cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.22bc3
title: Data from: The oceanic concordance of phylogeography and biogeography: a case study in Notochthamalus

description: Dispersal and adaptation are the two primary mechanisms that set the range
 distributions for a population or species. As such, understanding how
 these mechanisms interact in marine organisms in particular – with
 capacity for long-range dispersal and a poor understanding of what
 selective environments species are responding to – can provide useful
 insights for the exploration of biogeographic patterns. Previously, the
 barnacle Notochthamalus scabrosus has revealed two evolutionarily distinct
 lineages with a joint distribution that suggests an association with one
 of the two major biogeographic boundaries (~30°S) along the coast of
 Chile. However, spatial and genomic sampling of this system has been
 limited until now. We hypothesized that given the strong oceanographic and
 environmental shifts associated with the other major biogeographic
 boundary (~42°S) for Chilean coastal invertebrates, the southern
 mitochondrial lineage would dominate or go to fixation in locations
 further to the south. We also evaluated nuclear polymorphism data from 130
 single nucleotide polymorphisms to evaluate the concordance of the signal
 from the nuclear genome with that of the mitochondrial sample. Through the
 application of standard population genetic approaches along with a
 Lagrangian ocean connectivity model, we describe the codistribution of
 these lineages through a simultaneous evaluation of coastal lineage
 frequencies, an approximation of larval behavior, and current-driven
 dispersal. Our results show that this pattern could not persist without
 the two lineages having distinct environmental optima. We suggest that a
 more thorough integration of larval dynamics, explicit dispersal models,
 and near-shore environmental analysis can explain much of the coastal
 biogeography of Chile.
description: Supplement S2 SNP
 DataGenotypic and mitotype
 data for all individuals analyzed in our publication.
DOI: 10.5061/dryad.g2b7n
title: Data from: An experimental test of the transmission−virulence trade-off hypothesis in a plant virus

description: The transmission–virulence trade-off hypothesis is one of the few adaptive
 explanations of virulence evolution, and assumes that there is an overall
 positive correlation between parasite transmission and virulence. The
 shape of the transmission–virulence relationship predicts whether
 virulence should evolve toward either a maximum or to an intermediate
 optimum. A positive correlation between each of these traits and
 within-host growth is often suggested to underlie the relationship between
 virulence and transmission. There are few experimental tests of this
 hypothesis; this study reports on the first empirical test on a plant
 pathogen. We infected Brassica rapa plants with nine natural isolates of
 Cauliflower mosaic virus and then estimated three traits: transmission,
 virulence, and within-host viral accumulation. As predicted by the
 trade-off hypothesis, we observed a positive correlation between
 transmission and virulence, suggestive of the existence of an intermediate
 optimum. We discovered the unexpected existence of two groups of
 within-host accumulation, differing by at least an order of magnitude.
 When accumulation groups were not accounted for, within-host accumulation
 was correlated neither to virulence nor transmission, although our results
 suggest that within each group these correlations exist.
description: Doumayrou et
 al_trade-off_dataThis data file contains
 life history data (i.e. virulence, transmission rate and within-host
 accumulation) of nine natural isolates of Cauliflower mosaic virus
 infecting Brassica rapa to test the virulence-transmission trade-off
 hypothesis discussed in the manuscript.Doumayrou et
 al_evolution_traits_dataThis data file contains
 life history data (i.e. virulence, transmission rate and within-host
 accumulation) of four natural isolates of Cauliflower mosaic virus
 infecting Brassica rapa to test the evolution of the virulence,
 transmission and viral accumulation of isolates with low and high
 within-host accumulation discussed in the manuscript.
DOI: 10.15468/dl.fkv63f
title: Occurrence Download

description: A dataset containing 1778 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Mabea speciosa, Mabea speciosa speciosa, Mabea caudata)"
 ]
}

 The dataset includes 1778 records from 112 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000498-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yhdfc4
title: Occurrence Download

description: A dataset containing 4990 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Peru, Colombia, Venezuela (Bolivarian Republic of), Ecuador, Bolivia (Plurinational State of), Chile, Argentina, Pakistan, Bhutan, India, Nepal)",
 "TaxonKey is Aedes aegypti"
 ]
}

