cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9rn92
title: Data from: Comparison of dogs and humans in visual scanning of social interaction

description: Previous studies have demonstrated similarities in gazing behaviour of
 dogs and humans, but comparisons under similar conditions are rare, and
 little is known about dogs' visual attention to social scenes. Here,
 we recorded the eye gaze of dogs while they viewed images containing two
 humans or dogs either interacting socially or facing away: the results
 were compared with equivalent data measured from humans. Furthermore, we
 compared the gazing behaviour of two dog and two human populations with
 different social experiences: family and kennel dogs; dog experts and
 non-experts. Dogs' gazing behaviour was similar to humans: both
 species gazed longer at the actors in social interaction than in
 non-social images. However, humans gazed longer at the actors in dog than
 human social interaction images, whereas dogs gazed longer at the actors
 in human than dog social interaction images. Both species also made more
 saccades between actors in images representing non-conspecifics, which
 could indicate that processing social interaction of non-conspecifics may
 be more demanding. Dog experts and non-experts viewed the images very
 similarly. Kennel dogs viewed images less than family dogs, but otherwise
 their gazing behaviour did not differ, indicating that the basic
 processing of social stimuli remains similar regardless of social
 experiences.
description: Tornqvist_et al_human
 & dog data_2015
DOI: 10.5061/dryad.n50t281
title: Data from: Social cues affect quantitative genetic variation and covariation in animal personality traits

description: The social environment is expected to have substantial effects on
 behavior, and as a consequence its heritability and evolvability. We
 investigated these effects by exposing Australian field crickets
 (Teleogryllus oceanicus) to either silence or recordings of male acoustic
 sexual signals. We used a combined pedigree and full-sib/half-sib breeding
 design to estimate the repeatability, heritability, and evolvability of
 behaviors related to boldness, exploration, and activity. All behaviors
 measured were significantly repeatable in both social environments.
 Additionally, most behaviors showed significant heritabilities in the two
 environments. We found no difference in repeatabilities between the silent
 and the acoustic environment but did find significant differences in the
 heritabilities and evolvabilities between these environments. There was a
 high degree of similarity between the phenotypic covariance matrices
 across the two environments, while the genotypic covariance matrices were
 highly dissimilar. Reflecting this, we found significant
 genotype-by-environment interactions for most of the behaviors. Lastly, we
 found that the repeatable aspect of behavior (‘personality’) was
 significantly heritable for most behaviors, but that these heritabilities
 were higher in the acoustic than in the silent environment. We conclude
 that the social environment can have a significant impact on the
 heritability and evolvability of behavior, and argue that evolutionary
 inferences from phenotypic studies should be made with caution.
description: Behavioural trials
 dataThis file includes the
 behavioural measures obtained from behavioural trials conducted 1 week
 apart (first trial = 1, second trial = 2; e.g. Velocity 1 was the velocity
 measured during the first trial), as well as the size (pronotum width)
 measures of each individual. The file also includes all information
 necessary for conducting the quantitative genetic analyses, i.e. sire and
 dam identities. The second tab ('Pedigree') includes the
 pedigree that was used in ASReml for the genetic
 analyses.Rudin et al.
 data.xlsx
DOI: 10.5061/dryad.024bn
title: Data from: Scaling of phloem structure and optimality of photoassimilate transport in conifer needles

