cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9ghx3ffg9
title: Taxonomic sampling and rare genomic changes overcome long-branch attraction in the phylogenetic placement of pseudoscorpions

description: Long-branch attraction is a systematic artifact that results in erroneous
 groupings of fast-evolving taxa. The combination of short, deep internodes
 in tandem with LBA artifacts has produced empirically intractable parts of
 the Tree of Life. One such group is the arthropod subphylum Chelicerata,
 whose backbone phylogeny has remained unstable despite improvements in
 phylogenetic methods and genome-scale datasets. Pseudoscorpion placement
 is particularly variable across datasets and analytical frameworks, with
 this group either clustering with other long-branch orders or with
 Arachnopulmonata (scorpions and tetrapulmonates). To surmount LBA, we
 investigated the effect of taxonomic sampling via sequential deletion of
 basally branching pseudoscorpion superfamilies, as well as varying gene
 occupancy thresholds in supermatrices. We show that concatenated
 supermatrices and coalescent-based summary species tree approaches support
 a sister group relationship of pseudoscorpions and scorpions, when more of
 the basally branching taxa are sampled. Matrix completeness had
 demonstrably less influence on tree topology. As an external arbiter of
 phylogenetic placement, we leveraged the recent discovery of an ancient
 genome duplication in the common ancestor of Arachnopulmonata as a litmus
 test for competing hypotheses of pseudoscorpion relationships. We
 generated a high-quality developmental transcriptome and the first genome
 for pseudoscorpions to assess the incidence of arachnopulmonate-specific
 duplications (e.g., homeobox genes and miRNAs). Our results support the
 inclusion of pseudoscorpions in Arachnopulmonata (new definition), as the
 sister group of scorpions. Panscorpiones (new name) is proposed for the
 clade uniting Scorpiones and Pseudoscorpiones.
description: Please refer to the file README.txt for an explanation of
 directory structure and contents. This readme file includes an explanation
 of which folders correspond to which analyses and figures in the
 manuscript.
DOI: 10.5061/dryad.2547d7wps
title: Recovered microbiome of an oviparous lizard differs across gut and reproductive tissues, cloacal swabs, and feces

description: Microbial diversity and community function are related, and both can be
 highly specialized in different regions of the gut. The cloacal microbiome
 of Sceloporus virgatus lizards has low diversity, suggesting a specialized
 function, and is known to transfer antifungal microbes to eggshells during
 oviposition. We hypothesize that the cloacal microbiome is distinct from
 other parts of the digestive and reproductive systems. Here, we compare
 the microbiome of tissue samples from the cloaca, lower intestine, upper
 intestine, and oviduct. We further assessed whether common methods of
 microbial sampling – cloacal swabs and feces – provide accurate
 representations of these tissues, and whether feces might “seed” the
 cloacal microbiome. We found that the upper intestine and oviduct had
 unique microbial communities, while the lower intestine and cloaca had
 similar communities with lower diversity indicative of regional
 specialization. The cloacal community, in particular, showed extreme
 specialization averaging 99% Proteobacteria (Phylum) and 83%
 Enterobacteriacaea (Family). Cloacal swabs recovered communities similar
 to that of lower intestine and cloacal tissues, but fecal samples had much
 higher diversity and a distinct composition (62% Firmicutes and 39%
 Lachnospiraceae) relative to all gut regions. This result serves as a
 caution against the frequent assumption that fecal samples provide an
 accurate representation of the gut. Finally, we found that defecation did
 not alter the cloacal microbiome, suggesting that community is robust to
 perturbations from transient microbiota.  
description: Sequences of the 16s V4 regions were
 generated at IBest Genomics Core (University of Idaho) on the Illumina
 MiSeq platform. Detailed methodology can be found in Bunker et al., 2021,
 Specialization of the cloacal microbiome relative to gut, oviduct, and
 feces of an oviparous lizard.
DOI: 10.5061/dryad.r2280gbbz
title: RNA m6A methylation in unilateral ureteral ligations model

