cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3pc3j00
title: Data from: Management trade-offs on ecosystem services in apple orchards across Europe: direct and indirect effects of organic production

description: 1. Apple is considered the most important fruit crop in temperate areas
 and profitable production depends on multiple ecosystem services,
 including the reduction of pest damage and the provision of sufficient
 pollination levels. Management approaches present an inherent trade-off as
 each affects species differently. 2. We quantified the direct and indirect
 effects of management (organic versus integrated pest management (IPM)) on
 species richness, ecosystem services and fruit production in 85 apple
 orchards in three European countries. We also quantified how habit
 composition influenced these effects at three spatial scales: within
 orchards, adjacent to orchards and in the surrounding landscape. 3.
 Organic management resulted in 48% lower yield than IPM, but also that the
 variation between orchards was large with some organic orchards having a
 higher yield than the average yield of IPM orchards. The lower yield in
 organic orchards resulted directly from management practices, and from
 higher pest damage in organic orchards. These negative yield effects were
 partly offset by indirect positive effects from more natural enemies and
 higher flower visitation rates in organic orchards. 4. Two factors other
 than management affected species richness and ecosystem services. Higher
 cover of flowering plants within and adjacent to the apple trees increased
 flower visitation rates by pollinating insects and a higher cover of apple
 orchards in the landscape decreased species richness of beneficial
 arthropods. 5. The species richness of beneficial arthropods in orchards
 was uncorrelated with fruit production, suggesting that diversity can be
 increased without large yield loss. At the same time, organic orchards had
 38% higher species richness than IPM orchards, an effect that is likely
 due to differences in pest management. 6. Synthesis and applications. Our
 results indicate that organic management is more efficient than integrated
 pest management in developing environmentally friendly apple orchards with
 higher species richness. We also demonstrate that there is no inherent
 trade-off between species richness and yield. A priority of sustainable
 apple production needs to be the development of more environmentally
 friendly means for pest control that do not negatively affect pollination
 services.
description: Data matrix used for
 structural equation modelThe data matrix includes
 all variables included in the structural equation model analysed in the
 paper. The variable descriptions and the statistical code is found in the
 README-fileSupplementary
 table.csv
DOI: 10.5061/dryad.qh46k18
title: Data from: Context-dependent evolution of ostracod morphology along the ecogeographical gradient of ocean depth

description: Ecogeographical rules inform our understanding of biodiversity by seeking
 reliable associations between organismal phenotypes and environmental
 factors. Reminiscent of classic ecogeographical rules, environmental
 factors vary in predictable ways with ocean depth, leading to predictions
 about organismal phenotypes. A valuable group for studying associations
 between habitat depth and phenotype is cylindroleberidid ostracods
 (Crustacea) because of previous phylogenetic analyses and their enormous
 depth range. Using phylogenetic comparative methods, we asked how habitat
 depth relates to body size and eye morphology in 232 cylindroleberidid
 species measured from museum specimens and literature descriptions. For
 each species, we recorded maximum habitat depth, body size, absolute eye
 size, number of ommatidia (facets) per eye, and diameter of the largest
 ommatidium. We find that the relationship between morphology and habitat
 depth in cylindroleberidids depends on pelagic zone: as depth increases in
 the photic zone, body size increases and eyes have fewer ommatidia; as
 depth increases in the disphotic zone, body size does not change and eyes
 have more ommatidia. We did not find a relationship between absolute eye
 size and depth in either pelagic zone. Overall, we find that associations
 between phenotypes and ecogeographical gradients depend on interactions
 between contexts such as pelagic zone, character state, and evolutionary
 history.
description: Juarez_et_al_dataThis zip file contains data and metadata for: 1) species maximum values, 2) individual values for specimens from the NMNH, and 3) species maximum values sent to us by Dr. Anna Syme.
DOI: 10.25824/redu/adyd9d
title: Modelos de aprendizado auto-supervisionado utilizados para classificação de sinais de eletroencefalograma no contexto de interfaces cérebro-computador

