cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.12jm63xz8
title: Data from: A new composite abundance metric detects stream fish declines and community homogenization during six decades of invasions

description: Aim: We developed a new technique, utilizing species-specific counts of
 individuals from historical fish community samples, to examine
 landscape-level, spatiotemporal trends in relative abundance
 distributions. Abundance-based historical distribution analyses are often
 plagued by data comparability issues, but provide critical information
 about community composition trends inaccessible to those using analyses
 based only on species presence-absence. We established trends in native
 and non-native fish abundance and community homogenization, uniqueness,
 and diversity to help local conservation managers prioritize targets and
 motivate similar studies globally to support fish conservation.
 Location:  Upper and middle New River (UMNR) basin, Appalachian
 Mountains, USA. Methods: We compiled catch data from 61 years of fish
 community surveys (1958-2019) and tested for community homogenization by
 comparing data from repeatedly sampled sites (1900s versus 2000s samples)
 using dispersion analyses. We measured community uniqueness (site
 contributions to beta diversity) and species diversity (Shannon index) at
 sampled streams to identify potential conservation hotspots. We then used
 regression analyses and Wilcoxon signed-rank tests to examine
 species-specific basin-wide and local abundance trends and identify
 species of potential conservation concern. Results: Dispersion of sites in
 species-abundance space was significantly greater in the 1900s compared to
 the 2000s, indicating homogenization had occurred. Of 36 native species
 analyzed, 44.4% (16) showed basin-wide declines. Non-native species
 exhibited mixed patterns; site-level abundance increased in 2 of 15
 species analyzed (13%). Main conclusions: Our results indicate basin-wide
 community homogenization has occurred within the UMNR, but many unique and
 diverse communities persist. If conserved, these could help maintain
 regional fish diversity. We found basin-wide declines in four endemic
 species, as well as spread patterns of non-native and native species that
 were not detected by a presence-absence analysis applied within the same
 study area. This finding illustrates the importance of considering both
 species’ abundance and occurrence patterns as separate dimensions of
 biodiversity to inform conservation planning.
description: These data represent Scaled Composite Species Abundance scores
 (SCSAs; described in text) across 638 unique year- and NHD+ v2 flowline
 segment-specific records, derived from historical fish community data
 across the upper and middle New River basin (UMNR). For more
 information please contact Logan Sleezer at slogan3@vt.edu.
DOI: 10.5061/dryad.5dv41ns6b
title: Evolution of winter moulting strategies in European and North American migratory passerines

description: Moult is critical for birds as it replaces damaged feathers and worn
 plumage, enhancing flight performance, thermoregulation, and
 communication. In passerines, moult generally occurs on the breeding
 grounds during the post-breeding period once a year. However, some species
 of migrant passerines that breed in the Nearctic and western Palearctic
 regions have evolved different moulting strategies that involve moulting
 on the overwintering grounds. Some species forego moult on the breeding
 grounds and instead complete their prebasic moult on the overwintering
 grounds. Other species moult some or all feathers a second time
 (prealternate moult) during the overwintering period. Using phylogenetic
 analyses, we explored the potential drivers of the evolution of winter
 moults in Nearctic and western Palearctic breeding passerines. Our results
 indicate an association between longer photoperiods and the presence of
 prebasic and prealternate moults on the overwintering grounds for both
 Nearctic and western Palearctic species. We also found a relationship
 between prealternate moult and generalist and water habitats for western
 Palearctic species. Finally, the complete prealternate moult in western
 Palearctic passerines was linked to longer days on the overwintering
 grounds and longer migration distance. Longer days may favour the
 evolution of winter prebasic moult by increasing the time window when
 birds can absorb essential nutrients for moult. Alternatively, for birds
 undertaking a prealternate moult at the end of the overwintering period,
 longer days may increase exposure to feather-degrading ultra-violet
 radiation, necessitating the replacement of feathers. Our study underlines
 the importance of the overwintering grounds in the critical process of
 moult for many passerines that breed in the Nearctic and western
 Palearctic regions.
DOI: 10.5061/dryad.z8w9ghxcp
title: Ethnobotanical study of medicinal plants used by Ensaro people to treat human diseases

