cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q0sr5p5
title: Data from: Genomes reveal drastic and recurrent phenotypic divergence in Firetip skipper butterflies (Hesperiidae: Pyrrhopyginae)

description: Biologists marvel at the powers of adaptive convergence, when distantly
 related animals look alike. While mimetic wing patterns of butterflies
 have fooled predators for millennia, entomologists inferred that mimics
 were distant relatives despite similar appearance. However, the obverse
 question has not been frequently asked. Who are the close relatives of
 mimetic butterflies and what are their features? As opposed to close
 convergence, divergence from a non-mimetic relative would also be extreme.
 When closely related animals look unalike, it is challenging to pair them.
 Genomic analysis promises to elucidate evolutionary relationships and shed
 light on molecular mechanisms of divergence. We chose the Firetip skipper
 butterflies as a model due to their phenotypic diversity and abundance of
 mimicry. We sequenced and analyzed whole genomes of nearly 120
 representative species. Genomes partitioned this subfamily Pyrrhopyginae
 into 5 tribes (1 new), 23 genera and, additionally, 22 subgenera (10 new).
 The largest tribe Pyrrhopygini is divided into 4 subtribes (3 new).
 Surprisingly, we found 5 cases where a uniquely patterned butterfly was
 formerly placed in a genus of its own and separately from its close
 relatives. In several cases, extreme and rapid phenotypic divergence
 involved not only wing patterns, but also the structure of the male
 genitalia. The visually striking wing pattern difference between close
 relatives frequently involves disappearance or suffusion of spots and
 color exchange between orange and blue. These differences, in particular a
 transition between unspotted black and striped wings, happen recurrently
 on a short evolutionary time-scale, and are therefore likely achieved by a
 small number of mutations.
description: Barcodes for
 Pyrrhopyginae samplesBarcode sequences for
 Pyrrhopyginae samplesPyrr_barcodes.faProtein coding regions of Pyrrhopyginae mitogenomesProtein coding regions of Pyrrhopyginae mitogenomesPyrr_mitos.fastaInput for constructing time-calibrated tree by BEASTBEAST input filePyrrhopyginae_BEAST_input.xml.gzConcatenated nuclear protein coding sequences for Pyrrhopyginae samplesConcatenated nuclear protein coding sequences for Pyrrhopyginae samplesPyrr_nuclear.fasta.gz
DOI: 10.5061/dryad.2h87r1f
title: Data from: Predator-induced collapse of niche structure and coexistence on islands

description: Biological invasions represent both a pressing environmental challenge and
 an opportunity to investigate fundamental ecological processes, such as
 the role of top predators in regulating species diversity and food-web
 structure. In whole-ecosystem manipulations of small Caribbean islands
 where brown anole lizards (Anolis sagrei) were the native top predator, we
 experimentally staged invasions by competitors (green anoles, A.
 smaragdinus) and/or novel top predators (curly-tailed lizards,
 Leiocephalus carinatus). We show that curly-tails destabilized coexistence
 of competing prey species, contrary to the classic idea of keystone
 predation. Fear-driven avoidance of predators collapsed the spatial and
 dietary niche structure that otherwise stabilized coexistence,
 intensifying interspecific competition within predator-free refuges and
 contributing to green-anole population extinctions. Moreover, whereas
 adding either green anoles or curly-tails lengthened food chains, adding
 both species reversed this effect, in part because apex predators were
 trophic omnivores. Our results underscore the importance of top-down
 control in community ecology, but show that its outcomes hinge on prey
 behavior, spatial structure, and omnivory. Diversity-enhancing effects of
 top predators cannot be assumed, and non-consumptive effects of predation
 risk may be a widespread constraint on species coexistence.
description: Metabarcode sequence
 data and MID tagsSequence data obtained
 DNA metabarcoding of fecal samples. The ReadMe file contains
 "MID" tag identifiers used to demultiplex samples with the
 Obitools software prior to analysis. The ReadMe file contains a column
 referencing 5 raw Illumina fastq files that contain the data. One of these
 raw Illumina fastq files is available to download from this Dryad DOI;
 four raw Illumina fastq files are available from a previous Dryad DOI,
 which is linked below: Kartzinel TR, Pringle RM (2014) Data from:
 Molecular detection of invertebrate prey in vertebrate diets: trophic
 ecology of Caribbean island lizards. Dryad Digital Repository.
 https://doi.org/10.5061/dryad.f18k5s_1_1_reads_passed_filter.fastq.gzMetabarcode sequence data and MID tags at doi:10.5061/dryad.f18k5
DOI: 10.5061/dryad.mv06pv1
title: Data from: Some like it dry: water restriction overrides heterogametic sex determination in two reptiles

