cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mkkwh713m
title: Correlation between fine root traits and pathogen richness depends on plant mycorrhizal types

description: Root uptake strategies are associated with the strength of negative
 plant–soil feedback induced (PSF) induced by soil pathogens. Given the
 intensified effect of pathogen richness in fine roots on the strength of
 negative PSF through the synergistic effects of multiple pathogens,
 researchers have proposed a trade-off between nutrient acquisition and
 pathogen defence in roots. However, empirical evidence is lacking. In
 addition, because the interaction between pathogens and fine roots depends
 on the mycorrhizal types of tree species, both fine root traits and
 mycorrhizal types should be incorporated to reveal covariation in pathogen
 richness and the strength of negative PSF. In this study, we selected 50
 arbuscular mycorrhizal (AM) tree species and 7 ectomycorrhizal (ECM) tree
 species in a subtropical forest to investigate the relationships between
 fine root traits and pathogen richness in fine roots and determined
 whether their relationships depended on plant mycorrhizal types. Our
 results showed that pathogen richness was negatively correlated with fine
 root diameter but was positively correlated with specific root length for
 the AM-associated species, while for the ECM-associated species, the
 pathogen richness was only found to have a significant negative
 relationship with the relative abundance of ECM fungi. These findings
 highlight the difference between AM- and ECM-associated species in
 pathogen defence and bridge the gap between root traits and pathogen
 richness, which is significant for improving our understanding of the
 potential factors mediating the strength of PSF and thus maintaining tree
 species diversity.
description: Please see manuscript (Correlation between fine root traits and
 pathogen richness depends on plant mycorrhizal types) in OIKOS.
description: Please see manuscript (Correlation between fine root traits and
 pathogen richness depends on plant mycorrhizal types) in OIKOS.
DOI: 10.5061/dryad.hx3ffbghq
title: Effect of the free healthcare policy on the health services' utilisation by children under five years in Burkina Faso

description: Objectives: This study aimed to analyse, at national level, the effects of
 the free healthcare policy for children on the use of health services by
 children under five in Burkina Faso. We hypothesized that this policy has
 led to an immediate and sustained increase in the use of health services
 for these children in the country. Setting: We conducted a controlled
 interrupted time series. Monthly data at district level, spanning from
 January 2013 to December 2018 and corresponding to 72 monthly data points
 (39 before and 33 after), were extracted from the Burkina Faso National
 Health Information System. The analysed dataset included data from all the
 70 health districts of the country. Participants: The study consisted of
 aggregated data from children under five as the target for the policy with
 children aged between 5-14 years old as control group. Intervention: The
 intervention was the introduction of the free healthcare policy for women
 and children under five years from April 2016. Outcome: The primary
 outcome was the mean monthly rate of health services visits by children
 Results: Among the children under five, the rate of visits increased of
 57% (IRR= 1.57; 95% CI=1.2 to 2.0) in the month immediately following the
 launching of the free healthcare policy. An increase in the rate of health
 facility visits of 1% (IRR=1.01; 95% CI=1.0 to 1.1) per month was also
 noted during post-intervention. Compared to the control group, we observed
 an increase of the rate of visits of 2.5% (IRR=1.025; 95%CI= 1.023 to
 1.026) per month. Conclusion: Findings suggest that the free healthcare
 policy increased the use of health facilities for care in Burkina Faso
 immediately after the implementation of the policy with a small increase
 in the rate overtime. Strategies to maintain the policy effect over time
 are necessary.
description: Monthly data were
 retrospectively extracted from the National Health Information System from
 January 2013 to December 2018. All the data were
 extracted in May 07–30, 2021 and updated on May 05 –12, 2022. The dataset included observations on 39 months for the pre-intervention period and 33 months for the post-intervention period for all 70 health districts in the country.
description: The Excel software
DOI: 10.5061/dryad.z34tmpghs
title: Assessing potential hybridization between a hypothetical gene drive-modified Drosophila suzukii and non-target Drosophila species