description: Abstract Introduction: - People all over the world have been using
 medicinal plants to treat various ailments and diseases throughout
 history. It is still common in developing countries. Because is easily
 accessible, affordable, and trusted by the communities. Although there are
 several ethnobotanical studies on medicinal plants in Ethiopia, the number
 of medicinal plant species and indigenous knowledge documented is still
 low compared to the high diversity of culture and habitats. Methods: -
 Ethnobotanical data were collected during the 13th of February 2019 and
 the 26th of October 2020 through Semi-structured interviews, field
 observation, a guided field walk, and focus group discussions Result: -
 the study documented 142 medicinal plant species distributed in 125 genera
 and 56 families which used to treat 52 ailments. Most of these species
 were collected from wild habitats. The most used plant families were
 Fabaceae (14) followed by lamiaceae (9) and Solanaceae (9). Most of these
 medicinal plants were herbs followed by shrubs. Conclusion The study
 revealed a relatively high diversity of medicinal plants that indicated
 the existence of indigenous knowledge of using medicinal plants to treat
 ailments and diseases. The findings of this study supported up the idea
 that indigenous knowledge of using medicinal plants is still alive in
 highly degraded areas. To make sustainable use of these medicinal plants
 in the study area, local people must collaborate with natural resource
 administrators to manage them before they become seriously threatened.
 Both ex-situ and In-situ conservation strategies should be combined and
 employed urgently for optimal conservation results
DOI: 10.5061/dryad.cjsxksn66
title: Dimethyl sulfide mediates microbial predator-prey interactions between zooplankton and algae in the ocean

description: Phytoplankton are key components of the oceanic carbon and sulfur cycles.
 During bloom events, some species can emit large amounts of the
 organosulfur volatile dimethyl sulfide (DMS) into the ocean, and
 consequently the atmosphere, where it can modulate aerosol formation and
 affect climate. In aquatic environments, DMS plays an important role as a
 chemical signal mediating diverse trophic interactions. Yet, its role in
 microbial predator-prey interactions remains elusive with contradicting
 evidence for its role in either algal chemical defense or in the
 chemoattraction of grazers to prey cells. Here, we investigated the
 signaling role of DMS during zooplankton-algae interactions by genetic and
 biochemical manipulation of the algal DMS-generating enzyme
 dimethylsulfoniopropionate lyase (DL) in the bloom-forming alga Emiliania
 huxleyi. We inhibited DL activity in E. huxleyi cells in-vivo using the
 selective DL-inhibitor 2-bromo-3-(dimethylsulfonio)-propionate (Br-DMSP),
 and overexpressed the DL encoding gene in the model diatom Thalassiosira
 pseudonana. We showed that algal DL activity did not serve as an
 anti-grazing chemical defense, but paradoxically enhanced predation by the
 grazer Oxyrrhis marina and other micro- and mesozooplankton, including
 ciliates and copepods. Consumption of algal prey with induced DL activity
 also promoted O. marina growth. Overall, our results demonstrate that
 DMS-mediated grazing may be ecologically important and prevalent during
 prey-predator dynamics in aquatic ecosystems. The role of algal DMS
 revealed here, acting as an eat-me signal for grazers, raises fundamental
 questions regarding the retention of its biosynthetic enzyme through the
 evolution of dominant bloom-forming phytoplankton in the ocean.
description: This data set includes prey and predator cell count analysis from
 grazing experiments. The data was collected by flow cytometry or manually
 with a microscope. In addition, microscopy images are
 provided for the phytoplankton and microzooplankton used in the
 study.
DOI: 10.5061/dryad.fn2z34ttx
title: Electrophysiological recordings and a liposome-based assay showing the absence of chloride and proton conduction in TTYH proteins

description: The Tweety homologues (TTYHs) are members of a conserved family of
 eukaryotic membrane proteins that are abundant in the brain. The three
 human paralogs were assigned to function as anion channels that are either
 activated by Ca2+ or cell swelling. To uncover their unknown architecture
 and its relationship to function, we have determined the structures of
 human TTYH1–3 by cryo-electron microscopy. All structures display
 equivalent features of a dimeric membrane protein that contains five
 transmembrane segments and an extended extracellular domain.  As
 none of the proteins shows features reminiscent of an anion channel, we
 revisited functional experiments and did not find any indication of ion
 conduction. Instead, we find density in an extended hydrophobic pocket
 contained in the extracellular domain that emerges from the lipid bilayer,
 which suggests a role of TTYH proteins in the interaction with lipid-like
 compounds residing in the membrane.
DOI: 10.5061/dryad.9p8cz8wgq
title: Scoring of research priorities for the Philippine Liver Research Network

