cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.cr1m5
title: Data from: Ecogeographical patterns of morphological variation in pygmy shrews Sorex minutus (Soricomorpha: Soricinae) within a phylogeographic and continental-and-island framework

description: Ecogeographical patterns of morphological variation were studied in the
 Eurasian pygmy shrew Sorex minutus aiming to understand the species’
 morphological diversity in a continental and island setting, and within
 the context of previous detailed phylogeographical studies. In total, 568
 mandibles and 377 skulls of S. minutus from continental and island
 populations from Europe and Atlantic islands were examined using a
 geometric morphometrics approach, and the general relationships of
 mandible and skull size and shape with geographical and environmental
 variables were studied. Samples were then pooled into predefined
 geographical groups to evaluate the morphological differences among them
 using analyses of variance, aiming to contrast the morphological and
 genetic relationships based on morphological and genetic distances and
 ancestral state reconstructions, as well as assess the correlations of
 morphological, genetic, and geographical distances with Mantel tests. We
 found significant relationships of mandible size with geographical and
 environmental variables, fitting the converse Bergmann's rule;
 however, for skull size, this was less evident. Continental groups of S.
 minutus could not readily be differentiated from each other by shape. Most
 island groups of S. minutus were easily discriminated from the continental
 groups by being larger, indicative of an island effect. Moreover,
 morphological and genetic distances differed substantially and, again,
 island groups were distinctive morphologically. Morphological and
 geographical distances were significantly correlated, although this was
 not the case for morphological and genetic distances, indicating that
 morphological variation does not reflect genetic subdivision in S.
 minutus. Our analyses showed that environmental variables and insularity
 had important effects on the morphological differentiation of S. minutus.
description: DRYAD Vega et al BJLS
 Ecogeographical patterns in pygmy shrewsDRYAD Sorex minutus data
 mandibles and skullsExcel file with
 geographical and environmental data for mandible and skull samples of
 Sorex minutusVega et al BJLS Sorex
 minutus mandiblesPhotographs of mandibles
 of Sorex minutusVega et al BJLS Sorex
 minutus skullsPhotographs of skulls of
 Sorex minutus (ventral side)Sorex minutus Eurasia
 mandibles LeftTPS file with landmark
 configurations for Sorex minutus mandiblesSorex minutus Eurasia
 Skulls LeftTPS file with landmark
 configurations for Sorex minutus skulls
DOI: 10.5281/zenodo.18385844
title: Dataset for Omnichannel Marketing Strategy and Hospital Service Quality Study in Indonesia

description: This dataset contains anonymized survey data collected for a study examining the impact of omnichannel marketing strategy on hospital service quality in a private hospital in Indonesia. The dataset includes responses from inpatient and outpatient participants and was analyzed using quantitative statistical methods. Personal identifiers have been removed to protect participant confidentiality. Access to the dataset is restricted due to ethical considerations and institutional regulations.
DOI: 10.5281/zenodo.18385843
title: Dataset for Omnichannel Marketing Strategy and Hospital Service Quality Study in Indonesia

description: This dataset contains anonymized survey data collected for a study examining the impact of omnichannel marketing strategy on hospital service quality in a private hospital in Indonesia. The dataset includes responses from inpatient and outpatient participants and was analyzed using quantitative statistical methods. Personal identifiers have been removed to protect participant confidentiality. Access to the dataset is restricted due to ethical considerations and institutional regulations.
DOI: 10.5061/dryad.h6s5j
title: Data from: Species discovery and validation in a cryptic radiation of endangered primates: coalescent-based species delimitation in Madagascar's mouse lemurs

