cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.xhc8n9
title: Occurrence Download

description: A dataset containing 308532 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Laridae",
 "Country is France",
 "HasCoordinate is true",
 "Year is greater than or equal to 2024"
 ]
}

 The dataset includes 308532 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001599-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.0nk1p
title: Data from: Injuries, death, and disability associated with 11 years of conflict in Baghdad, Iraq: a randomized household cluster survey

description: Background: The objective of this study was to characterize injuries,
 deaths, and disabilities arising during 11 years of conflict in Baghdad.
 Methods: Using satellite imagery and administrative population estimated
 size for Baghdad, 30 clusters were selected, proportionate to population
 size estimates. Interviews were conducted during April and May 2014 in 900
 households containing 5148 persons. Details about injuries and
 disabilities occurring from 2003 through May 2014 and resultant
 disabilities were recorded. Findings: There were 553 injuries reported by
 Baghdad residents, 225 of which were intentional, and 328 unintentional.
 For intentional injuries, the fatality rate was 39.1% and the disability
 rate 56.0%. Gunshots where the major cause of injury through 2006 when
 blasts/explosions became the most common cause and remained so through
 2014. Among unintentional injuries, the fatality rate was 7.3% and the
 disability rate 77.1%. The major cause of unintentional injuries was falls
 (131) which have increased dramatically since 2008, followed by traffic
 related injuries (81), which have steadily increased. The proportion of
 injuries ending in disabilities remained fairly constant through the
 survey period. Interpretation: Intentional injuries added substantially to
 the burden of unintentional injuries for the population. For Baghdad, the
 phases of the Iraqi conflict are reflected in the patterns of injuries and
 consequent deaths reported. The scale of injuries during conflict is most
 certainly under-reported. Difficulties recalling injuries in a survey
 covering 11 years is a limitation, but it is likely that minor injuries
 were under-reported more than severe injuries. The in- and out-migration
 of Baghdad populations likely had effects on the events reported which we
 could not measure or estimate. Damage to the health infrastructure and the
 flight of health workers may have contributed to mortality and morbidity.
 Civilian injuries as well as mortality should be measured during
 conflicts, though not currently done.
description: Iraq Injury
 DataIraq_Injury_10_Aug_Deidentified.dta
DOI: 10.5061/dryad.54137
title: Data from: The building of a biodiversity hotspot across a land-bridge in the Mediterranean

description: Many of the macroevolutionary processes that have shaped present-day
 phylogenetic patterns were caused by geological events such as plate
 tectonics and temporary land-bridges. The study of spatial patterns of
 phylogenetic diversity can provide insights into these past events. Here
 we focus on a western Mediterranean biodiversity hotspot located in the
 southern Iberian Peninsula and northwest Africa, two regions that are
 separated by the Strait of Gibraltar. We explore the spatial structure of
 the phylogenetic relationships within and across large-scale plant
 assemblages. Significant turnover in terminal lineages tends to occur
 between landmasses, whereas turnover in deep lineages tends to occur
 within landmasses. Plant assemblages in the western ecoregions of this
 hotspot tend to be phylogenetically overdispersed but are phylogenetically
 clustered on its eastern margins. We discuss our results in the light of
 potential scenarios of niche evolution (or conservatism) and lineage
 diversification. The significant turnover between landmasses suggests a
 common scenario of allopatric speciation that could have been facilitated
 by the intermittent joining of the two continents. This may have
 constituted an important stimulus for diversification and the emergence of
 this western Mediterranean biodiversity hotspot.
description: SUPP_INF_3Site-by-species matrices for angiosperms and eudicots respectively (presence/absence data), PCA1 for temperature- and precipitation-related variables and spatial coordinates of the centroids of ecoregion polygons.Genus_level_TreeGenus-level time-calibrated phylogeny used in the study (Newick format)
DOI: 10.5061/dryad.8790
title: Data from: Understanding angiosperm diversification using small and large phylogenetic trees

