cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.djh9w0vzz
title: Moving out of town? The status of alien plants in high-Arctic Svalbard, and a method for monitoring of alien flora in high-risk, polar environments

description: Rising human activity in the Arctic, combined with a warming climate,
 increases the probability of the introduction and establishment of alien
 plant species. While settlements are known hotspots for persistent
 populations, little is known about colonization of particularly
 susceptible natural habitats. Systematic monitoring is lacking and
 available survey methods vary greatly. Here we present the most
 comprehensive survey of alien vascular plant species in the high-Arctic
 archipelago of Svalbard to date, aimed at: i) providing a status within
 settlements; ii) surveying high-risk habitats such as those with high
 visitor numbers and nutrient enrichment from sea bird colonies; iii)
 presenting a systematic monitoring method that can be implemented in
 future work on alien plant species in Arctic environments; and iv) discuss
 possibilities for mapping alien plant habitats using Unmanned Arial
 Vehicles (UAVs). The systematic grid survey, covering 1.7km2 over three
 settlements and six bird cliffs, detected 36 alien plant species. Alien
 plant species were exclusively found in areas of human activity,
 particularly areas associated with current, or historic animal husbandry.
 The survey identified the successful eradication of Anthricus sylvestris
 in Barentsburg, as well as the rapid expansion of Taraxacum sect.
 Ruderalia over the last few decades. As there is currently no consistent
 method for monitoring alien plant species tailored to polar environments,
 we propose a systematic methodology that could be implemented within a
 structured monitoring regime as part of an adaptive monitoring strategy
 towards alien species in the Arctic.
DOI: 10.5061/dryad.4qrfj6q94
title: Data from: Pathogenic effect of TP73 gene variants in people with amyotrophic lateral sclerosis

description: Objective: To identify novel disease associated loci for amyotrophic
 lateral sclerosis (ALS), we utilized sequencing data and performed in
 vitro and in vivo experiments to demonstrate pathogenicity of mutations
 identified in TP73. Methods: We analyzed exome sequences of 87 sporadic
 ALS patients and 324 controls, with confirmatory sequencing in independent
 ALS cohorts of &gt;2,800 patients.  For the top hit, TP73, a
 regulator of apoptosis, differentiation, and a binding partner as well as
 homolog of the tumor suppressor gene TP53, we assayed mutation effects
 using in vitro and in vivo experiments.  C2C12 myoblast
 differentiation assays, characterization of myotube appearance, and
 immunoprecipitation of p53-p73 complexes were perform in vitro. 
 In vivo, we used CRISPR/Cas9 targeting of zebrafish tp73 to assay motor
 neuron number and axon morphology. Results: Four heterozygous rare,
 nonsynonymous mutations in TP73 were identified in our sporadic ALS
 cohort. In independent ALS cohorts, we identified an additional 19 rare,
 deleterious variants in TP73.   Patient TP73 mutations
 caused abnormal differentiation and increased apoptosis in the myoblast
 differentiation assay, with abnormal myotube appearance.
  Immunoprecipitation of mutant ΔN-p73 demonstrated that patient
 mutations hinder ΔN-p73’s ability to bind p53.  CRISPR/Cas9
 knockout of tp73 in zebrafish led to impaired motor neuron development and
 abnormal axonal morphology, concordant with ALS pathology. 
 Conclusion: Together, these results strongly suggest that variants in TP73
 correlate with risk for ALS and indicate a novel role for apoptosis in ALS
 disease pathology.
DOI: 10.5061/dryad.0cfxpnw1s
title: Restricted dispersal in a sea of gene flow

