cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25338/b8z61m
title: Data from: Integrative species delimitation reveals cryptic diversity in the southern Appalachian Antrodiaetus unicolor (Araneae: Antrodiaetidae) species complex

description: Although species delimitation can be highly contentious, the development
 of reliable methods to accurately ascertain species boundaries is an
 imperative step in cataloguing and describing Earth’s quickly disappearing
 biodiversity. Spider species delimitation remains largely based on
 morphological characters; however, many mygalomorph spider populations are
 morphologically indistinguishable from each other yet have considerable
 molecular divergence. The focus of our study, Antrodiaetus unicolor
 species complex which contains two sympatric species, exhibits this
 pattern of relative morphological stasis with considerable genetic
 divergence across its distribution. A past study using two molecular
 markers, COI and 28S, revealed that A. unicolor is paraphyletic with
 respect to A. microunicolor. To better investigate species boundaries in
 the complex, we implement the cohesion species concept and employ multiple
 lines of evidence for testing genetic exchangeability and ecological
 interchangeability. Our integrative approach includes extensively sampling
 homologous loci across the genome using a RADseq approach (3RAD),
 assessing population structure across their geographic range using
 multiple genetic clustering analyses that include STRUCTURE, PCA, and a
 recently developed unsupervised machine learning approach (Variational
 Autoencoder). We evaluate ecological similarity by using large-scale
 ecological data for niche-based distribution modeling. Based on our
 analyses, we conclude that this complex has at least one additional
 species as well as confirm species delimitations based on previous less
 comprehensive approaches. Our study demonstrates the efficacy of
 genomic-scale data for recognizing cryptic species, suggesting that
 species delimitation with one data type, whether one mitochondrial gene or
 morphology, may underestimate true species diversity in morphologically
 homogenous taxa with low vagility.
DOI: 10.5061/dryad.9zw3r22b0
title: Development and testing of a novel Killer-Rescue self-limiting gene drive system in Drosophila melanogaster

description: Here we report the development and testing of a novel self-limiting gene
 drive system, Killer-Rescue, in Drosophila melanogaster. This system is
 composed of an auto-regulated Gal4 Killer (K) and a Gal4-activated Gal80
 Rescue (R). Overexpression of Gal4 is lethal, but in the presence of R
 activation of Gal80 leads to much lower levels of Gal4 and rescue of
 lethality. We demonstrate that with a single 2:1 engineered to wildtype
 release, K drives R through the population and after nine generations more
 than 98% of the population carry R and less than 2% of the population are
 wildtype flies. We discuss how this simple Killer-Rescue gene drive system
 may be readily adapted for population replacement in a human health pest,
 Aedes aegypti, or for population suppression in an agricultural pest,
 Drosophila suzukii.
description: Fly counts, list of fly genotypes, primer sequences and figures
 to accompany paper
description: Data and figures to accompany paper
DOI: 10.5061/dryad.pk0p2ngjp
title: Hard to get, easy to lose: Evolution of mantle photoreceptor organs in bivalves (Bivalvia, Pteriomorphia)

