cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.wstqjq2r1
title: Data from: Phylogenetic conflict between species tree and maternally inherited gene trees in a clade of Emberiza buntings (Aves: Emberizidae)

description: Different genomic regions may reflect conflicting phylogenetic topologies
 on account of incomplete lineage sorting and/or gene flow. Genomic data
 are necessary to reconstruct the true species tree and explore potential
 causes of phylogenetic conflict. Here, we investigate the phylogenetic
 relationships of four Emberiza species (Aves: Emberizidae) and discuss the
 potential causes of the observed mitochondrial non-monophyly of Emberiza
 godlewskii (Godlewski's bunting) using phylogenomic analyses based on
 whole genome resequencing data from 41 birds. Phylogenetic analyses based
 on both the whole mitochondrial genome and ~39 kilobases from the
 non-recombining W chromosome reveal that the northern and southern
 populations of E. godlewskii are each sister to E. cioides and E. cia,
 respectively. In contrast, phylogenetic analysis based on genome-wide data
 support the monophyly of E. godlewskii with the following tree topology:
 (((E. godlewskii, E. cia), E. cioides), E. jankowskii). Using
 D-statistics, we detected multiple gene flow events among different
 lineages, indicating pervasive introgressive hybridization within this
 clade. Introgression from an unsampled lineage that is sister to E.
 cioides or introgression from an unsampled mitochondrial + W chromosomal
 lineage of E. cioides into northern E. godlewskii may explain the
 phylogenetic conflict between the species tree estimated from genome-wide
 data and mtDNA/W trees. These results underscore the importance of using
 genomic data for phylogenetic reconstruction and species delimitation.
description: Dataset and supporting information from the manuscript of
 Phylogenetic conflict between species tree and maternally inherited gene
 trees in a clade of Emberiza buntings (Aves: Emberizidae).
description: These files contains original fasta or vcf file for phylogenetic analyses
 in the manuscript USYB-2023-045 File "Concatenated_NRW.fas"
 contains aligned NRW sequences; File "Dsuite_output_data.txt"
 contains output data of Dsuite analysis; huimei, liban, sandaomei, south
 and north represent E. cia, E. jankowskii, E. cioides, southern E.
 godlewskii and northern E. godlewskii, respectively; BBAA, ABBA and BABA
 represents the counts conform to the corresponding site patterns; for
 other parameters, please refer to Dsuite tutorial; File
 "ldfil.recode.vcf.gz" contains linkage disequilibrium pruned vcf
 file; File "mitochondrial_cytb.fas" contains aligned
 mitochondrial cytb sequences; File
 "mitochondrial_other_sequences.fas" contains aligned
 mitochondrial sequences without cytb gene File "MP-EST_input_20000
 trees.rar" contains 20000 sliding window trees for the input to
 MP-EST analysis; File
 "ALSTRAL_input_trees_of_Z_chromosome.trees" contains 3583
 sliding window trees from chromosome Z for the input to ASTRAL analysis;
 File "Supporting_information.pdf" contains supplementary
 methods, tables and figures.
DOI: 10.5061/dryad.w0vt4b8w6
title: Tsetse flies (Glossina m. morsitans) choose birthing sites guided by substrate cues with no evidence for a role of pheromones

description: Tsetse flies significantly impact public health and economic development
 in sub-Saharan African countries by transmitting the fatal disease African
 trypanosomiasis. Unusually, instead of laying eggs, tsetse birth a single
 larva that immediately burrows into the soil to pupate.  Where
 the female chooses to larviposit is therefore crucial for offspring
 survival. Previous laboratory studies suggested that a putative larval
 pheromone, n-pentadecane, attracts gravid female Glossina morsitans
 morsitans to appropriate larviposition sites. However, this attraction
 could not be reproduced in field experiments. Here, we resolve this
 disparity by designing naturalistic laboratory experiments that closely
 mimic the physical characteristics found in the wild. We show that gravid
 G. m. morsitans were neither attracted to the putative pheromone nor,
 interestingly, to pupae placed in the soil.  In contrast, females
 appear to choose larviposition sites based on environmental substrate
 cues. We conclude that, among the many cues that likely contribute to
 larviposition choice in nature, substrate features are a main determinant,
 while we failed to find evidence of a role of pheromones.
description: The dataset was collected in grouped non-forced two-choice
 experiments as described in 10.1098/rspb.2023.0030. Briefly, heavily
 pregnant female <em>Glossina morsitans morsitans</em> were
 given the choice between a) sand and leaf litter, b) putative pheromone
 and control (under leaf litter), and c) sand conditioned with fresh pupae
 and unconditioned sand (under leaf litter). Larviposition choice was
 recorded based on where the pupae were found: in the stimulus tray
 ("stim"), in the control tray ("con"), on the floor on
 the stimulus side ("stim.out"), or on the floor on the control
 side ("con.out"). Larvae could not cross the boundary between
 the two sides of the floor. Pupae were collected daily, and their average
 weight was determined at the end of each experiment. A
 Bayesian model of the data was built to verify the results.
 All data was analysed in R using custom-designed analysis
 scripts. 
description: The data is stored in .csv files. All data was analysed in R
 using custom-designed analysis scripts. The code for
 the Bayesian model is provided as an R markdown file.
DOI: 10.5061/dryad.8cz8w9gvx
title: Data for: A taxonomic revision of ten whitefish species from lakes Lucerne, Sarnen, Sempach, and Zug, Switzerland, with descriptions of seven new species (Teleostei, Coregonidae)

