cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2bvq83bt3
title: Publications on snake biology

description: The trajectory of biological research may be affected by historical
 factors (such as the study species and locations of influential
 researchers) as well as by underlying biological dimensions (such as
 species diversity and location of potential study taxa). Such influences
 on research focus can be clarified by examining the topics of published
 papers. Based on 93,816 scientific papers published on snake biology since
 1804 (from the Web of Science), we found a non-random distribution of
 research output among snake clades, fields of research, and geographic
 locations, and strong changes through time in overall research effort as
 well as in the foci of that work. Snakes are the subjects of more
 scientific papers than are other lineages of reptiles, but research on
 turtles has been increasing faster, and research effort per species is
 higher for smaller reptile lineages. Studies on systematics and taxonomy
 dominated snake research until the mid-20th century when this field was
 overtaken by studies of venoms, ecology, morphology, and physiology.
 Colubrids and vipers have been the most popular study taxa, reflecting a
 concentration of research in continents (Europe and the Americas) where
 these taxa are diverse and abundant. Research effort on vipers increased
 from around 1920, reflecting advances in antivenom and radiotelemetry
 technology. Blindsnakes and smaller Families remain relatively neglected
 in absolute terms. Numbers of papers per species are tenfold greater for
 North American and European snakes than in most other regions. We
 attribute these non-random patterns to temporal and spatial variation in
 research priorities, methodology, and the availability of scientific
 infrastructure.
description: Web of Science search for publications on snake biology. We
 searched the Web of Science (WoS) in March 2022 using snake Family names
 as the search terms, and the title, abstract, and keywords of each paper
 as the fields to be interrogated. All years from 1900 to 2022 were
 included. The nomenclature of snake Families has changed frequently over
 recent years so for simplicity, we treated each lineage as a Family even
 if it meant including “Families” that are often given subfamilial status
 within large lineages (e.g., we searched on “Pareidae” as well as the
 broader “Colubridae”). Likewise, we searched for “Hydrophiidae” and
 “Laticaudidae” even though modern literature relegates these groups to
 subfamilial status within the Elapidae. Papers that listed a group as a
 Subfamily rather than a Family would be captured in searches based on the
 more inclusive Family (in this case, Elapidae). 
description: Excel
DOI: 10.5061/dryad.34tmpg4nt
title: Functional traits and metacommunity theory reveal that habitat filtering and competition maintain bird diversity in a human shared landscape

description: Human shared landscapes cover much of Earth, yet their conservation value
 is contested. This controversy may persist because previous studies have
 examined species diversity, rather than the processes through which such
 diversity is maintained. For example, a site exhibiting high diversity may
 not actually bolster populations if the diversity is only maintained
 through net immigration. Recent research has begun to isolate the
 processes that maintain metacommunities and develop functional trait
 methods to identify these processes. However, the processes underlying
 bird communities remain obscure. Here, we leverage metacommunity theory,
 functional trait partitioning, and a Bayesian multispecies abundance model
 to assess whether a shared landscape – woody perennial polyculture farms –
 bolsters bird diversity. Such farms grow multiple species of
 food-producing woody perennials together with vegetative groundcover. We
 surveyed birds and their in situ functional traits across the US Midwest
 in traditional agriculture, woody perennial polyculture, prairie, and
 woods. We found that woody perennial polycultures exhibited the highest
 bird diversity and were the most preferred by many species (including
 threatened ones). Moreover, our functional trait analysis suggests that
 this diversity is maintained through habitat filtering and competition,
 rather than merely immigration. Thus, shared landscapes can likely
 conserve birds by providing a distinct habitat. These results suggest that
 woody perennial polyculture farms offer substantial potential to support
 bird populations in the US Midwest. Our study demonstrates the utility of
 in situ functional trait partitioning within a Bayesian framework to
 unmask ecological processes and help assess the conservation value of
 landscapes.
description: This data was collected in the US Midwest in summer 2018, and
 processed using R and Stan.
description: R, Stan, text editor.
DOI: 10.5061/dryad.m0cfxpp6g
title: Data from: Improving quartet graph construction for scalable and accurate species tree estimation from gene trees

