cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.85cg1d3
title: Data from: Genetic Diversity and Demographic History of an Upper Hill Dipterocarp (Shorea platyclados): Implications for Conservation

description: Southeast Asian rainforests at upper hill elevations are increasingly
 vulnerable to degradation because most lowland forest areas have been
 converted to different land uses. As such, understanding the genetics of
 upper hill species is becoming more crucial for their future management
 and conservation. Shorea platyclados is an important, widespread upper
 hill dipterocarp in Malaysia. To elucidate the genetic structure of S.
 platyclados and ultimately provide guidelines for a conservation strategy
 for this species, we carried out a comprehensive study of the genetic
 diversity and demographic history of S. platyclados. Twenty-seven
 populations of S. platyclados across its range in Malaysia were genotyped
 at 15 polymorphic microsatellite loci and sequenced at seven noncoding
 chloroplast DNA (cpDNA) regions. A total of 303 alleles were derived from
 the microsatellite loci, and 29 haplotypes were identified based on 2892
 bp of concatenated cpDNA sequences. The populations showed moderately high
 genetic diversity (mean HE = 0.680 for microsatellite gene diversity and
 HT = 0.650 for total haplotype diversity) and low genetic differentiation
 (FST = 0.060). Bayesian clustering divided the studied populations into
 two groups corresponding to western and eastern Malaysia. Bottleneck
 analysis did not detect any recent bottleneck events. Extended Bayesian
 skyline analyses showed a model of constant size for the past population
 history of this species. Based on our findings, priority areas for in situ
 and ex situ conservation and a minimum population size are recommended for
 the sustainable utilization of S. platyclados.
description: StructureInput_15Loci_1032IndivStructure input file for 1032 unrelated individuals sampled from 27 populations, genotyped at 15 microsatellite loci
DOI: 10.5061/dryad.c610m8n
title: Data from: A bidirectional network for appetite control in larval zebrafish

description: Medial and lateral hypothalamic loci are known to suppress and enhance
 appetite, respectively, but the dynamics and functional significance of
 their interaction have yet to be explored. Here we report that, in larval
 zebrafish, primarily serotonergic neurons of the ventromedial caudal
 hypothalamus (cH) become increasingly active during food deprivation,
 whereas activity in the lateral hypothalamus (LH) is reduced. Exposure to
 food sensory and consummatory cues reverses the activity patterns of these
 two nuclei, consistent with their representation of opposing internal
 hunger states. Baseline activity is restored as food-deprived animals
 return to satiety via voracious feeding. The antagonistic relationship and
 functional importance of cH and LH activity patterns were confirmed by
 targeted stimulation and ablation of cH neurons. Collectively, the data
 allow us to propose a model in which these hypothalamic nuclei regulate
 different phases of hunger and satiety and coordinate energy balance via
 antagonistic control of distinct behavioral outputs.
description: Figure3_SourceData1Processed calcium imaging data (matlab files) for all 14 fish analyzed in Figure 3
DOI: 10.5061/dryad.5sk68cd
title: Data from: Historical contingency, niche conservatism and the tendency for some taxa to be more diverse towards the poles

description: Aim We test the ability of the biotic exchange across the Bering
 land-bridge coupled to niche conservatism to explain current day mammalian
 diversity gradients. Location the Holarctic Taxon mammals Methods We
 compared the diversity within clades that participated in the exchange
 (colonizers), whose ancestors withstood the Beringian cold temperatures,
 with that within clades that did not participate (sedentaries). We
 contrasted biogeographical patterns, tested the ability of environmental
 models to predict species richness of colonizers and sedentaries across
 continents and, compared richness-climate relationships between colonizers
 and sedentaries controlling for phylogenetic effects. Results We find that
 assemblages of colonizers are more diverse towards higher latitudes,
 opposing the traditional latitudinal diversity gradient which is followed
 by sedentaries. Despite the long passage of time since this major
 dispersal event, we find that the geographic distribution of colonizers is
 more strongly correlated to the distributions of other colonizers
 inhabiting a different continent than to the distribution of sedentary
 species. Main conclusions Our results highlight the importance of
 historical migrations and dispersal in configuring present-day diversity
 gradients. We also suggest that colonizers may be particularly vulnerable
 to future climate change because of the predicted disproportionate
 decrease in climate space in the extra-tropical realm where they are
 currently most diverse.
description: Table S1 -
 Classification of Holarctic mammals into colonizer and sedentary
 speciesTable S1. Species list
 including a classification of each species as P-N colonizer, N-P
 colonizer, P sedentary, N sedentary, attending to their belonging to
 clades that participated or not in the biotic exchange through the Bering
 land-bridge during the Plio-Pleistocene. Note that P denotes Palearctic,
 and N is for Nearctic.Table S1. Species list and
 classification.xlsx
DOI: 10.15468/dl.9vmtb4
title: Occurrence Download

description: A dataset containing 977 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "OccurrenceStatus is Present",
 "TaxonKey is Paratrechina longicornis"
 ]
}

