cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.wpzgmsbk8
title: Phylogeny and biogeography of Fagus (Fagaceae) based on 28 nuclear single/low‐copy loci

description: Fagus L. is a key component in temperate deciduous broadleaf forests of
 the Northern Hemisphere. However, its biogeographic history has not been
 examined under the framework of a fully resolved and reasonably
 time-calibrated phylogeny. In this study, we sequenced 28 nuclear
 single/low-copy loci (18,555 bp in total) of 11 Fagus species/segregates
 and seven outgroups. Phylogenetic trees were reconstructed using both
 concatenation-based (ML, MP, BI) and coalescent-based methods (StarBEAST2,
 ASTRAL). The monophyly of two subgenera (Fagus and Engleriana) and most
 sections was well supported, except for sect. Lucida, which was
 paraphyletic with respect to sect. Longipetiolata. We also found a major
 phylogenetic conflict among North American, East Asian and West Eurasian
 lineages of subgen. Fagus. Three segregates that have isolated
 distribution (F. mexicana, F. multinervis, and F. orientalis) were
 independent evolutionary units. Biogeographic analysis with fossils
 suggested that Fagus could have originated in North Pacific region in late
 Early Eocene. Major diversifications coincided with a climate aberration
 at the Eocene/Oligocene boundary and the global cooling since Mid-Miocene.
 The Late Miocene accelerated global cooling and the Pleistocene
 glaciations would have driven beeches into East Asia, North America and
 West Eurasia. Meanwhile, range reduction and extinction in high latitudes,
 in central Asia and in western North America converged to form beech
 modern distribution pattern. This study provides a first attempt to
 disentangle the biogeographic history of beeches in the context of a
 nearly resolved and time-calibrated phylogeny, which may shed new insights
 into the formation of the temperate biome in the Northern Hemisphere.
description: Total genomic DNA was isolated from silica-gel dried leaves,
 using a modified CTAB protocol. Twenty-eight nuclear loci were
 successfully amplified using the primers designed in this paper. All PCR
 reactions were performed in a volume of 25 μL, including 1 μl 40–100 ng of
 template DNA, 22 μl 1.1×T3 Super PCR Mix (Tsingke, Beijing), 1 μl 10 μM of
 each primer. The PCR programs for all 28 loci were as follows: 98 ℃ for 3
 min; 30 cycles at 98 ℃ for 10 s, 50–60 ℃ for 10 s, 72 ℃ for 15 s; followed
 by a single cycle at 72 ℃ for 2 min; finally stopped at 10 ℃. The PCR
 products were sequenced on an ABI 3730XL sequencer (Applied Biosystems,
 Foster City, CA, USA) using the PCR primers. The fragments with
 heterozygous sites were sequenced bidirectionally. New sequences generated
 in this study were deposited in GenBank (under accession numbers
 MT727083–MT729360). The orthologous sequences in seven published
 genomes,<i>C. mollissima</i>, <i>Quercus suber
 </i>L., <i>Q. robur</i> L., <i>Q. lobata</i>
 Née and <i>F. sylvatica</i>, were extracted using Blastn
 algorithm. All sequences of a locus were aligned using the online service
 MAFFT.
DOI: 10.5061/dryad.1rn8pk0s0
title: Towards a taxonomically unbiased EU Biodiversity Strategy for 2030