description: How will the emerging possibility of inferring ultra-large phylogenies
 influence our ability to identify shifts in diversification rate? For
 several large angiosperm clades (Angiospermae, Monocotyledonae,
 Orchidaceae, Poaceae, Eudicotyledonae, Fabaceae, and Asteraceae), we
 explore this issue by contrasting two approaches: (1) using small backbone
 trees with an inferred number of extant species assigned to each terminal
 clade and (2) using a mega-phylogeny of 55473 seed plant species
 represented in GenBank. The mega-phylogeny approach assumes that the
 sample of species in GenBank is at least roughly proportional to the
 actual species diversity of different lineages, as appears to be the case
 for many major angiosperm lineages. Using both approaches, we found that
 diversification rate shifts are not directly associated with the major
 named clades examined here, with the sole exception of Fabaceae in the
 GenBank mega-phylogeny. These agreements are encouraging and may support a
 generality about angiosperm evolution: major shifts in diversification may
 not be directly associated with major named clades, but rather with clades
 that are nested not far within these groups. An alternative explanation is
 that there have been increased extinction rates in early-diverging
 lineages within these clades. Based on our mega-phylogeny, the shifts in
 diversification appear to be distributed quite evenly throughout the
 angiosperms. Mega-phylogenetic studies of diversification hold great
 promise for revealing new patterns, but we will need to focus more
 attention on properly specifying null expectation.
description: final_treeThe 55473 tip phylogeny in newick format presented in the paper.big_plants.tarThe 55473 tip phylogenetic dataset including the extended phylip format alignment and the model file identifying the gene and partitions.
DOI: 10.5061/dryad.b7g8p
title: Data from: A multiscale vibrational spectroscopic approach for identification and biochemical characterization of pollen

description: Background: Analysis of pollen grains reveals valuable information on
 biology, ecology, forensics, climate change, insect migration, food
 sources and aeroallergens. Vibrational (infrared and Raman) spectroscopies
 offer chemical characterization of pollen via identifiable spectral
 features without any sample pretreatment. We have compared the level of
 chemical information that can be obtained by different multiscale
 vibrational spectroscopic techniques. Methodology: Pollen from 15
 different species of Pinales (conifers) were measured by seven infrared
 and Raman methodologies. In order to obtain infrared spectra, both
 reflectance and transmission measurements were performed on ground and
 intact pollen grains (bulk measurements), in addition, infrared spectra
 were obtained by microspectroscopy of multigrain and single pollen grain
 measurements. For Raman microspectroscopy measurements, spectra were
 obtained from the same pollen grains by focusing two different
 substructures of pollen grain. The spectral data from the seven
 methodologies were integrated into one data model by the Consensus
 Principal Component Analysis, in order to obtain the relations between the
 molecular signatures traced by different techniques. Results: The
 vibrational spectroscopy enabled biochemical characterization of pollen
 and detection of phylogenetic variation. The spectral differences were
 clearly connected to specific chemical constituents, such as lipids,
 carbohydrates, carotenoids and sporopollenins. The extensive differences
 between pollen of Cedrus and the rest of Pinaceae family were
 unambiguously connected with molecular composition of sporopollenins in
 pollen grain wall, while pollen of Picea has apparently higher
 concentration of carotenoids than the rest of the family. It is shown that
 vibrational methodologies have great potential for systematic collection
 of data on ecosystems and that the obtained phylogenetic variation can be
 well explained by the biochemical composition of pollen. Out of the seven
 tested methodologies, the best taxonomical differentiation of pollen was
 obtained by infrared measurements on bulk samples, as well as by Raman
 microspectroscopy measurements of the corpus region of the pollen grain.
 Raman microspectroscopy measurements indicate that measurement area, as
 well as the depth of focus, can have crucial influence on the obtained
 data.
description: Data from: A multiscale
 vibrational spectroscopic approach for identification and biochemical
 characterization of pollen PLOS ONEData for PlosOne
 articleDatadyrad_PlosOne.zip
DOI: 10.5061/dryad.676tf
title: Data from: The role of regional survivor incumbency in the evolutionary recovery of calcareous nannoplankton from the Cretaceous/Paleogene (K/Pg) mass extinction

