cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.41ns1rn9w
title: Biotic exchange leaves detectable genomic patterns in the Australian rainforest flora

description: The movement (or invasion) of plant lineages from Sunda (the Malay
 Archipelago) into Sahul (mainland Australia) has resulted in a present-day
 Australian rainforest flora of mixed ancestries. Floristic integration
 increased during the Quaternary when continental vegetation was subjected
 to recurrent expansion/contraction cycles. To date, this expansion history
 has yet to be investigated through multi-species, landscape-level genetic
 analyses within tropical Northern Australia, presumably the main point of
 contact for Sunda lineages. Here, we characterise and compare the dynamics
 of 53 species of Sunda and Sahul ancestry co-distributed across the
 Australian Tropics and Subtropics. We use whole-chloroplast genomic
 datasets to obtain comparable measures of species-level diversity and
 estimate community dynamics through time across multiple rainforest sites.
 Unlike Sahul-derived species, Sunda-derived species show consistently low
 genomic diversities, with recent accumulation rates for Sunda species
 being detected across all sites, confirming recent arrival and expansion
 across eastern Australia. A subset of Sunda-derived species with
 continental distributions consistently exhibited highest diversity at the
 most northerly site sampled, suggesting north to south colonisation
 processes. The same species however, differed in the levels of genomic
 differentiation between the Tropics and Subtropics, suggesting that
 continental expansion occurs at different temporal scales, with some
 species experiencing a northern time lag before a southern expansion along
 the east coast of Australia.
description: Refer to the methodology of the paper Each
 file contains an alignment of species-specific chloroplast
 genomic sequences created from the relevant NGS
 libraries.
DOI: 10.5061/dryad.kd51c5b2h
title: Seroprevalence of Entamoeba histolytica at a voluntary counselling and testing centre in Tokyo: a cross-sectional study

description: Background Amebiasis, which is caused by Entamoeba histolytica, is a
 re-emerging public health issue owing to sexually transmitted infection
 (STI) in Japan. However, epidemiological data are quite limited. Methods
 To reveal the relative prevalence of sexually transmitted E. histolytica
 infection to other STIs, we conducted a cross-sectional study at a
 voluntary counselling and testing (VCT) centre in Tokyo. Seroprevalence of
 E. histolytica was assessed according to positivity with an enzyme-linked
 immunosorbent assay for E. histolytica-specific IgG in serum samples
 collected from anonymous VCT clients. Results Among 2,083 samples,
 seropositive rate for E. histolytica was 2.64%, which was higher than that
 for HIV-1 (0.34%, p &lt; 0.001) and comparable to that for syphilis
 (rapid plasma reagin (RPR) 2.11%, p = 0.31). Positivity for Chlamydia
 trachomatis in urine by transcription-mediated amplification (TMA) was
 4.59%. Seropositivity for E. histolytica was high among RPR- or Treponema
 pallidum hemagglutination (TPHA)-positive individuals and it was not
 different between clients with and without other STIs. Both seropositivity
 of E. histolytica and RPR were high among male clients. The seropositive
 rate for anti-E. histolytica antibody was positively correlated with age.
 TMA positivity for urine C. trachomatis was high among female clients and
 negatively correlated with age. Regression analysis identified that male
 sex, older age, and TPHA-positive results are independent risk factors of
 E. histolytica seropositivity. Conclusions Seroprevalence of E.
 histolytica was 7.9 times higher than that of HIV-1 at a VCT centre in
 Tokyo, with a tendency to be higher among people at risk for syphilis
 infection. There is a need for education and specific interventions
 against this parasite, as a potentially re- 65 emerging pathogen.
description: The design of this study was a cross-sectional study. The total
 2,083 serum samples used in this study were collected at the Tokyo
 Metropolitan Minami Shinjuku Testing – Counselling Centre where more than
 10,000 anonymous clients seek HIV-1 screening tests each year. Collected
 samples are transferred to the Tokyo Metropolitan Institute of Public
 Health for laboratory testing, then stored at 4°C. Fourth generation HIV-1
 screening is performed routinely throughout the year. However, in 2 months
 of the year (e.g., June and December in the case of 2017), the Tokyo
 Metropolitan Government intensifies STI screening, and rapid plasma reagin
 (RPR) and Treponema pallidum hemagglutination (TPHA) tests for syphilis
 screening are additionally performed for all clients. In addition, urinary
 sampling and transcription-mediated amplification (TMA) assay testing for
 Chlamydia trachomatis and Neisseria gonorrhoeae are performed for clients
 who are willing to undergo these tests.
DOI: 10.15139/s3/oij4pc
title: Data Management and Sharing Plan for: Enhancing Mental Health Treatment Engagement among Probationers - Adapting an Organizational Linkage Implementation Strategy for Specialty Mental Health Probation

