cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r14s8s8
title: Data from: Evolution of interspecies unilateral incompatibility in the relatives of Arabidopsis thaliana

description: The evolutionary concurrence of intraspecies self-incompatibility (SI) and
 explosive angiosperm radiation in the Cretaceous has led to the hypothesis
 that SI was one of the predominant drivers of rapid speciation in
 angiosperms. Interspecies unilateral incompatibility (UI) usually occurs
 when pollen from a self-compatible (SC) species is rejected by the pistils
 of a SI species, while the reciprocal pollination is compatible (UC).
 Although this SI x SC type UI is most prevalent and viewed as a prezygotic
 isolation barrier to promote incipient speciation of angiosperms,
 comparative evidence to support such a role is lacking. We show that SI x
 SI type UI in SI species pairs is also common in the well-characterized
 accessions representing the 4 major lineages of the Arabidopsis genus and
 is developmentally regulated. This allowed us to reveal a strong
 correlation between UI strength and species divergence in these
 representative accessions. In addition, analyses of a SC accession and the
 pseudo-self-compatible (psc) spontaneous mutant of A. lyrata indicate that
 UI share, at least, common pollen rejection pathway with SI. Furthermore,
 genetic and genomic analyses of SI x SI type UI in A. lyrata x A. arenosa
 species pair showed that two major-effect quantitative trait loci are the
 stigma and pollen side determinant of UI respectively, which could be
 involved in heterospecies pollen discrimination. By revealing a close link
 between UI and SI pathway, particularly between UI and species divergence
 in the representative accessions, our findings establish a connection
 between SI and speciation. Thus, the preexistence of SI system would have
 facilitated the evolution of UI and accordingly promote speciation.
description: Marker
 informationSequence
 AlignmentSequenceAlignment
DOI: 10.5061/dryad.3q08v
title: Data from: Effects of riparian forest harvest on streams: a meta-analysis

description: 1. Riparian forest harvesting impacts streams in many ways, from altering
 temperature regimes, shifting geomorphic structure, increasing sediment
 fluxes and affecting fish populations. However, we have noted considerable
 variation in the results between studies that led us to ask whether the
 effects of forest harvesting on streams were consistent between studies.
 We used meta-analysis of 34 replicated studies to address the effects of
 riparian logging on biological and chemical components of streams in
 contrast to control sites. 2. We found that the overall effect sizes of
 several response variables in replicated studies were significantly higher
 than zero, especially benthic invertebrates, and nitrogen and potassium
 concentrations. However, there was a very large amount of variation in the
 effect sizes between studies, and for many measures, the effect sizes from
 different studies were positive or negative, indicating site-specific
 responses. 3. We explored whether stream size, stream gradient and
 regional potential evapotranspiration could explain some of the effect
 size variation between studies. Relations with these environmental
 variables were weak, but suggestive that some of the context-specific,
 individual outcomes might be due to underlying environmental differences
 between sites. 4. Synthesis and applications. Despite relatively low
 numbers of replicated studies, we found significant overall effects of
 riparian forest harvesting although the magnitude and direction of
 responses within individual studies were site specific. This lack of
 consistency in the direction of effect sizes suggests we need a more
 context-dependent approach to the protection of freshwaters from forest
 management.
description: Supplementary
 Material-S1Citations to data
 sources. Two tables include the extracted data for each variable from each
 study included for control (unharvested) and clear-cut treatments. Data
 for replicated studies (2 or more replicates in each category) include
 Means, Standard Errors, and the calculated effect sizes. The data for
 unreplicated studies (1 in each category, or 2 in one category and 1 in
 the other) are in a separate table, along with the values and calculated
 effect size.
DOI: 10.5061/dryad.23pk1
title: Data from: Are red bishops red enough? On the persistence of a generalized receiver bias in Euplectes

