cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q83bk3jfg
title: Data from: Inter-colony variation in foraging flight characteristics of black-headed gulls Chroicocephalus ridibundus during the incubating period

description: Using GPS-loggers, we examined the influence of colony, sex, and bird
 identity on foraging flight characteristics of black-headed gulls
 Chroicocephalus ridibundus during the incubation period. We studied tracks
 of 36 individuals breeding in one urban and two rural colonies in Poland.
 Birds from both rural colonies performed the furthest flights (mean 8-12
 km, up to 27 km) foraging mainly in agricultural areas. Gulls from the
 urban colony performed shorter flights (median 5 km, up to 17 km) visiting
 mainly urbanized areas and water bodies. We found that females performed
 longer flights and their flights parameters were less repeatable compared
 to males. Males from both rural colonies visited water bodies more
 frequently than females. In all colonies males (but not females) used
 habitats unproportionally to their availability in the vicinity.
 Relatively low inter-individual and relatively high intra-individual
 overlap in home ranges indicated considerable foraging site fidelity.
 Individuals specialized in the use of particular type of habitat performed
 shorter foraging flights compared to individuals using diverse habitats
 during their foraging flights. Our results indicate diverse foraging
 strategies of black-headed gulls, including generalists that explore
 various habitats and specialists characterized by high foraging site and
 habitat fidelity.
description: To characterize flights of black-headed gulls breeding in three
 colonies located across Central and Northern Poland during the incubation
 period, we used 18 PinPoint-10 GPS store-on-board loggers (1.3 g, Lotek
 Wireless Inc.) recording time and position. In total, we deployed loggers
 on one pair member from 37 nests (10 at Bydgoszcz, 16 at Koronowo and 11
 at Przykona). We captured birds on nests during the 2nd-4th week of the
 incubation period using spring traps or loops made of nylon
 lines. Loggers were programmed to collect data at 15
 min intervals and were used in 2018: 10-26 May at Bydgoszcz, 28 April - 23
 May at Koronowo, and 19-31 May at Przykona. After about 48 h from logger
 deployment we tried to recapture birds and retrieve tags. We successfully
 recaptured 36 (97.3%) marked birds. A foraging trip was
 defined as a trip with at least three positions recorded with a minimum
 distance of 1 km from the colony. We analysed only flights performed
 during day hours (4:00-23:00), as some individuals from Bydgoszcz colony
 were regularly spending nights on the roofs of buildings in the city
 centre and returning to the colony during the daylight hours.
description: See more details in the file Read_me.txt
DOI: 10.5061/dryad.83bk3j9nn
title: Data from: Fire and grazing controlling a tropical tree line: Effects of long‐term grazing exclusion in Bale Mountains, Ethiopia

description: Aims: Tropical tree lines are often associated with abrupt shifts in
 vegetation, soils and disturbance regimes, but the underlying mechanisms
 are poorly understood. We analysed the role of grazing, fuels and fire in
 maintaining a sharp tree line with flammable heathland above non-flammable
 forest. Location: Bale Mountains, Ethiopia. Methods: Grazing exclosures,
 repeated vegetation sampling, soil analyses and burning and sowing
 experiments along an altitudinal gradient with Hagenia abyssinica forest,
 Erica trimera forest and Erica heathland; all heavily grazed, the latter
 burnt on short rotation. Results: Contrary to expectation, livestock
 exclusion did not increase forest fuel flammability, but instead resulted
 in a dense carpet of non-flammable herbs. In the heathland, livestock
 exclusion led to somewhat faster post-fire fuel recovery, but no major
 vegetation change. Seeding of tree species resulted in some seedling
 establishment, but notably Hagenia grew poorly in the heathland, even when
 protected from livestock. A bioassay, as well as observations of outpost
 trees on atypical soil above the treeline, suggest that this poor growth
 is caused by the acidic soils, rather than harsh climate. Despite frequent
 fires, heathland soils had lower pH and higher organic matter content than
 forest soils. Below the tree line, tree seedling establishment was
 successful only in forest gaps, and if livestock was excluded. In both
 forest and heathland rapid vegetative regeneration in the ground flora
 after disturbance restricted major species shifts. Conclusions: These
 results suggest that the contrasting fire potential between heathland and
 forest, and thus the sharp tree line would be maintained, or possibly even
 accentuated, in the absence of livestock grazing, and that Hagenia
 colonisation upwards into the heathland is restricted not only by fire and
 grazing, but also the acidic soils, a legacy of centuries of Erica
 dominance.
description: Collected by ourselves in the field 2005-2011,processed in Excel
 and Minitab
DOI: 10.5061/dryad.6hdr7sqxc
title: Female-driven intersexual coevolution in beetle genitalia