description: Genetically engineered gene drives (geGD) are potentially powerful tools
 for suppressing or even eradicating populations of pest insects. Before
 living geGD insects can be released into the environment, they must pass
 an environmental risk assessment (ERA) to ensure that their release will
 not harm valued and protected entities of the environment. A key research
 question concerns the likelihood that non-target species will acquire the
 functional GD elements; such acquisition could lead to the loss of those
 species and to a disruption of the ecosystem services they provide. The
 main route for gene flow is through hybridization between the GD insect
 strain and closely related species that co-occur in the area of release.
 Using the invasive spotted-wing drosophila, Drosophila suzukii, as a case
 study, we demonstrate how a combination of interspecific hybridization
 experiments, behavioral observations, and molecular genetic analyses can
 be used to assess the potential for hybridization.
DOI: 10.5061/dryad.c2fqz61cg
title: U.S. freshwater mussel occurrence data

description: Natural history collections are uniquely positioned to chronicle
 biodiversity change and are a fundamental data source in taxon-based
 research and conservation. With 85 species federally protected under the
 Endangered Species Act, freshwater mussels are one of the most imperiled
 animal assemblages in the United States and are the focus of extensive
 conservation efforts. Unfortunately, natural history collections data are
 underleveraged in taxon-based conservation efforts because much of the
 data are decentralized and nonstandard, and thus, difficult to access and
 analyze. Our objective herein is to synthesize, standardize, enrich, and
 distribute digitized US freshwater mussel collections data to better suit
 the needs of conservation stakeholders. We aggregated specimen records
 from 45 US natural history collections and enriched these records by
 programmatically standardizing taxonomic information, flagging potentially
 problematic records, and joining records with freshwater-specific spatial
 frameworks and their associated hydrological metadata. The assembled
 dataset includes 410,813 records from 302 species and 1,538 hydrological
 units (8 digit-level). Using these enriched records, we estimated
 ecological attributes for 286 freshwater mussel species including aspects
 of range size and hydrological preferences. Imperiled species had
 significantly fewer occurrences, smaller area of occupancy, and
 experienced greater declines in area of occupancy than non-imperiled
 species. Imperiled species also had higher stream order and discharge
 preferences than non-imperiled species. The synthesized, standardized, and
 enriched natural history collections data and our novel ecological
 estimates have revealed and corroborated important insights into
 freshwater mussel diversity, distribution, and decline. Stakeholders can
 access this data via download or interactively at the companion web app,
 MusselMapR (https://musselmapr.shinyapps.io/hic_sunt_naiades/).
description: Additional supporting information may be found in the online version of
 the article at the publisher’s website. All data and code necessary for
 reproduction are availablehere and
 . Appendix S1:
 Code to standardize, process, analyze, and visualize collections data
 Appendix S2: All .csv data files Appendix S3: Species range shapefiles for
 programmatic flagging
DOI: 10.5061/dryad.tb2rbp03t
title: Dataset for: Indirect nitrous oxide emission factors of fluvial networks can be predicted by dissolved organic carbon and nitrate from local to global scales

