cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fp3fp
title: Data from: DNA metabarcoding diet analysis for species with parapatric versus sympatric distribution: a case study on subterranean rodents

description: Closely related sympatric species commonly develop different ecological
 strategies to avoid competition. Ctenomys minutus and C. flamarioni are
 subterranean rodents parapatrically distributed in the southern Brazilian
 coastal plain, showing a narrow sympatric zone. To gain understanding on
 food preferences and possible competition for food resources, we evaluated
 their diet composition performing DNA metabarcoding analyzes of 67 C.
 minutus and 100 C. flamarioni scat samples, collected along the species
 geographical ranges. Thirteen plant families, mainly represented by
 Poaceae, Araliaceae, Asteraceae and Fabaceae, were identified in the diet
 of C. minutus. For C. flamarioni, 10 families were recovered, with a
 predominance of Poaceae, Araliaceae and Asteraceae. A significant
 correlation between diet composition and geographical distance was
 detected in C. minutus, whereas the diet of C. flamarioni was quite
 homogeneous throughout its geographical distribution. No significant
 differences were observed between males and females of each species.
 However, differences in diet composition between species were evident
 according to multivariate analysis. Our results suggest some level of diet
 partitioning between C. flamarioni and C. minutus in the sympatric region.
 While the first species is more specialized on few plant items, the second
 showed a more varied and heterogeneous diet pattern among individuals.
 These differences might have been developed to avoid competition in the
 region of co-occurrence. Resource availability in the environment also
 seems to influence food choices. Our data indicate that C. minutus and C.
 flamarioni are generalist species, but that some preference for Poaceae,
 Asteraceae and Araliaceae families can be suggested for both rodents.
description: ast_feces_unfilteredgh_feces_unfilteredpoa_feces_unfilteredmav_feces_unfilteredreference_db_ghSequences of the reference database of the P6 loop of the chloroplast trnL (UAA) intronreference_db_ITS_AsteraceaeSequences of the reference database of the ITS1 molecular marker of Asteraceaereference_db_ITS_PoaceaeSequences of the reference database of the ITS1 molecular marker of Poaceae
DOI: 10.5061/dryad.3jh4r
title: Data from: The effect of parasites on sex differences in selection

description: The life history strategies of males and females are often divergent,
 creating the potential for sex differences in selection. Deleterious
 mutations may be subject to stronger selection in males, owing to sexual
 selection, which can improve the mean fitness of females and reduce
 mutation load in sexual populations. However, sex differences in selection
 might also maintain sexually antagonistic genetic variation, creating a
 sexual conflict load. The overall impact of separate sexes on fitness is
 unclear, but the net effect is likely to be positive when there is a large
 sex difference in selection against deleterious mutations. Parasites can
 also have sex-specific effects on fitness, and there is evidence that
 parasites can intensify the fitness consequences of deleterious mutations.
 Using lines that accumulated mutations for over 60 generations, we studied
 the effect of the pathogenic bacterium Pseudomonas aeruginosa on sex
 differences in selection in the fruit fly Drosophila melanogaster.
 Pseudomonas infection increased the sex difference in selection, but may
 also have weakened the intersexual correlation for fitness. Our results
 suggest that parasites may increase the benefits of sexual selection.
description: fitness_dataFitness measures from replicate reproductive success assays. 25 mutant (MA) genotypes; 25 control (non-MA) genotypes; two sexes; three inoculation treatments (infection levels). These data are made available in two file formats, for use with Numbers or Excel.immediately_plated_bacterial_countsBacterial counts taken from diluted homogenate of males and females immediately following inoculation. These data are made available in two file formats, for use with Numbers or Excel.
DOI: 10.5281/zenodo.18390837
title: Supplementary Tables

description: Supplementary tables
DOI: 10.5061/dryad.p680f
title: Data from: Phylum-wide comparative genomics unravel the diversity of secondary metabolism in Cyanobacteria

