cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6p4f83q
title: Data from: Evolutionary relationships among bullhead sharks (Chondrichthyes: Heterodontiformes)

description: The evolution of modern sharks, skates and rays (Elasmobranchii) is
 largely enigmatic due to their possession of a labile cartilaginous
 skeleton; consequently, taxonomic assignment often depends on isolated
 teeth. Bullhead sharks (Heterodontiformes) are a group of basal
 neoselachians, thus their remains and relationships are integral to
 understanding elasmobranch evolution. Here we fully describe
 †Paracestracion danieli – a bullhead shark from the Late Jurassic
 plattenkalks of Eichstätt, Germany (150–154 Ma) – for its inclusion in
 cladistic analyses (employing parsimonious principles) using morphological
 characters from complete †Paracestracion and Heterodontus fossil specimens
 as well as extant forms of the latter. Results confirm the presence of two
 separate monophyletic clades within Heterodontiformes based on
 predominantly non-dental characters, which show a strong divergence in
 body morphology between †Paracestracion and Heterodontus (the latter
 possessing a first dorsal fin and pectoral fins that are placed more
 anterior and pelvic fins that are placed more posterior). This study
 emphasizes the importance of including non-dental features in
 heterodontiform systematics (as compared to the use of dental characters
 alone) and supports the erection of the family †Paracestracionidae.
 Further, phylogenetic analysis of molecular data from five extant species
 suggests that crown heterodontiforms arose from a diversification event
 42.58 Ma off the west coast of the Americas.
description: Heterodontiform discrete
 character matrix Discrete character
 matrix for heterodontiform cladistic analysis. Heterodontiformes discrete
 character matrix.nex FIG S1
 FIG S1.
 Photograph of a complete fossil heterodontiform, specimen SMNS 11150.
 Scale bar represents 1 cm.   
 Supplementary
 text Supplementary text
 providing a list of specimens examined for morphological character
 assessments, a list of morphological characters and character states for
 cladistic analysis and character distributions using ACCTRAN and DELTRAN
 optimizations.   
 Table S1
 Distance
 measurements taken from extinct and extant heterodontids.
  
 
 Table
 S2 Allometrically scaled
 distance measurements taken from extinct and extant
 heterodontids.
DOI: 10.5061/dryad.8tr03f8
title: Accuracy of de novo assembly of DNA sequences from double‐digest libraries varies substantially among software

description: Advances in DNA sequencing have made it feasible to gather genomic data
 for non-model organisms and large sets of individuals, often using methods
 for sequencing subsets of the genome. Several of these methods sequence
 DNA associated with endonuclease restriction sites (various RAD and GBS
 methods). For use in taxa without a reference genome, these methods rely
 on de novo assembly of fragments in the sequencing library. Many of the
 software options available for this application were originally developed
 for other assembly types and we do not know their accuracy for reduced
 representation libraries. To address this important knowledge gap, we
 simulated data from the Arabidopsis thaliana and Homo sapiens genomes and
 compared de novo assemblies by six software programs that are commonly
 used or promising for this purpose (ABySS, CD-HIT, Stacks, Stacks2, Velvet
 and VSEARCH). We simulated different mutation rates and types of
 mutations, and then applied the six assemblers to the simulated datasets,
 varying assembly parameters. We found substantial variation in software
 performance across simulations and parameter settings. ABySS failed to
 recover any true genome fragments, and Velvet and VSEARCH performed poorly
 for most simulations. Stacks and Stacks2 produced accurate assemblies of
 simulations containing SNPs, but the addition of insertion and deletion
 mutations decreased their performance. CD-HIT was the only assembler that
 consistently recovered a high proportion of true genome fragments. Here,
 we demonstrate the substantial difference in the accuracy of assemblies
 from different software programs and the importance of comparing
 assemblies that result from different parameter settings.
description: Data and scripts to
 reproduce de novo assembly analysisThis directory contains
 all data and scripts necessary to reproduce our analysis of de novo
 assembler performance. We include the scripts to produce simulated reads
 and the reads themselves; the assemblies produced by each assembler for
 each parameter combination and the scripts to produce them; and all
 scripts needed to calculate results.de_novo_assem_scripts_data.tar.gz
DOI: 10.5061/dryad.j4869rd
title: Data from: A quantitative method for inferring locomotory shifts in amniotes during ontogeny, its application to dinosaurs, and its bearing on the evolution of posture