description: The phloem vascular system facilitates transport of energy-rich sugar and
 signalling molecules in plants, thus permitting long-range communication
 within the organism and growth of non-photosynthesizing organs such as
 roots and fruits. The flow is driven by osmotic pressure, generated by
 differences in sugar concentration between distal parts of the plant. The
 phloem is an intricate distribution system, and many questions about its
 regulation and structural diversity remain unanswered. Here, we
 investigate the phloem structure in the simplest possible geometry: a
 linear leaf, found, for example, in the needles of conifer trees. We
 measure the phloem structure in four tree species representing a diverse
 set of habitats and needle sizes, from 1 (Picea omorika) to 35 cm (Pinus
 palustris). We show that the phloem shares common traits across these four
 species and find that the size of its conductive elements obeys a power
 law. We present a minimal model that accounts for these common traits and
 takes into account the transport strategy and natural constraints. This
 minimal model predicts a power law phloem distribution consistent with
 transport energy minimization, suggesting that energetics are more
 important than translocation speed at the leaf level.
description: Conifer needle phloem
 geometryThis data contains the
 measurements for phloem geometry (number of sieve tubes, sieve tube area
 as function of distance from the tip) for 3-6 needles of four conifer
 species (Abies nordmanniana, Pinus cembra, Pinus palustris, Picea
 omerika)DataSupplement.zip
DOI: 10.5061/dryad.mq0gb
title: Data from: Fresh Is best: accurate SNP genotyping from koala scats

description: Maintaining genetic diversity is a crucial component in conserving
 threatened species. For the iconic Australian koala, there is little
 genetic information on wild populations that is not either skewed by
 biased sampling methods (e.g. sampling effort skewed towards urban areas)
 or of limited usefulness due to low numbers of microsatellites used. The
 ability to genotype DNA extracted from koala scats using next-generation
 sequencing technology will not only help resolve location sample bias but
 also improve the accuracy and scope of genetic analyses (e.g. neutral
 versus adaptive genetic diversity, inbreeding, and effective population
 size). Here we present the successful SNP genotyping (1272 SNP loci) of
 koala DNA extracted from scat, using a proprietary DArTseq™ protocol. We
 compare genotype results from two day old scat DNA and 14 day old scat DNA
 to a blood DNA template, to test accuracy of scat genotyping. We find that
 DNA from fresher scat results in fewer loci with missing information than
 DNA from older scat, however, 14 day old scat can still provide useful
 genetic information, depending on the research question. We also find that
 a subset of 209 conserved loci can accurately identify individual koalas,
 even from older scat samples. In addition, we find that DNA sequences
 identified from scat samples through the DArTseq™ process can provide
 genetic identification of koala diet species, bacterial and viral
 pathogens, and parasitic organisms.
description: Koala genotypes (1272
 SNP loci)This file contains
 genotype data for the five koalas used in this study. The data is in
 single-row format for 1272 SNP loci identified through DArT-Seq TM
 protocols. The 209 loci used for individual identification testing in our
 paper are identified here, and genotypes are shown for scat and blood DNA
 samples from each koala.Schultz et al Koala SNP
 genotypes.xlsx
DOI: 10.5061/dryad.693pn12
title: Data from: Inbred burying beetles suffer fitness costs from making poor decisions

description: There is a growing interest in how environmental conditions, such as
 resource availability, can modify the severity of inbreeding depression.
 However, little is known about whether inbreeding depression is associated
 with differences in individual decision-making. For example, decisions
 about how many offspring to produce are also often based upon the
 prevailing environmental conditions, such as resource availability, and
 getting these decisions wrong may have important fitness consequences for
 both parents and offspring. We tested for effects of inbreeding on
 individual decision-making in the burying beetle, Nicrophorus
 vespilloides, which uses the size of a carrion resource to make decisions
 about offspring number. Both inbred and outbred females adjusted their
 initial decisions about the number of eggs to lay based on carcass size.
 However, when we forced individuals to update this initial decision by
 providing them with a different-sized carcass partway through
 reproduction, inbred females failed to update their decision about how
 many larvae to cull. Consequently, inbred females reared too many larvae,
 resulting in negative fitness consequences in the form of smaller
 offspring and reduced female post-reproductive condition. Our study
 provides novel insights into the effects of inbreeding by showing that
 poor decision-making by inbred individuals can negatively affect fitness.
description: Data from: Inbred
 burying beetles suffer fitness costs from making poor
 decisionsFile is a spreadsheet
 containing data from an experiment on the effects of inbreeding on
 decision-making in the burying beetle Nicrophorus
 vespilloides.RichardsonCominSmiseth -
 data.csv
DOI: 10.5061/dryad.v4j1p
title: Data from: Beneficiary feedback effects on alpine cushion benefactors become more negative with increasing cover of graminoids and in dry conditions