 The dataset includes 977 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001910-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.97h25b0
title: Data from: Consequences of past and present harvest management in a declining flyway population of common eiders Somateria mollissima

description: 1. Harvested species population dynamics are shaped by the relative
 contribution of natural and harvest mortality. Natural mortality is
 usually not under management control, so managers must continuously adjust
 harvest rates to prevent overexploitation. Ideally, this requires regular
 assessment of the contribution of harvest to total mortality and how this
 affects population dynamics. 2. To assess the impact of hunting mortality
 on the dynamics of the rapidly declining Baltic/Wadden Sea population of
 common eiders Somateria mollissima we first estimated vital rates of ten
 study colonies over the period 1970–2015. By means of a multi-event
 capture-recovery model we then used the cause of death of recovered
 individuals to estimate proportions of adult females that died due to
 hunting or other causes. Finally, we adopted a stochastic matrix
 population modelling approach based on simulations to investigate the
 effect of past and present harvest regulations on changes in flyway
 population size and composition. 3. Results showed that even the complete
 ban on shooting females implemented in 2014 in Denmark, where most hunting
 takes place was not enough to stop the population decline given current
 levels of natural female mortality. Despite continued hunting of males our
 predictions suggest that the proportion of females will continue to
 decline unless natural mortality of the females is reduced. 4. Although
 levels of natural mortality must decrease to halt the decline of this
 population, we advocate that the current hunting ban on females is
 maintained while further investigations of factors causing increased
 levels of natural mortality among females are undertaken. 5. Synthesis and
 applications. At the flyway scale, continuous and accurate estimates of
 vital rates and the relative contribution of harvest versus other
 mortality causes are increasingly important as the population effect of
 adjusting harvest rates is most effectively evaluated within a model-based
 adaptive management framework.
description:   A short description of each
 dataset is found within the datafiles!
DOI: 10.5061/dryad.k7m020r
title: Data from: A strong east–west Mediterranean divergence supports a new phylogeographic history of the carob tree (Ceratonia siliqua, Leguminosae) and multiple domestications from native populations

description: Aim: Phylogeography of fruit trees is challenging due to the recurrent
 exchanges between domesticated and wild populations. Here we tested the
 eastern refugium hypothesis (ERH) for the carob tree, Ceratonia siliqua,
 which supports its natural and domestication origins in the Eastern
 Mediterranean and a feral origin in the West. Location: Mediterranean
 basin Taxon: Ceratonia siliqua L., Leguminosae Methods: Divergence time of
 the divergence between the carob tree and its sister species (C.
 oreothauma) was estimated based on two nuclear and one plastid sequences.
 Variation from four plastid regions and 17 nuclear microsatellite loci
 were used to decipher genetic structure in the carob tree and to test
 coalescent-based models by an Approximate Bayesian Computation (ABC)
 approach. We assessed our hypotheses by examining palaeobotanical records
 and hindcasting the past distribution of the carob tree at the
 Mid-Holocene, Last Glacial Maximum (LGM) and Last Interglacial (LIG) using
 species distribution modelling (SDM). Results: The split between C.
 oreothauma and C. siliqua was estimated at 6.4 Ma, and a first divergence
 within C. siliqua at 1.3 Ma. After a presence since the Oligocene,
 Ceratonia was found in the Western and the Eastern Mediterranean in the
 fossil records during the Pleistocene. Plastid and nuclear markers,
 characterized by low allelic richness, revealed a strong west-east genetic
 structuring. Approximate Bayesian computation (ABC) analyses rejected the
 ERH. Main conclusions: Our study supports a severe population decline
 during LIG. The strong west-east divergence and the occurrence of four
 lineages within C. siliqua provided support for a new hypothesis of
 multiple domestications of the carob tree from native populations
 throughout the Mediterranean basin.
description: Viruel_JBiogeo_Carob_Phylogeography_Sequence_microsat_and occurrence_data_files
DOI: 10.5061/dryad.rc739b0
title: Data from: Immune response declines with age in a wild lizard

description: The immune system allows animals to survive the constant attacks of
 pathogens. Even though it is essential for survival and fitness, the
 performance of the immune system can decline with age -a process known as
 immunosenescence- which may be responsible for the increased mortality of
 older individuals. There are few studies regarding the effect of age on
 the immune system in reptiles, and no evidence of immunosenescence has yet
 been reported in lizards. In a wild population of Dickerson's
 collared lizards, Crotaphytus dickersonae, we evaluated the effect of age
 (estimated by skeletochronology) on the male’s immune response to a novel
 antigen (phytohemagglutinin). We found a strong negative relationship
 between immune response and age, the first evidence of immunosenescence in
 a lizard. Our results show that immunosenescence can occur even in
 relatively short-lived reptiles and underline the importance of age on
 performance in fitness-related traits.
description: Age and immune response
 in the lizard Crotaphytus dickersonae
DOI: 10.5061/dryad.228986b
title: Data from: Adaptive landscape genetics and malaria across divergent island bird populations

