cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qjq2bvqjg
title: EcoPhyloMapper: an R package for integrating geographic ranges, phylogeny, and morphology

description: 1. Spatial patterns of species richness, phylogenetic and morphological
 diversity are key to answering many questions in ecology and evolution.
 Across spatial scales, geographic and environmental features, as well as
 evolutionary history and phenotypic traits, are thought to play roles in
 shaping both local species communities and regional assemblages. By
 examining these geographic patterns, it is possible to infer how different
 axes of biodiversity influence one another, and how their interaction with
 abiotic factors has led to the spatial distribution of species assemblages
 – and their attributes – that we observe in the present. Although there
 has been interest in this area of research for some time, it has recently
 become more tractable to include multivariate shape data in such analyses.
 Shape information has the potential to provide a more direct measure of
 the functional morphology of species as compared to individual trait
 measurements and might be more relevant to understanding community
 composition. However, few tools currently exist to explore geographic
 patterns of both phylogenetic and shape diversity. 2. We present the
 ecoPhyloMapper R package (epm) that aims to streamline the handling of
 geographic range polygons or point occurrences and integration of
 resulting species metacommunities with phylogenetic trees and
 morphological shape. 3. Geographic maps can be generated that demonstrate
 spatial patterns in diversity metrics pertaining to phylogenetic
 similarity, multivariate shape similarity and disparity, and combinations
 of the two. Patterns of taxonomic, phylogenetic and shape disparity
 turnover can also be visualized. Biodiversity indices summarized across
 grid cells can easily be exported to GIS software as well as to other R
 packages that specialize in community assembly or geospatial statistics.
 4. This R package will facilitate the geographic exploration of
 multivariate shape data in concert with phylogenetic diversity, which will
 in turn support macroecological research exploring how species assemblages
 are structured. Further, this R package should prove useful across a wide
 range of macroecological applications that extend beyond the study of
 morphology.
description: Note that the tutorials and walk-throughs are available on the
 related Zenodo page: https://zenodo.org/record/6585672
DOI: 10.57707/fmi-b2share.012tq-kk733
title: Derived data products analyzed and presented in the manuscript "Ter-diurnal Atmospheric Tide on Mars"

description: There are altogether 29 files including the all the data of the results. The filenames are self-explaining, because they refer to the figures in the publication.
DOI: 10.57707/fmi-b2share.1m9fw-z2053
title: Derived data products analyzed and presented in the manuscript "Ter-diurnal Atmospheric Tide on Mars"

description: There are altogether 29 files including the all the data of the results. The filenames are self-explaining, because they refer to the figures in the publication.
DOI: 10.5061/dryad.0p2ngf245
title: Natural variation at a single gene generates sexual antagonism across fitness components in Drosophila

description: Mutations with conflicting fitness effects in males and females accumulate
 in sexual populations, reducing their adaptive capacity. Although
 quantitative genetic studies indicate that sexually antagonistic
 polymorphisms are common, their molecular basis and population genetic
 properties remain poorly understood. Here, we show in fruit flies how
 natural variation at a single gene generates sexual antagonism through
 phenotypic effects on cuticular hydrocarbon (CHC) traits that function as
 both mate signals and protectors against abiotic stress across a
 latitudinal gradient. Tropical populations of Drosophila serrata have
 polymorphic CHCs producing sexual antagonism through opposing but
 sex-limited effects on these two fitness-related functions. We dissected
 this polymorphism to a single fatty-acyl CoA reductase gene, DsFAR2-B,
 that is expressed in oenocyte cells where CHCs are synthesised. RNAi
 mediated disruption of the DsFAR2-B ortholog in D. melanogaster oenocytes
 affected CHCs in a similar way to that seen in D. serrata. Population
 genomic analysis revealed that balancing selection likely operates at the
 DsFAR2-B locus in the wild. Our study provides insights into the genetic
 basis of sexual antagonism in nature and connects sexually varying
 antagonistic selection on phenotypes with balancing selection on genotypes
 that maintains molecular variation.
DOI: 10.5061/dryad.msbcc2g1b
title: Paninvasion severity assessment of a U.S. grape pest to disrupt the global wine market

