cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7280/d12108
title: Database of human alternative 5' and 3' splice sites

description: To determine the impact of the intron-exon architecture and splice site
 strength on splice site selection, we created a database of alternative
 splice sites (ALTssDB) using the Human Exon Splicing Event Database
 HEXEvent, the Intron DB, and GeneBase. MaxEntScan, a computational tool
 was used to assign splice site scores. To minimize variability, we focused
 on competing alternative 5′ or 3′ splice site pairs of internal exons with
 only one alternative splice pattern. Thus, two alternative 5′ splice sites
 compete for a common 3′ss, or two alternative 3′ splice sites compete for
 a common 5′ss. As a result, ALTssDB reports the location of the major
 splice site and its competing alternative 3′ or 5′ splice site,
 corresponding exon sizes, usage levels, splice site scores and flanking
 intron lengths.
description: ALTssDB was created using EST data from the Human Exon splicing
 Events (HEXEvent) database. HEXEvent contains information regarding the
 location of competing splice sites, the resulting exon sizes, alternative
 splice site usage levels and the gene associated with each mRNA. The
 HEXEvent data was filtered to obtain a dataset comprising of only pairs of
 competing 5' and 3' splice sites separately. This database was
 subsequently modified to include splice site junction information and
 MaxENT scores using MaxEntScan. Using an R script and IntronDB dataset, (a
 database detailing eukaryotic intron features) flanking intron lengths
 were added to the database. Alternative splicing events were further
 filtered to include only events that have 10 or more EST counts.
DOI: 10.5061/dryad.fttdz08vf
title: Rabbit spotlight counts are a better index of population density when density is high

description: Context: The management of the European rabbit is of strong interest to
 land managers. However, rabbits can be difficult to detect due to being
 nocturnal and living in dense vegetation or burrows. Consequently, rabbit
 spotlight counts are frequently used as an index of their density, but
 they are generally not expected to accurately reflect their true density.
 Indices place paramount importance on the precision of the estimator,
 which is directly driven by variability in individual estimates. Aims: To
 investigate how the variability of rabbit spotlight counts changes with
 the number of rabbits counted, repeated counts, and environmental
 variables. Key results: We identified a significant negative association
 between the number of rabbits counted and count variability; spotlight
 counts as an index of rabbit density have greater statistical power and
 are more likely to detect similar proportional differences in density when
 density is high compared to when density is low. We did not find any
 effects of rainfall, temperature, cloud cover, wind strength, season or
 additional consecutive spotlight count nights on count variability.
 Conclusions: Despite our comparatively large dataset, our results
 contrasted those of several previous studies; this suggests that many of
 the environmental factors that have previously been shown to impact rabbit
 activity or spotlight counts likely have small effects in reality.
 Implications: Appreciating and recognising that spotlight counts are less
 likely to accurately detect or reflect changes in population size when
 rabbit numbers are low is critical to their effective use.
description: We defined variability as the relative deviation of a single
 spotlight count from the mean of a set of three consecutive spotlight
 counts on the same population. We modelled spotlight count variability
 across 22 Australian sites over the period 2006-2020 using generalised
 linear mixed models.
DOI: 10.5061/dryad.z8w9ghxdz
title: Soil incubation data along a water gradient

description: The dataset is from an incubation experiment which was carried out in the
 dark at the temperature of 15°C and the relative humidity of 40% for 72
 days. The predominant soil is sandy loam, with sand, silt and clay
 percentages of 54%, 41% and 5%, respectively. The SOC content of the 0 –
 10 cm layer is 4.2% and the pH is 6.9. Four treatments with four
 replicates were set up at the SWC of 12%, 24%, 43% and 61%, respectively.
 The average cumulative respiration of the four replicates and its standard
 deviation (SD) are provided in the dataset.
description: Fresh soil samples were collected from four
 separate locations several meters apart in September 2020. Plants and
 surface litter were cleared away before sampling and the soil from the 0 –
 10 cm layer was collected. The soil samples were then transported to
 the laboratory in containers with ice. In the laboratory, rocks and plant
 materials were removed before the soil was homogenized and passed a 2-mm
 sieve. Soil samples were stored at -20 ℃ until the incubation experiment
 started. During the incubation, 66.3 g fresh soil (equivalent to 50 g
 air-dried soil) was put in a 200 ml open-top mason jar. The soil water
 content was maintained at the treatment levels by weighing the jars and
 adding the corresponding amount of water every day. All the jars were
 pre-incubated for seven days. During each measurement, the jar was covered
 by a rubber lid with two gas paths and connected to an LI-8100A infrared
 gas analysis system (LI-COR, USA). After stabilizing the system for 10
 minutes, CO<sub>2</sub> concentration changes within one
 minute in the headspace of each jar were recorded to calculate the
 CO<sub>2</sub> emission rate. The measurement was conducted
 daily in the first eight days, every two days for the next 19 days, and
 every four days thereafter. Overall, there were 28 sampling occasions over
 the 72-day incubation.
DOI: 10.25338/b8j33m
title: A barcode-based phylogenetic characterization of Phytophthora cactorum identifies two cosmopolitan lineages with distinct host affinities and the first report of Phytophthora pseudotsugae in California

