cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.30kp1qg
title: Data from: Bony lesions in early tetrapods and the evolution of mineralized tissue repair

description: Bone healing is an important survival mechanism, allowing vertebrates to
 recover from injury and disease. Here we describe newly recognized
 paleopathologies in the hindlimbs of the early tetrapods Crassigyrinus
 scoticus and Eoherpeton watsoni from the Early Carboniferous of
 Cowdenbeath, Scotland. These pathologies are among the oldest known
 instances of bone healing in tetrapod limb bones in the fossil record
 (about 325 Myr old). X-ray microtomographic imaging of the internal bone
 structure of these lesions shows that they are characterized by a mass of
 trabecular bone separated from the shaft’s trabeculae by a layer of
 cortical bone. We frame these paleopathologies in an evolutionary context,
 including additional data on bone healing and its pathways across extinct
 and extant sarcopterygians. These data allowed us to synthesize
 information on cell-mediated repair of bone and other mineralized tissues
 in all vertebrates, to reconstruct the evolutionary history of skeletal
 tissue repair mechanisms. We conclude that bone healing is ancestral for
 sarcopterygians. Furthermore, other mineralized tissues (aspidin and
 dentine) were also capable of healing and remodeling early in vertebrate
 evolution, suggesting that these repair mechanisms are synapomorphies of
 vertebrate mineralized tissues. The evidence for remodeling and healing in
 all of these tissues appears concurrently, so in addition to healing these
 early vertebrates had the capacity to restore structure and strength by
 remodeling their skeleton. Healing appears to be an inherent property of
 these mineralized tissues, and its linkage to their remodeling capacity
 has previously been under-appreciated.
description: Supplementary Text 1-3,
 Supplementary Figure 1 Includes Supplementary
 Text 1 (information about Crassigyrinus specimens), Supplementary Text 2
 (information about Eoherpeton specimens), Supplementary Text 3 (image
 processing macro used for main text Figure 1), and Supplementary Figure 1
 (comparing Crassigyrinus and Ossinodus pathologies). Also includes
 references for all supplementary material. Final_Supplementary_Information_Text_and_Figure.doc Supplementary Table 1 Supplementary Table 1 lists early tetrapod specimens scanned to investigate paleopathologies. Includes specimen numbers and scanning information. final_Supplementary_Information_Table1.doc
DOI: 10.5061/dryad.p7k5610
title: Data from: High incidence of hypopigmented marks in the endangered Florida bonneted bat (Eumops floridanus)

description: Aberrant patches of white skin and/or fur known as hypopigmented marks,
 have been observed in many mammal species worldwide, but they are
 typically limited to only a few individuals in a population. Hypopigmented
 marks were documented in only two museum specimens of the federally
 endangered Florida bonneted bat (Eumops floridanus) as early as 1950, but
 recent observations suggest that these marks may be more common in this
 species than previously believed. To better understand the occurrence and
 persistence of hypopigmented marks in Florida bonneted bats, we evaluated
 the variation in frequency, compared effects on survival, and assessed
 spatial and temporal differences of specimens at an intensively studied
 site and across the species range. From 2014 through 2017, we regularly
 captured Florida bonneted bats for demographic studies at Babcock-Webb
 Wildlife Management Area in Charlotte County and we observed hypopigmented
 marks on 172 (80.8%) of 213 individuals, the highest incidence ever
 reported for bats. The proportion of hypopigmented marks did not differ
 with sex, age at first capture, or reproductive status, and importantly,
 we documented the persistence of hypopigmented marks in individuals over
 multiple months. We also found no difference in survival or capture
 probability between hypopigmented and solid-colored individuals. Using
 data from concurrent mist net studies, we assessed the proportion of
 Florida bonneted bats with hypopigmented marks across the species range
 and found a higher proportion of individuals with hypopigmented marks in
 the two northern counties (80.8% in Charlotte County and 61.5% in Polk
 County) compared to the two southern counties (21.1% in Miami-Dade County
 and 16.7% in Collier County). Additionally, we compared the proportion of
 hypopigmented individuals in Miami-Dade County between recently
 captured/collected bats (post-2004) and historically (pre-1965) collected
 museum specimens and found more hypopi gmented marks in recently captured
 bats. The persistence of hypopigmented marks over time, the presence of
 marks on bats from different locations, and our finding of no effect of
 age on the presence of marks all strongly suggest that the hypopigmented
 marks in Florida bonneted bats are the result of genetic rather than
 environmental factors. Further study is required to understand the
 mechanism underlying the high incidence of hypopigmented marks and to
 determine whether the prevalence of hypopigmented marks indicates low
 genetic diversity that could threaten Florida bonneted bats.
description: Hypopigmented_SupplementalData includes individual bat data, measurements of white marks, recapture data, and museum specimen data.
DOI: 10.5061/dryad.852h5m8
title: Data from: Carryover effects of larval environment on individual variation in a facultatively diadromous fish

