cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.37g5sk5
title: Data from: Effect of larval density and substrate quality on the wing geometry of Stomoxys calcitrans L. (Diptera: Muscidae)

description: Background: In insects, oviposition decisions may lead to egg deposition
 in substrates with different larval density and nutritional levels.
 Individuals developing in such substrates may present plasticity in their
 phenotype. Here, we investigated the effect of two factors related to
 oviposition decisions, namely larval density and substrate quality, on the
 wing size and wing shape of the stable fly, Stomoxys calcitrans L.
 (Diptera: Muscidae). Methods: We reared S. calcitrans larvae at different
 densities (5, 15 and 25) and on different substrates (camel, cow, donkey
 and sheep dung). For each fly that emerged, we recorded body weight, and
 detached, slide-mounted and photographed the right wing. Next, we
 collected 15 landmarks on each photographed wing, and applied geometric
 morphometric analysis to assess variation in wing size and wing shape of
 S. calcitrans across the different larval densities and substrate types.
 Results: We observed that wing size and wing shape of S. calcitrans were
 affected by larval density and the nature of the developmental substrate.
 Flies reared in a group of 5 had larger wing centroid size, wing length,
 wing width, wing area and wing loading compared with those reared in a
 group of 25. Also, flies developed in donkey and sheep dung had larger
 wing centroid size, wing length, wing width, wing area and wing loading in
 comparison with those grown in camel and cow dung. Canonical variate
 analysis followed by discriminant analysis revealed significant wing shape
 variation in S. calcitrans across the different densities and substrates.
 Wing size had a significant but weak positive effect on wing shape.
 Conclusions: This study demonstrates the high sensitivity of S. calcitrans
 wings to variation in larval density and developmental substrate, and that
 use of landmark-based geometric morphometric analysis could improve our
 understanding of how flies of veterinary importance respond to
 environmental variability.
description: Wing landmark
 coordinates of stable fly, Stomoxys calcitrans L 1758 (Diptera: Muscidae)
 reared at different densities and substrate types.This dataset contains
 wing landmark coordinates of stable fly, Stomoxys calcitrans L 1758
 (Diptera: Muscidae) collected following this protocol. We reared S.
 calcitrans larvae at different densities (5, 15 and 25) and on different
 substrates (camel, cow, donkey and sheep dung). For each fly that emerged,
 we recorded body weight, and detached, slide-mounted and photographed the
 right wing. Next, we collected 15 landmarks on each photographed wing and
 applied geometric morphometric analysis to assess variation in wing size
 and wing shape of S. calcitrans across the different larval densities and
 substrate types.stable fly wing landmark
 coordinates (Density and substrates
 types).txt
DOI: 10.5061/dryad.7rm572m
title: Data from: Decoding the locational information in the orb web vibrations of Araneus diadematus and Zygiella x-notata

description: A spider's web is a multifunctional structure that captures prey and
 provides an information platform that transmits vibrational information.
 Many physical factors interact to influence web vibration and information
 content, from vibration source properties and input location, to web
 physical properties and geometry. The aim of the study was to test whether
 orb web vibration contains information about the location of the source of
 vibration. We used finite-element analysis model webs to control and vary
 major physical factors, investigating webs where spiders use a direct or
 remote monitoring strategy. When monitoring with eight sensors (legs) at
 the web centre, a comparison of longitudinal and transverse wave amplitude
 between the sensors gave sufficient information to determine source
 direction and distance, respectively. These localization cues were robust
 to changes in source amplitude, input angle and location, with increased
 accuracy at lower source amplitudes. When remotely monitoring the web
 using a single thread connected to the web's hub (a signal thread),
 we found that locational information was not available when the angle of
 the source input was unknown. Furthermore, a free sector and a stiff hub
 were physical mechanisms to aid information transfer, which provides
 insights for bioinspired fibre networks for sensing technologies.
description: Data and matlab codes
 from article94 files in 10 folders
 (c. 10MB when unzipped): one README file; two pdfs giving input and output
 locations for Araneus and Zygiella webs; 40 text files with Araneus web A6
 time displacement data for lateral, longitudinal and transverse waves; 49
 text files with Zygiella Z6 time displacement data for lateral,
 longitudinal and transverse waves; two matlab codes for Araneus and
 Zygiella analysisDatav2.zip
DOI: 10.15468/dl.wqaq7t
title: Occurrence Download

description: A dataset containing 32008 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Acris blanchardi"
 ]
}

