cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9025
title: Data from: Phylogenetic analyses of mitochondrial and nuclear data in haematophagous flies support the paraphyly of the genus Stomoxys (Diptera: Muscidae)

description: The genus Stomoxys Geoffroy (Diptera; Muscidae) contains species of
 parasitic flies that are of medical and economic importance. We conducted
 a phylogenetic analysis including 10 representative species of the genus
 including multiple exemplars, together with the closely related genera
 Prostomoxys Zumpt, Haematobosca Bezzi, and Haematobia Lepeletier &
 Serville. Phylogenetic relationships were inferred using maximum
 likelihood and Bayesian methods from DNA fragments from the cytochrome c
 oxidase subunit I (COI, 753 bp) and cytochrome b (CytB, 587 bp)
 mitochondrial genes, and the nuclear ribosomal internal transcribed spacer
 2 (ITS2, 426 bp). The combination of mitochondrial and nuclear data
 strongly supports the paraphyly of the genus Stomoxys because of the
 inclusion of Prostomoxys saegerae Zumpt. This unexpected result suggests
 that Prostomoxys should be renamed into Stomoxys. Also, the deep molecular
 divergence observed between the subspecies Stomoxys niger niger Macquart
 and S. niger bilineatus Grünbreg led us to propose that they should rather
 be considered as distinct species, in agreement with ecological data.
 Bayesian phylogenetic analyses support three distinct lineages within the
 genus Stomoxys with a strong biogeographical component. The first lineage
 consists solely of the divergent Asian species S. indicus Picard which
 appears as the sister-group to all remaining Stomoxys species. The second
 clade groups the strictly African species Stomoxys inornatus Grünbreg,
 Stomoxys transvittatus Villeneuve, Stomoxys omega Newstead, and Stomoxys
 pallidus Roubaud. Finally, the third clade includes both African occurring
 and more widespread species such as the livestock pest Stomoxys calcitrans
 Linnaeus. Divergence time estimates indicate that the genus Stomoxys
 originated in the late Oligocene around 30 million years ago, with the
 major lineages diversifying in the Early Miocene between 20 and 15 million
 years ago at a time when temperate forests developed in the Northern
 Hemisphere.
description: Dsouli-InfectGenetEvol11
 nexus fileNexus file for the
 concatenation of 2 mitochondrial (COX1 and CYTB) and 1 nuclear (ITS2)
 genes for 39 dipterans.Dsouli-InfectGenetEvol11.nexDsouli-InfectGenetEvol11 phylogramThis phylogram is the 50% majority rule consensus tree presented in Figure 1. It was obtained with Bayesian inference using MrBayes under the GTR + G model. Numbers at nodes indicate posterior probabilities (PP).Dsouli-InfectGenetEvol11.tre
DOI: 10.5061/dryad.rn192
title: Data from: Biotic resistance to an alien amphibian: larval competition between Japanese frogs and invasive cane toads

description: Understanding negative effects of native species on introduced taxa may
 suggest novel ways to control the invasive species by enhancing such
 effects. Previous studies have reported that the larvae of invasive cane
 toads (Rhinella marina) are suppressed by competition with the larvae of
 native anurans in Australia, but not in North America. We conducted
 laboratory trials to measure the effect of exposure to the larvae of
 Japanese frogs (Microhyla ornata, Fejervarya sakishimensis, Rhacophorus
 owstoni) on rates of survival, growth and development of cane toad
 tadpoles in Ishigaki Island, in southern Japan. Survival rates were not
 affected by native species, but competition with Dicroglossids and
 Rhacophorids (but not Microhylids) strongly reduced rates of growth and
 development in the tadpoles of cane toads. Dicroglossid tadpoles also
 reduced the body condition to toad tadpoles in addition to effects on SVL
 and mass. Encouraging populations of native frogs in toad-invaded areas of
 Japan thus may help to reduce the numbers of invasive cane toads.
description: Plos one raw data
 (native tad vs toad tad)Survival rate, svl, and
 weight of cane toad tadpole in Ishikgai island, Japan
DOI: 10.5061/dryad.m4452
title: Data from: Biparental care is predominant and beneficial to parents in the burying beetle Nicrophorus orbicollis (Coleoptera: Silphidae)