description: In facilitative interactions, the beneficiary feedback effect (BFE) has
 been defined as the effect of beneficiary species (facilitated species) on
 their benefactor. BFEs have been shown to be dependent on environmental
 conditions and the composition of the beneficiary community. In alpine
 cushion systems, BFEs are more negative with more abundant, diverse and
 phylogenetically aggregated communities of beneficiary species. We tested
 the hypothesis that the functional composition of the beneficiary
 communities correlates with the direction and strength of BFE received by
 alpine cushion benefactors and specifically that a more negative BFE would
 occur with increasing density of graminoids and a more positive BFE would
 occur with increasing density of forbs and legumes. Additionally, we
 predicted that the negative BFE of graminoids would increase with
 increasing summer aridity. We used a data base of alpine cushion
 communities from 30 sites throughout the world to assess the overall
 relationship between the composition of beneficiary communities and the
 total flower density of cushion benefactors, and its variation with
 increasing drought. Additionally, in order to assess more precisely the
 role of the functional composition of the beneficiary communities on BFE
 in a very dry site with cushion benefactors exhibiting contrasting
 functional compositions of beneficiary communities, we also designed a
 field study in the Qilian Shan mountain range (China). At this site with a
 highly continental climate, we compared the number of flowers and fruits
 of different phenotypes of the alpine cushion species Thylacospermum
 caespitosum hosting numerous graminoids, numerous forbs or very few
 beneficiary species. In the intercontinental study, we found a negative
 relationship between graminoids and cushion benefactor flower density but
 no effect of other functional groups. The negative BFE of graminoids
 increased with increasing summer drought. In the dry Qilian Shan range, we
 found both a negative effect of graminoids on total flower density and a
 positive effect of forbs on flower density and fruit set. Our study
 indicates that the context dependence of BFE may be partially explained by
 the composition of beneficiary communities and in particular the negative
 effect of graminoids.
description: Global
 studyExcel data file with the
 data from the intercontinental study.Qilian
 ShanExcel data file with the
 data from the Qilian Shan study site.
DOI: 10.5061/dryad.7tk51
title: Data from: GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown roots systems

description: Root systems develop different root types that individually sense cues
 from their local environment and integrate this information with systemic
 signals. This complex multi-dimensional amalgam of inputs enables
 continuous adjustment of root growth rates, direction and metabolic
 activity that define a dynamic physical network. Current methods for
 analyzing root biology balance physiological relevance with imaging
 capability. To bridge this divide, we developed an integrated imaging
 system called Growth and Luminescence Observatory for Roots (GLO-Roots)
 that uses luminescence-based reporters to enable studies of root
 architecture and gene expression patterns in soil-grown, light-shielded
 roots. We have developed image analysis algorithms that allow the spatial
 integration of soil properties, gene expression and root system
 architecture traits. We propose GLO-Roots as a system that has great
 utility in presenting environmental stimuli to roots in ways that evoke
 natural adaptive responses and in providing tools for studying the
 multi-dimensional nature of such processes.
description: figure_7figure_8figure_6figure_4figure_3figure_2figure_1
DOI: 10.5061/dryad.m3d42
title: Data from: Coordination of fictive motor activity in the larval zebrafish is generated by non-segmental mechanisms

