cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.wh70rxwjp
title: Female black brant body mass, ninth primary data

description: Body mass declines during wing moult in numerous, but not all, populations
 of Anatidae. We assessed two leading hypotheses for body mass dynamics
 during the wing moult: (1) body mass dynamics are adapted to attain a
 target body mass at the end of the wing moult (restraint hypothesis),
 versus (2) body mass dynamics reflect environmental constraint on the
 nutrient-energy balance during wing moult (constraint hypothesis). We used
 regressions of mass of breeding female Black Brent, Branta bernicla
 nigricans, on ninth primary length (a measure of moult stage) for each of
 16 years to assess mass dynamics during wing moult and used regression
 equations to predict mass at the beginning and end of wing moult each
 year.  We also included gosling mass at 30 days (an indicator of
 forage availability) in models of adult mass to assess how mass dynamics
 varied as a function of foraging conditions. Predicted body mass (± 95%
 CI) at the start of wing moult (ninth primary = 0 mm) varied significantly
 among years ranging from 1032 ± 52g to 1169 ± 27g.  Similarly,
 predicted mass in late wing moult (ninth primary = 142 mm) ranged from
 1048 ± 25g to 1222 ± 28g. Rate of mass gain was significantly related to
 gosling mass at 30 days: interaction between adult ninth primary length
 and gosling mass = 0.0031 ± 0.0020 (P = 0.003). Females initiated wing
 moult at lower body masses, gained mass more rapidly, and ended wing moult
 heaviest when goslings were heaviest. Body mass dynamics of female Black
 Brent during wing moult were consistent with the constraint
 hypothesis.  Positive association between gosling mass and rate
 of body mass gain by adult females during wing moult was also consistent
 with the constraint hypothesis. 
description: Moulting adults and broods were herded into corral traps during
 the adult remigial moult (9th primary <em>x</em>  = 59.56 mm ± 30.62 [SD]) after which we applied metal U. S. Geological Survey bands and uniquely engraved plastic tarsal bands (Sedinger <em>et al.</em> 1997).  We determined sex by cloacal examination and assessed breeding status of female Brent based on the presence or absence of a brood patch (Owen 1980). We measured body mass of goslings and adults using an electronic balance (± 1.0 g, after 2000) or a spring scale (± 10 g, before 2000), and total tarsus and culmen using dial calipers (± 0.1 mm; Dzubin & Cooch 1992).  Goslings had been tagged in their webs with uniquely stamped fish fingerling tags while in the nest (Alliston 1975, Sedinger & Flint 1991) so we knew their age in days.  We measured ninth-primary length (± 1 mm) of female Brent with brood patches on the distal side of the rachis between the ninth and tenth primaries (Dzubin & Cooch 1992, Taylor 1995).  All handling of animals was approved by the Institutional Animal Care and Use Committee of the University of Nevada Reno, most recent protocol no. 00056.
DOI: 10.5061/dryad.2280gb5nt
title: Light organ photosensitivity in deep-sea shrimp may suggest a novel role in counterillumination