description: Morphologically diverse eyes have evolved numerous times, yet little is
 known about how eye gain and loss is related to photic environment. The
 pteriomorphian bivalves (e.g., oysters, scallops, and ark clams), with a
 remarkable range of photoreceptor organs and ecologies, are a suitable
 system to investigate the association between eye evolution and ecological
 shifts. The present phylogenetic framework was based on amino acid
 sequences from transcriptome datasets and nucleotide sequences of five
 additional genes. In total, 197 species comprising 22 families from all
 five pteriomorphian orders were examined, representing the greatest
 taxonomic sampling to date. Morphological data were acquired for 162
 species and lifestyles were compiled from the literature for all 197
 species. Photoreceptor organs occur in 11 families and have arisen
 exclusively in epifaunal lineages, i.e., living above the substrate, at
 least five times independently. Models for trait evolution consistently
 recovered higher rates of loss over gain. Transitions to crevice-dwelling
 habit appear associated with convergent gains of eyespots in epifaunal
 lineages. Once photoreceptor organs have arisen, multiple losses occurred
 in lineages that shift to burrowing lifestyles and deep-sea habitats. The
 observed patterns suggest that eye evolution in pteriomorphians might have
 evolved in association with light-guided behaviors, such as phototaxis,
 body posture, and alarm responses.
description: Dataset for 197 pteriomorphian species and eight other bivalve
 species, including amino acid sequences (from 277 orthologs in Matrix 2,
 see Lemer et al. 2016) and five additional nucleotide sequences (16S
 rRNA, COI,18S rRNA, 28S rRNA, and Histone H3) available in
 <i>GenBank</i>. All molecular data with respective accession
 numbers are listed in supporting information (Table S1). Alignments were
 performed in MAFFT v7.311 under the L-INS-i method (Katoh and Standley
 2013). The phylogenetic tree file (nexus format) was obtained in a
 partitioned analysis performed in IQ-TREE v1.6.12 (Nguyen et al. 2014)
 under maximum likelihood and the following models of sequence evolution:
 GTR+I+G (for nucleotide sequences) and LG+F+I+G (for amino acid sequences
 from the transcriptome dataset).
DOI: 10.5061/dryad.66t1g1jzc
title: Habitat transitions alter the adaptive landscape and shape phenotypic evolution in needlefishes (Belonidae)

description: Habitat occupancy can have a profound influence on macroevolutionary
 dynamics, and a switch in major habitat type may alter the evolutionary
 trajectory of a lineage. In this study we investigate how evolutionary
 transitions between marine and freshwater habitats affect
 macroevolutionary adaptive landscapes, using needlefishes (Belonidae) as a
 model system. We examined the evolution of body shape and size in marine
 and freshwater needlefishes and tested for phenotypic change in response
 to transitions between habitats. Using micro-computed tomographic (µCT)
 scanning and geometric morphometrics, we quantified body shape, size, and
 vertebral counts of 31 belonid species. We then examined the pattern and
 tempo of body shape and size evolution using phylogenetic comparative
 methods. Our results show that transitions from marine to freshwater
 habitats have altered the adaptive landscape for needlefishes and expanded
 morphospace relative to marine taxa. We provide further evidence that
 freshwater taxa attain reduced sizes either through dwarfism (as inferred
 from axial skeletal reduction) or developmental truncation (as inferred
 from axial skeletal loss). We propose that transitions to freshwater
 habitats produce morphological novelty in response to novel prey resources
 and changes in locomotor demands. We find that repeated invasions of
 different habitats have prompted predictable changes in morphology.
description: from FishBase, evaluated, refined and augmented with museum
 data
DOI: 10.5061/dryad.6wwpzgmv2
title: Protein expression of hepatocellular carcinoma in a fibrotic liver in mice