description: Streams and rivers are important sources of nitrous oxide (N2O), a
 powerful greenhouse gas. Estimating global riverine N2O emissions
 is critical for the assessment of anthropogenic N2O emission
 inventories. The indirect N2O emission factor (EF5r) model, one
 of the bottom-up approaches, adopts a fixed EF5r value to
 estimate riverine N2O emissions based on IPCC methodology.
 However, the estimates have considerable uncertainty due to the large
 spatiotemporal variations in EF5r values. Factors regulating
 EF5r are poorly understood at the global scale. Here, we combine
 4-year in situ observations across rivers of different land use types in
 China, with a global meta-analysis over six continents, to explore the
 spatiotemporal variations and controls on EF5r values. Our
 results show that the EF5r values in China and other regions with
 high N loads are lower than those for regions with lower N loads. Although
 the global mean EF5r value is comparable to the IPCC default
 value, the global EF5r values are highly skewed with large
 variations, indicating that adopting region-specific EF5r values
 rather than revising the fixed default value is more appropriate for the
 estimation of regional and global riverine N2O emissions. The
 ratio of dissolved organic carbon to nitrate (DOC/NO3-) and
 NO3- concentration are identified as the dominant predictors of
 region-specific EF5r values at both regional and global scales
 because stoichiometry and nutrients strictly regulate denitrification and
 N2O production efficiency in rivers. A multiple linear regression
 model using DOC/NO3- and NO3- is proposed to predict
 region-specific EF5r values. The good fit of the model associated
 with easily obtained water quality variables allows its widespread
 application. This study fills a key knowledge gap in predicting
 region-specific EF5r values at the global scale and provides a
 pathway to estimate global riverine N2O emissions more accurately
 based on IPCC methodology. This dataset is a global integrated N2O dataset
 including data from 4-year (2017-2020) in situ measurements of six large
 rivers in China, 3-year (2018-2020) in situ measurements of urban river
 networks in Beijing of China, and 825 measurements from 70
 published papers over six continents. The data includes dissolved N2O
 concentration, biogeochemical (DOC, NO3-, NH4+, temperature, and
 DO), climatological (climate zones), and geographic (region, location, and
 land cover) information.
description: Methods of data collection/generation are described in the
 manuscript for details.
DOI: 10.5061/dryad.djh9w0w3n
title: Colour moult phenology and camouflage mismatch in polymorphic populations of Arctic foxes

description: Species that seasonally moult from brown to white to match snowy
 backgrounds become conspicuous and experience increased predation risk as
 snow cover duration declines. Long-term adaptation to camouflage mismatch
 in a changing climate might occur through phenotypic plasticity in colour
 moult phenology and or evolutionary shifts in moult rate or timing. Also,
 adaptation may include evolutionary shifts towards winter brown phenotypes
 that forgo the winter white moult. Most studies of these processes have
 occurred in winter white populations, with little attention to polymorphic
 populations with sympatric winter brown and winter white morphs. Here, we
 used remote camera traps to record moult phenology and mismatch in two
 polymorphic populations of Arctic foxes in Sweden over 2 years. We found
 that the colder, more northern population moulted earlier in the fall and
 later in the spring. Next, foxes moulted earlier in the fall and later in
 the spring during colder and snowier years. Finally, white foxes
 experienced relatively low camouflage mismatch while blue foxes were
 mismatched against snowy backgrounds most of the fall through the spring.
 Because the brown-on-white mismatch imposes no evident costs, we predict
 that as snow duration decreases, increasing blue morph frequencies might
 help facilitate species persistence.
DOI: 10.5061/dryad.zw3r228bj
title: Oenothera Section Calylophus population genetic study

description: Premise: Animal pollinators play an important role in pollen dispersal.
 Differences in foraging patterns, flight distances and grooming behaviors
 are assumed to have consequences for genetic diversity of plants but are
 rarely tested explicitly. Here, we assess the role of pollinator
 functional groups with different foraging behaviors (hawkmoth and bee) in
 generating patterns of genetic diversity over similar geographic ranges
 for two closely related taxa. Methods: This study focuses on two members
 of Oenothera section Calylophus that co-occur on gypsum outcrops
 throughout the Chihuahua Desert but differ in floral phenotype and primary
 pollinator: Oenothera gayleana (bee) and O. hartwegii subsp.
 filifolia (hawkmoth). We measured breeding system and floral traits in the
 greenhouse and conducted a population genetic study at the local
 (&lt;13km; four populations) and landscape (60–440km; five
 populations) scales using 10–11 nuclear (pollen dispersal) and three
 plastid (seed dispersal) microsatellite markers.  Key Results:
 Both taxa were self-incompatible and floral traits were consistent with
 expectations for different pollinators. We found no evidence of genetic
 structure at the local scale, but at the landscape scale, O. gayleana
 showed greater differentiation and significant isolation by distance than
 O. hartwegii subsp. filifolia. The plastid data were consistent with
 gravity dispersal of seeds and suggest that pollen dispersal is the
 principal driver of genetic structure in both species.
 Conclusions: We demonstrate that pollinator functional groups can
 impact genetic differentiation in different and predictable ways.
 Hawkmoths, with larger foraging distances, can maintain gene flow across
 greater spatial scales than bees.
description: Floral morphology and leaf tissue for genetic samples were
 collected in wild populations in New Mexico and Texas, USA.
 Floral morphology data and the breeding system assessment were
 conducted on plants grown in a growth chamber at the Chicago Botanic
 Garden, Illinois, USA. Additional details of methods
 used can be found in the published manuscript (to be updated upon
 publication).
DOI: 10.5061/dryad.d7wm37q4j
title: A chromosomal-scale reference genome of the New World Screwworm, Cochliomyia hominivorax

