cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m37pvmcxr
title: How co-distribution of two related azaleas (Rhododendron) developed in the Japanese archipelago: Insights from evolutionary and demographic analyses

description: Plants growing in similar climates with extensively overlapping
 distributions may exhibit similar phylogeographic patterns, due to
 similarities in range shifts during past climatic oscillations. We tested
 and exploited this expectation in a comparison of the evolutionary and
 demographic histories of two related and co-distributed species endemic to
 Japan – Rhododendron pentaphyllum and R. quinquefolium. Genetic variation
 in sequences of noncoding chloroplast DNA regions and hundreds of nuclear
 single nucleotide polymorphisms were used to investigate 191 individuals
 from 13 populations of R. pentaphyllum and 142 individuals from 10
 populations of R. quinquefolium. We found that the two species were not
 each other’s closest relative and we found different times to the most
 recent common ancestor of extant populations based on both chloroplast DNA
 and nuclear SNPs. Rhododendron pentaphyllum exhibited higher genetic
 variation between populations than R. quinquefolium, while the two species
 had similar patterns of genetic divergence between regions with slightly
 different divergence times. These lines of evidence suggest that the
 similar ranges of the two species are the result of repeated range shifts
 since speciation during climatic oscillations.
DOI: 10.15468/dl.vxhm8z
title: Occurrence Download

description: A dataset containing 9223 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is DEU.2.40_1",
 "OccurrenceStatus is Present",
 "Year 2005-2026"
 ]
}

 The dataset includes 9223 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001954-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.bcc2fqz7c
title: Data from: Primary pollinator exclusion has divergent consequences for pollen dispersal and mating in different populations of a bird-pollinated tree

description: Pollination by nectarivorous birds is predicted to result in different
 patterns of pollen dispersal and plant mating compared to pollination by
 insects. We tested the prediction that paternal diversity, outcrossing
 rate and realised pollen dispersal will be reduced when the primary
 pollinator group is excluded from bird-pollinated plants. Pollinator
 exclusion experiments in conjunction with paternity analysis of progeny
 were applied to Eucalyptus caesia Benth. (Myrtaceae), a predominantly
 honeyeater-pollinated tree that is visited by native insects and
 introduced honeybees. Microsatellite genotyping at 14 loci of all adult E.
 caesia at two populations (n = 580 and 315) followed by paternity
 analysis of 705 progeny revealed contrasting results between populations.
 At the Chiddarcooping site, the exclusion of honeyeaters led to lower
 outcrossing rates, a threefold reduction in the average number sires per
 fruit, a decrease in intermediate-distance mating, and an increase in
 near-neighbour mating. These findings suggest that bird pollination
 increases plant paternal diversity, potentially leading to higher fitness
 of progeny and favouring the evolution of this strategy. In contrast,
 honeyeater exclusion did not significantly impact pollen dispersal or
 plant mating at Mount Caroline, suggesting that insects may be effective
 pollinators in some populations of bird-adapted plants, but ineffective in
 others.
DOI: 10.5061/dryad.7h44j0zqd
title: Effects of latitudinal, seasonal, and daily temperature variations on chytrid fungal infections in a North American frog

description: As human activities alter environmental conditions, the emergence and
 spread of disease represents an increasing threat to wildlife. Studies
 that examine how host–pathogen relationships play out across seasons and
 latitudes can serve as proxies for understanding how natural and
 anthropogenic changes in climate may influence infection and disease
 dynamics. Amphibians are ideal host organisms for studying the impacts of
 climate on disease because they are ectothermic and threatened by
 chytridiomycosis, a recently emerged and globally important disease caused
 by fungal pathogens in the genus Batrachochytrium. Previous studies
 suggest that temperature affects the interaction between amphibians and
 Batrachochytrium pathogens. However, a clearer understanding of this
 host–pathogen–environment interaction is needed to predict how the risk of
 chytridiomycosis will vary in space and time. Here, we investigate how
 daily, seasonal, and latitudinal variations in temperature affect the
 incidence and impact of Batrachochytrium dendrobatidis (Bd) infection in a
 broadly distributed host, the northern cricket frog (Acris crepitans),
 using a combination of field and laboratory studies. In a four-year field
 study conducted at three latitudes, we found that daily maximum air
 temperature over a 15-d period prior to sampling best-predicted patterns
 of Bd infection and that the lightest infection loads followed periods
 when these temperatures exceeded 25°C. In a laboratory exposure
 experiment, we found pathogen load and mortality to be greater at
 temperatures that mimic winter temperatures at the southern extent of this
 host’s range than for scenarios that mimic temperature conditions
 experienced in other areas and seasons. Taken together, our findings
 suggest that changes in temperature across timescales and latitudes
 interact to influence the dynamics of infection and disease in temperate
 amphibians.
description: Data provided include results from an exposure experiment with
 <em>Acris crepitans</em> and <em>Batrachochytrium
 dendrobatidis</em>, results from a field study of <em>Acris
 crepitans</em> across latitudes, and mark-recapture data for
 <em>Acris crepitans</em>. See publication in Ecosphere (Sonn
 et al. 2019) for full methods description.
DOI: 10.5061/dryad.37pvmcvf5
title: The data of ~160 worms during odor avoidance behavior before or after learning