description: Extraocular photoreception, the ability to detect and respond to light
 outside of the eye, has not been previously described in deep-sea
 invertebrates. Here, we investigate photosensitivity in the bioluminescent
 light organs (photophores) of deep-sea shrimp, an autogenic system in
 which the organism possesses the substrates and enzymes to produce light.
 Through the integration of transcriptomics, in
 situ hybridization and immunohistochemistry we find evidence for
 the expression of opsins and phototransduction genes known to play a role
 in light detection in most animals. Subsequent shipboard light exposure
 experiments showed ultrastructural changes in the photophore similar to
 those seen in crustacean eyes, providing further evidence that photophores
 are light sensitive. In many deep-sea species, it has long been documented
 that photophores emit light to aid in counterillumination – a dynamic form
 of camouflage that requires adjusting the organ’s light intensity to
 “hide” their silhouettes from predators below. However, it remains a
 mystery how animals fine-tune their photophore luminescence to match the
 intensity of downwelling light. Photophore photosensitivity allows us to
 reconsider the organ’s role in counterillumination - not only in light
 emission but also light detection and regulation.
description: Live specimens (n = 5) were
 preserved in RNAlater and stored at −80 °C. Eye and photophore tissue
 replicates were carefully dissected and homogenized in TRIzol reagent
 (ThermoFisher Scientific). Total RNA was discretely extracted from tissues
 and rDNase (Macherey-Nagel) treated following recommendations in DeLeo et
 al. 2018 (doi: 10.1093/biomethods/bpy012). Libraries were prepared from
 isolated mRNA using the NEBNext Ultra II Directional RNA Library Prep Kit
 for Illumina. Barcoded libraries were size selected (Pippin Prep, Sage
 Science) and sequenced across an Illumina HiSeq4000 lane. Raw sequencing
 data was quality assessed using FastQC to inform quality and adaptor
 trimming with Trimmomatic v0.36. Trimmed reads were processed with
 Rcorrector and BBnorm to error-correct reads and normalize read coverage.
 Trinity v2.6.5 was used to assemble tissue-specific (eye and photophore)
 reference assemblies <i>de novo </i>(minimum contig length of
 200 bp, k-mer size of 23). Contamination was removed from each assembly
 using Kraken v1.0 with default parameters and NCBI’s (Refseq) bacteria,
 archaea and viral databases. Contaminate free assemblies were then passed
 through BBduk and dedupe (BBTools suite, available at:
 http://sourceforge.net/projects/bbmap) to remove duplicate transcripts and
 rRNA.
description: A description of the assemblies can be found in the
 ReadMe.txt
DOI: 10.15468/dl.pzsyye
title: Occurrence Download

description: A dataset containing 646 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Astragalus cusickii"
 ]
}

 The dataset includes 646 records from 56 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002241-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.x0k6djhg2
title: Pasture trees contribute to structural heterogeneity and plant distributions in post-agricultural forests decades after canopy closure

description: Questions: Open-grown shade trees retained in pastures are legacies of
 agricultural history that influence recolonization dynamics and create
 structural heterogeneity in post-agricultural forests. This work addresses
 the long-term influence of pasture trees on forest structure and
 composition. I ask: Do signs of successional nucleation in microhabitat,
 structure and composition near pasture trees persist decades after canopy
 closure? If so, does variation primarily reflect seed deposition or
 environmental facilitation? Location: Southeastern Ohio, USA Methods:
 Thirteen open-grown trees greater than 70 cm in diameter in second-growth
 forests 40-90 years old were selected as study sites. Trees, saplings,
 herbs, and environmental variables were sampled and compared at three
 positions around each tree: under the canopy, at the dripline, and in the
 forest matrix. Results: Soil pH was lower and coarse woody debris most
 abundant under pasture tree canopies. Stems &gt;10 cm in diameter at
 breast height were nearly absent under each focal tree’s canopy and most
 abundant at its dripline. Composition under the canopy was limited to
 shade-tolerant trees, whereas the dripline was characterized by
 vertebrate-dispersed species. Ant-dispersed, adhesive, and unassisted herb
 species were most abundant under embedded pasture trees compared with the
 forest matrix. Discussion: Evidence of nucleation around open-grown trees
 persists for decades after canopy closure. Contrasts in structure and
 composition reflect spatially segregated interactions of competitive
 suppression and facilitation mediated by both dispersal and environment.
 Pasture trees contribute variation in microhabitat, composition, and
 structure to post-agricultural forests, and their retention should be
 encouraged.
DOI: 10.5061/dryad.pg4f4qrk1
title: The skin microbiome facilitates adaptive tetrodotoxin production in poisonous newts

