cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.905qfttq9
title: Data for: Nanopore R10.4.1 LSK114 HG002: subset of 20000 reads in BLOW5 format

description: HG002 (NA24385) is a reference human genome sample used for benchmarking
 and comparing bioinformatics applications. This dataset contains a subset
 of 20,000 reads from the HG002 human reference sample, sequenced using an
 Oxford Nanopore Technologies PromethION sequencer on an R10.4.1 flowcell.
 Sheared DNA libraries (~17Kb) were prepared using the ONT LSK114 ligation
 library prep and an R10.4.1 flow cell was used to generate ~30X genome
 coverage. The original data in the FAST5 format was converted to BLOW5
 format using slow5tools v0.8.0. This is a downsampled subset containing
 20,000 reads in BLOW5 format.
description: Sheared DNA libraries (~17Kb) were prepared using the ONT LSK114
 ligation library prep and a R10.4.1 flow cell was used to generate ~30X
 genome coverage and this is a downsampled subset containing 20,000 reads
 in BLOW5 format. FAST5 data was converted to BLOW5 using slow5tools
 v0.8.0. The uploaded dataset contains a tarball of a merged BLOW5 file and
 a BLOW5 file index. More information on BLOW5 format can be found at https://doi.org/10.1038/s41587-021-01147-4. 
description: Use slow5tools (available: https://github.com/hasindu2008/slow5tools) to view, query and manipulate the dataset. Examples of the use of slow5tools are provided at https://hasindu2008.github.io/slow5tools/.
DOI: 10.5061/dryad.dfn2z356c
title: Data from: Can body mass and skull morphology predict seed and fruit ingestion potential for mammal species? A test using extant species and its application to extinct species

description: Larger animals are assumed to ingest larger seeds and consume larger
 fruits, but empirical studies reveal inconsistent trends between body mass
 and the average size of fruits and seeds ingested. Further, no studies
 have explored seed size relationships with morphological traits, such as
 skull dimensions. Such characteristics might provide more reliable
 estimates of ingestion ability and allow for accurate predictions of seed
 dispersal capacity in species for which we lack empirical data, especially
 extinct species. To determine whether (i) mammalian skull dimensions are
 better predictors of the maximum size of ingested seeds and fruits,
 compared to body mass and (ii) body mass are the better predictors of mean
 fruit and seed sizes, we studied these relationships across three
 mammalian orders: Chiroptera, Primates, and Carnivora. We collected novel
 data on skull dimensions and collated available data on body mass and
 maximum and mean sizes of ingested fruits and seeds for mammals (N=100)
 across the Neotropics, Asia, Africa, and Madagascar. We explored the
 relationships between anatomical traits and fruit and seed sizes of extant
 species and made predictions for five extinct species. Our results
 revealed that body mass and skull dimensions are essential determinants of
 ingested fruit and seed size in mammals. The latter traits can generate
 predictions for extinct species, especially coronoid height and maximum
 jaw gape. Nevertheless, body mass predicted larger ingested fruits and
 seeds than skull dimensions and explained a greater part of the variance
 for both maximum and mean sizes in our dataset. Our results show how body
 mass and cranial anatomy constrain seed size and reinforce the importance
 of maintaining functional diversity in seed dispersers to maintain
 tropical forest structure. We also show that scientists can use
 morphological characteristics to predict the seed dispersal potential of
 extinct mammals allowing better inferences on past and future consequences
 of frugivore extinctions within tropical forests.
description: This dataset represents an
 international collaboration compiling many years of research in the field,
 collecting and measuring seeds/fruits (i.e. 1,100 plant species) ingested
 and consumed by 100 mammal species across the Neotropics (i.e., Central
 and South America) and Paleotropics (i.e., Asia and Africa). In addition,
 we compiled their body masses and measured their skulls from the
 collections of the Paris and London natural history
 museums.
DOI: 10.5061/dryad.8kprr4xsd
title: Palaeoloxodon mitochondrial genome

