cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t8v81
title: Data from: Characterizing wildlife behavioural responses to roads using integrated step selection analysis

description: Roads are a prevalent, ever-increasing form of human disturbance on the
 landscape. In many places in western North America, energy development has
 brought human and road disturbance into seasonal winter range areas for
 migratory elk. We sought to evaluate the predictions from the
 risk-disturbance hypothesis when studying elk response to roads during
 winter. Road proximity and crossing were used to evaluate these
 behaviours, which offered a rare comparison between two common measures of
 roads. We used integrated step selection analysis (iSSA) to evaluate four
 alternative hypotheses regarding the influence of roads on space-use
 behaviour across 175 elk-years of elk telemetry data, and we quantified
 both population-level and individual-level variations in responses. We
 demonstrated, for the first time, how iSSA can be used to combine movement
 analysis in a refined approach to habitat selection. Elk responded to
 roads as they would natural predation risk. Elk selected areas farther
 from roads at all times of day with avoidance being greatest during
 twilight. In addition, elk sought cover and moved more when in the
 vicinity of roads. Road crossings were generally avoided, but this
 avoidance was weakest during daytime when elk were both moving and closer
 to roads. Synthesis and applications. Energy development is transforming
 landscapes in western North America with the proliferation of roads, which
 we show is having substantial and multifaceted negative effects on elk
 movement and behaviour. These adverse effects can be mitigated by
 minimizing new road construction and by restricting traffic on roads as
 well as providing the protection of tree cover on elk winter ranges.
description: ElkYrRelocationsGPS relocations from elk collared in Southwestern Alberta from 2007 to 2013 with associated step attributes and habitat covariates. Data are from the winter seasons and files are separated by unique elk ID and year ('elk-year').
DOI: 10.5061/dryad.d0h71
title: Data from: "Transcriptome resources for two highly divergent Silene latifolia populations" in Genomic Resources Notes accepted 1 February 2015 – 31 March 2015

description: Here we have used next-generation Illumina sequencing to generate
 transcriptomes of four S. latifolia individuals from two morphologically
 divergent populations from disparate habitats, including including two
 females from Xativa, Spain and two males from Zagreb, Croatia. Spanish
 plants experience a much hotter, drier climate than Croatian plants, and
 the populations have ecologically relevant differences in floral and leaf
 characteristics (e.g., Spain has thicker leaves and produces fewer, larger
 flowers in comparison) (data not shown). This transcriptome data will
 provide population-specific SNPs for planned QTL studies using these
 populations to connect phenotypic diversity with the underlying genetic
 architecture. This transcriptome resource will also contribute to a
 growing set of genomics resources for S. latifolia.
description: Annotation
 SummarySummary of annotations
 generated using the Trinotate pipeline.meta_assembly.fastaTrinity generated assembly of all four individuals pooled together in a gzipped fasta format.ZAG5_1.fasta.gzTrinity generated assembly of ZAG5_1 individual in a gzipped fasta format.ZAG2_1.fasta.gzTrinity generated assembly of ZAG2_1 individual in a gzipped fasta format.CN9_1.fasta.gzTrinity generated assembly of CN9_1 individual in a gzipped fasta format.CN7_1.fasta.gzTrinity generated assembly of CN7_1 individual in a gzipped fasta format.blacklight_script.txtList of commands used to conduct assembly of pooled transcriptome on Blacklight cluster.silene_transcriptomes.vcf.gzCompressed vcf file containing snps identified in all four transcriptomes against Trinity derived pooled assembly as reference. PF01 = CN7_1, PF02 = ZAG2_1, PF03 = ZAG5_1, PF04 =CN9_1.Annotation_report.xlsContains full description of assembly component annotation generated by Trinotate.analysis_scripts.txtCommands used for conducting non-assembly based analysis.
DOI: 10.5061/dryad.54f1jc2
title: Data from: Synchronized shift of oral, fecal and urinary microbiotas in bats and natural infection dynamics during seasonal reproduction