description: The earliest Paleocene record of calcareous nannoplankton presents a
 unique opportunity to understand the evolutionary recovery of life from
 mass extinction. Nannoplankton were devastated at the Cretaceous/Paleogene
 boundary and their subsequent recovery can be studied in great detail
 because of their abundance in sediments, continuous stratigraphic
 occurrence, and near global distribution. Here we determine when and where
 new species of nannoplankton originated and how they dispersed following
 the Cretaceous/Paleogene mass extinction. Initially, we focus our efforts
 on North Pacific and South Atlantic deep sea sites with orbital age
 control to compare the precise timing and dynamics of the recovery between
 the locations. We then broaden our investigation to six sites from
 different basins and a variety of environments to study global patterns of
 the initial recovery. Our results show that many taxa in key Paleogene
 lineages originated in the North Pacific Ocean and that assemblages
 comprised primarily of new Paleogene taxa were not observed at other sites
 for several hundred thousand years. Survivors that were adapted to
 eutrophic post extinction conditions rapidly expanded in Southern
 Hemisphere sites where they dominated assemblages for most of the initial
 recovery. We therefore hypothesize that groups of survivors formed
 regionally incumbent assemblages in the Southern Hemisphere that limited
 diversification and dispersal of new Paleogene taxa. The end of survivor
 dominance correlates to the recovery of the biologic pump and subsequent
 decrease in surface ocean nutrient concentration 300–400 Kyr after the
 boundary. Only after survivors were removed did new Paleogene
 nannoplankton assemblages become abundant globally. Our results indicate
 that competition from regionally incumbent survivors was as an important
 control on the K/Pg recovery of nannoplankton.
description: Schueth et al. K/Pg
 nannofossil recovery SupplementSupplemental Materials
 for the manuscript "The role of regional survivor incumbency in the
 evolutionary recovery of calcareous nannoplankton from the
 Cretaceous/Paleogene (K/Pg) mass extinction." Includes supplemental
 figures, supporting information for main text and age models used in
 analysis.Schueth_et_al_Supplement-final.pdfSchueth et al. K/Pg nannofossil recovery Supplement - Cluster DendrogramAdditional supplement for the article "The role of regional survivor incumbency in the evolutionary recovery of calcareous nannoplankton from the Cretaceous/Paleogene (K/Pg) mass extinction" - contains the cluster analysis results with dendrograms and taxa abundances plotted along with dendrograms.Cluster_Dendrogram_SM.pdf
DOI: 10.5061/dryad.6f1r2
title: Data from: Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties

description: Background: Krishna Tulsi, a member of Lamiaceae family, is a herb well
 known for its spiritual, religious and medicinal importance in India. The
 common name of this plant is ‘Tulsi’ (or ‘Tulasi’ or ‘Thulasi’) and is
 considered sacred by Hindus. We present the draft genome of Ocimum
 tenuiflurum L (subtype Krishna Tulsi) in this report. The paired-end and
 mate-pair sequence libraries were generated for the whole genome sequenced
 with the Illumina Hiseq 1000, resulting in an assembled genome of 374 Mb,
 with a genome coverage of 61 % (612 Mb estimated genome size). We have
 also studied transcriptomes (RNA-Seq) of two subtypes of O. tenuiflorum,
 Krishna and Rama Tulsi and report the relative expression of genes in both
 the varieties. Results: The pathways leading to the production of
 medicinally-important specialized metabolites have been studied in detail,
 in relation to similar pathways in Arabidopsis thaliana and other plants.
 Expression levels of anthocyanin biosynthesis-related genes in leaf
 samples of Krishna Tulsi were observed to be relatively high, explaining
 the purple colouration of Krishna Tulsi leaves. The expression of six
 important genes identified from genome data were validated by performing
 q-RT-PCR in different tissues of five different species, which shows the
 high extent of urosolic acid-producing genes in young leaves of the Rama
 subtype. In addition, the presence of eugenol and ursolic acid, implied as
 potential drugs in the cure of many diseases including cancer was
 confirmed using mass spectrometry. Conclusions: The availability of the
 whole genome of O.tenuiflorum and our sequence analysis suggests that
 small amino acid changes at the functional sites of genes involved in
 metabolite synthesis pathways confer special medicinal properties to this
 herb.
description: Supplementary Figure
 5Supplementary Figure
 6
DOI: 10.5061/dryad.c418b
title: Data from: Influence of niche similarity on hybridisation between Myriophyllum sibiricum and M. spicatum

