cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7272/q6n29v5n
title: Supplemental Data: Low bone mineral density in early pubertal transgender/gender diverse youth: Findings from the Trans Youth Care Study

description: Context. Transgender youth may initiate gonadotropin-releasing hormone
 agonists (GnRHa) to suppress puberty, a critical period for bone-mass
 accrual. Low bone mineral density (BMD) has been reported in late-pubertal
 transgender girls prior to gender-affirming therapy, but little is known
 about BMD in early-pubertal transgender youth. Objective. To describe BMD
 in early-pubertal transgender youth. Design. Cross-sectional analysis of
 the prospective, observational, longitudinal Trans Youth Care Study
 cohort. Setting. Four multi-disciplinary academic pediatric gender centers
 in the United States. Participants. Early-pubertal transgender youth
 initiating GnRHa. Main Outcome Measures. Areal and volumetric BMD
 Z-scores. Results. Designated males at birth (DMAB) had below-average BMD
 Z-scores when compared with male reference standards, and designated
 females at birth (DFAB) had below-average BMD Z-scores when compared with
 female reference standards except at hip sites. At least one BMD Z-score
 was &lt; -2 in 30% of DMAB and 13% of DFAB. Youth with low BMD scored
 lower on the Physical Activity Questionnaire for Older Children than youth
 with normal BMD, 2.32 ± 0.71 vs. 2.76 ± 0.61 (p = 0.01). There were no
 significant deficiencies in vitamin D, but dietary calcium intake was
 suboptimal in all youth. Conclusions. In early-pubertal transgender youth,
 BMD was lower than reference standards for sex designated at birth. This
 lower BMD may be explained, in part, by suboptimal calcium intake and
 decreased physical activity – potential targets for intervention. Our
 results suggest a potential need for assessment of BMD in pre-pubertal
 gender-diverse youth and continued monitoring of BMD throughout the
 pubertal period of gender-affirming therapy.
DOI: 10.5061/dryad.3bk3j9kgc
title: Data from: Lowest drought sensitivity and decreasing growth synchrony towards the dry distribution margin of European beech

description: Aim: Climate limits the potential distribution ranges of species.
 Establishment and growth of individuals at range margins is assumed to be
 more limited by extreme events such as drought or frost events than in the
 centre of their range. We explore whether the growth of beech is more
 sensitive to drought towards the dry distribution margin and more
 sensitive to frost towards the cold distribution margin. Furthermore, we
 aim to gain insight into the adaptive potential of beech towards both the
 dry and cold distribution margins. Location: European gradient from the
 dry (Spain) to the cold (Poland, Sweden) distribution margin of beech.
 Taxon: European beech (Fagus sylvatica L.) Methods: We applied a
 range-wide dendroecological study to analyse spatial and temporal trends
 in climate-growth relationships. We further investigated negative growth
 anomalies and growth synchrony towards the range margins. Results: We
 found beech to be drought sensitive across its whole range, except at the
 dry distribution margin. Further, sensitivity to winter temperature was
 not found in the centre or at the cold distribution margin, but at the
 southern distribution margin. Growth synchrony was lower at the dry than
 at the cold distribution margin. Main conclusions: Beech seems to be
 adapted to drought at the dry distribution margin with a high adaptive
 potential indicated by the lowest growth synchrony along the gradient. At
 the cold distribution margin, cold events in winter and spring were less
 important for growth than drought. Still, the importance of spring frost
 for beech growth appears to increase in recent decades. Considering a
 projected north-eastward shift of the distribution range, beech is likely
 facing drought stress in combination with spring frost risk at the cold
 margin which could lead to a hampered range expansion.
DOI: 10.5061/dryad.mkkwh70wm
title: Data from: Nonnative old-field species inhabit early-season phenological niches and exhibit unique sensitivity to climate