description: The Data Management and Sharing Plan describes the scientific data to be generated and/or used in the research and outlines a strategy for managing and sharing project data.
description: Data Management and Sharing Plan
DOI: 10.5061/dryad.m63xsj3z3
title: Congruent population genetic structures and divergence histories in anther-smut fungi and their host plants Silene italica and the S. nutans species complex

description: The study of population genetic structure congruence between hosts and
 pathogens gives important insights into their shared phylogeographic and
 coevolutionary histories. We studied the population genetic structure of
 castrating anther-smut fungi (Microbotryum genus) and of their host
 plants, the Silene nutans species complex, and the morphologically and
 genetically close S. italica, which can be found in sympatry.
 Phylogeographic population genetic structure related to persistence in
 separate glacial refugia has been recently revealed in the S. nutans plant
 species complex across Western Europe, identifying several distinct
 lineages. We genotyped 171 associated plant-pathogen pairs of anther-smut
 fungi and their host plant individuals using microsatellite markers and
 plant chloroplastic SNPs. We found clear differentiation between fungal
 populations parasitizing S. nutans and S. italica plants. The population
 genetic structure of fungal strains parasitizing the S. nutans plant
 species complex mirrored the host plant genetic structure, suggesting that
 the pathogen was isolated in glacial refugia together with its host and/or
 that it has specialized on the plant genetic lineages. Using random forest
 approximate Bayesian computation (ABC-RF), we found that the divergence
 history of the fungal lineages on S. nutans was congruent with the one
 previously inferred for the host plant and likely occurred with ancient
 but no recent gene flow. Genome sequences confirmed the genetic structure
 and the absence of recent gene flow between fungal genetic lineages. Our
 analyses of host-pathogen individual pairs contribute to a better
 understanding of co-evolutionary histories between hosts and pathogens in
 natural ecosystems, in which such studies are still scarce.
description: -Table.genotype_microsatellite_170_strains-microsat-fungus.csv Diploid genotypes of 170 <em>Microbotryum</em> fungal strains (rows) for 22 microsatellite markers (columns). Microsatellite markers alleles of each sample are separated by a "/" symbol. Missing genotypes are indicated by a "NA".    -Table.genotype_microsatellite_plastidsnps_136_silene_samples.csv Diploid genotypes of 136 <i>Silene </i>host plants (rows) for 21 microsatellite markers (columns) and plastid SNPs (two last columns). Microsatellite markers alleles of each sample are separated by a "/" symbol. Missing genotypes are indicated by a "NA".
DOI: 10.5061/dryad.b5mkkwh8w
title: Untangling the imprints of climate, geography and land use/cover on bird diversity in the South American Gran Chaco