description: The evolution of sex determination is complex and yet crucial in our
 understanding of population stability. In ectotherms, sex determination
 involves a variety of mechanisms including genetic determination (GSD),
 environment determination (ESD), but also interactions between the two via
 sex reversal. In this study, we investigated whether water deprivation
 during pregnancy could override GSD in two heterogametic squamate
 reptiles. We demonstrated that water restriction in early gestation
 induced a male-biased secondary sex ratio in both species, which could
 only be explained by water sex reversal as the more likely mechanism. We
 further monitored some long term fitness estimates of offspring, which
 suggested that water sex determination (WSD) represented a compensatory
 strategy to ensure a balanced operational sex ratio. This study provides
 new insights into sex determination modes and calls for a general
 investigation of mechanisms behind WSD and to examine the evolutionary
 implications.
description: data_femalesThe female dataset includes all data on females (each female per line) of the two species and for each year of experiment. The table also gives the females' identification (mother ID), their affiliated hydric treatment and reproductive timing as described in the manuscript. For each mother, the number of offspring females and males at birth are available to calculate secondary sex ratio.data_juvenilesThe juvenile dataset includes all data on juveniles (each juvenile per line) of the two species and for each year of experiment. Each juvenile is identified with a number (juvenile ID) and affiliated to its mother (mother ID) and relevant maternal hydric treatment. Each juvenile has been sexed and measured for body growth rate as described in the manuscript. In lizard analyses, we also accounted for outdoor enclosure in analyses, so the table also includes this information.
DOI: 10.5061/dryad.m4r0cn0
title: Data from: Monitoring large and complex wildlife aggregations with drones

description: Recent advances in drone technology have rapidly led to their use for
 monitoring and managing wildlife populations but a broad and generalised
 framework for their application to complex wildlife aggregations is still
 lacking. We present a generalised semi-automated approach where machine
 learning can map targets of interest in drone imagery, supported by
 predictive modelling for estimating wildlife aggregation populations. We
 demonstrated this application on four large spatially complex breeding
 waterbird colonies on floodplains, ranging from ~20,000 to ~250,000 birds,
 providing estimates of bird nests. Our mapping and modelling approach was
 applicable to all four colonies, without any modification, effectively
 dealing with variation in nest size, shape, colour and density and
 considerable background variation (vegetation, water, sand, soil etc.).
 Our semi-automated approach was between 3 to 8 times faster than manually
 counting nests from imagery at the same level of accuracy. This approach
 is a significant improvement for monitoring large and complex aggregations
 of wildlife, offering an innovative solution where ground counts are
 costly, difficult or not possible. Our framework requires minimal
 technical ability, is open-source (Google Earth Engine and R), and easy to
 apply to other surveys
description: Eulimbah ibis colony
 drone imageryOrthorectified image
 mosaic derived from drone (Phantom 3 professional, stock camera) imagery,
 processed via Pix4D Mapper. Location is Eulimbah on the Murrumbidgee River
 in New South Wales, Australia. The imagery was acquired in October
 2016eulimbah_nov2016_p4_transparent_mosaic_group1.tif
DOI: 10.5061/dryad.fv278qs
title: Data from: Small RNA sequencing reveals a novel tsRNA-26576 mediating tumorigenesis of breast cancer

