cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.xsj3tx9b4
title: Multiple traits and multifarious environments: integrated divergence of morphology and life history

description: Understanding complex responses of multiple character suites (e.g.,
 behaviour, life history, morphology) to multifarious environments is a
 challenging task. Here we use a multivariate approach (partial least
 squares structural equation modelling) to disentangle drivers (i.e.,
 predation, resource availability, and population demographics) of
 phenotypic divergence among populations of Bahamas mosquitofish (Gambusia
 hubbsi) inhabiting blue holes. We further employ a two-block partial least
 squares analysis in a novel approach to uncovering integrated and
 independent aspects of divergence in correlated character suites. Results
 suggest that phenotypic divergence mainly resulted from
 differences in predation regimes, with population demography and resource
 availability also influencing particular aspects of divergence. We
 uncovered statistically significant covariation of life histories
 and morphologies, and revealed that phenotypic divergence between
 predation regimes involved both integrated and independent responses. For
 instance, female life histories diverged mostly independently of
 morphology, although some morphological shifts (abdominal distension)
 resulted from changes in fecundity. In contrast, males showed strong
 morphological divergence independent of life history, but much of their
 life-history shifts reflected joint morphological changes (lean weight and
 body shape). Our study illustrates the utility of gathering disparate data
 types from multiple populations/species to understand the causes and
 nature of phenotypic divergence in the wild.
description: This dataset consists of two separate files.
 The first file (individual data.xlsx) has all the individual
 level data for both male and female Gambusia hubbsi used in the 2B-PLS
 analyses and in the MANCOVAs for life histories and morphologies (centroid
 size and relative warps 1-18), where we either included or didn’t include
 2B-PLS vectors to test for integrated/independent responses of the
 character suites. For each fish it also provides details on the population
 (i.e, identity of the blue hole), whether it was high-predation or
 low-predation. The second file (PLS-SEM data.xlsx) has
 all population-specific data for all 14 populations used in the PLS-SEM
 analyses (both the original variables used to construct the latent
 variables, and the latent variable scores themselves).
DOI: 10.25574/16128
title: Chandra X-ray Observatory ObsId 16128

description: SNAPSHOTS IN THE HISTORY OF DISSOCIATIVE MAJOR MERGERS
DOI: 10.5061/dryad.v41ns1rrx
title: Activity niches outperform thermal physiological limits in predicting global ant distributions

description: Aim: Thermal physiology is commonly used in mechanistic models to predict
 species distributions and project distribution change. Such thermal
 constraints for ants are often measured under laboratory conditions as
 critical thermal limits (CTmax and CTmin), but have also been observed in
 the field as foraging thermal limits (FTmin and FTmax). Here we compared
 distribution projections based on ant physiological and behavioural
 thermal limits with their realized distributions to assess the validity of
 using ecophysiological models to predict species ranges over large scales.
 Location: Global Taxon: Ants Methods: From published literature, we
 compiled a database of 148 lab-measured critical thermal limits and 137
 field-observed foraging thermal limits for 20 ant genera distributed
 around the world. We projected their potential ranges using active hour
 thresholds by matching their thermal limits or preferred thermal breadth
 (incorporating thermal optima) with hourly surface temperature data. We
 then compared the projections against a comprehensive global database of
 ant distributions to assess the validity of physiologically and
 behaviorally based models. Results: We found that surface temperature
 plays a clear role in generic-level ant biogeography. Projections based on
 foraging thermal limits were more conservative in constraining ranges to
 observed distributions, while projections based on critical thermal limits
 often overestimated ranges. Furthermore, thermal limit models can be
 improved by incorporating behaviourally derived thermal optima. Main
 conclusions: Our results suggest that temperature-dependent activity
 niches and thermal optima better reveal species realized thermal niches
 than critical thermal limits, and hence can improve predictions of species
 distributions and future distribution changes under climate change.
description: See Metadata tab of spreadsheet for variable descriptions
DOI: 10.5061/dryad.p5hqbzkkz
title: A possible Cambrian stem-group gnathiferan-chaetognath from the Weeks Formation (Miaolingian) of Utah