description: Parenting strategies can be flexible within a species and may have varying
 fitness effects. Understanding this flexibility and its fitness
 consequences is important for understanding why parenting strategies
 evolve. In the present study, we investigate the fitness consequences of
 flexible parenting in the burying beetle Nicrophorus orbicollis, a species
 known for its advanced provisioning behaviour of regurgitated vertebrate
 carrion to offspring by both sexes. We show that, even when a parent is
 freely allowed to abandon the carcass at any point in time, biparental
 post-hatching care is the most common pattern of care adopted in N.
 orbicollis. Furthermore, two parents together raised more offspring than
 single parents of either sex, showing that the presence of the male can
 directly influence parental fitness even in the absence of competitors.
 This contrasts with studies in other species of burying beetle, where
 biparental families do not differ in offspring number. This may explain
 why biparental care is more common in N. orbicollis than in other burying
 beetles. We suggest how the fitness benefits of two parents may play a
 role in the evolution and maintenance of flexible biparental care in N.
 orbicollis.
description: Data from Benowitz &
 Moore 2016, BJLSBenowitz&Moore_BJLS_2016_data.xlsx
DOI: 10.5061/dryad.300k7
title: Data from: Prey size diversity hinders biomass trophic transfer and predator size diversity promotes it in planktonic communities

description: Body size exerts multiple effects on plankton food-web interactions.
 However, the influence of size structure on trophic transfer remains
 poorly quantified in the field. Here, we examine how the size diversity of
 prey (nano-microplankton) and predators (mesozooplankton) influence
 trophic transfer efficiency (using biomass ratio as a proxy) in natural
 marine ecosystems. Our results support previous studies on single trophic
 levels: transfer efficiency decreases with increasing prey size diversity
 and is enhanced with greater predator size diversity. We further show that
 communities with low nano-microplankton size diversity and high
 mesozooplankton size diversity tend to occur in warmer environments with
 low nutrient concentrations, thus promoting trophic transfer to higher
 trophic levels in those conditions. Moreover, we reveal an interactive
 effect of predator and prey size diversities: the positive effect of
 predator size diversity becomes influential when prey size diversity is
 high. Mechanistically, the negative effect of prey size diversity on
 trophic transfer may be explained by unicellular size-based metabolic
 constraints as well as trade-offs between growth and predation avoidance
 with size, whereas increasing predator size diversity may enhance diet
 niche partitioning and thus promote trophic transfer. These findings
 provide insight into size-based theories of ecosystem functioning, with
 implications for ecosystem predictive models.
description: GarciaComasetal_ProcB_DatasetSamples were collected in the field during cruises across the East China Sea. 'PPBR' corresponds to Predator-Prey Biomass Ratio. 'Predator' corresponds to mesozooplankton excluding carnivore species (water column sampled with a net of 330 µm mesh size; 1.6 m mouth diameter). 'Prey' corresponds to nano-microplankton (sampled from 10-m below the detected cola to surface with Niskin bottles). Individual size was obtained with the ZooSCAN for mesozooplankton, and the FlowCAM for nano-microplankton. Size diversity corresponds to the continuous version of the Shannon index. SST and SSS correspond to sea surface temperature and salinity, respectively. Nutrient concentrations are integrated above the mixed layer depth.
DOI: 10.5061/dryad.8g73f
title: Data from: Analysis of hypoxia-inducible factor alpha polyploidization reveals adaptation to Tibetan plateau in the evolution of schizothoracine fish

description: Background: Hypoxia-inducible factor (HIF) is a master regulator that
 mediates major changes in gene expression under hypoxic conditions. Though
 HIF family has been identified in many organisms, little is known about
 this family in schizothoracine fish. Results: Duplicated hif-α (hif-1αA,
 hif-1αB, hif-2αA, and hif-2αB) genes were identified in schizothoracine
 fish. All the deduced HIF-α proteins contain the main domains (bHLH-PAS,
 ODDD, and TAD), also found in humans. Evidence suggests a
 Cyprinidae-specific deletion, specifically, a conserved proline
 hydroxylation motif LxxLAP, in the NODD domain of schizothoracine fish
 HIF-1αA. In addition, a schizothoracine-specific mutation was observed in
 the CODD domain of the specialized and highly specialized schizothoracine
 fish HIF-1αB, which is the proline hydroxylation motif mutated into
 PxxLAP. Standard and stochastic branch-site codon model analysis indicated
 that only HIF-1αB has undergone positive selection, which may have led to
 changes in function. To confirm this hypothesis, HIF-αs tagged with Myc
 were transfected into HEK 293 T cells. Each HIF-1αB was found to
 significantly upregulate luciferase activity under normoxic and hypoxic
 conditions, which indicated that the HIF-1αB protein was more stable than
 other HIF-αs. Conclusions: All deduced HIF-α proteins of schizothoracine
 fish contain important domains, like their mammalian counterparts, and
 each HIF-α is shorter than that of human. Our experiments reveal that
 teleost-specific duplicated hif-α genes played different roles under
 hypoxic conditions, and HIF-1αB may be the most important regulator in the
 adaptation of schizothoracine fish to the environment of the Tibetan
 Plateau.
description: hifAll the sequences were
 amplified from cDNA and sequenced by ABI3730XL
 sequencer.
DOI: 10.5061/dryad.c3k16
title: Data from: Fine litterfall in the Brazilian Atlantic Forest

