cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dn498
title: Data from: Comparing herbaceous plant communities in active and passive riparian restoration

description: Understanding the efficacy of passive (reduction or cessation of
 environmental stress) and active (typically involving planting or seeding)
 restoration strategies is important for the design of successful
 revegetation of degraded riparian habitat, but studies explicitly
 comparing restoration outcomes are uncommon. We sampled the understory
 herbaceous plant community of 103 riparian sites varying in age since
 restoration (0 to 39 years) and revegetation technique (active, passive,
 or none) to compare the utility of different approaches on restoration
 success across sites. We found that landform type, percent shade, and
 summer flow helped explain differences in the understory functional
 community across all sites. In passively restored sites, grass and forb
 cover and richness were inversely related to site age, but in actively
 restored sites forb cover and richness were inversely related to site age.
 Native cover and richness were lower with passive restoration compared to
 active restoration. Invasive species cover and richness were not
 significantly different across sites. Although some of our results suggest
 that active restoration would best enhance native species in degraded
 riparian areas, this work also highlights some of the context-dependency
 that has been found to mediate restoration outcomes. For example, since
 the effects of passive restoration can be quite rapid, this approach might
 be more useful than active restoration in situations where rapid dominance
 of pioneer species is required to arrest major soil loss through erosion.
 As a result, we caution against labeling one restoration technique as
 better than another. Managers should identify ideal restoration outcomes
 in the context of historic and current site characteristics (as well as a
 range of acceptable alternative states) and choose restoration approaches
 that best facilitate the achievement of revegetation goals.
description: VegEnv
 data.esg_for_dryadFull data set used for
 paper
DOI: 10.5061/dryad.8jh04
title: Data from: Simulated seal scarer sounds scare porpoises, but not seals: species-specific responses to 12 kHz deterrence sounds

description: Acoustic harassment devices (AHD) or ‘seal scarers’ are used extensively,
 not only to deter seals from fisheries, but also as mitigation tools to
 deter marine mammals from potentially harmful sound sources, such as
 offshore pile driving. To test the effectiveness of AHDs, we conducted two
 studies with similar experimental set-ups on two key species: harbour
 porpoises and harbour seals. We exposed animals to 500 ms tone bursts at
 12 kHz simulating that of an AHD (Lofitech), but with reduced output
 levels (source peak-to-peak level of 165 dB re 1 µPa). Animals were
 localized with a theodolite before, during and after sound exposures. In
 total, 12 sound exposures were conducted to porpoises and 13 exposures to
 seals. Porpoises were found to exhibit avoidance reactions out to ranges
 of 525 m from the sound source. Contrary to this, seal observations
 increased during sound exposure within 100 m of the loudspeaker. We
 thereby demonstrate that porpoises and seals respond very differently to
 AHD sounds. This has important implications for application of AHDs in
 multi-species habitats, as sound levels required to deter less sensitive
 species (seals) can lead to excessive and unwanted large deterrence ranges
 on more sensitive species (porpoises).
description: PorpoiseDataSheet 1: Observation data from the harbour porpoise study at Helgenæs. Sheet 2: Exposure timesSealDataSheet 1: Observation data from the seal study at Anholt. Sheet 2: Exposure timesAnholt_SoundfilesExamples of the signals (first 5 from each trial) recorded on each of the four acoustic recording stations at Anholt, from a subset of the sound trials (trial number: 9,10,14,17,18). Start times of sound exposures can be found in the seal observation excel file. Sound files are named as such: stationname_distance_yyyyymmdd_hhmmssAnholt.zipHelgenaes_SoundfilesExamples of the signals (first 5 from each trial) recorded on each of the four acoustic recording stations at Helgenaes, from a subset of the sound trials (trial number: 9,11-15). Start times of sound exposures can be found in the porpoise observation excel file. Sound files are named as such: stationname_distance_yyyyymmdd_hhmmssHelgenaes.zip
DOI: 10.5061/dryad.95s1k
title: Data from: TSSK6 is required for γH2AX formation and the histone-to-protamine transition during spermiogenesis