description: Environmental conditions play a major role in shaping the spatial
 distributions of pathogens, which in turn can drive local adaptation and
 divergence in host genetic diversity. Haemosporidians, such as plasmodium
 (malaria) are a strong selective force, impacting survival and fitness of
 hosts, with geographic distributions largely determined by habitat
 suitability for their insect vectors. Here, we have tested whether
 patterns of fine-scale local adaptation to malaria are replicated across
 discrete, ecologically differing island populations of Berthelot's
 pipits Anthus berthelotii. We sequenced TLR4, an innate immunity gene that
 is potentially under positive selection in Berthelot's pipits, and
 two SNPs previously identified as being associated with malaria infection
 in a genome-wide association study (GWAS) in Berthelot's pipits in
 the Canary Islands. We determined the environmental predictors of malaria
 infection, using these to estimate variation in malaria risk on Porto
 Santo, and found some congruence with previously identified environmental
 risk factors on Tenerife. We also found a negative association between
 malaria infection and a TLR4 variant in Tenerife. In contrast, one of the
 GWAS SNPs showed an association with malaria risk in Porto Santo, but in
 the opposite direction to that found in the Canary Islands GWAS. Together,
 these findings suggest that disease-driven local adaptation may be an
 important factor in shaping variation among island populations.
description: Pipit sample
 dataDetails on collection,
 age, malaria strains and genetic data for each sample.TF_PS_pipits.csvTenerife GIS dataGIS data for samples collected in 2011 on TenerifeTF_pipits_2011.csvPorto Santo GIS dataGIS data for samples collected in 2016 on Porto SantoPS_pipits_2016.csv
DOI: 10.5061/dryad.bt3938p
title: Data from: Diversification of the North American Doellingeria-Eucephalus clade

description: Doellingeria and Eucephalus form the earliest-diverging clade of the North
 American Astereae lineage. Phylogenetic analyses of both nuclear and
 plastid sequence data show that the Doellingeria-Eucephalus clade consists
 of two main subclades that differ from current circumscriptions of the two
 genera. Doellingeria is the sister group to E. elegans, and the
 Doellingeria + E. elegans subclade in turn is sister to the subclade
 containing all remaining species of Eucephalus. In the plastid phylogeny,
 the two subclades are deeply divergent, a pattern that is consistent with
 an ancient hybridization event involving ancestral species of the
 Doellingeria-Eucephalus clade and an ancestral taxon of a related North
 American or South American group. Divergence of the two
 Doellingeria-Eucephalus subclades may have occurred in association with
 northward migration from South American ancestors. We combine these two
 genera under the older of the two names, Doellingeria, and propose 12 new
 combinations (10 species and two varieties) for all species of Eucephalus.
description: nrDNA ETS alignment (all
 samples)aligned DNA sequences in
 FASTA formatDE_nrDNA_ETS_alignment_2018.txtnrDNA ITS alignment (all samples)aligned DNA sequences in FASTA formatDE_nrDNA_ITS_alignment_2018.txtplastid trnCycf6 alignment (all samples)aligned DNA sequences in FASTA formatDE_plastid_trnCycf6_alignment_2018.txtinput file for Bayesian analysis of nrDNA sequencesfile in NEXUS formatDE_nrDNA_input_file_for_MrBayes_2018.txtinput file for Bayesian analysis of plastid sequencesfile in NEXUS formatDE_plastid_input_file_for_MrBayes_2018.txtnrDNA Bayesian treeNewick file for published treeDE_nrDNA.treplastid Bayesian treeNewick file for published treeDE_plastid.treData for morphological analysisFile is 123 specimens X 11 characters. Specimens are identified by species and IDCODE (= herbarium + accession #). Abbreviated names for morphological characters, along with measurement units, are explained in the published paper.DE_data_for_morph_analyses_2018.csvOutput from principal component analysis of morphological dataOutput file created by Statistix v. 9 software (available at www.statistix.com).DE_PCA_eigenvalues_and_eigenvectors.csvdiscriminant analysis with 2 groupsAnalysis results from SYSTAT v.10 (SPSS 2000) software.DE_discrim_analysis_with_2_groups.csvdiscriminant analysis with 3 groupsanalysis results from SYSTAT v.10 (SPSS 2000) softwareDE_discrim_analysis_with_3_groups.csvSamples used for molecular analysesTable with taxonomic names, voucher information, localities, and GenBank accession numbers for all samples used for phylogenetic analysesDNA_vouchers_and_GenBank_info.csvherbarium specimens used for morphometric analysisList of specimens by species, herbarium of origin, and accession/collection number.Specimens_for_morph_analysis.txt
DOI: 10.5061/dryad.mn257gm
title: Data from: The origin of the central dogma through conflicting multilevel selection