description: Rough-skinned newts (Taricha granulosa) use tetrodotoxin (TTX) to block
 voltage-gated sodium (Nav) channels as a chemical defense against
 predation. Interestingly, newts exhibit extreme population-level variation
 in toxicity attributed to a coevolutionary arms race with TTX-resistant
 predatory snakes, but the source of TTX in newts is unknown. Here, we
 investigated whether symbiotic bacteria isolated from toxic newts could
 produce TTX. We characterized the skin-associated microbiota from a toxic
 and non-toxic population of newts and established pure cultures of
 isolated bacterial symbionts from toxic newts. We then screened bacterial
 culture media for TTX using LC-MS/MS and identified TTX-producing
 bacterial strains from four genera,
 including Aeromonas, Pseudomonas, Shewanella,
 and Sphingopyxis. Additionally, we sequenced the
 Nav channel gene family in toxic newts and found that newts
 expressed Nav channels with modified TTX binding sites, conferring extreme
 physiological resistance to TTX. This study highlights the complex
 interactions among adaptive physiology, animal-bacterial symbiosis, and
 ecological context. 
description: These data were generated from bacterial DNA samples collected
 from wild-caught rough-skinned newts (<em>Taricha
 granulosa</em>). The V4 hypervariable region of the 16S rRNA gene
 was amplified from each bacterial DNA sample, and resulting amplicons were
 sequenced on the Illumina MiSeq v3 platform with
 paired-end 300-bp protocol for 600 cycles. The
 resulting sequence data were assembled and processed using mothur
 (https://www.mothur.org) and the MiSeq SOP protocol
 (https://www.mothur.org/wiki/MiSeq_SOP). Mothur generates a
 "shared" file, which is an OTU abundance table (file:
 newts.OTU.shared). Mothur also generates a taxonomy file, with SILVA rRNA
 database taxonomic classifications for each OTU (file:
 newts.OTU.taxonomy). We manually generated a corresponding metadata file
 (file: newts.OTU.metadata). We also include a processed shared file that
 we used in our analyses, in which singletons and doubletons have been
 removed and each bacterial community sample has been subsampled to 5,000
 seqs/sample.
DOI: 10.5061/dryad.h70rxwdfw
title: An age-dependent ovulatory strategy explains the evolution of dizygotic twinning in humans

description: Dizygotic twinning, the simultaneous birth of siblings when multiple ova
 are released, is an evolutionary paradox. Twin bearing mothers often have
 elevated fitness1-5; but despite twinning being heritable6, twin births
 only occur at low frequencies in human populations7. We resolve this
 paradox by showing that twinning and non-twinning are not competing
 strategies, instead dizygotic twinning is the outcome of an adaptive
 conditional ovulatory strategy of switching from single to double
 ovulation with increasing age. This conditional strategy when coupled with
 the well-known decline in fertility as women age, maximizes reproductive
 success and explains the increase and subsequent decrease in twinning rate
 with maternal age that is observed across human populations8-10. We show
 that the most successful ovulatory strategy would be to always double
 ovulate as an insurance against early fetal loss, but to never bear twins.
 This finding supports the hypothesis that twinning is a byproduct of
 selection for double ovulation rather than twinning.
description: These data are used to generate the figures in the
 manuscript. Figure 1 is a composite data set where
 twinning rates are taken from different populations and fitted with the
 model as described in the ms. Fig 2 are data generated
 from the simulation model. Fig 3 are generated from the
 analytical model The R code is supplied by the authors
 with the request that future users of the code are aware that this is code
 represents an ongoing research enterprise of ours and that they
 contact the authors in a spirit of collaboration (joseph.tomkins@uwa.edu.au). We think that there are lots of interesting things to do with the simulation and we are happy to engage in collaborations and test new ideas. We are currently working on variation within and across populations. The code runs the simulation, numerous replicates of which, with appropriate adjustment to the input variables, are used to generate the data in Figure 2.  The manual is a help file for the code.
description: Because the R code is a simulation where, at numerous stages, the
 probabilities of various events are drawn from distributions, exact
 replication of the Fig 2 data is not anticipated, however the
 <em>pattern </em>should be very similar when numerous runs of
 the simulation are combined.
DOI: 10.5061/dryad.kd51c5b2r
title: Hybridization selects for prime-numbered life cycles in Magicicada: an individual-based simulation model of a structured periodical cicada population

description: We investigate competition between separate periodical cicada populations
 each possessing different life cycle lengths. We build an individual-based
 model to simulate the cicada life cycle and allow random migrations to
 occur between patches inhabited by the different populations. We show that
 if hybridization between different cycle lengths produces offspring that
 have an intermediate life-cycle length, then predation acts
 disproportionately to select against the hybrid offspring. This happens
 because they emerge in low densities without the safety-in-numbers
 provided by either parent population. Thus, prime-numbered life cycles
 that can better avoid hybridization are favored. However, we find that
 this advantage of prime-numbered cycles occurs only if there is some
 mechanism that can occasionally synchronize emergence between local
 populations in sufficiently many patches.
description: This data encompasses all the codes and relevant simulation data
 generated for the analysis in the article "Hybridization selects for
 prime-numbered life cycles in Magicicada: and individual-based simulation
 model of a structured periodical cicada population". The simulations
 were done using Matlab.
description: The .mat-files can be opened using Matlab.
DOI: 10.5061/dryad.wh70rxwjq
title: Characterization of nuclear and mitochondrial genomes of Leptosphaerulina chartarum and Curvularia trifolii and their contributions to phylogenetic implications in the Pleosporales