description: Background: Cyanobacteria are an ancient lineage of photosynthetic
 bacteria from which hundreds of natural products have been described,
 including many notorious toxins but also potent natural products of
 interest to the pharmaceutical and biotechnological industries. Many of
 these compounds are the products of non-ribosomal peptide synthetase
 (NRPS) or polyketide synthase (PKS) pathways. However, current
 understanding of the diversification of these pathways is largely based on
 the chemical structure of the bioactive compounds, while the evolutionary
 forces driving their remarkable chemical diversity are poorly understood.
 Results: We carried out a phylum-wide investigation of genetic
 diversification of the cyanobacterial NRPS and PKS pathways for the
 production of bioactive compounds. 452 NRPS and PKS gene clusters were
 identified from 89 cyanobacterial genomes, revealing a clear burst in
 late-branching lineages. Our genomic analysis further grouped the clusters
 into 286 highly diversified cluster families (CF) of pathways. Some CFs
 appeared vertically inherited, while others presented a more complex
 evolutionary history. Only a few horizontal gene transfers were evidenced
 amongst strongly conserved CFs in the phylum, while several others have
 undergone drastic gene shuffling events, which could result in the
 observed diversification of the pathways. Conclusions: Therefore, in
 addition to toxin production, several NRPS and PKS gene clusters are
 devoted to important cellular processes of these bacteria such as nitrogen
 fixation and iron uptake. The majority of the biosynthetic clusters
 identified here have unknown end products, highlighting the power of
 genome mining for the discovery of new natural products.
description: SpeciesTree concatenated
 alignment datasetThe alignment used to
 generate the species tree corresponds to the concatenation of twenty-nine
 conserved proteins as described in the material and method section of the
 paper.SpeciesTree_aln.fastaMaximum Likelihood phylogeny tree of all cyanobacteria included in the studyThe Maximum-Likelihood phylogenetic species tree was generated using PhyML 3.1.0.2 with the alignment of a concatenation of twenty-nine conserved proteins.SpeciesTree_MLphylogeny.treeKS PUFA alignment datasetThe alignment used to generate the phylogeny of bacterial ketoacyl synthase domains.KS_PUFA_aln.fastaPhylogeny of bacterial ketoacyl synthase domainsMaximum likelihood phylogenetic tree of bacterial KS based on gene clusters encoding secondary lipids biosynthesis and enediynes.KS_PUFA_ML.treeKS domains alignementAlignment of the 472 KS domains detected in the 452 gene clusters.KSdomains_472_aln.fastaMaximum-likelihood phylogenetic tree of the 472 KS domainsKSdomains_472_ML.treeC domains alignementAlignement of the 939 C domains detected in the 452 gene clusters.allC_domains_939_aln.fastaMaximum-likelihood phylogenetic tree of the 939 C domainsallC_domains_939_JTT_ML.tree
DOI: 10.5281/zenodo.18390836
title: Supplementary Tables

description: Supplementary tables
DOI: 10.5061/dryad.qc3s0
title: Data from: High stakes species delimitation in eyeless cave spiders (Cicurina, Dictynidae, Araneae) from central Texas

description: A remarkable radiation of completely eyeless, cave-obligate spider species
 (Cicurina) has been described from limestone caves of Texas. This
 radiation includes over 50 described species, with a large number of
 hypothesized single-cave endemics, and four species listed as US Federally
 Endangered. Because of this conservation importance, species delimitation
 in the group is “high stakes” - it is imperative that species hypotheses
 are data-rich, objective, and robust. This paper focuses on a complex of
 four cave-dwelling Cicurina distributed on the northwestern edge of
 Austin, Texas. Several of the existing species hypotheses in this complex
 are weak, based on morphological comparisons of small samples of adult
 female specimens; one species description (for C. wartoni) is based on a
 single adult specimen. Species limits in this group were newly assessed
 using morphological, mitochondrial, and nuclear DNA sequence data
 evidence, analyzed using a variety of approaches. All data support a clear
 lineage separation between C. buwata versus the C. travisae complex
 (including C. travisae, C. wartoni, and C. reddelli). Observed congruence
 across multiple analyses indicate that the C. travisae complex represents
 a single species, and the formal species synonymy presented here has
 important conservation implications. The integrative framework utilized in
 this study serves as a potential model for other Texas cave Cicurina,
 including US Federally Endangered species. More generally, this study
 illustrates how and why taxon-focused conservation efforts must prioritize
 modern species delimitation research (if the existing taxonomy is weak),
 before devoting precious downstream resources to conservation efforts. The
 study also highlights the issue of taxonomic type II error that diversity
 biologists increasingly face as species delimitation moves into the
 genomics era.
description: Cicurina Nuclear
 AlignmentsDNA sequence alignments
 of phased nuclear dataCic_NucMatrices_Dryad.txtCic_COI_DryadCicurina mitochondrial (COI) alignmentRAxML and BEAST tre filestre files from RAxML and BEAST analyses, both nuclear & mitochondrialArchive.zipMorphology Imagesoriginal JPG files for male/female genital morphologiesMorphologyImages_Archive.zip
DOI: 10.5061/dryad.82k0q
title: Data from: An evaluation of fossil tip-dating versus node-age calibrations in tetraodontiform fishes (Teleostei: Percomorphaceae)