description: Genital coevolution is a pervasive phenomenon as changes in one sex tend
 to impose fitness consequences on the other generating sexual conflict.
 Sexual conflict is often thought to cause stronger selection on males due
 to the Darwin-Bateman’s anisogamy paradigm. However, recent studies have
 demonstrated that female genitalia may be equally elaborated and perform
 diverse extra-copulatory functions. These characteristics suggest that
 female genitals can also be primary targets of selection, especially where
 natural selection acts on female-exclusive functions such as oviposition.
 Here, we test this hypothesis in a statistical phylogenetic framework
 across the whole beetle (Coleoptera) phylogeny, investigating whether
 coevolution of specific genital traits may be triggered by changes in
 females. We focus on traits of the proctiger, which composes part of the
 male terminalia and the female ovipositor. Our results present a
 comprehensive case of male-female genital coevolution, and provide solid
 statistical evidence for a female-initiated coevolutionary process where
 the vast majority of evolutionary transitions in males have occurred only
 after changes in females. We corroborate the hypothesis that female traits
 may change independently and elicit counter-adaptations in males.
 Furthermore, by showing a consistent pattern across the phylogeny of the
 most diverse group of animals, our results suggest that this female-driven
 dynamics may persist through long time scales.
description: The files herein contain morphological datasets (Baculi.csv and
 Membranization.csv) used for all MCMC modelling procedures and the
 phylogenetic tree inferred in the same work (coleopteraTREE.tre). These
 files allow for replication of all our analyses. Raw morphological
 information were collected from Lawrence et al. (Annales Zoologici, 2011,
 61(1):1-217), then re-coded as two binary traits: (a) proctegier
 membranization (absence/presence) for males and females and (b)
 proctigeral baculi (absence/presence) for males and females. In the
 morphological datasets, "0" denotes absence and "1"
 denotes presence. Please, see the methods section in our paper for
 detailed description of the analytical procedures.
DOI: 10.5061/dryad.zcrjdfn7k
title: Data from: A molecular phylogeny for the genus Coccoloba (Polygonaceae) with an assessment of biogeographic patterns

description: Species in the genus Coccoloba are trees, shrubs, and lianas present in
 low elevation tropical and sub-tropical forests. Since 1756, well over 400
 taxa have been described for Coccoloba. Coccoloba species are natively
 distributed throughout the New World in a variety of habitats. Despite
 being distributed throughout the Neotropics, the concentration of
 Coccoloba species in a given area varies considerably, with four centers
 of diversity for the genus: Southern and Coastal Brazil, the West Indies,
 Mesoamerica, and Amazonia. We here present the first molecular phylogeny
 of Coccoloba and use this phylogeny to investigate geographic patterns of
 diversity within the genus. The topology of the phylogeny and the closest
 related genera to Coccoloba suggest a Mesoamerican origin for the genus.
 The South American species are recovered as the crown group of the
 phylogeny with one instance of a separate migration event from Mesoamerica
 to South America. Coccoloba species in Mesoamerica and the Caribbean show
 little to no geographic pattern to their diversification. Mesoamerica and
 the Caribbean are best considered as one phytogeographic region for
 Coccoloba.
description: Concatenated DNA sequences from three chloroplast regions: rbcL,
 trnL-trnF, psbA-trnH. Sanger sequences generated from DNA extracted from
 leaf tissue. Raw sequences were aligned using MUSCLE and trimmed using
 MESQUITE.  
description: Final sequence alignment. This is a NEXUS file format.
DOI: 10.5061/dryad.37pvmcvg9
title: Data from: Friction of Longmaxi shale gouges and implications for seismicity during hydraulic fracturing

