cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4f4qrfj7t
title: Within-island diversification in a passerine bird

description: The presence of congeneric taxa on the same island suggests the
 possibility of in situ divergence, but can also result from multiple
 colonizations of previously diverged lineages. Here, using genome-wide
 data from a large population sample, we test the hypothesis that
 intra-island divergence explains the occurrence of four geographic forms
 meeting at hybrid zones in the Reunion grey white-eye (Zosterops
 borbonicus), a species complex endemic to the small volcanic island of
 Reunion. Using population genomic and phylogenetic analyses, we
 reconstructed the population history of the different forms. We confirmed
 the monophyly of the complex and found that one of the lowland forms is
 paraphyletic and basal relative to others, a pattern highly consistent
 with in situ divergence. Our results suggest initial colonization of the
 island through the lowlands, followed by expansion into the highlands,
 which led to the evolution of a distinct geographical form, genetically
 and ecologically different from the lowland ones. Lowland forms seem to
 have experienced periods of geographical isolation, but they diverged from
 one another by sexual selection rather than niche change. Overall, low
 dispersal capabilities in this island bird combined with both geographical
 and ecological opportunities seem to explain how divergence occurred at
 such a small spatial scale.
description: SNP dataset from genotyping-by-sequencing (GBS) of
 372 individuals representing all Reunion grey white-eye geographic forms
 (316 individuals) and three closely related species. This vcf file that
 was generated by GATK v. 3.7. See methods and electronic supplementary
 material, text S2 for details about the generation of this
 dataset.
description: Correspondence between individual names, species and sampling
 site can be found in: infos_ind_species_loc_GBS_MS_in_situ.csv
DOI: 10.5061/dryad.v15dv41sd
title: (2019) Fieldtrip booklet for GSA Grand Canyon Thompson Field Forum I, "Age and Carving of Grand Canyon: Towards a resolution of 150 years of debate" (September 14-21, 2019)

description: Booklet containing USGS Grand Canyon Geologic River Maps. The Conveners
 for the 2019 GSA Thompson Field Forum were Karl Karlstrom and Laura
 Crossey, University of New Mexico, Eugene Humphreys, University of Oregon,
 David Shuster, University of California Berkeley, and Kelin Whipple,
 Arizona State University. The age and evolution of the 1.6-km-deep,
 270-mile-long Grand Canyon have been debated since J.W. Powell’s
 exploration of the Colorado River in 1869. This GSA Thompson Field Forum
 honored the 150th anniversary of Powell’s trip. It involved 28 researchers
 and young scientists who discussed the evidence for the age and incision
 history of Grand Canyon in the context of recent advances and ongoing
 debates. The objective was to promote a next generation of research on the
 evolution and tectonic geomorphology of this iconic region, as well as
 similar studies globally, and debate the evidence for and against
 mantle-driven dynamic topography. The field forum started and ended in Las
 Vegas, Nevada, USA, and was run under a charter with Grand Canyon
 Expeditions. The eight-day river trip covered 280 river miles from Lees
 Ferry to Pearce Ferry. Each participant gave a short seminar as
 discussions on the outcrop, “plenary” discussions at morning and evening
 seminars, or short talks and discussions on boats while floating past key
 areas. This booklet became known as "the hymnal"; each
 participnat had one in a waterproof bag and their pages, sent in ahead of
 time by each participant, served as the "slides" for the river
 seminars.
DOI: 10.5061/dryad.9s4mw6mbz
title: (2019) Grand Canyon Geology and Geoscience Education Public Symposium (April 18-20, 2019): final program and abstracts

