cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.d315q
title: Data from: Divergent evolution and niche differentiation within the common peatmoss Sphagnum magellanicum

description: PREMISE OF THE STUDY: Populations with phenotypic polymorphism in discrete
 characters may be good models for investigating genome evolution and
 speciation. Sphagnum magellanicum Brid. is found throughout the northern
 hemisphere, and despite considerable variation in morphological
 characters, it is considered one of the least taxonomically controversial
 peatmoss species. We have observed two main morphs of the species
 associated with different microhabitats. Here we investigated the genomic
 and environmental basis of this intraspecific morphological variation.
 METHODS: We conducted transplant and common garden experiments to test
 whether the two morphs are genetically differentiated. We then used
 RAD-sequencing to quantify the genomic divergence between the morphs and
 approximate Bayesian computation (ABC) to infer the most likely
 demographic scenario explaining the genome-wide differentiation of the two
 morphs. KEY RESULTS: We found that genomic differentiation between the two
 morphs is unexpectedly high and that several of the differentiated
 morphological characters have a genetic basis. Using simulation
 approaches, we found support for a scenario of ancient divergence followed
 by recent secondary contact. CONCLUSIONS: We show that the two morphs
 represent the two main genetic clusters previously found worldwide. Our
 results demonstrate that relatively minor morphological differentiation in
 a presumed phenotypically plastic peatmoss may be associated with massive
 divergence across the genome.
description: Phylogenetic
 relationships between expanse and margin morphs of Sphagnum
 magellanicumPhylogenetic
 relationships between expanse and margin morphs of Sphagnum magellanicum
 using a maximum likelihood analysis in RAxML. The tree is rooted with the
 outgroup species, S. fallax. The two morphs form reciprocally monophyletic
 lineages with 100% bootstrap support. Branch support higher than 50 is
 shown.Fig
 7.tifRAxML_bipartitionsThe tree file generated by RAxML v. 8.2.4 and annotated by FigTree v. 1.4.3.The FASTA file of concatenated SNPsThe alignment file used to reconstruct the phylogenetic relationships of the plants representing the two morphs using maximum likelihood (ML) analysis in RAxML. SNPs were concatenated and converted to FASTA format (4274 SNPs). The sequence data corresponding to the SNP locations on the reference genome of S. fallax was extracted using a custom R script to be used as outgroup.magellanicum_fallax.fa
DOI: 10.17632/p5xpj4v73r
title: Spatial transcriptomic analysis reveals dysregulated pro-inflammatory signaling in the aged lung

description: Older individuals are more susceptible to viral and bacterial respiratory infections than younger people. While structural lung changes and a hyperinflammatory milieu have been proposed to contribute to worsened clinical outcomes, exact mechanisms remain elusive. Clinical specimens are challenging to obtain and although rodents are valuable models of human disease, their specific pathogen free status and inbred genetics limit translation of findings obtained from these models. We sought to address this question by analyzing the transcriptional landscape of lung tissue obtained from young and aged rhesus macaque using Visium spatial transcriptomics. Unlike rodents, captive rhesus macaques are genetically outbred and exposed to natural particulates and respiratory microbes that modulate their lung immunity. Analysis identified immune and structural cells clusters. Differential gene expression revealed a strong pro-inflammatory bias in aged animals while transcriptional signatures in young animals were consistent with a regulatory phenotype. Moreover, cellular signaling important for adhesion, tissue maintenance, and cell migration was significantly reduced in the aged compared to young lungs. These data indicate that aged lungs are skewed towards hyperinflammatory responses which are likely to result in higher immune mediated damage following challenge.
DOI: 10.17632/p5xpj4v73r.1
title: Spatial transcriptomic analysis reveals dysregulated pro-inflammatory signaling in the aged lung