description: How far do marine larvae disperse in the ocean? Decades of population
 genetic studies have revealed generally low levels of genetic structure at
 large spatial scales (hundreds of km). Yet this result, which is typically
 based on discrete sampling designs, does not necessarily imply extensive
 dispersal. Here, we adopt a continuous sampling strategy along 950 km of
 coast in the Northwestern Mediterranean Sea to address this question in
 four species. In line with expectations, we observe weak genetic structure
 at large spatial scale. Nevertheless, our continuous sampling strategy
 uncovers a pattern of genetic isolation by distance at small spatial
 scales (few tens of km). Individual-based simulations indicate that this
 signal is an expected signature of restricted dispersal. At the other
 extreme of the connectivity spectrum, two pairs of individuals that are
 closely related genetically were found up to 250 km apart, indicating
 long-distance dispersal. Such a combination of restricted dispersal with
 rare long-distance dispersal events is supported by a high-resolution
 biophysical model of larval dispersal in the study area, and we posit that
 it may be common in marine species. Our results bridge population genetic
 studies with direct dispersal studies and have implications for the design
 of marine reserve networks.
DOI: 10.5061/dryad.280gb5mph
title: Supplementary information for Jones et al., 2021: "Size and shape variation in the calcareous nannoplankton genus Braarudosphaera following the Cretaceous-Paleogene (K/Pg) mass extinction: clues as to its evolutionary success"

description: Calcareous nannoplankton have been one of the dominant primary producers
 in the surface oceans since the late Triassic. The bolide impact at the
 Cretaceous-Paleogene (K/Pg) boundary ~66.0 Ma, led to the elimination of
 &gt; 90% of nannoplankton species: the largest extinction event in
 their evolutionary history.  One of the few nannoplankton genera
 to survive the K/Pg mass extinction and even thrive in its aftermath was
 Braarudosphaera, which precipitates pentagonal calcite plates
 (pentaliths).  The only Braarudosphaera species to span the K/Pg
 boundary (B. bigelowii) is extant, and has formed geographically and
 temporally restricted “blooms” throughout geologic time. Four
 morphologically and genetically distinct cryptic species of B. bigelowii
 have been identified in the modern ocean. However, it is uncertain whether
 these cryptic species have disparate eco-physiological tolerances that
 have allowed them to adapt to varying environmental conditions. For the
 first time, we assess changes in the size and shape of Braarudosphaera
 pentaliths following the K/Pg mass extinction at three geographically and
 environmentally disparate sites that have early Paleocene Braarudosphaera
 blooms. Our results show that different Braarudosphaera morphotypes were
 dominant in the Gulf of Mexico compared to the paleo-Tethys, likely due to
 regional environmental differences. In addition, we provide evidence that
 the dominant Braarudosphaera morphotypes shifted in response to changes in
 upper water column stratification. This ability to rapidly adapt to
 unstable environments likely helped Braarudosphaera thrive in the
 aftermath of the K/Pg extinction, and explains why this lineage has
 enjoyed such a long evolutionary history.
DOI: 10.5061/dryad.63xsj3v1s
title: Joermungandr bolti, an exceptionally preserved microsaur from Mazon Creek, Illinois, reveals patterns of integumentary evolution in Recumbirostra

description: The Carboniferous Pennsylvanian-aged (309-307 Ma) Mazon Creek Lagerstätte
 produces some of the earliest fossils of major Paleozoic tetrapod
 lineages. Recently, several new tetrapod specimens collected from Mazon
 Creek have come to light, including the earliest fossorially-adapted
 recumbirostrans. Here we describe a new long-bodied recumbirostran,
 Joermungandr bolti gen et sp. nov., known from a single part and
 counterpart concretion bearing a virtually complete skeleton. Uniquely,
 Joermungandr preserves a full suite of dorsal, flank, and ventral dermal
 scales, together with a series of thinned and reduced gastralia.
 Investigation of these scales using Scanning Electron Microscopy (SEM)
 reveals ultrastructural ridge and pit morphologies, revealing complexities
 comparable to the scale ultrastructure of extant snakes and fossorial
 reptiles, which have scales modified for body based propulsion and
 shedding substrate. Our new taxon also represents an important early
 record of an elongate recumbirostran bauplan, wherein several features
 linked to fossoriality, including a characteristic recumbent snout, are
 present. We utilized parsimony phylogenetic methods to conduct
 phylogenetic analysis using the most recent recumbirostran-focused matrix.
 The analysis recovers the new taxon within the Cocytinoidea clade as
 sister taxon to all brachystelechids. Finally, we review integumentary
 patterns in Recumbirostra, noting reductions and losses of gastralia and
 osteoderms associated with body elongation and, thus, likely also
 associated with increased fossoriality.
description: Data Matrix.
description: Run in Paup.
DOI: 10.5061/dryad.34tmpg4js
title: A method to evaluate body length of live aquatic vertebrates using digital images