description: The Excel files contain x and y positions (mm), the odor concentration at
 the position (micro-M) and the behavioral states (Run or Pirouette) of
 ~160 Caenorhabditis elegansin naive (before learning) or preexposed (after
 learning) conditionduring 121-720 s of the odor avoidance assay.
DOI: 10.15468/dl.d5r44r
title: Occurrence Download

description: A dataset containing 196 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-98.45788 19.13831,-98.36623 19.13831,-98.36623 19.20012,-98.45788 19.20012,-98.45788 19.13831))",
 "OccurrenceStatus is Present",
 "TaxonKey is Tracheophyta"
 ]
}

 The dataset includes 196 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001956-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.612jm63zq
title: High contrast yellow mosaic patterns are prey attractants for orb-weaving spiders

description: Many animals improve their foraging success by producing signals that
 exploit the sensory biases of potential prey, but the specific properties
 that make these sensory traps effective remain unclear. We combine field
 experiments with phylogenetic comparative analyses to investigate the
 visual luring properties of different signal designs in web‐building
 spiders. Our field experiments used cardboard spider models to examine the
 effects of area of colour patches, colour and pattern on the foraging
 success of the colourful giant wood spider, Nephila pilipes.
 These experiments revealed that both the colour (yellow) and pattern
 (yellow and black mosaic) are essential for luring prey in a high ambient
 light environment. We subsequently used phylogenetic comparative analyses
 to demonstrate an evolutionary association between prey viewing
 environment and spider ventral signal among 63 species of orb‐weavers from
 53 genera. Combined, our data show that (a) the colour of the bright body
 parts of orb‐weavers is essential for both diurnal and nocturnal prey
 attraction, whereas the pattern and area of colour patches are important
 for diurnal foraging and (b) the evolution of these visual lures is
 associated with the viewing environment, specifically ambient light
 intensity. We conclude that the effectiveness of colour luring might be a
 major driver of the convergent evolution of yellow mosaic patterns in
 phylogenetically divergent orb‐weavers. Our discoveries indicate that prey
 colour preferences and signal efficacy play a significant role in the
 evolution of visually mediated prey‐luring systems.
description: The field data and spectral reflectance measurements of paper
 used for field experiments are included in "prey_data.xlsx" and
 "spectral_reflectance_measurements_of_paper .xlsx". The datasets
 used for comparative analyses (Table S1 and S2) listed in "Datasets
 used in the comparative analyses.xlsx".
DOI: 10.5061/dryad.dv41ns1td
title: Macronutrients modulate survival to infection and immunity in Drosophila