description: Implementation of the coalescent model in a Bayesian framework is an
 emerging strength in genetically based species delimitation studies. By
 providing an objective measure of species diagnosis, these methods
 represent a quantitative enhancement to the analysis of multilocus data,
 and complement more traditional methods based on phenotypic and ecological
 characteristics. Recognized as two species 20 years ago, mouse lemurs
 (genus Microcebus) now comprise more than 20 species, largely diagnosed
 from mtDNA sequence data. With each new species description, enthusiasm
 has been tempered with scientific scepticism. Here, we present a
 statistically justified and unbiased Bayesian approach towards mouse lemur
 species delimitation. We perform validation tests using multilocus
 sequence data and two methodologies: (i) reverse-jump Markov chain Monte
 Carlo sampling to assess the likelihood of different models defined a
 priori by a guide tree, and (ii) a Bayes factor delimitation test that
 compares different species-tree models without a guide tree. We assess the
 sensitivity of these methods using randomized individual assignments,
 which has been used in bpp studies, but not with Bayes factor delimitation
 tests. Our results validate previously diagnosed taxa, as well as new
 species hypotheses, resulting in support for three new mouse lemur
 species. As the challenge of multiple researchers using differing criteria
 to describe diversity is not unique to Microcebus, the methods used here
 have significant potential for clarifying diversity in other taxonomic
 groups. We echo previous studies in advocating that multiple lines of
 evidence, including use of the coalescent model, should be trusted to
 delimit new species.
description: Nuclear and mtDNA
 lociSequence data files in
 NEXUS format for all four nuclear and two mtDNA loci used in this study.
 These files contain the sequence data analyzed in Weisrock et al. (2010)
 as well as new sequence data from this study.Study
 Loci.zipLemur Map
 LocalitiesA list of coordinate
 information for the localities presented in Figure 1.STRUCTURE
 AnalysesA folder containing all
 input and results files for STRUCTURE analyses performed in this
 study.BPP
 AnalysesA folder containing all
 input and results files from BPP analyses. Also included are .xlsx files
 summarizing the full set of BPP runs.Bayes Factor
 AnalysesThis folder contains all
 input and result files associated with *BEAST-based Bayes factor analyses
 performed in this study. Also included is an .xlsx file summarizing
 results across all analyses, including HME, sHME, Path Sampling, and
 Stepping Stone sampling calculations.
DOI: 10.5061/dryad.hf124
title: Data from: Electroreception in early vertebrates: survey, evidence and new information

description: Electroreception is widespread in living vertebrates, and is often
 considered a primitive vertebrate character. However, the early evolution
 of electroreception remains unclear. A variety of structures in early
 vertebrate fossils have been put forward as potential electroreceptors,
 but these need to be reassessed in light of the now substantial literature
 on electroreceptors in living vertebrates. Here we review the evidence for
 all putative electroreceptors in early vertebrates, and provide new
 information from CT scans. In the jawless osteostracans, the pore canal
 system in the dermal skeleton and the lateral and dorsal fields do not
 resemble electroreceptors in living species. Nevertheless the presence of
 a recurrent ramus of the anterior lateral line nerve in osteostracans
 suggests electroreceptors were present, by comparison with lampreys. In
 placoderms, cutaneous sense organs on arthrodire cheek plates are possible
 electroreceptors. CT data shows that the orientation of these pits is
 anomalous for electroreceptors, and intimately associated with bone
 growth. A newly identified type of cheek pit, for which the term “Young’s
 apparatus” is introduced, is known so far only from two arthrodire
 specimens. It is closely associated with the underlying jaw joint, but its
 precise function is unknown. In osteichthyans, the “pore-group” clusters
 of early sarcopterygians may have housed electroreceptors. CT data from
 Devonian lungfish support this interpretation, showing internal morphology
 consistent with electroreceptors, and innervation via the rostral tubuli
 underlying the dermal bone of the snout. The early osteichthyan
 Ligulalepis has pit structures which may be electroreceptors, and they
 were possibly innervated by lateral line nerves. Specialised
 electroreceptor systems, including elaborated “pore-group” pits in
 Devonian lungfish and rostral organs in the earliest coelacanths, show
 that electroreception may have had an important role in niche
 specialisation in early vertebrates. Finally, fossil data does not support
 the hypothesis that vertebrate hard tissues initially evolved to shield
 electroreceptors.
description: Camuropiscis_Suborbital_SAMP53772Eastmanosteus_postsuborbital_MVP231104Eastmanosteus_Postsuborbital_subsection_MVP231104Kimberleyichthys_Postsuborbital_ANUV1037Ligulalepis_ANUV3628_sensory pitsParabuchanosteus_Suborbital_ANUV1686Speonesydrion_ANU49340_anteriorSpeonesydrion_ANU49340_posteriortorosteidsp_Postsuborbital_SAMP50606Torosteus_Postsuborbital_MVP230808Torosteus_Suborbital_MVP230808V79_large_modelV79_small_modelV244_suborbitalV79
DOI: 10.15470/77bhey
title: Dataset of Bottlenose Dolphin Acoustic Recordings from Boat-Based Encounters Using HydroMoth Devices, Event 006 (2024-12-01)

description: This dataset contains acoustic information derived from underwater recordings of a group of bottlenose dolphins (Tursiops truncatus) during a boat-based encounter on 1 December 2024 off Costes del Garraf (Natura 2000: ES5110020; Catalonia, Spain, NW Mediterranean). Recordings were made using a HydroMoth device (AudioMoth Firmware Basic v1.11.0) by the Institut de Ci?ncies del Mar (ICM-CSIC), with field support from Associaci? Cet?cea.