description: Previous studies reported that symbiont endophytic fungi are widely
 distributed in all tissues of tobacco plants and played important roles.
 It is therefore important to determine the species distribution and
 characteristics of endophytic fungi in tobacco. Here, two parasitic fungi
 Leptosphaerulina chartarum and Curvularia trifolii were isolated from
 normal tobacco tissue, then were used to sequence their nuclear and
 mitogenomes. Finally, we yield 41.68 Mb and 37.95 Mb nuclear genome for C.
 trifolii and L. chartarum with the contig N50 as 638.94 Kb and 284.12 Kb,
 respectively. The average GC content of these two species were 49.74% and
 50.64%. And the C. trifolii and L. chartarum mitochondrial genomes were
 68,926 bp and 59,100 bp long circular molecules with average GC contents
 of 28.60% and 29.31%, respectively. In order to gain additional evidence
 for the classification of C. trifolii and L. chartarum, we calculated the
 evolutionary rate of 7 nuclear and 12 mitochondrial genes and then
 performed phylogenetic analyses. The results showed that the phylogenetic
 trees performed by combining nuclear and mitochondrial genes showed
 similar topologies, only existing tiny difference. Combined with our
 studies, we further confirmed that the phylogenetic relationships of
 endophytic fungi in tobacco is better to construct based on the datasets
 of multi-protein coding genes either from nuclear or mitochondrial
 genomes. These data therefore provide an understanding of the gene content
 and evolutionary history of species within the Pleosporales.
description: Two parasitic fungi <i>Leptosphaerulina chartarum
 </i>and <i>Curvularia trifolii </i>were isolated from
 normal tobacco tissue, then were used to sequence their nuclear and
 mitogenomes on Illumina platform.
DOI: 10.5061/dryad.59zw3r247
title: Ecological traits and the spatial structure of competitive coexistence among carnivores

description: Competition is a widespread interaction among carnivores, ultimately
 manifested through one or more dimensions of the species’ ecological
 niche. One of the most explicit manifestations of competitive interactions
 regards spatial displacement. Its interpretation under a theoretical
 context provides an important tool to deepen our understanding of
 biological systems and communities, but also for wildlife management and
 conservation. We used Bayesian multi-species occupancy models on camera
 trapping data from multiple sites in Southwestern Europe (SWE) to
 investigate competitive interactions within a carnivore guild, and to
 evaluate how species' ecological traits are shaping coexistence
 patterns. Seventeen out of 26 pairwise interactions departed from a
 hypothesis of independent occurrence, with spatial association being twice
 as frequent as avoidance. Association behaviours were only detected among
 mesocarnivores, while avoidance mainly involved mesocarnivores avoiding
 the apex predator (n=4) and mesocarnivore-only interactions (n=2). Body
 mass ratios, defined as the dominant over the subordinate species body
 mass, revealed an important negative effect (β ̂=-0.38
 [〖CI〗_95=-0.81,-0.06]) on co-occurrence probability, and support that
 spatially-explicit competitive interactions are mostly expressed by larger
 species able to dominate over smaller ones, with a threshold in body mass
 ratios of ca. 4, above which local-scale intraguild coexistence is
 unlikely. We found a weak relationship between pairwise trophic niche
 overlap and the probability of coexistence (β ̂=-0.19
 [〖CI〗_95=-0.58,0.21]), suggesting that competition for feeding resources
 may not be a key driver of competition, at least at the scale of our
 analysis. Despite local-scale avoidance, regional-scale coexistence
 appears to be maintained by the spatial structuring of the competitive
 environment. We provide evidence that SWE ecosystems consist of
 spatially-structured competitive environments, and propose that
 coexistence among near-sized species is likely achieved through the
 interplay of “facultative” and “behavioral” character displacements.
 Factors influencing carnivore coexistence likely include context-dependent
 density and trait mediated-effects, which should be carefully considered
 for a sound understanding of the mechanisms regulating these communities.
DOI: 10.5061/dryad.3tx95x6c5
title: Liana communities exhibit different species composition, diversity and community structure across forest types in the Congo Basin