description: This symposium was held April 18-20, 2019 at the Shrine of the Ages
 Auditorium at the South Rim of Grand Canyon in honor of Grand Canyon
 National Park’s 2019 Centennial celebration, the 150th anniversary of John
 Wesley Powell’s 1869 pioneering Colorado River expedition, and Earth Day
 2019. The conveners were Karl Karlstrom and Laurie Crossey, University of
 New Mexico, Steven Semken, Arizona State University, Todd Stoeberl, Chief
 of Interpretation, and Jeanne Calhoun, Chief of Science and Resource
 Management, Grand Canyon National Park. The objective was to provide an
 update on geologic research and on innovations in geoscience education
 that have taken place at Grand Canyon and help promote the next century of
 geologic research and outreach in this iconic region. The symposium was
 open to the public as well as the geoscience community. It involved two
 days of meetings with 14 talks from researchers on all aspects of Grand
 Canyon geology, and 7 geoscience education talks. It ended with a public
 walk on the Trail of time guided by geologists. The time perspective that
 geology conveys is crucial for a sustainable future as we grapple with
 many issues such as climate dynamism, extinctions, and other resources --
 including water. Grand Canyon’s 6 million annual visitors can play an
 important role internationally in gaining and promoting science literacy
 and geoscience awareness. A basic geology message for visitors is that
 Grand Canyon is a geologically young landscape being sculpted from very
 old rocks. Knowing some of the stories encoded in the rock layers and the
 landscapes enriches your understanding of our planet and enhances your
 experience at Grand Canyon.
description: This was a 2-day public meeting held at the Shrine of the Ages at
 Grand Canbyon's South Rim in honor of Grand Canyon National Park’s
 2019 Centennial celebration, Earth Day 2019, and the 150th anniversary of
 John Wesley Powell’s 1869 pioneering Colorado River expedition.
DOI: 10.5061/dryad.g1jwstqmz
title: Belowground interactions differ between sympatric desert shrubs under water stress

description: Understanding the relationships among species is central to ecological
 research, however, many knowledge gaps remain regarding how desert plant
 species interact. In the present study, we assessed the effect of rainfall
 on the belowground interactions and root morphology of two desert shrubs,
 Reaumuria soongorica (Tamaricaceae) and Salsola passerina
 (Chenopodiaceae), from three communities with similar landforms and soil
 environments. The roots of both R. soongorica and S. passerina were deeper
 when grown together than grown singly. Interestingly, the belowground
 biomass of R. soongorica was higher but the belowground biomass of S.
 passerina was lower when grown together than when grown alone. This
 suggests that S. passerina benefitted from the association with R.
 soongorica. When grown together under conditions of low rainfall, the
 roots of R. soongorica were deeper than those of S. passerina, which
 suggests that R. soongorica is more robust than S. passerina when
 subjected to periods of decreased rainfall. We concluded that the
 symbiotic relationship between these two shrub species can lead to deeper
 roots and that the plants are affected by rainfall availability. Combined
 with the output results of climate change models, we speculated that the
 distribution area of these two species will expand to the west, which has
 important implications on how the interactions of other desert species may
 change in response to climate variability.
DOI: 10.5061/dryad.fxpnvx0ng
title: Bayesian network analysis of immune signaling networks FACS data

description: Cancer immunotherapy, specifically immune checkpoint blockade therapy, has
 been found to be effective in the treatment of metastatic cancers.
 However, many patients do not show marked clinical response. Consequently,
 elucidating immune system-related pre-treatment biomarkers that are
 predictive with respect to sustained clinical response is a major research
 priority. Another research priority is evaluating changes in immune
 signaling networks before and after treatment in responders and
 non-responders. High-dimensional flow cytometry data (FACS,
 Fluorescence-activated cell sorting) characterizing immune signaling
 network markers in gastrointestinal (GI) cancer patients was used by us to
 perform such analyses. We developed a novel computational pipeline to
 perform secondary analyses of FACS data using systems biology / machine
 learning / information-theoretic techniques and concepts, namely Bayesian
 networks and maximum entropy. Application of the pipeline resulted in
 elucidation of immune markers, combinations and interactions thereof, and
 corresponding immune cell population types, that are associated with
 clinical response in the GI cancer cohorts. Future studies are planned to
 generalize our analytical approach to different cancer types and
 corresponding multimodal high-dimensional datasets.
description: FACS data:<br>   Peripheral blood
 mononuclear cells (PBMCs) from patients were isolated from heparinized
 blood by Ficoll-Paque density centrifugation and cryopreserved in 10% DMSO
 FBS. Cryopreserved PBMCs were thawed and stained with antibodies for the
 following flow cytometry panels: Checkpoint panel:
 CD4, CD8, CD45RA, KLGR1, CCR7, CXCR5, 4-1BB, BTLA4, LAG3, OX40, CD160,
 TIGIT, PD1 and TIM3; Innate panel: CD3, CD14, CD16, CD20, CD33, CD56,
 CD11c, CD141, CD1c, CD123, CD83, HLA-DR, TCRgδ, PD-L1; Adaptive panel:
 CD4, CD8, CCR10, CCR6, CD73, ICOS, CXCR3, CXCR5, CD45RA, CCR4, CCR7, CD25,
 CD127, PD1. Flow cytometry was performed using Fortessa Flow Cytometers
 and flow cytometry data was analyzed using FlowJo software (BD
 Biosciences). Please see
 patients.txt file for the datasets breakdown.
description: Please see patients.txt file for the
 datasets breakdown.
DOI: 10.5061/dryad.0zpc866tt
title: Data from: Sleep disorders in anti-NMDAR encephalitis

