cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5m3338v
title: Data from: Drivers of spatio-temporal patterns of salinity in Spanish rivers: a nationwide assessment

description: The salinization of freshwaters is a global water quality problem that
 leads to the biological degradation of aquatic ecosystems. However, little
 is known about the spatial extent of freshwater salinization and the
 relative contribution of each human activity (e.g. agriculture,
 urbanization, mining or shale-gas extraction). Here, we investigated
 environmental factors that explain spatio-temporal patterns of water
 salinity and examined the causes, the extent and the degree of
 salinization of Spanish rivers. Results showed a strong variation in water
 salinity among river typologies and between river reaches in good and poor
 ecological status according to the Water Framework Directive. The
 variation in water salinity was largely explained by a combination of
 natural (i.e. climate and geology) and anthropogenic (i.e. land use)
 factors. By contrast, land use factors as urbanization and agriculture
 were the main drivers of salinization, which affected more than one
 quarter of the rivers and streams in Spain, especially those in the most
 arid regions (central and southern regions) and in the main courses of the
 largest rivers such as the Ebro, Douro and Tajo rivers. The information
 provided here can be relevant to set priority regions and actions to
 ameliorate freshwater salinization.
description: Spain_Conductivity_DatasetR codes and datasets necessary to analyses spatio-temporal patterns of water conductivity in Spanish rivers
DOI: 10.5061/dryad.d9p7h
title: Data from: Estimation of effective population size in continuously distributed populations: there goes the neighborhood

description: Use of genetic methods to estimate effective population size (N^e) is
 rapidly increasing, but all approaches make simplifying assumptions
 unlikely to be met in real populations. In particular, all assume a
 single, unstructured population, and none has been evaluated for use with
 continuously distributed species. We simulated continuous populations with
 local mating structure, as envisioned by Wright's concept of
 neighborhood size (NS), and evaluated performance of a single-sample
 estimator based on linkage disequilibrium (LD), which provides an estimate
 of the effective number of parents that produced the sample (N^b). Results
 illustrate the interacting effects of two phenomena, drift and mixture,
 that contribute to LD. Samples from areas equal to or smaller than a
 breeding window produced estimates close to the NS. As the sampling window
 increased in size to encompass multiple genetic neighborhoods, mixture LD
 from a two-locus Wahlund effect overwhelmed the reduction in drift LD from
 incorporating offspring from more parents. As a consequence, N^b never
 approached the global N^e, even when the geographic scale of sampling was
 large. Results indicate caution is needed in applying standard methods for
 estimating effective size to continuously distributed populations.
description: bw1ldneEffective population size estimates from LDNE and population genetic summary values for all Sample Window Sizes and Breeding Window 2.bw2ldnebw3ldneEffective population size estimates from LDNE and population genetic summary values for all Sample Window Sizes and Breeding Window 3.b4ldne
DOI: 10.5061/dryad.h11h7
title: Data from: Long livestock farming history and human landscape shaping revealed by lake sediment DNA