description: In the genus Euplectes (17 species of widowbirds and bishops), red
 carotenoid-based coloration has been found to function in male contest
 competition over territories and appears to exploit a generalized receiver
 bias by which redder (more longwave) hues are perceived as more aversive
 or intimidating. A major piece missing, however, is that among the 5 most
 extensively red species, forming the clade of “red bishops,” the agonistic
 function has remained unexplored or undetected. Moreover, does the
 receiver bias remain generalized (“open-ended”) after coevolution of the
 most exaggerated signal phenotypes? In this field experiment with southern
 red bishops E. orix, we increased the color hue 27nm, beyond its natural
 range, and compared the success in territorial competition of these
 supernormal red males to that of control-red and green (down-manipulated)
 males. The treatment, but no pre-manipulation colorimetrics or
 morphometrics, had a significant effect on territory establishment; 76% of
 super-red males, 45% of control-red males, and 17% of green males were
 recorded as territory holders at the end of the experiment. The receiver
 bias, that is, a generalized aversion of redder hues, thus appears to
 remain after the signal elaboration process, likely (but not necessarily)
 reinforced by adaptive receiver coevolution, through, for example,
 exploitation resistance or signal honesty.
description: Ninnes et al.
 DATAA
 workbook containing three spreadsheets, one with data for the main
 experiment, one with data for the supplementary experiment, and one with
 reflectance data. Column headers are easily
 interpretable.
DOI: 10.5061/dryad.k3b6sv7
title: Data from: Disruptive sexual selection on body size in the polyphenic black scavenger fly Sepsis thoracica

description: Sexual selection has two main components, female preference and male-male
 competition, which can lead males to adopt alternative reproductive
 tactics to optimize their reproductive success. Two traits that
 significantly influence reproductive success are body size and coloration,
 as they can facilitate access to females through male contests or as
 female attractors. We investigated whether, and if so which mechanism of
 sexual selection contributes to the maintenance, and possibly even the
 establishment, of two almost discrete male morphs in the polyphenic black
 scavenger fly Sepsis thoracica (Diptera: Sepsidae): small and black, or
 large and amber. We performed two complementary laboratory experiments to
 evaluate the mating success of the different male morphs and the behaviors
 (of both males and females) presumably mediating their mating success. We
 found evidence for intraspecific disruptive sexual selection on male body
 size that is mediated by male-male interactions, and significant positive
 directional selection on body size that interacted with (directional)
 selection on coloration, likely contributing to the origin and/or
 maintenance of the threshold relationship between the two traits in this
 species. The simultaneous occurrence of disruptive selection and
 polyphenism in S. thoracica supports the role of sexual selection in the
 intraspecific diversification of coupled traits (here body size and
 coloration), which could be a speciation starting point.
description: Sexual Selection Data
 S.thoracica FINAL BehEcol00445Data on sexual selection
 as a function of size and coloration of the sexually selected male
 forelegs of the dimorphic dung fly Sepsis thoracica
DOI: 10.5061/dryad.n0h37
title: Data from: Agonistic reciprocity is associated with reduced male reproductive success within haremic social networks

description: While individual variation in social behaviour is ubiquitous and causes
 social groups to differ in structure, how these structural differences
 affect fitness remains largely unknown. We used social network analysis of
 replicate bluebanded goby (Lythrypnus dalli) harems to identify the
 reproductive correlates of social network structure. In stable groups, we
 quantified agonistic behaviour, reproduction and steroid hormones, which
 can both affect and respond to social/reproductive cues. We identified
 distinct, optimal social structures associated with different reproductive
 measures. Male hatching success (HS) was negatively associated with
 agonistic reciprocity, a network structure that describes whether
 subordinates ‘reciprocated’ agonism received from dominants. Egg laying
 was associated with the individual network positions of the male and
 dominant female. Thus, males face a trade-off between promoting structures
 that facilitate egg laying versus HS. Whether this reproductive conflict
 is avoidable remains to be determined. We also identified different social
 and/or reproductive roles for 11-ketotestosterone, 17β-oestradiol and
 cortisol, suggesting that specific neuroendocrine mechanisms may underlie
 connections between network structure and fitness. This is one of the
 first investigations of the reproductive and neuroendocrine correlates of
 social behaviour and network structure in replicate, naturalistic social
 groups and supports network structure as an important target for natural
 selection.
description: Solomon-Lane et
 al_behavior, reproduction, hormones
DOI: 10.5061/dryad.23fg0
title: Data from: Quantifying the effects of ecological constraints on trait expression using novel trait-gradient analysis parameters