The workflow relies entirely on open-source tools and is designed to ensure FAIR data publication in biodiversity repositories: media files and supplementary materials are preserved in Zenodo, while structured data are published as a Darwin Core Archive (DwC-A) through GBIF.
DOI: 10.5061/dryad.0564q
title: Data from: Bayesian model selection with BAMM: effects of the model prior on the inferred number of diversification shifts

description: 1. Understanding variation in rates of speciation and extinction -- both
 among lineages and through time -- is critical to the testing of many
 hypotheses about macroevolutionary processes. BAMM is a flexible Bayesian
 framework for inferring the number and location of shifts in
 macroevolutionary rate across phylogenetic trees and has been widely used
 in empirical studies. BAMM requires that researchers specify a prior
 probability distribution on the number of diversification rate shifts
 before conducting an analysis. The consequences of this "model
 prior" for inference are poorly known but could potentially influence
 both the probability of accepting models that are more (high error rate)
 or less (low power) complex than the generating model. 2. The hierarchical
 Poisson process prior in BAMM reduces to a simple geometric distribution
 on number of rate shifts and we use this property to increase the
 efficiency of model selection with Bayes factors. Using BAMM v2.5, we
 analyzed phylogenies simulated with and without diversification
 heterogeneity across a broad range of prior parameterizations. We also
 assessed the impact of the model prior on MCMC convergence times and on
 diversification rate estimates. 3. For all simulation scenarios, model
 evidence (Bayes factor support) for the number of shifts is not sensitive
 to the choice of model prior over the wide range examined here. The
 best-supported model found using BAMM rarely includes spurious shifts
 (&lt;2% of all runs) when diversification models are selected using
 Bayes factors. BAMM was reliably able to infer the true number of
 diversification rate shifts across prior expectations that varied by three
 orders of magnitude. However, we find a strong effect of model prior on
 MCMC convergence properties: a flatter prior distribution (larger expected
 number of shifts) can dramatically increase the efficiency of the MCMC
 simulation. 4. Our results support the use of a liberal model prior in
 BAMM, as it reduces computation time without distorting the evidence for
 rate heterogeneity.
description: RscriptsR scripts and supplementary files for processing the BAMM analyses of the constant rate and diversity-dependent simulations. Please contact Jonathan S. Mitchell with questions about these files.constantTreesConstant-rate simulated phylogenies analyzed with two different versions of BAMM under many different model priors. Please contact Jonathan S Mitchell with questions about these files.plosTrees1-100First 100 trees from Dan Rabosky's original 2014 PlOS description of BAMM analyzed using three different priors. Please contact Jonathan S Mitchell with questions about these files.plosTrees101-300Simulated trees #101 to 300 from Dan Rabosky's original 2014 PLoS description of BAMM analyzed using three different priors. Please contact Jonathan S Mitchell with questions about these files.
DOI: 10.5061/dryad.58g217k
title: Data from: Genome-wide variation in nucleotides and retrotransposons in alpine populations of Arabis alpina (Brassicaceae)