description: Hepatocellular carcinoma (HCC) is a liver tumor that arises in patients
 with cirrhosis. One of the key players in the progression of cirrhosis to
 HCC is the hepatic stellate cell, which is activated during liver damage.
 Activated stellate cells play an essential role in the pathogenesis of HCC
 by creating a fibrotic micro-environment that sustains tumor growth and by
 producing growth factors and cytokines that enhance tumor cell
 proliferation and migration. We assessed the role of endoplasmic
 reticulum (ER) stress in the cross-talk between hepatic stellate cells and
 HCC-cells. Mice with a fibrotic HCC were treated with the IRE1A-inhibitor
 4mu8C. The oncogenic protein expression was assessed using
 a multiplex proximity extension assay for ninety-two biomarkers
 in the murine exploratory panel (Olink Bioscience, Uppsala, Sweden) in
 liver samples from healthy mice, mice with HCC and mice with HCC treated
 with the IRE1A-inhibitor 4mu8C.
description: Mouse model A chemically induced mouse model
 for hepatocellular carcinoma was used. Briefly, 5-week-oldmale sv129 mice
 received intraperitoneal injections once per week with 35mg/kg bodyweight
 diethylnitrosamine (DEN) diluted in saline. From week 10, mice were
 injected twice per week with 10μg/g bodyweight 4μ8C (Sigma) in saline.
 After 25 weeks mice were euthanized and samples were taken for analysis.
 The following conditions are included in the assay: healthy liver (CTL),
 liver cancer (DEN) and liver cancer treated with 4μ8C (DEN +
 4μ8C) Olink multiplex proximity extension
 assay Liver samples were homogenized in ice-cold RIPA
 containing protease inhibitors (Sigma Aldrich). Homogenates were kept on
 ice for 20–30 min, whilst mixing vigorously to enhance disruption of the
 cell membranes. The homogenates were centrifuged (20 min, 13 000 rpm, 4°C)
 and supernatant containing protein was collected. Supernatant was stored
 at -20°C until protein measurement. Protein concentration was measured
 using the BCA kit (ThermoFisher) and all samples were diluted to 1 mg/mL
 protein in RIPA. Samples from 3 biological replicates per group were
 analyzed with a multiplex proximity extension assay for ninety-two
 biomarkers in the murine exploratory panel (Olink Bioscience, Uppsala,
 Sweden) [30]. Samples were loaded random on the assay plates.
DOI: 10.5061/dryad.9w0vt4bbn
title: The impact of learning opportunities on the development of learning and decision making: an experiment with passerine birds

description: Learning abilities have been shown to be influenced by the developmental
 context, namely through experiments that imposed severe nutritional and/or
 environmental constraints (i.e. lack of enrichment). In contrast, we know
 little on the impact of opportunities for learning on the development of
 cognition in animals, despite that such opportunities are known to
 influence human cognitive development. We exposed young zebra finches
 (Taenopygia guttata) (n=26) to one of three experimental conditions, i.e.
 an environment where (i) the presence of food was predicted by one colour
 cue (associative learning), (ii) a combination of two-colour cues
 (conditional learning), or (iii) colour cues were non-informative
 (control). After conducting two different discrimination tasks, our
 results show that experience with predictive cues can cause increased
 choice accuracy and decision-making speed. Our first learning task showed
 that individuals in the associative treatment outperformed the control
 treatment, while task 2 showed that individuals in the conditional
 treatment shad shorter latencies when making choices compared to the
 control treatment. We found no support for a speed-accuracy trade-off.
 This dataset provides a rare longitudinal and experimental examination of
 the effect of predictive vs non-predictive cues during development on the
 cognition of adult animals.
description: (1) Experience2020: Dataset on 23 (N=23) juvenile zebra finches
 randomly assorted into three different experimental conditions i.e. an
 environment where (i) the presence of food was predicted by one colour cue
 (associative learning), (ii) a combination of two-colour cues (conditional
 learning), or (iii) colour cues were non-informative (control).
 Individuals experienced ~500 choices each with a simple discrimination
 task between a rewarding and non-rewarding feeder. Data includes:
 individual bird information, treatment, trial number, latency to choose,
 and correct choice.   (2) Learning2020: Dataset on
 22 (N=22) zebra finches randomly assorted into three different
 experimental conditions i.e. an environment where (i) the presence of food
 was predicted by one colour cue (associative learning), (ii) a combination
 of two-colour cues (conditional learning), or (iii) colour cues were
 non-informative (control). Individuals experienced ~50 choices for two
 different discrimination tasks. Data includes: individual bird
 information, treatment, trial number, latency to choose, and correct
 choice.
DOI: 10.5061/dryad.t3v71
title: Data from: Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding

