cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7g5b162
title: Data from: How conflict shapes evolution in poeciliid fishes

description: In live-bearing animal lineages, the evolution of the placenta is
 predicted to create an arena for genomic conflict during pregnancy, drive
 patterns of male sexual selection, and increase the rate of speciation.
 Here we test these predictions of the viviparity driven conflict
 hypothesis (VDCH) in live-bearing poecilid fishes, a group showing
 multiple independent origins of placentation and extreme variation in male
 sexually selected traits. As predicted, male sexually selected traits are
 only gained in lineages that lack placentas; while there is little or no
 influence of male traits on the evolution of placentas. Both results are
 consistent with the mode of female provisioning governing the evolution of
 male attributes. Moreover, it is the presence of male sexually selected
 traits (pre-copulatory), rather than placentation (post-copulatory), that
 are associated with higher rates of speciation. These results highlight a
 causal interaction between female reproductive mode, male sexual selection
 and the rate of speciation, suggesting a role for conflict in shaping
 diverse aspects of organismal biology.
description: READMEReproductive mode data
 filefull_reproductive_mode.xlsxPoeciliinae traits data filepoeciliinae_traits.xlsxPROPGL alternative scoring data filePROPGL_alternative_scoring.xlsxSDISL alternative scoring data fileSDISL_alternative_scoring.xlsxPoeciliinae species numbers data filepoeciliinae_species_numbers.xlsxPoeciliinae unresolved tips data filepoeciliinae_unresolved_tips.xlsxData set referencesdataset_references.xlsxPhylogenetic treeIR_hard_ultrametric.tre
DOI: 10.5061/dryad.kb135g6
title: Data from: Mouse whole embryo culture: evaluating the requirement for rat serum as culture medium

description: BACKGROUND. Whole embryo culture is a valuable research method in
 mammalian developmental biology and birth defects research, enabling
 longitudinal studies of explanted organogenesis-stage rodent embryos. Rat
 serum is the primary culture medium, and can sustain growth and
 development over limited periods as in utero. However, the cost, labour
 and time to produce culture serum are factors limiting the uptake of the
 methodology. The goal of replacing or at least reducing rat serum usage in
 culture would be in accordance with the principles of ‘replacement,
 reduction and refinement’ of animals in research (the 3Rs). METHODS. We
 performed cultures of mouse embryos for 24 h from embryonic day 8.5 in
 serum-free media or in rat serum diluted with defined media, compared with
 100% rat serum. Developmental parameters scored after culture included
 yolk sac circulation, dorsal axial length, somite number, protein content
 and completion of cranial neural tube closure. RESULTS. A literature
 review revealed use of both serum-free and diluted rat serum-based media
 in whole embryo culture studies, but with almost no formal comparisons of
 culture success against 100% rat serum. Two serum-free media were tested,
 but neither could sustain development as in 100% rat serum. Dilution of
 rat serum 1:1 with Glasgow Minimum Essential Medium plus Defined
 Supplements supported growth and development as well as whole rat serum,
 whereas other diluent media yielded sub-standard outcomes. CONCLUSIONS.
 Rat serum usage cannot be avoided, to achieve high quality mouse embryo
 cultures, but rat usage can be reduced using medium containing diluted
 serum.
description: Culshaw et al, dataset
 for BDR paperSpreadsheet containing
 raw data and statistical analyses for Figures 1, 4, 5, 6 and
 8.
DOI: 10.5061/dryad.56b7s48
title: Data from: Variation and correlations between sexual, asexual and natural enemy resistance life-history traits in a natural plant pathogen population