description: Health research networks are viewed as an avenue through which complex
 health problems can be solved. Networks apply multidisciplinary expertise
 and methodologies to strengthen current evidence for a particular disease
 or condition. In 2019, the Philippine Council for Health Research
 Development signed a bilateral agreement with the Fondazione Italiana
 Fegato. Recognizing the need for liver research in the Philippines, one of
 their main areas of collaboration is the creation of the Philippine Liver
 Research Network. This exercise aimed to develop a research agenda for the
 network. This research priority-setting exercise followed steps based on
 the Philippine National Health Research System Guidelines for Health
 Research Prioritization and the James Lind Alliance framework: 1) identify
 stakeholders to participate, 2) map existing liver studies in the
 Philippines, 3) generation of the interim list of priorities, 4) research
 priority-setting consultation, and 5) seeking feedback on the research
 agenda from stakeholders. Seven stakeholders participated in the research
 priority-setting exercise. Soliciting research questions from stakeholders
 resulted in sixty-five initial research priorities. The final research
 agenda was selected through criteria selection, weight assignment, and
 scoring of each research priority in a consultation. The Philippine Liver
 Research Network aims to consolidate and capitalize on multi-sectoral and
 mult-disciplinary collaboration opportunities to advance liver health
 research in the country. With the eventual establishment of the network,
 the interdisciplinary research agenda presents an important opportunity
 for further funding. Although the network is currently in its early stages
 of formation, this exercise may serve to aid in further organizing the
 network and its stakeholders under the research agenda for 2020-2022.
description: This dataset was generated as part of the research priority
 setting process, during the consutlation to finalize the research agenda
 of the Philippine Liver Research Network.  To determine
 the criteria through which the priorities will be evaluated, participants
 were asked to generate criteria individually. Each participant was given
 time to explain their suggested criteria to the group. The final criteria
 and weight assignments per criteria was decided as a plenary. Scoring of
 the research priorities was done individually and anonymously using the
 criteria and weights developed by the participants through paper forms. To
 minimize order bias, the list of research priorities were randomized in
 each paper form between participants. As recommended by the
 James Lind Alliance framework, only the top 10 research priorities were
 included in the research agenda and were presented to the
 participants.
DOI: 10.5061/dryad.mw6m905x4
title: Pollinator community predicts trait-matching between oil-producing flowers and a guild of oil-collecting bees

description: The impact of pollinator community diversity on trait-matching in
 plant-pollinator interactions is poorly studied, even though many
 mutualisms involve multiple interaction partners. We studied ten
 communities in which one to three species of oil-collecting Rediviva bee
 pollinate the long-spurred, oil-producing flowers of
 Diascia ‘floribunda’ to examine how pollinator diversity affects
 covariation of functional traits across sites and trait-matching within
 sites. Floral spur-length was significantly correlated with weighted grand
 mean foreleg length of the local bee community but not with foreleg length
 of individual bee species. The closeness of trait-matching varied among
 populations and was inversely related to pollinator community diversity.
 For all bee species, trait-matching was closest at sites characterized by
 exclusive, pairwise interactions. Reduced trait-matching associated with
 increased community diversity for individual pollinator species, but close
 matching at the community level support the importance of community
 context for shaping interacting traits of flowers and pollinators.
description: The dataset contains the data of forleg length and spur length of
 all collected <em>Rediviva </em>bees and <em>Diascia
 </em>flowers at each site.  Forelegs of 2–56
 females of each <i>Rediviva</i> species per site were
 measured. Bees were collected with a sweep net and stored in 96% ethanol.
 The right foreleg was removed and foreleg segments (disti + mediotarsus,
 basitarsus, tibia, femur, trochanter, coxa) were measured to the nearest
 0.01 mm using a Keyence VHX 500 F digital microscope following the method
 described by Steiner and Whitehead (1990). Foreleg length was calculated
 as the sum of the individual foreleg segments. The
 right spurs <em> </em>of freshly collected flowers of
 <em>Diascia floribunda </em>were longitudinally sectioned
 prior to measurement. Length of spur entrance area, proximal and apical
 elaiophores fields and the gap between fields were measured to the nearest
 0.01 mm using a Dino-Lite Digital Microscope AD-413T as per the methods
 described in Hollens et al. (2017). Total spur length was calculated as
 the sum of the individual segments. Hollens H, van
 der Niet T, Cozien R, Kuhlmann M. 2017 A spur-ious inference: Pollination
 is not more specialized in long-spurred than in spurless species in
 <i>Diascia</i>-<i>Rediviva</i> mutualisms. Flora
 232, 73–82. (doi:10.1016/j.flora.2016.12.006) Steiner KE,
 Whitehead VB. 1990 Pollinator adaptation to oil-secreting flowers –
 <i>Rediviva</i> and <i>Diascia</i>.
 Evolution<i> </i>44, 1701–1707.
 (doi:10.1111/j.1558-5646.1990.tb03857.x)
DOI: 10.5061/dryad.6djh9w11s
title: Recoding amino acids to a reduced alphabet may increase or decrease phylogenetic accuracy