description: The cellular and network basis for most vertebrate locomotor central
 pattern generators (CPGs) is incompletely characterized, but
 organizational models based on known CPG architectures have been proposed.
 Segmental models propose that each spinal segment contains a circuit that
 controls local coordination and sends longer projections to coordinate
 activity between segments. Unsegmented/continuous models propose that
 patterned motor output is driven by gradients of neurons and synapses that
 do not have segmental boundaries. We tested these ideas in the larval
 zebrafish, an animal that swims in discrete episodes, each of which is
 composed of coordinated motor bursts that progress rostrocaudally and
 alternate from side to side. We perturbed the spinal cord using spinal
 transections or strychnine application and measured the effect on fictive
 motor output. Spinal transections eliminated episode structure, and
 reduced both rostrocaudal and side-to-side coordination. Preparations with
 fewer intact segments were more severely affected, and preparations
 consisting of midbody and caudal segments were more severely affected than
 those consisting of rostral segments. In reduced preparations with the
 same number of intact spinal segments, side-to-side coordination was more
 severely disrupted than rostrocaudal coordination. Reducing glycine
 receptor signaling with strychnine reversibly disrupted both rostrocaudal
 and side-to-side coordination in spinalized larvae without disrupting
 episodic structure. Both spinal transection and strychnine decreased the
 stability of the motor rhythm, but this effect was not causal in reducing
 coordination. These results are inconsistent with a segmented model of the
 spinal cord and are better explained by a continuous model in which motor
 neuron coordination is controlled by segment-spanning microcircuits.
description: Rostrocaudal_DelayPeripheral nerve recordings of rostrocaudal delay in reduced spinal cord preparations. The details of the transection and recording locations are listed in the ReadMe file.Side_to_Side_AlternationPeripheral nerve recordings of side-to-side alternation in reduced spinal cord preparations. The details of the transection and recording locations are listed in the ReadMe file.StrychninePeripheral nerve recordings of rostrocaudal delay and side to side alternation in during strychnine wash-in and wash-out. The experimental stage and details of the recording locations are listed in the ReadMe file.Same_SegmentPeripheral nerve recordings of motor output from spinalized larvae reduced spinal cord preparations recorded either in the same body segment or different body segments. The details of the transection and recording locations are listed in the ReadMe file.
DOI: 10.5061/dryad.s95f1
title: Data from: Engineering ER-stress dependent non-conventional mRNA splicing

description: The endoplasmic reticulum (ER) protein folding capacity is balanced with
 the protein folding burden to prevent accumulation of un- or misfolded
 proteins. The ER membrane-resident kinase/RNase Ire1 maintains ER protein
 homeostasis through two fundamentally distinct processes. First, Ire1 can
 initiate a transcriptional response through a non-conventional mRNA
 splicing reaction to increase the ER folding capacity. Second, Ire1 can
 decrease the ER folding burden through selective mRNA decay. In
 Saccharomyces cerevisiae and Schizosaccharomyces pombe, the two Ire1
 functions have been evolutionarily separated. Here, we show that the
 respective Ire1 orthologs have become specialized for their functional
 outputs by divergence of their RNase specificities. In addition, RNA
 structural features separate the splicing substrates from the decay
 substrates. Using these insights, we engineered an S. pombe Ire1 cleavage
 substrate into a splicing substrate, which confers S. pombe with both Ire1
 functional outputs.
description: MegZ03_index13_AGTCAA_1MISS_lowerM_wildtype_polyA_PLUSstrand_COUNTSThis is .WIG file (processed from .fastq files) for DMS-seq data in S. pombe cells (plus strand) (generated by Meghan Zubradt)MegZ03_index13_AGTCAA_1MISS_lowerM_wildtype_polyA_MINUSstrand_COUNTSThis is .WIG file (processed from .fastq files) for DMS-seq data in S. pombe cells (minus strand) (generated by Meghan Zubradt)MegZ03_index13_AGTCAA_L005_R1_001.fastq.gzThis is the unprocessed sequencing .fastq file (compressed) for S. pombe DMS-seq experiment (generated by Meghan Zubradt)
DOI: 10.5061/dryad.54tp8q5
title: Data from: Local fields in human subthalamic nucleus track the lead-up to impulsive choices