description: In recent years the plethora of “weird wonders”, the vernacular for the
 apparently extinct major bodyplans documented in many of the Cambrian
 Lagerstätten, has been dramatically trimmed.  This is because
 various taxa have either been assigned to known phyla or at least
 accommodated in larger monophyletic assemblages.  Nevertheless, a
 number of Cambrian taxa retain their enigmatic status.  To this
 intriguing roster we add Dakorhachis thambus n. gen. n. sp., from the
 Miaolingian (Guzhangian) Weeks Formation Konservat-Lagerstätte of
 Utah.  Specimens consist of an elongate body lacking appendages,
 but which is apparently segmented.  A prominent feeding apparatus
 consists of a circlet of triangular teeth, while posteriorly there are
 three distinct skeletal components.  D. thambus n. sp. is
 interpreted as an ambush predator and may have been partially
 infaunal.  The wider affinities of this new taxon remain
 conjectural but it is suggested that it may represent a stem-group member
 of the Gnathifera, today represented by the gnathostomulids,
 micrognathozoans, rotifers, and possibly with links also to the
 chaetognaths.
DOI: 10.5061/dryad.jdfn2z378
title: Persistence of arctic-alpine flora during 24,000 years of environmental change in the Polar Urals

description: Plants adapted to extreme conditions can be at high risk from climate
 change; arctic-alpine plants, in particular, could “run out of space” as
 they are out-competed by expansion of woody vegetation. Mountain regions
 could potentially provide safe sites for arctic-alpine plants in a warmer
 climate, but empirical evidence is fragmentary. Here we present a
 24,000-year record of species persistence based on sedimentary ancient DNA
 (sedaDNA) from Lake Bolshoye Shchuchye (Polar Urals). We provide robust
 evidence of long-term persistence of arctic-alpine plants through
 large-magnitude climate changes but document a decline in their diversity
 during a past expansion of woody vegetation.  Nevertheless, most
 of the plants that were present during the last glacial interval,
 including all of the arctic-alpines, are still found in the region today.
 This underlines the conservation significance of mountain landscapes via
 their provision of a range of habitats that confer resilience to climate
 change, particularly for arctic-alpine taxa.
DOI: 10.5061/dryad.msbcc2fts
title: The only complete articulated early Miocene chameleon skull (Rusinga Island, Kenya) suggests an African origin for Madagascar’s endemic chameleons

description: We here present the first detailed study of the specimen KNM-RU 18340 from
 Rusinga Island (Kenya), the only known complete early Miocene chameleon
 skull, using micro-CT. This specimen represents one of the oldest
 chameleon fossils ever recovered. For the first time, the skull bone
 internal surfaces, their sutures, and elements contained inside the rocky
 matrix are observed. Our morphological comparisons and phylogenetic
 analyses place this specimen confidently in the genus Calumma and a new
 species, Calumma benovskyi sp. nov., is erected for it. Since all species
 of this genus are endemic to Madagascar, this fossil uniquely demonstrates
 the existence of Calumma on continental Africa in prehistoric time. Our
 results challenge the long-held view that chameleons originated on
 Madagascar and dispersed over water to Africa, and provide a strong
 evidence of an African origin for some Malagasy lineages. The
 Oligocene–early Miocene dispersal to Madagascar, using oceanic currents
 that favoured eastward dispersal at that time, is a highly supported
 scenario matching the suggested dispersal of lemurs to this island. This
 is consistent with a previously suggested hypothesis based on molecular
 data.
description: We µCT scanned this skull at the University of Witswatersrand
 (South Africa), using a Nikon Metrology  XTH 225/320 LC Xray
 microtomograph, with an acceleration tension of 100 kV and an intensity of
 50 µA. As much as 2000 radiographs were acquired with an exposure time of
 4 s and an averaging of 1. The resolution was 18.83 µm. The μCT data were
 analyzed using VG Studio Max 3.2 and Avizo 8.1.
DOI: 10.5061/dryad.6djh9w0x9
title: Less is more: on-board lossy compression of accelerometer data increases biologging capacity