description: This is supplemetal data (tables and methods) from a paper submitted for
 publication, whose objective was to describe the sleep disorders in
 anti-NMDA receptor encephalitis (anti-NMDARe).
description: Patients recovering from anti-NMDARe were invited to participate
 in a prospective observational single center study including comprehensive
 clinical, video-polysomnography (V-PSG) sleep assessment and
 neuropsychological evaluation. Age and sex-matched healthy participants
 served as controls.
 <strong>Results</strong>: Eighteen patients (89%
 female, median age 26 years, IQR 21-29) and 21 controls (81% female,
 median age 23 years, IQR 18-26) were included. In the acute stage, 16
 (89%) patients reported insomnia and 2 hypersomnia; nightmares occurred in
 7. After the acute stage, 14 (78%) had hypersomnia.  At study-admission
 (median 183 days after disease onset, IQR 110-242) 8 patients still had
 hypersomnia, 1 insomnia, and 9 normal sleep duration. Patients had more
 daytime sleepiness than controls (higher Barcelona Sleepiness Index,
 p=0.02, and Epworth Sleepiness Score, p=0.04). On V-PSG, sleep efficiency
 was similar in both groups, but patients had more frequently multiple and
 longer confusional arousals in NREM sleep (videos provided). Additionally,
 13 (72%) patients had cognitive deficits, 12 (67%) psychological, social,
 or occupational disability, and 33% depression or mania. Compared with
 controls, patients had a higher body mass index (median, IQR: 23.5,
 22.3-30.2 vs. 20.5, 19.1-21.1; p=0.007). Between disease onset and last
 follow-up, 14 (78%) patients developed hyperphagia, and 6 (33%)
 hypersexuality (2 requiring hospitalization), all associated with sleep
 dysfunction. <strong>Conclusions</strong>:
 Sleep disturbances are frequent in anti-NMDARe. They show a temporal
 pattern (predominantly insomnia at onset; hypersomnia during recovery),
 associate with behavioral and cognitive changes, and can occur with
 confusional arousals during NREM sleep.
DOI: 10.5061/dryad.0vt4b8gvd
title: Phylogenomics resolves the relationships within Antennaria (Asteraceae, Gnaphalieae) and yields new insights into its morphological character evolution and biogeography

description: Antennaria are dioecious perennial herbs distributed mainly in the
 Holarctic Region with their major center of diversity in the Rocky
 Mountains of Western North America. The genus comprises 33 known sexual
 diploid/tetraploid species and at least five polyploid agamic complexes
 which mostly reproduce by forming asexual seeds. We performed a
 phylogenetic reconstruction of the 31 sexually-reproducing Antennaria
 species using a novel target enrichment method that employs custom capture
 probes and is designed to work across Asteraceae. Both concatenated and
 coalescent-based analyses of DNA sequence data from hundreds of nuclear
 loci recovered Antennaria as a monophyletic group except for the
 long-disputed species, Antennaria linearifolia, which was recovered
 outside of the genus. Antennaria was further resolved into three distinct,
 major lineages. Analysis of ancestral state reconstruction of 12
 taxonomically important morphological characters elucidated patterns of
 character evolution throughout the genus. Estimations of ancestral
 geographic ranges and molecular dating analyses demonstrated the Rocky
 Mountain region, including the Vancouverian Province, as the center of
 origin for the genus Antennaria, around 5.8 MYA. Subsequent dispersals of
 Antennaria into the Arctic and Appalachian provinces, Canadian provinces,
 and Eurasia took place roughly 3.2 MYA, 2.4 MYA and 1.6 MYA, respectively.
 Biogeographical Stochastic Mapping indicated that 51.4% of biogeographical
 events were based on within-area speciation. The remaining 48.6% of the
 events were divided into two types of dispersals: i) range expansion
 dispersals (anagenic, 37%) and ii) founder/jump dispersals (cladogenic,
 11.6%). Our results provide a framework for future evolutionary studies of
 Antennaria, including speciation, origin(s) of polyploidy, and agamospermy
 in the genus.
description: The dataset is generated using Hyb_Seq technique. The datamatrix
 is produced by the alignment of putative orthologs of targeted 1061 single
 or low copy genes from the study species.
DOI: 10.5061/dryad.2jm63xsk6
title: An integrative phylogenomic approach illuminates the evolutionary history of Old World tree frogs (Anura: Rhacophoridae)

