cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1p55v
title: Data from: Oxygen limitations on marine animal distributions and the collapse of epibenthic community structure during shoaling hypoxia

description: Deoxygenation in the global ocean is predicted to induce ecosystem-wide
 changes. Analysis of multidecadal oxygen time-series projects the
 northeast Pacific to be a current and future hot spot of oxygen loss.
 However, the response of marine communities to deoxygenation is unresolved
 due to the lack of applicable data on component species. We repeated the
 same benthic transect (n = 10, between 45 and 190 m depths) over 8 years
 in a seasonally hypoxic fjord using remotely operated vehicles equipped
 with oxygen sensors to establish the lower oxygen levels at which 26
 common epibenthic species can occur in the wild. By timing our surveys to
 shoaling hypoxia events, we show that fish and crustacean populations
 persist even in severe hypoxia (&lt;0.5 mL L−1) with no mortality
 effects but that migration of mobile species occurs. Consequently, the
 immediate response to hypoxia expansion is the collapse of community
 structure; normally partitioned distributions of resident species
 coalesced and localized densities increased. After oxygen renewal and
 formation of steep oxygen gradients, former ranges re-established. High
 frequency data from the nearby VENUS subsea observatory show the average
 oxygen level at our site declined by ~0.05 mL L−1 year−1 over the period
 of our study. The increased annual duration of the hypoxic (&lt;1.4 mL
 L−1) and severely hypoxic periods appears to reflect the oxygen dynamics
 demonstrated in offshore source waters and the adjacent Strait of Georgia.
 Should the current trajectory of oxygen loss continue, community
 homogenization and reduced suitable habitat may become the dominant state
 of epibenthic systems in the northeast Pacific. In situ oxygen occurrences
 were not congruent with lethal and sublethal hypoxia thresholds calculated
 across the literature for major taxonomic groups indicating that research
 biases toward laboratory studies on Atlantic species are not globally
 applicable. Region-specific hypoxia thresholds are necessary to predict
 future impacts of deoxygenation on marine biodiversity.
description: Animal abundances and
 environment data in Saanich InletData are animal counts
 and environment data collected during remotely operated vehicle imagery
 surveys in Saanich Inlet, Vancouver Island, British Columbia, Canada from
 2006-2013. Each row entry equals a second of annotated ROV video with
 associated metadata (e.g. video file properties), water column data (e.g.
 depth, temperature, oxygen), or species data (presence/absence or counts).
 Extended details can be found with the associated README file. Data was
 collected as part of a PhD thesis (Chu) and is A Canadian Healthy Oceans
 Network Ecosystem Function project, EF-13.CHONe_EF-13_ChuJ_Data_GCB2015.xlsx
DOI: 10.5061/dryad.17n4d
title: Data from: The impact of tropical forest logging and oil palm agriculture on the soil microbiome

description: Selective logging and forest conversion to oil palm agriculture are
 rapidly altering tropical forests. However, functional responses of the
 soil microbiome to these land-use changes are poorly understood. Using 16S
 rRNA gene and shotgun metagenomic sequencing, we compared composition and
 functional attributes of soil biota between unlogged, once-logged and
 twice-logged rainforest, and areas converted to oil palm plantations in
 Sabah, Borneo. Although there was no significant effect of logging
 history, we found a significant difference between the taxonomic and
 functional composition of both primary and logged forests and oil palm.
 Oil palm had greater abundances of genes associated with DNA, RNA, protein
 metabolism and other core metabolic functions, but conversely, lower
 abundance of genes associated with secondary metabolism and cell–cell
 interactions, indicating less importance of antagonism or mutualism in the
 more oligotrophic oil palm environment. Overall, these results show a
 striking difference in taxonomic composition and functional gene diversity
 of soil microorganisms between oil palm and forest, but no significant
 difference between primary forest and forest areas with differing logging
 history. This reinforces the view that logged forest retains most features
 and functions of the original soil community. However, networks based on
 strong correlations between taxonomy and functions showed that network
 complexity is unexpectedly increased due to both logging and oil palm
 agriculture, which suggests a pervasive effect of both land-use changes on
 the interaction of soil microbes.
description: 16S rRNA gene OTU
 table16S rRNA gene
 OTUsM5NR taxonomic profile
 at class levelM5NR taxonomic profile
 at class levelSEED functional profile
 at subsystem level 3Functional gene
 categories at subsystem level 3 (SEED database)Soil chemical
 variablesValues of soil chemical
 variables in different land uses
DOI: 10.5061/dryad.cs6t6
title: Data from: Implementation of complex biological logic circuits using spatially distributed multicellular consortia