description: Through the Habitats Directive (92/43/EEC) and the LIFE projects financial
 investments, Europe has been the world’s experimental arena for biological
 conservation. With an estimated budget of €20 billion/year, the EU
 Biodiversity Strategy for 2030 has set an ambitious goal of reaching 30%
 Protected Areas and ensure no deterioration in conservation trends and
 status of all protected species. We analyzed LIFE projects focused on
 animals from 1992 to 2018 and we found that investment towards vertebrates
 has been six times higher than that for invertebrates (€970 vs €150
 million), with birds and mammals alone accounting for 72% species and 75%
 total budget. Budget allocation is primarily explained by species’
 popularity. We propose a roadmap to achieve unbiased conservation targets
 for 2030 and beyond.
description: We extracted information on the amount of funding allocated to various species using the LIFE projects database (https://ec.europa.eu; accessed between February and May 2020). Note that we focused here on a species-level conservation approach [9], in contrast to other more general conservation measures (such as socio-ecological approaches [15,16] and others [17]) that are only indirectly covered by LIFE projects. We first filtered LIFE projects specifically aimed at species conservation, using the query STRAND = “All”; YEAR = “All”; COUNTRY = “All”; THEMES = “Species”; SUB-THEMES = “Amphibians”; “Birds”; “Fish”; “Invertebrates”; “Mammals”; “Reptiles”. This query resulted in 819 LIFE projects that met the search criteria. A second query focused on THEMES = “Biodiversity issues”; SUB-THEMES = “Ecological coherence”; “Invasive species”; “Urban biodiversity”, which matched an additional 298 LIFE projects. For the latter query, we examined summaries of the LIFE projects and extracted further information only from those specifically aimed at the conservation of animal species (n = 16). For example, projects aimed at generically enhancing biodiversity through measures targeting ecosystems or the impacts of anthropic activities were not considered. In total, we included 835 projects in our analyses—819 with the theme “Species” and 16 with the theme “Biodiversity issues”. To define the amount of funds allocated to each species for each LIFE project, the budget of each project with multiple species was divided equally among the target species. To obtain a deeper understanding of the factors underlying the observed pattern of conservation measures among species, we further associated traits to each species (risk of extinction, body size, and online popularity). See main text for details.
description: Data: Tab-delimited .csv file (See R script
 for the description of relevant columns.)
 Code: .R file
DOI: 10.5061/dryad.tqjq2bvxg
title: Global & Community Health: Implementation of and patient satisfaction with the first neurologic telemedicine program in Mexico during COVID-19

description: Since the coronavirus disease 2019 (COVID-19) pandemic outbreak, due to
 the large number of patients requiring in-hospital care, hospitals
 worldwide were converted into COVID-19 referral centers. In addition, as
 part of the mitigation strategies besides social distancing and mandatory
 use of facemasks, other measures to reduce the risk of infection among
 healthcare workers such as increasing the time between work shifts and
 sending high-risk personnel to in-home isolation were taken, leading to a
 significantly reduced workforce, requiring relocation of medical personnel
 from multiple specialties to the frontline.  By April 2020, due
 to the reduction of medical and administrative staff in addition to the
 steadily increasing number of patients, our center decided to stop all
 face-to-face non-COVID-19 consultations. Therefore, we decided to adapt to
 the challenges and started researching how to implement a teleneurology
 program to re-open our neurology continuity clinic. Here, we describe our
 experience developing and implementing a teleneurology program in Mexico
 and patient satisfaction with our program. To assess patient satisfaction
 and quality of the healthcare received, at the end of the consultations,
 to those who had internet access, we sent via e-mail or text message an
 anonymous 24-question online-based questionnaire (modified for the
 COVID-19 pandemic) developed and validated for the Spanish-speaking
 population. We included 304 patients. The most common neurologic disorders
 we attended were neuromuscular disorders in 33.6% of patients, headache
 disorders in 32.9%, epilepsy in 11.5%, cerebrovascular diseases in 5.9%,
 and movement disorders in 5.6%. None of the patients required an in-person
 visit. Of the 304 patients, only 125 (41%) answered the survey, 86.4%
 preferred teleneurology instead of an in-person consultation, 83.3%
 (90/108) of them because of concerns about getting COVID-19; 92%
 completely agree that they felt comfortable when talking to the
 neurologist through a camera and a microphone; 96% reported being
 satisfied with their consultation; 87.2% completely agree in trusting that
 their privacy would be protected. However, 4% were not satisfied, but
 their reasons were not specified. Our findings suggest that telemedicine
 is a feasible and acceptable option to continue with neurological patient
 care during the COVID-19 pandemic.
DOI: 10.5061/dryad.2ngf1vhm8
title: Data supporting Fear of sex: Sexual conflict exposed as avoidance in a parthenogenetic invertebrate