description: Traditional methods to measure body lengths of aquatic vertebrates rely on
 anesthetics, and extended handling times. These procedures can increase
 stress, potentially affecting the animal’s welfare after its release. We
 developed a simple procedure using digital images to estimate body lengths
 of coastal cutthroat trout (Oncorhynchus clarkii clarkii) and larval
 coastal giant salamander (Dicamptodon tenebrosus). Images were
 post-processed using ImageJ2. We measured more than 1,800 individuals of
 these two species from 200 pool habitats along 9.6 river kilometers. The
 percent error (mean ± SE) of our approach compared to the use of a
 traditional graded measuring board was relatively small for all metrics of
 the two species. Total length of trout was -2.2% ± 1.0. Snout-vent length
 and total length of larval salamanders was 3.5% ± 3.3 and -0.6% ± 1.7,
 respectively. We cross-validated our results by two independent observers
 that followed our protocol to measure the same animals and found no
 significant differences (p &gt; 0.7) in body size distributions for
 all metrics of the two species. Our procedure provides reliable
 information of body size reducing stress and handling time in the field.
 The method is transferable across taxa and the inclusion of multiple
 animals per image increases sampling efficiency with stored images that
 can be reviewed multiple times. This practical tool can improve data
 collection of animal size over large sampling efforts and broad
 spatiotemporal contexts.
description: The attached spreadsheet includes the data to conduct the
 analyses shown in the associated manuscript.
DOI: 10.15468/dl.hq4c4x
title: Occurrence Download

description: A dataset containing 91 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-5000.0",
 "TaxonKey is Euphorbia neriifolia"
 ]
}

 The dataset includes 91 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002804-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.k6djh9w5t
title: Genomic distinctness despite shared color patterns among threatened populations of a tiger beetle

description: Conservation biologists have long debated the value of subspecies, which
 are morphologically and geographically identifiable but not necessarily
 evolutionarily distinctive. One example of a controversial subspecies is
 Cicindela formosa gibsoni, a tiger beetle that is nationally listed as
 threatened in Canada and whose taxonomic status is based primarily on its
 unique elytral (forewing) color pattern. To determine whether C. f.
 gibsoni represents one or more genetically distinctive units, we sampled
 14 populations within or near this subspecies’ disjunct North American
 range and assessed their genetic differentiation from neighboring and
 phenotypically distinctive populations of C. f. formosa and C. f.
 fletcheri. Instead of clustering by color pattern, analyses of
 mitochondrial and nuclear markers recovered three geographically
 structured genetic groupings: a northern cluster from Canada, a
 southwestern cluster from northwestern Colorado, and a southeastern
 cluster of US populations east of the Continental Divide. These data,
 coupled with previously documented differences in larval morphology,
 suggest that populations of C. formosa in western Canada and northwestern
 Colorado may have independently evolved similar color patterns. Thus, we
 consider C. f. gibsoni to be endemic to Canada and describe the novel
 subspecies C. f. gaumeri ssp. nov. from northwestern Colorado. Both
 subspecies are evolutionarily significant units, and each deserves
 consideration for conservation listing. Collectively, our results reveal
 general congruence between mitochondrial and nuclear genetic data but
 conflict with color pattern, the conventional basis for subspecies
 designations in tiger beetles.
DOI: 10.5061/dryad.8931zcrq8
title: Community phylogeographic patterns reveal how a barrier filters and structures taxa in North American warm deserts