 The dataset includes 4990 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000499-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rrde64
title: Occurrence Download

description: A dataset containing 7278 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Betula lenta"
 ]
}

 The dataset includes 7278 records from 147 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000500-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.gd501
title: Data from: Phylogenetic placement of the unusual jumping spider Depreissia Lessert, and a new synapomorphy uniting Hisponinae and Salticinae (Araneae, Salticidae)

description: The relationships of the unusual salticid spider Depreissia from central
 Africa and Borneo have been difficult to resolve, obscured by its highly
 modified ant-like body. Phylogenetic analysis of the gene 28S strongly
 supports its placement outside the major clade Salticinae and within the
 clade of cocalodines, spartaeines and lapsiines, with weaker support for a
 relationship with the cocalodines in particular. Excluding the genus from
 the Salticinae is supported also by the presence of a median apophysis on
 the male palp, and by the lack of a cymbial apical groove cradling the tip
 of embolus, which is newly presented here as a synapomorphy of Hisponinae
 plus Salticinae.
description: 28S alignment for
 Depreissia salticid study, plus treesThis file includes the
 28S alignment, the full constraint tree, and trees resulting from various
 analyses, as indicated in the names of the tree blocksDepreissia28s-05-ForDryad.nex
DOI: 10.5061/dryad.6m98m
title: Data from: Inclusive fitness and differential productivity across the life course determine intergenerational transfers in a small-scale human society

description: Transfers of resources between generations are an essential element in
 current models of human life-history evolution accounting for prolonged
 development, extended lifespan and menopause. Integrating these models
 with Hamilton's theory of inclusive fitness, we predict that the
 interaction of biological kinship with the age-schedule of resource
 production should be a key driver of intergenerational transfers. In the
 empirical case of Tsimane’ forager–horticulturalists in Bolivian Amazonia,
 we provide a detailed characterization of net transfers of food according
 to age, sex, kinship and the net need of donors and recipients. We show
 that parents, grandparents and siblings provide significant net downward
 transfers of food across generations. We demonstrate that the extent of
 provisioning responds facultatively to variation in the productivity and
 demographic composition of families, as predicted by the theory. We
 hypothesize that the motivation to provide these critical transfers is a
 fundamental force that binds together human nuclear and extended families.
 The ubiquity of three-generational families in human societies may thus be
 a direct reflection of fundamental evolutionary constraints on an
 organism's life-history and social organization.
description: hooper_et_al_2015_individual_dyadsField dataset utilized to analyze transfers between Tsimane' individuals. Net transfers from individual i to individual j are represented in units of calories per day. See text and electronic supplementary materials for details.hooper_et_al_2015_family_dyadsField dataset utilized to analyze transfers between Tsimane' nuclear families. Measured net need, estimated net need, and net transfers from family i to family j are represented in units of calories per day. See text and electronic supplementary materials for details.
DOI: 10.5061/dryad.4cj42
title: Data from: Loss of genetic integrity in wild lake trout populations following stocking: insights from an exhaustive study of 72 lakes from Québec, Canada

description: Stocking represents the most important management tool worldwide to
 increase and sustain commercial and recreational fisheries in a context of
 overexploitation. Genetic impacts of this practice have been investigated
 in many studies, which examined population and individual admixture, but
 few have investigated determinants of these processes. Here, we addressed
 these questions from the genotyping at 19 microsatellite loci of 3341
 adult lake trout (Salvelinus namaycush) from 72 unstocked and stocked
 lakes. Results showed an increase in genetic diversity and a twofold
 decrease in the extent of genetic differentiation among stocked
 populations when compared to unstocked. Stocked populations were
 characterized by significant admixture at both population and individual
 levels. Moreover, levels of admixture in stocked populations were strongly
 correlated with stocking intensity and a threshold value of total
 homogenization between source and stocked populations was identified. Our
 results also suggest that under certain scenarios, the genetic impacts of
 stocking could be of short duration. Overall, our study emphasizes the
 important alteration of the genetic integrity of stocked populations and
 the need to better understand determinants of admixture to optimize
 stocking strategies and to conserve the genetic integrity of wild
 populations.
description: Lake trout
 genotypesThe raw genotype of all
 individuals used in this study.SANA_QC_2011.xlsxAncient lake trout genotypesThe subset of historical genotypes compared to contemporary ones.SANA_QC_Ancient.xlsx
DOI: 10.5061/dryad.53vs3
title: Data from: Response of deep-sea biodiversity to abrupt deglacial and Holocene climate changes in the North Atlantic Ocean