description: Evolutionary transitions between quadrupedal and bipedal postures are
 pivotal to the diversification of amniotes on land, including in our own
 lineage (Hominini). Heterochrony is suggested as a macroevolutionary
 mechanism for postural transitions, but understanding postural evolution
 in deep time is hindered by a lack of methods for inferring posture in
 extinct species. Dinosaurs are an excellent natural laboratory for
 understanding postural transitions, because their lineage contains at
 least four instances of quadrupedality evolving from bipedality, and
 because heterochronic processes have been put forward as an explanatory
 model for these transitions. We extend a quantitative method for reliably
 inferring posture in tetrapods to the study of ontogenetic postural
 transitions, using measurements of proportional limb robusticity. We apply
 this method to ontogenetic series of living and extinct amniotes, with a
 focus on dinosaurs. Our method correctly predicts the general pattern of
 ontogenetic conservation of quadrupedal and bipedal postures in many
 living amniote species and infers the same pattern in some dinosaurs.
 Furthermore, it correctly predicts the ontogenetic postural shift from
 quadrupedal crawling to bipedal walking in humans. We also infer a
 transition from early ontogenetic quadrupedality to late-ontogenetic
 bipedality in the transitional sauropodomorph dinosaur Mussaurus
 patagonicus and possibly in the early branching ceratopsian Psittacosaurus
 lujiatunensis. The phylogenetic positions of these ontogenetic shifts
 suggest that heterochrony may indeed play a role in the macroevolution of
 posture, at least in dinosaurs. Our method has substantial potential for
 testing evolutionary transitions between locomotor modes, especially in
 elucidating the role of evolutionary mechanisms such as heterochrony.
description: S1
 TableMeasurement
 sourcesS2
 TableLog10HC vs Log10FC
 regression coefficientsS3
 TableDFA results using
 femoral and humeral circumferencesS4
 FigsHistograms displaying
 the distribution of the posterior probabilities of being bipedal over the
 10 000 replicates in dinosaurs (using Log10HC and
 Log10FC).S5
 FigureFigure: Log10HL vs
 Log10FL. Line and point colours reflect observed posture during habitual
 locomotion (travel), Homo sapiens in grey. Point shapes reflect posture
 predicted by the DFA. Silhouettes for small, medium and large size class
 bipeds|quadrupeds and dinosaurs.S6
 TableLog10HL vs Log10FL
 regression coefficientsS7
 TableDFA results using
 femoral and humeral lengths
DOI: 10.5061/dryad.m1674h1
title: Data from: The neuropeptide Drosulfakinin regulates social isolation-induced aggression in Drosophila

description: Social isolation strongly modulates behavior across the animal kingdom. We
 utilized the fruit fly Drosophila melanogaster to study social
 isolation-driven changes in animal behavior and gene expression in the
 brain. RNA-seq identified several head-expressed genes strongly responding
 to social isolation or enrichment. Of particular interest, social
 isolation downregulated expression of the gene encoding the neuropeptide
 Drosulfakinin (Dsk), the homologue of vertebrate cholecystokinin (CCK),
 which is critical for many mammalian social behaviors. Dsk knockdown
 significantly increased social isolation-induced aggression. Genetic
 activation or silencing of Dsk neurons each similarly increased
 isolation-driven aggression. Our results suggest a U-shaped dependence of
 social isolation-induced aggressive behavior on Dsk signaling, similar to
 the actions of many neuromodulators in other contexts.
description: 3
 Supplementary Tables related to RNA-seq analysis.
 Supplementary Table S1: Table containing differentially expressed
 genes identified by three different methods of RNA-seq analysis.
 Supplementary Table S2: Table includes Gene Ontology (GO) Terms
 enriched in GH and SH fly heads.  Supplementary Table
 S3: Table comparing differentially expressed genes identified by RNA-seq
 analysis by Agrawal et al. with previously published microarray and
 RNA-seq studies.
DOI: 10.5061/dryad.kk63d49
title: Data from: Spatial encoding in primate hippocampus during free navigation