description: GPS-tracking devices have been used in combination with a wide range of
 additional sensors to study animal behaviour, physiology and interaction
 with their environment. Tri-axial accelerometers allow researchers to
 remotely infer the behaviour of individuals, at all places and times.
 Collection of accelerometer data is relatively cheap in terms of energy
 usage, but the amount or raw data collected generally requires much
 storage space and is particularly demanding in terms of energy needed for
 data transmission. Here we propose compressing the raw ACC data into
 summary statistics within the tracking device (before transmission) to
 reduce data size, as a means to overcome limitations in storage and energy
 capacity. We explored this type of lossy data compression in the
 accelerometer data of tagged Bewick’s swans (Cygnus columbianus bewickii)
 collected in spring 2017. By using software settings in which bouts of 2 s
 of both raw ACC data and summary statistics were collected in parallel but
 with different bout intervals to keep total data size comparable, we
 created the opportunity for a direct comparison of time budgets derived by
 the two data collection methods. We found that the data compression in our
 case yielded a 6 time reduction in data size per bout, and concurrent,
 similar decreases in storage and energy use of the device. We show that
 with the same accuracy of the behavioural classification, the freed memory
 and energy of the device can be used to increase the monitoring effort,
 resulting in a more detailed representation of the individuals’ time
 budget. Rare and/or short behaviours such as daily roost flights, were
 picked up significantly more when collecting summary statistics instead of
 raw ACC data (but note differences in sampling rate). Such level of detail
 can be of essential importance, for instance to make a reliable estimate
 of the energy budgets of individuals. In conclusion, we argue that this
 type of lossy data compression can be a well-considered choice in study
 situations where limitations in energy and storage space of the device
 pose a problem. Ultimately these developments can allow for long-term and
 nearly continuous remote-monitoring of the behaviour of free-ranging
 animals.
DOI: 10.5061/dryad.z612jm683
title: Differential impact of nevirapine on artemether-lumefantrine pharmacokinetics in individuals stratified by CYP2B6 c.516G&gt;T genotypes

description: There is an increased recognition of the need to identify and quantify the
 impact of genetic polymorphisms on drug-drug interactions. This study
 investigated the pharmacogenetics of the pharmacokinetic drug-drug
 interaction between nevirapine and artemether-lumefantrine in HIV-positive
 and HIV-negative adult Nigerian subjects. Thirty each of HIV-infected
 patients on nevirapine-based antiretroviral therapy and HIV-negative
 volunteers without clinical malaria, but with predetermined CYP2B6 c.516GG
 and TT genotypes were administered a complete treatment dose of 3-days of
 artemether-lumefantrine. Rich pharmacokinetic sampling prior to and
 following the last dose was conducted and plasma concentrations of
 artemether/dihydroartemisinin and, lumefantrine/desbutyl-lumefantrine were
 quantified using tandem mass spectrometry. Pharmacokinetic parameters of
 artemether-lumefantrine and its metabolites in HIV-infected patients on
 nevirapine were compared with those in the absence of nevirapine in
 HIV-negative volunteers. Overall, nevirapine reduced exposure to
 artemether and desbutyl-lumefantrine by 39% and 34% respectively. These
 reductions were significantly greater in GG versus TT subjects for
 artemether [ratio of geometric mean (90% confidence interval): 0.42 (0.29
 – 0.61) versus 0.81 (0.51 – 1.28)] and for desbutyl-lumefantrine [0.56
 (0.43 – 0.74) versus 0.75 (0.56 – 1.00)]. On the contrary, it increased
 exposure to dihydroartemisinin and lumefantrine by 47% and 30%
 respectively. These increases were significantly higher in TT versus GG
 subjects for dihydroartemisinin [1.67 (1.20 – 2.34) versus 1.25 (0.88 –
 1.78)] and for lumefantrine [1.51 (1.20 – 1.90) versus 1.08 (0.82 –
 1.42)]. This study underscores the importance of incorporating
 pharmacogenetics into all drug-drug interaction studies with potential for
 genetic polymorphisms to influence drug disposition.
DOI: 10.15468/dl.9q5686
title: Occurrence Download

description: A dataset containing 1213 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Germany",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Nyctalus noctula",
 "Year 2018-2026"
 ]
}