description: Aim: Little is known about how marine biodiversity responds to
 oceanographic and climatic changes over the decadal to centennial
 time-scales which are most relevant for predicted climate changes due to
 greenhouse gas forcing. This paper aims to reveal decadal–centennial scale
 deep-sea biodiversity dynamics for the last 20,000 years and then explore
 potential environmental drivers. Location: The North Atlantic Ocean.
 Methods: We investigated deep-sea benthic microfossil records to reveal
 biodiversity dynamics and subsequently applied comprehensive ecological
 modelling to test possible environmental factors (i.e. surface
 productivity, seasonality of productivity or deepwater circulation related
 to bottom-water temperature) that may have influenced deep-sea
 biodiversity over these time-scales. Results: Deep-sea biodiversity
 changed synchronously with stadial–interstadial climate changes over the
 last 20,000 years across a large area of the North Atlantic in both
 ostracod crustaceans and foraminiferan protozoa (in spite of their
 different dispersal abilities). Species diversity rapidly increased during
 abrupt stadial events during the last deglacial and the Holocene
 interglacial periods. These include the well-known Heinrich 1, the Younger
 Dryas and the 8.2 ka events when the strength of Atlantic Meridional
 Overturning Circulation (AMOC) decreased. There is also evidence for
 quasi-cyclic changes in biodiversity at a c. 1500-year periodicity,
 consistent with the well-known ‘1500-year climatic cycle’. Statistical
 analyses revealed that AMOC variability (probably specifically the
 variability in AMOC-driven bottom-water temperature) is correlated with
 deep-sea biodiversity. Main conclusions: Our finding of a significant
 AMOC–diversity relationship may indicate pervasive control of the
 diversity of deep-sea benthic species by rapidly changing climate,
 specifically bottom-water temperature, over decadal to centennial
 time-scales. Our results, based on highly resolved fossil records, may
 portend pervasive, synchronous and sudden ecosystem responses to
 human-induced changes to climate and ocean circulation in this century.
description: Raw ostracode census
 dataOstracode count data of
 the core EW9302 23GGC.Yasuhara_raw_census.xls3-point moving sum ostracode census dataset3-point moving sum ostracode census dataset of the core EW9302 23GGC.Yasuhara_3pt_mov_sum_census.xls3-point moving sum ostracode census dataset for R modeling3-point moving sum ostracode census dataset of the core EW9302 23GGC for R modeling. Shallow-water and non-benthic species are removed. See the paper for the full details.Yasuhara_3pt_movsum_census_R.xlsTable S1Table S1 in MS Excel formatYasuhara_TableS1.xlsTable S2Table S2 in MS Excel formatYasuhara_TableS2.xlsTable S5Table S5 in MS Excel formatYasuhara_TableS5.xlsTable S6Table S6 in MS Excel formatYasuhara_TableS6.xlsTable S7Table S7 in MS Excel formatYasuhara_TableS7.xls
DOI: 10.5061/dryad.j7028s5
title: Data from: Regional climate and local-scale biotic acceptance explain native-exotic diversity relationships in Australian annual plant communities