description: Spermiogenesis includes transcriptional silencing, chromatin condensation
 and extensive morphological changes as spermatids transform into sperm.
 Chromatin condensation involves histone hyperacetylation, transitory DNA
 breaks, histone H2AX Ser139 phosphorylation (γH2AX), and replacement of
 histones by protamines. Previously, we reported that the spermatid protein
 kinase TSSK6 is essential for fertility in mice, but its specific role in
 spermiogenesis is unknown. Here, we show that TSSK6 expression is
 spatiotemporally coincident with γH2AX formation in nuclei of developing
 mouse spermatids. RNA-Seq analysis demonstrates that genetic ablation of
 Tssk6 does not impact gene expression or silencing in spermatids. However,
 loss of TSSK6 blocks γH2AX formation, even though the timing and level of
 the transient DNA breaks is unaltered. Further, Tssk6 KO sperm contained
 increased histones H3 and H4, and protamine 2 precursor/intermediate(s)
 indicative of a defective histone to protamine transition. These results
 demonstrate that TSSK6 is required for γH2AX formation during
 spermiogenesis, and also link γH2AX to the histone-to-protamine transition
 and male fertility.
description: RNA-Seq data of WT and
 Tssk6 KO spermatidsSpermatids were purified
 from three sets of adult wild type (WT) and Tssk6 knockout (KO), total RNA
 was isolated, RNA-Seq libraries were prepared using Illumina TruSeq
 Stranded mRNA sample preparation kit, and sequenced on Illumina HiSeq
 2500. Quality of raw data was assessed and passed by FastQC and reads were
 mapped to the reference genome (Mus musculus_UCSC_mm10). Cufflinks
 (v2.2.1) was used to estimate transcript levels represented by FPKM
 (fragments per kilo bases per million mapped reads) and differential
 expression between samples was determined by Cuffdiff (v.2.2.1). Student’s
 t-test was performed to calculate the P values.RNA Seq Data_Jha et
 al.xlsx
DOI: 10.5061/dryad.8m2t5
title: Data from: A genetic signature of the evolution of loss of flight in the Galapagos cormorant

description: We have a limited understanding of the genetic and molecular basis of
 evolutionary changes in the size and proportion of limbs. We studied wing
 and pectoral skeleton reduction leading to flightlessness in the Galapagos
 cormorant (Phalacrocorax harrisi). We sequenced and de novo assembled the
 genomes of four cormorant species and applied a predictive and comparative
 genomics approach to find candidate variants that may have contributed to
 the evolution of flightlessness. These analyses and cross-species
 experiments in Caenorhabditis elegans and in chondrogenic cell lines
 implicated variants in genes necessary for transcriptional regulation and
 function of the primary cilium. Cilia are essential for Hedgehog
 signaling, and humans affected by skeletal ciliopathies suffer from
 premature bone growth arrest, mirroring skeletal features associated with
 loss of flight.
description: Cormorant gene
 alignmentNEXUS file used to
 generate the Phylogram in Figure 1 using MrBayesCormorant_alignment.nexCormorant Bayesian PhylogramPhylogram generated using MrbayesCormorant_phylogeny.con.treDCHS1 alignmentDCHS1 alignment (fasta format) for PAML positive selection analysisDCHS1.algDVL1 alignmentDVL1 alignment (fasta format) for PAML positive selection analysisDVL1.algDYNC2H1 alignmentDYNC2H1 alignment (fasta format) for PAML positive selection analysisDYNC2H1.algEVC alignmentEVC alignment (Fasta format) for PAML positive selection analysisEVC.algFAT1 alignmentFAT1 alignment (Fasta format) for PAML positive selection analysisFAT1.algGLI2 alignmentGLI2 alignment (Fasta format) for PAML positive selection analysisGLI2.algGLI3 alignmentGLI3 alignment (Fasta format) for PAML positive selection analysisGLI3.algIFT122 alignmentIFT122 alignment (Fasta format) for PAML positive selection analysisIFT122.algKIF7 alignmentKIF7 alignment (Fasta format) for PAML positive selection analysisKIF7.algOFD1 alignmentOFD1 alignment (Fasta format) for PAML positive selection analysisOFD1.algTALPID3 alignmentTALPID3 alignment (Fasta format) for PAML positive selection analysisTALPID3.algWDR34 alignmentWDR34 alignment (Fasta format) for PAML positive selection analysisWDR34.alg
DOI: 10.5061/dryad.c134g
title: Data from: Atoll-scale patterns in coral reef community structure: Human signatures on Ulithi Atoll, Micronesia