description: Native and nonnative plant species can exhibit differences in the timing
 of their reproductive phenology as well as their phenological sensitivity
 to climate. These contrasts may influence species’ interactions and the
 invasion potential of nonnative species; however, a limited number of
 phenology studies expressly consider phenological mismatches among native
 and nonnative species over broad spatial or temporal scales. To fill this
 knowledge gap, we used two complementary approaches: first, we quantified
 the flowering phenology of native and nonnative plants at five old-field
 sites across a spatially extensive range of eastern North America. Second,
 we used herbarium records to compare the sensitivity of flowering and
 fruiting phenology to climate across a 114-year time period in a subset of
 common old field species in southwestern Pennsylvania. Across the study
 region, nonnatives reproduced substantially earlier in the growing season
 than natives, suggesting that nonnatives occupy a unique phenological
 niche (0.55 months earlier flowering across the North American study
 sites; 50.1 days earlier flowering and 17.5 days earlier fruiting in
 southwestern Pennsylvania). Both natives and nonnatives advanced their
 reproductive phenology between 1900 to 2014 but exhibited contrasting
 phenological sensitivity to climate factors. During the flowering stage of
 phenology, nonnatives were more sensitive to changes in precipitation than
 natives and generally delayed flowering in wetter years.
  Nonnative plants had greater sensitivity and advanced fruiting
 when the month preceding fruiting was warmer while native plants had
 greater sensitivity and advanced fruiting when the three-month period
 preceding fruiting was warmer. Our findings suggest that nonnative
 old-field species occupy an earlier phenological niche relative to native
 species, which may facilitate their invasion into old-field communities.
 However, given the different sensitivities of native and nonnative plants
 to climate factors, present-day patterns of phenology are likely to shift
 with future climate changes, potentially leading to novel species
 interactions that may influence the outcomes of invasion.
description: See methods of the associated manuscript and the attached ReadMe
 file.
description: See ReadMe file for more information about datasets.
 <strong>Flowering_Phenology_Survey: </strong>Survey
 of flowering phenology of eastern North American old-field
 plants.
 <strong>FINAL_Herbarium_Phenology:</strong> Herbarium
 records used for final analysis (duplicate records removed)
 <strong>RAW_Herbarium_Phenology:</strong> Herbarium
 records, pre-cleaning <strong>Temperature_Data:
 </strong>Monthly temperature records 
 <strong>Precipitation_Data: </strong>Monthly
 precipitation records
DOI: 10.5061/dryad.p8cz8w9mh
title: Do alignment and trimming methods matter for phylogenomic (UCE) analyses?

description: Alignment is a crucial issue in molecular phylogenetics because different
 alignment methods can potentially yield very different topologies for
 individual genes. But it is unclear if the choice of alignment methods
 remains important in phylogenomic analyses, which incorporate data from
 dozens, hundreds, or thousands of genes. For example, problematic biases
 in alignment might be multiplied across many loci, whereas alignment
 errors in individual genes might become irrelevant. The issue of alignment
 trimming (i.e. removing poorly aligned regions or missing data from
 individual genes) is also poorly explored. Here, we test the impact of 12
 different combinations of alignment and trimming methods on phylogenomic
 analyses. We compare these methods using published phylogenomic data from
 ultraconserved elements (UCEs) from squamate reptiles (lizards and
 snakes), birds, and tetrapods. We compare the properties of alignments
 generated by different alignment and trimming methods (e.g., length,
 informative sites, missing data). We also test whether these datasets can
 recover well-established clades when analyzed with concatenated (RAxML)
 and species-tree methods (ASTRAL-III), using the full data (~5,000 loci)
 and subsampled datasets (10% and 1% of loci). We show that different
 alignment and trimming methods can significantly impact various aspects of
 phylogenomic datasets (e.g. length, informative sites). However, these
 different methods generally had little impact on the recovery and support
 values for well-established clades, even across very different numbers of
 loci. Nevertheless, our results suggest several “best practices” for
 alignment and trimming. Intriguingly, the choice of phylogenetic methods
 impacted the results most strongly, with concatenated analyses recovering
 significantly more well-established clades (with stronger support) than
 the species-tree analyses.
DOI: 10.15468/dl.xuaqj5
title: Occurrence Download

description: A dataset containing 2343 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Astragalus canadensis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 2343 records from 138 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002378-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7291/d1j66x
title: Año Nuevo Island Animal Count: analyzing citizen science pinniped counts from drone imagery

description: Fluctuations in marine mammal abundance can reveal changes in local
 ecosystem health and inform conservation strategies. Unmanned aircraft
 systems (UAS) such as drones are increasingly being used to photograph and
 count marine mammals in remote locations; however, counting animals in
 images is a laborious task. Crowd-sourced science has the potential to
 considerably reduce the time required to conduct these censuses but must
 first be validated against expert counts to confirm accuracy. Our
 objectives were to examine the citizen science counts for accuracy,
 identify costs and benefits of drone imagery and citizen science for
 pinniped censuses, and make recommendations for future uses of the data.
 We obtained and uploaded drone imagery of Año Nuevo Island in California
 to a custom citizen science website (sealcount.com) that instructed
 volunteers to count seals and sea lions. Across 212 days, over 1,500
 volunteers counted northern elephant seals, harbor seals, California sea
 lions, and Steller sea lions in 90,000 photographs. We created five simple
 algorithms to extract one count per photograph from the crowd-sourced data
 and then analyzed each algorithm for accuracy by comparing to expert
 counts. We found that the median was the most accurate metric for
 extracting counts of seals but not sea lions. Volunteers consistently
 underestimated sea lions, so removing minimum values was the best strategy
 for extracting accurate counts of sea lions. We also found that while
 citizen scientists were able to accurately count adult seals, their
 accuracy was lower during pupping season, when small pups were present but
 difficult to detect. With proper precautions, citizen science saves money,
 labor, and time, while producing large amounts of accurate data that can
 be used to analyze a suite of biological patterns. Future applications
 include analyses of geo-spatial patterns within and between species,
 quantifying interspecific niche partitioning, and life history phenology.
DOI: 10.5061/dryad.n8pk0p2s8
title: Evolution in novel environments: do restored prairie populations experience strong selection?