description: Time-calibrated phylogenies based on molecular data provide a framework
 for comparative studies. Calibration methods to combine fossil information
 with molecular phylogenies are, however, under active development, often
 generating disagreement about the best way to incorporate paleontological
 data into these analyses. This study provides an empirical comparison of
 the most widely used approach based on node-dating priors for relaxed
 clocks implemented in the programs BEAST and MrBayes, with two recently
 proposed improvements: one using a new fossilized birth–death process
 model for node dating (implemented in the program DPPDiv), and the other
 using a total-evidence or tip-dating method (implemented in MrBayes and
 BEAST). These methods are applied herein to tetraodontiform fishes, a
 diverse group of living and extinct taxa that features one of the most
 extensive fossil records among teleosts. Previous estimates of
 time-calibrated phylogenies of tetraodontiforms using node-dating methods
 reported disparate estimates for their age of origin, ranging from the
 late Jurassic to the early Paleocene (ca. 150–59 Ma). We analyzed a
 comprehensive dataset with 16 loci and 210 morphological characters,
 including 131 taxa (95 extant and 36 fossil species) representing all
 families of fossil and extant tetraodontiforms, under different molecular
 clock calibration approaches. Results from node-dating methods produced
 consistently younger ages than the tip-dating approaches. The older ages
 inferred by tip dating imply an unlikely early-late Jurassic (ca. 185–119
 Ma) origin for this order and the existence of extended ghost lineages in
 their fossil record. Node-based methods, by contrast, produce time
 estimates that are more consistent with the stratigraphic record,
 suggesting a late Cretaceous (ca. 86–96 Ma) origin. We show that the
 precision of clade age estimates using tip dating increases with the
 number of fossils analyzed and with the proximity of fossil taxa to the
 node under assessment. This study suggests that current implementations of
 tip dating may overestimate ages of divergence in calibrated phylogenies.
 It also provides a comprehensive phylogenetic framework for
 tetraodontiform systematics and future comparative studies.
description: Appendix_1Appendix1_GenBank_Accession_Numbers.xlsxMrBayes_ND_CommandsMrBayes_TD_CommandsSupplementary_FilesTrees_TD_ND
DOI: 10.5061/dryad.66jr2
title: Data from: Evidence for high dispersal ability and mito-nuclear discordance in the small brown planthopper, Laodelphax striatellus

description: Understanding dispersal ability in pest species is critical for both
 theoretical aspects of evolutionary and population biology and from a
 practical standpoint, such as implementing effective forecasting systems.
 The small brown planthopper (SBPH), Laodelphax striatellus (Fallén), is an
 economically important pest, but few data exist on its dispersal ability.
 Here, we used mitochondrial and nuclear markers to elucidate the
 population genetic structure of SBPH and of the parasitic bacterium
 Wolbachia throughout temperate and subtropical China. Our results showed
 that the SBPH populations in China lack significant differences in genetic
 structure, suggesting extensive gene flow. Multilocus sequence typing
 revealed that Wolbachia infection was systematic and due to the same
 strain (wStri) within and across populations. However, the mtDNA
 haplogroups had a nonrandom distribution across the sampling localities,
 which correlated to latitudinal and climatic gradients. We explain this
 mito-nuclear discordance as a result of historical population
 recolonization or mitochondria adaptation to climate.
description: Laodelphax striatellus
 microsatellite datamicrosatellite genotype
 of 26 Laodelphax striatellus populations sampled in
 ChinaData matrix of
 concatenated partial COI and COII sequences from 1323
 individualsConcatenated partial COI
 and COII sequences of 26 laodelphax striatellus populations sampled in
 China.107 haplotype sequences
 of concatenated partial COI and COII sequences from 1323
 individualsGPS
 valuesGPS values of the
 sampling locationsGPS
 value.xlsx
DOI: 10.5061/dryad.9jc16
title: Data from: Metabolomic perfusate analysis during kidney machine perfusion: the pig provides an appropriate model for human studies