description: The dynamic relationship between reefs and the people who utilize them at
 a subsistence level is poorly understood. This paper characterizes
 atoll-scale patterns in shallow coral reef habitat and fish community
 structure, and correlates these with environmental characteristics and
 anthropogenic factors, critical to conservation efforts for the reefs and
 the people who depend on them. Hierarchical clustering analyses by site
 for benthic composition and fish community resulted in the same 3 major
 clusters: cluster 1–oceanic (close proximity to deep water) and
 uninhabited (low human impact); cluster 2–oceanic and inhabited (high
 human impact); and cluster 3–lagoonal (facing the inside of the lagoon)
 and inhabited (highest human impact). Distance from village, reef exposure
 to deep water and human population size had the greatest effect in
 predicting the fish and benthic community structure. Our study
 demonstrates a strong association between benthic and fish community
 structure and human use across the Ulithi Atoll (Yap State, Federated
 States of Micronesia) and confirms a pattern observed by local people that
 an ‘opportunistic’ scleractinian coral (Montipora sp.) is associated with
 more highly impacted reefs. Our findings suggest that small human
 populations (subsistence fishing) can nevertheless have considerable
 ecological impacts on reefs due, in part, to changes in fishing practices
 rather than overfishing per se, as well as larger global trends. Findings
 from this work can assist in building local capacity to manage reef
 resources across an atoll-wide scale, and illustrates the importance of
 anthropogenic impact even in small communities.
description: benthic composition
 summary dataBenthic surveys of reefs
 in the Atoll of Ulithi, Yap State, Micronesiafish_transects_2012_13_14Fish transects in the Atoll of Ulithi, Yap State, Federated states of Micronesia
DOI: 10.5061/dryad.qb29h
title: Data from: Screening of duplicated loci reveals hidden divergence patterns in a complex salmonid genome

description: A whole-genome duplication (WGD) doubles the entire genomic content of a
 species and is thought to have catalysed adaptive radiation in some
 polyploid-origin lineages. However, little is known about general
 consequences of a WGD because gene duplicates (i.e., paralogs) are
 commonly filtered in genomic studies; such filtering may remove
 substantial portions of the genome in data sets from polyploid-origin
 species. We demonstrate a new method that enables genome-wide scans for
 signatures of selection at both nonduplicated and duplicated loci by
 taking locus-specific copy number into account. We apply this method to
 RAD sequence data from different ecotypes of a polyploid-origin salmonid
 (Oncorhynchus nerka) and reveal signatures of divergent selection that
 would have been missed if duplicated loci were filtered. We also find
 conserved signatures of elevated divergence at pairs of homeologous
 chromosomes with residual tetrasomic inheritance, suggesting that joint
 evolution of some nondiverged gene duplicates may affect the adaptive
 potential of these genes. These findings illustrate that including
 duplicated loci in genomic analyses enables novel insights into the
 evolutionary consequences of WGDs and local segmental gene duplications.
description: Limborg et al.
 2017_MEC-16-1473This file contains three
 sheets with data for PolyFreqs based allele frequency estimates for all
 non-duplicated and all duplicated SNPs as well as co-dominant genotype
 data for all 4,077 non-duplicated SNPs. In this data file population
 samples are also named according to their location so that: Copper River
 resident = COPPL08, Copper River anadromous = TANA09, Columbia River
 resident = MEAD00, Columbia River anadromous = WENAT06.Copper River
 resident = COPPL08, Copper River anadromous = TANA09, Columbia River
 resident = MEAD00, Columbia River anadromous = WENAT06.Data for
 Dryad_MEC-16-1473.xlsx
DOI: 10.5061/dryad.b4c70
title: Data from: Distance sampling with camera traps