description: Background:Understanding the mechanisms by which diversity is maintained
 in pathogen populations is critical for epidemiological predictions.
 Life-history trade-offs have been proposed as a hypothesis for explaining
 long-term maintenance of variation in pathogen populations, yet the
 empirical evidence supporting trade-offs has remained mixed. This is in
 part due to the challenges of documenting successive pathogen life-history
 stages in many pathosystems. Moreover, little is understood of the role of
 natural enemies of pathogens on their life-history evolution. Results: We
 characterize life-history-trait variation and possible trade-offs in
 fungal pathogen Podosphaera plantaginis infecting the host plant Plantago
 lanceolata. We measured the timing of both asexual and sexual stages, as
 well as resistance to a hyperparasite of seven pathogen strains that vary
 in their prevalence in nature. We find significant variation among the
 strains in their life-history traits that constitute the infection cycle,
 but no evidence for trade-offs among pathogen development stages, apart
 from fast pathogen growth coninciding with fast hyperparasite growth.
 Also, the seemingly least fit pathogen strain was the most prevalent in
 the nature. Conclusions: We conclude that in the nature environmental
 variation, and interactions with the antagonists of pathogens themselves
 may maintain variation in pathogen populations.
description: SingleInfectionInoculationsData on the single-leaf inoculations without the hyperparasiteInoculationsWithAmpelomycesThe data on single-leaf inoculations together with a hyperparasite
DOI: 10.5061/dryad.tr4v447
title: Data from: Consistent temperature dependence of functional response parameters and their use in predicting population abundance

description: 1. Global warming is one of the greatest threats to the persistence of
 populations: increased metabolic demands should strengthen pairwise
 species interactions, which could destabilise food webs at the higher
 organisational levels. Quantifying the temperature dependence of
 consumer-resource interactions is thus essential for predicting ecological
 responses to warming. 2. We explored feeding interactions between
 different predator-prey pairs in temperature-controlled chambers and in a
 system of naturally-heated streams. We found consistent temperature
 dependence of attack rates across experimental settings, though the
 magnitude and activation energy of attack rate was specific to each
 predator, which varied in mobility and foraging mode. 3. We used these
 parameters along with metabolic rate measurements to estimate energetic
 efficiency and population abundance with warming. Energetic efficiency
 accurately estimated field abundance of a mobile predator that struggled
 to meet its metabolic demands, but was a poor predictor for a sedentary
 predator that operated well below its energetic limits. Temperature
 effects on population abundance may thus be strongly dependent on whether
 organisms are regulated by their own energy intake or interspecific
 interactions. 4. Given the widespread use of functional response
 parameters in ecological modelling, reconciling outcomes from laboratory
 and field studies increases the confidence and precision with which we can
 predict warming impacts on natural systems.
description: Abundance, respiration,
 and feeding rates of freshwater invertebrates in the laboratory and field
 at increasing temperaturesContains: data on the
 abundance of Limnophora riparia, Potamophylax cingulatus, and Simuliidae
 in the Hengill geothermal stream system, Iceland, along with data on
 respiration rates of L. riparia and P. cingulatus, and feeding rate data
 of both species (on Simuliidae prey) in the laboratory and field across a
 gradient of temperatures. These datasets also contain information on the
 natal stream (IS = stream identifier), natal stream temperature,
 experimental temperature, mass, species, initial prey number, and
 experimental setting (laboratory or field) where
 appropriate.Archer et al
 data.zip
DOI: 10.5061/dryad.g708nd7
title: Data from: The effects of heterospecific mating frequency on the strength of cryptic reproductive barriers

