cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.p34h3
title: Data from: Recombination-dependent replication and gene conversion homogenize repeat sequences and diversify plastid genome structure

description: PREMISE OF THE STUDY: There is a misinterpretation in the literature
 regarding the variable orientation of the small single copy region of
 plastid genomes (plastomes). The common phenomenon of small and large
 single copy inversion, hypothesized to occur through intramolecular
 recombination between inverted repeats (IR) in a circular, single
 unit-genome, in fact more likely occurs through recombination-dependent
 replication (RDR) of linear plastome templates. If RDR can be primed
 through both intra- and intermolecular recombination, then this mechanism
 could not only create inversion isomers of so-called single copy regions,
 but also an array of alternative sequence arrangements. METHODS: We used
 Illumina paired-end and PacBio single-molecule real-time (SMRT) sequences
 to characterize repeat structure in the plastome of Monsonia emarginata
 L'Hér. (Geraniaceae). We used OrgConv and inspected nucleotide
 alignments to infer ancestral nucleotides and identify gene conversion
 among repeats and mapped long (&gt;1 kb) SMRT reads against the
 unit-genome assembly to identify alternative sequence arrangements.
 RESULTS: Although M. emarginata lacks the canonical IR, we found that
 large repeats (&gt;1 kilobase; kb) represent ~22% of the plastome
 nucleotide content. Among the largest repeats (&gt;2 kb) we identified
 GC-biased gene conversion and mapping filtered, long SMRT reads to the M.
 emarginata unit-genome assembly revealed alternative, substoichiometric
 sequence arrangements. CONCLUSION: We offer a model based on RDR and gene
 conversion between long repeated sequences in the M. emarginata plastome,
 and provide support that both intra-and intermolecular recombination
 between large repeats, particularly in repeat-rich plastomes, varies
 unit-genome structure while homogenizing the nucleotide sequence of
 repeats.
description: rpl20 repeat
 alignmentMAFFT alignment used to
 generate phylogram. Alignment was trimmed to exclude overhanging sequences
 and used to infer putative gene conversion sites.R20
 alignment.nex3904 PacBio raw reads of
 Monsonia emarginataCorrected PacBio reads
 greater than 1 kbmon_pacbio_3904
DOI: 10.5061/dryad.j4594
title: Data from: Propulsion in hexapod locomotion: how do desert ants traverse slopes?

description: The employment of an alternating tripod gait to traverse uneven terrains
 is a common characteristic shared among many Hexapoda. Because this could
 be one specific cause for their ecological success, we examined the
 alternating tripod gait of the desert ant Cataglyphis fortis together with
 their ground reaction forces and weight-specific leg impulses for level
 locomotion and on moderate (±30 deg) and steep (±60 deg) slopes in order
 to understand mechanical functions of individual legs during inclined
 locomotion. There were three main findings from the experimental data. (1)
 The hind legs acted as the main brake (negative weight-specific impulse in
 the direction of progression) on both the moderate and steep downslopes
 while the front legs became the main motor (positive weight-specific
 impulse in the direction of progression) on the steep upslope. In both
 cases, the primary motor or brake was found to be above the centre of
 mass. (2) Normalised double support durations were prolonged on steep
 slopes, which could enhance the effect of lateral shear loading between
 left and right legs with the presence of direction-dependent attachment
 structures. (3) The notable directional change in the lateral ground
 reaction forces between the moderate and steep slopes implied the
 utilisation of different coordination programs in the extensor–flexor
 system.
description: Woehrl etal 2017
 DATAWoehrl_etal_2017_DATA.zip contains Cataglyphis fortis locomotion data in 1) data.mat (MATLAB Version 8.6.0.267246 R2015b): weight-specific leg impulses at different slopes; ground reaction force; trajectories of petiole, tarsi and neck-thorax joint; body masses; 2) MATLAB script index.m; 3) HTML file with a sample video and figuresWoehrl_etal_2017_DATA.zip
DOI: 10.5061/dryad.fq068
title: Data from: Oilbirds produce echolocation signals beyond their best hearing range and adjust signal design to natural light conditions