description: Immunity and nutrition are two essential modulators of individual fitness.
 However, while the implications of immune function and nutrition on an
 individual’s lifespan and reproduction are well established, the interplay
 between feeding behaviour, infection, and immune function, remains poorly
 understood. Asking how ecological and physiological factors affect immune
 responses and resistance to infections is a central theme of
 eco-immunology. In this study, we used the fruit fly, Drosophila
 melanogaster, to investigate how infection through septic injury modulates
 nutritional intake, and how macronutrient balance affects survival to
 infection by the pathogenic Gram-positive bacterium Micrococcus luteus.
 Our results show that infected flies maintain carbohydrate intake, but
 reduce protein intake, thereby shifting from a protein-to-carbohydrate
 (P:C) ratio of ~1:4 to ~1:10 relative to non-infected and sham-infected
 flies. Strikingly, the proportion of flies dying after M. luteus infection
 was significantly lower when flies were fed a low-P high-C diet, revealing
 that flies shift their macronutrient intake as means of nutritional
 self-medication against bacterial infection. These results are likely due
 to the effects of the macronutrient balance on the regulation of the
 constitutive expression of innate immune genes, as a low-P high-C diet was
 linked to an up-regulation in the expression of key antimicrobial
 peptides. Together, our results reveal the intricate relationship between
 macronutrient intake and resistance to infection, and integrate the
 molecular cross-talk between metabolic and immune pathways into the
 framework of nutritional immunology.
DOI: 10.5061/dryad.fxpnvx0n2
title: Data from: Limitation of complementary resources affects colony growth, foraging behavior, and reproduction in bumble bees

description: Resource availability has been disturbed for many organisms in
 agricultural landscapes including pollinator species. Abundance and
 diversity in flower availability benefit bee populations, however, little
 is known about which of protein or carbohydrate resources may limit their
 growth and reproductive performance. Here, we test the hypothesis of
 complementary resource limitation using a supplemental feeding approach.
 We applied this assumption with bumble bees (Bombus terrestris), assuming
 that colony growth and reproductive performance should depend on the
 continuous supply of carbohydrates and proteins, through the foraging for
 nectar and pollen respectively. We placed wild-caught bumble bee colonies
 along a landscape gradient of semi-natural habitats, and monitored the
 colonies’ weight, foraging activity and reproductive performance during
 the whole colony cycle. We performed supplemental feeding as an indicator
 of landscape resource limitation, using a factorial design consisting of
 the addition of sugar-water (carbohydrate, supplemented or not) crossed by
 pollen (protein, supplemented or not). Bumble bee colony dynamics showed a
 clear seasonal pattern with a period of growth followed by a period of
 stagnation. Higher abundance of semi-natural habitats resulted in reducing
 the proportion of pollen foragers relative to all foragers in both
 periods, and in improving the reproductive performance of bumble bees.
 Interestingly, the supplemental feeding of sugar-water positively affected
 the colony weight during the stagnation period, while the supplemental
 feeding of pollen mitigated the landscape effect on pollen collection
 investment. Single and combined supplementation of sugar-water and pollen
 increased the positive effect of semi-natural habitats on reproductive
 performance. This study reveals a potential co-limitation in pollen and
 nectar resources affecting foraging behavior and reproductive performance
 in bumble bees, and indicates that even in mixed agricultural landscapes
 with higher proportions of semi-natural habitats, bumble bee populations
 face resource limitations. We conclude that the seasonal management of
 floral resources must be considered in conservation to support bumble bee
 populations and pollination services in farmlands.
DOI: 10.5061/dryad.j0zpc868z
title: Data from: Genetic Monogamy despite frequent extra-pair Copulations in “strictly monogamous” wild Jackdaws