description: Engineered synthetic biological devices have been designed to perform a
 variety of functions from sensing molecules and bioremediation to energy
 production and biomedicine. Notwithstanding, a major limitation of in vivo
 circuit implementation is the constraint associated to the use of standard
 methodologies for circuit design. Thus, future success of these devices
 depends on obtaining circuits with scalable complexity and reusable parts.
 Here we show how to build complex computational devices using
 multicellular consortia and space as key computational elements. This
 spatial modular design grants scalability since its general architecture
 is independent of the circuit’s complexity, minimizes wiring requirements
 and allows component reusability with minimal genetic engineering. The
 potential use of this approach is demonstrated by implementation of
 complex logical functions with up to six inputs, thus demonstrating the
 scalability and flexibility of this method. The potential implications of
 our results are outlined.
description: Supporting Information:
 IMPLEMENTATION OF COMPLEX BIOLOGICAL LOGIC CIRCUITS USING SPATIALLY
 DISTRIBUTED MULTICELLULAR CONSORTIASupporting Experimental
 DataSupporting_Information.zip
DOI: 10.5061/dryad.62q6n
title: Data from: Genetic basis of adult migration timing in anadromous steelhead discovered through multivariate association testing

description: Migration traits are presumed to be complex and to involve interaction
 among multiple genes, thus we employed both univariate analyses and
 multivariate Random Forest (RF) machine learning algorithm to conduct
 association mapping of 15,239 single nucleotide polymorphisms (SNPs) for
 adult migration-timing phenotype in steelhead (Oncorhynchus mykiss). Our
 study focused on a model natural population of steelhead that exhibits two
 distinct migration-timing life histories with high levels of admixture in
 nature. Neutral divergence was limited between fish exhibiting summer- and
 winter-run migration owing to high levels of interbreeding, but a
 univariate mixed linear model found three SNPs from a major effect gene to
 be significantly associated with migration-timing (p &lt; 0.000005)
 that explained 46% of trait variation. Alignment to the annotated S. salar
 genome provided evidence that all three SNPs localize within a 46 kb
 region overlapping GREB1-like (an estrogen target gene) on chromosome
 Ssa03. Additionally, multivariate analyses with RF identified that these 3
 SNPs plus 15 additional SNPs explained up to 60% of trait variation. These
 candidate SNPs may provide the ability to predict adult migration-timing
 of steelhead to facilitate conservation management of this species and
 this study demonstrates the benefit of multivariate analyses for
 association studies.
description: TASSLEgeno15239Ind237vfinal_genotype.hmpThe input file of genotypes for the program TASSLE which was used to perform the univariate GWAS for this study.TASSLE_input15239Ind237vfinal_covtraitsThis file contains the population structure individual Q values that were used as trait covariates in the program TASSLE to perform a univariate GWAS. Included are the individual proportions of ancestry using a K=6 and a K=10. For the analyses reported in the study, we used K=10, but we mentioned examining results with K=6 in the supplemental methods.TASSLE_input15239Ind237vfinal_traitsThis file contains additional traits and covariates that were used to perform a univariate GWAS in TASSLE. Covariates include collection "year", and gender (1=male, 2=female). The trait phenotype is listed as "Dayreorder" which represents migration-timing in units of ordinal day as the phenotype. We "re-ordered" these days to reflect the biological sequence of annual steelhead migrations. Refer to the methods in the study for more detail.
DOI: 10.5061/dryad.1rs12
title: Data from: Manipulation of the N-terminal sequence of the Borna disease virus X protein improves its mitochondrial targeting and neuroprotective potential