description: Chronic kidney disease (CKD) is a high incidence disease. Renal fibrosis
 is the ultimate pathological pathway for chronic kidney diseases leading
 to end-stage renal failure. There is currently no effective treatment to
 prevent the renal fibrosis. Renal EMT is a key mechanism of renal
 fibrosis. Recent evidence suggests m6A modification in RNA can regulate
 EMT in tumor cells. However, a role of m6A RNA modification in renal
 fibrosis has not been reported. Therefore, we investigate whether m6A RNA
 methylation plays an important role in the epithelial-to-mesenchymal
 transition (EMT) process of renal fibrosis. Unilateral ureteral
 ligations were performed in C57BL/6 mice to establish a mouse model of
 renal fibrosis and TGF-b intervention was used in HK2 cells to
 establish a cellular model of renal fibrosis. The effects of m6A and the
 role of Mettl14 on kidney disease and HK2 cells were
 studied. 
description: Cloudseq Biotech Inc. (Shanghai, China) provided MeRIP-Seq service. Clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4). Methylated sites on RNAs were identified by MACS software. Identified m6A peaks were subjected to motif enrichment analysis by HOMER, and metagene m6A distribution was characterized by R package MetaPlotR. Differentially methylated sites (fold change ≥2 and p &lt; 0.05) were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and chosen by homemade scripts.
DOI: 10.5061/dryad.3tx95x6fj
title: Microsatellite data of 21 EST-SSR loci from all 503 Emmenopterys henryi samples

description: Aim: Several hypotheses are available to predict change in genetic
 diversity at expanding peripheral ranges. However, empirical evidence to
 test predictions of the centre-periphery hypothesis (CPH) at contracting
 range limits is scarce. To address this issue, we assessed spatial
 patterns of genetic variation, effective population size, and contemporary
 and historical gene flow in a widespread, Tertiary relict tree species
 from subtropical China. Location: Warm-temperate deciduous forests of
 subtropical China. Taxon：Emmenopterys henryi (Rubiaceae) Methods: We
 applied kernel density estimation to determine the centre of the species’
 geographical range. Using microsatellite markers, we assessed genetic
 structure and diversity in 36 populations (503 individuals) sampled in the
 centre and periphery across the species’ range. We further examined both
 historical and contemporary gene flow. Finally, we applied coalescent
 methods to simulate population demography. Results: In support of CPH
 predictions, the highest density of E. henryi coincided with the
 geographical centre of the species’ distribution range, and genetic
 diversity significantly declined with distance from this range centre.
 Historical migration from the core to the edge was significantly higher
 than in the opposite direction, whereas contemporary migration followed an
 opposite pattern. Central and peripheral populations had similar levels of
 genetic differentiation. Main conclusions: Core-to-edge patterns of
 genetic diversity, but not genetic differentiation, were consistent with
 the CPH in E. henryi. Also in line with the CPH, historical (but not
 contemporary) migration from the core to the edge was significantly higher
 than in the opposite direction. Results suggest that the complex
 topography in subtropical China and population demographic processes may
 strongly influence whether CPH predictions are met in different population
 genetic parameters.
description: Total genomic DNA was
 extracted from the dried leaf tissue using DNA Plantzol Reagent
 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol.
 Following protocols of Zhu et al. (2016), we developed a total of 21
 polymorphic EST-SSR (expressed sequence tags-simple sequence repeat)
 markers from the transcriptome of <i>E. henryi </i>(GenBank
 accession number: SRR9878962). The EST-SSR loci were polymerase chain
 reaction (PCR) amplified following Zhu et al. (2016) and loaded on a
 3730xl DNA Analyzer (Applied Biosystems, Foster City, CA, USA). Alleles
 were manually scored and determined using GeneMarker 2.4.0 (SoftGenetics,
 State College, PA, USA).
DOI: 10.5061/dryad.x3ffbg7hn
title: Genomic population structure of sympatric sexual and asexual populations in a parasitic wasp, Meteorus pulchricornis (Hymenoptera: Braconidae), inferred from six hundred single-nucleotide polymorphism loci