description: “Monogamy” refers to different components of pair exclusiveness: the
 social pair, sexual partners, and the genetic outcome of sexual
 encounters. Avian monogamy is usually defined socially or genetically,
 while quantifications of sexual behavior remain scarce. Jackdaws (Corvus
 monedula) are considered a rare example of strict monogamy in songbirds,
 with lifelong pair bonds and little genetic evidence for extra-pair
 offspring. Yet jackdaw copulations, although accompanied by loud
 copulation calls, are rarely observed, since they occur visually concealed
 inside nest cavities. Using full-day nest-box video surveillance and
 on-bird acoustic bio-logging, we directly observed jackdaw sexual behavior
 and compared it to the corresponding genetic outcome obtained via
 molecular parentage analysis. In the video-observed nests, we found
 genetic monogamy, but frequently detected forced extra-pair sexual
 behavior, accompanied by characteristic male copulation calls. We thus
 challenge the long-held notion of strict jackdaw monogamy at the sexual
 level. Our data suggest that male mate-guarding and frequent intra-pair
 copulations during the female fertile phase, as well as the forced nature
 of the copulations could explain the absence of extra-pair offspring.
 Since extra-pair copulation behavior appeared to be costly for both sexes,
 we suggest that immediate fitness benefits are an unlikely explanation for
 its prevalence. Instead, sexual conflict and dominance effects could
 interact to shape the spatio-temporal pattern of extra-pair sexual
 behavior in this species. Our results call for larger-scale investigations
 of jackdaw sexual behavior and parentage, and highlight the importance of
 combining social, sexual and genetic datasets for a more complete
 understanding of mating systems.
description: This study combines behavioural and genetic information
 collected from a breeding colony of wild jackdaws in Bavaria, Germany.
 Social and sexual behaviour and genetics were directly compared to
 evaluate the levels of social*, sexual** and genetic*** monogamy of this
 supposedly strictly monogamous songbird. *Breeding
 data were collected via nest checks and observations.
 **Behavioural data were collected using nest-box video
 surveillance, acoustic bio-logging (microphone backpacks) and observations
 of banded individuals. ***Information on genetic
 monogamy was obtained via molecular parentage analysis on chick (buccal
 swabs) and adult (blood samples) DNA.  
description: Statistical analyses and figures of the behavioural and
 breeding data were performed in R and can be reproduced using the R-script
 and numbered .csv files. Other files:
 -Genotypes for parentage -Audio example
 of on-board recording: focal male jackdaw copulation call sequence
 accompanied by wingbeats; short calls of non-focal bird in background;
 end: focal male exits nest-box
DOI: 10.15468/dl.fn3xz8
title: Occurrence Download

description: A dataset containing 29651 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "Country is Norway",
 "TaxonKey is Vulpes vulpes",
 "Year 2000-2026"
 ]
}

 The dataset includes 29651 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001953-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.wh70rxwhs
title: Data from: Endemism patterns are scale dependent

description: Areas of endemism are important in biogeography because they capture
 facets of biodiversity not represented elsewhere. However, the scales at
 which they are relevant to research and conservation are poorly analysed.
 Here, we calculate weighted endemism (WE) and phylogenetic endemism (PE)
 separately for all birds and amphibians across the globe. We show that
 scale dependence is widespread for both indices and manifests across grain
 sizes, spatial extents and taxonomic treatments. Variations in taxonomic
 opinions – whether species are treated by systematic ‘lumping’ or
 ‘splitting’ – can profoundly affect the allocation of WE hotspots. Global
 patterns of PE can provide insights into complex evolutionary processes
 but this congruence is lost at the continental to country extents. These
 findings are explained by environmental heterogeneity at coarser grains,
 and to a far lesser extent at finer resolutions. Regardless of scale, we
 find widespread deficits of protection for endemism hotspots. Our study
 presents a framework for assessing areas for conservation that are robust
 to assumptions on taxonomy, spatial grain and extent.
description: Range maps from the IUCN spatial datasets
DOI: 10.5061/dryad.1g1jwstqs
title: Data from: Differential clinicopathological features of EGPA-associated neuropathy with and without ANCA