description: Aim: To evaluate the structure of bird communities throughout the South
 American Gran Chaco determining the effects of climate, geography, and
 land use/land cover in bird beta diversity, as well as to understand the
 beta-diversity processes underlying land-use changes across broad spatial
 ranges. Taxon: Birds. Location: South American Gran Chaco. Methods: We
 constructed a site-by-species matrix with occurrence probabilities of 293
 bird species across 2669 spatial units tiling completely the study area.
 Based on this matrix, we calculated pairwise dissimilarities scores and
 performed a hierarchical cluster analysis for describing the spatial
 configuration of dissimilarities. The clustering result was spatially
 represented through an original venation map with boundaries between sites
 widened in the function of their distance in the dendrogram. We used the
 Generalized Dissimilarity Modelling approach to model beta diversity,
 using geographic distance, climatic and land use/land cover information as
 predictors. We mapped beta-diversity patterns using color theory and the
 HSV color model. Results: We identified two main clusters of sites across
 the Gran Chaco, which represent environmentally different sites and
 harbour very distinct assemblages of species. These main groups are
 separated by two natural delimiters: The Bermejo-Pilcomayo interfluvium
 and the Lower Paraná floodplain. Overall, we observed that the percentage
 of cropland and climatic variables were important shapers of bird beta
 diversity. Main conclusions: We provide the first area-wide assessment of
 land use/land cover effects on bird beta diversity for the Gran Chaco. The
 distribution of croplands has a marked influence on bird beta diversity at
 regional scale highlighting the role of anthropic changes in reshaping
 bird beta diversity within the ecoregion. Taking into account the global
 increasing conversion of forests into croplands, a growing footprint of
 land use changes over geographical patterns of bird diversity in forest
 biomes can be anticipated.
DOI: 10.5061/dryad.wstqjq2h0
title: Supplement to: Hippocampal neurochemical profile and glucose transport kinetics in patients with type 1 diabetes

description: Context Longstanding type 1 diabetes (T1D) may lead to alterations in
 hippocampal neurochemical profile. Upregulation of hippocampal glucose
 transport as a result of recurrent exposure to hypoglycemia may preserve
 cognitive function during future hypoglycemia in subjects with T1D and
 impaired awareness of hypoglycemia (IAH). The effect of T1D on hippocampal
 neurochemical profile and glucose transport is unknown. Objective To test
 the hypothesis that hippocampal neurochemical composition is altered in
 T1D and glucose transport is upregulated in T1D with IAH. Design and
 participants Hippocampal neurochemical profile was measured with
 single-voxel magnetic resonance spectroscopy at 3T during euglycemia in 18
 healthy controls (HC), 10 T1D with IAH, and 12 T1D with normal awareness
 to hypoglycemia (NAH). Additionally, 12 HC, 8 T1D-IAH, and 6 T1D-NAH were
 scanned during hyperglycemia to assess hippocampal glucose transport with
 metabolic modeling. Setting University medical center. Main Outcome
 Measures Concentrations of hippocampal neurochemicals measured during
 euglycemia and ratios of maximal transport rate to cerebral metabolic rate
 of glucose (Tmax/CMRGlc), derived from magnetic resonance
 spectroscopy–measured hippocampal glucose as a function of plasma glucose.
 Results Comparison of hippocampal neurochemical profile revealed no group
 differences (HC, T1D, T1D-IAH, and T1D-NAH). The ratio
 Tmax/CMRGlc was not significantly different between the groups,
 T1D-IAH (1.58 ± 0.09) and HC (1.65 ± 0.07, P = 0.54),
 between T1D-NAH (1.50 ± 0.09) and HC (P = 0.19), and between
 T1D-IAH and T1D-NAH (P = 0.53). Conclusions Subjects with T1D
 with sufficient exposure to recurrent hypoglycemia to create IAH did not
 have alteration of Tmax/CMRglc or neurochemical profile compared
 with participants with T1D-NAH or HC.
description: Suppemental figures and tables.
DOI: 10.5061/dryad.mkkwh70w0
title: Data from: A revised sectional classification of Plukenetia L. (Euphorbiaceae, Acalyphoideae) with four new species from South America