description: My dataset includes the mitogenomes sequence (bam format file) of two
 Chinese straight-tusked elephants (genus: Palaeoloxodon, sample number:
 CADG1074 and CADG841).
description: We perform DNA extraction, library preparation, pre-sequencing,
 target-enrichment capture and sequencing procedures for fossil samples.
 After obtaining the Illumina raw reads, fastp v0.22.0 was used to trim
 adapters, remove reads shorter than 30 bp, and merge overlapping reads.
 Complete mitochondrial genome of <em>P. antiquus</em> (Genbank
 No: KY499558) was used as mapping references using the ‘aln’ algorithm in
 BWA v0.7.17. Reads with minimum mapping quality score below 30 were
 discarded by running ‘view’ and the remaining ones were sorted from
 5' mapping position by using ‘sort’ in SAMtools v1.9. Potential PCR
 duplicates were removed using “rmdup”, and a final bam format file was
 obtained by merging all libraries using “merge” in SAMtools
 v1.9.
description: The data files will be required to be opened and edited using
 software GENEIOUS v.10 (http://www.geneious.com/).
DOI: 10.5061/dryad.573n5tbc2
title: Data from: The Reissner fiber under tension in vivo shows dynamic interaction with ciliated cells contacting the cerebrospinal fluid

description: The Reissner fiber (RF) is an acellular thread positioned in the midline
 of the central canal that forms together with cerebrospinal fluid
 (CSF)-contacting neurons (CSF-cNs) an axial sensory system detecting
 curvature in the spinal cord. How these components interact is unknown.
 Using in vivo imaging in larval zebrafish, we show that RF is under
 tension and resonates dorsoventrally. Focal RF ablations trigger
 retraction and relaxation of the fiber cut ends, with larger retraction
 speeds for rostral ablations. We built a mechanical model that estimates
 RF stress diffusion coefficient at 10 mm2/s and reveals that tension
 builds up rostrally along the fiber. After RF ablation, CSF-cN spontaneous
 activity decreased and ciliary motility changed, suggesting physical
 interactions between RF and cilia projecting into the central canal. We
 observed that motile cilia were caudally-tilted and frequently interacted
 with RF. We propose that the numerous ependymal motile monocilia
 contribute to RF heterogenous tension via weak interactions. Our work
 demonstrates that under tension, the Reissner fiber dynamically interacts
 with motile cilia generating CSF flow and spinal sensory neurons.
DOI: 10.5061/dryad.dbrv15f5b
title: Data from: A caste differentiation mutant elucidates the evolution of socially parasitic ants

description: Most ant species have two distinct female castes – queens and workers –
 yet the developmental and genetic mechanisms that produce these
 alternative phenotypes remain poorly understood. Working with the clonal
 raider ant, Ooceraea biroi, we discovered a variant strain that expresses
 queen-like traits in individuals that would normally become workers. The
 variants show changes in morphology, behavior, and fitness that cause them
 to rely on workers in wild-type (WT) colonies for survival. Overall, they
 resemble the queens of many obligately parasitic ants that have
 evolutionarily lost the worker caste and live inside colonies of closely
 related hosts. To understand the genetic basis of this variant
 strain, which we term the queen-like mutants (QLM), we re-analyzed
 published PacBio and Hi-C data (McKenzie and Kronauer 2018) using the
 Falcon pipeline. 
description: To improve the
 assembly of Chromosome 13, we re-analyzed published data using the Falcon
 pipeline. First, we ran Falcon-unzip using published PacBio data (McKenzie
 & Kronauer 2018, Genome Biology). This yielded primary (212Mbp,
 322 contigs with N50 of 2.2Mbp) and alternate (67.8Mbp, 2685 contigs with
 N50 of 27.37kbp) assemblies. These assemblies were phased with published
 Hi-C data (McKenzie & Kronauer 2018, Genome Biology) using
 Falcon-phase, and then scaffolded using the NCBI Obir v5.4 genome assembly
 using RaGOO. Finally, this primary assembly, which we refer to as the Obir
 v5.6 assembly, was polished and masked as described previously. These
 assemblies were uploaded as primary_chroms_ragoo.fasta and
 secondary_chroms_ragoo.fasta, respectively.<br><br>Next, we
 performed high molecular weight extractions of O. biroi following a
 published protocol and sequenced two barcoded libraries using the Oxford
 Nanopore PromethION platform. Raw reads were assembled de novo using Flye
 (version 2.8.2) and aligned to the Obir v5.6 contigs using Mauve (snapshot
 2015-02-25). These de novo assemblies were uploaded as assembly_QLM.fasta
 and assembly_WT.fasta, respectively. <br><br>For more details,
 see Trible et al 2023, Current Biology. 
description: The falcon pipeline (falcon-unzip and falcon-phase) and RaGOO
 were used to generate the primary and secondary 5.6 assemblies. RaGOO also
 generated structural variant statistics. Contigs from the de-novo Flye
 assemblies were aligned to the primary RaGOO assembly using
 Mauve.
DOI: 10.5061/dryad.3n5tb2rn6
title: Commodity canola and seed canola visitation and plant data