description: Heterospecific mating frequency is critical to hybrid zone dynamics and
 can directly impact the strength of reproductive barriers and patterns of
 introgression. The ef‐ fectiveness of post‐mating prezygotic (PMPZ)
 reproductive barriers, which include reduced fecundity via heterospecific
 matings and conspecific sperm precedence, may depend on the number,
 identity and order of mates. Studies of PMPZ barriers suggest that they
 may be important in many systems, but whether these barriers are effective
 at realistic heterospecific mating frequencies has not been tested. Here,
 we evaluate the strength of cryptic reproductive isolation in two leaf
 beetles (Chrysochus auratus and C. cobaltinus) in the context of a range
 of heterospecific mating frequen‐ cies observed in natural populations. We
 found both species benefited from multiple matings, but the benefits were
 greater in C. cobaltinus and extended to heterospecific matings. We found
 that PMPZ barriers greatly limited hybrid production by C. aura- tus
 females with moderate heterospecific mating frequencies, but that their
 effec‐ tiveness diminished at higher heterospecific mating frequencies. In
 contrast, there was no evidence for PMPZ barriers in C. cobaltinus females
 at any heterospecific mating frequency. We show that integrating realistic
 estimates of cryptic isolation with information on relative abundance and
 heterospecific mating frequency in the field substantially improves our
 understanding of the strong directional bias in F1 production previously
 documented in the Chrysochus hybrid zone. Our results dem‐ onstrate that
 heterospecific mating frequency is critical to understanding the impact of
 cryptic post‐copulatory barriers on hybrid zone structure and dynamics,
 and that future studies of such barriers should incorporate field‐relevant
 heterospecific mat‐ ing frequencies.
description: RawData_2004All of the raw data collected in 2004 associated with this analysis. Each tab includes descriptions of column labels.Data_2004.xlsxRawData_2005All of the raw data collected in 2005 associated with this analysis. Each tab includes descriptions of column labels.Data_2005.xlsx
DOI: 10.5061/dryad.56qq231
title: Data from: The many faces of synapsid cranial allometry

description: Previous studies of cranial shape have established a consistent
 interspecific allometric pattern relating the relative lengths of the face
 and braincase regions of the skull within multiple families of mammals. In
 this interspecific allometry, the facial region of the skull is
 proportionally longer than the braincase in larger species. The regularity
 and broad taxonomic occurrence of this allometric pattern suggests that it
 may have an origin near the base of crown Mammalia, or even deeper in the
 synapsid or amniote forerunners of mammals. To investigate the possible
 origins of this allomeric pattern, we used geometric morphometric
 techniques to analyze cranial shape in 194 species of non-mammalian
 synapsids, which constitute a set of successive outgroups to Mammalia. We
 recovered a much greater diversity of allometric patterns within
 non-mammalian synapsids than has been observed in mammals, including
 several instances similar to the mammalian pattern. However, we found no
 evidence of the mammalian pattern within Therocephalia and non-mammalian
 Cynodontia, the synapsids most closely related to mammals. This suggests
 that the mammalian allometric pattern arose somewhere within
 Mammaliaformes, rather than within non-mammalian synapsids. Further
 investigation using an ontogenetic series of the anomodont Diictodon
 feliceps shows that the pattern of interspecific allometry within
 anomodonts parallels the ontogenetic trajectory of Diictodon. This
 indicates that in at least some synapsids allometric patterns associated
 with ontogeny may provide a “path of least resistance” for interspecific
 variation, a mechanism that we suggest produces the interspecific
 allometric pattern observed in mammals.
description: Morphometric Data and
 Scripts for AnalysisThis .zip file contains
 the following folders, with the following contents: "Raw Data" -
 TPS files containing raw landmark data collected from photographs of
 specimens; "Morphometric Data" - .TPS files containing shape
 data used in our analyses by the scripts in the "Scripts"
 folder; "Time Data" - Phylogenies and stratigraphic occurrence
 data for all species in our analyses; "Scripts" - R scripts used
 to analyze our datasets.Data &
 Code.zip
DOI: 10.15468/dl.ej9jpa
title: Occurrence Download

description: A dataset listing the 1683 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((9.87252 49.74261,10.00654 49.74261,10.00654 49.8239,9.87252 49.8239,9.87252 49.74261))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae",
 "Year 2010-2020"
 ]
}

 The dataset's 1683 records were derived from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001776-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.mt6mp43
title: Data from: Importance of infection of haemosporidia blood parasites during different life history stages for long-term reproductive fitness of collared flycatchers