description: Older individuals are more susceptible to viral and bacterial respiratory infections than younger people. While structural lung changes and a hyperinflammatory milieu have been proposed to contribute to worsened clinical outcomes, exact mechanisms remain elusive. Clinical specimens are challenging to obtain and although rodents are valuable models of human disease, their specific pathogen free status and inbred genetics limit translation of findings obtained from these models. We sought to address this question by analyzing the transcriptional landscape of lung tissue obtained from young and aged rhesus macaque using Visium spatial transcriptomics. Unlike rodents, captive rhesus macaques are genetically outbred and exposed to natural particulates and respiratory microbes that modulate their lung immunity. Analysis identified immune and structural cells clusters. Differential gene expression revealed a strong pro-inflammatory bias in aged animals while transcriptional signatures in young animals were consistent with a regulatory phenotype. Moreover, cellular signaling important for adhesion, tissue maintenance, and cell migration was significantly reduced in the aged compared to young lungs. These data indicate that aged lungs are skewed towards hyperinflammatory responses which are likely to result in higher immune mediated damage following challenge.
DOI: 10.5061/dryad.j1692
title: Data from: Antifungal activity of water-stable copper-containing metal–organic frameworks

description: Although metal-organic frameworks (MOFs) or porous coordination polymers
 have been widely studied, their antimicrobial activities have not yet been
 fully investigated. In this work, antifungal activity of copper-based
 benzene-tricarboxylate MOF (Cu-BTC MOF), which is water stable and
 industrially interesting, is investigated against Candida albicans,
 Aspergillus niger, Aspergillus oryzae and Fusarium oxysporum. The Cu-BTC
 MOF can effectively inhibit the growth rate of C. albicans and remarkably
 inhibit the spore growth of A. niger, A. oryzae and F. oxysporum. This
 finding shows the potential of using Cu-BTC MOF as a strong biocidal
 material against representative yeasts and moulds that are commonly found
 in the food and agricultural industries.
description: Physical properties of
 Cu-BTC and Antifungal activity results of CuBTC againt
 YeastPhysical properties of
 Cu-BTC and Antifungal activity results of CuBTC againt
 YeastAntifungal activity
 results of CuBTC againt Fungi
DOI: 10.5061/dryad.4c6t3
title: Data from: Pteris borneensis (Pteridaceae), a New Species from Borneo, with Re-circumscription of Pteris decrescens and Pteris parviloba

description: A new species was collected during a fern expedition in Nuluhon Trusmadi
 Forest Reserve, Sabah, Borneo. Morphologically, it is similar to both
 Pteris decrescens Christ and P. parviloba Christ but can be distinguished
 by the frond characters. Specifically, the new species differs from the
 other two species by having basiscopic secondary pinnae (vs. without
 basiscopic secondary pinnae), petiolulate pinnae (vs. sessile pinnae),
 without bristles on the stipes (vs. with bristles on the stipes), a
 crenate margin of the pinna-segment apex (vs. a serrate apex), and entire
 pseudoindusia (vs. ciliate pseudoindusia). Furthermore, P. decrescens and
 P. parviloba differ in the number of lateral pinnae (5 or 6 vs. 8–16
 pairs) and the length of the basal pinna-segments being shortest or
 longest of all lateral pinnae. Two plastid genes, rbcL and matK, were used
 to decipher their phylogenetic relationships. The new species was resolved
 in different clades from P. decrescens and P. parviloba, providing further
 support of its uniqueness. The morphology, illustrations, ecology, and
 distribution of the new species are provided. We also found that the type
 materials of P. decrescens included two different species, P. decrescens
 and P. parviloba. A lectotype of P. decrescens was therefore designated.
 Based on the results of this study, P. decrescens and P. parviloba are
 re-circumscribed, and the new species is described as P. borneensis sp.
 nov.
description: nex file for phylogeny
 reconstructiondec.nexTree filedec.best.treFIG. S1. A specimen with collection number J. Cavalerie 2038 in the herbarium at Royal Botanic Garden Edinburgh (E 00414276)Fig S1 Pteris decrescens_type_E00414276.tifFIG. S2. A specimen with collection number J. Cavalerie 2038 in the herbarium at New York Botanical Garden (NY00127508)Fig S2 Pteris decrescens Christ ( type )_NY00127508.tifFIG. S3. Lectotype of Pteris parviloba Christ in the herbarium at Royal Botanic Garden Edinburgh (E 00414277)Fig S3 Pteris parviloba_type_E00414277.tif
DOI: 10.15468/dl.ut4g79
title: Occurrence Download

description: A dataset containing 1782 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Laurus novocanariensis"
 ]
}