description: Native and exotic species richness is expected to be negatively related at
 small spatial scales where individuals interact, and positive at larger
 spatial scales as a greater variety of habitats are sampled. However, a
 range of native-exotic richness relationships (NERRs) have been reported,
 including positive at small scales and negative at larger scales. We
 present a hierarchical metacommunity framework to explain how contrasting
 NERRs may emerge across scales and study systems, and then apply this
 framework to NERRs in an invaded winter annual plant system in south-west
 Western Australia. We analysed NERRs at increasing spatial scales from
 neighbourhoods (0.09 m2) to communities (225 m2) to metacommunities
 (&gt;10 ha) within a multi-level structural equation model. In
 contrast to many previous studies, native and exotic richness were
 positively related at the neighbourhood scale and were not significantly
 associated at larger scales. Heterogeneity in soil surface properties was
 weakly, but positively, associated with native and exotic richness at the
 community-scale. Metacommunity exotic richness increased strongly with
 regional temperature and moisture availability, but relationships for
 native richness were negative and much weaker. Thus, we show that neutral
 NERRs can emerge at larger scales due to differential climatic filtering
 of native and exotic species pools.
description: Neighbourhood
 Composition within QuadratsEach row corresponds
 with a species and its abundance within each quadrat.plants.core.2011.csvQuadrat Scale InformationEach row corresponds with a quadrat and the associated information.quadrat_scale_data.csvTowers_Dwyer_2018_ScriptThe R code used to conduct the analyses used in the manuscript.
DOI: 10.5061/dryad.81hn422
title: Data from: Exploring preferences for variable delays over fixed delays to high-value food rewards as a model of food-seeking behaviours in humans

description: Foraging and operant models suggest that animals will tolerate uncertainty
 or risk to obtain food quickly. In modern food environments, sustained
 access to quick energy-dense foods can promote weight gain. Here, we used
 a discrete-choice procedure to examine peoples' decisions about when
 next to eat high-value, palatable food rewards, probabilistically
 delivered immediately or following longer delays. In Experiment 1,
 moderately hungry young females showed consistent preferences for a
 variable delay option that delivered food rewards immediately or following
 long delays over a fixed delay option that delivered the same rewards
 following intermediate delays. These preferences were stronger in females
 with higher BMIs compared with lower BMIs, suggesting that quick food can
 enhance the value of uncertain or ‘risky’ food-seeking strategies in
 individuals vulnerable to future weight gain. In Experiment 2, prior
 exposure to a subtle and not easily identifiable food aroma increased
 selections of the variable delay option following delayed food rewards in
 a mixed sample of male and female adults, providing preliminary evidence
 that food cues can sustain uncertain food-seeking strategies. These data
 highlight a working hypothesis that the rapid delivery and consumption of
 food rewards, and food cues, can increase risk-tolerance in the
 food-seeking behaviours of individuals who are vulnerable to weight gain.
description: Multi-level models for
 food-scheduling dataR script for multi-level
 models for experiments 1 & 2 containing sequence of models for
 variable/fixed delay selections, selection time and collection time
 models.Phil_trans_Models_FINAL.RFood scheduling Experiment 1 - participant dataData file for participant data for Experiment 1 of food scheduling experimentsS1_FINAL_Participant_data.csvFood scheduling Experiment 2 - participant dataData file of participant data for Experiment 2 of food scheduling experimentsS2_FINAL_Participant_data.csv
DOI: 10.5061/dryad.v5m24
title: Data from: Assessing pre- and post-zygotic barriers between North Atlantic eels (Anguilla anguilla and A. rostrata)