description: Advances in high-throughput sequencing have promoted the collection of
 reference genomes and genome-wide diversity. However, the assessment of
 genomic variation among populations has hitherto mainly been surveyed
 through single-nucleotide polymorphisms (SNPs) and largely ignored the
 often major fraction of genomes represented by transposable elements
 (TEs). Despite accumulating evidence supporting the evolutionary
 significance of TEs, comprehensive surveys remain scarce. Here, we
 sequenced the full genomes of 304 individuals of Arabis alpina sampled
 from four nearby natural populations to genotype SNPs as well as
 polymorphic long terminal repeat retrotransposons (polymorphic TEs; i.e.
 presence/absence of TE insertions at specific loci). We identified 291,396
 SNPs and 20,548 polymorphic TEs, comparing their contributions to genomic
 diversity and divergence across populations. Few SNPs were shared among
 populations and overall showed high population-specific variation, whereas
 most polymorphic TEs segregated among populations. The genomic context of
 these two classes of variants further highlighted candidate adaptive loci
 having a putative impact on functional genes. In particular, 4.96% of the
 SNPs were identified as non-synonymous or affecting start/stop codons. In
 contrast, 43% of the polymorphic TEs were present next to Arabis genes
 enriched in functional categories related to the regulation of
 reproduction and responses to biotic as well as abiotic stresses. This
 unprecedented dataset, mapping variation gained from SNPs and
 complementary polymorphic TEs within and among populations, will serve as
 a rich resource for addressing microevolutionary processes shaping genome
 variation.
description: PolyTE_Final_ClassifiedPolymorphic TEs are genotyped as 0,1,2 0 = TE not present in the given coordinates 1 = TE present in heterozygous state 2 = TE present in homozygous state NA = Information not available Genomic coordinates for each polymorphic TE is given by 'chrom', 'start' and 'stop' 'PolyTE names' starting with 'A' are the polyTE loci called by deletion with respect to the reference pipeline and those starting with 'I' are the loci called by insertion with respect to the reference pipeline of TEPID. Family, Tribe and Superfamily classification for each polymorphic TE is provided. Polymorphic TEs beloning to Solo-LTR or Full length elements are provided in TEID.SNPs dataSNPs dataset (containing also SNPs within the transposable element sequences) in vcf format. Called with FreeBayes v.1.0.2 from whole genome sequencing (Illumina Hiseq 2500) 304 individuals from four regions: Ma: Martinet Pa: Para Es: Essets Pi: PierredarSNPs.vcf.gznon-TE SNPs datasetSNPs dataset that do not contain the SNPs within the transposable elements sequences in a vcf format called with FreeBayes v.1.0.2 from whole genome sequencing (Illumina Hiseq 2500). 304 individuals from four regions: Ma: Martinet Pa: Para Es: Essets Pi: Pierredarnon-TE_SNPs.vcf.gz
DOI: 10.5061/dryad.1632h
title: Data from: Predicting Stroop effect from spontaneous neuronal activity: a study of regional homogeneity

description: The Stroop effect is one of the most robust and well-studied phenomena in
 cognitive psychology and cognitive neuroscience. However, little is known
 about the relationship between intrinsic brain activity and the individual
 differences of this effect. In the present study, we explored this issue
 by examining whether resting-state functional magnetic resonance imaging
 (rs-fMRI) signals could predict individual differences in the Stroop
 effect of healthy individuals. A partial correlation analysis was
 calculated to examine the relationship between regional homogeneity (ReHo)
 and Stroop effect size, while controlling for age, sex, and framewise
 displacement (FD). The results showed positive correlations in the left
 inferior frontal gyrus (LIFG), the left insula, the ventral anterior
 cingulate cortex (vACC), and the medial frontal gyrus (MFG), and negative
 correlation in the left precentral gyrus (LPG). These results indicate the
 possible influences of the LIFG, the left insula, and the LPG on the
 efficiency of cognitive control, and demonstrate that the key nodes of
 default mode network (DMN) may be important in goal-directed behavior
 and/or mental effort during cognitive control tasks.
description: FunRaw_replaceThese 44 subjects were randomly selected from 175 participants. Therefore, subject NO. is discrete. In the folder named FunRaw, the T2-weighted images of subjects were included and the data were collected during the resting stateFunRaw.rarT1Img_replaceThese 44 subjects were randomly selected from 175 participants. Therefore, subject NO. is discrete. In the folder named T1Img, the T1-weighted images of subjects were included.T1Img.rarbehavior_replaceThese 44 subjects were randomly selected from 175 participants. Therefore, subject NO. is discrete. In the folder named behavior, the behavioral data of subjects were included.behavior.zip
DOI: 10.5061/dryad.104kg
title: Data from: Metabarcoding of freshwater invertebrates to detect the effects of a pesticide spill