 The dataset includes 1782 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001505-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.jj264
title: Data from: Intraspecific niche models for ponderosa pine (Pinus ponderosa) suggest potential variability in population-level response to climate change.

description: Unique responses to climate change can occur across intraspecific levels,
 resulting in individualistic adaptation or movement patterns among
 populations within a given species. Thus, the need to model potential
 responses among genetically distinct populations within a species is
 increasingly recognized. However, predictive models of future
 distributions are regularly fit at the species level, often because
 intraspecific variation is unknown or is identified only within limited
 sample locations. In this study, we considered the role of intraspecific
 variation to shape the geographic distribution of ponderosa pine (Pinus
 ponderosa), an ecologically and economically important tree species in
 North America. Morphological and genetic variation across the distribution
 of ponderosa pine suggest the need to model intraspecific populations: the
 two varieties (var. ponderosa and var. scopulorum) and several haplotype
 groups within each variety have been shown to occupy unique climatic
 niches, suggesting populations have distinct evolutionary lineages adapted
 to different environmental conditions. We utilized a recently-available,
 geographically-widespread dataset of intraspecific variation (haplotypes)
 for ponderosa pine and a recently-devised lineage distance modeling
 approach to derive additional, likely intraspecific occurrence locations.
 We confirmed the relative uniqueness of each haplotype-climate
 relationship using a niche-overlap analysis, and developed ecological
 niche models (ENMs) to project the distribution for two varieties and
 eight haplotypes under future climate forecasts. Future projections of
 haplotype niche distributions generally revealed greater potential range
 loss than predicted for the varieties. This difference may reflect
 intraspecific responses of distinct evolutionary lineages. However,
 directional trends are generally consistent across intraspecific levels,
 and include a loss of distributional area and an upward shift in
 elevation. Our results demonstrate the utility in modeling intraspecific
 response to changing climate and they inform management and conservation
 strategies, by identifying haplotypes and geographic areas that may be
 most at risk, or most secure, under projected climate change.
description: Sampled occurrences and
 climate data..csv files for each
 variety and haplotype containing presence/absence locations and associated
 climate data used to fit ecological niche models.Occurrences.zipOnline AppendixOnline_Appendix_FINAL.pdf
DOI: 10.5061/dryad.3v2v5
title: Data from: Effective population sizes of a major vector of human diseases, Aedes aegypti