description: Insect-mediated pollination of crops is an important service to
 agriculture, as increased insect visitation can increase fruit production
 by increasing pollen deposition. Unfortunately, pollination is often
 treated as a “black box”, and pollination management suffers from key
 knowledge gaps that hinder its greater utility, particularly the specific
 mechanisms underlying the processes of visitation, pollination, and fruit
 production. We present a causal model that links insect visitation to
 pollination to three separate components of yield, using field data from
 two types of canola (Brassica napus) production systems. Our results
 demonstrate that yield in commodity canola fields is primarily determined
 by plant size, and we found no relationship between honey bee (Apis
 mellifera) visitation and pollen deposition, or pollen deposition and seed
 yield. In contrast, yield in seed production canola fields was similarly
 controlled by plant size, but there was also a strong relationship between
 alfalfa leafcutting bee (Megachile rotundata) visitation and pollen
 deposition, as well as pollen deposition and seed yield. Leafcutting bee
 visitation in particular strongly increased pollen deposition in seed
 canola fields, whereas honey bee visitation did not. This model serves as
 a step towards a dynamic model of pollination services and highlights the
 relative importance of bee pollination in canola production.
description: Visitation and pollen data were collected from hybrid seed canola
 fields in Alberta, Canada during the summers of 2015 and 2016. Observers
 watched 1m<sup>2</sup> plots for 5 to 10 minutes and recorded
 the number of visits to within each plot. They then sampled stigmas from
 five random flowers and counted the density of flowers and plants per
 m<sup>2</sup>. Stigmas were mounted on slides and
 <em>Brassica</em> pollen was counted. Three plants were
 collected from the same plots at the end of the season; the vegetative
 mass and seed mass were recorded, and seeds per pod and seed mass was
 counted for five pods per plant. Additionally, we counted the number of
 pods per plant, number of primary branches, and the number of pedicels
 without a pod (flower was aborted).<br><br>Similar visitation
 data was collected from commodity canola fields during the summers of 2014
 and 2015 (see https://doi.org/10.5061/dryad.vhhmgqnvj). Three plants were also collected from the same plots at the end of the season, and the same metrics of plant mass, seed mass, and pod counts were recorded.
description: See README.md for column metadata. All missing data are
 represented as NA.
DOI: 10.5061/dryad.vdncjsxzv
title: Symbiotic nitrogen fixation does not stimulate soil phosphatase activity under temperate and tropical trees

description: Symbiotic nitrogen (N)-fixing plants can enrich ecosystems with N, which
 can alter the cycling and demand for other nutrients. Researchers have
 hypothesized that fixed N could be used by plants and soil microbes to
 produce extracellular phosphatase enzymes, which release P from organic
 matter. Consistent with this speculation, the presence of N-fixing plants
 is often associated with high phosphatase activity, either in the soil or
 on root surfaces, although other studies have not found this association,
 and the connection between phosphatase and rates of N fixation—the
 mechanistic part of the argument—is tenuous. Here, we measured soil
 phosphatase activity under N-fixing trees and non-fixing trees
 transplanted and grown in tropical and temperate sites in the USA: two
 sites in Hawaii, and one each in New York and Oregon. This provides a rare
 example of phosphatase activity measured in a multi-site field experiment
 with rigorously quantified rates of N fixation. We found no difference in
 soil phosphatase activity under N-fixing vs. non-fixing trees nor across
 rates of N fixation, though we note that no sites were P limited and only
 one was N limited. Our results add to the literature showing no connection
 between N fixation rates and phosphatase activity.
DOI: 10.5061/dryad.tb2rbp04s
title: Data from: Role of horizontal temperature advection in Arctic surface warming in early spring