description: Summary methods are one of the dominant approaches for estimating species
 trees from genome-scale data. However, they can fail to produce accurate
 species trees when the input gene trees are highly discordant due to gene
 tree estimation error as well as biological processes, like incomplete
 lineage sorting. Here, we introduce a new summary method TREE-QMC that
 offers improved accuracy and scalability under these challenging
 scenarios. TREE-QMC builds upon the algorithmic framework of QMC (Snir and
 Rao 2010) and its weighted version wQMC (Avni et al. 2014). Their approach
 takes weighted quartets (four-leaf trees) as input and builds a species
 tree in a divide-and-conquer fashion, at each step constructing a graph
 and seeking its max cut. We improve upon this methodology in two ways.
 First, we address scalability by providing an algorithm to construct the
 graph directly from the input gene trees. By skipping the quartet
 weighting step, TREE-QMC has a time complexity of O(n^3 k) with some
 assumptions on subproblem sizes, where n is the number of species and k is
 the number of gene trees. Second, we address accuracy by normalizing the
 quartet weights to account for "artificial taxa," which are
 introduced during the divide phase so that solutions on subproblems can be
 combined during the conquer phase. Together, these contributions enable
 TREE-QMC to outperform the leading methods (ASTRAL-III, FASTRAL, wQFM) in
 an extensive simulation study. We also present the application of these
 methods to an avian phylogenomics data set.
DOI: 10.5068/d1p96n
title: Winter connectivity and leapfrog migration in a migratory passerine

description: Aim: Every year birds prepare for their migration journey, and
 understanding how this phenomenon is carried out allows us to infer
 whether human activities have influenced and modified the way in which the
 birds migrate. Many bird species perform long-distance movements to find
 sites with better conditions and optimize the use of resources during the
 annual cycle. These migration movements in birds have been studied using
 different methods, from mist nets, mark and recapture techniques,
 geolocators to document movements, and stable hydrogen isotopes. In this
 study, we used a genetic tool to create a graphic representation of the
 genetic variation across the species breeding range or genoscape as a
 reference to assess the connectivity of a migratory bird across its annual
 cycle. The advantage of the genoscape approach is that it allows us to
 identify distinct genetic units in the breeding range and then detect the
 migration pattern of those units through time and space. Methods: We
 studied migration in the Painted Bunting (Passerina ciris) using genetic
 data from 386 individuals across the breeding range, 230 samples from 28
 migration stopover locations, and 178 samples from 16 wintering locations.
 We also combined population and individual-level genetic assignments to
 breeding areas in order to study migratory connectivity patterns in
 greater depth. Results: Our results show the existence of four main
 genetic groups within the species: Eastern, Southwestern, Central, and
 Louisiana. We also found that most of the individuals migrate during the
 fall towards Western Mexico and Central America and return to their
 breeding sites through the coastal plains of the Gulf of Mexico; the
 Louisiana breeding unit migrates to the Yucatan Peninsula and Central
 America, returning to their breeding sites in the spring through the
 coastal plains of the Gulf of Mexico. We found strong support for the
 existence of a Leap-frog migration pattern. Main conclusions: We use a
 genoscape approach to investigate population structure and broad-scale
 migration patterns in the Painted Bunting. By screening samples from
 across the annual cycle, we can reveal clear patterns of population
 structure across the breeding range and provide strong support for the
 existence of leapfrog migration.
DOI: 10.5061/dryad.70rxwdc1b
title: Population admixtures in medaka inferred by multiple arbitrary amplicon sequencing