description: Elucidating barriers to gene flow is important for understanding the
 dynamics of speciation. Here we investigate pre- and post-zygotic
 mechanisms acting between the two hybridizing species of Atlantic eels:
 Anguilla anguilla and A. rostrata. Temporally varying hybridization was
 examined by analyzing 85 species-diagnostic single-nucleotide
 polymorphisms (SNPs; FST greater than or equal to0.95) in eel larvae
 sampled in the spawning region in the Sargasso Sea in 2007 (N=92) and 2014
 (N=460). We further investigated whether genotypes at these SNPs were
 nonrandomly distributed in post-F1 hybrids, indicating selection. Finally,
 we sequenced the mitochondrial ATP6 and nuclear ATP5c1 genes in 19
 hybrids, identified using SNP and restriction site associated DNA (RAD)
 sequencing data, to test a previously proposed hypothesis of cytonuclear
 incompatibility leading to adenosine triphosphate (ATP) synthase
 dysfunction and selection against hybrids. No F1 hybrids but only later
 backcrosses were observed in the Sargasso Sea in 2007 and 2014. This
 suggests that interbreeding between the two species only occurs in some
 years, possibly controlled by environmental conditions at the spawning
 grounds, or that interbreeding has diminished through time as a result of
 a declining number of spawners. Moreover, potential selection was found at
 the nuclear and the cytonuclear levels. Nonetheless, one glass eel
 individual showed a mismatch, involving an American ATP6 haplotype and
 European ATP5c1 alleles. This contradicted the presence of cytonuclear
 incompatibility but may be explained by that (1) cytonuclear
 incompatibility is incomplete, (2) selection acts at a later life stage or
 (3) other genes are important for protein function. In total, the study
 demonstrates the utility of genomic data when examining pre- and
 post-zyotic barriers in natural hybrids.
description: FLUIDIGM SNP data in
 genepop formatFLUIDIGM SNP data in
 genepop format from all genotyped individuals analyzed in the present
 study. The data includes both data from the paper of pujolar et al. 2014a
 and new data.FLUIDIGM_SNP_data.genepopRAD_SNPdata_47eels_1330SNPs_STRUCTURESNP file in STRUCTURE format. The data encompases 47 individuals: 7 hybrids and 20 individuals considered to be pure specimens from each species. The data set was used for estimating hybrid classes for the 7 hybrids. Please see Supporting Information Note 3 for more information.
DOI: 10.7910/dvn/vasmxu
title: Smart Village and Climate-Smart Agriculture Researches, Publication Networks, Author Collaborations and Keyword Interactions

description: Bibliometric analysis was used to examine research trends and thematic structures related to smart villages and climate-smart agriculture. Using CiteSpace and VOSviewer, publication networks, collaborations, and keyword relationships were mapped, revealing coherent thematic clusters.
DOI: 10.5061/dryad.k3m55
title: Data from: Comprehensive transcriptome analysis of Crocus sativus for discovery and expression of genes involved in apocarotenoid biosynthesis

description: Background: Crocus sativus stigmas form rich source of apocarotenoids like
 crocin, picrocrocin and saffranal which besides imparting color, flavour
 and aroma to saffron spice also have tremendous pharmacological
 properties. Inspite of their importance, the biosynthetic pathway of
 Crocus apocarotenoids is not fully elucidated. Moreover, the mechanism of
 their stigma specific accumulation remains unknown. Therefore, deep
 transcriptome sequencing of Crocus stigma and rest of the flower tissue
 was done to identify the genes and transcriptional regulators involved in
 the biosynthesis of these compounds. Results: Transcriptome of stigma and
 rest of the flower tissue was sequenced using Illumina Genome Analyzer IIx
 platform which generated 64,604,402 flower and 51,350,714 stigma reads.
 Sequences were assembled de novo using trinity resulting in 64,438
 transcripts which were classified into 32,204 unigenes comprising of 9853
 clusters and 22,351 singletons. A comprehensive functional annotation and
 gene ontology (GO) analysis was carried out. 58.5 % of the transcripts
 showed similarity to sequences present in public databases while rest
 could be specific to Crocus. 5789 transcripts showed similarity to
 transcription factors representing 76 families out of which Myb family was
 most abundant. Many genes involved in carotenoid/apocarotenoid pathway
 were identified for the first time in this study which includes
 zeta-carotene isomerase and desaturase, carotenoid isomerase and lycopene
 epsilon-cyclase. GO analysis showed that the predominant classes in
 biological process category include metabolic process followed by cellular
 process and primary metabolic process. KEGG mapping analysis indicated
 that pathways involved in ribosome, carbon and starch and sucrose
 metabolism were highly represented. Differential expression analysis
 indicated that key carotenoid/apocarotenoid pathway genes including
 phytoene synthase, phytoene desaturase and carotenoid cleavage dioxygenase
 2 are enriched in stigma thereby providing molecular proof for stigma to
 be the site of apocarotenoid biosynthesis. Conclusions: This data would
 provide a rich source for understanding the carotenoid/apocarotenoid
 metabolism in Crocus. The database would also help in investigating many
 questions related to saffron biology including flower development.
description: Phylogenythe folder contains files which contains sequences of CCD genes and their accession numbers. it also contains alignment file and the resulting phylogenetic tree