description: The reconstruction of human-driven, Earth-shaping dynamics is important
 for understanding past human/environment interactions and for helping
 human societies that currently face global changes. However, it is often
 challenging to distinguish the effects of the climate from human
 activities on environmental changes. Here we evaluate an approach based on
 DNA metabarcoding used on lake sediments to provide the first
 high-resolution reconstruction of plant cover and livestock farming
 history since the Neolithic Period. By comparing these data with a
 previous reconstruction of erosive event frequency, we show that the most
 intense erosion period was caused by deforestation and overgrazing by
 sheep and cowherds during the Late Iron Age and Roman Period. Tracking
 plants and domestic mammals using lake sediment DNA (lake sedDNA) is a
 new, promising method for tracing past human practices, and it provides a
 new outlook of the effects of anthropogenic factors on landscape-scale
 changes.
description: Giguet_Covex_MamP007_sequence_data_run1this file contains all unique sequences produced by MamP007F (5’- CGAGAAGACCCTATGGAGCT-3’) and MamP007R (5’- CCGAGGTCRCCCCAACC-3’) primers for the first run.Giguet_Covex_MamP007_sequence_data_run2This file contains all unique sequences produced by MamP007F (5’- CGAGAAGACCCTATGGAGCT-3’) and MamP007R (5’- CCGAGGTCRCCCCAACC-3’) primers, for the second run with new lake sediment samples.Giguet-Covex_MamP007_filtered_data_run1This file contains the filtered sequences produced by MamP007F (5’- CGAGAAGACCCTATGGAGCT-3’) and MamP007R (5’- CCGAGGTCRCCCCAACC-3’) primers for the first run.Giguet-Covex_MamP007_filtered_data_run2This file contains the filtered sequences produced by MamP007F (5’- CGAGAAGACCCTATGGAGCT-3’) and MamP007R (5’- CCGAGGTCRCCCCAACC-3’) primers for the second run on new lake sediment samples.Giguet_Covex_gh_sequence_data_run1This file contains all unique sequences produced by g (5’-GGGCAATCCTGAGCCAA-3’) and h (5’-CCATTGAGTCTCTGCACCTATC-3’) primers for the first run.Giguet_Covex_gh_sequence_data_run2This file contains all unique sequences produced by g (5’-GGGCAATCCTGAGCCAA-3’) and h (5’-CCATTGAGTCTCTGCACCTATC-3’) primers for the second run with new lake sediment samples.Giguet_Covex_gh_filtered_data_run1This file contains the filtered sequences produced by g (5’-GGGCAATCCTGAGCCAA-3’) and h (5’-CCATTGAGTCTCTGCACCTATC-3’) primers for the first run.Giguet_Covex_gh_filtered_data_run2This file contains the filtered sequences produced by g (5’-GGGCAATCCTGAGCCAA-3’) and h (5’-CCATTGAGTCTCTGCACCTATC-3’) primers for the second run with new lake sediment sample.
DOI: 10.5061/dryad.5gd00
title: Data from: Phylotranscriptomic analysis and genome evolution of the Cypripedioideae (Orchidaceae)

description: Premise of Study: The slipper orchids (Cypripedioideae) are a
 morphologically distinct subfamily of Orchidaceae. They also have some of
 the largest genomes in the orchids, which may be due to polyploidy or some
 other mechanism of genome evolution. We generated ten transcriptomes and
 incorporated existing RNA-seq data to infer a multi-locus nuclear
 phylogeny of the Cypripedioideae and to determine if a whole genome
 duplication event (WGD) correlated to the large genome size of this
 subfamily. Knowing more about timing of ancient polyploidy events can help
 us understand the evolution of one of the most species-rich plant
 families. Methods: Transcriptome data was used to identify low-copy
 orthologous genes to infer a phylogeny of Orchidaceae and to identify
 paralogs to place any WGD events on the species tree. Key results: Our
 transcriptome phylogeny confirmed relationships published in previous
 studies that used fewer markers but incorporated more taxa. We did not
 find a WGD event at the base of the slipper orchids; however, we did
 identify one on the Orchidaceae stem lineage. We also confirmed the
 presence of a previously identified WGD event deeper in the monocot
 phylogeny. Conclusions: Although WGD has played a role in the evolution of
 Orchidaceae, polyploidy does not appear to be responsible for the large
 genome size of slipper orchids. The conserved set of 775 largely
 single-copy nuclear genes identified in this study should prove useful in
 future studies of orchid evolution.
description: Phylotranscriptomics of
 CypripedioideaeUnruh_Cypripedioideae_Phylotranscriptomics_2018.tar.gz
DOI: 10.5061/dryad.1kc2c
title: Data from: Conformational dynamics in TRPV1 channels reported by an encoded coumarin amino acid