description: Litterfall is an essential component of tropical forest productivity,
 transferring nutrients from the vegetation back to soils. Here, we
 summarize the data from 105 estimates of fine litterfall production from
 45 sites in the Atlantic Forest domain, including two types of forests,
 evergreen and seasonal, and two successional stages, secondary and old
 growth. The overall litterfall average was 8.0 ± 2.5 Mg/ha. Litterfall was
 significantly in higher seasonal forests than in evergreen forests and in
 old growth versus secondary forests. Leaves were the major component of
 litterfall, contributing 68 percent to the total. The second most
 important component was branches, contributing 22 percent, followed by
 reproductive organs (flowers and fruits), at 6 percent. Accurate
 measurements of tropical forest productivity are crucial for estimating
 their role in sequestering atmospheric carbon, and we suggest some ways to
 standardize litterfall sampling to obtain better estimates.
description: Fine litterfall data -
 Atlantic ForestThis file contains fine
 litterfall data from several sites of the Brazilian Atlantic
 Forest.Litterfall data - Martinelli et
 al. - Biotropica.xlsx
DOI: 10.5061/dryad.4p6pf
title: Data from: Entomopathogenic Nematodes Combined with Adjuvants Presents a New Potential Biological Control Method for Managing the Wheat Stem Sawfly, Cephus cinctus (Hymenoptera: Cephidae)

description: The wheat stem sawfly, (Cephus cinctus Norton) Hymenoptera: Cephidae, has
 been a major pest of winter wheat and barley in the northern Great Plains
 for more than 100 years. The insect's cryptic nature and lack of safe
 chemical control options make the wheat stem sawfly (WSS) difficult to
 manage; thus, biological control offers the best hope for sustainable
 management of WSS. Entomopathogenic nematodes (EPNs) have been used
 successfully against other above-ground insect pests and adding adjuvants
 to sprays containing EPNs has been shown to improve their effectiveness.
 We tested the hypothesis that adding chemical adjuvants to sprays
 containing EPNs will increase the ability of EPNs to enter wheat stems and
 kill diapausing WSS larvae. This is the first study to test the ability of
 EPNs to infect the WSS, C. cinctus, and test EPNs combined with adjuvants
 against C. cinctus in both the laboratory and the field. Infection assays
 showed that three different species of EPNs caused 60-100% mortality to
 WSS larvae. Adding Penterra, Silwet L-77, Sunspray 11N, or Syl-Tac to
 solutions containing EPNs resulted in higher WSS mortality than solutions
 made with water alone. Field tests showed that sprays containing S.
 feltiae added to 0.1% Penterra increased WSS mortality up to 29.1%. These
 results indicate a novel control method for WSS, and represent a
 significant advancement in the biological control of this persistent
 insect pest.
description: Data File WSS vs.
 EPNs
DOI: 10.5061/dryad.d04s0
title: Data from: Cold adaptation increases rates of nutrient flow and metabolic plasticity during cold exposure in Drosophila melanogaster