description: The New World Screwworm, Cochliomyia hominivorax (Calliphoridae), is the
 most important myiasis-causing species in America. Screwworm myiasis is a
 zoonosis that can cause severe lesions in livestock, domesticated and wild
 animals, and occasionally in people. Beyond the sanitary problems
 associated with this species, these infestations negatively impact
 economic sectors, such as the cattle industry. Here, we present a
 chromosome-scale assembly of C. hominivorax's genome, organized in 6
 chromosome-length and 515 unplaced scaffolds spanning 534 Mb. There was a
 clear correspondence between the D. melanogaster linkage groups A-E and
 the chromosomal-scale scaffolds. Chromosome Quotient (CQ) analysis
 identified a single scaffold from the X chromosome that contains most of
 the orthologs of genes that are on the D. melanogaster fourth chromosome
 (linkage group F or dot chromosome). CQ analysis also identified potential
 X and Y unplaced scaffolds and genes. Y-linkage for selected regions was
 confirmed by PCR with male and female DNA. Some of the long
 chromosome-scale scaffolds include Y-linked sequences, suggesting
 misassembly of these regions. These resources will provide a basis for
 future studies aiming at understanding the biology and evolution of this
 devastating obligate parasite.
description: The input de novo assembly, Chicago library reads, and Dovetail
 HiC library reads were used as input data for HiRise, a software pipeline
 designed specifically for using proximity ligation data to scaffold genome
 assemblies. An iterative analysis was conducted. First, Chicago library
 sequences were aligned to the draft input assembly using a modified SNAP
 read mapper (http://snap.cs.berkeley.edu). The separations of Chicago read pairs mapped within draft scaffolds were analyzed by HiRise to produce a likelihood model for genomic distance between read pairs, and the model was used to identify and break putative misjoins, to score prospective joins, and make joins above a threshold. After aligning and scaffolding Chicago data, Dovetail HiC library sequences were aligned and scaffolded following the same method. The genes predicted in our previous assembly using BRAKER (https://www.nature.com/articles/s42003-020-01152-4) were lifted-over to the current assembly using the pipeline ‘flo’.
description: Files open with a text editor.
DOI: 10.34740/kaggle/dsv/14650985
title: Global Genomic Neurofibromatosis Neoplasia
DOI: 10.5061/dryad.931zcrjpg
title: ZIKV in situ hybridization from full thickness placental center cuts, only positive samples included

description: These data accompany the manuscript "Infection of the maternal-fetal
 interface and vertical transmission following low-dose inoculation of
 pregnant rhesus macaques (Macaca mulattta) with an African-lineage Zika
 virus" The included images are low magnification scans of
 full-thickness placental sections (placenta containing decidua, placental
 villi, and chorionic plate) evaluated with in situ hybridization against
 ZIKV RNA. Details of methods are provided in the manuscript. Only slides
 that were deemed positive are included.
DOI: 10.34740/kaggle/dsv/14650981
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.gt56yv
title: Occurrence Download

description: A dataset containing 75 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Erichsenia uncinata",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 75 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003291-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6076/d1r30s
title: Data: Canonical host-pathogen tradeoffs subverted by mutations with dual benefits