description: Longmaxi formation shales are the major target reservoir for shale gas
 extraction in the Sichuan Basin, southwest China. Swarms of earthquakes
 accompanying hydraulic fracturing are observed at depths typified by the
 Longmaxi formation. Mineral composition varies broadly through the
 stratigraphic section due to different depositional environments. The
 section is generally tectosilicate-poor and phyllosilicate-rich with a
 minor portion (~5 wt.%) the converse. We measure the frictional and
 stability properties of shale gouges taken from the full stratigraphic
 section at hydrothermal conditions. Velocity-stepping experiments were
 performed on representative shale gouges at σc = 60 MPa, Pf = 30 MPa and T
 =150 ℃. Results show that the gouges are generally frictionally strong
 with friction coefficients spanning a range of 0.50-0.75. Two
 phyllosilicate+TOC-poor gouges exhibited higher frictional strength and
 velocity weakening behavior, capable of potentially unstable fault slips,
 while only velocity strengthening behavior was observed for the remaining
 phyllosilicate+TOC-rich gouges. These results confirm that the frictional
 and stability properties are mainly controlled by phyllosilicate+TOC
 content. Elevating the temperature further weakens the gouges and drives
 it towards velocity weakening. The presence of observed seismicity in
 majority velocity strengthening materials suggest the importance of the
 minority velocity weakening materials. We suggest a model where seismicity
 is triggered when high pore fluid pressures drive aseismic slip in the
 near-field and triggers seismic slip on adjacent faults. Our results have
 important implications in understanding the physics of earthquakes in
 Sichuan Basin and highlights the importance of identifying the location
 and characteristics of faults prior to hydraulic fracturing.
description: Experiment
 details, recorded data during each shear experiment, and friction data
 used to reflect the frictional properties of Longmaxi shale gouges in
 Sichuan Basin, southwest China.
DOI: 10.5061/dryad.hqbzkh1cd
title: Data from: Hemiptera phylogenomic resources: tree-based orthology prediction and conserved exon identification

description: High-throughput sequencing of transcriptomes and targeted genomic regions
 are advancing our knowledge of The Tree of Life. Building phylogenies with
 regions of the genome requires 1-to-1 ortholog resources of genes and
 non-coding loci. One organismal group that has received little attention
 in this area is the Hemiptera, the fifth largest insect order represented
 by approximately 103,590 named species. Here, we present a set of 3,872
 Hemiptera 1-to-1 orthogroups based on tree-based orthology inference of 8
 Hemiptera species with publicly available genome sequences. Furthermore,
 we also estimated a set of 406 orthologous exons with similar mRNA splice
 sites that can be used for Sanger sequencing and developing enrichment
 probes for targeted genome sequencing for phylogenomic inference. We show
 this novel set of orthologs is informative at the protein, coding
 sequence, and exon molecular levels and provide robust branch support in
 both gene tree - species tree methods and concatenated sequence
 phylogenies. In addition, we demonstrate the utility of these loci to
 resolve relationships in whiteflies, Bemisia tabaci, a large species
 complex with few phylogenomic resources. Lastly, we compare our Hemiptera
 phylogeny with previously published phylogenies and other ortholog
 databases, while providing suggestions on further improvement to this
 phylogenomic resource.
DOI: 10.5061/dryad.jh9w0vt7r
title: Concordance table for oral testosterone undecanoate