description: To favor their replication, viruses express proteins that target diverse
 mammalian cellular pathways. Due to the limited size of many viral
 genomes, such proteins are endowed with multiple functions, which require
 targeting to different subcellular compartments. One salient example is
 the X protein of Borna disease virus, which is expressed both at the
 mitochondria and in the nucleus. Moreover, we recently demonstrated that
 mitochondrial X protein is neuroprotective. In this study, we sought to
 examine the mechanisms whereby the X protein transits between subcellular
 compartments and to define its localization signals, to enhance its
 mitochondrial accumulation and thus, potentially, its neuroprotective
 activity. We transfected plasmids expressing fusion proteins bearing
 different domains of X fused to enhanced green fluorescent protein (eGFP)
 and compared their subcellular localization to that of eGFP. We observed
 that the 5–16 domain of X was responsible for both nuclear export and
 mitochondrial targeting and identified critical residues for mitochondrial
 localization. We next took advantage of these findings and constructed
 mutant X proteins that were targeted only to the mitochondria. Such
 mutants exhibited enhanced neuroprotective properties in compartmented
 cultures of neurons grown in microfluidic chambers, thereby confirming the
 parallel between mitochondrial accumulation of the X protein and its
 neuroprotective potential.
description: FerreAncillaryFasebAncillary Data 1 to 4 of the Manuscript by Cécile A; Ferré et al.
DOI: 10.5061/dryad.422sh
title: Data from: The majority of the pre-antiretroviral population who were lost to follow-up stopped their care in Freetown, Sierra Leone: a 12-month prospective cohort study starting with HIV diagnosis

description: Background: The heterogeneity of the pre-antiretroviral (pre-ART)
 population calls for more granular depictions of the cascade of HIV care.
 Methods: We studied a prospective cohort of persons newly diagnosed with
 HIV infection from a single center in Freetown, Sierra Leone, over a
 12-month period and then traced those persons who were lost to follow-up
 (LTFU) during pre-ART care (before ART initiation). ART eligibility was
 based on a CD4 cell count result of &lt; 350 mm/cells and/or WHO
 clinical stage 3 or 4. Persons who attended an appointment in the final
 three months were considered to be retained in care. Adherence to ART was
 measured using pharmacy refill dates. "Effective HIV care" was
 defined as completion of the cascade of care at 12-months regardless of
 whether patients are on ART. Tracing outcomes were obtained for those who
 were LTFU during pre-ART care. Results: 408 persons newly diagnosed with
 HIV infection were screened, 338 were enrolled, and 255 persons were
 staged for ART. ART-ineligible persons had higher retention rates than
 ART-eligible persons (59.6% vs 41.8%, p=0.03). 77 (22.8%) of 338 persons
 received effective HIV care. Most attrition (61.9%) occurred with persons
 during pre-ART care. 123 of 138 persons (89.1%) who were LTFU prior to ART
 initiation were found, and 91 of those 123 (74.0%) were alive. Of the 74
 persons who were alive and described their engagement in care, 40 (54.1%)
 stopped care. Nearly half (42.5%) of those 40 stopped after assessment of
 ART-eligibility but before ART initiation. The main limitation of this
 study was the lack of tracing outcomes for those lost during ART care.
 Conclusions: The majority of the pre-ART LTFU population stopped their
 care, particularly after ART-eligibility but before ART initiation.
 Interventions to hasten ART initiation and retain this at-risk group may
 have significant downstream impact on effective HIV care.
description: STEPS data PLOS
 ONE
DOI: 10.5061/dryad.vp42s
title: Data from: The power and promise of RNA-seq in ecology and evolution