description: Males and females often have divergent evolutionary interests, generating
 sexual conflicts. This is particularly true in organisms that exhibit
 facultative sexuality, whereby females are capable of reproducing
 without fitness costs of mating. Here we provide the first documented
 evidence with quantitative tracking showing that sex interacts with social
 context to determine space-use of females, in a pattern resembling
 predator avoidance. To achieve this, we labeled Daphnia
 magna with fluorescent nanoparticles and utilized a 3-D tracking
 platform to record pairs of individuals swimming. The recordings comprised
 either same-sex or opposite-sex pairings. We found that females swam
 faster, deeper, more horizontally and more linearly when exposed to males
 than when exposed to females. Simultaneously, we found that male behavior
 did not differ depending on swimming partner and, importantly, we observed
 no sexual dimorphism in swimming behaviors when swimming with the same
 sex. Our results suggest that the presence of males in a population has
 the potential to influence the distribution of individuals, similarly to
 known threats, such as predation. This highlights that sexual conflict has
 clear spatial consequences and should be considered in such ecological
 frameworks, like the Landscape of Fear (LOF) concept. In a broader
 context, the connection of the evolutionary and social concept of sexual
 conflict and the ecological concept of LOF may improve our understanding
 of population dynamics and the spatial and temporal distribution of
 individuals in natural ecosystems.
description: We recommend to see the Methods section and Supplementary
 Information of the corresponding paper which details the data acquisition
 and handling.
description: For detailed information regarding the datasets, please refer to
 the Fear_of_Sex_data_readme.txt file.
DOI: 10.5061/dryad.1c59zw3t6
title: Developmental instability and phenotypic evolution in a small and isolated bear population

description: We explored fluctuating asymmetry (FA) and morphological integration (MI)
 in the skull of the small, highly inbred and divergent Apennine bear
 (Ursus arctos marsicanus), to explore its uniqueness and investigate any
 potential effects of inbreeding depression. We used 3d geometric
 morphometrics contrasting 17 Apennine bears with other two large outbred
 bear populations (22 from Scandinavia and 9 from Kamchatka) as controls.
 Shape divergence and variability were explored by a PCA on aligned
 coordinates of 39 landmarks. Procrustes ANOVA, morphological disparity,
 and the Global Integration (GI) index were performed both to detect FA and
 to quantify shape variance and degree of MI. By remarking that Apennine
 bears share a highly divergent phenotype, we recorded the highest FA and
 deviation from self-similarity compared to the other two control
 populations. We conclude that Apennine bears are likely facing
 developmental instability as a consequence of inbreeding depression,
 whereas the divergent trait covariance pattern may represent a potential
 source of evolutionary novelties. We discuss the implications for the
 conservation and management of this imperiled taxon.
description: Thirty-nine 3d landmarks were collected on 3D models (from photgrammetry and CT scans) using the software Meshlab
description: <strong>Rscript, landmark
 coordinates:</strong> marsicano3D.csv
 # raw landmark coordinates Loy_et_al_Rcode.R #R code
 for GMM analysis  Land.symm.csv   # matrix
 containing matched pairs of symmetric landmarks
 orsolinks.csv   # matrix defining links between
 landmarks
DOI: 10.5061/dryad.fxpnvx0q3
title: Rapid beard darkening predicts contest outcome, not copulation success, in bearded dragon lizards

description: Rapid colour change is widespread in animals and allows them to respond
 dynamically to the physical and social environment. However, few studies
 have examined the information conveyed by dynamic colour signals in
 different social contexts, such as courtship and rivalry contests.
 Furthermore, dynamic colour change on different body regions may be
 subject to different selection pressures and therefore serve different
 functions. We tested whether male colour or colour change
 predict contest outcome in male-male interactions, or the
 likelihood of copulation attempts in male-female interactions in the
 central bearded dragon, Pogona vitticeps. The extent of beard
 darkening strongly predicted contest outcome, but neither colour (beard,
 dorsal) nor colour change predicted copulation attempts. Dorsal
 colour showed little consistent change and did not predict contest outcome
 or copulation attempts. Previous work shows that dorsal but not
 beard colour change occurs in response to both background colour and
 temperature in the laboratory and in the wild. Taken together,
 these results indicate that dynamic colour change in bearded dragons
 varies in relation to social context and can serve different functions
 depending on the body region. Our data add to the growing
 appreciation of how rapid colour change enables animals to accommodate the
 multiple functions of colour, including communication to different
 receivers, camouflage and thermoregulation.
DOI: 10.5061/dryad.4mw6m9086
title: Genome-scale target capture of mitochondrial and nuclear environmental DNA from water samples