description: 1. Complex processes related to biotic and abiotic forces can impose
 limitations to assembly and composition of plant communities. Quantifying
 the effects of these constraints on plant functional traits across
 environmental gradients, and among communities, remains challenging. We
 define ecological constraint (Ci) as the combined, limiting effect of
 biotic interactions and environmental filtering on trait expression (i.e.,
 the mean value and range of functional traits). 2. Here we propose a set
 of novel parameters to quantify this constraint by extending the
 trait-gradient analysis (TGA) methodology. The key parameter is ecological
 constraint, which is dimensionless and can be measured at various scales,
 e.g., on population and community levels. It facilitates comparing the
 effects of ecological constraints on trait expressions across
 environmental gradients, as well as within and among communities. 3. We
 illustrate the implementation of the proposed parameters using the bark
 thickness of 14 woody species along an aridity gradient on granite
 outcrops in southwestern Australia. We found a positive correlation
 between increasing environmental stress and strength of ecological
 constraint on bark thickness expression. Also, plants from more stressful
 habitats (shrublands on shallow soils and in sun-exposed locations)
 displayed higher ecological constraint for bark thickness than plants in
 more benign habitats (woodlands on deep soils and in sheltered locations).
 4. The relative ease of calculation and dimensionless nature of Ci allow
 it to be readily implemented at various scales and make it widely
 applicable. It therefore has the potential to advance the mechanistic
 understanding of the ecological processes shaping trait expression. Some
 future applications of the new parameters could be investigating the
 patterns of ecological constraints i) among communities from different
 regions, ii) on different traits across similar environmental gradients,
 and iii) for the same trait across different gradient-types.
description: Ottaviani et al
 2017_Ecol Evol_bark thickness dataBark thickness data were
 collected in the field for 14 plant species, from seven granite outcrops
 across an aridity gradient in Southwestern Australia, in 2012. In each
 study site, 3-4 species were sampled. For each species 10 individuals were
 sampled (in each outcrop). For each plant sampled, 5 different bark
 thickness measurements were collected, then averaged.
DOI: 10.5061/dryad.g064k
title: Data from: The developmental race between maturing host plants and their butterfly herbivore – the influence of phenological matching and temperature

description: 1. Interactions between herbivorous insects and their host plants that are
 limited in time are widespread. Therefore, many insect–plant interactions
 result in a developmental race, where herbivores need to complete their
 development before plants become unsuitable, while plants strive to
 minimize damage from herbivores by outgrowing them. 2. When spring
 phenologies of interacting species change asymmetrically in response to
 climate warming, there will be a change in the developmental state of host
 plants at the time of insect herbivore emergence. In combination with
 altered temperatures during the subsequent developmental period, this is
 likely to affect interaction strength as well as fitness of interacting
 species. 3. Here, we experimentally explore whether the combined effect of
 phenological matching and thermal conditions influence the outcome of an
 insect–host interaction. We manipulated both developmental stages of the
 host plants at the start of the interaction and temperature during the
 subsequent developmental period in a model system of a herbivorous
 butterfly, Anthocharis cardamines, and five of its Brassicaceae host plant
 species. 4. Larval performance characteristics were favoured by earlier
 stages of host plants at oviposition as well as by higher developmental
 temperatures on most of the host species. The probability of a larva
 needing a second host plant covered the full range from no influence of
 either phenological matching or temperature to strong effects of both
 factors, and complex interactions between them. The probability of a plant
 outgrowing a larva was dependent only on the species identity. 5. This
 study demonstrates that climatic variation can influence the outcome of
 consumer–resource interactions in multiple ways and that its effects
 differ among host plant species. Therefore, climate warming is likely to
 change the temporal match between larval and plant development in some
 plant species, but not in the others. This is likely to have important
 implications for host plant use and possibly influence competitive
 relationships.
description: Data on larval
 performance (except establishment), development race outcome for the
 butterflies and for the host plant speciesMain
 dataset.xlsxData on larval
 establishmentNot established
 larvae.xlsx
DOI: 10.5061/dryad.590
title: Data from: c-Myc gene sequences and the phylogeny of bats and other eutherian mammals