description: The interaction between birds and haemosporidia blood parasites is a
 well-used system in the study of parasite biology. However where, when and
 how parasites are transmitted is often unclear and defining parasite
 transmission dynamics is essential because of how they influence
 parasite-mediated costs to the host. In this study, we used
 cross-sectional and longitudinal data taken from a collared flycatcher
 (Ficedula albicollis) population to investigate the temporal dynamics of
 haemosporidia parasite infection and parasite-mediated costs to host
 fitness. We investigated host-parasite interactions starting at the
 nestling stage of the bird’s life-cycle and then followed their progress
 over three possible breeding attempts to quantify their fitness—measured
 as the number of offspring they produced that recruited back into the
 breeding population. We found that the majority of haemosporidia blood
 parasite infections occurred within the first year of life and that the
 most common parasite lineages that infected the breeding population also
 infected juvenile birds in the natal environment. Moreover, our findings
 suggest that nestlings in poorer condition could be at a higher risk of
 haemosporidia blood parasite infection. In this study, only female and not
 male bird fitness was adversely affected by parasite infection and the
 cost of infection on female fitness depended on the timing of
 transmission. In conclusion, our study indicates that in collared
 flycatchers, early-life is potentially important for many of the
 interactions with haemosporidia parasite lineages, and evidence of
 parasite-mediated costs to fitness suggest that these parasites may have
 influenced the host population dynamics.
description: Ficedula haemosporidia
 infection dataThe data in this file
 was collected in the field and the file was created using excel. The
 column names refer to the following data: Birth (year of birth), BCI
 (nestling body condition index), Recruit (year first recruited), Add.year
 (Additional recruitment years), Status (Infection status), YOI (Year of
 infection), Lineage (Parasite lineage), Genus (Parasite genus), Clutch
 (Total number of eggs produced by females), Fledge (Total number of
 fledged offspring), Fitness (Total number of offspring that recruited back
 into the breeding population).
DOI: 10.5061/dryad.506p9k0
title: Data from: Temperature mediated responses of carbon fluxes to precipitation variabilities in an alpine meadow ecosystem on the Tibetan Plateau

description: Effects of climate warming and changing precipitation on ecosystem carbon
 fluxes have been intensively studied. However, how they co-regulate carbon
 fluxes is still elusive for some under-studied ecosystems. To fill the
 gap, we examined net ecosystem productivity (NEP), gross ecosystem
 productivity (GEP) and ecosystem respiration (ER) responses to multi-level
 of temperature increments (control, warming 1, warming 2, warming 3,
 warming 4) in three contrasting hydrological growing seasons in a typical
 semiarid alpine meadow. We found that carbon fluxes responded to
 precipitation variations more strongly in low-level warming treatments
 than in high-level ones. The distinct responses were attributable to
 different soil water conditions and community composition under low-level
 and high-level warming during the three growing seasons. In addition,
 carbon fluxes were much more sensitive to decreased than to increased
 precipitation in low-level warming treatments, but not in high-level ones.
 At a regional scale, this negative asymmetry was further corroborated.
 This study reveals that future precipitation changes, particularly
 decreased precipitation would induce significant change in carbon fluxes,
 and the effect magnitude is regulated by climate warming size.
description: Data
DOI: 10.5061/dryad.j78f467
title: Data from: Genomic differentiation tracks earth-historic isolation in an Indo-Australasian archipelagic pitta (Pittidae; Aves) complex