description: Cost-effective genotyping can be achieved by sequencing PCR amplicons.
 Short 3–10 base primers can arbitrarily amplify thousands of loci using
 only a few primers. To improve the sequencing efficiency of the multiple
 arbitrary amplicon sequencing (MAAS) approach, we designed new primers and
 examined their efficiency in sequencing and genotyping. To demonstrate the
 effectiveness of our method, we applied it to examine the population
 structure of the small freshwater fish, medaka (Oryzias latipes). We
 obtained 2,987 informative SNVs with no missing genotype calls for 67
 individuals from 15 wild populations and three artificial strains. The
 estimated phylogenic and population genetic structures of the wild
 populations were consistent with previous studies, corroborating the
 accuracy of our genotyping method. We also attempted to reconstruct the
 genetic backgrounds of a commercial orange mutant strain, Himedaka, which
 has caused a genetic disturbance in wild populations. Our admixture
 analysis focusing on Himedaka showed that at least two wild populations
 had genetically contributed to the nuclear genome of this mutant strain.
 Our genotyping methods and results will be useful in quantitative
 assessments of genetic disturbance by this commercially available strain.
description: The original DNA was obtained from the individuals collected from
 the wild or inbred strains of <em>Oryzias</em>
 <em>latipes</em> and <em>O</em>.
 <em>sakaizumii</em>. Genomewide single
 nucleotide variants were obtained using PCR-amplicon based genotyping by
 sequencing with HiseqX. Fastq files were processed and
 genotyped by fastp ver. 0.20.0, BWA mem ver. 0.7.17, SAMtools ver. 1.7,
 Genome Analysis Tool Kit (GATK ver. 3.8.0).
DOI: 10.5061/dryad.gb5mkkwsd
title: Dataset of punctual observations along soil moisture gradients in France

description: The interface between wetlands and uplands is characterized by gradients
 in hydrological, soil and biological components. Consequently, the exact
 spatial distribution of this transitional area is not well known because
 it often occurs as a fuzzy moisture gradient. However, ecological
 assessment and conservation require mapping and characterizing this
 interface to better understand and model biotic and abiotic interactions
 between wetlands and uplands. To this end, in 2021 and 2022, we observed
 soil properties and vegetation types along soil moisture gradients
 throughout the Atlantic, Continental, Mediterranean and Alpine
 biogeographic regions of France. The dataset contains 2 236
 georeferenced plots (accuracy ± 5 m) distributed along 1 088
 transects placed along the slope at 377 sites. Each plot in the database
 is characterized by 21 fields that describe the vegetation habitat type
 based on the European Nature Information System (EUNIS) and soil
 properties (i.e. depth of appearance and thickness of redoximorphic
 features in the soil profile, moisture). These data are useful for
 researchers and engineers in a variety of disciplines (e.g. Earth and life
 sciences) to calibrate and validate models to predict the spatial
 distribution of habitats or to analyze flows.
DOI: 10.5061/dryad.4mw6m90d4
title: Data from: The fat body cortical actin network regulates Drosophila inter-organ nutrient trafficking, signaling, and adipocyte cell size

description: Defective nutrient storage and adipocyte enlargement (hypertrophy) are
 emerging features of metabolic syndrome and type 2 diabetes. How the
 cytoskeletal network contributes to nutrient uptake, fat storage, and
 adipocyte size remains poorly understood. Utilizing the Drosophila larval
 fat body (FB) as a model adipose tissue, we show that a specific actin
 isoform—Act5C—forms the cortical actin network necessary for inter-organ
 lipid trafficking. Act5C also promotes FB tissue expansion during larval
 development so larvae can store sufficient biomass for metamorphosis. We
 find FB-specific loss of Act5C, but not other Drosophila actins, perturbs
 FB triglyceride (TG) storage in lipid droplets (LDs), resulting in
 developmentally delayed larvae that fail to develop into flies. Act5C
 localizes to the FB cell surface where it intimately contacts peripheral
 LDs (pLDs), forming a cortical actin network together with spectrins for
 cell architectural support. While both the cortical actin and spectrin
 cytoskeletons maintain FB cell surface architecture, we find that only the
 actin network is required for fat storage. Mechanistically, we show that
 FBs lacking the Act5C cortical cytoskeleton exhibit a block in lipoprotein
 (Lpp) secretion from FB cells, and a subsequent disruption of gut:FB
 inter-organ lipid transport, resulting in mid-gut fat accumulation.
 Utilizing temporal RNAi-depletion approaches, we also reveal that Act5C is
 indispensable post-embryogenesis during larval feeding to promote FB cell
 expansion. Act5C-deficient FBs fail to expand cell sizes, leading to
 lipodystrophic larvae unable to accrue sufficient biomass for
 metamorphosis. Collectively, we propose that the Act5C-mediated cortical
 actin network of Drosophila adipose tissue plays an essential role in
 post-embryonic inter-organ nutrient transport and FB cell size
 determination for organismal energy homeostasis and development.
description: These are datasets associated with cell size quantification.
DOI: 10.5061/dryad.s1rn8pkbq
title: Long-term nitrogen fertilization alters arbuscular mycorrhizal fungi community phylogenetic structure in plant roots across fine spatial scales