description: The central dogma of molecular biology rests on two kinds of asymmetry
 between genomes and enzymes: informatic asymmetry, where information flows
 from genomes to enzymes but not from enzymes to genomes; and catalytic
 asymmetry, where enzymes provide chemical catalysis but genomes do not.
 How did these asymmetries originate? Here, we show that these asymmetries
 can spontaneously arise from conflict between selection at the molecular
 level and selection at the cellular level. We developed a model consisting
 of a population of protocells, each containing a population of replicating
 catalytic molecules. The molecules are assumed to face a trade-off between
 serving as catalysts and serving as templates. This trade-off causes
 conflicting multilevel selection: serving as catalysts is favoured by
 selection between protocells, whereas serving as templates is favoured by
 selection between molecules within protocells. This conflict induces
 informatic and catalytic symmetry breaking, whereby the molecules
 differentiate into genomes and enzymes, establishing the central dogma. We
 show mathematically that the symmetry breaking is caused by a positive
 feedback between Fisher’s reproductive values and the relative impact of
 selection at different levels. This feedback induces a division of labour
 between genomes and enzymes, provided variation at the molecular level is
 sufficiently large relative to variation at the cellular level, a
 condition that is expected to hinder the evolution of altruism. Taken
 together, our results suggest that the central dogma is a logical
 consequence of conflicting multilevel selection.
description: C++ source code implementing the agent-based model
 source.tar.gz
DOI: 10.5061/dryad.n1d7c01
title: Data from: Ecology and signal structure drive the evolution of synchronous displays

description: Animal synchrony is found in phylogenetically distant animal groups,
 indicating behavioural adaptations to different selective pressures and in
 different signaling modalities. A notable example of synchronous display
 is found in fiddler crabs in that males wave their single enlarged claw
 during courtship. They present species-specific signals, which are
 composed of distinctive movement signatures. Given that synchronous waving
 has been reported for several fiddler crab species, the display pattern
 could influence the ability of a given species to sufficiently adjust wave
 timing to allow for synchrony. In this study we quantified the wave
 displays of fiddler crabs to predict their synchronous behaviour. We
 combined this information with the group’s phylogenetic relationships to
 trace the evolution of display synchrony in an animal taxon. We found no
 phylogenetic signal in interspecific variation in predicted wave
 synchrony, which mirrors the general non-phylogenetic pattern of synchrony
 across animal taxa. Interestingly, our analyses show that the phenomenon
 of synchronization stems from the peculiarities of display pattern, mating
 systems and the complexity of microhabitats. This is the first study to
 combine mathematical simulations and phylogenetic comparative methods to
 reveal how ecological factors and the mechanics of animal signals affect
 the evolution of the synchronous phenomena.
description: normalizedContains the normalized wave display series for each of the 5 individuals and 32 species.Competition_for_leadershipFortran file. Competition for leadership simulationPredicted_synchorny_Rayleigh_testR file. Using the Rayleigh test to obtain the p-values for synchrony. Calculates the percentage of simulations that presented synchrony: predicted synchrony values.finalPhylogenetic treePGLS_dataFinal data for PGLS analysisPGLS_analysis
DOI: 10.5281/zenodo.15472377
title: Code of Magnetoelastic
DOI: 10.5281/zenodo.15472378
title: Code of Magnetoelastic
DOI: 10.15468/dl.64jwnc
title: Occurrence Download

description: A dataset containing 53 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Sesbania grandiflora (L.) Poir."
 ]
}

 The dataset includes 53 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009638-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5rzzvu
title: Occurrence Download

description: A dataset containing 644 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Dominican Republic",
 "Geometry POLYGON((-69.23591 18.86858,-69.02836 18.86858,-69.02836 19.16877,-69.23591 19.16877,-69.23591 18.86858))",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 644 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009868-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8nb565
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is Philippines",
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "TaxonKey is Pithecophaga jefferyi",
 "Year 2000-2025"
 ]
}

 The dataset includes 23 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009869-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wr5qma
title: Occurrence Download

description: A dataset containing 2901 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is DEU.13.6_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Ailanthus altissima"
 ]
}

 The dataset includes 2901 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009871-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zcx66x
title: Occurrence Download

description: A dataset containing 30637 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leopardus pardalis",
 "DecimalLongitude is not null",
 "DecimalLatitude is not null"
 ]
}

 The dataset includes 30637 records from 379 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009870-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.