description: The effective population size (Ne) is a fundamental parameter in
 population genetics that determines the relative strength of selection and
 random genetic drift, the effect of migration, levels of inbreeding, and
 linkage disequilibrium. In many cases where it has been estimated in
 animals, Ne is on the order of 10-20% of the census size. In this study,
 we use 12 microsatellite markers and 14,888 single nucleotide
 polymorphisms (SNPs) to empirically estimate Ne in Aedes aegypti, the
 major vector of yellow fever, dengue, chikungunya, and Zika viruses. We
 used the method of temporal sampling to estimate Ne on a global dataset
 made up of 46 samples of Ae. aegypti that included multiple time points
 from 17 widely distributed geographic localities. Our Ne estimates for Ae.
 aegypti fell within a broad range (~25-3,000), and averaged between 400
 and 600 across all localities and time points sampled. Adult census size
 (Nc) estimates for this species range between one and five thousand, so
 the Ne/Nc ratio is about the same as for most animals. These Ne values are
 lower than estimates available for other insects and have important
 implications for the design of genetic control strategies to reduce the
 impact of this species of mosquito on human health.
description: Ae.aegypti_Ne_genepop_filesAedes aegypti microsatellite alleles and SNP-chip genotypes from a worldwide sample of populations in "genepop" format, used in estimates of Ne for this paper. Details of the "genepop" format can be found at http://genepop.curtin.edu.au. For the microsatellite genotyping, we used the protocol described in (Brown et al, 2011) for 12 loci; A1, B2, B3, A9, AC2, CT2, AG2, AC4, AC1, AC5, AG1, and AG4. Briefly, amplifications were performed using standard PCR protocol (35 cycles at 54˚C) with fluorescently labeled M13 primers (6-FAM and HEX) in 10.0 μl reaction volumes using the Type-it Microsatellite PCR Master Mix (Qiagen), then diluted, multiplexed, and submitted for fragment analysis with GS 500 ROX internal size standard (Applied Biosystems, Foster City, CA, USA) on an Applied Biosystems 3730xl DNA Genetic Analyzer at the DNA Analysis Facility on Science Hill at Yale. Alleles were scored using GeneMapper v4.0 (Applied Biosystems). For the SNP-chip genotyping, 167 samples were analyzed on the Axiom_aegypti1 SNP-chip (Evans et al, 2015) at the Functional Genomics Core at University of North Carolina, Chapel Hill, using manufacturer protocols. Raw data were processed and converted into genotype calls following Evans et al. (2015) using Genotyping Console v4.2 (Affymetrix, Santa Clara, CA, USA) and SNPolisher v1.4 (Affymetrix) in the R environment with the call threshold set to 95%. SNPs were pruned to remove any linked SNPs in PLINK v1.7 (Purcell et al, 2007) with the command “--indep 100 10 2”, which recursively removed SNPs within a sliding window of 100 SNPs wide, shifting 10 SNPs per step, with a variance inflation factor (i.e. VIF) threshold of 2.
DOI: 10.5061/dryad.kk04r
title: Data from: Aquatic animals promote antibiotic resistance gene dissemination in water via conjugation: role of different regions within the zebra fish intestinal tract, and impact on fish intestinal microbiota

description: The aqueous environment is one of many reservoirs of antibiotic resistance
 genes (ARGs). Fish, as important aquatic animals which possess ideal
 intestinal niches for bacteria to grow and multiply, may ingest antibiotic
 resistance bacteria from aqueous environment. The fish gut would be a
 suitable environment for conjugal gene transfer including those encoding
 antibiotic resistance. However, little is known in relation to the impact
 of ingested ARGs or antibiotic resistance bacteria (ARB) on gut
 microbiota. Here, we applied the cultivation method, qPCR, nuclear
 molecular genetic marker and 16S rDNA amplicon sequencing technologies to
 develop a plasmid-mediated ARG transfer model of zebrafish. Furthermore,
 we aimed to investigate the dissemination of ARGs in microbial communities
 of zebrafish guts after donors carrying self-transferring plasmids that
 encode ARGs were introduced in aquaria. On average, 15% of faecal bacteria
 obtained ARGs through RP4-mediated conjugal transfer. The hindgut was the
 most important intestinal region supporting ARG dissemination, with
 concentrations of donor and transconjugant cells almost 25 times higher
 than those of other intestinal segments. Furthermore, in the hindgut where
 conjugal transfer occurred most actively, there was remarkable
 upregulation of the mRNA expression of the RP4 plasmid regulatory genes,
 trbBp and trfAp. Exogenous bacteria seem to alter bacterial communities by
 increasing Escherichia and Bacteroides species, while decreasing Aeromonas
 compared with control groups. We identified the composition of
 transconjugants and abundance of both cultivable and uncultivable bacteria
 (the latter accounted for 90.4%–97.2% of total transconjugants). Our study
 suggests that aquatic animal guts contribute to the spread of ARGs in
 water environments.
description: Raw sequencing data of
 conjugative mixturesThis file gives the raw
 sequencing data of conjugative mixtures in zebrafish guts and feces, which
 provides information on the composition and abundance of
 transconjugants.Raw sequencing
 data.rar
DOI: 10.5061/dryad.4pb80
title: Data from: Novel and divergent genes in the evolution of placental mammals