description: When populations colonize new habitats, they are likely to experience
 novel environmental conditions, and as a consequence may experience strong
 selection. While selection and the resulting evolutionary responses may
 have important implications for establishment success in colonizing
 populations, few studies have estimated selection in such scenarios. Here
 we examined evidence of selection in recently established plant
 populations in two prairie restorations in close proximity (&lt; 15 km
 apart) using two approaches: 1) we tested for evidence of past selection
 on a suite of traits in two Chamaecrista fasciculata populations by
 comparing the restored populations to each other and their shared source
 population in common gardens to quantify evolutionary responses and 2) we
 measured selection in the field. We found evidence of past selection on
 flowering time, specific leaf area, and root nodule production in one of
 the populations, but detected contemporary selection on only one trait
 (plant height). Our findings demonstrate that while selection can occur in
 colonizing populations, resulting in significant trait differences between
 restored populations in less than 6 generations, evolutionary responses
 differ across even nearby populations sown with the same source
 population. Because contemporary measures of selection differed from
 evolutionary responses to past selection, our findings also suggest that
 selection likely differs over the early stages of succession that
 characterize young prairies.
DOI: 10.15468/dl.t4cs66
title: Occurrence Download

description: A dataset containing 170232 records in GBIF matching the query:
SELECT
 '432' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 41.89415215079384
 AND decimalLatitude &lt;= 46.479780028101516
 AND decimalLongitude &gt;= -88.12157328514692
 AND decimalLongitude &lt;= -77.9229717807129
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 170232 records were derived from 257 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002365-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.jwstqjq69
title: The origin of the parrotfish species Scarus compressus in the Tropical Eastern Pacific: region-wide hybridization between ancient species pairs

description: Background: An increasing number of hybrid zones with varying
 evolutionary outcomes have been documented from different reef fish
 families. In the Tropical Eastern Pacific (TEP), four species of
 parrotfishes occur in sympatry on rocky reefs from Baja California to
 Ecuador: Scarus. compressus,S. ghobban, S. perrico,
 and S. rubroviolaceus; and have complex phylogeographic
 histories. The most divergent,S. perrico, belongs to a Tropical American
 clade that diverged from a Central Indo-Pacific ancestor in the late
 Miocene (6.6 Ma). We tested the hypothesis that S. compressuswas
 the result of ongoing hybridization among the other three species by
 sequencing four nuclear markers and a mitochondrial locus in samples
 spanning 2/3 of the latitudinal extent of the TEP. 
 Results: A structure model of all samples indicated that K=3 was
 the best fit to the nuclear data and that individuals identified
 as S. compressushad admixed assignment values (Q). Power analyses
 indicated our data could correctly detect and assign pure adults and F1
 hybrids with &gt; 0.90 probability, and correct assignment of F2 was
 also high in some cases. NewHybrids models revealed that 89.8% (n= 59) of
 the Scarus compressus samples were F1 hybrids of crosses
 between divergent species pairs: S.
 perrico × S. ghobbanand S.
 perrico × S. rubroviolaceus.
 Similarly, S.ghobban and S. rubroviolaceuswere
 also hybridizing, with ½ of the admixed individuals assigned to F1 hybrids
 and the remainder likely deep generation hybrids. We observed strong
 mito-nuclear discordance in all three hybrid pairs, but found little
 evidence for accelerated mt vs. nuclear evolution in the paternal species.
 Bayesian analysis of Migrate models favours gene flow between S.
 perricoand S. ghobban, but not other species pairs. 
 Conclusions: Mating between species whose ancestors diverged in
 the late Miocene is giving rise to region wide, hybrid complex,
 characterized by a high frequency of parental and F1 genotypes but a low
 frequency of deep generation hybrids. Trimodal structure, combined with
 reproductive evidence for fertility of both male and female F1 hybrids,
 suggest that fitness declines sharply in later generation hybrids. In
 contrast, the hybrid population of the two younger species had similar
 frequencies of F1 and &gt; F1 hybrids. These differences are
 consistent with a model of accelerating post-mating incompatibility with
 time. Mitochondrial genotypes in hybrids, suggests indiscriminate mating
 by male S. perricois driving pre-zygotic breakdown, which may
 reflect the isolation of this endemic species in the TEP for millions of
 years and weak selection for conspecific mate recognition. Despite
 overlapping habitat use, high rates of hybridization, and evidence for
 historical gene flow, species boundaries are maintained by post-mating
 processes in this complex.
DOI: 10.5061/dryad.r4xgxd28x
title: Data from: Characterization of rhizome transcriptome and identification of a rhizomatous ER body in the clonal plant Cardamine leucantha