description: Metabolic flexibility is an important component of adaptation to stressful
 environments, including thermal stress and latitudinal adaptation. A long
 history of population genetic studies suggest that selection on core
 metabolic enzymes may shape life histories by altering metabolic flux.
 However, the direct relationship between selection on thermal stress
 hardiness and metabolic flux has not previously been tested. We
 investigated flexibility of nutrient catabolism during cold stress in
 Drosophila melanogaster artificially selected for fast or slow recovery
 from chill coma (i.e. cold-hardy or -susceptible), specifically testing
 the hypothesis that stress adaptation increases metabolic turnover. Using
 13C-labelled glucose, we first showed that cold-hardy flies more rapidly
 incorporate ingested carbon into amino acids and newly synthesized
 glucose, permitting rapid synthesis of proline, a compound shown elsewhere
 to improve survival of cold stress. Second, using glucose and leucine
 tracers we showed that cold-hardy flies had higher oxidation rates than
 cold-susceptible flies before cold exposure, similar oxidation rates
 during cold exposure, and returned to higher oxidation rates during
 recovery. Additionally, cold-hardy flies transferred compounds among body
 pools more rapidly during cold exposure and recovery. Increased metabolic
 turnover may allow cold-adapted flies to better prepare for, resist and
 repair/tolerate cold damage. This work illustrates for the first time
 differences in nutrient fluxes associated with cold adaptation, suggesting
 that metabolic costs associated with cold hardiness could invoke
 resource-based trade-offs that shape life histories.
description: Experiment 1 –
 Quantifying anabolism from glucose in cold-hardy versus -susceptible fly
 linesCold hardy and
 susceptible flies were fed a dilute U13C-6-glucose tracer, left to
 metabolize for 4h, then homogenized and enrichments in glucose and amino
 acids were analyzed using GC-MS as described in Williams et al. (in
 review). Data are Atom Percent Excess (APE).Expt 1_glucose and AA
 synthesis_15Jun2016.xlsxExperiments 2 and 3 -
 Oxidation rates of glucose and leucine tracersOxidation rates of
 glucose and leucine tracers before, during and after cold exposure for
 cold-hardy and -susceptible flies.Expt2and3_Breathoxidationrates_15Jun2016.xlsxExperiments 2 and 3 - Tracer enrichments in body pools13C enrichments in lipid, carbohydrate and protein pools resulting from glucose and leucine tracer ingestion, before during and after cold exposure for cold-hardy and cold-susceptible flies.Expts2and3_body enrichments_15Jun2016.xlsx
DOI: 10.5061/dryad.mg42jj1
title: Data from: Responses of insect herbivores and their food plants to wind exposure and the importance of predation risk

description: 1. Wind is an important abiotic factor that influences an array of
 biological processes, but it is rarely considered in studies on
 plant-herbivore interactions. 2. Here, we tested whether wind exposure
 could directly or indirectly affect the performance of two insect
 herbivores, Plutella xylostella and Pieris brassicae, feeding on Brassica
 nigra plants. 3. In a greenhouse study using a factorial design, B. nigra
 plants were exposed to different wind regimes generated by fans before and
 after caterpillars were introduced on plants in an attempt to separate the
 effects of direct and indirect wind exposure on herbivores. 4. Wind
 exposure delayed flowering, decreased plant height and increased leaf
 concentrations of amino acids and glucosinolates. 5. Plant-mediated
 effects of wind on herbivores, i.e., effects of exposure of plants to wind
 prior to herbivore feeding, were generally small. However, development
 time of both herbivores was extended and adult body mass of P. xylostella
 was reduced when they were directly exposed to wind. By contrast,
 wind-exposed adult P. brassicae butterflies were significantly larger,
 revealing a trade-off between development time and adult size. 6. Based on
 these results, we conducted a behavioral experiment to study preference by
 an avian predator, the Great Tit (Parus major) for last instar P.
 brassicae caterpillars on plants that were exposed to either control (no
 wind) or wind (fan-exposed) treatments. Tits captured significantly more
 caterpillars on still than on wind-exposed plants. 7. Our results suggest
 that P. brassicae caterpillars are able to perceive the abiotic
 environment and to trade off the costs of extended development time
 against the benefits of increased size depending on the perceived risk of
 predation mediated by wind exposure. Such adaptive phenotypic plasticity
 in insects has not yet been described in response to wind exposure.
description: The excel file include
 all data that were used in the analysesJAE-2017-00752.xlsx
DOI: 10.5061/dryad.b2m1n
title: Data from: Evolutionary dynamics of Rh2 opsins in birds demonstrate an episode of accelerated evolution in the New World warblers (Setophaga)