description: Introduction: Hypothermic machine perfusion offers great promise in kidney
 transplantation and experimental studies are needed to establish the
 optimal conditions for this to occur. Pig kidneys are considered to be a
 good model for this purpose and share many properties with human organs.
 However it is not established whether the metabolism of pig kidneys in
 such hypothermic hypoxic conditions is comparable to human organs.
 Methods: Standard criteria human (n = 12) and porcine (n = 10) kidneys
 underwent HMP using the LifePort Kidney Transporter 1.0 (Organ Recovery
 Systems) using KPS-1 solution. Perfusate was sampled at 45 minutes and 4
 hours of perfusion and metabolomic analysis performed using 1-D 1H-NMR
 spectroscopy. Results: There was no inter-species difference in the number
 of metabolites identified. Of the 30 metabolites analysed, 16 (53.3%) were
 present in comparable concentrations in the pig and human kidney
 perfusates. The rate of change of concentration for 3-Hydroxybutyrate was
 greater for human kidneys (p&lt;0.001). For the other 29 metabolites
 (96.7%), there was no difference in the rate of change of concentration
 between pig and human samples. Conclusions: Whilst there are some
 differences between pig and human kidneys during HMP they appear to be
 metabolically similar and the pig seems to be a valid model for human
 studies.
description: perfusate_sampleszip archive of Bruker format NMR data. Contains 12 human perfusate sample spectra after both 45 minutes and 4 hours of perfusion (24 in total). Also contains 10 porcine perfusate samples at the same timepoints (20 in total).
DOI: 10.5061/dryad.5845b
title: Data from: Integrating fossils, phylogenies, and niche models into biogeography to reveal ancient evolutionary history: the case of Hypericum (Hypericaceae)

description: In disciplines such as macroevolution that are not amenable to
 experimentation, scientists usually rely on current observations to test
 hypotheses about historical events, assuming that “the present is the key
 to the past”. Biogeographers, for example, used this assumption to
 reconstruct ancestral ranges from the present distribution of extant
 species. Yet, under scenarios of high extinction rates, the biodiversity
 we observe today might not be representative of the historical diversity
 and this could result in incorrect biogeographic reconstructions. Here, we
 introduce a new approach to incorporate into biogeographic inference the
 temporal, spatial, and environmental information provided by the fossil
 record, as a direct evidence of the extinct biodiversity fraction. First,
 inferences of ancestral ranges for those nodes in the phylogeny calibrated
 with the fossil record are constrained to include the geographic
 distribution of the fossil. Second, we use fossil distribution and past
 climate data to reconstruct the climatic preferences and potential
 distribution of ancestral lineages over time, and use this information to
 build a biogeographic model that takes into account “ecological
 connectivity” through time. To show the power of this approach, we
 reconstruct the biogeographic history of the large angiosperm genus
 Hypericum, which has a fossil record extending back to the Early Cenozoic.
 Unlike previous reconstructions based on extant species distributions, our
 results reveal that Hypericum stem-lineages were already distributed in
 the Holarctic before diversification of its crown-group, and that the
 geographic distribution of the genus has been relatively stable throughout
 the climatic oscillations of the Cenozoic. Geographical movement was
 mediated by the existence of climatic corridors, like Beringia, while the
 equatorial tropical belt acted as a climatic barrier, preventing Hypericum
 lineages to reach the southern temperate regions. Our study shows that an
 integrative approach to historical biogeography —that combines sources of
 evidence as diverse as paleontology, ecology, and phylogenetics— could
 help us obtain more accurate reconstructions of ancient evolutionary
 history. It also reveals the confounding effect different rates of
 extinction across regions have in biogeography, sometimes leading to
 ancestral areas being erroneously inferred as recent colonization events.
description: Online-Appendix1Supplementary information tablesOnline-Appendix2Supplementary information textOnline-Appendix3Supplementary information figures
DOI: 10.5061/dryad.707rk
title: Data from: EdAl-2 (Educació en Alimentació) programme: reproducibility of a cluster randomised, interventional, primary-school-based study to induce healthier lifestyle activities in children