description: Reference is regularly made to the power of new genomic sequencing
 approaches. Using powerful technology, however, is not the same as having
 the necessary power to address a research question with statistical
 robustness. In the rush to adopt new and improved genomic research
 methods, limitations of technology and experimental design may be
 initially neglected. Here, we review these issues with regard to RNA
 sequencing (RNA-seq). RNA-seq adds large-scale transcriptomics to the
 toolkit of ecological and evolutionary biologists, enabling differential
 gene expression (DE) studies in non-model species without the need for
 prior genomic resources. High biological variance is typical of
 field-based gene expression studies and means that larger sample sizes are
 often needed to achieve the same degree of statistical power as clinical
 studies based on data from cell lines or inbred animal models. Sequencing
 costs have plummeted, yet RNA-seq studies still underutilise biological
 replication. Finite research budgets force a trade-off between sequencing
 effort and replication in RNA-seq experimental design. However, clear
 guidelines for negotiating this trade-off, while taking into account
 study-specific factors affecting power, are currently lacking. Study
 designs that prioritise sequencing depth over replication fail to
 capitalise on the power of RNA-seq technology for DE inference.
 Significant recent research effort has gone into developing statistical
 frameworks and software tools for power analysis and sample size
 calculation in the context of RNA-seq DE analysis. We synthesise progress
 in this area and derive an accessible rule-of-thumb guide for designing
 powerful RNA-seq experiments relevant in eco-evolutionary and clinical
 settings alike.
description: RNA-seq expression count
 data for T. bifasciatum forebrainRNA-seq expression data
 for three male and three female bluehead wrasse (T. bifasciatum) forebrain
 samples. Data is presented as a table of raw read counts per transcript
 (rows) in each sample (columns), processed in RSEM.bluehead_3F3M_rawcounts_brain_table.tsvRNA-seq expression count data for T. bifasciatum gonadRNA-seq expression data for three male and three female bluehead wrasse (T. bifasciatum) gonad samples. Data is presented as a table of raw read counts per transcript (rows) in each sample (columns), processed in RSEM.bluehead_3F3M_rawcounts_gonad_table.tsv
DOI: 10.5061/dryad.np6b8
title: Data from: Vegetation as self-adaptive coastal protection: reduction of current velocity and morphologic plasticity of a brackish marsh pioneer

description: By reducing current velocity, tidal marsh vegetation can diminish storm
 surges and storm waves. Conversely, currents often exert high mechanical
 stresses onto the plants and hence affect vegetation structure and plant
 characteristics. In our study, we aim at analysing this interaction from
 both angles. On the one hand, we quantify the reduction of current
 velocity by Bolboschoenus maritimus, and on the other hand, we identify
 functional traits of B. maritimus’ ramets along environmental gradients.
 Our results show that tidal marsh vegetation is able to buffer a large
 proportion of the flow velocity at currents under normal conditions.
 Cross-shore current velocity decreased with distance from the marsh edge
 and was reduced by more than 50% after 15 m of vegetation. We were
 furthermore able to show that plants growing at the marsh edge had a
 significantly larger diameter than plants from inside the vegetation. We
 found a positive correlation between plant thickness and cross-shore
 current which could provide an adaptive value in habitats with high
 mechanical stress. With the adapted morphology of plants growing at the
 highly exposed marsh edge, the entire vegetation belt is able to better
 resist the mechanical stress of high current velocities. This
 self-adaptive effect thus increases the ability of B. maritimus to grow
 and persist in the pioneer zone and may hence better contribute to
 ecosystem-based coastal protection by reducing current velocity.
description: Data Carus et
 alData files contain data
 from velocity measurements in the pioneer zone of the Elbe estuary and
 measured plant traits of Bolboschoenus maritimus.
DOI: 10.5061/dryad.g56f4
title: Data from: Evolutionary implications of mitochondrial genetic variation: Mitochondrial genetic effects on OXPHOS respiration and mitochondrial quantity change with age and sex in fruit flies