description: Abstract—We present a phylogenetic classification for Plukenetia
 (Euphorbiaceae, Acalyphoideae) based on morphology and molecular
 phylogenetic studies using nuclear (ETS, ITS, KEA1 introns 11 and 17, TEB
 exon 17) and plastid (matK, ndhF, psbA-trnH) DNA data. Plukenetia
 comprises 25 species divided into six sections, with three new sections
 and four new species described here. The circumscription of Plukenetia is
 unaltered from recent treatments and we continue to recognize Romanoa as
 distinct. The sections of Plukenetia correspond with the subclade system
 proposed by Cardinal-McTeague and Gillespie (2016): P1 = P. sect.
 Fragariopsis comb. et stat. nov.; P2 = P. sect. Penninerviae sect. nov.;
 P3 = P. sect. Plukenetia; P4 = P. sect. Angostylidium; and P5 = P. sect.
 Hedraiostylus + P. sect. Madagascarienses sect. nov. The sections are
 distinguished by a combination of leaf venation, staminate flower
 morphology, pistillate flower number, style morphology, fruit type, and
 seed size. Additionally, we describe three new species from South America
 belonging to sect. Penninerviae: Plukenetia brevistyla and Plukenetia
 megastyla from the Amazon basin and Plukenetia chocoensis from the Chocó
 Biogeographic Region of Colombia. The new Amazonian species are
 morphologically similar to P. brachybotrya but distinguished by their
 style shape and size. The new Colombian species is morphologically similar
 to P. penninervia but distinguished by its elongate basilaminar
 extrafloral nectaries, presence of abaxial laminar extrafloral nectaries,
 and longer inflorescences. We also describe a new species from sect.
 Plukenetia, Plukenetia sylvestris, which is found in central and southern
 Peru. This species is suggested to be the wild progenitor of the
 cultivated P. carolis-vegae, differing by its smaller seeds/fruits and
 fewer stamens. Molecular data, including a new ETS phylogeny sampling P.
 brevistyla, support our new taxa as distinct. Keys to the sections and
 species of Plukenetia are provided and we designate 12 new lectotypes for
 Plukenetia and Romanoa.
description: This package includes the archived ETS alignment and resulting
 MrBayes tree file for <em>Plukenetia</em> and close
 relatives, as well as an R script needed to reproduce the species
 distribution base map from the following paper: Cardinal-McTeague and
 Gillespie (2020) A revised sectional classification of
 <em>Plukenetia</em> L. (Euphorbiaceae, Acalyphoideae) with
 four new species from South America. Systematic Botany.
DOI: 10.5061/dryad.02v6wwq07
title: Frequent burning causes large losses of carbon from deep soil layers in a temperate savanna

description: 1. Fire activity is changing dramatically across the globe, with uncertain
 effects on ecosystem processes, especially belowground. Fire‐driven losses
 of soil carbon (C) are often assumed to occur primarily in the upper soil
 layers because the repeated combustion of aboveground biomass limits
 organic matter inputs into surface soil. However, C losses from deeper
 soil may occur if frequent burning reduces root biomass inputs of C into
 deep soil layers or stimulates losses of C via leaching and priming. 2. To
 assess the effects of fire on soil C, we sampled 12 plots in a
 51‐year‐long fire frequency manipulation experiment in a temperate oak
 savanna, where variation in prescribed burning frequency has created a
 gradient in vegetation structure from closed‐canopy forest in unburned
 plots to open‐canopy savanna in frequently burned plots. 3. Soil C stocks
 were non‐linearly related to fire frequency, with soil C peaking in
 savanna plots burned at an intermediate fire frequency and declining in
 the most frequently burned plots. Losses from deep soil pools were
 significant, with the absolute difference between intermediately burned
 plots versus. most frequently burned plots more than doubling when the
 full 1 m sample was considered rather than the top
 0–20 cm alone (losses of 98.5 MgC ha‐1 (−76%) and 42.3
 MgC ha‐1 (−68%) in the full 1 m and 0–20 cm
 layers, respectively). Compared to unburned forested plots, the most
 frequently burned plots had 65.8 MgC ha‐1 (−58%) less C in the
 full 1 m sample. Root biomass below the top 20 cm also
 declined by 39% with more frequent burning. Concurrent fire‐driven losses
 of nitrogen and gains in calcium and phosphorus suggest that burning may
 increase nitrogen limitation and play a key role in the calcium and
 phosphorus cycles in temperate savannas. 4. Synthesis: Our
 results illustrate that fire‐driven losses in soil C and root biomass in
 deep soil layers may be critical factors regulating the net effect of
 shifting fire regimes on ecosystem C in forest‐savanna transitions.
 Projected changes in soil C with shifting fire frequencies in savannas may
 be 50% too low if they only consider changes in the topsoil.
DOI: 10.5061/dryad.n8pk0p2rs
title: The magnitude of large-scale tree mortality caused by the invasive pathogen Phytophthora ramorum