description: Background: Allopatric speciation has played a particularly important role
 in archipelagic settings where populations evolve in isolation after
 colonizing different islands. The Indo-Australasian island realm is an
 unparalleled natural laboratory of biotic diversification. Here we explore
 how the level of earth-historic isolation has influenced genetic
 differentiation across the region by investigating phylogeographic
 patterns in the Pitta sordida species complex. Results: We generated a de
 novo genome and compared population genomics of 29 individuals of Pitta
 sordida from the entire distributional range and we reconstructed
 phylogenetic relationship using mitogenomes, a multi-nuclear gene dataset
 and single nucleotide polymorphisms (SNPs). We found deep divergence
 between an eastern and a western group of taxa across Indo-Australasia.
 Within both groups we have identified major lineages that are
 geographically separated into Philippines, Borneo, western Sundaland, and
 New Guinea, respectively. Although these lineages are genetically
 well-differentiated, suggesting a long-term isolation, there are
 signatures of extensive gene flow within each lineage throughout the
 Pleistocene, despite the wide geographic range occupied by some of them.
 We found little evidence of hybridization or introgression among the
 studied taxa, but forsteni from Sulawesi makes an exception. This
 individual, belonging to the eastern clade, is genetically admixed between
 the western and eastern clades. Geographically this makes sense as
 Sulawesi is not far from Borneo that houses a population of hooded pittas
 that belongs to the western clade. Conclusions: We found that geological
 vicariance events cannot explain the current genetic differentiation in
 the Pitta sordida species complex. Instead, the glacial-interglacial
 cycles may have played a major role therein. During glacials the sea level
 could be up to 120 m lower than today and land bridges formed within both
 the Sunda Shelf and the Sahul Shelf permitting dispersal of floral and
 faunal elements. The geographic distribution of hooded pittas shows the
 importance of overwater, “stepping-stone” dispersals not only to deep-sea
 islands, but also from one shelf to the other. The most parsimonious
 hypothesis is an Asian ancestral home of the Pitta sordida species complex
 and a colonization from west to east, probably via Wallacea.
description: EVOB-D-18-00410 Data
 used in analysesData used in
 phylogenomic analyses and population genomics.EVOB-D-18-00410_data_for_analyses.zip
DOI: 10.5061/dryad.6rg781m
title: Data from: A single session of hyperbaric oxygen therapy demonstrates acute and long-lasting neuroplasticity effects in humans: a replicated, randomized controlled clinical trial

description: Purpose: Animal studies have demonstrated anti-inflammatory, and
 anti-nociceptive properties of hyperbaric oxygen therapy (HBOT). However,
 physiological data are scarce in humans. In a recent experimental study,
 the authors used the burn injury (BI) model observing a decrease in
 secondary hyperalgesia area (SHA) in the HBOT-group compared to a
 control-group.Surprisingly, a long-lasting neuroplasticity effect
 mitigating the BI-induced SHA-response was seen in the HBOT-preconditioned
 group. The objective of the present study, therefore, was to confirm our
 previous findings using an examiner-blinded, block-randomized, controlled,
 crossover study design. Patients and methods: Nineteen healthy subjects
 attended two BI-sessions with an inter-session interval of ≥28 days. The
 BIs were induced on the lower legs by a contact thermode (12.5 cm2, 47C°,
 420 s). The subjects were block-randomized to receive HBOT (2.4 ATA, 100%
 O2, 90 min) or ambient conditions ([AC]; 1 ATA, 21% O2), dividing cohorts
 equally into two sequence allocations: HBOT-AC or AC-HBOT. All sensory
 assessments performed during baseline, BI, and post-intervention phases
 were at homologous time points irrespective of sequence allocation. The
 primary outcome was SHA, comparing interventions and sequence allocations.
 Data are mean (95% CI). Results: During HBOT-sessions a mitigating effect
 on SHAs was demonstrated compared to AC-sessions, ie, 18.8 (10.5–27.0) cm2
 vs 32.0 (20.1–43.9) cm2 (P=0.021), respectively. In subjects allocated to
 the sequence AC-HBOT a significantly larger mean difference in SHA in the
 AC-session vs the HBOT-session was seen 25.0 (5.4–44.7) cm2 (P=0.019). In
 subjects allocated to the reverse sequence, HBOT-AC, no difference in SHA
 between sessions was observed (P=0.55), confirming a preconditioning,
 long-lasting (≥28 days) effect of HBOT. Conclusion: Our data demonstrate
 that a single HBOT-session compared to control is associated with both
 acute and long-lasting mitigating effects on BI-induced SHA, confirming
 central anti-inflammatory, neuroplasticity effects of hyperbaric oxygen
 therapy.
description: Supplemental Document
 1Specifications of the
 blinding procedure.Supplemental Figure
 1Specifications of the
 blinding procedure.Supplemental Table
 1Specifications of the
 blinding procedure.Supplemental Video
 1Video file of baseline
 sensory assessments.Supplemental Table
 2Inclusion and exclusion
 criteria.Supplemental Document
 2Supplementary data
 analyses.Supplemental File
 1Dataset.