description: Extreme Arctic warming scenario is studied with an idealized numerical
 experiment of polar warming. We employ the Community Earth System Model
 version 1.0 (CESM1.0) in this study. The control starts from the rest of
 the data with standard configurations (using a CO2 concentration of 285
 ppm). Overall, the model climate reaches a quasi-equilibrium state after
 1,000 years of integration (Yang et al., 2015). A surface albedo
 perturbation experiment (0.1A) is carried out to achieve global warming
 and AA. During years 1501-2000, 0.1A is “parallel” to control, with the
 same initial conditions at the end of year 1500, and it reaches
 quasi-equilibrium after the 500-year integration. In the numerical result
 study, we focus on the equilibrium responses using the monthly averaged
 fields over the last 200 years of integration. Here we offered SAT
 anomaly, 500 hPa geopotential height, surface wind anomaly, and surface
 horizontal heat advection anomaly.
DOI: 10.5061/dryad.stqjq2c7b
title: Multivariate mapping of ontogeny, taphonomy, and phylogeny to reconstruct problematic fossil taxa

description: Exceptionally preserved fossils of soft-bodied organisms provide unique
 evidence of evolutionary history, but they are often contentious;
 different approaches frequently produce radically different
 reconstructions of taxa and their affinities. Conflict arises due
 to difficulties in disentangling the three non-independent factors that
 underlie all morphological variation within and between fossils: ontogeny,
 taphonomy, and phylogeny. Comparative data from extant organisms can be
 extremely powerful in this context, but is often difficult to apply given
 the multidimensionality of anatomical variation. Here we present a
 multivariate ordination method using discrete morphological character data
 from modern taxa at different ontogenetic and taphonomic stages
 (semaphoront and ‘semataphonts’). Analysing multiple axes of morphological
 variation simultaneously allows us to visualise character combinations
 that are likely to exist in fossil specimens at intersecting stages of
 growth and decay, and thus constrain interpretation of fossils.
 Application to early vertebrates finds variation in fossil specimens to be
 accounted for by all three axes: primarily decay in Mayomyzon, ontogeny in
 Priscomyzon, and phylogeny in ‘euphaneropoids’ and Palaeospondylus. Our
 demonstration of empirical multifactorial variation underscores the need
 for multivariate approaches to fossil interpretation, especially
 non-biomineralized taxa. As such, this conceptual approach provides a new
 method for resolving enigmatic taxa throughout the fossil record.
DOI: 10.5061/dryad.66t1g1k5w
title: Bioacoustic dataset assessing the impact of festival music on bat activity

description: Sound is a critical component of an animal’s habitat, where it is used to
 glean important environmental information from their surroundings. The
 modification of natural soundscapes due to the global rise in
 anthropogenic noise pollution over recent decades can have serious
 negative impacts on species fitness and survival. Nocturnal species such
 as bats are reliant on sound for many aspects of their life history and
 are therefore highly sensitive to anthropogenic noise. Music festivals are
 a source of unregulated and potentially harmful, acute noise pollution
 however they have become ubiquitous across our landscapes throughout the
 summer months and are increasingly being held in settings important for
 wildlife. Using an experimental approach, we provide the first evidence of
 negative impacts of music festivals on bat activity in a habitat that
 represents a typical festival setting i.e. woodland edge. We found that
 loud music playback alone can reduce the activity of bats even in the
 absence of other anthropogenic factors commonly associated with music
 festivals such as lighting and habitat disturbance.  Activity of
 Nyctalus/Eptesicus spp. was reduced along woodland edge habitats exposed
 to loud music whereas no effect was recorded for Myotis spp., P. pygmaeus
 and P. pipistrellus compared to quiet nights. We also provide the first
 evidence of the spatial scale of negative effects from festival music on
 activity for P.pygmaeus as well as highlighting differential responses
 between cryptic species. In light of the paucity of research or guidance
 into acute noise impacts on nocturnal biodiversity, we outline the
 potential negative impacts of music festivals for bats. We show that music
 alone can reduce the activity of bats even in the absence of other
 anthropogenic factors commonly associated with music festivals which could
 potentially fragment important habitats for certain species, leading to a
 degradation of functional connectivity across the landscape.
DOI: 10.5061/dryad.79cnp5j0h
title: Construction of microneedle of Atractylodes macrocephala aqueous extract and effect on mammary gland hyperplasia based on intestinal flora