 The dataset includes 32008 records from 62 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001671-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.f47d293
title: Data from: Immunogenetic response of the bananaquit in the face of malarial parasites

description: Background: In the arms race between hosts and parasites, genes involved
 in the immune response are targets for natural selection. Toll-Like
 Receptor (TLR) genes play a role in parasite detection as part of the
 innate immune system whereas Major Histocompatibility Complex (MHC) genes
 encode proteins that display antigens as part of the vertebrate adaptive
 immune system. Thus, both gene families are under selection pressure from
 pathogens. The bananaquit (Coereba flaveola) is a passerine bird that is a
 common host of avian malarial parasites (Plasmodium sp. and Haemoproteus
 sp.). We assessed molecular variation of TLR and MHC genes in a wild
 population of bananaquits and identified allelic associations with
 resistance/susceptibility to parasitic infection to address hypotheses of
 avian immune response to haemosporidian parasites. Results: We found that
 allele frequencies are associated with infection status at the immune loci
 studied. A consistent general trend showed the infected groups possessed
 more alleles at lower frequencies, and exhibited unique alleles, compared
 to the uninfected group. Conclusions: Our results support the theory of
 natural selection favoring particular alleles for resistance while
 maintaining overall genetic diversity in the population, a mechanism which
 has been demonstrated in some systems in MHC previously but understudied
 in TLRs.
description: INF_AmpliSAS_outputAllele frequency data for INF groupLA07_AmpliSAS_outputAllele frequency data for LA07 groupUNI_AmpliSAS_outputAllele frequency data for UNI groupResampling_allelefreqsResampling data for determining significantly high and low allele frequencies for all groups and lociMHC1UAA1_GenAlEx_amovaAnalysis of molecular variance for MHC1-UAA-1MHC1-UAA-1_XLSTAT_associationAssociation/Correlation Tests between allele frequencies and groups for MHC1-UAA-1MHC1UAA2_GenAlEx_amovaAnalysis of molecular variance for MHC1-UAA-2MHC1-UAA-2_XLSTAT_associationAssociation/Correlation Tests between allele frequencies and groups for MHC1-UAA-2TLR1A_GelAlEx_amovaAnalysis of molecular variance for TLR1ATLR1A_XLSTAT_associationAssociation/Correlation Tests between allele frequencies and groups for TLR1ATLR2B_GelAlEx_amovaAnalysis of molecular variance for TLR2BTLR2B_XLSTAT_associationAssociation/Correlation Tests between allele frequencies and groups for TLR2BTLR7_GelAlEx_amovaAnalysis of molecular variance for TLR7TLR7_XLSTAT_associationAssociation/Correlation Tests between allele frequencies and groups for TLR7INF-GROUP_R1_001.fastq.gzRaw sequencing reads for INF group read 1INF-GROUP_R2_001.fastqRaw sequencing reads for INF group read 2LA07-GROUP_R1_001.fastqRaw sequencing reads for LA07 group read 1LA07-GROUP_R2_001.fastqRaw sequencing reads for LA07 group read 2UNI-GROUP_R1_001.fastqRaw sequencing reads for UNI group read 1UNI-GROUP_R2_001.fastqRaw sequencing reads for UNI group read 2
DOI: 10.5061/dryad.fn457gr
title: Data from: The influence of size on body shape diversification across Indo-Pacific shore fishes