description: Economic impacts from plant pests are often felt at the regional scale,
 yet some impacts expand to the global scale through the alignment of a
 pest’s invasion potentials. Such globally invasive species (i.e.,
 paninvasives) are like the human pathogens that cause pandemics. Like
 pandemics, assessing paninvasion risk for an emerging regional pest is key
 for stakeholders to take early actions that avoid market disruption. Here,
 we develop the paninvasion severity assessment framework and use it to
 assess a rapidly spreading regional U.S. grape pest, the spotted
 lanternfly planthopper (Lycorma delicatula; SLF), to spread and disrupt
 the global wine market. We found that SLF invasion potentials are aligned
 globally because important viticultural regions with suitable environments
 for SLF establishment also heavily trade with invaded U.S. states. If the
 U.S. acts as an invasive bridgehead, Italy, France, Spain, and other
 important wine exporters are likely to experience the next SLF
 introductions. Risk to the global wine market is high unless stakeholders
 work to reduce SLF invasion potentials in the U.S. and globally.
description: Please see corresponding study and readme file.
description: Please see corresponding study and readme file.
DOI: 10.5061/dryad.bg79cnpd2
title: On the computational reproducibility of molecular phylogenies

description: Reports on the lack of computational reproducibility of molecular
 phylogenies, produced in multiple runs of the same program or by different
 programs, cast a long shadow on downstream research using these
 phylogenies and on efforts to build the tree of life. We show that this
 irreproducibility does not decrease the accuracy of the reconstructed
 evolutionary relationships. Also, we find inferred molecular phylogenies
 to have log-likelihoods comparable to or better than the true phylogeny.
 Therefore, the lack of computational reproducibility of molecular
 phylogenies is not a problem for evolutionary studies.
description: The simulated datasets were generated by a previous study
 under an autocorrelated rate
 model (Tamura et al. 2012).
DOI: 10.5061/dryad.ghx3ffbrj
title: Open habitats in a tropical biodiversity hotspot support pollinator diversity in both protected and unprotected areas

description: Protected areas (PAs) are vital in the global effort to preserve
 biodiversity, particularly for disturbance-intolerant pollinator species
 in the tropics. As there is little information on the potential of PAs for
 pollinator conservation in sensitive tropical ecosystems, we assessed here
 insect pollinator diversity in protected vs. unprotected areas in two
 vegetation zones in Nigeria, within the West African Guinea Biodiversity
 Hotspot. We selected two land-use types based on predominant canopy cover
 type (open and tree-shaded habitats) and these were sampled in both
 protected and unprotected areas of tropical rain forest and savanna
 vegetation zones. Pollinator composition varied significantly between
 protected vs. unprotected areas in each vegetation zone, signifying both
 areas support unique assemblages of insect pollinators. However,
 pollinator diversity varied according to land-use type (open vs. shaded
 habitats) rather than protected area per se, such that pollinators were
 more abundant and species-rich in open habitat than shaded habitat. These
 findings emphasize that beyond the protection of ecosystems, fine scale
 habitat management promoting the availability of adequate floral resources
 in natural areas is critical for ensuring conservation of these
 pollinators in tropical ecosystems.   
description: Sampling of insect pollinators was
 carried out four times between August 2018 and July 2019 on each sampling
 plot. The sampling times were during early rain (May/June), late rain
 (September/October), early dry (January) and late dry (March) seasons
 within the one-year sampling period to cover the variation during the
 prolonged flowering season (Kaiser-Bunbury et al., 2017). The sampling of
 flowering plants in the study plots was carried out only after insect
 sampling to avoid disturbing the insect flower visitors. A 1 m × 1 m
 quadrat was randomly thrown ten times in each 25 m × 25 m plot. All
 flowering plants were shrubs and herbs with a maximum height of
 approximately 1m above ground level. Species richness and abundance of the
 flowering plants were estimated within the quadrats. The abundance and
 species richness of the different taxa (bees, wasps, beetles, butterflies,
 and flies) recorded in each vegetation zone from all sampling periods were
 pooled per insect taxon for the analyses. Species richness was estimated
 as the number of species recorded in each observation plot during the
 sampling period.  
description: None
DOI: 10.5061/dryad.b5mkkwhg6
title: Parasitism dramatically alters the ecosystem services provided by freshwater mussels