description: The hippocampus comprises two neural signals – place cells and theta
 oscillations - that contribute to facets of spatial navigation. 
 While their complementary relationship has been well established in
 rodents, their respective contributions in the primate brain during free
 navigation remains unclear.  Here we recorded neural activity in
 the hippocampus of freely-moving marmosets as they naturally explored a
 spatial environment to more explicitly investigate this issue. We report
 place cells in marmoset hippocampus during free-navigation that exhibit
 remarkable parallels to analogous neurons in other mammalian species.
 Although theta oscillations were prevalent in the marmoset hippocampus,
 the patterns of activity were notably different than in other taxa. This
 local field potential oscillation occurred in bouts – rather than
 continuously – and was neither significantly modulated by locomotion nor
 consistently coupled to place cell activity. These findings suggest that
 the relationship between place cell activity and theta oscillations in
 primate hippocampus during free navigation differs substantially from
 rodents and paint an intriguing comparative picture regarding the neural
 basis of spatial navigation across mammals.
description: PLoSBio_Data_01PLoSBio_Data_02PLoSBio_Data_03PLoSBio_Data_04PLoSBio_Data_05PLoSBio_Data_06PLoSBio_Data_07Data_Organization
DOI: 10.5061/dryad.36rn1k2
title: Data from: Validation of a simple extraction procedure for bisphenol A identification from human plasma

description: The general population is exposed to bisphenol A (BPA) orally,
 parenterally, transdermally, and environmentally as a result of the use of
 BPA in food packaging, plastics, and personal care products. The majority
 of the population nowadays (91–99%) has detectable levels of BPA inside
 their body. In this study, we successfully performed an inexpensive,
 rapid, and simple protein precipitation procedure for extraction of BPA
 from human plasma, followed by analysis by LC-MS/MS. This method was
 specifically developed for handling large numbers of samples with minimum
 cost and volume of sample. The developed method was accurate, precise, and
 reproducible for quantification of BPA from human plasma samples in the
 concentration range of 10–2000 ng/mL. The method was performed on samples
 from 150 healthy volunteers who were enrolled in the study. The mean of
 observed BPA level was 2.22 ± 9.91 ng/mL. Higher BPA levels were observed
 for females compare to that of males (p-value = 0.002), the BPA levels
 were higher in participants 33 years of age and older compared to those
 less than 33 years of age (p-value = 0.000), then the BPA levels higher in
 subjects with tap water as source of drinking (p-value = 0.005). This
 method may be valuable for general risk assessment of BPA for a large and
 varied population because of its efficiency and economical aspects.
description: Questionnaire Data Idha
 edit
DOI: 10.5061/dryad.8j8p90s
title: Data from: Constraints on fruit-tracking by birds at the range edge

description: Aims: Biotic interactions may be disrupted at the range boundary if the
 involved species are rare in the most distant sectors. This study assesses
 fruit-tracking by seed-dispersing birds wintering on the border of the
 Palaearctic, a region where many species become scarcer before reaching
 the limits of their distribution in the Sahara. Since vagrancy improves
 fruit-tracking, this study tests if vagrant birds track fruit resources
 better than non-vagrant birds and if their tracking ability is reduced at
 the range edge. Location: The Iberian Peninsula and the Maghreb Methods:
 Seed-dispersing passerines (O. Passeriformes) were counted in 134 sampling
 sites along a 2000 km long latitudinal belt. Relationships between bird
 numbers and latitude, temperature, shrub cover and fruit abundance were
 explored by multivariate analyses. In addition, the habitat matching rule
 was used to assess the ability of birds to track fruit changes along the
 latitudinal belt. Results: Fruit abundance and temperature were the main
 drivers of the distribution of vagrant birds (all of them migratory
 species) while for non-vagrant birds (most of them sedentary species)
 distribution was weakly correlated to the study variables. Vagrant birds
 tracked the spatial-temporal variations in fruit abundance but showed a
 reduced ability to fit numbers to fruit abundance changes in southern
 sectors. Main conclusions: Vagrant, migratory birds are responsible for
 large-scale tracking of fruit outputs but face some constraints on
 fruit-tracking at the far edge of the Palaearctic. Since the movements of
 these birds southwards are declining due to climate warming effects, these
 results suggest a future weakening of their role as seed dispersers in the
 most peripheral areas of the Palaearctic.
description: Bird numbers and
 environmental variablesRaw data on the
 geographical distribution, environmental variables and bird numbers of
 sampling sitesSupplementary_material.txt
DOI: 10.5061/dryad.302jq43
title: Data from: Sleep disordered breathing is associated with brain vascular reactivity in spinal cord injury