description: Concordance analysis was performed to identify the best post-dose T assay
 time-point to guide any necessary dose-adjustment in oral TU
 patients.  Concordance is defined herein to describe the extent
 of agreement between a decision to adjust the oral TU dose (up or down)
 when a single circulating T concentration in remains in the hypogonadal
 range [i.e., &lt;252 ng/dl (9 nmol/L) for this study] or
 supraphysiological range [i.e., &gt;907 ng/dL (31 nmol/L)] and the
 desired outcome of that decision (i.e., a circulating T level in the
 eugonadal range) is achieved.
DOI: 10.5061/dryad.905qftth4
title: The filtered VCF file containing SNPs detected from the Vitis bryoniifolia clade using RAD-seq.

description: The grape genus (Vitis L.) is of great agronomic importance and represents
 an economically valuable resource. Researchers have explored the
 phylogenetic relationships of subgenus Vitis for decades. However, the
 evolutionary patterns of many morphological characters of subgenus Vitis
 have not yet been explored in the context of a robust phylogenetic
 framework. Within the East Asian clade, V. bryoniifolia and its closely
 related taxa form the V. bryoniifolia clade, which is taxonomically
 complex. The phylogenetic relationships and species delimitation within
 this clade remain poorly resolved, due to the limited sampling in prior
 studies. We tested morphological trait evolution based on ancestral
 character state reconstruction using a phylogenomic framework. With 89
 accessions from the East Asian subgenus Vitis sampled, a robust
 phylogenetic relationship of the V. bryoniifolia clade is reconstructed
 using the restriction-site associated DNA sequencing (RAD-seq) data, which
 support the monophyly of most taxa of the V. bryoniifolia clade. Ancestral
 character state reconstructions suggest that the weak climbing ability and
 simplified tendrils of Vitis each evolved multiple times. This study
 provides a reliable phylogenomic framework for the V. bryoniifolia clade.
 Coupled with morphological analyses, we discuss the taxonomic status of
 some taxa in the V. bryoniifolia clade and untangle a taxonomic dilemma in
 the grape genus.
DOI: 10.15468/dl.muvt3f
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "CatalogNumber" : [
 "is one of (PDD 86131, PDD 86152, K-M000195447, K-M000153678, K-M000951583, K-M000202918, K-M000193552, K-M000193555, K-M000193559, K-M000193549, K-M000819799)"
 ]
}

 The dataset includes 11 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002304-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wvhawz
title: Occurrence Download

description: A dataset containing 1311 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Astragalus vexilliflexus"
 ]
}

 The dataset includes 1311 records from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002302-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qvsfpc
title: Occurrence Download

description: A dataset containing 689 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Andira vermifuga",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 689 records from 69 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002303-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.wm37pvmjh
title: Data from: Hurricane effects on Neotropical lizards span geographic and phylogenetic scales

description: Extreme climate events such as droughts, cold snaps, and hurricanes can be
 powerful agents of natural selection, producing acute selective pressures
 very different from the everyday pressures acting on organisms. However,
 it remains unknown whether these infrequent but severe disruptions are
 quickly erased by quotidian selective forces, or whether they have the
 potential to durably shape biodiversity patterns across regions and
 clades. Here, we show that hurricanes have enduring evolutionary impacts
 on the morphology of anoles, a diverse Neotropical lizard clade. We first
 demonstrate a transgenerational effect of extreme selection on toepad area
 for two populations struck by hurricanes in 2017. Given this short-term
 effect of hurricanes, we then asked whether populations and species that
 more frequently experienced hurricanes have larger toepads. Using 70 y of
 historical hurricane data, we demonstrate that, indeed, toepad area
 positively correlates with hurricane activity for both 12 island
 populations of Anolis sagrei and
 188 Anolis species throughout the Neotropics. Extreme
 climate events are intensifying due to climate change and may represent
 overlooked drivers of biogeographic and large-scale biodiversity patterns.
description: These morphology data are largely measured from toepad scans of
 anolis species toepads. They have been synced with hurricane occurence
 data from NOAA. See main text for full data description. 
description: Data is complete, to the best of our knowledge.
 We recommend
 accessing Donihue_etal_PNAS_HurricaneEffectsNeotropicalLizards_CodeArchive.R in the Rproj. All code is available there and all data can be accessed through that code.  For re-use of data or questions about data descriptions please contact colindonihue@gmail.com
DOI: 10.6075/j0bc3wzs
title: Data from: Anticholinergic medications: A potentially modifiable risk factor for development of MCI