description: The impact of ecological factors on natural hybridization is of widespread
 interest. Here, we asked whether climate niche influences hybridization
 between the two closely related plant species Myriophyllum sibiricum and
 M. spicatum. Eight microsatellite loci and two chloroplast fragments were
 used to investigate the occurrence of hybridization between these two
 species in two co-occurring regions: north-east China (NEC) and the
 Qinghai-Tibetan Plateau (QTP). The climate niches of the species were
 quantified by principal component analysis with bioclimatic data, and
 niche comparisons were performed between the two species in each region.
 Reciprocal hybridization was observed, and M. sibiricum was favoured as
 the maternal species. Furthermore, hybrids were rare in NEC but common in
 the QTP. Accordingly, in NEC, the two species were climatically distinct,
 and hybrids only occurred in the narrow geographical or ecological
 transition zone, whereas in the QTP, obvious niche overlaps were found for
 the two species, and hybrids occurred in multiple contact zones. This
 association between hybridization pattern and climate niche similarity
 suggests that the level of hybridization was promoted by niche overlap.
 Compared with the parental species, similar climate niches were found for
 the hybrid populations in the QTP, indicating that other environmental
 factors rather than climate were important for hybrid persistence. Our
 findings highlight the significance of climate niche with respect to
 hybridization patterns in plants.
description: allele
 sizeMultilocus genotypes
 based on allele size of 474 Myriophyllum individuals in northeast China
 (NEC) and the Qinghai-Tibetan Plateau (QTP)Bioclim data of
 NEC19
 bioclimatic variables of northeast China (NEC) with a resolution of
 10'bioclim_NEC.txtBioclim data of the QTP19 bioclimatic variables of the Qinghai-Tibetan Plateau (QTP) with a resolution of 10'bioclim_QTP.txt
DOI: 10.5061/dryad.8826
title: Data from: Using CRISPRs as a metagenomic tool to identify microbial hosts of a diffuse flow hydrothermal vent viral assemblage

description: Metagenomic analyses of viruses have revealed widespread diversity in the
 viriosphere, but it remains a challenge to identify specific hosts for a
 viral assemblage. To address this problem, we analyze the viral metagenome
 of a northeast Pacific hydrothermal vent with a comprehensive database of
 spacers derived from the CRISPR (Clustered Regularly Interspaced Short
 Palindromic Repeat) putative immune system. CRISPR spacer matches to the
 marine vent virome suggest that viruses infecting hosts from diverse
 taxonomic groups are present in this vent environment. Comparative virome
 analyses show that CRISPR spacers from vent isolates and from thermophiles
 in general have a higher percentage of matches to the vent virome than to
 other marine or terrestrial hot spring viromes. However, a high percentage
 of hits to spacers from mesophilic hosts, combined with a moderately high
 modeled alpha diversity, suggest that the marine vent virome is comprised
 of viruses that have the potential to infect diverse taxonomic groups of
 multiple thermal regimes in both the bacterial and archaeal domains.
description: CRISPR spacer
 databaseThis data file consists
 of a FASTA file containing all spacers in the CRISPR spacer database used
 for this publication. The name of each sequence describes the NC number of
 the species in which the CRISPR spacer is found, the number of the CRISPR
 locus in which it is found, and the number of the spacer within that
 CRISPR locus. The manuscript describes how this database was
 created.all_spacers_updated.txtSupplementary Table 2This file, designated Supplementary Table 2 in the manuscript, consists of a resemblance matrix used to compare the set of all CRISPR spacers in each genome in the NCBI database against the set of CRISPR spacers in every other genome. X- and Y- axes of the matrix list all sequenced strains in the NCBI database as of April 20th, 2010. Numbers corresponding to each pair indicate the number of CRISPR spacers shared between the two strains, divided by the sum total of all CRISPR spacers between the two strains."Shared" here indicates an alignment of 100% identity across at least 20 base pairs.Supplementary_Table_2.txt
DOI: 10.5061/dryad.r8dv2
title: Data from: Eye-spots in Lepidoptera attract attention in humans