description: 1. Intraspecific trait variation may result from “carryover effects” of
 variability of environments experienced at an earlier life stage. This
 phenomenon is particularly relevant in partially migrating populations
 composed of individuals with divergent early life histories. While many
 studies have addressed the causes of partial migration, few have
 investigated the consequences for between-individual variability later in
 life. 2. We studied carryover effects of larval environment in a
 facultatively diadromous New Zealand fish, Gobiomorphus cotidianus, along
 an estuarine salinity gradient. We investigated the implications of
 varying environmental conditions during this critical stage of ontogeny
 for adult phenotype. 3. We inferred past environmental history of
 wild-caught adult fish using otolith microchemistry (Sr/Ca) as a proxy for
 salinity. We tested for main and interactive effects of larval and adult
 environment on a suite of traits, including growth rates, behaviour
 (exploration and activity), parasite load, and diet (stable isotopes and
 gut contents).4. We found a Sr/Ca consistent with a continuum from
 freshwater to brackish environments, and with different trajectories from
 juvenile to adult habitat. Aside from a near-significant effect of larval
 salinity on juvenile growth rates, growth rates did not seem to be
 affected by past environment. Fish with Sr/Ca indicating upstream
 migration were more vulnerable to trematode infection, suggesting a
 mismatch to freshwater habitat. Diet analysis suggested an interactive
 effect of larval and adult environments on trophic position and diet
 preference, while behavioural traits were unrelated to environment at any
 life stage. 5. Overall, we show that early life environment can have
 multiple effects on adult performance and ecology, with the potential for
 lifetime fitness trade-offs associated with life history. Our study
 highlights that even relatively minor variation in rearing conditions may
 be enough to generate individual variation in natural populations.
description: Fish
 dataData from common bullies
 (Gobiomorphus cotidianus) collected on February 12-13 2018 in lake Waipori
 system, South Island, New Zealand. NA indicates missing
 data.FishData.xlsxInvertebrateDataStable C-N isotope of invertebrates collected on February 12, 2018 in lake Waipori, South Island, New Zealand. NA ndicates missing data.WaterDataWater parameters and element concentrations of natural water in the Taieri basin, South Island, New Zealand.
DOI: 10.5061/dryad.40br385
title: Data from: Always a price to pay: hibernation at low temperatures comes with a trade-off between energy savings and telomere damage

description: We experimentally tested the costs of deep torpor at low temperatures by
 comparing telomere dynamics in two species of rodents hibernating at
 either 3°C or 14°C. Our data show that hibernators kept at the warmer
 temperature had higher arousal frequencies, but maintained longer
 telomeres than individuals hibernating at the colder temperature. We
 suggest that the high-energy demand of frequent arousals is counteracted
 by a lower temperature differential between torpid and euthermic body
 temperature and that telomere length is restored during arousals, when the
 body temperature is returned to normothermic values. Taken together, our
 study shows that hibernation at low body temperatures comes with costs on
 a cellular level and that hibernators need to actively counterbalance the
 shortening of telomeres.
description: Dormice_metabolicrate_data_fo_respositoryData on metabolic costs of hibernation at 3°C or 14°C in two species of dormice.Dormice_data_fo_respositoryData from experiment testing the influence that deep torpor has on telomere attrition in two species of dormice, hibernating at 3°C or 14°C.
DOI: 10.5061/dryad.7hs993m
title: Data from: Widespread infection of Areospora rohanae in southern king crab (Lithodes santolla) populations across south Chilean Patagonia