description: Oilbirds are active at night, foraging for fruits using keen olfaction and
 extremely light-sensitive eyes, and echolocate as they leave and return to
 their cavernous roosts. We recorded the echolocation behaviour of wild
 oilbirds using a multi-microphone array as they entered and exited their
 roosts under different natural light conditions. During echolocation, the
 birds produced click bursts (CBs) lasting less than 10 ms and consisting
 of a variable number (2–8) of clicks at 2–3 ms intervals. The CBs have a
 bandwidth of 7–23 kHz at −6 dB from signal peak frequency. We report on
 two unique characteristics of this avian echolocation system. First,
 oilbirds reduce both the energy and number of clicks in their CBs under
 conditions of clear, moonlit skies, compared with dark, moonless nights.
 Second, we document a frequency mismatch between the reported best
 frequency of oilbird hearing (approx. 2 kHz) and the bandwidth of their
 echolocation CBs. This unusual signal-to-sensory system mismatch probably
 reflects avian constraints on high-frequency hearing but may still allow
 oilbirds fine-scale, close-range detail resolution at the upper extreme
 (approx. 10 kHz) of their presumed hearing range. Alternatively, oilbirds,
 by an as-yet unknown mechanism, are able to hear frequencies higher than
 currently appreciated.
description: Aripo Cave, single bird,
 exit in darkness.wav file, top
 microphoneAripo_030212_219_ch10top.wavDunstans Cave, single bird, exit in darkness.wav fileDunstansCave_250112_088_ch5_combi.wavDunstans Cave, single bird, exit in moonlight.wav file, centre microphoneDunstans_light_single_exit_14_ch4center.wavDunstans Cave, single bird, enter in darkness.wav file, centre microphoneSingle_Entering_Dunstans_Darkness_250112_082_ch4center.wavDunstans Cave, two birds, exit in darkness.wav file, top microphoneDunstans_2birds_260112_003_ch8top.wavRaw data deposit Oilbird paper.mat files
DOI: 10.5061/dryad.b640d
title: Data from: Muscle-tendon mechanics explain unexpected effects of exoskeleton assistance on metabolic rate during walking

description: The goal of this study was to gain insight into how ankle exoskeletons
 affect the behavior of the plantarflexor muscles during walking. Using
 data from previous experiments, we performed electromyography-driven
 simulations of musculoskeletal dynamics to explore how changes in
 exoskeleton assistance affected plantarflexor muscle–tendon mechanics,
 particularly for the soleus. We used a model of muscle energy consumption
 to estimate individual muscle metabolic rate. As average exoskeleton
 torque was increased, while no net exoskeleton work was provided, a
 reduction in tendon recoil led to an increase in positive mechanical work
 performed by the soleus muscle fibers. As net exoskeleton work was
 increased, both soleus muscle fiber force and positive mechanical work
 decreased. Trends in the sum of the metabolic rates of the simulated
 muscles correlated well with trends in experimentally observed whole-body
 metabolic rate (R2=0.9), providing confidence in our model estimates. Our
 simulation results suggest that different exoskeleton behaviors can alter
 the functioning of the muscles and tendons acting at the assisted joint.
 Furthermore, our results support the idea that the series tendon helps
 reduce positive work done by the muscle fibers by storing and returning
 energy elastically. We expect the results from this study to promote the
 use of electromyography-driven simulations to gain insight into the
 operation of muscle–tendon units and to guide the design and control of
 assistive devices.
description: OpenSim
 Results.mat file that includes
 the data used to produce our figures and results. Data for all subjects
 for the muscles of interest are provided -- averages can be computed as
 needed.DATA_OPENSIM.mat
DOI: 10.5061/dryad.02j5s
title: Data from: Genetic diversity and gene flow decline with elevation in montane mayflies

description: Montane environments around the globe are biodiversity ‘hotspots’ and
 important reservoirs of genetic diversity. Montane species are also
 typically more vulnerable to environmental change than their low-elevation
 counterparts due to restricted ranges and dispersal limitations. Here we
 focus on two abundant congeneric mayflies (Baetis bicaudatus and B.
 tricaudatus) from montane streams over an elevation gradient spanning
 1400 m. Using single-nucleotide polymorphism genotypes, we measured
 population diversity and vulnerability in these two species by: (i)
 describing genetic diversity and population structure across elevation
 gradients to identify mechanisms underlying diversification; (ii)
 performing spatially explicit landscape analyses to identify environmental
 drivers of differentiation; and (iii) identifying outlier loci
 hypothesized to underlie adaptive divergence. Differences in the extent of
 population structure in these species were evident depending upon their
 position along the elevation gradient. Heterozygosity, effective
 population sizes and gene flow all declined with increasing elevation,
 resulting in substantial population structure in the higher elevation
 species (B. bicaudatus). At lower elevations, populations of both species
 are more genetically similar, indicating ongoing gene flow. Isolation by
 distance was detected at lower elevations only, whereas landscape barriers
 better predicted genetic distance at higher elevations. At higher
 elevations, dispersal was restricted due to landscape effects, resulting
 in greater population isolation. Our results demonstrate differentiation
 over small spatial scales along an elevation gradient, and highlight the
 importance of preserving genetic diversity in more isolated high-elevation
 populations.
description: B.bicudatus genepop
 fileBbi.genB. tricaudatus genepop fileBtrAll.genCO_Final_Circuit_Data_S1Landscape resistance data
DOI: 10.5061/dryad.3kj10
title: Data from: Differential responses by stream and riparian biodiversity to in-stream restoration of forestry-impacted streams