description: TRPV1 channels support the detection of noxious and nociceptive input.
 Currently available functional and structural data suggest that TRPV1
 channels have two gates within their permeation pathway: one formed by a
 ′bundle-crossing′ at the intracellular entrance and a second constriction
 at the selectivity filter. To describe conformational changes associated
 with channel gating, the fluorescent non-canonical amino acid
 coumarin-tyrosine was genetically encoded at Y671, a residue proximal to
 the selectivity filter. Total internal reflection fluorescence microscopy
 was performed to image the conformational dynamics of the channels in live
 cells. Photon counts and optical fluctuations from coumarin encoded within
 TRPV1 tetramers correlates with channel activation by capsaicin, providing
 an optical marker of conformational dynamics at the selectivity filter. In
 agreement with the fluorescence data, molecular dynamics simulations
 display alternating solvent exposure of Y671 in the closed and open
 states. Overall, the data point to a dynamic selectivity filter that may
 serve as a gate for permeation.
description: Figure 1-Steinberg et
 alFigure 1 - Source
 data.Figure 2-Steinberg et
 alFigue 2 - Source
 dataFigure 3-Steinberg et
 alFigure 3 - Source
 dataFigure 4-Steinberg et
 alFigure 4 - Source
 dataMATLAB
 CODEMatlab code used to
 readout the SPAD array.
DOI: 10.5061/dryad.0nm8t
title: Data from: Using spatial capture–recapture to elucidate population processes and space-use in herpetological studies

description: The cryptic behavior and ecology of herpetofauna make estimating the
 impacts of environmental change on demography difficult; yet, the ability
 to measure demographic relationships is essential for elucidating
 mechanisms leading to the population declines reported for herpetofauna
 worldwide. Recently developed spatial capture–recapture (SCR) methods are
 well suited to standard herpetofauna monitoring approaches. Individually
 identifying animals and their locations allows accurate estimates of
 population densities and survival. Spatial capture–recapture methods also
 allow estimation of parameters describing space-use and movement, which
 generally are expensive or difficult to obtain using other methods. In
 this paper, we discuss the basic components of SCR models, the available
 software for conducting analyses, and the experimental designs based on
 common herpetological survey methods. We then apply SCR models to
 Red-backed Salamander (Plethodon cinereus), to determine differences in
 density, survival, dispersal, and space-use between adult male and female
 salamanders. By highlighting the capabilities of SCR, and its advantages
 compared to traditional methods, we hope to give herpetologists the
 resource they need to apply SCR in their own systems.
description: Sal_DataThis RData file contains the three seasons of mark-recapture data used for our analyses.EncHistBuilder_ClosedThis R script contains functions to subset and format the salamander spreadsheet into a multi-catch SCR encounter history for a closed-population analysis.EncHistBuilder_RDThis R script contains functions to subset and format the salamander spreadsheet into a multi-catch SCR encounter history for a robust design analysis.Analysis_ClosedThis R script contains all the steps to load the data, format it, and run the MCMC estimation through program JAGS for the closed-population spatial capture-recapture analysis.Analysis_RD.RThis R script contains all the steps to load the data, format it, and run the MCMC estimation through program JAGS for the robust design spatial capture-recapture analysis.ClosedPop JAGS ModelA model file for program JAGS. Contains the actual closed-population model whose parameters will be estimated in JAGS. Includes a covariate for sex of the individual.ClosedPop.txtRD JAGS ModelA model file for program JAGS. Contains the actual robust design model whose parameters will be estimated in JAGS. Includes a covariate for sex of the individual.RD.txtSeason1_Closed_ResultsThe results from the autumn 2013 closed-population analysis.Season2_Closed_ResultsThe results from the spring 2014 closed-population analysis.Season3_Closed_ResultsThe results from the autumn 2014 closed-population analysis.RD_ResultsThe results from the robust design analysis.WorkflowThis file gives detailed instructions on how to use all of the scripts found in this repository and provides a step-by-step guide to run the analyses discussed in the manuscript.
DOI: 10.5061/dryad.p5t21
title: Data from: Monitoramento Independente da Cobertura Florestal das Bacias Setentrionais do Extremo Sul da Bahia

description: O presente relatório apresenta refere-se à conclusão do projeto de
 mapeamento das bacias setentrionais do Extremo Sul da Bahia, compreendendo
 uma área total de 2.300.000 ha. Foram mapeadas imagens de alta resolução
 para os anos de 1996 (1 milhão de ha) e 2006/2007 (2,3 milhão de ha), e de
 baixa resolução para os anos de 1990 e 2002. Para realização do presente
 mapeamento foram utilizadas todas as informações registradas em campo com
 auxílio de GPS (3700 pontos), referente aos principais tipos de cobertura
 vegetal e de uso do solo da região. Também contou com a experiência
 regional dos coordenadores das equipes de trabalho, tanto em Porto Seguro
 quanto Ilhéus, além de consultores especializados neste tipo de serviço
 executado, bem como com vasta experiência de campo na região.
description: Maps South of Bahia from
 1990, 1996, 2001 and 2007Maps South of Bahia from
 1990, 1996, 2001 and 2007Maps_1990_1996_2001_2007.7z
DOI: 10.5061/dryad.61m60
title: Data from: Transcriptional variation associated with cactus host plant adaptation in Drosophila mettleri