description: Objective: To determine the cognitive consequences of anticholinergic
 medications (aCH) in cognitively normal older adults as well as
 interactive effects of genetic and cerebrospinal fluid (CSF) Alzheimer’s
 disease (AD) risk factors. Methods: 688 cognitively normal participants
 from the Alzheimer’s Disease Neuroimaging Initiative were evaluated (mean
 age = 73.5, 49.6% female). Cox regression examined risk of progression to
 mild cognitive impairment (MCI) over a 10-year period, and linear mixed
 effects models examined 3-year rates of decline in memory, executive
 function, and language as a function of aCH. Interactions with APOE 4
 genotype and CSF biomarker evidence of AD pathology were also assessed.
 Results: aCH+ participants had increased risk of progression to MCI (HR =
 1.42, p = .02), and there was a significant aCH x AD-risk interaction such
 that (aCH+)(&[epsilon]4+) individuals showed greater than 2-fold
 increased risk (HR = 2.47, p &lt; .001) for incident MCI relative to
 (aCH-)(&[epsilon]4-), while (aCH+)(p-tau/Aß+) individuals
 demonstrated greater than 4-fold (HR = 4.25, p &lt; .001) increased
 risk relative to (aCH-)(p-tau/Aß-). Linear mixed effects models revealed
 that aCH predicted a steeper slope of decline in memory (t = -2.31, p =
 .02) and language (t = -2.35, p = .02), with effects exacerbated in
 individuals with AD risk factors. Conclusions: aCH increased risk of
 incident MCI and cognitive decline, and effects were significantly
 enhanced among individuals with genetic risk factors and CSF-based AD
 pathophysiological markers. Findings underscore the adverse impact of aCH
 medications on cognition and the need for deprescribing trials,
 particularly among individuals with elevated risk for AD.
description: The uploaded data comprise several appendices that include
 sensitivity analyses for the manuscript "Anticholinergic medications:
 A potentially modifiable risk factor for development of MCI" by
 Weigand et al. Methods details for these data can be found in the
 manuscript text.
DOI: 10.5061/dryad.3r2280gcw
title: Personality predicts innovation and social learning in children; Implications for cultural evolution

description: Innovation and social learning are the pillars of cultural evolution,
 allowing cultural behaviours to cumulatively advance over generations.
 Yet, little is known about individual differences in the use of social and
 asocial information. We examined whether personality influenced children’s
 propensity to observe others or independently generate solutions to novel
 problems. Conscientiousness was associated with electing for no
 demonstrations, while agreeableness was associated with opting for
 demonstrations. For children receiving demonstrations, openness to
 experience consistently predicted deviation from observed methods.
 Children who opted for no demonstrations were also more likely than those
 opting for demonstrations to exhibit tool manufacture on an innovation
 challenge and displayed higher creativity. These results highlight how new
 cultural traditions emerge, establish and advance by identifying which
 individuals generate new cultural variants in populations and which are
 influential in the diffusion of these variants, and help reduce the
 apparent tension within the ‘ratchet’ of cumulative culture.
description: This data was collected using from an experiment. It has been
 processed using SPSS and R.
description: Some of the coded scores only applies to participants who elected
 for social demonstrations on the puzzlebox. This should be clear but is
 explained in the readme.
DOI: 10.25934/pr00012558.0
title: Available datapackage for study 'Randomized COVID-19 Testing in Vulnerable Communities and Risk Tool Creation (FightCOVIDMKE)'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.