description: Parasites can indirectly affect ecosystem function by altering host
 phenotype, but the trait-mediated impacts of parasitism at an ecosystem
 level remain poorly characterised. However, understanding the influence of
 parasites is central to understanding the ecosystem services provided by
 host species, especially in an era of global environmental change. We
 examined the effect of native (the trematode Rhipidocotyle campanula) and
 invasive (the bitterling fish Rhodeus amarus) parasites, and their
 interaction, on the clearance rates of unionid mussels, a dominant
 ecosystem-engineering group that modifies freshwater ecosystems worldwide.
 We used a combination of field experiments, laboratory experiments, and
 ecological simulations to demonstrate the phenotypic impact of parasites
 on the functional response of two mussel species across an environmental
 gradient (suspended particle concentration), and extended this with host
 and parasite community data to demonstrate the consequences for a
 real-world ecosystem, the Old West River in Cambridgeshire, England. Both
 parasites altered the clearance rates of their hosts but in contrasting
 fashion: while R. campanula increased host clearance rates relative to
 uninfected conspecifics under all conditions, R. amarus suppressed
 clearance rates at high suspended particle concentrations (eutrophic
 conditions) but elevated them otherwise. The parasites displayed different
 infection patterns in the two host species, and the invasive R. amarus
 rarely co-infects mussels with R. campanula. Given their disparate
 effects, the parasites’ distributions reversed the relative filtration
 capacity of the two host species under high vs. low concentrations of
 suspended particles, demonstrating how differences between the infection
 patterns of native and invasive parasites, as well as their individual
 effects, need to be considered. Overall, the proportion of daily river
 discharge filtered by the combined mussel community changed by up to 96%
 in the presence of parasites. By incorporating multiple host species and
 multiple parasite species, we provide ecologically relevant evidence for
 the trait-mediated effects of parasites on ecosystem processes. Our study
 demonstrates that parasitism can significantly alter wider ecosystem
 processes by changing the phenotype of their host. Future work on
 ecosystem function should take parasitism into account, and consider both
 trait-mediated and density-mediated effects.
description: Please see the paper associated with this dataset for detailed
 methods (section 2.2). 
description: We have deposited three files: the two .csv files contain data
 for the bitterling and trematode experiments respectively, and the .R code
 provides complete code to run the analyses and ecosystem models, and
 produce the figures. Please see the README file for full
 details.
DOI: 10.5061/dryad.xgxd254jp
title: Highly-multiplexed mass cytometry screen of human bone marrow hematopoietic stem and progenitor cells

description: In contrast to the rich single-cell transcriptomic and epigenetic data,
 the corresponding protein level information of human hematopoietic stem
 and progenitor cell (HSPC) populations is still missing. We used a
 highly-multiplexed single-cell screen to quantify the protein expression
 of 353 surface molecules and 79 functional intracellular molecules (TFs,
 chromatin regulators, and metabolic enzymes) with mass cytometry. In doing
 this, we created a core panel with probes against functional protein
 molecules associated with specific lineage potentials to better illuminate
 the differentiation potentials of the progenitors. In total, we analyzed
 556,226 CD34+ bone marrow HSPCs across three individuals. Our analysis
 identified ten distinct clusters among HSPCs by unsupervised method and
 defined their unique proteomic composition. We compare our data-driven
 populations to the canonical HSPC cell types identified by cell surface
 proteins and observe discrepancies, especially in the lympho-myeloid axis.
 Overall, we supply a quantified summary of the proteomes of human HSPCs
 and create a framework to redefine progenitor populations with unique
 functional states along hematopoiesis.
DOI: 10.5061/dryad.hqbzkh1jk
title: The social network of target of rapamycin complex 1 in plants