description: Purpose: Nitrogen deposition due to human activities is known to have a
 substantial impact on arbuscular mycorrhizal fungi (AMF) community in
 plant roots. However, the influence of elevated nitrogen on the
 phylogenetic structure of AMF across fine spatial scales, as well as the
 mechanisms behind such alterations, are remained poorly understood.
 Results: Nitrogen addition significantly increased the phylogenetic alpha
 diversity (diversity within a plot) and the ‘within-treatment’
 phylogenetic beta diversity (dissimilarity among replicate plots) of AMF
 communities, which resulted in an increased ‘within-treatment’
 phylogenetic gamma diversity (overall diversity among all the replicate
 plots within a treatment). These changes were caused by the relative
 abundance decline of a dominant genus (Glomus) and an increase in
 non-dominant genera. Mechanically, nitrogen addition affected phylogenetic
 alpha diversity mainly by influencing soil properties. Likewise, the
 increased ‘within-treatment’ dissimilarity of plant community composition
 and changes in soil properties caused by nitrogen addition and plot
 distance contributed to an increase in within-treatment phylogenetic beta
 diversity. Conclusions: We conclude that deterministic environmental
 filtering (both abiotic and biotic) and dispersal limitation effect played
 critical roles in AMF community assembly under global change scenarios.
 Insightfully, this study provides a mechanistic understanding of the
 response of AMF to nitrogen addition across fine scales.
description: We collected 256 root samples of 16 common plant species that
 occurred along a gradient of nitrogen addition and then calculated the AMF
 phylogenetic alpha, beta and gamma diversity.
DOI: 10.5061/dryad.dncjsxm2q
title: An ordinal severity scale for COVID-19 retrospective studies using electronic health record data

description: Objectives: Although the World Health Organization (WHO) Clinical
 Progression Scale for COVID-19 is useful in prospective clinical trials,
 it cannot be effectively used with retrospective Electronic Health Record
 (EHR) datasets. Modifying the existing WHO Clinical Progression Scale, we
 developed an ordinal severity scale (OS) and assessed its usefulness in
 the analyses of COVID-19 patient outcomes using retrospective EHR data.
 Results: The data set used in this analysis consists of 2,880,456
 patients. PCA of the day-to-day variation in OS levels over the totality
 of the 28-day period revealed contrasting patterns of variation in disease
 severity within the first and second 14 days and illustrated the
 importance of evaluation over the full 28-day period. Discussion: An OS
 with well-defined, robust features, based on discrete EHR data elements,
 is useful for assessments of COVID-19 patient outcomes, providing insights
 on progression of COVID-19 disease severity over time. Conclusion: The OS
 provides a framework which can facilitate better understanding of the
 course of acute COVID-19, informing clinical decision-making and resource
 allocation.
description: An OS was developed to assign COVID-19 disease severity using the
 Observational Medical Outcomes Partnership common data model within the
 National COVID Cohort Collaborative (N3C) data enclave. We then evaluated
 usefulness of the developed OS using heterogenous EHR data from January
 2020 to October 2021 submitted to N3C by 63 healthcare organizations
 across the United States. Principal Components Analysis (PCA) was employed
 to characterize changes in disease severity among patients during the
 28-day period following COVID-19 diagnosis.
DOI: 10.5061/dryad.wpzgmsbqf
title: Reduction in biomass of freshwater arctic vegetation by foraging and nesting hyperabundant herbivores shows recovery