description: Purpose: As a malignancy that develops from breast tissue, breast cancer
 has been widely regarded as the most common type of cancer threatening the
 health of women worldwide. Emerging evidence has demonstrated that tsRNAs
 might play a vital part in the tumorigenesis and progression of several
 types of cancers. However, the functions of tsRNAs in breast cancer remain
 largely unknown. Here, we investigated the functions of tsRNA-26576 in
 tumorigenesis of breast cancer. Patients and methods: In this study, the
 tsRNA deregulation states in breast cancer patients (four cancer tissues
 and four adjacent normal tissues) were evaluated using small RNA
 sequencing. And then, RT-PCR was used to detected the tsRNA-26576
 expression level in breast cancer patients. Results: A total of 263 tsRNAs
 were identified as significantly differentially expressed, of which 75
 were upregulated, and 188 were downregulated. The functional
 classification through KEGG pathway database illustrated that the most
 significant pathway enriched by the targets of differentially expressed
 tsRNAs was the pathway in cancer. Among these differently expressed
 tsRNAs, we found that tsRNA-26576 was remarkably upregulated in cancer
 tissue in comparison with adjacent normal tissue. Meanwhile, RT-PCR
 results verified that tsRNA-26576 expression level was highly upregulated
 in 10 paired samples from breast cancer patients. Besides, tsRNA-26576 was
 found to motivate cellular multiplication and migration while suppressing
 cellular apoptosis in MDA-MB-231 cells. Moreover, mRNA sequencing results
 showed that several tumor suppressor genes, including FAT4 and SPEN, were
 upregulated after delivering tsRNA-26576 inhibitor in MDA-MB-231 cells.
 Conclusion: We found tsRNA-26576 was upregulated in breast cancer tissue,
 and it could promote the cell growth while inhibite cell apoptosis.
 Therefore, tsRNA-26576 might serve as a potential clinical therapy target
 and a predictive marker for breast cancer.
description: Table
 S1Table
 S2Table
 S3
DOI: 10.5061/dryad.3f83707
title: Data from: A phylogenomic rodent tree reveals the repeated evolution of masseter architectures

description: Understanding the number of times a trait has evolved is a necessary
 foundation for comprehending its potential relationships with selective
 regimes, developmental constraints, and evolutionary diversification.
 Rodents make up over 40% extant of mammalian species and their ecological
 and evolutionary success has been partially attributed to the increase in
 biting efficiency that resulted from a forward shift of one or two
 portions of the masseter muscle from the zygomatic arch onto the rostrum.
 This forward shift has occurred in three discrete ways, but the number of
 times it has occurred has never been explicitly quantified. We estimated
 an ultrametric phylogeny, the first to include all rodent families, using
 thousands of ultraconserved elements. We examined support for evolutionary
 relationships among the five rodent suborders and then incorporated
 relevant fossils, fit models of character evolution, and used stochastic
 character mapping to determine that a portion of the masseter muscle has
 moved forward onto the rostrum at least seven times (with one reversal)
 during the ca. 70 MY history of rodents. Combined, the repeated evolution
 of this key innovation, its increasing prevalence through time, and the
 species diversity of clades with this character underscores the adaptive
 value of improved biting efficiency and the relative ease with which some
 advantageous traits arise.
description: Rodentia Concatenated
 Alignment for RAxMLThis is the concatenated
 alignment in phylip format used for RAxML.rodentia_concatenated_alignment_for_raxml.phylipCharsets file for concatenated alignmentCharsets file for concatenated alignment used for RAxMLrodentia_concatenated_alignment_for_raxml.charsetsRodentia UCE locus alignmentsRodentia UCE alignments by locus in nexus format.rodentia_uce_locus_alignments.zipRAxML concatenated and calibrated treeRAxML concatenated tree with treePL divergence time estimation using fossil constraints listed in Table 1.raxml_concatenated_treepl_calibrated.treeRAxML concatenated best treeUncalibrated RAxML concatenated tree fileraxml_concatenated_uncalibrated.txt
DOI: 10.5061/dryad.7d028rp
title: Data from: Egg investment in response to the helper presence in cooperatively breeding Tibetan ground tits