description: A collection of 30 Phytophthora cactorum and 12 P. pseudotsugae (subclade
 1a) strains isolated from several recent surveys across California was
 phylogenetically compared to a worldwide collection of 112 conspecific
 strains using sequences from three barcoding loci. The surveys baited P.
 cactorum from soil and water across a wide variety of forested ecosystems
 with a geographic range of more than 1000 km. Two cosmopolitan lineages
 were identified within the widespread P. cactorum, one being mainly
 associated with strawberry production and the other more closely
 associated with apple orchards, oaks and ornamental trees. Two other
 well-sampled P. cactorum lineages, including one that dominated
 Californian restoration outplantings, were only found in the western
 United States, while a third was only found in Japan. Coastal California
 forest isolates of both Phytophthora species exhibited considerable
 diversity, suggesting both may be indigenous to the state. Many isolates
 with sequence accessions deposited as P. cactorum were determined to be P.
 hedraiandra and P. ×serendipita, with one hybrid lineage appearing
 relatively common across Europe and Asia. This study contains the first
 report of P. pseudotsugae from the state of California and one of the only
 reports of that species since its original description.
description: Sequences were derived by BLASTing a moving window of each locus
 against data in the sequence read archive corresponding to the listed
 BioSamples. Alignments are phylip files (.phy) and a nexus file (.nex)
 used as the input for IQTREE2.
DOI: 10.15468/dl.as5gh9
title: Occurrence Download

description: A dataset containing 2069 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Material sample, Specimen, Occurrence evidence)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Hypoponera opaciceps",
 "Year 1000-2025"
 ]
}

 The dataset includes 2069 records from 39 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003059-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.d7wm37q33
title: Data from: Organic-walled microfossils from the Kistedalen Formation, Norway: acritarch chronostratigraphy of the Baltic Miaolingian and evolutionary trends of placoid acritarchs

description: New acritarch data from the Kistedalen Formation based on two sections
 with continuous exposure allow to establish the most detailed Miaolingian
 acritarch biozonation in Baltica to date. Six interval zones previously
 established in Gondwana, the Eliasum llaniscum, Cristallinium cambriense,
 Adara alea, Timofeevia lancarae, Cristallinium dubium and Vulcanisphaera
 turbata zones, are identified, and their correlations within the
 Acado-Baltic Province examined. The diagnoses of Retisphaeridium,
 Cristallinium, Retisphaeridium dichamerum, Retisphaeridium lechistanium,
 Cristallinium dubium and Cristallinium cambriense are emended and the new
 species Retisphaeridium rugulatum sp. nov. and Retisphaeridium minimum sp.
 nov. are described. The diagnosis of Retisphaeridium ovillense (Cramer
 & Díez) Vanguestaine is emended and the species assigned to
 Dictyotidium ovillense comb. nov. The main evolutionary changes of the
 placoid acritarchs during the Miaolingian are analysed. Comparison with
 previous acritarch data from the Kistedalen Formation suggest that
 different extraction methodologies may result in significant bias in the
 recovered fossil record.
description: All field samples were collected by Teodoro Palacios and
 processed by Teodoro Palacios in the acid laboratory in Área de
 Palentologia, Universidad de Extremadura, Badajoz, Spain. Identical
 processing techniques were used for all samples, as outlined in the
 present manuscript and in Palacios et al. (2021).
 Palacios, T., Jensen, S., Alvaro, J.J., Santos Zaldeugui, J.F.,
 Eguiluz, L., Corfu, F. & Gil Ibarguchi, J.I. 2021. Acritarch-based
 chronostratigraphic and radiometric calibration of the Cambrian
 volcanosedimentary Vallehondo and Play´on formations in the Cambrian
 Ossa-Morena Rift, Spain. Palaeogeography, Palaeoclimatology,
 Palaeogeography 565, 110216 (32 pp).
DOI: 10.5061/dryad.866t1g1sd
title: Cranial kinesis facilitates quick retraction of stuck woodpecker beaks