description: Seasonal reproduction is a period of extreme physiological and behavioral
 changes, yet we know little about how it may affect host microbial
 communities (i.e. microbiota) and pathogen transmission. Here, we
 investigated shifts of the bacterial microbiota in saliva, urine and
 faeces during the seasonal reproduction of bats in South Africa, and test
 for an interaction in shedding patterns of both bacterial (Leptospira) and
 viral (adeno- and herpes-viruses) agents. Based on a comparative approach
 in two cave-dwelling bat species and high-throughput sequencing of the 16S
 rRNA gene, we demonstrated a clear signature in microbiota changes over
 the reproduction season, consistent across the multiple body habitats
 investigated, and associated with sex, age and reproductive condition of
 bats. We observed in parallel highly dynamic shedding patterns for both
 bacteria and viruses, but did not find a significant association between
 viral shedding and bacterial microbiota composition. Indeed, only
 Leptospira shedding was associated with alterations in both the diversity
 and composition of the urinary microbiota. These results illustrate how
 seasonal reproduction in bats substantially affects microbiota composition
 and infection dynamics, and have broad implications for the understanding
 of disease ecology in important reservoir hosts, such as bats.
description: Rousettus_SampleList_SalivaList and details of Rousettus samples.Miniopterus_SampleList_Saliva-Urine-FaecesList and details of Miniopterus samples.Rousettus fasta DryadA zip folder with fasta files for Rousettus.Miniopterus fasta dryadA zip folder with fasta files for Miniopterus.Rousettus_Saliva_OTUsOTU table for Rousettus saliva samples.Miniopterus_Saliva_OTUsOTU table for Miniopterus saliva samples.Miniopterus_Faeces_OTUsOTU table for Miniopterus faeces samples.Miniopterus_Urine_OTUsOTU table for Miniopterus urine samples.
DOI: 10.5061/dryad.r7201
title: Data from: Natural hybridization between genera that diverged from each other approximately 60 million years ago

description: A fern from the French Pyrenees—×Cystocarpium roskamianum—is a recently
 formed intergeneric hybrid between parental lineages that diverged from
 each other approximately 60 million years ago (mya; 95% highest posterior
 density: 40.2–76.2 mya). This is an extraordinarily deep hybridization
 event, roughly akin to an elephant hybridizing with a manatee or a human
 with a lemur. In the context of other reported deep hybrids, this finding
 suggests that populations of ferns, and other plants with abiotically
 mediated fertilization, may evolve reproductive incompatibilities more
 slowly, perhaps because they lack many of the premating isolation
 mechanisms that characterize most other groups of organisms. This
 conclusion implies that major features of Earth’s biodiversity—such as the
 relatively small number of species of ferns compared to those of
 angiosperms—may be, in part, an indirect by-product of this slower
 “speciation clock” rather than a direct consequence of adaptive
 innovations by the more diverse lineages.
description: DatingAnalysis1_combnd_burninoutDatingAnalysis1_combnd_burninoutPosterior sample of divergence times, etc., from the four DatingAnalysis1 (eupolypods II) runs, combined, with the burnin removed.DatingAnalysis1_run1of4logPosterior sample of divergence time, etc., from one of the four DatingAnalysis1 (eupolypods II) runs.DatingAnalysis1_run1of4.logDatingAnalysis1_run1of4treesPosterior sample of time trees from one of the four DatingAnalysis1 (eupolypods II) runs.DatingAnalysis1_run1of4.treesDatingAnalysis1_run1of4xmlBeast XML (alignment, settings, etc.) from one of the four DatingAnalysis1 (eupolypods II) runs.DatingAnalysis1_run1of4.xmlDatingAnalysis2_combd_burninouttreePosterior sample of time trees from the four DatingAnalysis2 (Cystopteridaceae) runs, combined, with the burnin removed.DatingAnalysis2_combd_burninout.treDatingAnalysis2_combnd_burninoutlogPosterior sample of divergence times, etc., from the four DatingAnalysis2 (Cystopteridaceae) runs, combined, with the burnin removed.DatingAnalysis2_combnd_burninout.logDatingAnalysis2_run1of4logPosterior sample of divergence times, etc., from one of the four DatingAnalysis2 (Cystopteridaceae) runs.DatingAnalysis2_run1of4.logDatingAnalysis2_run1of4treesPosterior sample of time trees from one of the four DatingAnalysis2 (Cystopteridaceae) runs.DatingAnalysis2_run1of4.treesDatingAnalysis2_run1of4xmlBeast XML (alignment, settings, etc.) from one of the four DatingAnalysis2 (Cystopteridaceae) runs.DatingAnalysis2_run1of4.xmlRscript_xCysto_posterior_distributions_fitting_etcAn R script for extracting the posterior node age distributions from the Beast outputs, and then fit parametric distributions to them. And to compare distributions (plot them).xCysto_posterior_distributions_fitting_etc.RxCysto_alleles_garli configuration fileThe Garli configuration file for the Cystopteridaceae alleles dataset analysis.xCysto_alleles_garli.conf
DOI: 10.5061/dryad.7n1q4
title: Data from: Global biogeography and evolution of Cuvierina pteropods