description: Analysis of genome sequences within a phylogenetic context can give
 insight into the mode and tempo of gene and protein evolution, including
 inference of gene ages. This can reveal whether new genes arose on
 particular evolutionary lineages and were recruited for new functional
 roles. Here, we apply MCL clustering with all-vs-all reciprocal BLASTP to
 identify and phylogenetically date ‘Homology Groups’ amongst vertebrate
 proteins. Homology Groups include new genes and highly divergent duplicate
 genes. Focussing on the origin of the placental mammals within the
 Eutheria, we identify 357 novel Homology Groups that arose on the stem
 lineage of Placentalia, 87 of which are deduced to play core roles in
 mammalian biology as judged by extensive retention in evolution. We find
 the human homologues of novel eutherian genes are enriched for expression
 in preimplantation embryo, brain, and testes, and enriched for functions
 in keratinization, reproductive development, and the immune system.
description: List of all protein IDs
 and Homology GroupsList of protein IDs
 (combined Ensembl/NCBI) for a range of vertebrate species, and their
 assignment to Homology GroupsTable S1 - List of all protein
 IDs and Homology Groups.xlsx
DOI: 10.5061/dryad.n08sv
title: Data from: Spatiotemporal scaling of plant species richness and functional diversity in a temperate semi-natural grassland

description: The accumulation of biodiversity in space and time has been modelled
 extensively using the species-area relationship and the species-time
 relationship, respectively. Recently, these models have been combined into
 time-area curves in order to investigate spatiotemporal scaling of species
 richness. This study expands on previous research by applying these
 spatiotemporal models to functional diversity. Understanding
 spatiotemporal dynamics of ecological traits is important due to their
 crucial role in ecosystem functioning and mediating species responses to
 environmental change. We present a new function based on the
 semi-logarithmic species-area relationship, which was applied with a power
 function to vegetation survey data from Scottish machair grassland for
 both species richness and two measures of functional diversity. When
 taking a whole-study approach using non-linear mixed effects models, the
 semi-logarithmic function used here shows a positive time-area interaction
 for species richness, contrasting with the negative interaction of the
 power law found in previous investigations. Although there was a negative
 time-area interaction for functional diversity measures at the whole-study
 scale, parameter estimates were inconsistent at the individual site level.
 Overall, the results reveal differing spatiotemporal dynamics of species
 and their traits and suggest that the appropriate scale for space-for-time
 substitutions depends on the aspect of biodiversity being investigated.
 The new model developed in this study, and the novel application to
 functional diversity, opens up future possible research into
 spatiotemporal dynamics of biodiversity.
description: MachairSurvey2004_2008The data file contains percentage cover of grass, sedge and forb species from surveys carried out in the Western Isles of Scotland at three nested quadrat scales. Quadrats at each scale were arranged in a 5x5 grid indicated by the columns Refno and Refletter.
DOI: 10.15468/dl.2phuqg
title: Occurrence Download

description: A dataset containing 32342761 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Continent is South America",
 "Country is Brazil",
 "Year 1858-2025"
 ]
}

 The dataset includes 32342761 records from 1796 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007209-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b2rs4m
title: Occurrence Download

description: A dataset containing 864 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 {
 "or" : [
 "Geometry POLYGON((-48.57102 -1.53094,-47.97687 -1.53094,-47.97687 -1.15285,-48.57102 -1.15285,-48.57102 -1.53094))",
 "Geometry POLYGON((-48.51997 -1.4854,-48.3359 -1.4854,-48.3359 -1.3808,-48.51997 -1.3808,-48.51997 -1.4854))"
 ]
 },
 "OccurrenceStatus is Present",
 "TaxonKey is Tracheophyta",
 "Year 2020-2025"
 ]
}

 The dataset includes 864 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013765-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9yygb6
title: Occurrence Download

description: A dataset containing 12862 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pterocarpus erinaceus Poir."
 ]
}

 The dataset includes 12862 records from 164 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013767-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.74n4vh
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "CoordinateUncertaintyInMeters 0.0-500.0",
 "Country is India",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Gossypium hirsutum",
 "Year 2020-2026"
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005848-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qqmahv
title: Occurrence Download

description: A dataset containing 399 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ixora philippinensis"
 ]
}

 The dataset includes 399 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005847-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.