description: The ability to adaptively minimize not only motor but cognitive symptoms
 of neurological diseases, such as Parkinson's Disease (PD) and
 obsessive-compulsive disorder (OCD), is a primary goal of next-generation
 deep brain stimulation (DBS) devices. On the basis of studies
 demonstrating a link between beta-band synchronization and severity of
 motor symptoms in PD, the minimization of beta band activity has been
 proposed as a potential training target for closed-loop DBS. At present,
 no comparable signal is known for the impulsive side effects of PD, though
 multiple studies have implicated theta band activity within the
 subthalamic nucleus (STN), the site of DBS treatment, in processes of
 conflict monitoring and countermanding. Here, we address this challenge by
 recording from multiple independent channels within the STN in a
 self-paced decision task to test whether these signals carry information
 sufficient to predict stopping behavior on a trial-by-trial basis. As in
 previous studies, we found that local field potentials (LFPs) exhibited
 modulations preceding self-initiated movements, with power ramping across
 multiple frequencies during the deliberation period. In addition, signals
 showed phasic changes in power around the time of decision. However, a
 prospective model that attempted to use these signals to predict decision
 times showed effects of risk level did not improve with the addition of
 LFPs as regressors. These findings suggest information tracking the
 lead-up to impulsive choices is distributed across multiple frequency
 scales in STN, though current techniques may not possess sufficient
 signal-to-noise ratios to predict—and thus curb—impulsive behavior on a
 moment-to-moment basis.
description: Behavior, spikes, and
 local field potentialsData for Local Fields in
 Human Subthalamic Nucleus Track the Lead-up to Impulsive
 Choicesbart.hdf5
DOI: 10.5061/dryad.pg8q56g
title: Data from: Inter-chromosomal coupling between vision and pigmentation genes during genomic divergence

description: Recombination between loci underlying mate choice and ecological traits is
 a major evolutionary force acting against speciation with gene flow. The
 evolution of linkage disequilibrium between such loci is therefore a
 fundamental step in the origin of species. Here, we show that this process
 can take place in the absence of physical linkage in hamlets—a group of
 closely related reef fishes from the wider Caribbean that differ
 essentially in colour pattern and are reproductively isolated through
 strong visually-based assortative mating. Using full-genome analysis, we
 identify four narrow genomic intervals that are consistently
 differentiated among sympatric species in a backdrop of extremely low
 genomic divergence. These four intervals include genes involved in
 pigmentation (sox10), axial patterning (hoxc13a), photoreceptor
 development (casz1) and visual sensitivity (SWS and LWS opsins) that
 develop islands of long-distance and inter-chromosomal linkage
 disequilibrium as species diverge. The relatively simple genomic
 architecture of species differences facilitates the evolution of linkage
 disequilibrium in the presence of gene flow.
description: READMEMD5 checksums for data
 filesThis file contains the
 checksums to verify file integrity of the data files.MD5.txtHamlet genome annotationThis file contains the genome annotation of the hamlet genome (Hypoplectrus puella).HP.annotation.named.gff.gzPhased genotypes of Caribbean reef fishes (Hypoplectrus sp.)Genotypes of 110 hamlets (H. nigricans, H. puella and H. unicolor). Based on ~24x Illumina sequencing data, created with GATK and phased using SHAPEIT.6_phased_mac2.vcf.gzFst resultsFst results for pairwise population comparisonsfst.tar.gzGxP resultsGxP results for pairwise population comparisonsGxP.tar.gz
DOI: 10.25919/3g08-m977
title: Beaufort River AEM Project Data

description: A compilation of airborne electromagnetic (AEM) survey data for the area surrounding Beaufort River, Western Australia. The AEM data was collected using the SkyTEM 312 system. 

Data have been processed and inverted using stitched 1D layered earth models including induced polarisation effects using Cole-Cole parameters for chargeability, time-constant, and exponent factor.

Included are the processed data and inverted models. Cross sections of the modeled electrical conductivity