description: The rhizome is a plant organ that develops from a shoot apical meristem
 but penetrates into belowground environments. To characterize the gene
 expression profile of rhizomes, we compared the rhizome transcriptome with
 those of the leaves, shoots and roots of a rhizomatous Brassicaceae plant,
 Cardamine leucantha. Overall, rhizome transcriptomes were characterized by
 the absence of genes that show rhizome-specific expression and expression
 profiles intermediate between those of shoots and roots. Our results
 suggest that both endogenous developmental factors and external
 environmental factors are important for controlling the rhizome
 transcriptome. Genes that showed relatively high expression in the rhizome
 compared to shoots and roots included those related to belowground
 defense, control of reactive oxygen species, and cell elongation under
 dark conditions. A comparison of transcriptomes further allowed us to
 identify the presence of an ER body, a defense-related belowground
 organelle, in epidermal cells of the C. leucantha rhizome, which is the
 first report of ER bodies in rhizome tissue.
description: The reference transcriptome sequences file of <em>Cardamine
 leucantha</em>.
DOI: 10.5061/dryad.1jwstqjrs
title: Data from: An integrative phylogenomic approach to elucidate the evolutionary history and divergence times of Neuropterida (Insecta: Holometabola)

description: Background The latest advancements in DNA sequencing technologies have
 facilitated the resolution of the phylogeny of insects, yet parts of the
 tree of Holometabola remain unresolved. The phylogeny of Neuropterida has
 been extensively studied, but no strong consensus exists concerning the
 phylogenetic relationships within the order Neuroptera, and the timeline
 of diversification of thelineages of Neuropterida. Here, we assembled a
 novel transcriptomic dataset to address previously unresolved issues in
 the phylogeny of Neuropterida and to infer divergence times within the
 group. We tested the robustness of our phylogenetic estimates by comparing
 summary coalescent and concatenation-based phylogenetic approaches and by
 employing different quartet-based measures of phylogenomic incongruence,
 combined with data permutations. Results Our results suggest that the
 order Raphidioptera is sister to Neuroptera + Megaloptera. Coniopterygidae
 was inferred as sister to all remaining neuropteran families, indicating
 that larval cryptonephry could be a ground plan feature of Neuroptera. A
 clade that includes Nevrorthidae, Osmylidae, and Sisyridae (i.e.
 Osmyloidea) was inferred as sister to all other Neuroptera except
 Coniopterygidae. Dilaridae was placed as sister to all remaining families
 except Coniopterygidae and Osmyloidea. Ithonidae was inferred as sister
 group to monophyletic Myrmeleontiformia. The phylogenetic affinities of
 Chrysopidae and Hemerobiidae were dependent on the data type analyzed, and
 quartet-based analyses showed only weak support for the placement of
 Hemerobiidae as sister to Ithonidae + Myrmeleontiformia. Our molecular
 dating analyses suggest that most families of Neuropterida started to
 diversify in the Jurassic, while the common ancestor of extant
 Neuropterida was estimated to have lived in the middle of the
 Carboniferous. Conclusion Our extensive phylogenomic analyses consolidate
 several aspects in the backbone phylogeny of Neuropterida, such as the
 basal placement of Coniopterygidae within Neuroptera and the monophyly of
 Osmyloidea. Furthermore, they provide new insights into the timing of
 diversification of Neuropterida. Despite the vast amount of analyzed
 molecular data, we found that certain nodes in the tree of Neuroptera are
 not robustly resolved. Therefore, we emphasize the importance of
 integrating the results of morphological analyses with those of
 sequence-based phylogenomics. We also suggest that comparative analyses of
 genomic meta-characters should be incorporated into future phylogenomic
 studies of Neuropterida.
description: Supplementary data deposited on DRYAD and README of the study
 <strong>Vasilikopoulos <em>et al.</em>
 (2020)</strong>: An integrative phylogenmic approach to elucidate
 the evolutionary history and divergence times of Neuropterida (Insecta:
 Holometabola). BMC
 Evolutionary Biology. DOI: 10.1186/s12862-020-01631-6.