description: Life-history theory predicts a trade-off between current and future
 reproduction to maximize lifetime fitness. In cooperatively breeding
 species, where offspring care is shared between breeders and helpers,
 helper presence may influence the female breeders’ egg investment, and
 consequently, survival and future reproductive success. For example,
 female breeders may reduce egg investment in response to helper presence
 if this reduction is compensated by helpers during provisioning.
 Alternatively, female breeders may increase egg investment in response to
 helper presence if helpers allow the breeders to raise more or higher
 quality offspring successfully. In the facultatively cooperative-breeding
 Tibetan ground tit Pseudopodoces humilis, previous studies found that
 helpers improve total nestling provisioning rates and fledgling
 recruitment, but have no apparent effects on the number and body mass of
 fledglings produced, while breeders with helpers show reduced provisioning
 rates and higher survival. Here, we investigated whether some of these
 effects may be explained by female breeders reducing their investment in
 eggs in response to helper presence. In addition, we investigated whether
 egg investment is associated with the female breeder’s future fitness. Our
 results showed that helper presence had no effect on the female breeders’
 egg investment, and that egg investment was not associated with breeder
 survival and reproductive success. Our findings suggest that the responses
 of breeders to helping should be investigated throughout the breeding
 cycle, because the conclusions regarding the breeders’ adjustment of
 reproductive investment in response to being helped may depend on which
 stage of the breeding cycle is considered.
description: Egg investment, female
 breeder survival and reproductive successData used to analyse egg
 investment and its consequences on female breeder's fitness in
 cooperatively breeding Ground tits on the Tibetan plateau,
 China.Data.xlsx
DOI: 10.5061/dryad.v7t77ts
title: Data from: Carbon sequestration and soil restoration potential of grazing lands under exclosure management in a semi-arid environment of northern Ethiopia

description: Exclosures are used to regenerate native vegetation as a way to reduce
 soil erosion, increase rain water inﬁltration and provide fodder and woody
 biomass in degraded grazing lands. Therefore, this study assessed the
 impact of grazing exclosure on vegetation biomass, carbon sequestration
 and soil nutrients under five and ten years of grazing exclosures and
 freely grazed areas in Tigray, northern Ethiopia. Vegetation biomass,
 carbon stocks and soil nutrients increased with increasing grazing
 exclusion. However, open grazing lands and five years of grazing exclosure
 did not differ in aboveground biomass, above-and-belowground carbon
 stocks. Moreover, ten years of grazing exclosure had a higher
 (P&lt;0.01) grass, herb and litter carbon stocks compared to five
 years exclosure and open grazing lands. The total carbon stock was higher
 for ten years exclosure (75.65 t C ha-1) than the five years exclosure
 (55.06 t C ha-1) and in open grazing areas (51.98 t C ha-1). Grazing lands
 closed for ten years had a higher SOC, organic matter, total N, available
 P, and exchangeable K+ and Na+ compared to five year’s exclosure and open
 grazing lands. Therefore, establishment of grazing exclosures had a
 positive effect in restoring degraded grazing lands, thus improving
 vegetation biomass, carbon sequestration potentials and soil nutrients.
description: Carbon stock and soil
 properties DataSoil properties and
 carbon stock data for semi-arid environment of northern
 Ethiopia
DOI: 10.5061/dryad.sc65030
title: Data from: Validation of the GARD™skin assay for assessment of chemical skin sensitizers – ring trial results of predictive performance and reproducibility

description: Proactive identification of chemicals with skin sensitizing properties is
 a key toxicological endpoint within chemical safety assessment. In order
 to meet recent legislations and increase animal welfare, considerable
 efforts have been made to develop non-animal approaches to replace current
 animal testing. Genomic Allergen Rapid Detection (GARD™) is a
 state-of-the-art technology platform, the most advanced application of
 which is the assay for assessment of skin sensitizing chemicals,
 GARD™skin. The methodology is based on a dendritic cell (DC)-like cell
 line, thus mimicking the mechanistic events leading to initiation and
 modulation of downstream immunological responses. Induced transcriptional
 changes are measured following exposure to test chemicals, providing a
 detailed evaluation of cell activation. These changes are associated with
 the immunological decision-making role of DCs in vivo and include among
 other phenotypic modifications, up-regulation of co-stimulatory molecules,
 induction of cellular and oxidative stress pathways and xenobiotic
 responses. Here, results from an inter-laboratory ring trial of GARD™skin,
 conducted in compliance with OECD guidance documents and comprising a
 blinded chemical test set of 28 chemicals, are summarized. The assay was
 found to be transferable to naïve laboratories, with an inter-laboratory
 reproducibility of 92.0%. The within-laboratory reproducibility ranged
 between 82.1-88.9%, while the cumulated predictive accuracy across the
 three laboratories was 93.8%. Based on these and previously published
 data, it is concluded that GARD™skin is a robust and reliable method for
 the identification of skin sensitizing chemicals and suitable for use as a
 stand-alone assay. These data form the basis for the regulatory validation
 of GARD™skin.
description: Supplementary Material
 S1GARD SOP
 v.05.01Supplementary Material
 S2Results calculation
 spreadsheat.Supplementary Material
 S3 revisedHistorical
 data.
DOI: 10.5061/dryad.bj20jr7
title: Data from: A natural point mutation in the bitter taste receptor TAS2R16 causes inverse agonism of arbutin in lemur gustation