description: Aqui encontram-se disponibilizados os códigos dos modelos e transformações de data augmentation utilizados durante a pesquisa de mestrado que gerou a dissertação: "Aplicação de aprendizado auto-supervisionado em interfaces cérebro-computador". Além disso, também foram disponibilizados os arquivos.py para pré-processamento e organização dos dados em dataloaders, assim como as funções de treinamento/fine-tuning/teste utilizados. Os dados brutos utilizados durante a pesquisa estão disponíveis publicamente e podem ser encontrados nos repositórios indicados pelos próprios autores nos respectivos artigos.
DOI: 10.5061/dryad.df546b8
title: Data from: Niches in the Anthropocene: passerine assemblages show niche expansion from natural to urban habitats

description: Human‐mediated habitat transformation is increasingly evident around the
 world. Yet, how this transformation influences species’ niche width and
 overlap remains unclear. On the one hand, human‐mediated habitat
 transformation promotes increased species similarity through trait‐based
 filtering, and an increased prevalence of generalist species with broad
 niches, resulting in functional homogenization. On the other hand, species
 that colonize transformed habitats could use empty niches, resulting in
 decreased species similarity and an expansion of assemblage‐level niche
 space. Here we explore these two alternatives in eight highly diverse
 passerine assembles in natural, rural and urban habitats in South and
 Southwest China, a rapidly developing region of the world. Based on stable
 isotopes, we found that species’ niche width increased from natural to
 human‐made habitats, but there were no differences in niche overlap among
 habitats. Therefore, we found evidence for niche expansion, with
 generalists appearing to use empty niches created by human habitat
 modification, and with assemblages being comprised of complementary
 species. Further research is needed to determine whether increased
 between‐ or within‐individual niche variation is the main driver of niche
 expansion in transformed habitats.
description: PaganiNunezetal2019_NichesAnthropocene_EcographyFive files are available. The two first files contain species' abundances (full and reduced sample) to compute rarefied richness. The third file contains raw individual isotopic data (d13C and d15N). The fourth file contains niche characteristics at the species level. The fifth file is a phylogenetic tree modified to incorporate several populations of the same species.
DOI: 10.5061/dryad.8kb68mr
title: Data from: New Neogene taxa of the tribe Chlamydini Teppner, 1922 (Pectinidae, Bivalvia) of southern South America

description: The Chilean species traditionally assigned to the genera Chlamys Röding,
 1798 or Zygochlamys Ihering, 1907 are now placed in two new endemic South
 American taxa: Dietotenhosen n. gen. (middle Miocene–early middle
 Pliocene) to include the southeastern Pacific Ocean species D. hupeanus
 (Philippi, 1887) n. comb. and D. remondi (Philippi, 1887) n. comb., and
 Ckaraosippur n. gen. (earliest middle Miocene–Pliocene) for C. calderensis
 (Möricke, 1896) n. comb. (Chile) and C. camachoi n. sp. (Argentina). Both
 genera are the youngest survivors of the tribe Chlamydini in southern
 South America. None of them are related to the circumpolar genus
 Psychrochlamys Jonkers, 2003, and the previous proposal of the dispersal
 through the Antarctic Circumpolar Current for the species included herein
 in Dietotenhosen is rejected.
description: Supplementary Data
 1List
 of stratigraphic and geographic occurrences of the analyzed
 materialsupplemental data 1 santelli
 and del rio.xlsx
DOI: 10.5061/dryad.02cr88f
title: Data from: Diversity and spacio-temporal distribution of mushrooms in a Nigerian savanna: implication for their conservation