description: Much like nails that are hammered into wood, the beaks of woodpeckers
 regularly get stuck upon impact. A kinematic video analysis of pecking by
 black woodpeckers shows how they manage to quickly withdraw their beaks,
 revealing a two-phase pattern: first a few degrees of nose-down rotation
 about the nasofrontal hinge causes the tip of the upper beak to be
 retruded while its proximal end is lifted. Next, the head is lifted,
 causing nose-up rotation about the nasofrontal hinge while the lower beak
 starts retruding and initiates the final freeing. We hypothesise that
 these consecutive actions, taking place in about 0.05 s, facilitate beak
 retraction by exploiting the presumably low frictional resistance between
 the upper and lower beak keratin surfaces, allowing them to slide past
 each other. It also demonstrates the counter-intuitive value of
 maintaining cranial kinesis in a species adapted to deliver forceful
 impacts.
description: See publication.
description: See README file.
DOI: 10.5061/dryad.vhhmgqnw0
title: Data from: Growth productivity as a determinant of the inoculum effect for bactericidal antibiotics

description: Understanding the mechanisms by which populations of bacteria resist
 antibiotics has implications for evolution, microbial ecology, and public
 health. The inoculum effect (IE), where antibiotic efficacy
 declines as the density of a bacterial population increases, has been
 observed for multiple bacterial species and antibiotics. Several
 mechanisms to account for IE have been proposed, but most lack
 experimental evidence or cannot explain IE for multiple antibiotics. We
 show that growth productivity, the combined effect of growth and
 metabolism, can account for IE for multiple bactericidal antibiotics and
 bacterial species. Guided by flux balance analysis and whole genome
 modeling, we show that the carbon source supplied in the growth medium
 determines growth productivity. If growth productivity is sufficiently
 high, IE is eliminated. Our results may lead to approaches to reduce IE in
 the clinic, help standardize the analysis of new antibiotics, and further
 our understanding of how bacteria evolve resistance.
DOI: 10.5061/dryad.7pvmcvdvm
title: Evaluating the roles of microbial functional breadth and home-field advantage in leaf litter decomposition

description: Soil biota are increasingly recognized as a primary control on litter
 decomposition at both local and regional scales, but the precise
 mechanisms by which biota influence litter decomposition have yet to be
 identified. There are multiple hypothesized mechanisms by which biotic
 communities may influence litter decomposition – for example, decomposer
 communities may be specially adapted to local litter inputs and therefore
 decompose litter from their home ecosystem at elevated rates. This
 mechanism is known as the home-field advantage (HFA) hypothesis.
 Alternatively, litter decomposition rates may simply depend upon the range
 of metabolic functions present within a decomposer community. This
 mechanism is known as the functional breadth (FB) hypothesis. However, the
 relative importance of HFA and FB in litter decomposition are unknown, as
 are the microbial community drivers of HFA and FB. Potential
 relationships/tradeoffs between microbial HFA and FB are also unknown. To
 investigate the roles of HFA and FB in litter decomposition, we collected
 litter and soil from six different ecosystems across the continental US
 and conducted a full factorial litter × soil inoculum experiment. We
 measured litter decomposition (i.e., cumulative CO2-C respired) over 150
 days and used an analytical model to calculate the HFA and FB of each
 microbial decomposer community.  Our results indicated clear
 functional differences among decomposer communities, i.e., litter sources
 were decomposed differently by different decomposer communities. These
 differences were primarily due to differences in FB between different
 communities, while HFA effects were less evident. We observed a positive
 relationship between HFA and the disturbance-sensitive bacterial phylum
 Verruomicrobia, suggesting that HFA may be an important mechanism in
 undisturbed environments. We also observed a negative relationship between
 bacterial r vs. K strategists and FB, suggesting an important link between
 microbial life history strategies and litter decomposition functions.
 Microbial FB and HFA exhibited a strong unimodal relationship, where high
 HFA was observed at intermediate FB values, while low HFA was associated
 with both low and high FB. This suggests that adaptation of decomposers to
 local plant inputs (i.e., high HFA) constrains FB, which requires broad
 rather than specialized functionality. Further, this relationship suggests
 that HFA effects will not be apparent when communities exhibit high FB and
 therefore decompose all litters well and also when FB is low and
 communities decompose all litters poorly. Overall, our study provides new
 insights into the mechanisms by which microbial communities influence the
 decomposition of leaf litter.
DOI: 10.5061/dryad.tb2rbp02h
title: Watershed DOC uptake occurs mostly in lakes in the summer and in rivers in the winter: The CUPS-OF-DOC model