description: Reliable estimates of animal density and abundance are essential for
 effective wildlife conservation and management. Camera trapping has proven
 efficient for sampling multiple species, but statistical estimators of
 density from camera trapping data for species that cannot be individually
 identified are still in development. We extend point-transect methods for
 estimating animal density to accommodate data from camera traps, allowing
 researchers to exploit existing distance sampling theory and software for
 designing studies and analysing data. We tested it by simulation, and used
 it to estimate densities of Maxwell's duikers (Philantomba maxwellii)
 in Taï National Park, Côte d'Ivoire. Densities estimated from
 simulated data were unbiased when we assumed animals were not available
 for detection during long periods of rest. Estimated duiker densities were
 higher than recent estimates from line transect surveys, which are
 believed to underestimate densities of forest ungulates. We expect these
 methods to provide an effective means to estimate animal density from
 camera trapping data and to be applicable in a variety of settings.
description: Observed distances from
 camera traps to Maxwell's duikersFilmed Maxwell's
 duikers were assigned to distance intervals; recorded distances are the
 midpoints of the intervals. "Sample.Label" references the trap
 location. "Effort" is temporal effort, i.e. the number of
 2-second time-steps over which the camera operated. "multiplier"
 describes spatial effort, as the proportion of a circle covered by the
 angle of view of the camera. The data is formatted as a
 "flatfile" suitable for use with distance sampling software
 including Distance and associated R packages.DaytimeDistances.txtObserved distances from camera traps to Maxwell's duikers at times of peak activityFilmed Maxwell's duikers were assigned to distance intervals; recorded distances are the midpoints of the intervals. "Sample.Label" references the trap location. "Effort" is temporal effort, i.e. the number of 2-second time-steps over which the camera operated. "multiplier" describes spatial effort, as the proportion of a circle covered by the angle of view of the camera. The data is formatted as a "flatfile" suitable for use with distance sampling software including Distance and associated R packages. This file includes only observations recorded at times of peak activity.PeakDistances.txtStart times of videos of Maxwell's duikersStart times of videos of Maxwell's duikers recorded at camera traps. We included only videos recorded on days when cameras operated, and were not visited by researchers, for the entire day.VideoStartTimes_FullDays.txt
DOI: 10.5061/dryad.q2m2v
title: Data from: A new cynodont from the Santa Maria Formation, south Brazil, improves Late Triassic probainognathian diversity

description: The fossil record of non-mammaliaform probainognathian cynodonts is
 outstanding in the Late Triassic rocks of Brazil and Argentina.
 Approximately 15 genera are known, providing unique insights in the study
 of the major skeletal transformations prior to the mammalian condition.
 Globally, the diversity of probainognathians is possibly
 under-represented, as the discovery of small- to very small-sized taxa
 based on relatively well-preserved specimens is rare. Several species, for
 example much of the Laurasian record, are based on isolated teeth and jaw
 fragments. Here, we describe a new probainognathian from the Late Carnian
 Hyperodapedon Assemblage Zone of the Santa Maria Formation, south Brazil.
 Alemoatherium huebneri gen. et sp. nov. is based on a left lower jaw with
 almost complete dentition that exhibits a combination of features not seen
 in any other known probainognathian. Its slender lower jaw, anterodorsally
 bent process of the dentary, high number of lower incisors, reduced
 canine, triconodont-like postcanine teeth with mesiolingual and
 distolingual cingular cusps are all features that support the inclusion of
 A. huebneri as a member of the Prozostrodontia clade. This new find
 highlights the conspicuous probainognathian cynodont fossil record in
 southern Brazil, with a plethora of forms near the mammalian origin.
description: Supplementary
 Information for Martinelli et alThis file includes: the
 character list (1), the changes in character-states for Therioherpeton
 cargnini (2), the modified data matrix (3), the strict consensus trees of
 three different analyses (4), and photographs of the humerus of T.
 cargnini (5).Supplementary Information
 Martinelli et al.docx
DOI: 10.5061/dryad.j2n8q
title: Data from: Finding a needle in a haystack: distinguishing Mexican maize landraces using a small number of SNPs

description: In Mexico's territory, the center of origin and domestication of
 maize (Zea mays), there is a large phenotypic diversity of this crop. This
 diversity has been classified into “landraces.” Previous studies have
 reported that genomic variation in Mexican maize is better explained by
 environmental factors, particularly those related with altitude, than by
 landrace. Still, landraces are extensively used by agronomists, who
 recognize them as stable and discriminatory categories for the
 classification of samples. In order to investigate the genomic foundation
 of maize landraces, we analyzed genomic data (35,909 SNPs from Illumina
 MaizeSNP50 BeadChip) obtained from 50 samples representing five maize
 landraces (Comiteco, Conejo, Tehua, Zapalote Grande, and Zapalote Chico),
 and searched for markers suitable for landrace assignment. Landrace
 clusters could not be identified taking all the genomic information, but
 they become manifest taking only a subset of SNPs with high FST among
 landraces. Discriminant analysis of principal components was conducted to
 classify samples using SNP data. Two classification analyses were done,
 first classifying samples by landrace and then by altitude category.
 Through this classification method, we identified 20 landrace-informative
 SNPs and 14 altitude-informative SNPs, with only 6 SNPs in common for both
 analyses. These results show that Mexican maize phenotypic diversity can
 be classified in landraces using a small number of genomic markers, given
 the fact that landrace genomic diversity is influenced by environmental
 factors as well as artificial selection due to bio-cultural practices.
description: ScriptsFolder containing the scripts for the analyses presented in the article.Data_and_MetadataFolder containing data for the analyses presented in the article.
DOI: 10.5061/dryad.tj4p2
title: Data from: Optimizing the spatial planning of prescribed burns to achieve multiple objectives in a fire-dependent ecosystem.