description: Background: Shelled pteropods are planktonic gastropods that are
 potentially good indicators of the effects of ocean acidification. They
 also have high potential for the study of zooplankton evolution because
 they are metazoan plankton with a good fossil record. We investigated
 phenotypic and genetic variation in pteropods belonging to the genus
 Cuvierina in relation to their biogeographic distribution across the
 world’s oceans. We aimed to assess species boundaries and to reconstruct
 their evolutionary history. Results: We distinguished six morphotypes
 based on geometric morphometric analyses of shells from 926 museum and 113
 fresh specimens. These morphotypes have distinct geographic distributions
 across the Atlantic, Pacific and Indian oceans, and belong to three major
 genetic clades based on COI and 28S DNA sequence data. Using a
 fossil-calibrated phylogeny, we estimated that these clades separated in
 the Late Oligocene and Early to Middle Miocene. We found evidence for
 ecological differentiation among all morphotypes based on ecological niche
 modelling with sea surface temperature, salinity and phytoplankton biomass
 as primary determinants. Across all analyses, we found highly congruent
 patterns of differentiation suggesting species level divergences between
 morphotypes. However, we also found distinct morphotypes (e.g. in the
 Atlantic Ocean) that were ecologically, but not genetically
 differentiated. Conclusions: Given the distinct ecological and phenotypic
 specializations found among both described and undescribed Cuvierina taxa,
 they may not respond equally to future ocean changes and may not be
 equally sensitive to ocean acidification. Our findings support the view
 that ecological differentiation may be an important driving force in the
 speciation of zooplankton.
description: Centroid size and
 uncorrected RW (relative warp) data of Cuvierina
 pteropods.Centroid size and
 uncorrected RW data of all Cuvierina shells in ventral as well as
 apertural orientations. Relative contributions of RW axes to shell shape
 variation are included. The first sheet contains ventral data of 113
 fresh, 712 reference museum, and 214 other museum specimens. The second
 sheet contains apertural data of 115 fresh, 352 reference museum, and 83
 other museum specimens.Morphometrics_Data_Cuvierina_AKBurridge.xlsPhotographs of Cuvierina shells in a ventral orientation.Photographs of 1039 Cuvierina shells in a ventral orientation used for geometric morphometric analyses in this study.Morphometrics_Ventral_Cuvierina_AKBurridge.zipPhotographs of Cuvierina shells in an apertural orientation.Photographs of 550 Cuvierina shells in an apertural orientation used for geometric morphometric analyses in this study.Morphometrics_Apertural_Cuvierina_AKBurridge.zip
DOI: 10.5061/dryad.7c4g3
title: Data from: Improving HybrID: how to best combine indirect and direct encoding in evolutionary algorithms

description: Many challenging engineering problems are regular, meaning solutions to
 one part of a problem can be reused to solve other parts. Evolutionary
 algorithms with indirect encoding perform better on regular problems
 because they reuse genomic information to create regular phenotypes.
 However, on problems that are mostly regular, but contain some
 irregularities, which describes most real-world problems, indirect
 encodings struggle to handle the irregularities, hurting performance.
 Direct encodings are better at producing irregular phenotypes, but cannot
 exploit regularity. An algorithm called HybrID combines the best of both:
 it first evolves with indirect encoding to exploit problem regularity,
 then switches to direct encoding to handle problem irregularity. While
 HybrID has been shown to outperform both indirect and direct encoding, its
 initial implementation required the manual specification of when to switch
 from indirect to direct encoding. In this paper, we test two new methods
 to improve HybrID by eliminating the need to manually specify this
 parameter. Auto-Switch-HybrID automatically switches from indirect to
 direct encoding when fitness stagnates. Offset-HybrID simultaneously
 evolves an indirect encoding with directly encoded offsets, eliminating
 the need to switch. We compare the original HybrID to these alternatives
 on three different problems with adjustable regularity. The results show
 that both Auto-Switch-HybrID and Offset-HybrID outperform the original
 HybrID on different types of problems, and thus offer more tools for
 researchers to solve challenging problems. The Offset-HybrID algorithm is
 particularly interesting because it suggests a path forward for
 automatically and simultaneously combining the best traits of indirect and
 direct encoding.
description: Improving HybrID:
 Champion Genomes and Fitness ValuesAn archive containing
 champion genomes and fitness values for algorithms tested in the paper
 Improving HybrID: How to best combine indirect and direct encoding in
 evolutionary algorithms, as well as the configuration files used to
 produce the populations.ImprovingHybrID.tar.gz
DOI: 10.5061/dryad.cb506
title: Data from: Can reinforcement complete speciation?