description: A total of ninety-three different species of mushrooms were found in the
 study area. These species belong to twenty-nine different families, most
 species belonging to the family Agaricaceae, Lyophyllaceae, Bolbitiaceae,
 Pluteaceae and Polyporaceae. They are dominated by the Agaricaceae family,
 which has a total of 48 species; followed by Lyophyllaceae represented by
 6 species. The micro-habitats of mushrooms in the study area include Wood;
 soil around dead Tree Stump; Waste Dump; Cow Dung; Fallow; Arable land;
 and 22 different living trees species. More important habitats in term of
 mushroom species diversity are Parkia biglobosa, Tamarindus indica, and
 Dead Wood. The Parkia biglobosa tree has the highest species richness (45)
 and species diversity (Shannon Diversity index, SDI: 3.6). Tamarindus
 indica was the second, having 28 species richness and 2.7 SDI. These were
 followed by Dead Wood where 22 different mushroom species were recorded.
 Also, these three habitats (Parkia biglobosa, Dead Wood and Tamarindus
 indica) have the highest number of mushroom species (14, 8 and 6
 respectively) that were peculiar to them. Most of the other mushroom
 species were peculiar to only one microhabitat. Different in mushroom
 abundance between the Arable land (SDI =3.2) and the Fallow (SDI =3.66)
 was not statistically significant (P=0.40). Collectively, the indigenous
 trees habited more mushroom species (63) than the exotic trees (20). Also,
 the indigenous trees (SDI =3.828) has significantly (P=0.00) more mushroom
 abundance than the exotic trees (SDI =2.45). Inter-annual variation of
 mushroom species diversity was also observed. Human activities contribute
 positively to mushroom diversity in the study area by creating some unique
 micro-habitats that are peculiar for the growth of certain mushroom
 species. Therefore, for maximum conservation of mushroom diversity,
 extremism by which all human activities will be completely removed should
 be avoided.
description: Mushroom Data For
 Dyad
DOI: 10.5281/zenodo.15427260
title: A standardized approach to terrestrial arthropod sampling
DOI: 10.5281/zenodo.15427261
title: A standardized approach to terrestrial arthropod sampling
DOI: 10.5061/dryad.qm4j1
title: Data from: Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales

description: Comparative genetic studies of non-model organisms are transforming
 rapidly due to major advances in sequencing technology. A limiting factor
 in these studies has been the identification and screening of orthologous
 loci across an evolutionarily distant set of taxa. Here, we evaluate the
 efficacy of genomic markers targeting ultraconserved DNA elements (UCEs)
 for analyses at shallow evolutionary timescales. Using sequence capture
 and massively parallel sequencing to generate UCE data for five
 co-distributed Neotropical rainforest bird species, we recovered 776–1516
 UCE loci across the five species. Across species, 53–77% of the loci were
 polymorphic, containing between 2.0 and 3.2 variable sites per polymorphic
 locus, on average. We performed species tree construction, coalescent
 modeling, and species delimitation, and we found that the five
 co-distributed species exhibited discordant phylogeographic histories. We
 also found that species trees and divergence times estimated from UCEs
 were similar to the parameters obtained from mtDNA. The species that
 inhabit the understory had older divergence times across barriers,
 contained a higher number of cryptic species, and exhibited larger
 effective population sizes relative to the species inhabiting the canopy.
 Because orthologous UCEs can be obtained from a wide array of taxa, are
 polymorphic at shallow evolutionary timescales, and can be generated
 rapidly at low cost, they are an effective genetic marker for studies
 investigating evolutionary patterns and processes at shallow timescales.
description: Supplemental
 FiguresSupplemental-data-
 GPhoCS-outputSupplementary
 TablesSupplementary
 MethodsSupp
 Methods.docxfullFasta alignments of
 sequences from ultraconserved elements containing up to eight individuals
 from each of five study species. All alignments in a given species that
 contain at least one individual in each of four areas of endemism are
 included.orthologsFasta alignments of sequences from ultraconserved elements containing up to eight individuals from each of five study species. Only the 166 loci that are present in all five full datasets are included.interspecies_fullFasta alignments of sequences from ultraconserved elements containing up to thirty-six individuals from five study species. Alignments include samples from all species, and any loci for which data was recovered for at least two individuals.interspecies_reducedFasta alignments of sequences from ultraconserved elements containing up to thirty-six individuals from five study species. Alignments include samples from all species, but only loci for which at least one individual is represented in every area of endemism in all study species.mtDNA_UCE_taxaMitochondrial DNA sequences from the gene cytochrome b from the same samples for which UCE data were obtained.
DOI: 10.5061/dryad.8kt5d
title: Data from: Ancient hybrid origin of the eastern wolf not yet off the table: a comment on Rutledge et al.