description: Common molecular phylogenetic characteristics such as long branches and
 compositional heterogeneity can be problematic for phylogenetic
 reconstruction when using amino acid data. Recoding alignments to reduced
 alphabets before phylogenetic analysis has often been used both to explore
 and potentially decrease the effect of such problems. We tested the
 effectiveness of this strategy on topological accuracy using simulated
 data on four-taxon trees. We simulated alignments in phylogenetically
 challenging ways to test the phylogenetic accuracy of analyses using
 various recoding strategies together with commonly-used homogeneous
 models. We tested three recoding methods based on amino acid
 exchangeability, and another recoding method based on lowering the
 compositional heterogeneity among alignment sequences as measured by the
 Chi-squared statistic. Our simulation results show that on trees with long
 branches where sequences approach saturation, accuracy was not greatly
 affected by exchangeability-based recoding, but Chi-squared-based recoding
 decreased accuracy. We then simulated sequences with different kinds of
 compositional heterogeneity over the tree. Recoding often increased
 accuracy on such alignments. Exchangeability-based recoding was rarely
 worse than not recoding, and often considerably better. Recoding based on
 lowering the Chi-squared value improved accuracy in some cases but not in
 others, suggesting that low compositional heterogeneity by itself is not
 sufficient to increase accuracy in the analysis of these alignments. We
 also simulated alignments using site-specific amino acid profiles, making
 sequences that had compositional heterogeneity over alignment sites.
 Exchangeability-based recoding coupled with site-homogeneous models had
 poor accuracy for these datasets but Chi-squared-based recoding on these
 alignments increased accuracy. We then simulated datasets that were
 compositionally both site- and tree-heterogeneous, like many real
 datasets. The effect on accuracy of recoding such doubly problematic
 datasets varied widely, depending on the type of compositional
 tree-heterogeneity and on the recoding scheme. Interestingly, analysis of
 unrecoded compositionally heterogeneous alignments with the NDCH or CAT
 models was generally more accurate than homogeneous analysis, whether
 recoded or not. Overall, our results suggest that making trees for recoded
 amino acid datasets can be useful, but they need to be interpreted
 cautiously as part of a more comprehensive analysis. The use of better
 fitting models like NDCH and CAT, which directly account for the patterns
 in the data, may offer a more promising long-term solution for analysing
 empirical data.
description: Datasets were simulated.
description: Dataset lengths are 10 million sites, which were divided into 100
 alignments of 100,000 sites each for analysis.
DOI: 10.5061/dryad.vmcvdncsz
title: Data from: Taxon-level assessment of the data collection quality in Atlas Florae Europaeae: insights from the case of Rosa (Rosaceae) in Eastern Europe

description: By the method of data re-collection and re-assessment, we tested the
 completeness of distribution areas of the species and species aggregates
 of Rosa in Eastern Europe as mapped in volume 13 of Atlas Florae
 Europaeae, and discussed insights into the issues connected with the data.
 We have found many new occurrences which are additions to the published
 maps: 1068 records of species and 570 records of species aggregates. The
 new occurrences are listed with references to the sources, and the updated
 AFE maps are provided. The greatest increase by new native occurrences was
 revealed for the species that are widespread or taxonomically complicated,
 and by new alien occurrences for the species that expand their secondary
 distribution areas. The mapping work published in 2004 is considered good,
 with minor omissions caused by possible oversights and incomplete
 sampling. The majority of new additions originated in the period after the
 original data collection. Nearly the same amount of new data originated
 from larger and smaller herbarium collections, underlining the value of
 small collections for chorological studies. We found that only ca. 20% of
 new records based on herbarium specimens have been published, thus
 highlighting the need of data papers for publication of distributional
 data. The greatest increase by new records based on herbarium specimens
 was found for insufficiently studied territories (Belarus, central,
 northern and eastern parts of Russia), whereas the same level of increase
 for the territories with reasonably good coverage (Latvia) was achieved by
 observations. We conclude that the overall sparsity of published records
 in Eastern Europe was caused by a lower level of data collection rather
 than by the poor data availability, and that floristic surveys based on
 herbarium specimens cannot compete in speed and density of records with
 observation-based surveys, which may become the main source of
 distributional information in the future.
description: The dataset was formed from distributional records available as
 herbarium specimens in public herbarium collections. The specimens were
 taxonomically verified by the authors.
DOI: 10.15468/dl.brp5a9
title: Occurrence Download

description: A dataset containing 7611812 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Artiodactyla"
 ]
}

 The dataset includes 7611812 records from 5976 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002886-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y3kzgg
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Sectoria heterognathos)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024849-250811113504898/datasets/export for details.
DOI: 10.15468/dl.xmwyss
title: Occurrence Download

description: A dataset containing 2729 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is one of (Asia, Africa, Europe)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Issue is one of (Continent derived from coordinates, Country derived from coordinates)",
 "OccurrenceStatus is Present",
 "TaxonKey is Crex crex (Linnaeus, 1758)",
 "Year 1901-1990"
 ]
}

 The dataset includes 2729 records from 76 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009850-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wvyy9j
title: Occurrence Download

description: A dataset containing 170 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Occurrence evidence, Specimen)",
 "Country is one of (Spain, Portugal)",
 "OccurrenceStatus is Present",
 "TaxonKey is Tricholoma acerbum (Bull.) Quél."
 ]
}

 The dataset includes 170 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009848-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.