description: Understanding the causes of body shape variability across the tree of life
 is one of the central issues surrounding the origins of biodiversity. One
 potential mechanism driving observed patterns of shape disparity is a
 strongly conserved relationship between size and shape. Conserved
 allometry has been shown to account for as much as 80% of shape variation
 in some vertebrate groups. Here, we quantify the amount of body shape
 disparity attributable to changes in body size across nearly 800 species
 of Indo-Pacific shore fishes using a phylogenetic framework to analyze 17
 geometric landmarks positioned to capture general body shape and
 functionally-significant features. In marked contrast to other vertebrate
 lineages, we find that changes in body size only explain 2.9% of the body
 shape variation across fishes, ranging from 3-50% within our 11 sampled
 families. We also find a slight but significant trend of decreasing rates
 of shape evolution with increasing size. Our results suggest that the
 influence of size on fish shape has largely been overwhelmed by
 lineage-specific patterns of diversification that have produced the modern
 landscape of highly diverse forms that we currently observe in nature.
description: Landmark
 DataCSV file with landmark
 data for all species present in the phylogeny. This is a subset of
 previously unpublished data that were used in Claverie T, Wainwright PC
 (2014) A Morphospace for Reef Fishes: Elongation Is the Dominant Axis of
 Body Shape Evolution. PLoS ONE 9(11): e112732.
 https://doi.org/10.1371/journal.pone.0112732
 Data provided
 courtesy of the authors.trimmed_tps_Claverie2014.csvTime Tree FileTime tree file trimmed to species with TPS data. Original tree published by Rabosky et al. (2013). If you use these data, please also credit the original source: Rabosky DL, Santini F, Eastman J, Smtih SA, Sidlauskas B, Chang J, Alfaro ME (2013) Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation. Nature Communications 4: 1958. https://doi.org/10.1038/ncomms2958 and Rabosky DL, Santini F, Eastman J, Smtih SA, Sidlauskas B, Chang J, Alfaro ME (2013) Data from: Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation. Dryad Digital Repository. https://doi.org/10.5061/dryad.j4802 trimmed_Rabosky2013.tre
DOI: 10.5061/dryad.r4s16vs
title: Data from: Inbreeding alters context‐dependent reproductive effort and immunity in male crickets

description: Infection can cause hosts to drastically alter their investment in key
 life‐history traits of reproduction and defence. Infected individuals are
 expected to increase investment in defence (e.g., by increasing immune
 function) and, due to trade‐offs, investment in other traits (e.g.,
 current reproduction) should decrease. However, the terminal investment
 hypothesis postulates that decreased lifespan due to infection and the
 associated reduction in the expectation for future offspring will favour
 increased investment towards current reproduction. Variation in intrinsic
 condition will likely influence shifts in reproductive investment
 post‐infection, but this is often not considered in such assessments. For
 example, the extent of inbreeding can significantly impact an
 individual's lifetime fitness and may influence its reproductive
 behaviour following a threat of infection. Here, we investigated the
 effects of inbreeding status on an individual's reproductive
 investment upon infection, including the propensity to terminally invest.
 Male crickets (Gryllodes sigillatus) from four genetically distinct inbred
 lines and one outbred line were subjected to a treatment from an
 increasing spectrum of simulated infection cue intensities, using
 heat‐killed bacteria. We then measured reproductive effort (calling
 effort), survival and immune function (antibacterial activity, circulating
 haemocytes and haemocyte microaggregations). Inbred and outbred males
 diverged in how they responded to a low‐dose infection cue: relative to
 unmanipulated males, outbred males decreased calling effort, whereas
 inbred males increased calling effort. Moreover, we found that inbred
 males exhibited higher antibacterial activity and numbers of circulating
 haemocytes compared with outbred males. These results suggest that an
 individual's inbreeding status may have consequences for
 context‐dependent shifts in reproductive strategies, such as those
 triggered by infection.
description: Duffield et al
 2019_CallingEffortCalling effort of inbred
 (across 4 genetically distinct inbred lines) and outbred male crickets
 following treatment from an increasing spectrum of infection cue intensity
 using heat-killed bacteria.Duffield et al
 2019_TIinbreeding_RE_Dryad.txtDuffield et al
 2019_ImmuneAssaysImmune measurements of
 inbred (across 4 genetically distinct inbred lines) and outbred male
 crickets following treatment from an increasing spectrum of infection cue
 intensity using heat-killed bacteria.Duffield et al
 2019_TIinbreeding_IF_Dryad.txt
DOI: 10.5061/dryad.mc443qs
title: Data from: Multi-driver and multi-scale assessment of vine community structure and composition across a complex tropical environmental matrix