description: Cottage cheese disease is caused by microsporidian parasites that infect a
 wide range of animal populations. Despite its potential to affect
 economically important activities, the spatial patterns of prevalence of
 this disease are still not well understood. Here, we analyze the
 occurrence of the microsporidian Areospora rohanae in populations of the
 king crab Lithodes santolla over ca. 800 km of the southeastern Pacific
 shore. In winter 2011, conical pots were deployed between 50 and 200 m
 depth to capture crabs of a wide range of sizes. The infection was widely
 distributed along the region, with a mean prevalence of 16 %, and no
 significant association between prevalence and geographic location was
 detected. Males, females, and ovigerous females showed similar prevalence
 values of 16.5 (13 – 18.9), 15 (9.2 – 15), and 16.7 % (10 – 19 %),
 respectively. These patterns of prevalence were consistent across crab
 body sizes, despite the ontogenetic and sex-dependent variations in
 feeding behavior and bathymetric migrations previously reported for king
 crabs. This study provided the first report of the geographic distribution
 of A. rohanae infecting southern king crabs.
description: Rodríguez et al.
 data_kingcrabPrevalence data of
 Areospora rohanae parasitizing to Lithodes sandlot along Magellan region,
 southeastern Pacific shore of ChileRodríguez et al. data_king
 crab.xls
DOI: 10.5061/dryad.9kj2fr6
title: Data from: Strangers in a strange land: Ecological dissimilarity to metatherian carnivores may partly explain early colonization of South America by Cyonasua-group procyonids

description: It was once thought that the endemic carnivorous mammals of South America,
 the metatherian sparassodonts, were driven extinct by North American
 carnivores through competitive exclusion. However, sparassodonts went
 extinct before most groups of carnivorans entered South America; only the
 endemic Cyonasua-group procyonids (Cyonasua and Chapalmalania), which
 immigrated to South America nearly four million years earlier than other
 carnivorans, significantly overlapped with sparassodonts in time. In this
 study, we examine the functional morphology of the dentition of Cyonasua
 and Chapalmalania through quantitative analysis to determine the dietary
 habits of these taxa and the degree to which they may have ecologically
 overlapped sparassodonts and large predatory Neogene didelphimorphians. We
 find Cyonasua and Chapalmalania to be more carnivorous than extant
 procyonids other than Bassariscus, in agreement with previous studies, but
 more omnivorous than most other carnivorans and all meat-eating South
 American metatherians, including sparassodonts. The extreme ecological
 dissimilarity between Cyonasua-group procyonids and members of the endemic
 South American predator guild may explain why procyonids were able to
 successfully establish themselves in South America several million years
 earlier than most other northern mammals (including all other
 carnivorans): they moved into a previously unoccupied ecological niche
 (large omnivore) and avoided direct competition with incumbent native
 species, a situation similar to that documented in historical cases of
 biological invasion. The omnivorous diets and climbing/swimming abilities
 of procyonids may have increased their chances for a successful over-water
 dispersal relative to other carnivorans, further favoring their successful
 establishment in South America.
description: EC Cyonasua Figure
 S1FIGURE S1. Enlarged
 version of Figure 1 of the main text, showing the positions of the various
 non-sparassodont taxa mentioned in the main article. Legend for symbols is
 the same as Figure 1.EC Cyonasua Figure
 S2FIGURE S2. Enlarged
 region of the sparassodont morphospace, with the four groups discussed in
 the main article circled. Legend for symbols is the same as Figure
 1.EC Cyonasua Paper
 Supplementary InformationOnline supplementary
 information for "Strangers in a strange land: Ecological
 dissimilarity to metatherian carnivores may partly explain early
 colonization of South America by Cyonasua-group
 procyonids"
DOI: 10.5061/dryad.gf7hc1r
title: Data from: Human-mediated disturbance in multitrophic interactions results in outbreak levels of North America’s most venomous caterpillar