description: The complete protein-coding sequences of the c-myc proto-oncogene were
 determined for five species of four new orders of eutherian (placental)
 mammals. These newly obtained sequences were aligned to each other and to
 other available orthologues for the phylogenetic estimation of eutherian
 interordinal relationships. Several measures of sequence difference and
 base composition were first calculated to assess the major evolutionary
 properties of the three codon positions and two protein-coding exons of
 the gene. On the basis of these calculations, different parsimony,
 distance, and maximum likelihood approaches were adopted, with the most
 sophisticated involving the separate, then combined, likelihood analyses
 of the third codon positions of exon 2 vs. all other sites. These
 phylogenetic approaches provide clear support for the grouping of
 Chiroptera (bats) with Artiodactyla (ruminants, camels, and pigs) and
 Carnivora (cats, dogs, and their allies), an interordinal arrangement that
 receives strong corroboration from other lines of evidence including
 complete mitochondrial DNA sequences. In contrast, these analyses fail to
 provide strong to reasonable support for any other interordinal group.
 This study concludes with specific recommendations about sampling and
 other strategies for maximizing the phylogenetic contributions of the
 c-myc gene to the continued resolution of the eutherian ordinal tree.
description: Miyamoto et al Data
 Setmiyamoto.txt
DOI: 10.5061/dryad.8jq92
title: Data from: An eighteen serum cytokine signature for discriminating glioma from normal healthy individuals

description: Glioblastomas (GBM) are largely incurable as they diffusely infiltrate
 adjacent brain tissues and are difficult to diagnose at early stages.
 Biomarkers derived from serum, which can be obtained by minimally invasive
 procedures, may help in early diagnosis, prognosis and treatment
 monitoring. To develop a serum cytokine signature, we profiled 48
 cytokines in sera derived from normal healthy individuals (n = 26) and
 different grades of glioma patients (n = 194). We divided the normal and
 grade IV glioma/GBM serum samples randomly into equal sized training and
 test sets. In the training set, the Prediction Analysis for Microarrays
 (PAM) identified a panel of 18 cytokines that could discriminate GBM sera
 from normal sera with maximum accuracy (95.40%) and minimum error (4.60%).
 The 18-cytokine signature obtained in the training set discriminated GBM
 sera from normal sera in the test set as well (accuracy 96.55%; error
 3.45%). Interestingly, the 18-cytokine signature also differentiated grade
 II/Diffuse Astrocytoma (DA) and grade III/Anaplastic Astrocytoma (AA) sera
 from normal sera very efficiently (DA vs. normal–accuracy 96.00%, error
 4.00%; AA vs. normal–accuracy 95.83%, error 4.17%). Kyoto Encyclopedia of
 Genes and Genomes (KEGG) pathway analysis using 18 cytokines resulted in
 the enrichment of two pathways, cytokine-cytokine receptor interaction and
 JAK-STAT pathways with high significance. Thus our study identified an
 18-cytokine signature for distinguishing glioma sera from normal healthy
 individual sera and also demonstrated the importance of their differential
 abundance in glioma biology.
description: An eighteen serum
 cytokine signature for discriminating glioma from normal healthy
 individualsSerum cytokine profiling
 was done using serum samples from normal (n=26), GBM (n=148), DA (n=24)
 and AA (n=22) by bead array method. We used commercially available human
 cytokine kits: 21-plex and 27-plex (Bio-rad) and followed the protocol
 according to manufacturer’s instructions. The basic principle is based on
 sandwich ELISA. In this assay, serum samples were diluted 4 times with
 dilution buffer and incubated with beads containing specific antibodies
 directed against different cytokines. After thorough washing step, a
 biotinylated detection antibody was added. Next, a
 streptavidin-phycoerythrin reporter complex was added and incubated for 15
 mins. The plate was washed and read using bio-plex system, a dual-laser
 flow-based microplate reader. The lasers and associated optics detect the
 internal fluorescence of the individual bead as well as the fluorescent
 reporter signal on the bead surface. The standard curve was generated
 using known concentrations of purified cytokines which later allowed the
 quantification (pico gram /mL) of each cytokine in the serum
 samples.
DOI: 10.5061/dryad.tc0184k
title: Data from: Thermal sensitivity of gypsy moth (Lepidoptera: Erebidae) during larval and pupal development