description: Environmental DNA (eDNA) provides a promising supplement to traditional
 sampling methods for population genetic inferences, but current studies
 have almost entirely focused on short mitochondrial markers. Here, we
 develop one mitochondrial and one nuclear set of target capture probes for
 the whale shark (Rhincodon typus) and test them on seawater samples
 collected in Qatar to investigate the potential of target capture for
 eDNA-based population studies. The mitochondrial target capture
 successfully retrieved ~235x (90x-352x per base position) coverage of the
 whale shark mitogenome. Using a minor allele frequency of 5%, we find 29
 variable sites throughout the mitogenome, indicative of at least five
 contributing individuals. We also retrieved numerous mitochondrial reads
 from an abundant non-target species mackerel tuna (Euthynnus affinis),
 showing a clear relation between sequence similarity to the capture probes
 and the number of captured reads. The nuclear target capture probes
 retrieved only few reads and polymorphic variants from the whale shark,
 but we successfully obtained millions of reads and thousands of
 polymorphic variants with different allele frequencies from E. affinis. We
 demonstrate that target capture of complete mitochondrial genomes and
 thousands of nuclear loci is possible from aquatic eDNA samples. Our
 results highlight that careful probe design, taking into account the range
 of divergence between target and non-target sequences as well as presence
 of non-target species at the sampling site, is crucial to consider.
 Environmental DNA sampling coupled with target capture approaches provide
 an efficient means with which to retrieve population genomic data from
 aggregating and spawning aquatic species.
description: This data is the raw sequencing output for a mitochondrial
 capture and a nuclear capture using custom-made myBaits target capture.
 Both captures are based on a single sample (two one-liter eDNA samples
 combined after extraction) collected in Qatari waters in the middle of a
 whale shark aggregation, in an area with an expected high abundance of
 <em>Euthynnus affinis</em>. There is thus no need for
 demultiplexing.  The sequencing was performed on a
 MiSeq with 301 bp PE sequencing. 
description: The mitochondrial target capture data consists of two zipped
 fastq-files (paired-end sequencing):<br>
 "MKRJ_S3_L001_R1_001.fastq.gz" and
 "MKRJ_S3_L001_R2_001.fastq.gz"  The nuclear
 target capture data consists of two zipped fastq-files (paired-end
 sequencing):<br> "M6_S1_L001_R1_001.fastq.gz" and
 "M6_S1_L001_R2_001.fastq.gz"
DOI: 10.15468/dl.e29p4g
title: Occurrence Download

description: A dataset containing 304 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Caryota maxima"
 ]
}

 The dataset includes 304 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002625-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.vmcvdncr7
title: Leaf traits predict water‐use eficiency in U.S. Pacific Northwest grasslands under rain exclusion treatment

description: Does drought stress in temperate grasslands alter the relationship between
 plant structure and function? Here we report data from an experiment
 focusing on growth form and species traits that affect the critical
 functions of water‐ and nutrient‐use efficiency in prairie and pasture
 plant communities. A total of 139 individuals of 12 species (11 genera and
 four families) were sampled in replicated plots maintained for three years
 across a 520-km latitudinal gradient in the Pacific Northwest, USA. Rain
 exclusion did not alter the interspecific relationship between foliar
 traits and stoichiometry or intrinsic water‐use efficiency (iWUE). Rain
 exclusion reduced iWUE in grasses, and effect was primarily
 species‐specific, although leaf morphology, life history strategy, and
 phylogenetic distance predicted iWUE for all 12 species when analyzed
 together. Variation in specific leaf area explained most of the variation
 in iWUE between different functional groups, with annual forbs and annual
 grasses at opposite ends of the resource‐use spectrum. Our findings are
 consistent with expected trait‐driven tradeoffs between productivity and
 resource‐use efficiency and provide insight into strategies for the
 sustainable use and conservation of temperate grasslands.
DOI: 10.5061/dryad.vx0k6djq6
title: V374A KCND3 pathogenic variant associated with paroxysmal ataxia exacerbations