description: A recent study of North American canids by Rutledge et al. (Biol. Lett.
 11, 20150303 (doi:10.1098/rsbl.2015.0303)) refutes the hypothesized hybrid
 origin of the eastern wolf (EW) based on genomic evidence against very
 recent hybridization. However, the analyses do not rule out the
 possibility of more ancient hybridization. Claims to have resolved the
 evolutionary origin of the EW are therefore inappropriate. Importantly,
 though, we plead that uncertainty about the ancient history of the taxon
 should not affect current conservation policy.
description: hybrid
 fastafasta file simulations
 hybrid modeldryad
 hybrid.txt3 species
 fastafasta file simulation 3
 species modeldryad
 3species.txt
DOI: 10.5061/dryad.ph2c5
title: Data from: The microbiome of the ant-built home: the microbial communities of a tropical arboreal ant and its nest.

description: Microbial life is ubiquitous, yet we are just beginning to understand how
 microbial communities are assembled. We test whether relationships between
 ant microbiomes and their environments resemble patterns identified in the
 human home microbiome. We examine the microbial communities and chemical
 composition of ants, their waste, their nest and the surrounding soil. We
 predicted that the microbiome of the canopy ant, Azteca trigona, like that
 of humans, represents a distinct, relatively invariant, community compared
 to the soil community. Because Azteca build aboveground nests constructed
 from ant exudates mixed with chewed plant fibers, we predicted that
 nest-associated microorganisms should reflect their ants, not the
 surrounding environment. The ant microbiome was distinct from the soil,
 but contrary to initial predictions, ant microbiomes varied dramatically
 across colonies. This variation was largely driven by the relative
 abundance of Lactobacillus, a genus frequently associated with
 hymenopteran diets. Despite the origin of nests and their means of
 construction, nest-associated microorganisms were most similar to the
 surrounding soil. The microbiota of Azteca ants is thus distinct, but
 dimorphic across colonies, for reasons likely due to inter-colony
 differences in diet; microbiotas of the nests however mirror the
 surrounding soil community in similar to patterns of human home
 microbiota.
description: all_otu_table
DOI: 10.5061/dryad.4nr63
title: Data from: Estimating diversity through time using molecular phylogenies: old and species-poor frog families are the remnants of a diverse past.

description: Estimating how the number of species in a given group varied in the deep
 past is of key interest to evolutionary biologists. However, current
 phylogenetic approaches for obtaining such estimates have limitations,
 such as providing unrealistic diversity estimates at the origin of the
 group. Here we develop a robust probabilistic approach for estimating
 Diversity-Through-Time (DTT) curves and uncertainty around these estimates
 from phylogenetic data. We show with simulations that under various
 realistic scenarios of diversification, this approach performs better than
 previously proposed approaches. We also characterize the effect of tree
 size and undersampling on the performance of the approach. We apply our
 method to understand patterns of species diversity in anurans (frogs and
 toads). We find that Archaeobatrachia -- a species-poor group of old frog
 clades often found in temperate regions -- formerly had much higher
 diversity and net diversification rate, but the group declined in
 diversity as younger, nested clades diversified. This diversity decline
 seems to be linked to a decline in speciation rate rather than an increase
 in extinction rate. Our approach, implemented in the R package RPANDA,
 should be useful for evolutionary biologists interested in understanding
 how past diversity dynamics have shaped present-day diversity. It could
 also be useful in other contexts, such as for analyzing clade-clade
 competitive effects or the effect of species richness on phenotypic
 divergence.
description: DTT_Supplementary_MaterialSupplementary results about illustrations of simulated diversity trajectories, over/underestimation of the three approaches, test of significativity, diversity trajectories and inferred rates of speciation and extinction for archaeobatrachian frogs and families subtenting diversification rate shiftsScriptsR scripts used for : - simulation of trees under the five diversification scenarios and computation of the global error (directory Simulation) - analysis of the frogs' phylogeny (directory Frogs_analysis)
DOI: 10.5061/dryad.t6t12
title: Data from: Disease-free monoculture farming by fungus-growing termites