description: Aim: The study of biogeographic barriers has been instrumental in
 understanding the evolution and distribution of taxa. With the increasing
 availability of empirical datasets, emergent patterns can be inferred from
 communities by synthesizing how barriers filter and structure populations
 across species. We assemble phylogeographic data across a barrier and
 perform spatially-explicit simulations to quantify spatiotemporal patterns
 of divergence, the influence of species traits on these patterns, and the
 statistical power needed to differentiate alternative diversification
 modes. Location: North America Methods: We incorporate published datasets
 to examine taxa around the Cochise Filter Barrier, separating the Sonoran
 and Chihuahuan Deserts of North America, to synthesize phylogeographic
 structuring across the community with respect to organismal functional
 traits. We then use simulation and machine learning to assess the power of
 phylogeographic model selection. Results: Taxa distributed across the
 Cochise Filter Barrier show heterogeneous responses to the barrier in
 levels of gene flow, phylogeographic structure, divergence timing, barrier
 width, and divergence mechanism. These responses correlate with locomotor
 and thermoregulatory traits. Many taxa show a Pleistocene population
 genetic break, often with introgression after divergence. Allopatric
 isolation and isolation-by-environment are the primary mechanisms
 structuring genetic divergence within taxa. Simulations reveal that in
 spatially-explicit isolation-with-migration models across the barrier, age
 of divergence, presence of gene flow, and presence of
 isolation-by-distance can confound the interpretation of evolutionary
 history and model selection by producing easily-confusable results. We
 re-analyze five empirical genetic datasets to illustrate the utility of
 these simulations despite these constraints. Main Conclusions: By
 synthesizing phylogeographic data for the Cochise Filter Barrier we show
 that barriers interact with species traits to differentiate taxa in
 communities over millions of years. Identifying diversification modes
 across the barrier for these taxa remains challenging because commonly
 invoked demographic models may not be identifiable across a range of
 likely parameter space.
DOI: 10.5061/dryad.6t1g1jwz2
title: The transcription factor PagLBD3 contributes to the regulation of secondary growth in Populus

description: Lateral organ boundaries domain (LBD) genes encode plant-specific
 transcription factors that participate in regulating various developmental
 processes. In this study, we genetically characterized PagLBD3 as an
 important regulator of secondary growth in Populus. Overexpression of
 PagLBD3 increased stem secondary growth in Populus with significantly
 higher rate of cambial cells differentiated into phloem, while dominant
 repression of PagLBD3 significantly decreased the rate of cambial cells
 differentiated into phloem. Furthermore, we identified 1756 PagLBD3
 genome-wide putative direct target genes (DTGs) through RNA sequencing
 (RNA-seq) coupled DNA affinity purification followed by sequencing
 (DAP-seq) assays. Gene Ontology analysis revealed that genes regulated by
 PagLBD3 were enriched in biological pathways regulating meristem
 development, xylem development, and auxin transport. Several central
 regulator genes for vascular development, including phloem intercalated
 with xylem (PXY), wuschel related homeobox4 (WOX4), Secondary
 Wall-Associated NAC Domain 1s (SND1-B2) and Vascular-Related NAC-Domain 6s
 (VND6-B1), were identified as PagLBD3 DTGs. Together, our results
 suggested that PagLBD3 and its DTGs form a complex transcriptional network
 to modulate cambium activity and phloem/xylem differentiation.
DOI: 10.5061/dryad.44j0zpcd9
title: Temporal and regional trends of antibiotic use in long-term aged care facilities across 39 countries, 1985-2019: systematic review and meta-analysis