description: To manage and conserve biodiversity, one must know what is being lost,
 where, and why, as well as which remedies are likely to be most effective.
 Metabarcoding technology can characterise the species compositions of mass
 samples of eukaryotes or of environmental DNA. Here, we validate
 metabarcoding by testing it against three high-quality standard data sets
 that were collected in Malaysia (tropical), China (subtropical) and the
 United Kingdom (temperate) and that comprised 55,813 arthropod and bird
 specimens identified to species level with the expenditure of 2,505
 person-hours of taxonomic expertise. The metabarcode and standard data
 sets exhibit statistically correlated alpha- and beta-diversities, and the
 two data sets produce similar policy conclusions for two conservation
 applications: restoration ecology and systematic conservation planning.
 Compared with standard biodiversity data sets, metabarcoded samples are
 taxonomically more comprehensive, many times quicker to produce, less
 reliant on taxonomic expertise and auditable by third parties, which is
 essential for dispute resolution.
description: Example_R_scriptExample R script for running the analyses used in the paper.arthropods.env.txtInput file (environmental information) for use with the example R scriptMBCarthropods.txtExample input file for the R script, containing species X site data.RSW2_Test.RR script for a Monte Carlo test to compare whether metabarcode and standard data select similar sets of sites for conservation, given a budget.RSW2SoftwareResults.txtInput dataset for RSW2_Test.R (output from the RSW2 software package)Ailaoshan dataset: all fna and qual filessee Readme file: dryad metadata.txtAilaoshan.1-4.TCA.454Reads.fna.qual.zipAilaoshan_all_Map.txtDanum Valley dataset: all fna and qual filessee Readme file: dryad metadata.txtDanum_Valley.1.2.TCA.454Reads.fna.qual.zipLahadDatu_all_Map.txtThetford dataset: all fna and qual filessee Readme file: dryad metadata.txtThetford.1.2.3.10.TCA.454Reads.fna.qual.zipUK1_all_Map.txtarthropods.txtExample input file for the R script, containing species X site data.
DOI: 10.5061/dryad.5hqbzkh2x
title: The evolution of fossorial locomotion in the transition from tetrapod to snake-like in lizards

description: Dramatic evolutionary transitions in morphology are often assumed to be
 adaptive in a new habitat. However, these assumptions are rarely tested
 because such tests require intermediate forms, which are often extinct. In
 vertebrates, the evolution of an elongate, limbless body is generally
 hypothesized to facilitate locomotion in fossorial and/or cluttered
 habitats. However, these hypotheses remain untested because few studies
 examine the locomotion of species ranging in body form from tetrapod to
 snake-like. Here, we address these functional hypotheses by testing
 whether trade-offs exist between locomotion in surface, fossorial, and
 cluttered habitats in Australian Lerista lizards, which include multiple
 intermediate forms. We found that snake-like species penetrated sand
 substrates faster than more lizard-like species, representing the first
 direct support of the adaptation to fossoriality hypothesis. In contrast,
 body form did not affect surface locomotion or locomotion through
 cluttered leaf litter. Furthermore, all species with hindlimbs used them
 during both fossorial and surface locomotion. We found no evidence of a
 trade-off between fossorial and surface locomotion. This may be either
 because Lerista employed kinematic strategies that took advantage of both
 axial and limb-based propulsion. This, may have led to differential
 occupation of their habitat, facilitating diversification of intermediate
 forms.
description: See README file for more instructions
DOI: 10.5061/dryad.jwstqjq5v
title: Biogeographic divides delineated by the three-step landforms of China and the East China Sea: insights from the phylogeography of Kerria japonica