description: Host-parasite coevolution is expected to drive the evolution of genetic
 diversity because the traits used in arms races, namely host range and
 parasite resistance, are hypothesized to trade off with traits used in
 resource competition. We therefore tested data for several tradeoffs among
 93 isolates of bacteriophage and 51 Escherichia coli genotypes that
 coevolved during a laboratory experiment. Surprisingly, we found multiple
 tradeups (positive trait correlations) but little evidence of several
 canonical tradeoffs. For example, some bacterial genotypes evaded a
 tradeoff between phage resistance and absolute fitness, instead evolving
 simultaneous improvements in both these traits. This was surprising
 because our experimental design was predicted to expose resistance-fitness
 tradeoffs by culturing E. coli in a medium where the phage
 receptor, LamB, is also used for nutrient acquisition. On reflection, LamB
 mediates not one but many tradeoffs, allowing for more complex trait
 interactions than just pairwise tradeoffs. Here, we report that
 mathematical reasoning and laboratory data highlight how tradeups should
 exist whenever an evolutionary system exhibits multiple interacting
 tradeoffs. Does this mean that coevolution should not promote genetic
 diversity? No, quite the contrary: we deduce that whenever positive trait
 correlations are observed in multi-dimensional traits, other traits may
 tradeoff and so provide the right circumstances for diversity maintenance.
 Overall, this study reveals there are predictive limits when data only
 account for pairwise trait correlations and it argues that a wider range
 of circumstances than previously anticipated can promote genetic and
 species diversity.
description: Many different sources of data including genome sequences, images
 of infection assays, OD-based growth curves, protein structural models,
 and bacterial competition experiments. 
description: See the README file.
DOI: 10.5061/dryad.wdbrv15s6
title: Collective navigation as a solution to noisy navigation and its vulnerability to population loss

description: Many animals use the geomagnetic field to migrate long distances with high
 accuracy; however, research has shown that individual responses to
 magnetic cues can be highly variable. Thus, it has been hypothesized that
 magnetoreception alone is insufficient for accurate migrations, and
 animals must either switch to a more accurate sensory cue or integrate
 their magnetic sense over time. Here we suggest that magnetoreceptive
 migrators could also use collective navigation strategies. Using
 agent-based models, we compare agents utilizing collective navigation to
 both the use of a secondary sensory system and time-integration. Our
 models demonstrate that collective navigation allows for 70% success rates
 for noisy navigators. To reach the same success rates, a secondary sensory
 system must provide perfect navigation for over 73% of the migratory
 route, and time integration must integrate over 50 time-steps, indicating
 that magnetoreceptive animals could benefit from using collective
 navigation. Finally, we explore the impact of population loss on animals
 relying on collective navigation. We show that as population density
 decreases, a greater proportion of individuals fail to reach their
 destination and that a 50% population reduction can result in up to a 37%
 decrease in the proportion of the individuals completing their migration.
description: Described in the Supplemental Section of the associated
 paper.
description: Netlogo version 6.2.2 R version 4.1.2
DOI: 10.5061/dryad.xd2547dm5
title: Data from: Local adaptation in shell shape traits of a brooding chiton with strong population genomic differentiation

description: Comparing divergence in quantitative traits and neutral molecular markers,
 such as QST–FST comparisons, provides a means to distinguish between
 natural selection and genetic drift as causes of population
 differentiation in complex polygenic traits. Onithochiton neglectus
 (Rochebrune, 1881) is a morphologically variable chiton endemic to New
 Zealand, with populations distributed over a broad latitudinal
 environmental gradient. In this species, the morphological variants
 cluster into two geographically separated shell shape groups, and the
 phenotypic variation in shell shape has been hypothesised to be adaptive.
 Here, we assessed this hypothesis by comparing neutral genomic
 differentiation between populations (FST) with an index of phenotypic
 differentiation (PST). We used 7,562 putatively neutral single nucleotide
 polymorphisms (SNPs) across 15 populations and three clades of O.
 neglectus throughout New Zealand to infer FST. PST was calculated from 18
 shell shape traits and gave highly variable estimates across populations,
 clades and shape groups. By systematically comparing PST with FST, we
 identified evidence of local adaptation in a number of the O. neglectus
 shell shape traits. This supports the hypothesis that shell shape could be
 an adaptive trait, potentially correlated with the ability to live and
 raft in kelp holdfasts.
description: Information on methods of collection and processing can be found
 in the associated publication.