description: The target of rapamycin complex 1 (TORC1) is a highly conserved
 serine–threonine protein kinase crucial for coordinating growth according
 to nutrient availability in eukaryotes. It works as a central integrator
 of multiple nutrient inputs such as sugar, nitrogen, and phosphate and
 promotes growth and biomass accumulation in response to nutrient
 sufficiency. Studies, especially in the past decade, have identified the
 central role of TORC1 in regulating growth through interaction with
 hormones, photoreceptors, and stress-signaling machinery in plants. In
 this review, we comprehensively analyse the interactome and
 phosphoproteome of the Arabidopsis TORC1 signaling network. Our analysis
 highlights the role of TORC1 as a central hub kinase communicating with
 the transcriptional and translational apparatus, ribosomes, chaperones,
 protein kinases, metabolic enzymes, and autophagy and stress response
 machinery to orchestrate growth in response to nutrient signals. This
 analysis also suggests that along with the conserved downstream components
 shared with other eukaryotic lineages, plant TORC1 signaling underwent
 several evolutionary innovations and co-opted many lineage-specific
 components. Based on the protein–protein interaction and phosphoproteome
 data, we also discuss several uncharacterized and unexplored components of
 the TORC1 signaling network, highlighting potential links for future
 studies.
DOI: 10.5061/dryad.bnzs7h4d8
title: Richness and abundance of both butterflies and floral resources in residential gardens across southwestern Melbourne, Australia’s greater metropolitan area

description: Wildlife gardening is a popular activity undertaken within residential
 areas. It is broadly promoted as a means of encouraging residents to make
 their gardens more ‘wildlife friendly’. While theory and anecdotal
 evidence suggest these schemes should be effective, quantitative
 evaluation of wildlife gardening practices and programs is lacking across
 most taxa they target. Our overall objective in collecting this data was
 to determine if there was a difference in butterfly richness or abundance
 between gardens managed and not managed to benefit wildlife. To
 test this, the data were collected at two spatial scales: landscape level
 representing our 500x500 m sampling cells and garden level representing
 our wildlife and traditional residential gardens. At the landscape level,
 butterfly and floral data were collected along a 1-km long Pollard walk
 through the sampling cell. At the garden level we conducted point counts
 for butterflies in residential gardens participating in a wildlife
 gardening program and compared them to non-participating control gardens
 within the same sampling cell and from areas not targeted by the gardening
 program. At both levels we counted floral resources and calculated tree
 cover (%) within the surrounding landscape as both are important potential
 resources for butterflies within the landscape. The amount (%) of
 impervious surface cover within the entire sampling cell and
 within the landscape surrounding each garden was also measured as it is
 known to have a negative effect on the butterfly community.
DOI: 10.5061/dryad.ttdz08m1t
title: Assessing population structure and genetic diversity in U.S. Suffolk sheep to define a framework for genomic selection

description: Long-term sustainability of breeds depends on having sufficient genetic
 diversity for adaptability to change, whether driven by climatic
 conditions or by priorities in breeding programs. Genetic diversity in
 Suffolk sheep in the U.S. was evaluated in four ways: 1) using genetic
 relationships from pedigree data [(n=64,310 animals recorded in the U.S.
 National Sheep Improvement Program (NSIP)]; 2) using molecular data (n=304
 Suffolk genotyped with the OvineHD BeadChip); 3) comparing Australian
 (n=109) and Irish (n=55) Suffolk sheep to those in the U.S. using
 molecular data; and 4) assessing genetic relationships (connectedness)
 among active Suffolk flocks (n=18) in NSIP. By characterizing genetic
 diversity, a goal was to define the structure of a reference population
 for use for genomic selection strategies in this breed. Pedigree-based
 mean inbreeding level for the most recent year of available data was 5.5%.
 Ten animals defined 22.8% of the current gene pool. The effective
 population size (Ne) ranged from 27.5 to 244.2 based on pedigree and was
 79.5 based on molecular data. Expected (HE) and observed (HO)
 heterozygosity were 0.317 and 0.306, respectively. Model-based population
 structure included 7 subpopulations. From Principal Component Analysis,
 countries separated into distinct populations. Within the U.S. population,
 flocks formed genetically disconnected clusters. A decline in genetic
 diversity over time was observed from both pedigree and genomic-based
 derived measures with evidence of population substructure as measured by
 FST. Using these measures of genetic diversity, a framework for
 establishing a genomic reference population in U.S. Suffolk sheep engaged
 in NSIP was proposed.
DOI: 10.5061/dryad.12jm63z11
title: Dataset for: Burma terrane amber fauna shows connections to Gondwana and transported Gondwanan lineages to the northern hemisphere (Araneae: Palpimanoidea)