description: Forest pathogens are important drivers of tree mortality across the globe
 but it is exceptionally challenging to gather and build unbiased
 quantitative models of their impacts, which has resulted in few estimates
 matching the scale of disease. Here we harness the rare dataset matching
 the spatial scale of pathogen invasion, host, and disease heterogeneity to
 estimate infection and mortality for the four most susceptible host
 species of Phytophthora ramorum, an invasive pathogen that drives the most
 important biological cause of tree mortality in a broad geographic region
 of coastal California and southwest Oregon. As of 2012, the most current
 field survey year, we estimate 17.5 (± 4.6 95% CI) million tanoak
 (Notholithocarpus densiflorus) stems were pathogen-killed with an
 additional 71 (± 21.5) million infected. We estimated 9.0 million (± 2.2)
 coast live oak (Quercus agrifolia) and 1.7 million (± 0.5) California
 black oak (Quercus kelloggii) stems are disease impacted (mortality and
 infection combined). Lastly, our estimates showed 95.23 million (± 8.6)
 million infected California bay laurel (Umbellularia californica), which
 does not suffer mortality from infection and represents a critical source
 of continued spread. Using an extensive dataset on mortality rates of
 infected individuals we estimate that cumulative mortality likely
 increased from 20.8 to 42.8 million individual stems between 2012 and 2019
 for all species. While these impacts are substantial, the majority of host
 populations occur in a yet to be invaded region of northern California
 indicating that the disease will intensify in the coming decades.
description: Field data were collected with a standardized fixed plot survey
 using 1/20 ha plots and a survey of all stems greater than or equal to 1cm
 diameter at breast height. Counts of infected trees are those from plots
 with laboratory confirmation of infection (direct pathogen culturing).
 Host maps and environmental variables are derived data and details of the
 methods and sources are described in the accompanying meta data. Field
 data was processed following entry into a standardized Access database and
 packages into individual queries for species counts, mortality, and
 infection within species. Model derived data can be reproduced via the
 accompanying R code by using the stacked sets of rasterized environmental
 data and host maps.
description: The document "Cobb_et_al_Metadata.docx" explains how
 the data were used in processing. The R file titled
 "Cobb_et_al_SOD_impact_estimation.r" computes the models,
 generates the outputs, and does model validation and assessment.
DOI: 10.5061/dryad.80gb5mknk
title: Does breeding season variation affect evolution of a sexual signaling trait in a tropical lizard clade?

description: Sexually selected traits can be expected to increase in importance when
 the period of sexual behavior is constrained, such as in seasonally
 restricted breeders. Anolis lizard male dewlaps are classic examples of
 multifaceted signaling traits, with demonstrated intraspecific
 reproductive function reflected in courtship behavior. Fitch and Hillis
 found a correlation between dewlap size and seasonality in mainland Anolis
 using traditional statistical methods. Here, we present two tests of the
 Fitch-Hillis Hypothesis using new phylogenetic and morphological data sets
 for 44 species of Mexican Anolis. A significant relationship between
 dewlap size and seasonality is evident in phylogenetically uncorrected
 analyses but erodes once phylogeny is accounted for. This loss of strong
 statistical support for a relationship between a key aspect of dewlap
 morphology and seasonality also occurs within a species complex (A.
 sericeus group) that inhabits seasonal and aseasonal environments. Our
 results fail to support seasonality as a strong driver of evolution of
 Anolis dewlap size. We discuss the implications of our results and the
 difficulty of disentangling the strength of single mechanisms on trait
 evolution when multiple selection pressures are likely at play.
description: Standardized photos of animals were taken in the field,
 localities recorded via GPS, and dewlap size data extracted using ImageJ.
 Seasonality data (BIO15 from Bioclim) from collection
 localities were extracted using QGIS.
description: Data are very straight-forward and there are no missing values.
 There are two primary datasets. One (interspecies data) represents 41
 species of Mexican anoles and another (silky anoles) represents only the
 <em>Anolis sericeus</em> complex. Data
 files contain locality (latitude and longitude), values for head length
 (in mm), values for dewlap size (in mm2), and seasonality (BIO15 from
 Bioclim). For the interspecies analyses, data for head length and dewlap
 size were log-transformed and names for each species from the phylogenetic
 tree used (Poe et al. 2017) for PGLS. Information on date and season (Dry
 or Wet) of collection are also included. Input files
 for calculating the intra-class correlation coefficients for dewlap size
 and seasonality are also included.