description: Background: A microneedle patch loaded with Atractylodes macrocephala
 water extract was prepared for the treatment of mammary gland hyperplasia
 to explore the relationship between MGH and intestinal flora. Materials
 and methods: Preparation of the microneedle patch by micromolding method,
 the prescription of the microneedle was optimized by the Box-Behnken
 Design response surface test, and the micro-morphology, penetration,
 toughness, and brittleness were investigated. In vitro release of
 drug-loaded microneedles was measured by diffusion cell method. The rat
 model of mammary gland hyperplasia was prepared by the combination of
 estradiol benzoate-progesterone, and the microneedle patch of Atractylodes
 macrocephala aqueous extract was used for intervention treatment. The
 change of levels in E2, P, and PRL in rat serum was determined. The
 intestinal contents of rats were collected and the changes in intestinal
 flora in MGH rats were analyzed by 16s rRNA high-throughput sequencing.
 Results: The optimized microneedle formula is a PVA concentration of 6.0%,
 HA concentration of 15.5%, and PVPK30 concentration of 16.0%. The prepared
 microneedle tip loaded with Atractylodes macrocephala aqueous extract has
 complete, sharp, and no bubbles and the needle rate of the microneedle
 array is in the range of 95%~100%. The bending rate of the microneedle is
 about 12.7%, and it has good flexibility, and the microneedle can puncture
 4 layers of ParafilmⓇ membrane smoothly, and the puncture rate is more
 than 96%. The in vitro release of the microneedle was characterized by
 rapid release. The results of animal experiments showed that Atractylodes
 macrocephala aqueous extract microneedle patch could significantly reduce
 the E2 level, significantly reduce the PRL level, and significantly
 increase the P level. At the same time, it can regulate the abundance and
 diversity of intestinal flora in MGH rats, improve the intestinal flora
 disorder caused by mammary gland hyperplasia, and balance the community
 structure. Conclusion: The prepared microneedle containing Atractylodes
 macrocephala aqueous extract has good toughness and brittle strength, can
 penetrate the skin and enter the dermis, and effectively deliver drugs to
 play a role in the treatment of mammary gland hyperplasia.
DOI: 10.5061/dryad.t1g1jwt6g
title: Singing on the nest is a widespread behavior in incubating Northern Mockingbirds and increases probability of nest predation

description: In this study, we documented for the first time singing on the nest (SOTN)
 in 74% of 65 Northern Mockingbird (Mimus polyglottos) nests that were
 monitored with continuous-running video cameras (8,353.9 hrs sampled). As
 predicted, higher rates of SOTN significantly decreased daily survival
 rates of nests. SOTN occurred almost exclusively by females during the egg
 stage and in 86% (48/56) of nests for which we had sampling from the egg
 stage. While extensive at the population level, the average rate of SOTN
 per individual was very low (5.24 ± 1.24 s SOTN per hr video sampled). We
 found mixed support for the hypothesis that SOTN functions in territory
 maintenance. We found no support for the hypotheses that SOTN functions to
 coordinate parental care, defend nests, or aid in vocal learning. Given
 the limited attention SOTN has received and the mostly anecdotal accounts
 of it, our understanding of its costs and benefits is lacking. We conclude
 that while individual rates of SOTN are quite low, SOTN may be more
 widespread in populations than previously thought and that studies
 specifically designed to test hypotheses regarding potential functions are
 critically needed.
description: Data were collected from video cameras placed near mockingbird
 nests. A Python program screened the audio tracks from the videos for
 potential instances of singing on the nest (SOTN) and researchers verified
 whether singing occurred. Rate of singing on the nest was calculated by dividing the total SOTN duration in
 seconds by the total hours
 sampled for that nest.
 Likewise, rate of SOTN in different nest stages and at different times of
 day was calculated by dividing the amount of SOTN in sec in each interval
 by the total hours sampled during that interval.