description: Although the importance of host plant chemistry in plant–insect
 interactions is widely accepted, the genetic basis of adaptation to host
 plants is not well understood. Here, we investigate transcriptional
 changes associated with a host plant shift in Drosophila mettleri. While
 D. mettleri is distributed mainly throughout the Sonoran Desert where it
 specializes on columnar cacti (Carnegiea gigantea and Pachycereus
 pringleii), a population on Santa Catalina Island has shifted to
 chemically divergent coastal prickly pear cactus (Opuntia littoralis). We
 compared gene expression of larvae from the Sonoran Desert and Santa
 Catalina Island when reared on saguaro (C. gigantea), coastal prickly pear
 and laboratory food. Consistent with expectations based on the complexity
 and toxicity of cactus relative to laboratory food, within-population
 comparisons between larvae reared on these food sources revealed
 transcriptional differences in detoxification and other metabolic
 pathways. The majority of transcriptional differences between populations
 on the cactus hosts were independent of the rearing environment and
 included a disproportionate number of genes involved in processes relevant
 to host plant adaptation (e.g. detoxification, central metabolism and
 chemosensory pathways). Comparisons of transcriptional reaction norms
 between the two populations revealed extensive shared plasticity that
 likely allowed colonization of coastal prickly pear on Santa Catalina
 Island. We also found that while plasticity may have facilitated
 subsequent adaptive divergence in gene expression between populations, the
 majority of genes that differed in expression on the novel host were not
 transcriptionally plastic in the presumed ancestral state.
description: Drosophila mettleri
 transcriptome assemblyTranscriptome assembled
 de novo using Trinity. Paired end Illumina sequencing reads were from
 third instar larvae from two populations reared on three food
 types.Trinity.fastaRead count matrix file used for DE analysisRead counts produced by RSEM, rounded to integer values.AllGenesint.counts.matrix copy.txt
DOI: 10.5061/dryad.5rg72
title: Data from: The use of an unsupervised learning approach for characterizing latent behaviors in accelerometer data

description: The recent increase in data accuracy from high resolution accelerometers
 offers substantial potential for improved understanding and prediction of
 animal movements. However, current approaches used for analysing these
 multivariable datasets typically require existing knowledge of the
 behaviors of the animals to inform the behavioral classification process.
 These methods are thus not well-suited for the many cases where limited
 knowledge of the different behaviors performed exist. Here, we introduce
 the use of an unsupervised learning algorithm. To illustrate the
 method's capability we analyse data collected using a combination of
 GPS and Accelerometers on two seabird species: razorbills (Alca torda) and
 common guillemots (Uria aalge). We applied the unsupervised learning
 algorithm Expectation Maximization to characterize latent behavioral
 states both above and below water at both individual and group level. The
 application of this flexible approach yielded significant new insights
 into the foraging strategies of the two study species, both above and
 below the surface of the water. In addition to general behavioral modes
 such as flying, floating, as well as descending and ascending phases
 within the water column, this approach allowed an exploration of
 previously unstudied and important behaviors such as searching and prey
 chasing/capture events. We propose that this unsupervised learning
 approach provides an ideal tool for the systematic analysis of such
 complex multivariable movement data that are increasingly being obtained
 with accelerometer tags across species. In particular, we recommend its
 application in cases where we have limited current knowledge of the
 behaviors performed and existing supervised learning approaches may have
 limited utility.
description: COGUsubset of 1 Common
 guillemot behavioural data recorded with accelerometer
 tags.RAZOsubset of 1 Razorbill
 behavioural data recorded with accelerometer tags.
DOI: 10.5061/dryad.dd60v
title: Data from: Joint prediction of multiple quantitative traits using a Bayesian multivariate antedependence model