description: As global temperatures rise, thermal limits play an increasingly important
 role in determining the persistence and spread of invasive species. Gypsy
 moth (Lymantria dispar L. Lepidotera: Erebidae) in North America provides
 an ideal system for studying the effect of high temperatures on invasive
 species performance. Here, we used fluctuating temperature regimes and
 exposed gypsy moth at specific points in development (first–fourth instar,
 pupa) to cycles of favorable(22–28°C) or high-temperature treatments
 030–36°C, 32–38°C, 34–40°C) for either 2 or 7 d. We measured survival,
 growth, and prolonged effects of exposure on development time and pupal
 mass. Survival generally decreased as the experimental temperature
 treatment and duration of exposure increased for all instars and pupae,
 with a narrow threshold for lethal effects. In response to increasing
 temperature and magnified by longer exposure times, growth abruptly
 declined for third instars and development time increased for pupae. For
 those surviving the 2-d exposure treatment, development time to pupation
 increased for all instars, but we did not find consistent effects on final
 pupal mass. These negative effects of high temperature provide important
 data on the susceptibility of gypsy moth to heat at different points in
 development. This work improves our understanding of thermal limits to
 growth and development in gypsy moth and can aid in determining invasion
 potential under current and future climates.
description: Data
 AnalysisR script used to analyze
 the data in the accompanying files for the associated
 manuscript.Dryad Banahene et al 2018
 Analysis.RLarvalDataCSV file of larval data. Described in accompanying text file.PupalDataCSV file of pupal data. Described in accompanying text file.Survival7dCSV file of survival data for larva exposed to 7 days of temperature treatment. Described in accompanying text file.ThirdMassDataCSV file of third instar mass data. Described in accompanying text file.
DOI: 10.15468/q2k74j
title: Kelp Fly Recording Scheme - records verified via iRecord

description: This dataset contains species records for 3 families of Diptera (Coelopidae, Helcomyzidae and Heterocheilidae) and that have been verified by the recording scheme. Records are from datasets made available via the iRecord verification process - these records may originate from direct addition of records to iRecord, or via other datasets that have been made available via iRecord for verification purposes.
DOI: 10.15468/5wegnv
title: Sciomyzidae Recording Scheme - iRecord

description: Records and submissions to the Sciomyzidae Recording Scheme by contributors through iRecord
Refer to Dipterists Forum website at https:// www.dipterists.org.uk/ for published accounts. Reports in Dipterists Forum Bulletins
DOI: 10.5061/dryad.172s5
title: Data from: Sex-specific evolutionary potential of pre- and postcopulatory reproductive interactions in the field cricket, Teleogryllus commodus

description: Mate choice often depends on the properties of both sexes, such as the
 preference and responsiveness of the female and the sexual display traits
 of the male. Quantitative genetic studies, however, traditionally explore
 the outcome of an interaction between males and females based solely on
 the genotype of one sex, treating the other sex as a source of
 environmental variance. Here we use a half-sib breeding design in the
 field cricket, Teleogryllus commodus, to estimate the additive genetic
 contribution of both partners to three steps of the mate choice process:
 the time taken to mate; the duration of spermatophore attachment; and, the
 intensity of mate guarding. Rather than each sex contributing equally to
 the interactions, we found that genetic variation for latency to mate and
 spermatophore attachment was sex-specific, and in the case of mate
 guarding intensity, largely absent. For a given interaction, genetic
 variation in one sex also appears to be largely independent of the other,
 and is also uncorrelated with the other traits. We discuss how pre- and
 post-copulatory interactions have the potential to evolve as an
 interacting phenotype, but that any co-evolution between these traits, due
 to sexual selection or sexual conflict, may be limited.
description: Half_sib_designArchive contains data in 3 .csv files and ReadMe.txt, which describes the data files.Trail_1_dataTrail_2_data