description: Rhacophoridae is one of the most speciose and ecologically diverse
 families of amphibians. Resolution of its evolutionary relationships is
 key to understanding the accumulation of biodiversity, yet previous
 hypotheses based on Sanger sequencing exhibit much
 discordance amongst generic relationships. This conflict
 precludes the making of sound macroevolutionary conclusions. Herein, we
 conduct the first phylogenomic study using broad-scale sampling and
 sequences of 352 nuclear DNA loci obtained using
 anchored hybrid enrichment targeted sequencing. The robust time-calibrated
 phylogenetic hypothesis clarifies several long-disputed relationships and
 facilitates the testing of evolutionary hypotheses on spatiotemporal
 diversiﬁcation and reproductive modes. The major extant lineages
 of Rhacophoridae appear to have radiated in mainland
 Asia, and the spatiotemporal process corresponds with
 several common accumulations of biodiversity
 in Asia. Analyses do not detect any case of “Out of
 Himalayas” in Rhacophoridae. All transitions of
 reproductive modes appear to have evolved in an ordered,
 gradual sequence associated with gaining independence of standing
 water for larval development. The different reproductive modes
 are phylogenetically conserved and the completion of
 their transitions appear to have occurred over a period of ~30
 Ma, which does not fit a pattern of a rapid burst of diversification.
 Innovations in reproductive modes associate statistically with the uneven
 distribution of species-richness between clades, where higher
 diversification is linked to increased terrestrial modes of reproduction.
 These results strengthen the hypothesis that breeding innovations
 drive diversification by providing new opportunities for
 ecological release and dispersion.
DOI: 10.15468/dl.rza5ku
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "PublishingOrg is c2ecae57-6701-485e-9ebd-5f87b2945cb2",
 "TaxonKey is Melanoplus boulderensis",
 "Year 1900-2026"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002128-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.vhhmgqnq2
title: The relative role of rivers, environmental heterogeneity and species traits in driving compositional changes in Southeastern Amazonian bird assemblages

description: Amazonian rivers have been proposed to act as geographic barriers to
 species dispersal, either driving allopatric speciation or defining
 current distribution limits. The strength of the barrier varies according
 to the species ecological characteristics and the river physical
 properties. Environmental heterogeneity may also drive compositional
 changes, but have hardly been assessed in Amazonia. Aiming to understand
 the contributions of riverine barriers and environmental heterogeneity in
 shaping compositional changes in Amazonian forest bird assemblages, we
 focus on the Tapajós River. We investigate how spatial variation in
 species composition is related to physical barriers (Tapajós and Jamanxim
 rivers), ecological characteristics of the species (distinct guilds) and
 environmental heterogeneity (canopy reflectance, soils and elevation). We
 sampled birds through point counts and mist nets on both banks of both the
 Tapajós and Jamanxim rivers. To test for relationships between bird
 composition and environmental data, we used Mantel and partial Mantel
 tests, NMDS and ANOVA + Tukey HSD. The Mantel tests showed that the
 clearest compositional changes occurred across the Tapajós River, which
 seems to act unequally as a significant barrier to the bird guilds. The
 Jamanxim River was not associated with differences in bird communities.
 Our results reinforce that the Tapajós River is a biogeographical boundary
 for birds, but environmental heterogeneity determines compositional
 variation within interfluves. These results contrast with diversity
 patterns described for other vertebrates, suggesting that upland forest
 birds singularly respond to large rivers as barriers in Amazonia, leading
 to erroneous extrapolations for interpreting biogeographic results for
 other Amazonian organisms.
DOI: 10.5061/dryad.ksn02v70t
title: Elevation and landscape change drive the distribution of a montane, endemic grassland bird