description: River networks transport dissolved organic carbon (DOC) from terrestrial
 uplands to the coastal ocean. The extent to which a reach or lake within a
 river network uptakes DOC depends on the stream order, the seasonal
 conditions, and the flow. At the watershed scale, it remains unclear
 whether DOC uptake is dominated by biological processes such as
 respiration, or abiotic processes like photomineralization. The
 partitioning of DOC uptake in lakes versus rivers is also unclear. In this
 study, we present a new model that unifies year-round controls on DOC
 cycling for an entire river network, including river-lake connectivity, to
 elucidate the importance of biotic vs. abiotic controls on DOC uptake. We
 present the Catchment Uptake and Sinks by Season, Order, and Flow for DOC
 (CUPS-OF-DOC) model, which quantifies terrestrial DOC loading, gross
 primary productivity (GPP), and uptake via microbes and
 photomineralization. The model is applied to the Connecticut River
 Watershed and accounts for cascading reach- and lake-scale DOC cycling
 across ninety-eight scenarios spanning combinations of flows, seasons, and
 stream orders. We show that riverine DOC uptake is nearly constant with
 stream order, but the proportion of DOC uptake from photomineralization
 varies. Photomineralization dominates in rivers in most flow conditions
 and stream orders, especially in winter, accounting for at least half of
 whole-watershed DOC uptake in February across all flows. Whole-watershed
 summer DOC uptake occurs mostly via biomineralization in lakes, accounting
 for 80% of DOC uptake during the growing season, despite accounting for
 less than 6% of watershed open water surface area.
description: This data contains code and output from the CUPS-OF-DOC model.
 Please refer to the 2023 publication by the same name in Limnology
 & Oceanography for complete methods, doi:
 10.1002/lno.12306.
description: Please see the READ_ME file for instructions on how to run this
 code.
DOI: 10.5281/zenodo.17038011
title: Bacillus cereus group genomes

description: The database contains complete and chromosome level assembled genomes of Bacillus cereus group strains available at NCBI Datasets Genome, downloaded at 2026-01-13  (https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=86661&assembly_level=2:3)
DOI: 10.5281/zenodo.18399429
title: Bacillus cereus group genomes

description: The database contains complete and chromosome level assembled genomes of Bacillus cereus group strains available at NCBI Datasets Genome, downloaded at 2026-01-13  (https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=86661&assembly_level=2:3)
DOI: 10.5061/dryad.k6djh9w87
title: Volatile social environments can favour investments in quality over quantity of social relationships

description: Cooperation does not occur in a vacuum: interactions develop over time in
 social groups that undergo demographic changes. Intuition suggests that
 stable social environments favour developing few but strong reciprocal
 relationships (a 'focused' strategy), while volatile social
 environments favour the opposite: more but weaker social relationships (a
 'diversifying' strategy). We model reciprocal investments under
 a quality-quantity tradeoff for social relationships. We find that
 volatility, counterintuitively, can favour a focused strategy. This result
 becomes explicable through applying the theory of antagonistic pleiotropy,
 originally developed for senescence, to social life. Diversifying
 strategies show superior performance later in life, but with costs paid at
 young ages while the social network is slowly being built. Under volatile
 environments, many individuals die before reaching sufficiently old ages
 to reap the benefits. Social strategies that do well early in life are
 then favoured: a focused strategy leads individuals to form their first
 few social bonds quickly and to make strong use of existing bonds. Our
 model highlights the importance of pleiotropy and population age structure
 for the evolution of cooperative strategies and other social traits, and
 shows that it is not sufficient to reflect on the fate of survivors only,
 when evaluating the benefits of social strategies.
description: Code C++ and R
description: Code to run simulations and
 produce the raw data, and produce the figures. See the README.txt file
 associated with the code for the installation procedure.
DOI: 10.5061/dryad.qbzkh18k3
title: Temporal and interspecific dietary variation in wintering ducks in agricultural landscapes

description: Farmlands are becoming more important as waterfowl foraging habitats,
 while natural wetlands are being lost globally. However, it is unclear how
 waterfowl coexist in agricultural landscapes by resource partitioning. We
 evaluated the diets of seven sympatric dabbling ducks foraging in rice
 paddy and lotus fields around Lake Kasumigaura, the second largest lake in
 Japan, during two wintering seasons (from November to February) by fecal
 DNA metabarcoding using chloroplast trnL and mitochondrial CO1 region
 sequences. We examined 420 fecal samples and found different patterns of
 dietary diversity and composition among the duck species. The pattern also
 differed between plant and invertebrate food. Dietary niche partitioning
 was clear in plant food. Large-bodied ducks intensively use crop plants,
 and other ducks might mediate competition by using terrestrial and aquatic
 plants that are suitable for their foraging behaviors or microhabitats.
 Dietary segregation among species was the most apparent in February, when
 the abundance of foraging ducks was the largest. This study illustrated
 the complex pattern of dietary niche partitioning of dabbling ducks in
 agricultural landscapes, which might be difficult to evaluate by
 conventional approaches. The availability of crop plants, as well as other
 plant food resources in flooded areas and farmland dikes, may enable ducks
 to coexist by spatial or behavioral resource partitioning.