description: Aim: East Asia exhibits complex geomorphological and climatic
 characteristics. The aim of this study was to test whether the so-called
 three-step landforms of China, together with the East China Sea (ECS),
 have acted to shape specific phylogeographic patterns and affected the
 biogeographic history of the species belonging to the East Asian Flora
 (EAF). Location: China and Japan Taxon: Kerria japonica (L.) DC Methods:
 Three chloroplast DNA (cpDNA) regions and 15 nuclear microsatellite (nSSR)
 loci were sequenced and genotyped in 576/450 individuals of K. japonica.
 Phylogeographical analyses were performed to assess the genetic structure,
 historical gene flow, and demographic history of these individuals, and
 climatic factors were examined to determine their effects on
 phylogeographical breaks. Furthermore, time-calibrated phylogenetic trees
 and ancestral range reconstruction were used to infer the biogeographic
 history of K. japonica. Potential habitats at present and during the last
 glacial maximum (LGM) were identified using ecological niche modelling
 (ENM). Results: Distinct phylogeographical breaks were found across the
 ECS and along the boundary of the three-step landforms of China. Low
 historical gene flow and significant climatic differences were detected in
 each pair of adjacent regions. The results of molecular dating and
 ancestral range reconstruction indicated that K. japonica originated in
 North America during the mid-Miocene (14.76 Ma), and intra-specific
 diversification began in the late Miocene (7.78 Ma). Compared to the
 relatively stable distribution range of Chinese populations, Japanese
 populations experienced range expansion after the LGM in response to
 Quaternary climate change. Main conclusions: Kerria japonica has a complex
 biogeographic history, with a mid-Miocene origin in North America and
 subsequent migration into East Asia via the Bering land bridge. The onset
 of intra-specific diversification was probably associated with Asian
 monsoon intensifications, while exposure to the ECS floor facilitated the
 formation of the Japanese lineage in the late Miocene. The spatiotemporal
 population differentiation on the Chinese mainland demonstrates the
 significant role of biogeographic divides delineated by the three-step
 landforms of China and provides clues to understand the floristic
 regionalization and evolutionary history of plant diversity in East Asia,
 especially with respect to the Hengduan Mountains, Central China, and East
 China.
DOI: 10.15468/dl.9p2e24
title: Occurrence Download

description: A dataset containing 116 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aenictophyton anomalum",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 116 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002225-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kcxfht
title: Occurrence Download

description: A dataset containing 506 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lestodon armatus"
 ]
}

 The dataset includes 506 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002226-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.9zw3r22b1
title: Prioritizing road-kill mitigation areas: a spatially explicit national-scale model for an elusive carnivore

description: Aim: Roads impact wildlife in different ways, among which road mortality
 has been the most studied. Budgets in conservation biology are usually
 small, and macroecological approaches have been employed in recent years
 as the first steps towards guiding management. Carnivores are particularly
 vulnerable to mortality on roads due to their elevated ecological needs
 (low population density, often low fecundity, and relatively large home
 ranges). Our aim was to develop a ranking methodology to prioritize
 specific areas for road-kill mitigation. Location: Continental Italy.
 Methods: We studied 271 occurrences of live polecats (Mustela
 putorius) and 212 polecat road-kill sites. We used the former to generate
 a species distribution model (SDM), and the latter to identify the
 variables that determined the road-kill risk. Habitat suitability was
 derived from a spatial distribution model that combined the polecat
 occurrence data with a set of environmental variables. Prey availability
 was derived from the combination of suitability maps of 26 prey species.
 We used generalized linear modelling to identify the set of variables that
 best explained the occurrence of road-kills. The variables included in the
 best-performing model were combined to produce the road risk map and to
 identify the areas with the highest densities of road sections with
 highest risk. Results: Road-kills were positively associated with the road
 sections with higher broad-leaved forest coverage. The number of
 casualties was found to be higher than expected on the national and
 provincial roads and lower than expected on the local roads. Main
 conclusions: This approach allowed us to identify the 10x10 km cells where
 mitigation actions to prevent road-kills should be prioritized. As
 mitigation actions (wildlife passage construction, fencing) are expensive,
 measures should be prioritized on the specific high-risk road sections
 inside these selected cells, avoiding generalized mitigation plans.
description: <b>Road Risk Model (RRM):</b>We used generalized
 linear modelling to identify the set of variables (Human influence, Water
 courses, Broad-leaved forests, Pastures, Grasslands, Prey availability,
 SDM, Type of road) that best explained the occurrence of road-kills for
 the polecats. The variables included in the best-performing model were
 combined to produce the road risk map and to identify the areas with the
 highest densities of road sections with highest risk.