description: Fungus-growing termites engage in an obligate mutualistic relationship
 with Termitomyces fungi, which they maintain in monocultures on
 specialised fungus comb structures, without apparent problems with
 infectious diseases. While other fungi have been reported in the
 symbiosis, detailed comb fungal community analyses have been lacking. Here
 we use culture-dependent and -independent methods to characterise fungus
 comb mycobiotas from three fungus-growing termite species (two genera).
 Internal Transcribed Spacer (ITS) gene analyses using 454 pyrosequencing
 and Illumina MiSeq showed that non-Termitomyces fungi were essentially
 absent in fungus combs, and that Termitomyces fungal crops are maintained
 in monocultures as heterokaryons with two or three abundant ITS variants
 in a single fungal strain. To explore whether the essential absence of
 other fungi within fungus combs is potentially due to the production of
 antifungal metabolites by Termitomyces or comb bacteria, we performed in
 vitro assays and found that both Termitomyces and chemical extracts of
 fungus comb material can inhibit potential fungal antagonists. Chemical
 analyses of fungus comb material point to a highly complex metabolome,
 including compounds with the potential to play roles in mediating these
 contaminant-free farming conditions in the termite symbiosis.
description: LC-ESIMS/MS data for
 fractionated comb extractsLC-ESIMS/MS data for
 fractionated comb extracts, acquired in positive ionisation
 modeOtani_2019_LCESIMSMS_pos_data.zipLC-ESIMS/MS data for fractionated comb extractsLC-ESIMS/MS data for fractionated comb extracts, acquired in negative ionisation modeOtani_2019_LCMSMS_neg_data.zip
DOI: 10.5061/dryad.gp50t40
title: Data from: Geometric morphometrics dismiss the polymorphic Hydrocotyle quinqueloba (Araliaceae) from the neotropics

description: Hydrocotyle taxonomy is poorly resolved due the traditional assessment of
 leaf morphology that has imposed difficulties to species delimitation and
 prompted the recognition of several infraspecific taxa. Hydrocotyle
 quinqueloba comprises ten infraspecific taxa that differ mainly by the
 shape of their leaf blade. The species occurs in montane forests of the
 Andes and eastern Brazil, along the Atlantic forest and Cerrado domains.
 However, the geographic distribution of the taxa under H. quinqueloba is
 poorly known, and their supposedly continuous morphological variation
 remains unverified. Here we analyze the morphological variation and
 documented correlated differences in geographic distribution of H.
 quinqueloba to assess whether they support the delimitation of distinct
 species or the recognition of infraspecific taxa. For this task, we
 applied landmark-based geometric morphometrics (GM) to leaves and
 traditional morphometrics to other structures of specimens of H.
 quinqueloba. Procrustes analysis of variance (Procrustes ANOVA) indicated
 that variation of leaf blade shape was weakly associated with geography
 and was mainly explained by taxa themselves. In contrast, variation of
 leaf blade size was significantly (p &lt; 0.001) associated with
 geography, but variation at the specimen level could account for it.
 Principal component analysis (PCA) of leaf blade shape indicated that taxa
 differed mainly by the angle and relative size between median and lateral
 primary veins, by the space between the petiole insertion and middle
 lobe’s sinuses, and by the width of middle lobe’s base. Canonical variate
 analysis (CVA) indicated significant (p &lt; 0.01) differences among
 seven infraspecific taxa that formed groups defined by leaf blade shape.
 Linear discriminant analysis (LDA) of 11 morphological characters
 separated five groups of taxa, which displayed significant (p &lt;
 0.001) differences among each other. Based on that, we propose an updated
 taxonomic treatment that restricts the circumscription of H. quinqueloba
 to plants from the Andes and accepts four species from eastern Brazil.
description: Data for geometric and
 traditional morphometricsIt includes raw landmark
 coordinates, semilandmarks curve, a table with classifiers (taxon,
 locality, and region) for specimens, a character matrix used in
 traditional morphometrics, and the R script for data
 analysis.