description: Objective Ataxia channelopathies share common features such as slow motor
 progression and variable degrees of cognitive dysfunction. Mutations in
 KCND3, encoding the K+ channel, Kv4.3, are associated with spinocerebellar
 ataxia 19 (SCA19), allelic with spinocerebellar ataxia 22 (SCA22).
 Mutations in KCNC3, encoding another K+ channel, Kv3.3, cause
 spinocerebellar ataxia 13 (SCA13). First, a comprehensive phenotype
 assessment was carried out in a family with autosomal dominant ataxia
 harboring two genetic variants in KCNC3 and KCND3. In order to evaluate
 the physiological impact of these variants on channel currents, in vitro
 studies were performed. Methods Clinical and psychometric evaluations,
 neuroimaging, and genotyping of a family (mother and son) affected by
 ataxia were carried out. Heterozygous and homozygous Kv3.3 A671V andKv4.3
 V374A variants were evaluated in Xenopus laevis oocytes using
 two-electrode voltage-clamp. The influence of Kv4 conductance on neuronal
 activity was investigated computationally using a Purkinje neuron model.
 Results The main clinical findings were consistent with adult-onset ataxia
 with cognitive dysfunction, and acetazolamide (ACZ)-responsive paroxysmal
 motor exacerbations in the index case. Despite cognitive deficits, FDG-PET
 displayed hypometabolism mainly in the severely atrophic cerebellum.
 Genetic analyses revealed the new variant c.1121T&gt;C (V374A), in
 KCND3 and c.2012T&gt;C (A671V) in KCNC3. In vitro electrophysiology
 experiments on Xenopus oocytes demonstrated that the V374A mutant was
 non-functional when expressed on its own. Upon equal co-expression of WT
 and V374A channel subunits, Kv4.3 currents were significantly reduced in a
 dominant negative manner, without alterations of the gating properties of
 the channel. In contrast, Kv3.3 A671V, when expressed alone, exhibited
 moderately reduced currents compared to WT, with no effects on channel
 activation or inactivation. Immunohistochemistry demonstrated adequate
 cell membrane translocation of the Kv4.3 V374A variant, thus suggesting an
 impairment of channel function, rather than of expression. Computational
 modeling predicted an increased Purkinje neuron firing frequency upon
 reduced Kv4.3 conductance. Conclusions Our findings suggest that Kv4.3
 V374A, is likely pathogenic and associated with paroxysmal ataxia
 exacerbations, a new trait for SCA19/22. The present FDG PET findings
 contrast with a previous study demonstrating widespread brain
 hypometabolism in SCA19/22.
DOI: 10.5061/dryad.cc2fqz64m
title: Lack of phenological shift leads to increased camouflage mismatch in mountain hares

description: Understanding whether organisms will be able to adapt to human-induced
 stressors currently endangering their existence is an urgent priority.
 Globally, multiple species moult from a dark summer to white winter coat
 to maintain camouflage against snowy landscapes. Decreasing snow cover
 duration due to climate change is increasing mismatch in seasonal
 camouflage. To directly test for adaptive responses to recent changes in
 snow cover, we repeated historical (1950s) field studies of moult
 phenology in mountain hares (Lepus timidus) in Scotland. We found little
 evidence that population moult phenology has shifted to align seasonal
 coat colour with shorter snow seasons, or that phenotypic plasticity
 prevented increases in camouflage mismatch. The lack of responses resulted
 in 35 additional days of mismatch between 1950 and 2016. We emphasize the
 potential role of weak directional selection pressure and low genetic
 variability in shaping the scope for adaptive responses to anthropogenic
 stressors.