description: In spite of the two-fold reproductive advantage, asexual reproduction is
 not common in nature, likely due to the associated genetic deterioration
 or reduced genetic variation. To understand how genetic diversity
 is maintained in existing asexual populations, we investigated the genetic
 diversity and population structure of sympatric sexual and asexual
 populations of a parasitic wasp, Meteorus pulchricornis, using
 614 genome-wide loci with single nucleotide polymorphisms. The genetic
 structures of the apomictic asexual populations were distinct, showing
 considerable genetic differentiation among them. Most of the asexual
 populations were highly differentiated from the sympatric sexual
 population, some asexual individuals could not be distinguished from
 members of the sexual population. Furthermore, significantly fewer
 multilocus genotypes were identified in the asexual populations (1–7)
 compared to the sexual population (42), which is consistent with their
 apomictic nature. The observed patterns of fixed heterozygous sites
 suggest that major asexual populations had the same evolutionary origin
 and have long since evolved individually; while the detected gene flow
 between the sexual population and minor asexual population may indicate
 independent origins of asexuality. The potential role of occasional males
 in apomictic wasps is also discussed in the study.
description: Data derived from 614 single nucleotide polymorphism (SNP) loci
 obtained using multiplexed inter-simple sequence repeat (ISSR) genotyping
 via sequencing (MIG-seq), and obtained by analysis using PYRAD. 
 Input data and intermediate output for analysis using ADMIXTURE,
 ARLEQUIN, BAYESASS, FINERADSTRUCTURE and GENODIVE.
description: All input data (containing missing loci and individuals),
 parameter files or population file and intermediate output are
 provided.
DOI: 10.5061/dryad.j3tx95xcs
title: Global quantitative synthesis of effects of biotic and abiotic factors on stemflow production in woody ecosystems

description: Aim: Stemflow has been increasingly recognized as an indispensable
 component in water and nutrient budgets within vegetated ecosystems. Here
 we aim to quantify the stemflow percentage (St, %) of incident
 precipitation (i.e., stemflow production) at a global scale, and to
 provide a systematic evaluation on how biotic and abiotic factors affect
 St. Location: Global Time period: 1970 – 2019 Major taxa studied: Woody
 plants (trees and shrubs) Methods: We compiled a global stemflow dataset
 from 234 peer-reviewed papers, which included 488 observations of St and
 the related biotic (stand characteristics) and abiotic factors (climate
 variables) at 283 sites within terrestrial woody plant ecosystems. We
 explored the global pattern of St and performed a machine learning method
 (boosted regression trees) to model the effects of biotic and abiotic
 variables on St. Results: Globally, the median (interquartile range, IQR)
 St was 2.7 % (1.0 – 6.3 %). We found that St in arid zones (type B in
 Köppen-Geiger climate classification) was significant higher (P &lt;
 0.01) than in other climate types, and we also detected a significant
 difference (P &lt; 0.01) in St between trees (median: 2.4 %; IQR: 1.0
 – 5.3 %) and shrubs (median: 7.2 %; IQR: 5.2 – 11.9 %). Predictor
 variables that substantially accounted for the explained deviance of the
 final model included vegetation height (27.0 %), mean annual precipitation
 (16.1 %), mean annual temperature (14.4 %), stand density (10.8 %), stand
 age (8.9 %), and bark type (5.5 %). In contrast, leaf area index, diameter
 at breast height, basal area, phenology type, life form, and leaf type
 were classified as low importance. Main conclusions: Our synthesis
 provides a cross-site comparison of St, and gives a holistic view on how
 climate variables and stand characteristics contribute to and affect
 global stemflow production.
DOI: 10.5061/dryad.jq2bvq87w
title: Interaction network for eleven Cucurbita pepo sites in Guatemala