description: Objective: Our goal was to determine the population-level odds of
 individuals with SCI experiencing fatigue and sleep apnea, to elucidate
 relationships with level and severity of injury, and to examine
 associations with abnormal cerebrovascular responsiveness. Methods: We
 used population-level data, meta-analyses, and primary physiological
 assessments to provide a large-scale integrated assessment of
 sleep-related complications after SCI. Population-level and meta-analyses
 included more than 60,000 able-bodied individuals and more than 1,800
 individuals with SCI. Physiological assessments were completed on a
 homogenous sample of individuals with cervical SCI, and matched controls.
 We examined the prevalence of 1) self-reported chronic fatigue, 2)
 clinically-identified sleep apnea, and 3) cerebrovascular responsiveness
 to changing CO2. Results: Logistic regression revealed a 7-fold elevated
 odds of chronic fatigue after SCI [OR: 7.9, 95% CI: 3.5-16.2], and that
 fatigue and trouble sleeping are correlated with the level and severity of
 injury. We further show that those with SCI experience elevated risk of
 clinically-defined sleep-disordered breathing in more than 600 individuals
 with SCI [pooled OR: 3.1, 95% CI: 1.3-7.5]. We confirmed that individuals
 with SCI experience a high rate of clinically-defined sleep-apnea using
 primary polysomnography assessments. We then provide evidence using
 syndromic analysis that sleep-disordered breathing is a factor strongly
 associated with impaired cerebrovascular responsiveness to CO2 in patients
 with SCI. Conclusions: Individuals with SCI have an increased prevalence
 of sleep-disordered breathing, which may partially underpin their
 increased risk of stroke. There is thus a need to integrate sleep-related
 breathing examinations into routine care for individuals with SCI.
description: Supplemental
 InformationTable
 e-4Table
 e-5
DOI: 10.5061/dryad.8359820
title: Data from: Movement and habitat selection of the western spadefoot (Spea hammondii) in southern California

description: Agricultural activity, urban development and habitat alteration have
 caused the disappearance of the western spadefoot (Spea hammondii) from
 80% of its geographic range in southern California. Despite the western
 spadefoot’s continuing decline, little research has been conducted on its
 natural history. The home range of adult spadefoots is unknown, and their
 use of upland habitat is poorly understood. Both factors are important for
 the long-term conservation of the species because adult spadefoots spend
 the majority of their lives away from breeding pools in self-excavated
 burrows. Between January 2012 and January 2013, we surgically implanted
 radio transmitters in 15 spadefoots at two locations and recorded their
 movements and habitat use. The mean distance moved between burrow
 locations was 18 m (SD ± 24.1 m, range1 --204 m). The mean distance of
 burrows from the breeding pools was 40 m (SD ± 37.42, range 1–262 m). Rain
 was a significant predictor of spadefoot movement, with more rain
 predicting higher probability of movement and larger distances moved. At
 remote sensing (1 m) scale spadefoots selected grassland habitat for their
 burrow locations. At the microsite scale (&lt; 1 m) spadefoots
 strongly selected duff over grass or shrub cover. Spadefoots burrowed in
 friable, sandy/loam soil with significantly less clay than random
 pseudoabsence points. This research enhances our understanding of a
 little-studied species and will contribute to the development of effective
 management plans for the western spadefoot.
description: Data for movement and
 habitat selection of the western spadefoot (Spea hammondii) in southern
 CaliforniaCSV file containing all
 data for the movement and habitat selection of the western spadefoot (Spea
 hammondii) study in southern California from 2012. Including habitat and
 random point plot data, grain size and loss on ignition data, and movement
 distances versus amount of rain. Actual location data was removed to
 protect the species.ModelAnalysis_20190609.csv
DOI: 10.5061/dryad.f4j0h83
title: Data from: The global biogeography of lizard functional groups