description: Ecological communities are structured by multiple processes operating at
 multiple scales yet understanding the scale-dependency of these processes
 remains an open challenge. This might be particularly true for parasites,
 for which biotic rather than abiotic processes may play a primary role in
 structuring communities. Focusing on vines, a group of structural
 parasites that gain access to the canopy using different climbing
 mechanisms, we examined the influence of abiotic factors in tandem with
 host-parasite and parasite-parasite interactions in the assembly of
 tropical vine communities. Two synthetic variables, namely Climate1 and
 landscape Variety, were consistently important in explaining variation in
 species richness and diversity, as well as species composition, but their
 importance varied with scale. Whereas Climate1 summarizes the largest
 variability among climatic variables, landscape Variety expresses
 landscape heterogeneity within a neighborhood. Significant patterns of
 species co-occurrences suggest that vine-vine interactions also contribute
 to vine community assembly. Our results may be critical to understand vine
 proliferation and help design management strategies for their control.
description: Vine community
 dataThe document includes
 vine diversity data along with other abiotic and biotic variables that
 characterize the vine communities at three different scales (180, 270 and
 360 m^2).
DOI: 10.5061/dryad.6t7sh85
title: Data from: Molecular analyses identify hybridization-mediated nuclear evolution in newly discovered fungal hybrids

description: Hybridization may be a major driver in the evolution of plant pathogens.
 In a high elevation Alpine larch stand in Montana, a novel hybrid fungal
 pathogen of trees originating from the mating of Heterobasidion irregulare
 with H. occidentale has been recently discovered. In this study, sequence
 analyses of one mitochondrial and four nuclear loci from 11 Heterobasidion
 genotypes collected in the same Alpine larch stand indicated that
 hybridization has increased allelic diversity by generating novel
 polymorphisms unreported in either parental species. Sequence data and
 ploidy analysis through flow cytometry confirmed that heterokaryotic (n+n)
 genotypes were not first generation hybrids, but were the result of
 multiple backcrosses, indicating hybrids are fertile. Additionally, all
 admixed genotypes possessed the H. occidentale mitochondrion, indicating
 that the hybrid progeny may have been backcrossing mostly with H.
 occidentale. Based on reticulate phylogenetic network analysis by
 PhyloNet, Bayesian assignment, and ordination tests, alleles can be
 defined as H. irregulare-like or H. occidentale-like. H. irregulare-like
 alleles are clearly distinct from all known H. irregulare alleles, and are
 derived from the admixing of both Heterobasidion species. Instead, all but
 one H. occidentale alleles found in hybrids, although novel, were not
 clearly distinct from alleles found in the parental H. occidentale
 population. This discovery demonstrates that Alpine larch can be a
 universal host favoring the interspecific hybridization between H.
 irregulare and H. occidentale and the hybridization-mediated evolution of
 a nucleus, derived from H. irregulare parental species but clearly
 distinct from it.
description: Alignment
 S1-S5FASTA Alignments of
 sequences (atp6, gpd, RPB2, EF-1α, ITS)Alignments_S1-S5.txt
DOI: 10.5061/dryad.n7s0g10
title: Data from: Dwarf brooder versus giant broadcaster: combining genetic and reproductive data to unravel cryptic diversity in an Antarctic brittle star