description: In recent years, evidence has been found that plant-pollinator
 interactions are altered by land-use and that genetic diversity also plays
 a role. However, how land-use and genetic diversity influence
 plant-pollinator interactions, particularly in the Neotropics, where many
 endemic plants exist is still an open question. Cucurbita pepo is a
 monoecious plant and traditional crop wide distributed, with high rates of
 molecular evolution, landraces associated with human cultural management
 and a history of coevolution with bees, which makes this species a
 promising model for studying the effect of landscape and genetic diversity
 on plant-pollinator interactions. Here, we assess 1) whether female and
 male flowers differences have an effect on the interaction network, 2) how
 C. pepo genetic diversity affects flower-bee visitation network structure,
 and 3) what is the effect that land-use, accounting for C. pepo genetic
 variability, has on pumpkin-bee interaction network variables. 
 Our results indicate that female and male flowers presented the same
 community composition and network structure suggesting that the
 differences do not have a significant effect on network evolution. Genetic
 diversity has a positive effect on modularity, nestedness, and number of
 interactions, which, when considered, allows to observe how land-use
 variables can have an enhancing or buffering effect on nestedness. Our
 results suggest that considering genetic diversity is relevant for a
 better understanding of the effect of landscape on interaction networks.
 Additionally, this understanding has great value in conserving
 biodiversity and enhancing the stability of interaction networks in a
 world facing great challenges of habitat and diversity loss.
DOI: 10.5061/dryad.sqv9s4n35
title: Tracking and retention time data from Larus fuscus feeding at Doñana ricefields in Andalusia

description: 1. Non-frugivorous waterbirds disperse a wide variety of plants by
 endozoochory, providing longer dispersal distances than other mechanisms.
 Many waterbirds visit both agricultural and natural landscapes during
 their daily movements, but potential bird-mediated dispersal of weed
 plants within and from agricultural landscapes to other habitats is
 commonly overlooked. Gulls (Laridae) are expanding in numbers and
 increasingly exploiting anthropogenic habitats worldwide, with possible
 growing implications for the spread of weeds. Yet, to date there are no
 studies on the spatial distribution of weed dispersal by waterbirds. 2. We
 developed a plant dispersal model based on movements of 19 Larus fuscus
 using ricefields, via GPS telemetry. We combined daily movements with two
 curves estimating the retention times (RT) of plant seeds in their guts:
 1) an experimental curve based on RT in captivity for four weeds with dry
 fruits known to be dispersed by gulls: Juncus bufonius, Cyperus difformis,
 Polypogon monspeliensis and Amaranthus retroflexus; 2) a theoretical curve
 based on the interspecific scaling relationship between body mass and mean
 RT. 3. Median dispersal distances of weed plant seeds by gulls ranged
 between 690-940 m, but maximum distances exceeded 100 km. The theoretical
 RT model showed higher median dispersal distances than the experimental RT
 model, but lower maxima (131 and 151 km, respectively). Spatial patterns
 of weed deposition were very similar between RT methods, and most strongly
 depended on gull movements. Variation between individual gulls had little
 influence on seed shadows. About 92% of all seeds (&gt;10,000 intact
 seeds per day) were dispersed within the ricefield area of 370 km2. The
 remaining 8% of seeds were deposited beyond ricefields into other
 habitats, 42% of which reached moist environments (other irrigated
 agriculture, rivers and natural wetlands) presumably suitable for weed
 establishment. 4. Synthesis: Gulls can disperse weed plants over long
 distances across a mosaic of habitats. This implies exchange of weed plant
 species between human-dominated and natural areas by waterbirds as
 dispersal vectors. This spatial study highlights the importance of
 non-frugivorous birds for long-distance plant dispersal, which is
 generally an overlooked mechanism in studies aiming to predict and manage
 expansion of weed plants.
description: Two datasets were provided: 1. GPS database
 (e.g. latitude, longitude, speed, datetime etc) information regarding
 individual movements of gulls feeding at the ricefields and their
 movements beyond ricefields. 2. Seed retention time to
 generate an experimental curve derived from 7 individuals in
 captitivity.
DOI: 10.5061/dryad.z08kprrbq
title: In-situ feeding as a new management tool to conserve orphaned Eurasian lynx (Lynx lynx)