description: The taxonomy of the endemic whitefish of the lakes of the Reuss River
 system (Lucerne, Sarnen, Zug) and Lake Sempach, Switzerland, is reviewed
 and revised. Lake Lucerne harbours five species. Coregonus
 intermundia sp. nov. and C.
 suspensus sp. nov., are described. Coregonus
 nobilis Haack, 1882, C. suidteri Fatio, 1885,
 and C. zugensis Nüsslin, 1882, are redescribed. Genetic
 studies have shown that C. suidteri and C.
 zugensis are composed of several distinct species endemic to
 different lakes. The names C. suidteri and C.
 zugensis are restricted to the species of lakes Sempach and Zug,
 respectively. The whitefish populations previously referred to
 as C. suidteri and C. zugensis from
 Lake Lucerne are described as C. litoralis sp.
 nov. and C. muelleri sp. nov., respectively.
 Furthermore, the whitefish from Lake Zug that were previously referred to
 as C. suidteri are described as C.
 supersum sp. nov. A holotype is designated for C.
 supersum that was previously one of two syntypes of C.
 zugensis. The other syntype is retained for C.
 zugensis. Coregonus obliterus sp. nov. is
 described from Lake Zug, and C.
 obliterus and C. zugensis from Lake Zug are
 extinct. Finally, we describe C. sarnensis sp.
 nov. from lakes Sarnen and Alpnach. Coregonus
 suidteri from Lake Sempach shows strong signals of introgression
 from deliberately translocated non-native whitefish species, which
 questions if the extant population still carries a genetic legacy from the
 original species and thus may need to be considered
 extinct. Coregonus suspensus is genetically partially of
 allochthonous origin, closely related to the radiation of Lake Constance.
 It is therefore compared to all known and described species of Lake
 Constance: C. wartmanni Bloch, 1784, C.
 macrophthalmus Nüsslin, 1882, C.
 arenicolus Kottelat,1997, and C.
 gutturosus Gmelin, 1818.
description: See Material and Methods section in Selz et al. (2020 and
 2022).
description: Selz_and_Seehausen_2023.xlsx
 Readme_Selz_and_Seehausen_2023.rtf
DOI: 10.5061/dryad.mgqnk993g
title: Survival data from: Canopy buffering effects

description: Forest ecosystems can buffer understorey microhabitats and provide refuge
 for understorey species in a warming world. These effects are dependent on
 forest complexity and management. However, the roles of soils and bedrock
 types are less known although they also may affect forest complexity. We
 assessed differences in buffering effects of deciduous broad-leaved
 forests from calcareous and siliceous soils in the temperate climate of
 south-west France predicted to become dryer with climate change. We
 transplanted during dry and wet years, without and with neighbours
 (herbaceous and shrubs from forest understories and gaps), six species in
 gaps and dense forests of the two soil types. Target species originated
 from contrasting light availabilities and the two soil types. We measured
 transplant survival, light transmission, air temperature and vapour
 pressure deficit (VPD) in all treatments. Forest structure and soil
 parameters were also quantified on both bedrocks. Forest structure
 complexity was higher and light transmission lower on calcareous than
 siliceous soils. Relative air humidity was higher and maximum air
 temperature and VPD lower in the understorey of calcareous than siliceous
 forests, while soil nutrients and moisture were lower in siliceous soils.
 We found strong direct facilitation of transplants from shaded habitats by
 calcareous forest canopies during dry years. Facilitation of forest
 canopies was much weaker on siliceous bedrocks, during wet years and for
 species from sunny habitats. Facilitative responses were less obvious but
 still observed in the presence of understorey neighbours. Calcareous
 forests showed a stronger buffering ability than siliceous ones due to
 both higher facilitative effects of calcareous woody dominants and lower
 survival in calcareous gaps during dry years. Considering that the two
 forest types were old forests with similar management histories,
 differences in buffering ability between them were likely due to
 differences in forest complexity and composition induced by differences in
 soil types.
description: Experiment on including species transplantations with and without
 neighbours under forests and in graslands during 4 years on two
 bedrocks.
description: Excel and Word
DOI: 10.5061/dryad.jsxksn0f3
title: Data from: A new species of the Triassic genus Ideliopsina (Grylloblattida: Ideliidae) from the Ominé locality (Momonoki Formation, southwest Japan)