description: 1. There is potential for negative consequences for the ecological
 integrity of fire-dependent ecosystems as a result of inappropriate fire
 regimes. This can occur when asset (property) protection is prioritised
 over conservation objectives in burn programs. 2. Optimisation of fire
 management for multiple objectives is rarely undertaken. Here, we use
 integer linear programming to identify burn scheduling solutions that will
 cost-effectively achieve asset protection and conservation objectives. 3.
 An approach to burn scheduling that favours a risk-averse asset protection
 strategy results in poor conservation outcomes. Conversely, a
 conservation-focused approach achieves only modest asset protection
 benefits. However, when formulated as a multi-objective problem, good
 conservation outcomes can be realised with only a small reduction in
 potential benefits for asset protection. 4. A conservation-focused
 approach resulted in substantially more heterogeneity in burns at multiple
 spatial scales and a marked reduction in mean time since fire among all
 forest patches relative to an asset protection scenario. This increase in
 heterogeneity improves ecological integrity, while the resulting reduction
 in fuel load is beneficial for asset protection. 5. Synthesis and
 applications. Mathematical optimisation is a powerful framework for
 informing fire management that improves the prioritisation and scheduling
 of controlled burns to efficiently achieve management objectives. By
 quantifying the trade-offs that exist between the two competing objectives
 of conservation and asset protection we demonstrate that compromise
 solutions can be identified that achieve good outcomes for both
 objectives. In a transparent and equitable manner, we show that
 conservation value may be improved within a fire-dependent ecosystem with
 only modest concession to asset protection performance. Explicitly
 evaluating trade-offs among competing objectives enables managers to
 identify potentially undesirable outcomes, and facilitate development of
 preferred solutions. Heterogeneous burning under the auspices of
 conservation also has the potential to reduce overall fuel loads within
 the ecosystem and thus its value for asset protection is likely
 underappreciated.
description: Attribute
 tableDerived data used for
 analysisAttribute_table.csvPlanning unitsESRI shape file, planning unitsPlanning_units.zip
DOI: 10.5061/dryad.8225n
title: Data from: The magnitude of ivacaftor effects on fluid secretion via R117H-CFTR channels: human in vivo measurements

description: We optically measured effects of orally available ivacaftor (Kalydeco®) on
 sweat rates of identified glands in 3 R117H subjects, each having a unique
 set of additional mutations, and compared them with 5 healthy control
 subjects tested contemporaneously. We injected β-adrenergic agonists
 intradermally to stimulate CFTR-dependent ‘C-sweat’ and methacholine to
 stimulate ‘M-sweat’, which persists in CF subjects. We focused on an
 R117H-7T/F508del subject who produced quantifiable C-sweat off ivacaftor
 and was available for 1 blinded, 3 off ivacaftor, and 3 on ivacaftor
 tests, allowing us to estimate in vivo fold-increase in sweat rates
 produced by ivacaftor’s effect on the open probability (PO) of R117H-CFTR.
 Measured sweat rates must be corrected for sweat losses. With estimated
 sweat losses of 0.023 to 0.08 nl·gland-1·min-1, ivacaftor increased the
 average C-sweat rates 3-7 fold, and estimated function as % of WT were
 4.1-12% off ivacaftor and 21.9-32% on ivacaftor (larger values reflect
 increased loss estimates). Based on single tests, an R117H-7T/ R117H-7T
 subject showed 6-9% WT function off ivacaftor and 28-43% on ivacaftor.
 Repeat testing of an R117H-5T/F508del subject detected only trace
 responding to ivacaftor. We conclude that in vivo, R117H PO is strongly
 increased by ivacaftor, but channel number, mainly determined by variable
 deletion of exon 10, has a marked influence on outcomes.
description: WT gland
 numberingS9 gland
 numberingS10 gland
 numberingS11 gland
 numberingCFTR-R gland
 dataWT gland
 data