description: Objective: To investigate the clinicopathological features of eosinophilic
 granulomatosis with polyangiitis (EGPA)-associated neuropathy with a focus
 on the presence or absence of anti-neutrophil cytoplasmic antibodies
 (ANCAs). Methods: We examined the clinical features and pathological
 findings of sural nerve biopsy specimens from 82 patients with
 EGPA-associated neuropathy. Of these patients, 32.9% were myeloperoxidase
 (MPO)-ANCA-positive, and 67.1% were MPO-ANCA-negative. PR3-ANCA was
 negative in all of 78 examined patients. Results: Upper-limb symptoms were
 more frequently reported as initial neuropathic manifestations in the
 MPO-ANCA-positive group than in the MPO-ANCA-negative group (44.4% vs.
 14.6%, p &lt; 0.01). The serum levels of C-reactive protein were
 significantly higher in the MPO-ANCA-positive group than in the
 MPO-ANCA-negative group (p &lt; 0.05). Sural nerve biopsy specimens
 showed findings suggestive of vasculitis (i.e., destruction of vascular
 structures) in epineurial vessels; these results were more frequently seen
 in the MPO-ANCA-positive group than in the MPO-ANCA-negative group (p
 &lt; 0.0001). Conversely, the numbers of eosinophils in the lumen of
 the epineurial vessels (p &lt; 0.01) and epineurial vessels occluded
 by intraluminal eosinophils (p &lt; 0.05) were higher in the
 MPO-ANCA-negative group than in the MPO-ANCA-positive group. Furthermore,
 the incidence of eosinophil infiltration in the endoneurium was higher in
 the MPO-ANCA-negative group than in the MPO-ANCA-positive group (p
 &lt; 0.01). Conclusions: This study suggests that the pathogenesis of
 EGPA comprises at least two distinct mechanisms: ANCA-associated
 vasculitis resulting in ischemic effects and inflammation, which is
 prominent in MPO-ANCA-positive patients, and eosinophil-associated
 vascular occlusion leading to ischemia and eosinophil-associated tissue
 damage, which is conspicuous in MPO-ANCA-negative patients.
description: <b>Supplementary figure e-1 </b> <b>Methods for quantitative analysis of the sural nerve.</b> Transverse sections. Hematoxylin and eosin staining. (A) A whole transverse section of the sural nerve scanned by a virtual slide system (VS120-S5, Olympus, Tokyo, Japan) using the ×20 objective lens is shown. (B) Epineurial area and endoneurial area measured using ImageJ software version 1.50i (NIH, Bethesda, Maryland, USA) are shown as Ep and En, respectively. (C) Epineurial vessels counted using the same software are shown as black dots. Scale bars = 500 μm.
DOI: 10.5061/dryad.s7h44j12q
title: Extracting physiological information in experimental biology via Eulerian video magnification

description: Background: Videographic material of animals can contain inapparent
 signals, such as color changes or motion that hold information about
 physiological functions, such as heart and respiration rate, pulse wave
 velocity and vocalization. Eulerian video magnification allows enhancement
 of such signals to enable their detection. The purpose of this study is to
 demonstrate how signals relevant to experimental physiology can be
 extracted from non-contact videographic material of animals. Results: We
 applied Eulerian video magnification to detect physiological signals in a
 range of experimental models and in captive and free ranging wildlife.
 Neotenic Mexican axolotls were studied to demonstrate the extraction of
 heart rate signal of non-embryonic animals from dedicated videographic
 material. Heart rate could be acquired both in single and multiple animal
 setups of leucistic and normally colored animals under different
 physiological conditions (resting, exercised or anesthetized) using a wide
 range of video qualities. Pulse wave velocity could also be measured in
 the low blood pressure system of the axolotl as well as in the high
 pressure system of the human being. Heart rate extraction was also
 possible from videos of conscious, unconstrained zebrafish and from
 non-dedicated videographic material of sand lizard and giraffe. This
 technique also allowed for heart rate detection in embryonic chickens in
 ovo through the eggshell and in embryonic mice in utero, and could be used
 as a gating signal to acquire two-phase volumetric micro-CT data of the
 beating embryonic chicken heart. Additionally, Eulerian video
 magnification was used to demonstrate how vocalization induced vibrations
 can be detected in infrasound producing Asian elephants. 
 Conclusions: Eulerian video magnification provides a technique to extract
 inapparent temporal signals from videographic material of animals. This
 can be applied in experimental and comparative physiology where contact
 based recordings (e.g. heart rate) cannot be acquired.
description: This dataset consists of 232 source video files in either MP4 or
 MOV format acquired with smartphone or DSLR cameras.
description: The file name of each source video file is structured according
 to the following hierarchy:
 <b>1</b>_<b>2</b>_<b>3</b>_<b>4</b>_<b>5</b>_<b>6</b>_<b>7</b>_<b>8</b> where numbers refer to <b>1:</b> Species name; <b>2:</b> Animal#; <b>3:</b> Animal strain if relevant; <b>4:</b> Experiment specific information 1; <b>5:</b> Experiment specific information 2; <b>6:</b> Spatial resolution of video; <b>7:</b> Temporal resolution of video; <b>8:</b> Camera name, for example: <b><i>(1)</i></b>Amex_<b><i>(2)</i></b>Axolotl1_<b><i>(3)</i></b>Leucistic_<b><i>(4)</i></b>Anaesthetized_<b><i>(5)</i></b>LateralViewWithUltrasound_<b><i>(6)</i></b>1920x1080px^2_<b><i>(7)</i></b>30fps_<b><i>(8)</i></b>SamsungGlaxyS6.