description: This dataset documents the presence and abundance of the Nilgiri
 pipit (Anthus nilghiriensis) in 170 survey sites across most of
 its global range. Between one and four surveys were carried out
 at each site between November 2017 and May 2018 by experienced
 observers. Survey duration was proportional to site area. A wide range of
 habitat characteristics were also surveyed, and additional habitat
 characteristics for each site were gathered from remotely sensed
 data.
DOI: 10.5061/dryad.66t1g1jz3
title: Lack of vulnerability segmentation among woody species in a diverse dry sclerophyll woodland community

description: 1. Recent findings suggest that tree mortality and post-drought recovery
 of gas exchange can be predicted from loss of function within the water
 transport system. Understanding the susceptibility of plants to hydraulic
 damage requires knowledge about the vulnerability of different plant
 organs to stress-induced hydraulic dysfunction. This is particularly
 important in the context of vulnerability segmentation between plant
 tissues which is believed to protect more energetically “costly” tissues,
 such as woody stems, by sacrificing “cheaper” leaves early under drought
 conditions. 2. Differences in vulnerability segmentation between
 co-occurring plant species could explain divergent behaviours during
 drought, yet there are few studies considering how this characteristic may
 vary within a plant community. Here we investigated community-wide
 vulnerability segmentation by comparing leaf/shoot and stem vulnerability
 in all coexistent dominant canopy and understory woody species in a
 diverse dry sclerophyll woodland community, including multiple angiosperms
 and one gymnosperm. 3. Previously published terminal leaf/shoot
 vulnerability to loss of water transport capacity was compared with stem
 xylem vulnerability to embolism measured on the same species at the same
 site. We calculated hydraulic safety margins for stems to determine
 variation in the risk of hydraulic failure during drought among species.
 4. The xylem of all species was found to be highly resistant to hydraulic
 dysfunction, with only two of the eight species exhibiting significantly
 different vulnerability to the overall mean. No evidence of vulnerability
 segmentation between shoots/leaves and stems was found in seven of the
 eight species. 5. Phylogenetically diverse canopy and understory species
 in this evergreen sclerophyll woodland appear to have evolved similar
 strategies of drought resistance, including low xylem vulnerability to
 embolism and general lack of vulnerability segmentation. This convergence
 in hydraulic safety indicates a lack of hydraulic niche partitioning in
 this woodland community.
description: Stem vulnerability to embolism measured with the optical
 vulnerability method at thresholds of water potential in megapascals (MPa)
 at which stem had lost 12% (P12_MPa), 50% (P50_MPa), and 88% (P88_Mpa) of
 hydraulic conductivity. Minimum leaf water potential (MinLWP_Mpa)
 experienced by these species at the same fieldsite during a severe drought
 caused by the 2015-2016 El Niño Pacific southern oscillation.
DOI: 10.5061/dryad.tb2rbnzwt
title: Comparison between the psychopathy checklist-revised and the comprehensive assessment of psychopathic personality in a representative sample of Spanish prison inmates

description: In the field of psychopathy, there is an ongoing debate about the core
 traits that define the disorder, and that therefore must be present to
 some extent in all psychopaths. The main controversy of this debate
 concerns criminal behaviour, as some researchers consider it a defining
 trait, while others disagree. Using a representative sample of 204 Spanish
 convicted inmates incarcerated at the Pereiro de Aguiar Penitentiary in
 Ourense, Spain, we tested two competing models, the Psychopathy
 Checklist-Revised (PCL-R), which includes criminal behaviour items, versus
 the Comprehensive Assessment of Psychopathic Personality (CAPP), which
 does not. We used two different PCL-R models, one that includes criminal
 items and another that does not. PCL-R factors, facets, and testlets from
 both models and CAPP dimensions were correlated and compared. Two
 different PCL-R cut-off scores, 25 or more and 30 or more, were used for
 the analysis. Overall, a strong correlation was found between PCL-R and
 CAPP scores in the whole sample, but as scores increased and inmates
 became more psychopathic, the correlations weakened. All these data
 indicate that psychopathy, understood to mean having high scores on the
 PCL-R and CAPP, is a multidimensional entity, and inmates can develop the
 disorder and then receive the diagnosis through different dimensions. The
 CAPP domains showed better correlations when compared with the PCL-R
 factors from both models, showing that an instrument for the assessment of
 psychopathy without a criminal dimension is valuable for clinical
 assessment and research purposes.