description: High human-caused mortality due to wildlife-vehicle-collisions and illegal
 killing leads to frequent cases of orphaned Eurasian lynx juveniles. Under
 natural conditions, this would result in starvation of the young. To avoid
 this, wildlife managers conventionally rear animals in captivity and
 release them later. However, this measure is an undesirable outcome for
 species conservation, managers and animals alike. Increased awareness of
 Eurasian lynx orphaned by human-caused mortality means managers must often
 intervene in endangered populations. In this study we report for the first
 time a successful case of in-situ feeding designed to avoid captivity of
 two orphaned Eurasian lynx. We exposed 13 roe deer and 7 red deer
 carcasses in the field to successfully support two orphans to the age of
 independence and confirm dispersal from the natal range. We present this
 management approach as a feasible and complimentary tool that can be
 considered in small or isolated large carnivore populations where every
 individual counts towards population viability.
description: Species occurence at carrion provisioning sites in the Bavarian
 Forest National Park collected via camera trapping. Including carcass
 deployment (date, location), daily occurence of Eurasian lynx (in
 particular orphans) at carcasses, scavenger occurence at carcasses
 summarised per location, and broader scale occurence of Eurasian lynx
 documented by continuous camera trap monitoring.
description: See ReadMe file.
DOI: 10.15468/dl.u8yf4s
title: Occurrence Download

description: A dataset containing 110 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Cadophora finlandica"
 ]
}

 The dataset includes 110 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002741-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.rxwdbrv77
title: Mesocarnivore community structuring in the presence of Africa’s apex predator

description: Apex predator reintroductions have proliferated across southern Africa,
 yet their ecological effects and proposed umbrella benefits of associated
 management lack empirical evaluations. Despite a rich theory on top-down
 ecosystem regulation via mesopredator (&lt;20kg) suppression, a
 knowledge gap exists relating to the influence of lions (Panthera leo)
 over Africa’s diverse mesocarnivore communities. We investigate how
 geographical variation in mesocarnivore community richness and occupancy
 across South African reserves is associated with the presence of lions.
  An interesting duality emerged: lion reserves held more
 mesocarnivore-rich communities, yet mesocarnivore occupancy rates and
 evenness-weighted diversity were lower in the presence of lions. Human
 population density in the reserve surroundings had a similarly ubiquitous
 negative effect on mesocarnivore occupancy. The positive association
 between species richness and lion presence corroborated the umbrella
 species concept but translated into small differences in community size.
 Distributional contractions of mesocarnivore species within lion reserves,
 and potentially corresponding numerical reductions, suggest
 within-community mesopredator suppression by lions, likely as a result of
 lethal encounters and responses to a landscape of fear. Our findings offer
 empirical support for theoretical understanding of processes underpinning
 carnivore community assembly and are of conservation relevance under
 current large-predator orientated management and conservation paradigms.
description: We used camera-trap data on mesocarnivore species collected
 across R=17 reserves and <i>S</i> = 33 reserve-by-year surveys
 in NE South Africa. We summarized mesocarnivore daily encounter frequency
 data to implement the multi-region community occupancy model used to
 jointly describe geographical variation in mesocarnivore community
 richness and occupancy.
description: This is the multi-species detection data used to fit the
 Multi-region community occupancy model described in Curveira-Santos et
 al. "Mesocarnivore community structuring in the presence of Africa’s
 apex predator". Model formulation details are reported in
 <i>SII Appendix</i> and the JAGS model code is given in
 <em>SIII Appendix</em> of the article's supplementary
 material. <br> The data file called
 “Mesocarnivore camera-trapping data.RData” contains the following
 objects: "covs":
 reserve-by-year-specific covariates (lion presence [“LION”], reserve size
 [“AREA”], habitat diversity [“DIV_SI”], human population density [“HUM”],
 and leopard density ["LEOP"]);
 "K_tot": number of sampling occasions for each site in
 each reserve-by-year survey; "nregionYear":
 total number of reserve-by-year surveys;
 "nsites": total number of sites per reserve-by-year
 survey; "nspecies": total number of
 observed species; "region": numeric ID for
 each region in each reserve-by-year survey;
 "Ytot_3D": species-by-sites-by-survey detection
 frequency matrix.