description: The ancient acquisition of the mitochondrion into the ancestor of
 modern-day eukaryotes is thought to have been pivotal in facilitating the
 evolution of complex life. Mitochondria retain their own diminutive
 genome, with mitochondrial genes encoding core subunits involved in
 oxidative phosphorylation. Traditionally, it was assumed that there was
 little scope for genetic variation to accumulate and be maintained within
 the mitochondrial genome. However, in the past decade, mitochondrial
 genetic variation has been routinely tied to the expression of
 life-history traits such as fertility, development and longevity. To
 examine whether these broad-scale effects on life-history trait expression
 might ultimately find their root in mitochondrially mediated effects on
 core bioenergetic function, we measured the effects of genetic variation
 across twelve different mitochondrial haplotypes on respiratory capacity
 and mitochondrial quantity in the fruit fly, Drosophila melanogaster. We
 used strains of flies that differed only in their mitochondrial haplotype,
 and tested each sex separately at two different adult ages. Mitochondrial
 haplotypes affected both respiratory capacity and mitochondrial quantity.
 However, these effects were highly context-dependent, with the genetic
 effects contingent on both the sex and the age of the flies. These sex-
 and age-specific genetic effects are likely to resonate across the entire
 organismal life-history, providing insights into how mitochondrial genetic
 variation may contribute to sex-specific trajectories of life-history
 evolution.
description: Alstonville_DryadBarcelona_DryadBrownsville_DryadDahomey_DryadHawaii_DryadIsrael_DryadJapan_DryadMadang_DryadMysore_DryadOregon_DryadPuerto Montt_DryadSweden_Dryad
DOI: 10.5061/dryad.9350r
title: Data from: Testing potential selective agents acting on leaf shape in Ipomoea hederacea: predictions based on an adaptive leaf shape cline

description: Leaf shape is a highly variable phenotype, and is likely influenced by
 many sources of selection. Ipomoea hederacea exhibits an adaptive
 latitudinal cline in leaf shape, which is controlled by a single Mendelian
 locus: lobed individuals dominate the north with entire-shaped individuals
 mostly in the south. We test if the following candidate selective agents,
 suggested by the literature, are responsible for the cline: differential
 insect herbivory, genetic correlations with other clinal traits like
 flowering time and growth rate, and thermoregulatory differences. We
 planted 1680 F3 individuals, segregating for leaf shape, in the north of
 I. hederacea's range, where we expected lobed genotypes to have
 higher fitness. Individuals were assigned to insect removal or control
 treatments, and we scored herbivory, flowering time, growth rate, leaf
 temperature, and fitness (seed number). Herbivory, flowering, and growth
 rate had significant fitness effects, but none differed between leaf
 shapes. Lobed leaves were consistently warmer at night, but no performance
 advantage was detected. Finally, we detected no overall fitness
 differences between leaf shape genotypes, whether we controlled for other
 traits under selection or not. Our data suggest these candidate selective
 agents may not be important contributors to the cline, and alternative
 approaches to understanding the mechanisms maintaining the leaf shape
 cline in I. hederacea may be necessary.
description: Campitelli &
 Stinchcombe 2014 - Raw data allContains all of the raw
 data from this experiment. There are three separate data sheets: Sheet 1
 contains raw quantitative phenotypic data (flowering time, growth rate,
 leaf damage, and fitness), which are described in the paper. Sheet 2
 contains leaf temperature data. Sheet 3 contains data on Fv/Fm
 (photosynthetic efficiency), as well as the corresponding instantaneous
 leaf temperature measurements, both of which are described in the
 paper.
DOI: 10.5061/dryad.cf03b
title: Data from: Origins of cattle on Chirikof Island, Alaska, elucidated from genome-wide SNP genotypes

description: Feral livestock may harbor genetic variation of commercial, scientific,
 historical or esthetic value. The origins and uniqueness of feral cattle
 on Chirikof Island, Alaska, are uncertain. The island is now part of the
 Alaska Maritime Wildlife Refuge and Federal wildlife managers want grazing
 to cease, presumably leading to demise of the cattle. Here we characterize
 the cattle of Chirikof Island relative to extant breeds and discern their
 origins. Our analyses support the inference that Yakut cattle from Russia
 arrived first on Chirikof Island, then ~120 years ago the first European
 taurine cattle were introduced to the island, and finally a large wave of
 Hereford cattle were introduced on average 40 years ago. In addition, this
 mixture of European and East-Asian cattle is unique compared with other
 North American breeds and we find evidence that natural selection in the
 relatively harsh environment of Chirikof Island has further impacted their
 genetic architecture. These results provide an objective basis for
 decisions regarding conservation of the Chirikof Island cattle.
description: Genotypes, SNP, sample,
 and population information for 1,615 cattle from 137
 breedsThis file contains the
 genotypes from 43,018 SNP markers scored in 1,615 cattle. Samples were
 genotyped with the Illumina BovineSNP50 BeadChip. Genotypes were called
 using GenomeStudio. Genotypes were filtered using
 PLINK.DeckerDryad.zip