description: Burmese amber is a significant source of fossils that documents the
 mid-Cretaceous biota. This deposit was formed around 99 Ma on the Burma
 Terrane, which broke away from Gondwana and later collided with Asia,
 although the timing is disputed. Palpimanoidea is a dispersal-limited
 group that was a dominant element of the Mesozoic spider fauna, and has an
 extensive fossil record, particularly from Burmese amber. Using
 morphological and molecular data, evolutionary relationships of living and
 fossil Palpimanoidea are examined. Divergence dating with fossils as
 terminal tips, followed by ancestral range estimations, shows timing of
 diversification is contemporaneous with continental break-up and that
 widespread ancestral ranges divide into lineages that inherit different
 Pangean fragments, consistent with vicariance. Our results suggest that
 the Burmese amber fauna has ties to Gondwana due to a historical
 connection in the Early Cretaceous, and that the Burma Terrane facilitated
 biotic exchange by transporting lineages from Gondwana into the Holarctic
 in the Cretaceous.
DOI: 10.5068/d1gq3s
title: De novo genome assembly of human cell line CHM13 nanopore ultra-long reads using Shasta

description: Advances in Oxford Nanopore Technologies (ONT) sequencing, basecalling,
 and updates to Shasta are outpacing the publishing cycle. We aim to update
 users on the state of the art using the latest and greatest ONT data
 assembled with Shasta. This release encompassed our latest assembly of
 CHM13, the AssemblySummary.html and Assembly.gfa along with our evaluation
 presented in tables and figures. We assembled ultra-long nanopore reads of
 CHM13 using Shasta 0.9.0 with the iterative assembly mode to produce a
 haploid de novo genome assembly.
description: We downloaded publicly available reads created by the "Telomere-to-Telomere" (T2T) Consortium to assemble CHM13. For a description of sequencing methods by the T2T Consortium, please see https://github.com/marbl/CHM13#oxford-nanopore-data. Release 8 of the data was re-called with Guppy v5.0.7 in super accuracy mode.<strong id="docs-internal-guid-7821e365-7fff-0752-c7a7-d90ceb231ff6" style="font-weight:normal;"></strong>   T2T CHM13 rel8 reads https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/nanopore/rel8-guppy-5.0.7/reads.fastq.gz   We assembled the reads using Shasta 0.9.0 (Shafin et al., 2020) in the iterative assembly mode by calling the -Nanopore-Sep2020 configuration, plus additional command line options listed below. We performed the assembly on McCloud, a service that runs Shasta in the cloud.   Shasta 0.9.0 command line options   --Reads.minReadLength 50000 --Kmers.k 10 --MinHash.minHashIterationCount 100 --Align.minAlignedFraction 0.35 --Align.minAlignedMarkerCount 600 --Align.maxSkip 50 --Align.maxDrift 30 --Align.maxTrim 30 --ReadGraph.creationMethod 0 --ReadGraph.maxAlignmentCount 12 --ReadGraph.crossStrandMaxDistance 0 --MarkerGraph.refineThreshold 0 --MarkerGraph.minCoveragePerStrand 3 --MarkerGraph.simplifyMaxLength 10,100,1000,10000 --Assembly.iterative --Assembly.pruneLength 10000 --Assembly.consensusCaller Bayesian:guppy-5.0.7-a References   Shafin,K. et al. (2020) Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. Nat. Biotechnol., 38, 1044–1053.  
description: Files Genome assembly file Assembly of CHM13 in FASTA format (one strand only). shasta_0.9.0_chm13_assembly.fasta   Genome assembly summary file Assembly summary information in html format. AssemblySummary.html   Graphical fragment assembly file Assembly in GFA format (one strand only). Assembly.gfa   Assembly evaluation Results of our evaluation of the assembly using QUAST and asmgene presented in tables and figures. shasta_0.9.0_chm13_evaluation.pdf