description: Lianas are poorly characterized for central African forests. We quantify
 variation in liana composition, diversity and community structure in
 different forest types in the Yangambi Man and Biosphere Reserve,
 Democratic Republic of Congo. These attributes of liana assemblages were
 examined in 12 1-ha plots, randomly demarcated within regrowth forest,
 old-growth monodominant forest, old-growth mixed forest and old-growth
 edge forest. Using a combination of multivariate and univariate community
 analyses, we visualize the patterns of these liana assemblage attributes
 and/or test for their significant differences across forest types. The
 combined 12 1-ha area contains 2,638 lianas (≥ 2 cm diameter) representing
 105 species, 49 genera and 22 families. Liana species composition differed
 significantly across forest types. Taxonomic diversity was higher in
 old-growth mixed forests compared to old-growth monodominant and regrowth
 forests. Trait diversity was higher than expected in the regrowth forest
 as opposed to the rest of forest types. Similarly, the regrowth forest
 differed from the rest of forest types in the pattern of liana species
 ecological traits and diameter frequency distribution. The regrowth forest
 was also less densely populated in lianas, and had lower liana total basal
 area than the rest of forest types. We speculate that the mechanism of
 liana competitive exclusion by dominant tree species is mainly responsible
 for the lower liana species diversity in monodominant compared to mixed
 forests. We attribute variation in liana community structure between
 regrowth and old-growth forests mostly to short development time of size
 hierarchies.
description: We identified, measured and mapped all liana individuals with
 diameter ≥ 2 cm in 12 1-ha plots, randomly demarcated within regrowth
 forest, old-growth monodominant forest, old-growth mixed forest and
 old-growth edge forest in the Yangambi Man and Biosphere Reserve,
 Democratic Republic of Congo. We assigned 4 ecological traits (climbing
 mechanism, leaf size, regeneration light requirement, diaspore type and
 primary dispersal syndrome) to each identified liana species. Using a
 combination of univariate and multivariate community analyses, we quantify
 variation in liana composition, diversity and community structure in these
 different forest types of the Yangambi Reserve.
DOI: 10.5061/dryad.fttdz08ph
title: Nerve ultrasound for diagnosing chronic inflammatory neuropathy: a multicenter validation study

description: Objective To validate the diagnostic accuracy of a previously described
 short sonographic protocol to identify chronic inflammatory neuropathy
 (CIN), including chronic inflammatory demyelinating polyneuropathy (CIDP),
 Lewis Sumner syndrome (LSS) and multifocal motor neuropathy (MMN) and to
 determine the added value of nerve ultrasound to detect
 treatment-responsive patients compared to nerve conduction studies (NCS)
 in a prospective multicenter study. Methods We included 100 consecutive
 patients clinically suspected of CIN in three centers. The study protocol
 consisted of neurological examination, laboratory tests, NCS and nerve
 ultrasound. We validated a short sonographic protocol (median nerve at
 forearm, upper arm, and C5 nerve root) and determined its diagnostic
 accuracy using the EFNS/PNS criteria of CIDP/MMN (reference standard). In
 addition, to determine the added value of nerve ultrasound in detecting
 treatment-responsive patients, we used previously published diagnostic
 criteria based on clinical, NCS, sonographic findings and treatment
 response (alternative reference standard). Results Sensitivity and
 specificity of the sonographic protocol for CIN according to the reference
 standard were 87.4% and 67.3%, respectively. Sensitivity and specificity
 of this protocol according to the alternative reference standard were
 84.6% and 72.8%, respectively, and of NCS 76.1% and 93.4%. With addition
 of nerve ultrasound 44 diagnoses of CIN were established compared to 33
 diagnoses with NCS alone. Conclusions A short sonographic protocol shows
 high diagnostic accuracy for detecting CIN. Nerve ultrasound is able to
 detect up to 25% more patients who respond to treatment. Classification of
 evidence This multicenter study provides Class IV evidence that nerve
 ultrasound improves diagnosing of CIN.