description: 1. Forestry can have detrimental impacts on stream ecosystems,
 particularly via excessive sedimentation. A key challenge to stream
 management is therefore to identify the best restoration practices to
 mitigate the harmful impacts of fine sediments on stream biodiversity and
 ecosystem functioning. 2. We studied the effects of restoration of
 sediment-impacted headwater streams on the habitat structure, hydrologic
 retention, biodiversity (microbes, bryophytes, benthic macroinvertebrates,
 riparian plants) and ecosystem functions (periphyton accrual rate and leaf
 breakdown) by comparing four treatments: wood-restored, boulder-restored,
 impacted (by fine sediments) and near-natural streams. The restored
 streams were sampled three to seven years post restoration. Restoration by
 wooden or boulder structures aimed to reduce deposited sediments and
 increase channel heterogeneity and hydraulic retention. 3. Wooden
 structures were ineffective in removing fine bed sediments and did not
 induce positive responses in aquatic biota. Boulder additions reduced
 substrate limitation and thereby proved beneficial for aquatic bryophytes.
 Benthic macroinvertebrates were clearly impaired by sedimentation but
 responded weakly to restoration. Leaf-decomposing microbes and ecosystem
 functions were unresponsive to restoration but neither did they differ
 between near-natural and impacted streams, suggesting that they were
 little harmed by sedimentation. 4. Wood addition enhanced hydraulic
 retention, and riparian plant assemblages along wood-restored streams
 resembled those in near-natural streams, suggesting that increased
 retention re-established a more natural flood regime. By contrast,
 riparian plant assemblages in boulder-restored streams did not differ from
 those in impacted streams. Synthesis and applications. Restoration
 improved several aspects of stream and/or riparian biodiversity, but had
 limited effects on ecosystem functions. Different restoration measures
 resulted in differing biodiversity outcomes: boulder addition was more
 effective at restoring in-stream heterogeneity and aquatic biodiversity,
 whereas wooden structures helped restore channel hydrology and
 retentiveness, and, consequently, riparian vegetation. Therefore applying
 both measures in the restoration of forested headwater streams with
 naturally stony substrates enhances stream habitat variability at the
 watershed scale, providing the most promising scenario for biodiversity
 benefits in broad-scale restoration designs. In-stream restoration that
 increases hydraulic retention has impacts that extend beyond ecosystem
 boundaries, reinforcing the need to restore, manage and protect streams
 and their riparian forests in an integrated effort.
description: Turunen_etal_2017_Journal_of_Applied_EcologyEnvironmental and biological variables.Turunen_etal_2017.xlsx
DOI: 10.5061/dryad.9gc00
title: Data from: Evolutionary ecology of beta-lactam gene clusters in animals

description: Beta-lactam biosynthesis was thought to occur only in fungi and bacteria,
 but we recently reported the presence of isopenicillin N synthase in a
 soil-dwelling animal, Folsomia candida. However, it has remained unclear
 whether this gene is part of a larger beta-lactam biosynthesis pathway and
 how widespread the occurrence of penicillin biosynthesis is among animals.
 Here, we analyzed the distribution of beta-lactam biosynthesis genes
 throughout the animal kingdom and identified a beta-lactam gene cluster in
 the genome of F. candida (Collembola), consisting of isopenicillin N
 synthase (IPNS), δ-(L-α-aminoadipoyl)-L-cysteinyl-D-valine synthetase
 (ACVS), and two cephamycin C genes (cmcI and cmcJ) on a genomic scaffold
 of 0.76 Mb. All genes are transcriptionally active and are inducible by
 stress (heat shock). A beta-lactam compound was detected in vivo using an
 ELISA beta-lactam assay. The gene cluster also contains an ABC transporter
 which is co-regulated with IPNS and ACVS after heat shock. Furthermore, we
 show that different combinations of beta-lactam biosynthesis genes are
 present in over 60% of springtail families but they are absent from
 genome- and transcript libraries of other animals including close
 relatives of springtails (Protura, Diplura, and insects). The presence of
 beta-lactam genes is strongly correlated with an eudaphic (soil-living)
 lifestyle. Beta-lactam genes IPNS and ACVS each form a phylogenetic clade
 in between bacteria and fungi, while cmcI and cmcJ genes cluster within
 bacteria. This suggests a single horizontal gene transfer event most
 probably from a bacterial host, followed by differential loss in more
 recently evolving species.
description: DRYAD_Suring_coll_aaFor a detailed description of the data and data depositiion we refer to the Readme file. This file contains taxonomic names of applied species, library IDs used for transcriptome sequencing, NCBI bioproject codes per dataset including NCBI accession numbers. Also, we provide the number of specimens used for RNA extraction, the locations where these animials were sampled, in which life stage they were during sampling, and at what date they were sampled.
DOI: 10.5061/dryad.qt834
title: Data from: Evidence of a conserved molecular response to selection for increased brain size in primates

