturbed environments,
 but differ from others with regards to spatial associations and
 topographic effects such as elevation and wetness. While our results
 suggest M. ulcerans is an environmental organism existing in a specific
 ecological niche, they also reveal variation in the elements defining this
 niche across the sites considered. In addition, despite the causal
 association between Buruli ulcer and M. ulcerans, we observed no
 significant statistical association between case reports of Buruli ulcer
 and presence of M. ulcerans in nearby waterbodies.
description: MU-BU-GhanaThe data presented here are a combination of in the field measurements, remotely sensed satellite imagery, and subsequent laboratory processing.
DOI: 10.5061/dryad.p7c8s
title: Data from: The effect of plant identity and the level of plant decay on molecular gut content analysis in a herbivorous soil insect

description: Plant roots represent an important food source for soil-dwelling animals,
 but tracking herbivore food choices below-ground is difficult. Here, we
 present an optimized PCR assay for the detection of plant DNA in the guts
 of invertebrates, using general plant primers targeting the trnT-F
 chloroplast DNA region. Based on this assay, we assessed the influence of
 plant identity on the detectability of ingested plant DNA in Agriotes
 click beetle larvae. Six different plant species were fed to the insects,
 comprising a grass, a legume, and four non-legume forbs. Moreover, we
 examined whether it is possible to amplify DNA of decaying plants and if
 DNA of decayed plant food is detectable in the guts of the larvae. DNA of
 the ingested roots could be detected in the guts of the larvae for up to
 72 h post-feeding, the maximum digestion time tested. When fed with living
 plants, DNA detection rates differed significantly between the plant
 species. This may be ascribed to differences in the amount of plant tissue
 consumed, root palatability, root morphology and/or secondary plant
 components. These findings indicate that plant identity can affect
 post-feeding DNA detection success, which needs to be considered for the
 interpretation of molecularly derived feeding rates on plants.
 Amplification of plant DNA from decaying plants was possible as long as
 any tissue could be retrieved from the soil. The consumption of decaying
 plant tissue could also be verified by our assay, but the insects seemed
 to prefer fresh roots over decaying plant material.
description: raw data Wallinger et al
 MER-12-0242Molecular detection
 rates of different Agriotes larvae feeding on different plant species -
 feeding experiments with fresh plants and decaying
 tissue
DOI: 10.5061/dryad.vv46k
title: Data from: High chlorpyrifos resistance in Culex pipiens mosquitoes: strong synergy between resistance genes

description: We investigated the genetic determinism of high chlorpyrifos resistance
 (HCR), a phenotype first described in 1999 in Culex pipiens mosquitoes
 surviving chlorpyrifos doses greater than or equal to1 mg l−1 and more
 recently found in field samples from Tunisia, Israel or Indian Ocean
 islands. Through chlorpyrifos selection, we selected several HCR strains
 that displayed over 10 000-fold resistance. All strains were homozygous
 for resistant alleles at two main loci: the ace-1 gene, with the resistant
 ace-1R allele expressing the insensitive G119S acetylcholinesterase, and a
 resistant allele of an unknown gene (named T) linked to the sex and ace-2
 genes. We constructed a strain carrying only the T-resistant allele and
 studied its resistance characteristics. By crossing this strain with
 strains harboring different alleles at the ace-1 locus, we showed that the
 resistant ace-1R and the T alleles act in strong synergy, as they elicited
 a resistance 100 times higher than expected from a simple multiplicative
 effect. This effect was specific to chlorpyrifos and parathion and was not
 affected by synergists. We also examined how HCR was expressed in strains
 carrying other ace-1-resistant alleles, such as ace-1V or the duplicated
 ace-1D allele, currently spreading worldwide. We identified two major
 parameters that influenced the level of resistance: the number and the
 nature of the ace-1-resistant alleles and the number of T alleles. Our
 data fit a model that predicts that the T allele acts by decreasing
 chlorpyrifos concentration in the compartment targeted in insects.
description: Bioassaydata_HeredityRaw data for the bioassays analyzed in the publication. Excel sheet for each treatment.
DOI: 10.5061/dryad.14fd6
title: Data from: A free lunch? No cost for acquiring defensive plant pyrrolizidine alkaloids in a specialist arctiid moth (Utetheisa ornatrix)

description: Many herbivorous insects sequester defensive chemicals from their host
 plants. We tested sequestration fitness costs in the specialist moth
 Utetheisa ornatrix (Lepidoptera: Arctiidae). We added pyrrolizidine
 alkaloids (PAs) to an artificial diet at different concentrations. Of all
 the larval and adult fitness components measured, only development time
 was negatively affected by PA concentration. These results were repeated
 under stressful laboratory conditions. On the other hand, the amount of
 PAs sequestered greatly increased with the diet PA concentration. Absence
 of a detectable negative effect does not necessarily imply a lack of costs
 if all individuals express the biochemical machinery of detoxification and
 sequestration constitutively. Therefore, we used qPCR to show that
 expression of the gene used to detoxify PAs,
 pyrrolizidine-alkaloid-N-oxygenase (pno), increased 41-fold in our highest
 PA treatment. Nevertheless, fitness components were affected only slightly
 or not at all, suggesting that sequestration in this species does not
 incur a strong cost. The apparent lack of costs has important implications
 for our understanding of the evolution of ecological interactions; for
 example, it implies that selection by specialist herbivores may decrease
 the levels of certain chemical defense in plant populations.
description: All fitness
 experimentsAll experiments
 measuring fitness components on the different PA
 treatments.PA
 contentPA content in adult
 moths reared on different PA concentrationsqPCRqPCr data on expression
 of PNO