description: A new species of Grylloblattida, Ideliopsina aristovi sp. nov., is
 described from the Upper Triassic Ominé locality (Momonoki Formation, Mine
 Group, Japan). It belongs to a typical Triassic
 genus, Ideliopsina Storozhenko, 1996, which species have
 been previously reported from the Kyrgyz Republic and the
 Kazakhstan in Central Asia. The new species shows that the
 corresponding family, the Ideliidae ranging from the Cisuralian
 to the Late Triassic, remained widely distributed during the
 latter period, before its extinction.
description: The dataset contains two RTI (Reflectance Transformation Imaging)
 of the fossil specimen MMHF-3-00101 (Mine City Museum of History and
 Folklore, Japan), with 'p' in the file name accounting for
 'part' (wing viewed as if observed dorsally) and 'cp’
 accounting for 'counter-part' (wing viewed as if observed
 ventrally). Each RTI file composing this dataset was
 derived from a set of 54 photographs obtained using a light dome of about
 30 cm in diameter and equipped with 54 LEDs. Both the light dome and
 camera (a Canon EOS 5DS equipped with a MP-E 65 mm macro lens, all Canon,
 Tokyo, Japan) were driven by a control box (dome and control box, Flydome,
 Paris, France). Obtained images were then batch-optimized using Adobe
 Photoshop CS6 and were further compiled into an RTI file using the RTI
 Builder software v. 2.0.2 using the HSH fitter (software freely available
 from Cultural Heritage Imaging, San Francisco, CA, USA).
description: The RTI files composing this dataset can be opened using
 RTIviewer (software freely available from Cultural Heritage Imaging, San
 Francisco, CA, USA).
DOI: 10.5061/dryad.3xsj3txm3
title: Habitat isolation interacts with top-down and bottom-up processes in a seagrass ecosystem

description: Habitat loss is accelerating at unprecedented rates, leading to the
 emergence of smaller, more isolated habitat remnants. Habitat isolation
 adversely affects many ecological processes independently, but little is
 known about how habitat isolation may interact with ecosystem processes
 such as top-down (consumer-driven) and bottom-up (resource-driven)
 effects. To investigate the interactive influence of habitat isolation,
 resource availability and consumer distribution and impact on community
 structure, we tested two hypotheses using invertebrate and algal epibionts
 on temperate seagrasses, an ecosystem of ecological and conservation
 importance. First, we hypothesized that habitat isolation will change the
 structure of the seagrass epibiont community, and isolated patches of
 seagrass will have lower epibiont biomass and different epibiont community
 composition. Second, we hypothesized that habitat isolation would mediate
 top-down (i.e., herbivory) and bottom-up (i.e., nutrient enrichment)
 control for algal epibionts. We used observational studies in natural
 seagrass patches, and experimental artificial seagrass to examine three
 levels of habitat isolation. We further manipulated top-down and bottom-up
 processes in artificial seagrass through consumer reductions and nutrient
 additions, respectively. We indeed found that habitat isolation of
 seagrass patches decreased epibiont biomass and modified epibiont
 community composition. This pattern was largely due to dispersal
 limitation of invertebrate epibionts that resulted in a decline in their
 abundance and richness in isolated patches. Further, habitat isolation
 reduced consumer abundances, weakening top-down control of algal epibionts
 in isolated seagrass patches. Nutrient additions, however, reversed this
 pattern, and allowed a top-down effect on algal richness to emerge in
 isolated habitats, demonstrating a complex interaction between patch
 isolation and top-down and bottom-up processes. Habitat isolation may
 therefore shape the relative importance of central processes in
 ecosystems, leading to changes in community composition and food web
 structure in marine habitats.
description: This data was collected using natural and artificial seagrass
 units. The epibionts on the seagrass blades were identified, enumerated,
 and incinerated for ash free dry weight.
description: Excel, Google Sheets
DOI: 10.25338/b8dh0c
title: Data from: Wound healing and pain sensitivity following caustic paste disbudding in dairy calves