description: The adaptive significance of human brain evolution has been frequently
 studied through comparisons with other primates. However, the evolution of
 increased brain size is not restricted to the human lineage but is a
 general characteristic of primate evolution. Whether or not these
 independent episodes of increased brain size share a common genetic basis
 is unclear. We sequenced and de novo assembled the transcriptome from the
 neocortical tissue of the most highly encephalized non-human primate, the
 tufted capuchin monkey (Cebus apella). Using this novel dataset, we
 conducted a genome-wide analysis of orthologous brain-expressed protein
 coding genes to identify evidence of conserved gene-phenotype associations
 and species-specific adaptations during three independent episodes of
 brain size increase. We identify a greater number of genes associated with
 either total brain mass or relative brain size across these 6 species than
 show species-specific accelerated rates of evolution in individual
 large-brained lineages. We test the robustness of these associations in an
 expanded dataset of 13 species, through permutation tests and by analyzing
 how genome-wide patterns of substitution co-vary with brain size. Many of
 the genes targeted by selection during brain expansion have glutamatergic
 functions or roles in cell cycle dynamics. We also identify accelerated
 evolution in a number of individual capuchin genes whose human orthologs
 are associated with human neuropsychiatric disorders. These findings
 demonstrate the value of phenotypically informed genome analyses, and
 suggest at least some aspects of human brain evolution have occurred
 through conserved gene-phenotype associations. Understanding these
 commonalities is essential for distinguishing human-specific selection
 events from general trends in brain evolution.
description: Primate 6-way
 alignmentsThis dataset includes
 4,770 six-way one-to-one orthologs from Cebus apella, published data for
 Homo sapiens, Pongo abelii, Papio anubis, Colobus angolensis and Saimiri
 boliviensis. These alignments are unfiltered PRANK alignments. Dataset
 also includes fasta ortholog files, that include IDs.6sp.zipPrimate 13-way alignmentsThis dataset includes 3,130 13-way one-to-one orthologs from Cebus apella, published data for Homo sapiens, Pongo abelii, Papio anubis, Colobus angolensis, Saimiri boliviensis, Pan troglodytes, Gorilla gorilla, Nomascus leucogenys, Chlorocebus aethiops, Macaca mulatta, Callithrix jacchus, Saguinus midas. These alignments are unfiltered PRANK alignments. Dataset also includes fasta ortholog files, that include IDs.13sp.zip
DOI: 10.5061/dryad.bq124
title: Data from: Estradiol-mediated improvements in adipose tissue insulin sensitivity are related to the balance of adipose tissue estrogen receptor α and β in postmenopausal women