description: Background Antibiotic misuse is a key contributor to antimicrobial
 resistance and a concern in long-term aged care facilities (LTCFs). Our
 objectives were to:  i) summarise key indicators of systemic
 antibiotic use and appropriateness of use, and ii) examine temporal and
 regional variations in antibiotic use, in LTCFs (PROSPERO registration
 CRD42018107125). Methods & Findings Medline and EMBASE were
 searched for studies published between 1990-2021 reporting antibiotic use
 rates in LTCFs. Random effects meta-analysis provided pooled estimates of
 antibiotic use rates (percentage of residents on an antibiotic on a single
 day [point prevalence] and over 12 months [period prevalence]; percentage
 of appropriate prescriptions). Meta-regression examined associations
 between antibiotic use, year of measurement and region.  A total
 of 90 articles representing 78 studies from 39 countries with data between
 1985-2019 were included. Pooled estimates of point prevalence and 12-month
 period prevalence were 5.2% (95% CI: 3.3-7.9; n=523,171) and 62.0% (95%
 CI: 54.0-69.3; n=946,127), respectively. Point prevalence varied
 significantly between regions (Q=224.1, df=7, p&lt;0.001), and ranged
 from 2.4% (95% CI: 1.7-2.7) in Eastern Europe to 9.0% in the British Isles
 (95% CI: 7.6-10.5) and Northern Europe (95% CI: 7.7-10.5). Twelve-month
 period prevalence varied significantly between region (Q=15.1, df-3,
 p=0.002) and ranged from 53.9% (95% CI: 48.3-59.4) in the British Isles to
 68.3% (95% CI: 63.6-72.7) in Australia. Meta-regression found no
 association between year of measurement and antibiotic use prevalence. The
 pooled estimate of the percentage of appropriate antibiotic prescriptions
 was 28.5% (95% CI: 10.3-58.0; n=17,245) as assessed by the McGeer
 criteria. Year of measurement was associated with decreasing
 appropriateness of antibiotic use over time (OR: 0.78, 95% CI:
 0.67-0.91).  The most frequently used antibiotic classes were
 penicillins (n=44 studies), cephalosporins (n=36),
 sulphonamides/trimethoprim (n=31), and quinolones (n=28). 
 Conclusions Coordinated efforts focusing on LTCFs are required to address
 antibiotic misuse in LTCFs. Our analysis provides overall baseline and
 regional estimates for future monitoring of antibiotic use in LTCFs.
  
description: Systematic review with searches conducted in 2021.
DOI: 10.5061/dryad.2rbnzs7n2
title: An empirical test of the bet-hedging polyandry hypothesis: female red flour beetles avoid extinction via multiple mating

description: Bet-hedging via polyandry (spreading the extinction risk of the female’s
 lineage over multiple males) may explain the evolution of female multiple
 mating, which is found in a wide range of animal and plant taxa. This
 hypothesis posits that females can increase their fitness via polyandrous
 mating when “unsuitable” males (i.e., males causing reproductive failure
 for various reasons) are frequent in the population and females cannot
 discriminate such unsuitable mates. Although recent theoretical studies
 have shown that polyandry can operate as a bet-hedging strategy, empirical
 tests are scarce. In the present study, we tested the bet-hedging
 polyandry hypothesis by using the red flour beetle Tribolium castaneum. We
 compared female reproductive success between monandry and polyandry
 treatments when females mated with males randomly collected from an
 experimental population, including 20% irradiated (infertile) males. In
 addition, we evaluated geometric mean fitness across multiple generations
 as the index of adaptability of bet-hedging traits. Polyandrous females
 showed a significantly higher egg hatching rate and higher geometric mean
 fitness than monandrous females. These results strongly support the
 bet-hedging polyandry hypothesis.
DOI: 10.5061/dryad.44j0zpcdb
title: Supplemental material from: Can transcranial direct current stimulation enhance post-stroke motor recovery? Development of a theoretical patient-tailored model

description: New treatments that can facilitate neural repair and reduce persistent
 impairments have significant value in promoting recovery following stroke.
 One technique that has gained interest is transcranial direct current
 stimulation (tDCS) as early research suggested it could enhance plasticity
 and enable greater behavioral recovery. However, several studies have now
 identified substantial inter-subject variability in response to tDCS and
 clinical trials revealed insufficient evidence of treatment effectiveness.
 A possible explanation for the varied and negative findings is that the
 physiological model of stroke recovery that researchers have used to guide
 the application of tDCS based treatments in stroke is overly simplistic
 and does not account for stroke heterogeneity or known determinants that
 affect the tDCS response. Here, we propose that tDCS could have a more
 clearly beneficial role in enhancing stroke recovery if greater
 consideration is given to individualizing treatment. By critically
 reviewing the proposed mechanisms of tDCS, stroke physiology across the
 recovery continuum, and known determinants of tDCS response, we propose a
 new, theoretical, patient-tailored approach to delivering tDCS after
 stroke. The proposed model includes a step-by-step principled selection
 strategy for identifying optimal neuromodulation targets and outlines key
 areas for further investigation. Tailoring tDCS treatment to individual
 neuroanatomy and physiology is likely our best chance at producing robust
 and meaningful clinical benefit for people with stroke and would,
 therefore, accelerate opportunities for clinical translation.