 The dataset includes 1213 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002098-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.x0k6djhff
title: Tree communities and soil properties influence fungal community assembly in neotropical forests

description: The influence exerted by tree communities, topography and soil chemistry
 on the assembly of macrofungal communities remains poorly understood,
 especially in highly diverse tropical forests. Here, we used a large
 dataset that combines inventories of macrofungal Basidiomycetes fruiting
 bodies, tree species composition and measurements for 16 soil
 physico-chemical parameters, collected in 34 plots located in four sites
 of lowland rainforests in French Guiana. Plots were established on three
 different topographical conditions: hilltop, slope and seasonally flooded
 soils. We found hyperdiverse Basidiomycetes communities, mainly comprising
 members of Agaricales and Polyporales. Phosphorus, clay contents and base
 saturation in soils strongly varied across plots and shaped the richness
 and composition of tree communities. The latter composition explained 23%
 of the variation in the composition of macrofungal communities, probably
 through high heterogeneity of the litter chemistry and selective effects
 of biotic interactions. The high local heterogeneity of habitats
 influenced the distribution of both macrofungi and trees, as a result of
 diversed local soil hydromorphic conditions associated to contrasting soil
 chemistry. This first regional study across habitats of French Guiana
 forests revealed new niches for macrofungi, such as ectomycorrhizal ones,
 and illustrate how macrofungi inventories are still paramount to can be to
 understand the processes at work in the tropics.
description: 34 forest plots in French Guiana were sampled to inventory trees
 floristic composition and Basidiomycetes diversit, together with soil
 physico-chemical characteristics. Estimates of diversity (indices of
 richness, shannon and simpson) of tree and fungel communities were
 calculated. The relative contribution of tree diversity and floristic
 composition, and soil nutrients and topography were determined
DOI: 10.25338/b8r31q
title: Genome Synteny Has Been Conserved Among the Octoploid Progenitors of Cultivated Strawberry Over Millions of Years of Evolution

description: Allo-octoploid cultivated strawberry
 (Fragaria × ananassa) originated through a combination
 of polyploid and homoploid hybridization, domestication of an
 interspecific hybrid lineage, and continued admixture of wild species over
 the last 300 years. While genes appear to flow freely between the
 octoploid progenitors, the genome structures and diversity of the
 octoploid species remain poorly understood. The complexity and absence of
 an octoploid genome frustrated early efforts to study chromosome
 evolution, resolve subgenomic structure, and develop a single coherent
 linkage group nomenclature. Here, we show that
 octoploid Fragaria species harbor millions of
 subgenome-specific DNA variants. Their diversity was sufficient to
 distinguish duplicated (homoeologous and paralogous) DNA sequences and
 develop 50K and 850K SNP genotyping arrays populated with co-dominant,
 disomic SNP markers distributed throughout the octoploid genome.
 Whole-genome shotgun genotyping of an interspecific segregating population
 yielded 1.9M genetically mapped subgenome variants in 5,521 haploblocks
 spanning 3,394 cM
 in F. chiloensis subsp. lucida, and
 1.6M genetically mapped subgenome variants in 3,179 haploblocks spanning
 2,017 cM in F. × ananassa. These studies provide a dense
 genomic framework of subgenome-specific DNA markers for seamlessly
 cross-referencing genetic and physical mapping information and unifying
 existing chromosome nomenclatures. Using comparative genomics, we show
 that geographically diverse wild octoploids are effectively diploidized,
 nearly completely collinear, and retain strong macro-synteny with diploid
 progenitor species. The preservation of genome structure among
 allo-octoploid taxa is a critical factor in the unique history of garden
 strawberry, where unimpeded gene flow supported its origin and
 domestication through repeated cycles of interspecific hybridization.
DOI: 10.5061/dryad.vt4b8gtnh
title: Data from: The impact of prescribed burning on native bee communities (Hymenoptera: Apoidea: Anthophila) in longleaf pine savannas in the North Carolina sandhills