description: Low rates of sequence evolution associated with purifying selection can be
 interrupted by episodic changes in selective regimes. Visual pigments are
 a unique system in which we can investigate the functional consequences of
 genetic changes, therefore connecting genotype to phenotype in the context
 of natural and sexual selection pressures. We study the RH2 and RH1 visual
 pigments (opsins) across 22 bird species belonging to two ecologically
 convergent clades, the New World warblers (Parulidae) and Old World
 warblers (Phylloscopidae) and evaluate rates of evolution in these clades
 along with data from 21 additional species. We demonstrate generally slow
 evolution of these opsins: both Rh1 and Rh2 are highly conserved across
 Old World and New World warblers. However, Rh2 underwent a burst of
 evolution within the New World genus Setophaga, where it accumulated
 substitutions at 6 amino acid sites across the species we studied.
 Evolutionary analyses revealed a significant increase in dN/dS in
 Setophaga, implying relatively strong selective pressures to overcome
 long-standing purifying selection. We studied the effects of each
 substitution on spectral tuning and found they do not cause large spectral
 shifts. Thus, substitutions may reflect other aspects of opsin function,
 such as those affecting photosensitivity and/or dark–light adaptation.
 Although it is unclear what these alterations mean for colour perception,
 we suggest that rapid evolution is linked to sexual selection, given the
 exceptional plumage colour diversification in Setophaga.
description: Time calibrated
 phylogeny of the New World warblers, Old World warblers and Bowerbirds
 used in this study.Phylogeny shown in Fig.
 1. Branch lengths are proportional to timeFig1_NewickVariation in Rh2 non-synonymous rates of evolution (dN ) across species in the limited datasetGene tree for Rh2 where branch lengths are scaled by dN rate (substitutions per codon) estimated along that branch by a free-ratio model as implemented in PAMLFig4_RH2_dN_LimDataSetVariation in Rh2 non-synonymous rates of evolution (dN ) across species in the main datasetGene tree for Rh2 where branch lengths are scaled by dN rate (substitutions per codon) estimated along that branch by a free-ratio model as implemented in PAMLFig4_RH2_dN_MainDataSetRH2 nucleotide sequencesRH1 nucleotide sequencesRH2 amino acid aligmentAlignment of RH2 amino acid sequences - corresponds to figure S1Variation in Rh1 non-synonymous rates of evolution (dN ) across PasserinesBranch lengths are scaled by dN rates. Branch lengths were estimated using a free ratio model as implemented in PAML, that estimates independent dN rates for each branch in the tree.FigS4_RH1_dN
DOI: 10.5061/dryad.rd05n
title: Data from: Remating and sperm competition in replicate populations of Drosophila melanogaster adapted to alternative environments

description: The prevalence of sexual conflict in nature, as well as the supposedly
 arbitrary direction of the resulting coevolutionary trajectories, suggests
 that it may be an important driver of phenotypic divergence even in a
 constant environment. However, natural selection has long been central to
 the operation of sexual conflict within populations and may therefore
 constrain or otherwise direct divergence among populations. Ecological
 context may therefore matter with respect to the diversification of traits
 involved in sexual conflict, and if natural selection is sufficiently
 strong, such traits may evolve in correlation with environment, generating
 a pattern of ecologically-dependent parallel evolution. In this study we
 assess among-population divergence both within and between environments
 for several traits involved in sexual conflict. Using eight replicate
 populations of Drosophila melanogaster from a long-term evolution
 experiment, we measured remating rates and subsequent offspring production
 of females when housed with two separate males in sequence. We found no
 evidence of any variation in male reproductive traits (offense or
 defense). However, the propensity of females to remate diverged
 significantly among the eight populations with no evidence of any
 environmental effect, consistent with sexual conflict promoting
 diversification even in the absence of ecological differences. On the
 other hand, females adapted to one environment (ethanol) tended to produce
 a higher proportion of offspring sired by their first mate as compared to
 those adapted to the other (cadmium) environment, suggesting
 ecologically-based divergence of this conflict phenotype. Because we find
 evidence for both stochastic population divergence operating outside of an
 ecological context and environment-dependent divergence of traits under
 sexual conflict, the interaction of these two processes is an important
 topic for future work.
description: female
 rematingremating status of
 experimental femalesremated females
 offspringoffspring phenotype and
 number for remated experimental femalesmale reproductive
 defense rematingremating status of
 females from the male reproductive defense assaymale reproductive
 defense offspringoffspring phenotype and
 number for remated females from the male reproductive defense
 assaymale reproductive
 offense rematingremating status of
 females from the male reproductive offense assaymale reproductive
 offense offspringoffspring phenotype and
 number for remated females from the male reproductive offense
 assay
DOI: 10.15468/dl.5z6x65
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Nolana platyphylla",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000962-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.