description: Biomonitoring underpins the environmental assessment of freshwater
 ecosystems and guides management and conservation. Current methodology for
 surveys of (macro)invertebrates uses coarse taxonomic identification where
 species-level resolution is difficult to obtain. Next-generation
 sequencing of entire assemblages (metabarcoding) provides a new approach
 for species detection, but requires further validation. We used
 metabarcoding of invertebrate assemblages with two fragments of the cox1
 "barcode" and partial nuclear ribosomal (SSU) genes, to assess
 the effects of a pesticide spill in the River Kennet (Southern England).
 Operational Taxonomic Unit (OTU) recovery was tested under72 parameters
 (read denoising, filtering, pair merging and clustering). Similar
 taxonomic profiles were obtained under a broad range of parameters. The
 SSU marker recovered Platyhelminthes and Nematoda, missed by cox1,while
 Rotifera were only amplified with cox1. A reference set was created from
 all available barcode entries for Arthropoda in the BOLD database and
 clustered into OTUs. The River Kennet metabarcoding produced matches to
 207 of these reference OTUs, five times the number of species recognised
 with morphological monitoring. The increase was due to: greater taxonomic
 resolution (e.g. splitting a single morphotaxon ‘Chironomidae’ into 55
 named OTUs); splitting of binomial species names into multiple molecular
 OTUs in species complexes; and the use of a filtration-flotation protocol
 for extraction of minute specimens (meiofauna). Community analyses
 revealed strong differences between "impacted" vs.
 "control" samples, detectable with each gene marker, for each
 major taxonomic group, and for meio- and macro-faunal samples separately.
 Thus, highly resolved taxonomic data can be extracted at a fraction of the
 time and cost of traditional non-molecular methods, opening new avenues
 for freshwater invertebrate biodiversity monitoring and molecular ecology.
description: Raw metabarcode data
 Slot 1 (12 libraries)Raw metabarcode data
 Slot 1 (12 libraries). Inlcudes R1 and R2 files for macrofauna samples
 from the 3 impacted and 3 control sites, each sampled at two times after
 pesticide spill. More info on paper.Raw_metabarcode_data_Slot_1_(12_libraries).rarRaw_metabarcode_data_Slot_2_(12_libraries)Raw metabarcode data Slot 2 (12 libraries). Inlcudes R1 and R2 files for meiofauna samples from the 3 impacted and 3 control sites, each sampled at two times after pesticide spill. More info on paper.
DOI: 10.5061/dryad.3jj7f
title: Data from: Comparative analyses of QTLs influencing obesity and metabolic phenotypes in pigs and humans

description: The pig is a well-known animal model used to investigate genetic and
 mechanistic aspects of human disease biology. They are particularly useful
 in the context of obesity and metabolic diseases because other widely used
 models (e.g. mice) do not completely recapitulate key pathophysiological
 features associated with these diseases in humans. Therefore, we
 established a F2 pig resource population (n = 564) designed to elucidate
 the genetics underlying obesity and metabolic phenotypes. Segregation of
 obesity traits was ensured by using breeds highly divergent with respect
 to obesity traits in the parental generation. Several obesity and
 metabolic phenotypes were recorded (n = 35) from birth to slaughter (242 ±
 48 days), including body composition determined at about two months of age
 (63 ± 10 days) via dual-energy x-ray absorptiometry (DXA) scanning. All
 pigs were genotyped using Illumina Porcine 60k SNP Beadchip and a combined
 linkage disequilibrium-linkage analysis was used to identify genome-wide
 significant associations for collected phenotypes. We identified 229 QTLs
 which associated with adiposity- and metabolic phenotypes at genome-wide
 significant levels. Subsequently comparative analyses were performed to
 identify the extent of overlap between previously identified QTLs in both
 humans and pigs. The combined analysis of a large number of obesity
 phenotypes has provided insight in the genetic architecture of the
 molecular mechanisms underlying these traits indicating that QTLs
 underlying similar phenotypes are clustered in the genome. Our analyses
 have further confirmed that genetic heterogeneity is an inherent
 characteristic of obesity traits most likely caused by segregation or
 fixation of different variants of the individual components belonging to
 cellular pathways in different populations. Several important genes
 previously associated to obesity in human studies, along with novel genes
 were identified. Altogether, this study provides novel insight that may
 further the current understanding of the molecular mechanisms underlying
 human obesity.
description: UNIK_Porcine_FinalReportOriginal SNP genotypes for alle individuals included for 'Comparative Analyses of QTLs influencing Obesity and Metabolic Phenotypes in Pigs and Humans', Pant et al. Plos ONE 2015