description: Objectives: To assess the reproducibility of an educational intervention
 EdAl-2 (Educació en Alimentació) programme in ‘Terres de l'Ebre’
 (Spain), over 22 months, to improve lifestyles, including diet and
 physical activity (PA). Design: Reproduction of a cluster randomised
 controlled trial. Setting: Two semi-rural town-group primary-school
 clusters were randomly assigned to the intervention or control group.
 Participants: Pupils (n=690) of whom 320 constituted the intervention
 group (1 cluster) and 370 constituted the control group (1 cluster).
 Ethnicity was 78% Western European. The mean age (±SD) was 8.04±0.6 years
 (47.7% females) at baseline. Inclusion criteria for clusters were towns
 from the southern part of Catalonia having a minimum of 500 children aged
 7–8 year; complete data for participants, including name, gender, date and
 place of birth, and written informed consent from parents or guardians.
 Intervention: The intervention focused on eight lifestyle topics covered
 in 12 activities (1 h/activity/session) implemented by health promoting
 agents in the primary school over three academic years. Primary and
 secondary outcomes: The primary outcome was obesity (OB) prevalence and
 the secondary outcomes were body mass index (BMI) collected every year and
 dietary habits and lifestyles collected by questionnaires filled in by
 parents at baseline and end-of-study. Results: At 22 months, the OB
 prevalence and BMI values were similar in intervention and control groups.
 Relative to children in control schools, the percentage of boys in the
 intervention group who performed ≥4 after-school PA h/week was 15% higher
 (p=0.027), whereas the percentage of girls in both groups remained
 similar. Also, 16.6% more boys in the intervention group watched ≤2
 television (TV) h/day (p=0.009), compared to controls; and no changes were
 observed in girls in both groups. Conclusions: Our school-based
 intervention is feasible and reproducible by increasing after-school PA
 (to ≥4 h/week) in boys. Despite this improvement, there was no change in
 BMI and prevalence of OB.
description: BBDD EdAl_2 study and
 glossariEdAl-2 (Educació en
 Alimentació) programme: reproducibility of a cluster randomised,
 interventional, primary-school-based study to induce healthier lifestyle
 activities in children
DOI: 10.5061/dryad.25j57
title: Data from: Local adaptation despite high gene flow in the waterfall-climbing Hawaiian goby, Sicyopterus stimpsoni.

description: Environmental heterogeneity can promote the emergence of locally adapted
 phenotypes among subpopulations of a species, whereas gene flow can result
 in phenotypic and genotypic homogenization. For organisms like
 amphidromous fishes that change habitats during their life history, the
 balance between selection and migration can shift through ontogeny, making
 the likelihood of local adaptation difficult to predict. In Hawaiian
 waterfall-climbing gobies, it has been hypothesized that larval mixing
 during oceanic dispersal counters local adaptation to contrasting
 topographic features of streams, like slope gradient, that can select for
 predator avoidance or climbing ability in juvenile recruits. To test this
 hypothesis, we used morphological traits and neutral genetic markers to
 compare phenotypic and genotypic distributions in recruiting juveniles and
 adult subpopulations of the waterfall-climbing amphidromous goby,
 Sicyopterus stimpsoni, from the islands of Hawai'i and Kaua'i.
 We found that body shape is significantly different between adult
 subpopulations from streams with contrasting slopes and that trait
 divergence in recruiting juveniles tracked stream topography more so than
 morphological measures of adult subpopulation differentiation. Although no
 evidence of population genetic differentiation was observed among adult
 subpopulations, we observed low but significant levels of spatially and
 temporally variable genetic differentiation among juvenile cohorts, which
 correlated with morphological divergence. Such a pattern of genetic
 differentiation is consistent with chaotic genetic patchiness arising from
 variable sources of recruits to different streams. Thus, at least in S.
 stimpsoni, the combination of variation in settlement cohorts in space and
 time coupled with strong postsettlement selection on juveniles as they
 migrate upstream to adult habitats provides the opportunity for
 morphological adaptation to local stream environments despite high gene
 flow.
description: SicyopterusStimpsoniMicrosatelliteDataMicrosatellite allelic data for each individual.MicrosatelliteDataforDryad.xlsxSicyopterusStimpsoniMorphologyDataMorphological data for each individualMorphologyforDryad.xlsxSicyopterusStimpsoniSamplingSiteInfoSamplingSiteInfoforDryad.xlsxJMPScriptsforMorphology