description: Predicting organismal phenotypes from genotype data is important for
 preventive and personalized medicine as well as plant and animal breeding.
 Although genome-wide association studies (GWAS) for complex traits have
 discovered a large number of trait- and disease-associated variants,
 phenotype prediction based on associated variants is usually in low
 accuracy even for a high-heritability trait because these variants can
 typically account for a limited fraction of total genetic variance. In
 comparison with GWAS, the whole-genome prediction (WGP) methods can
 increase prediction accuracy by making use of a huge number of variants
 simultaneously. Among various statistical methods for WGP, multiple-trait
 model and antedependence model show their respective advantages. To take
 advantage of both strategies within a unified framework, we proposed a
 novel multivariate antedependence-based method for joint prediction of
 multiple quantitative traits using a Bayesian algorithm via modeling a
 linear relationship of effect vector between each pair of adjacent
 markers. Through both simulation and real-data analyses, our studies
 demonstrated that the proposed antedependence-based multiple-trait WGP
 method is more accurate and robust than corresponding traditional
 counterparts (Bayes A and multi-trait Bayes A) under various scenarios.
 Our method can be readily extended to deal with missing phenotypes and
 resequence data with rare variants, offering a feasible way to jointly
 predict phenotypes for multiple complex traits in human genetic
 epidemiology as well as plant and livestock breeding.
description: simulation_datasetsThis dataset contains simulation data in the following paper: Jicai Jiang et al., Joint prediction of multiple quantitative traits using a Bayesian multivariate antedependence model. Heredity (2015) Accpeted.
DOI: 10.5061/dryad.r726b
title: Data from: Habitat heterogeneity, host population structure and parasite local adaptation

description: Reciprocal-transplant experiments have proven to be a powerful tool for
 detecting local adaptation (LA). More recently, reciprocal
 cross-inoculation experiments have been used to evaluate adaptation by
 parasites to their local host populations. These experiments are
 conceptually similar to reciprocal-transplant experiments, except that the
 "environment" (the host population) may have evolved in response
 to changes in the parasite population. Here, I use analytical tools and
 computer simulations to determine when parasites would be expected to be
 more infective to their local host populations than to allopatric host
 populations. The models assume that parasites have to genetically
 "match" their hosts in order to infect. I also assumed that
 different host clones were favored in different populations. When parasite
 virulence was low, clonal selection outweighed parasite-mediated
 selection, leading to low host diversity within populations and strong LA
 by parasites. At intermediate levels of virulence, parasite-mediated
 selection maintained high levels of host diversity within populations,
 which reduced or eliminated parasite LA. The loss of parasite LA was not
 associated with increased infectivity by parasites on allopatric hosts.
 Instead, the loss of LA was due to a reduction in infectivity of parasites
 on sympatric hosts. Finally, at high levels of parasite virulence,
 parasite-mediated selection lead to oscillatory host dynamics, and weak
 local adaption by parasites. Across all levels of virulence, the strength
 of parasite LA closely tracked the degree of host population structure
 (GST).
description: Simulation model for
 local adaptation by parasitesThis is a computer
 simulation, written in Excel. Instructions for running the simulation
 occur on the first tab, called "Instructions." The variable
 names are as defined in the published paper in Journal of
 Heredity.Lively_LA_template_dyrad.xlsx
DOI: 10.5061/dryad.dv56j
title: Data from: An effector of the Irish potato famine pathogen antagonizes a host autophagy cargo receptor

description: Plants use autophagy to safeguard against infectious diseases. However,
 how plant pathogens interfere with autophagy related processes is unknown.
 Here we show that PexRD54, an effector from the Irish potato famine
 pathogen Phytophthora infestans, binds host autophagy protein ATG8CL to
 stimulate autophagosome formation. PexRD54 depletes the autophagy cargo
 receptor Joka2 out of ATG8CL complexes and interferes with Joka2's
 positive effect on pathogen defense. Thus a plant pathogen effector has
 evolved to antagonize a host autophagy cargo receptor in order to
 counteract host defenses.
description: Figure 3-source data
 1