description: Abstract Anthropogenic environmental change is predicted to disrupt
 multitrophic interactions, which may have drastic consequences for
 population-level processes. Here, we investigate how a large-scale
 human-mediated disturbance affects the abundance of North America’s most
 venomous caterpillar species, Megalopyge opercularis. Specifically, we
 used a natural experiment where netting was deployed to cover the entire
 canopies of a subset of mature southern live oak trees (Quercus
 virginiana) to exclude urban pest birds (grackles and pigeons), throughout
 an 8.1-km2 area encompassing a medical center in Houston, Texas. We used
 this experimental exclusion to test the following hypothesis: release from
 avian predators increases caterpillar abundance to outbreak levels, which
 increases the risk to human health. Results from a multi-year survey show
 that caterpillar abundance increased, on average, &gt;7300% on netted
 versus non-netted trees. Thus, increases in caterpillar abundance, due to
 anthropogenic enemy release, increase human exposure to this venomous
 pest, and should be considered a health threat in the area. This study
 emphasizes the unforeseen consequences of ecological disturbance for
 species interactions and highlights the importance of considering ecology
 in urban planning.
description: Raw Data Hood et al.
 2019 Biology LettersSupplementa Table 1: Raw
 data from “Human-mediated disturbance in multitrophic interactions results
 in outbreak level of North America’s most venomous caterpillar” by G.R.
 Hood, M. Comerford2, A.K. Weaver, P.M. Morton, and S.P. Egan.Given are the
 number of asp counted in the survey in Houston, Texas, USA in 2015, 2017,
 and 2018. Noted is the date of the survey, if the tree was netted (Y) or
 non-netted (N), the number of asp (larvae and pupae) observed on each
 tree, the location of the survey (TMC = Texas Medical Center; Rice = Rice
 University; HP = Herman Park; SG = Southgate Neighborhood), the year the
 survey was conducted, and if the tree of previously netted (Y = previously
 netted; N = not previously netted).
DOI: 10.5061/dryad.qf36gd4
title: Data from: Legacy of prior host and soil selection on rhizobial fitness in planta

description: Measuring selection acting on microbial populations in natural or even
 semi-natural environments is challenging because many microbial
 populations experience variable selection. The majority of rhizobial
 bacteria are found in the soil. However, they also live symbiotically
 inside nodules of legume hosts and each nodule can release thousands of
 daughter cells back into the soil. We tested how past selection (i.e.,
 legacies) by two plant genotypes and by the soil alone, affected selection
 and genetic diversity within a population of 101 strains of Ensifer
 meliloti. We also identified allelic variants most strongly associated
 with soil- and host-dependent fitness. In addition to imposing direct
 selection on rhizobia populations, soil and host environments had lasting
 effects across host generations. Host presence and genotype during the
 legacy period explained respectively 22% and 12% of the variance in the
 strain composition of nodule communities in the second cohort. While
 strains with high host fitness in the legacy cohort tended to be enriched
 in the second cohort, the diversity of the strain community was greater
 when the second cohort was preceded by host rather than soil legacies. Our
 results indicate the potential importance of soil selection driving the
 evolution of these plant-associated microbes.
description: Main R code: statistical
 analysis and figuresR code to recreate all
 figures and analysis included in the Evolution paper. This file takes as
 inputs freq1.tsv, freq2.tsv, and
 SingleStrain_phenotype_summary.tsv.EvolutionLegacy_Rcode_Dryad.RStrain frequencies from first sequencing runStrain frequencies of 101 rhizobial strains in pools of Medicago nodules inferred from high coverage WGS data. Raw data used to calculate strain frequencies are on NCBI (Accessions SRR6029825–SRR6029912) with code in a previous Dryad repository ( https://doi.org/10.5061/dryad.fp1bg).freq1.tsvStrain frequencies from second sequencing runStrain frequencies of 101 rhizobial strains from pools of Medicago nodules inferred from high coverage WGS data. Raw data used to calculate strain frequencies are on NCBI (Accessions SRR6029825–SRR6029912) with code in a previous Dryad repository (https://doi.org/10.5061/dryad.fp1bg).freq2.tsvPlant phenotypes from single strain experimentPlant phenotype data from a previously published single strain experiment (Burghardt et al, 2018, PNAS, https://doi.org/10.1073/pnas.1714246115). This file is also found in the Dryad repository for that publication ( https://doi.org/10.5061/dryad.fp1bg). The file is used as input for calculations of plant benefit of strain communities in the main R code.SingleStrain_phenotype_summary.tsvSource, results, and summary of results from genome-wide tests of allele frequency shiftsSee Readmescans.zip
DOI: 10.5061/dryad.82mn2ht
title: Data from: Tissue mechanics govern the rapidly adapting and symmetrical response to touch