description: Arctic-nesting geese are specialist herbivores of grasses and sedges
 (collectively, graminoids). Under moderate grazing pressure, these
 migratory herbivores can create and maintain arctic grazing lawns with
 high nutritional content and low aboveground biomass. Nutrient and energy
 subsidies from southern agricultural landscapes during winter have
 improved survival among populations of Ross’s (Anser rossii) and lesser
 snow geese (Anser caerulescens caerulescens), leading to marked population
 growth. Resulting goose hyperabundance has raised conservation concern for
 resilience of arctic ecosystems to withstand cumulative and intense
 pressures of herbivory and nest construction. We used both design-based
 (experimental herbivore exclosures) and model-based methods to investigate
 changes to plant community structure in direct response to foraging and
 nesting by these species within the Queen Maud Gulf (Ahiak) Migratory Bird
 Sanctuary, Nunavut, Canada. Annual nest construction and foraging by up to
 ~1.3 million geese at a large colony at Karrak Lake markedly reduced
 aboveground biomass of forage (graminoids) and non-forage (foliose and
 fruticose lichens) vegetation, with spatial variation in reduction
 associated with intensity of use by geese. Within vast brood-rearing
 regions, foraging reduced above- and belowground plant biomass of lowland
 plant communities by 61% and 29%, respectively, between 1994 (when
 herbivore exclosures were established) and 2017. In addition to landscape
 diversity associated with abiotic properties created by geomorphic
 processes, long-term herbivory by geese further increased spatial
 heterogeneity in vegetation at the landscape scale. Although foraging
 geese nearly completely depleted aboveground plant biomass in some parts
 of their brood-rearing areas, belowground biomass was largely conserved,
 and thus, plant communities had strong potential for aboveground
 regeneration. We propose that effects of high-density nesting and foraging
 by Ross’s and lesser snow geese in the central Canadian Arctic, while
 extensive, are ephemeral and prone to reversion following cessation of
 grazing and nesting pressure, such as that afforded by shifts in herbivore
 distribution or local population decline.
DOI: 10.5061/dryad.9s4mw6mk4
title: Trait coordination in boreal mosses reveals a bryophyte economics spectrum

description: 1. The study of plant trait spectra and their association with trade-offs
 in resource use strategy has greatly advanced our understanding of
 vascular plant function, yet trait spectra remain poorly studied in
 bryophytes, particularly outside of the Sphagnum genus. Here, we measured
 25 traits related to carbon, nutrient, and water conservation in 60 moss
 canopies (each dominated by one of 15 moss species) across diverse boreal
 forest habitats, and used bi-variate correlations and multi-variate
 analyses to assess trait coordination and trait spectra. 2. We found
 substantial trait coordination along a main principal components axis
 driven by trade-offs in carbon, nutrient, and water conservation
 strategies. Along this trait spectrum, traits varied from
 resource-acquisitive at one end (e.g., high maximum photosynthetic
 capacity, high tissue nitrogen content, low water holding capacity) to
 resource-conservative at the other end, in line with resource economics
 theory. 3. Traits related to carbon turnover (photosynthesis and
 respiration rates, litter decomposability) were positively related to
 nitrogen content and to desiccation rates, in line with global trait
 spectra in vascular plants. However, architectural traits of the moss
 shoots and of the moss canopy were generally unrelated to the main axis of
 trait variation and formed a secondary axis of trait variation, contrary
 to what is observed for vascular plants. 4. Resource-conservative trait
 spectra dominated in moss canopies from open and wet habitats (i.e.,
 mires), indicating that high irradiance and possibly high moisture
 fluctuation induce a resource-conservative trait strategy in mosses. 5.
 Synthesis. Our work suggests that trait relationships that are well
 established for vascular plants can be extended for bryophytes as well.
 Bryophyte trait spectra can be powerful tools to improve our understanding
 of ecosystem processes in moss-dominated ecosystems, such as boreal or
 arctic environments, where bryophyte communities exert strong control on
 nutrient and carbon cycling.