description: Caustic paste disbudding is increasing in popularity on commercial dairy
 farms in the U.S., but little research has explored the pain and
 welfare implications beyond the acute period of this procedure.
 Researchers have reported it takes 7 to 9 wk, on average, for hot-iron
 disbudding wounds to re-epithelialize in dairy calves. Our objective was
 to describe wound healing and sensitivity following caustic paste
 disbudding. Jersey and Holstein female calves were disbudded using Dr.
 Naylor’s caustic paste at 3 d of age (n = 18) while control calves
 received a sham procedure (n = 15). Before disbudding, calves received a
 local block and an NSAID. Calves ≥ 34 kg and &lt; 34 kg at birth had
 0.3 or 0.25 ml of paste applied per unshaved horn bud, respectively.
 Following disbudding, wounds were scored 2x/wk for the presence/absence of
 8 tissue categories including the final stages: new epithelium and fully
 healed. Control calves were removed from the experiment after 6 wk to be
 hot-iron disbudded and avoid more invasive procedures. Mechanical
 nociceptive threshold (MNT) measures were collected weekly to evaluate
 wound sensitivity until calves were removed from the study or wounds were
 healed. Wounds were slow to re-epithelialize (16.2 ± 5.7 wk, mean ± SD;
 range: 6.2–32.5 wk) and contract to be considered fully healed (18.8 ± 6
 wk, mean ± SD; range: 8.7–34.1 wk). Compared to non-disbudded controls,
 paste calves exhibited lower MNT values for all 6 wk (mean ± SE,
 Control:1.46 ± 0.16; Paste:1.18 ± 0.12 N). These data indicate that wounds
 from caustic paste disbudding are more sensitive than undamaged tissue for
 at least 6 wk and take twice as long to heal compared to cautery methods
 described in the literature. In conclusion, caustic paste disbudding
 wounds took 18.8 wk to fully heal and were more sensitive than intact horn
 buds for 6 wk. Future work should examine if aspects of paste application
 (e.g., amount, time rubbed in, age, pain mitigation), could improve
 healing time and sensitivity.
description: Please see the description in the associated research
 publication. 
description: Please see the included README file.
DOI: 10.15468/dl.8jgfq6
title: Occurrence Download

description: A dataset containing 39802920 species occurrences available in GBIF matching the query:
{
 "Country" : [
 "is Mexico"
 ]
}

 The dataset includes 39802920 records from 4806 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002822-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d3smcx
title: Occurrence Download

description: A dataset containing 2338 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "OccurrenceStatus is Present",
 "TaxonKey is Vulpes velox (Say, 1823)"
 ]
}

 The dataset includes 2338 records from 58 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012338-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g8uhm5
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Platytroctes apus Günther, 1878",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((40.877 -22.4563,40.8172 -22.0642,40.48 -21.825,40.0801 -21.8881,39.8467 -22.172,39.8612 -22.5315,40.2159 -22.8442,40.6757 -22.7649,40.877 -22.4563))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012339-250525065834625/datasets/export for details.
DOI: 10.15468/dl.5bzrhf
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Gouinia paraguayensis (Kuntze) Parodi",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 18 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012340-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/12019988
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.exk82z
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Platytroctes apus Günther, 1878",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((43.4313 -17.5054,43.9059 -19.9421,43.0686 -21.0649,42.7023 -21.9969,43.1619 -23.5254,43.213 -24.5373,43.6164 -25.1504,44.9648 -25.1504,44.9648 -16.1504,43.978 -16.1504,43.9239 -16.5407,43.4313 -17.5054))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012342-250525065834625/datasets/export for details.
DOI: 10.15468/dl.krucmg
title: Occurrence Download

description: A dataset containing 153 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Gueldenstaedtia verna (Georgi) Boriss.",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 153 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012343-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jnfgpg
title: Occurrence Download

description: A dataset containing 61786 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Paspalum dilatatum Poir."
 ]
}

 The dataset includes 61786 records from 1043 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012320-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xhpysh
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Platytroctes apus Günther, 1878",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((42.8012 -16.5547,42.4342 -16.6376,42.2188 -17.038,42.391 -17.4288,42.6657 -17.5533,43.0375 -17.4752,43.2579 -17.0968,43.0959 -16.69,42.8012 -16.5547))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012345-250525065834625/datasets/export for details.
DOI: 10.60508/k3z8-cd24
title: NIDX: A Machine Learning Approach for Identifying People with Neuroinfectious Diseases in Electronic Health Records

description: We developed a machine learning model to identify neuroinfectious diseases
(NID) from electronic health record notes. Using 3,000 notes from Mass General
Brigham, we trained an XGBoost model on text features extracted from clinical
documentation. Our model achieved excellent performance with an AUROC of 0.977
and AUPRC of 0.894 on internal validation, significantly outperforming both
ICD-code based identification (which showed high sensitivity of 97.1% but poor
specificity of 59.1%) and zero-shot classification using LLaMA 3.2 (AUROC
0.80). The model maintained strong performance when tested on an external
dataset of 600 notes from Beth Israel Deaconess Medical Center (AUROC 0.976,
AUPRC 0.779). This approach provides an accurate, automated method for
identifying patients with neuroinfectious diseases from clinical notes,
enabling more precise cohort creation for research compared to traditional ICD
code-based methods.