description: We recently demonstrated that short-term estradiol (E2) treatment improved
 insulin-mediated suppression of lipolysis in postmenopausal women, but to
 a greater extent in those who were late compared to early postmenopausal.
 In this follow-up study we tested whether subcutaneous adipose tissue
 (SAT) expression of estrogen receptors (ER) α and β differs between early
 and late postmenopausal women. We further tested whether the balance of
 ERα to ERβ in SAT determined the effect of E2 on SAT insulin sensitivity.
 The present study included 35 women who were ≤6 years past menopause (EPM;
 n = 16) or ≥10 years past menopause (LPM; n = 19). Fasted SAT samples were
 taken following 1-week transdermal E2 treatment or placebo (PL) in a
 random cross-over design. Samples were analyzed for nuclear/cytosolic
 protein content and mRNA expression using Western blot and qPCR,
 respectively. While ESR1 increased slightly (~1.4-fold) following E2
 treatment in both groups, ERα and ERβ protein expression did not differ
 between groups at baseline or in response to E2. However, the balance of
 ERα/ERβ protein in the SAT nuclear fraction increased 10% in EPM compared
 to a 25% decrease in LPM women (group x treatment interaction,
 p&lt;0.05). A greater proportion of ERα/ERβ protein in the nuclear
 fraction of SAT at baseline (placebo day) was associated with greater
 reduction in SAT insulin resistance (i.e., better suppression of
 lipolysis, EC50) in response to E2 (r = -0.431, p&lt;0.05). In
 conclusion, there do not appear to be differences in the proportion of
 adipose tissue ERα/ERβ protein in late, compared to early, postmenopausal
 women. However, the balance of ERα/ERβ may be important for E2-mediated
 improvement in adipose tissue insulin sensitivity.
description: Fig 1A ERa nuclear and
 cytoFig 1A ERb
 cytoFig 1A ERb
 nuclearFig 1B aTubulin nuclear
 and cytoFig 1C bActin
 cytoFig 1C bActin
 nuclearFig 1C ERa cyto
 (1)Fig 1C ERa cyto
 (2)Fig 1C ERa nuclear
 (1)Fig 1C ERa nuclear
 (2)Fig 1C ERb
 cytoFig 1C ERb nuclear
 (1)Fig 1C ERb nuclear
 (2)Fig 2A EPM
 E2Fig 2A EPM
 PLFig 2A LPM
 E2Fig 2A LPM
 PLS1
 FigureTEMPUS AT ms_MasterData
 v022317
DOI: 10.5061/dryad.6g2c7
title: Data from: Testing the association of phenotypes with polyploidy: An example using herbaceous and woody eudicots

description: Although numerous studies have surveyed the frequency with which different
 plant characters are associated with polyploidy, few statistical tools are
 available to identify the factors that potentially facilitate polyploidy.
 We describe a new probabilistic model, BiChroM, designed to associate the
 frequency of polyploidy and chromosomal change with a binary phenotypic
 character in a phylogeny. BiChroM provides a robust statistical framework
 for testing differences in rates of polyploidy associated with phenotypic
 characters along a phylogeny while simultaneously allowing for
 evolutionary transitions between character states. We used BiChroM to test
 whether polyploidy is more frequent in woody or herbaceous plants, based
 on tree with 4,711 eudicot species. Although polyploidy occurs in woody
 species, rates of chromosome doubling were over six times higher in
 herbaceous species. Rates of single chromosome increases or decreases were
 also far higher in herbaceous than woody species. Simulation experiments
 indicate that BiChroM performs well with little to no bias and relatively
 little variance at a wide range of tree depths when trees have at least
 500 taxa. Thus, BiChroM provides a first step towards a rigorous
 statistical framework for assessing the traits that facilitate polyploidy.
description: BiChroM Raw R
 Files1. Dataset and tree 2.
 Raw R files for optimizations 3. Full model optimizations 4. Reduced model
 optimizations 5. Profile rhoH and Profile rhoW 6. Bivariate profile rhoqH
 and Bivariate profile rhoqW 7. Raw R files for simulations 8. Simulations
 number of taxa 9. Simulations for tree heightBiChroMRawRfiles.zip
DOI: 10.5061/dryad.n0s75
title: Data from: Zinc is a potent and specific inhibitor of IFN-λ3 signalling

description: Lambda interferons (IFNL, IFN-λ) are pro-inflammatory cytokines important
 in acute and chronic viral infection. Single-nucleotide polymorphisms
 rs12979860 and rs8099917 within the IFNL gene locus predict hepatitis C
 virus (HCV) clearance, as well as inflammation and fibrosis progression in
 viral and non-viral liver disease. The underlying mechanism, however, is
 not defined. Here we show that the rs12979860 CC genotype correlates with
 increased hepatic metallothionein expression through increased systemic
 zinc levels. Zinc interferes with IFN-λ3 binding to IFNL receptor 1
 (IFNLR1), resulting in decreased antiviral activity and increased viral
 replication (HCV, influenza) in vitro. HCV patients with high zinc levels
 have low hepatocyte antiviral and inflammatory gene expression and high
 viral loads, confirming the inhibitory role of zinc in vivo. We provide
 the first evidence that zinc can act as a potent and specific inhibitor of
 IFN-λ3 signalling and highlight its potential as a target of therapeutic
 intervention for IFN-λ3-mediated chronic disease.
description: Liver Biopsy
 MicroarrayThis data represents
 gene expression from genotype 1 HCV infected liver biopsies using an
 Illumina microarray. All data has been normalized.Array.xlsx