description: Poecilogony, or multiple developmental modes in a single species, is
 exceedingly rare. Several species described as poecilogenous were later
 demonstrated to be multiple (cryptic) species with a single developmental
 mode. The Southern Ocean is known to harbor a high proportion of brooders
 (Thorson's Rule) but with an increasing number of counter examples
 over recent years. Here we evaluated poecilogony versus crypticism in the
 brittle star Astrotoma agassizii across the Southern Ocean. This species
 was initially described from South America as a brooder before some
 pelagic stages were identified in Antarctica. Reproductive and
 mitochondrial data were combined to unravel geographic and genetic
 variation of developmental modes. Our results indicate that A. agassizii
 is composed of seven well supported and deeply divergent clades (I:
 Antarctica and South Georgia; II: South Georgia and Subantarctic locations
 including Kerguelen, Patagonian shelf, and New Zealand; III-VI-VII:
 Patagonian shelf, IV-V: South Georgia). Two of these clades demonstrated
 strong size dimorphism when in sympatry and can be linked to differing
 developmental modes (Clade V: dwarf brooder versus Clade I: giant
 broadcaster). Based on their restricted geographic distributions and on
 previous studies, it is likely that Clades III-VI-VII are brooders. Clade
 II is composed of different morphological species, A. agassizii and A.
 drachi, the latter originally used as the outgroup. By integrating
 morphology, reproductive and molecular data we conclude that the variation
 identified in A. agassizii is best described as crypticism rather than
 poecilogony.
description: Dwarf brooder versus
 giant broadcaster: combining genetic and reproductive data to unravel
 cryptic diversity in an Antarctic brittle starBayesian Tree file,
 Outputs from GMYC and mPTP analyses (TXT), COI haplotypes (FASTA),
 Metadata for each specimen (EXCEL)Astrotoma_Data.zip
DOI: 10.5061/dryad.71568mt
title: Data from: A spatial perspective on the phenological distribution of the spring woodland caterpillar peak

description: A classic system for studying trophic mismatch focuses on the timing of
 the spring caterpillar peak in relation to the breeding time and
 productivity of woodland passerine birds. Most work has been conducted in
 single-site oak woodlands and little is known about how insights
 generalise to other woodland types or across space. Here we present the
 results of a three-year study on the species composition and temporal
 distribution of the spring caterpillar peak on different tree taxa across
 40 woodland sites spanning two degrees of latitude in Scotland. We used
 molecular barcoding to identify 62 caterpillar species, with winter moth
 (Operophtera brumata) the most abundant, comprising a third of the sample.
 Oak (Quercus sp.) and willow (Salix sp.) hosted significantly higher
 caterpillar abundances than other tree taxa, with winter moth exhibiting
 similar trends and invariantly proportionate across tree taxa. Caterpillar
 peak phenology was broadly similar between tree taxa. While latitude had
 little effect, increasing elevation increased the height of the
 caterpillar peak and retarded timing by 3.7 days/100m. These findings
 extend our understanding of how mismatch may play out spatially, with
 caterpillar peak date varying with elevation, and tree taxa varying in the
 caterpillar resource that they host.
description: JSMBAP_CaterpillarsDetails of all individual caterpillars collected (by branch beating) and identified along our Scottish transect of 40 woodland field sites 2014-16.JSMBAP_Branch_BeatingDetails on each branch beating and whether or not a caterpillar was captured. From our Scottish transect 2014-16.JSMBAP_HabitatHabitat data of each of the 40 field sites along our Scottish transect.JSMBAP_Nestbox_DetailsGeographic details of each bird nestbox (and site) on our 40-site Scottish transect 2014-16.JSMBAP_Tree_PhenologyTree phenology data for each focal tree studied along our Scottish transect of 40 field sites 2014-16.
DOI: 10.5061/dryad.t46kr73
title: Data from: Horizontal and vertical diversity jointly shape food web stability against small and large perturbations

description: The biodiversity of food webs is composed of horizontal (i.e. within
 trophic levels) and vertical diversity (i.e. the number of trophic
 levels). Understanding their joint effect on stability is a key challenge.
 Theory mostly considers their individual effects and focuses on small
 perturbations near equilibrium in hypothetical food webs. Here, we study
 the joint effects of horizontal and vertical diversity on the stability of
 hypothetical (modelled) and empirical food webs. In modelled food webs,
 horizontal and vertical diversity increased and decreased stability,
 respectively, with a stronger positive effect of producer diversity on
 stability at higher consumer diversity. Experiments with an empirical
 plankton food-web, where we manipulated horizontal and vertical diversity
 and measured stability from species interactions and from resilience
 against large perturbations, confirmed these predictions. Taken together,
 our findings highlight the need to conserve horizontal biodiversity at
 different trophic levels to ensure stability.
description: small_largeone6two3one6two3three1one6two4one6two4three1one6two5one6two5three1one7two3one7two4one7two4three1one7two3three1one7two5one7two5three1