description: Many prey species exhibit defensive traits to decrease their chances of
 predation. Conspicuous eye-spots, concentric rings of contrasting colours,
 are one type of defensive trait that some species exhibit to deter
 predators. We examined the function of eye-spots in Lepidoptera to
 determine whether they are effective at deterring predators because they
 resemble eyes (‘eye mimicry hypothesis’) or are highly salient
 (‘conspicuous signal hypothesis’). We recorded the gaze behaviour of men
 and women as they viewed natural images of butterflies and moths as well
 as images in which the eye-spots of these insects were modified. The
 eye-spots were modified by removing them, scrambling their colours, or
 replacing them with elliptical or triangular shapes that had either dark
 or light centres. Participants were generally more likely to look at,
 spend more time looking at and be faster to first fixate the eye-spots of
 butterflies and moths that were natural compared with ones that were
 modified, including the elliptical eye-spots with dark centres that most
 resembled eyes as well as the scrambled eye-spots that had the same
 contrast as the natural eye-spots. Participants were most likely to look
 at eye-spots that were numerous, had a large surface area and were located
 close to the insects' heads. Participants' pupils were larger
 when viewing eye-spots compared with the rest of the insects' body,
 suggesting a greater arousal when viewing eye-spots. Our results provide
 some support for the conspicuous signal hypothesis (and minimal support
 for the eye mimicry hypothesis) and suggest that eye-spots may be
 effective at deterring predators because they are highly conspicuous
 signals that draw attention.
description: AttentionEyespotsThis file contains data that was used in the "Probability Look," "Latency to Fixate," and "Time Looking" analyses. The "VariableDescription" tab describes the variables in the "Data" tab.PupilEyespotsThis file contains data that was used in the "Pupil Size" analysis. The “VariableDescription" tab describes the variables in the "Data" tab.
DOI: 10.5061/dryad.8d6k1
title: Data from: Local effects drive heterozygosity-fitness correlations in an outcrossing long-lived tree

description: Heterozygosity-fitness correlations (HFCs) have been used to understand
 the complex interactions between inbreeding, genetic diversity and
 evolution. Although frequently reported for decades, evidence for HFCs was
 often based on underpowered studies or inappropriate methods, and hence
 their underlying mechanisms are still under debate. Here, we used 6,100
 genome-wide Single Nucleotide Polymorphisms (SNPs) to test for general and
 local effect HFCs in maritime pine (Pinus pinaster Ait.), an iconic
 Mediterranean forest tree. Survival was used as a fitness proxy, and HFCs
 were assessed at a four-site common garden under contrasting environmental
 conditions (total of 16,288 trees). We found no significant correlations
 between genome-wide heterozygosity and fitness at any location, despite
 variation in inbreeding explaining a substantial proportion of the total
 variance for survival. However, four SNPs (including two non-synonymous
 mutations) were involved in significant associations with survival, in
 particular in the common gardens with higher environmental stress, as
 shown by a novel heterozygosity-fitness association test at the
 species-wide level. Fitness effects of SNPs involved in significant HFCs
 were stable across maritime pine gene pools naturally growing in distinct
 environments. These results led us to dismiss the general effect
 hypothesis and suggested a significant role of heterozygosity in specific
 candidate genes for increasing fitness in maritime pine. Our study
 highlights the importance of considering the species evolutionary and
 demographic history and different spatial scales and testing environments
 when assessing and interpreting heterozygosity-fitness correlations.
description: Pinus pinaster 6100 SNP
 data for 509 individualsThe excel file contains
 genotype data (6100 SNPs) for 509 Pinus pinaster trees, from 34
 populations sampled along the species' natural distribution
 range.6100SNPs_ProcRoySocB.xlsx