description: PLEASE NOTE, THESE DATA WERE ALSO ANALYZED FOR A SUBSEQUENT PUBLICATION in
 eLife. PLEASE SEE https://doi.org/10.7554/eLife.43226 FOR MORE
 INFORMATION. Recordings from Pacinian corpuscles in the 1960s showed that
 touch elicits symmetric activation followed by rapid adaptation.
 Sinusoidal stimulation resulted in frequency doubling within a sensitive
 frequency band, suggesting that these receptors function as
 frequency-tuned vibration sensors. At the time, the surrounding lamellar
 capsule was proposed to generate these response dynamics by acting as a
 mechanical filter. However, similar response dynamics have since been seen
 in many other mechanoreceptors, leading to controversy over the
 specificity of this hypothesis. Using a combination of in vivo
 electrophysiology, feedback-controlled mechanical stimulation, and
 simulation, we resolve this controversy in favor of a systems-level
 mechanical filter that is independent of specific anatomical features or
 specific mechanoelectrical transduction channels.
description: Eastwood-Fig1CDEFSource data related to Figure 1.Eastwood-Fig2ABCDSource data for Figure 2Eastwood-Fig3ABCDSource data for Figure 3Eastwood-Fig4CDESource experimental data for Figure 4Eastwood-Fig5ABCSource experimental data for Figure 5
DOI: 10.5061/dryad.t03b7b8
title: Data from: CORIGAN: Assessing multiple species and interactions within images

description: 1.Images are resourceful data for ecologists and can provide a more
 complete information than other methods to study biodiversity and the
 interactions between species. Automated image analysis however often
 relies on extensive datasets, not implementable by small research teams.
 We are here proposing an object detection method that allows the analysis
 of high‐resolution images containing many animals interacting in a small
 dataset. 2.We developed an image analysis pipeline named ‘CORIGAN' to
 extract the characteristics of animal communities. CORIGAN is based on the
 YOLOv3 model as the core of object detection. To illustrate potential
 applications, we use images collected during a sentinel prey experiment.
 3.Our pipeline can be used to detect, count and study the physical
 interactions between various animals. On our example dataset, the model
 reaches 86.6% precision and 88.9% recall at the species level or even at
 the caste level for ants. The training set required fewer than 10 h of
 labelling. Based on the pipeline output it was possible to build the
 trophic and non‐trophic interactions network describing the studied
 community. 4.CORIGAN relies on generic properties of the detected animals
 and can be used for a wide range of studies and supports. Here, we study
 invertebrates on high‐resolution images, but the same processing can be
 transferred for the study of larger animals on satellite or aircraft
 images.
description: Corigan training
 dataset95 images from on-field
 sentinel experiments. These image files are associated with labelled
 files. These files have been used to train the Yolov3 detection model
 (Redmon & Farhadi 2018), which constitutes the core of the CORIGAN
 pipeline. For more details on data and CORIGAN, see the related manuscript
 and supplementary materials in Methods in Ecology &
 Evolution.Corigan testing
 dataset93 images from on-field
 sentinel experiments. These image files are associated with labelled
 files. These files have been used to test the Yolov3 detection model
 (Redmon & Farhadi 2018), which constitutes the core of the CORIGAN
 pipeline. For more details on data and CORIGAN, see the related manuscript
 and supplementary materials in Methods in Ecology &
 Evolution.
DOI: 10.5061/dryad.s3t2qn0
title: Data from: Ecological speciation in sympatric palms: 4. Demographic analyses support speciation of Howea in the face of high gene flow

description: The idea that populations must be geographically isolated (allopatric) to
 evolve into separate species has persisted for a long time. It is now
 clear that new species can also diverge despite ongoing genetic exchange,
 but few accepted cases of speciation in sympatry have held up when
 scrutinised using modern approaches. Here, we examined evidence for
 speciation of the Howea palms of Lord Howe Island, Australia, in light of
 new genomic data. We used coalescence-based demographic models combined
 with double digest restriction-site associated DNA sequencing of multiple
 individuals and provide support for previous claims by Savolainen et al.
 (Nature 441: 210–213, 2006) that speciation in Howea did occur in the face
 of gene flow.
description: SNPS for Demographic
 analysisA vcf file containing
 the SNP genotypes for Howea forsteraina and Howea belmoreana that were
 used to infer the demographic history of the speciesHowea_snps_sfs.vcf