description: Prescribed burning is a common silvicultural practice used in the
 management of longleaf pine (Pinus palustris Mill.) savannas to reduce
 hardwood encroachment and ground cover and to maintain biodiversity. We
 investigated the response of the native bee community (Hymenoptera:
 Apoidea: Anthophila) in the Sandhills of North Carolina to prescribed
 burning on a three-year rotation over two consecutive years (2012 and
 2013). We deployed bee bowl traps in sites that had been burned the year
 of sampling, one year before, two years before, and in unburned controls.
 A total of 2,276 bees of 109 species were captured. Bee abundance declined
 with time since fire, with 2.3 times more bees captured in the most
 recently burned sites than in unburned controls. Bee diversity also
 declined with time since fire, with 2.1 times more species captured in the
 most recently burned sites than in controls. Bee community composition
 also responded to fire; we present evidence that this response was
 mediated in part by the effect of fire on the amount of bare ground and
 canopy cover. Bees nesting aboveground were unaffected by fire, contrary
 to our expectation that fire would destroy the wood and stems in which
 these species nest. Our results indicate that prescribed burning is a
 silvicultural practice consistent with pollinator conservation in longleaf
 pine ecosystems of the North Carolina sandhills.
DOI: 10.5061/dryad.pvmcvdngt
title: Colorectal cancer scRNA-seq 10xG-format data matrix

description: Metastatic colorectal cancer (CRC) is a major cause of cancer-related
 death and incidence is rising in the younger population (&lt;50
 years).  Current chemotherapies can achieve response rates above
 50%, but immunotherapies have limited value for patients with
 microsatellite-stable (MSS) cancers.  The present study
 investigates the impact of chemotherapy on the tumor immune
 microenvironment.  We treat human liver metastases slices with
 5-Fluorouracil (5FU) plus either irinotecan or oxaliplatin, then perform
 single-cell transcriptome analyses.  Results from eight cases
 reveal two cellular subtypes with divergent responses to chemotherapy.
 Susceptible tumors are characterized by a stemness signature, an activated
 interferon pathway, and suppression of PD-1 ligands in response to
 5FU+irinotecan.  Conversely, immune checkpoint TIM-3 ligands are
 maintained or up-regulated by chemotherapy in CRC with an enterocyte-like
 signature, and combining chemotherapy with TIM-3 blockade leads to
 synergistic tumor killing.  Together, our analyses highlight
 chemo-modulation of the immune microenvironment and provide a framework
 for combined chemo-immunotherapies. 
description: Following surgical resection of CRLM specimens greater than 2 cm in diameter, sterile 6 mm tumor tissue cores were punch biopsied and immediately placed in BELZER-UW solution on ice. Within hours, cores were cut into 250 μm thick slices by vibratome and placed with media onto Millicell Cell Culture Inserts in a 24-well cell culture plate. Tumor slices were treated with 1 µg/ml 5-Fluorouracil in combination with 1 µg/ml oxaliplatin in the FOLFOX group or 1 µg/ml 5-Fluorouracil in combination with 2 µg/ml irinotecan in the FOLFIRI group. Control group consisted of slices treated with 0.2% DMSO in medium. Tumor slices were dissociated using the MACS Tumor Dissociation Kit according to the Miltenyi Biotec “dissociation of soft tumors” protocol. Cells were processed by 10xGenomics Chromium using the single-cell 3' RNA version 2 protocol.  RNAseq libraries were sequenced on the NextSeq500 instrument for 150 cycles (26 bp for Read 1 and 124 bp for Read 2). Reads were aligned to the human genome (GRCh38) and quantified using the Cell Ranger version 2.0 with default settings.  All gene expression data was saved to a single Cell Ranger-like Market Exchange Format (MEX) sparse data matrix. 
description: Python and R libraries exists for reading MEX data matrices.  In
 the style of 10x Cell Ranger, we provide here the MEX file
 (filtered_matrix.mtx) and TSV files (filtered_genes.tsv,
 filtered_barcodes.tsv) with feature and barcode sequences corresponding to
 row and column indices, respectively.  One such library is ScanPy (https://scanpy.readthedocs.io) with its "read_mtx" function. We also provide a CSV file (sample_identification.csv) with sample and treatment information.