description: Bitter taste enables the detection of potentially harmful substances and
 is mediated by bitter taste receptors, TAS2Rs, in vertebrates. Few
 antagonists and inverse agonists of TAS2Rs have been identified,
 especially natural compounds. TAS2R16s in humans, apes and Old World
 monkeys (Catarrhini, Anthropoidea) recognise β-glucoside analogues as
 specific agonists. Here, we investigated responses of TAS2R16 to
 β-glucosides in non-anthropoid primates, namely, lemurs (Lemuriformes,
 Strepsirrhini). Salicin acted as an agonist on lemur TAS2R16. Arbutin
 acted as an agonist in the ring-tailed lemur (Lemur catta) but as an
 inverse agonist in black lemur (Eulemur macaco) and black-and-white ruffed
 lemur (Varecia variegata). We identified a strepsirrhine-specific amino
 acid substitution responsible for the inverse agonism of arbutin. In a
 food preference test, salicin bitterness was inhibited by arbutin in the
 black lemur. Structural modelling revealed this locus was important for a
 rearrangement of the intracellular end of transmembrane helix 7 (TM7).
 Accordingly, arbutin is the first known natural inverse agonist of TAS2Rs,
 contributing to our understanding of receptor–ligand interactions and the
 molecular basis of the unique feeding habit diversification in lemurs.
 Furthermore, the identification of a causal point mutation suggests that
 TAS2R can acquire functional changes according to feeding habits and
 environmental conditions.
description: Fig1_calcium_assayFig2_behavoural_assayFig3_calcium_assay_mutant282Fig5_calcium_assay_mutant262-282FigS1_IP_assayFigS2_calcium_assay_syntheticFigS3_calcium_assay_screeningFigS4_calcium_assay_mutant_inhibitionFigS6_calcium_assay_mutant262-282
DOI: 10.5061/dryad.5mr5k99
title: Data from: Harvest selection on multiple traits in the wild revealed by aquatic animal telemetry

description: Harvesting can have profound impacts on the ecology and evolution of
 marine populations. However, little is known about the strength and
 direction of fisheries-induced selection acting on multiple traits in the
 wild. Here, we used acoustic telemetry to directly monitor individual
 behavior and fate in an intensively harvested species, the European
 lobster (Homarus gammarus, n = 100), in southern Norway. Overall, 24% of
 the tracked lobsters survived the two-month harvest season within the
 study area. Our results indicated that local survival was not random with
 respect to phenotype. We found no clear support for fisheries-induced
 selection acting directly on body size. However, lobsters with large
 crusher claws relative to their body size, typical of socially dominant
 individuals, appeared at higher risk of being captured in the conventional
 trap fishery. We also detected a fine-scale spatial gradient in survival.
 After accounting for this gradient, individuals displaying larger home
 ranges were more likely to survive the harvest season. Finally, we found
 significant repeatabilities for lobster behavior on a monthly time scale,
 indicating that individual behavioral attributes tended to persist and may
 reflect personality. Our study therefore provides empirical support for
 the need to consider an evolutionary enlightened approach to fisheries
 management that considers the influence of harvest on multiple traits of
 target species.
description: Lobster harvest
 selectionTagging information,
 morphological- and behavioural traits of male European lobster (Homarus
 gammarus) monitoried by acoustic telemetry before and during a trap
 fishery in coastal Skagerrak, SE Norway.lobharvsel_Dryad.xlsx