description: Aim - Understanding the mechanisms determining species richness is a
 primary goal of biogeography. Richness patterns of sub-groups within a
 taxon are usually assumed to be driven by similar processes. However, if
 richness of distinct ecological strategies respond differently to the same
 processes, inferences made for an entire taxon may be misleading. We
 deconstruct the global lizard assemblage into functional groups and
 examine the congruence among richness patterns between them. We further
 examine the species richness – functional richness relationship to
 elucidate the way functional diversity contributes to the overall species
 richness patterns. Location – Global. Methods – Using comprehensive
 biological trait databases we classified the global lizard assemblage into
 ecological strategies based on body size, diet, activity times and
 microhabitat preferences, using Archetypal Analysis. We then examined
 spatial gradients in the richness of each strategy at the one-degree grid
 cell, biomes and realm scales. Results – We found that lizards can best be
 characterized by seven ‘ecological strategies’: scansorial, terrestrial,
 nocturnal, herbivorous, fossorial, large and semi-aquatic. There are large
 differences among the global richness patterns of these strategies. While
 the major richness hotspot for lizards in general is in Australia, several
 strategies exhibit highest richness in the Amazon Basin. Importantly, the
 global maximum in lizard species richness is achieved at intermediate
 values of functional diversity and increasing functional diversity further
 result in a shallow decline of species richness. Main conclusions - The
 deconstruction of the global lizard assemblage along multiple ecological
 axes offers a new way to conceive lizard diversity patterns. It suggests
 that local lizard richness mostly increases when species belonging to
 particular ecological strategies become hyper-diverse there, and not
 because more ecological types are present in the most species rich
 localities. Thus maximum richness and maximum ecological diversity do not
 overlap. These results shed light on the global richness pattern of
 lizards, and highlight previously unidentified spatial patterns in
 understudied functional groups.
description: Vidan et al. Appendix
 S5table of all the lizard
 species analysed, their loading on the seven different archetypes, and how
 they were classified in the full analysis ("Archetype", Column
 I), and in the sensitivity analyses omiting data on either body mass
 (column J) or activity time (Column K).
DOI: 10.5061/dryad.h2cp37f
title: Data from: Maze learning and memory in a decapod crustacean

description: Spatial learning is an ecologically important trait well studied in
 vertebrates and a few invertebrates yet poorly understood in crustaceans.
 We investigated the ability of European shore crabs, Carcinus maenas, to
 learn a complex maze over four consecutive weeks using food as a
 motivator. Crabs showed steady improvement during this conditioning period
 in both the time taken to find the food and in the number of wrong turns
 taken whilst doing so. Crabs also clearly remembered the maze as when
 placed back in the maze two weeks later and without any food, they all
 returned to the end of the maze in under eight minutes. Crabs that had not
 been conditioned to the maze (naïve animals) took far longer to reach the
 end and many (42 %) did not venture to the end of the maze at all during
 the one-hour study period. This study provides an initial description of
 spatial learning in a benthic decapod; a better appreciation of this
 adaptive trait in these animals will develop our understanding of resource
 exploitation by benthic crustaceans and their ecological roles.
description: Supporting data for Maze Learning and Memory in a Decapod
 Crustacean - Davies, Gagen and Pope Data for 12 crabs
 (Carcinus maenas) conditioned to a complex maze over 4 weeks in the
 presence of food (weeks 1-4) and then placed in the maze again two weeks
 later (week 6) in the absence of food. Data are also provided for 12 naive
 (unconditioned) crabs placed in the maze without food.
 Davies et al data.xlsx
DOI: 10.5061/dryad.3rn48cm
title: Data from: The effect of conspecific density on honey bee foraging behavior

description: Foraging honey bees (Apis mellifera) seem to use the presence of
 conspecific foragers as cues for flower quality. However, there is
 disagreement regarding how a conspecific cue is perceived by other
 foragers (enhancement or inhibition). Most studies manipulate the total
 number of bees foraging in an arena or the presence or absence of a bee on
 a flower and then observe the behavior of one forager in response to a
 single conspecific, which does not reflect natural foraging. We tested how
 a range of conspecifics on flowers affected on which flowers foraging
 honey bees landed. We trained students from a biology class for non-STEM
 majors to collect data and tested whether the number of conspecifics on
 flowers influences on which flower foragers land. We found that foragers
 land more frequently on flowers occupied by more conspecifics, which
 supports the hypothesis that conspecifics are cues for local enhancement.
 Our results increase our understanding of how honey bees forage once at a
 flower patch.
description: Horna Lowell et al. 2019
 dataWe collected this data
 in the field and transferred it to excel. Please see READ ME file for more
 information.