description: Hybridization is common in nature, even between "good" species.
 This observation poses the question of why reinforcement is not always
 successful in leading to the evolution of complete reproductive isolation.
 To study this question, we developed a new "quasi-linkage
 disequilibrium" (QLD) approximation to obtain the first analytic
 results for the evolution of modifiers that increase mate discrimination
 against hybrids and heterospecifics. When such modifiers have small
 effects, they evolve more readily under a one-allele than a two-allele
 mechanism (sensu Felsenstein 1981). The strength of selection on the
 modifier decreases as hybrids decrease in frequency, and so further
 reinforcement may not occur once hybridization is sufficiently rare. The
 outcome is qualitatively different when modifiers have large effects,
 however, for example when a single mutation can cause complete
 reproductive isolation. In this case modifiers in a two-allele mechanism
 can be selected as or more strongly than those in a one-allele mechanism.
 Further, they can spread under quite general conditions. Thus whether
 complete closure of genetic introgression by reinforcement occurs may
 depend on the size of effects that mutations have on the sensory systems
 used in mate choice.
description: KJBrecursionsMultilocus recursions. This file needs to be placed in the current working directory in order to initialize the Mathematica supplement properly.
DOI: 10.5061/dryad.4384p
title: Data from: Color phenotypes are under similar genetic control in two distantly related species of Timema stick insect

description: Ecology and genetics are both of general interest to evolutionary
 biologists as they can influence the phenotypic and genetic response to
 selection. The stick insects Timema podura and T. cristinae exhibit a
 green/melanistic body color polymorphism that is subject to different
 ecologically-based selective regimes in the two species. Here we describe
 aspects of the genetics of this color polymorphism in T. podura, and
 compare this to previous results in T. cristinae. We first show that
 similar color phenotypes of the two species cluster in phenotypic space.
 We then use genome-wide association mapping to show that in both species,
 color is controlled by few loci, dominance relationships between color
 alleles are the same, and SNPs associated with color phenotypes
 co-localize to the same linkage group. Regions within this linkage group
 that harbor genetic variants associated with color exhibit elevated
 linkage disequilibrium relative to genome wide expectations, but more
 strongly so in T. cristinae. We use these results to discuss predictions
 regarding how the genetics of color could influence levels of phenotypic
 and genetic variation that segregate within and between populations of T.
 podura and T. cristinae, drawing parallels with other organisms.
description: data - phenotype and
 genotype tablesContains phenotypic and
 genotypic data used in our study. Example scripts containing information
 regarding analyses carried out on these data can be found in the
 "scripts.zip" archive.data.zipscriptsThis archive contains scripts that were used to analyze data presented in our manuscript. For phenotypic and genotypic data associated with these scripts please download the "data.zip" archive.
DOI: 10.5061/dryad.13n52
title: Data from: A two-state model of tree evolution and its applications to alu retrotransposition

description: Models of tree evolution have mostly focused on capturing the cladogenesis
 processes behind speciation. Processes that derive the evolution of
 genomic elements, such as repeats, are not necessarily captured by these
 existing models. In this paper, we design a model of tree evolution that
 we call the dual-birth model, and we show how it can be useful in studying
 the evolution of short Alu repeats found in the human genome in abundance.
 The dual-birth model extends the traditional birth-only model to have two
 rates of propagation, one for active nodes that propagate often, and
 another for inactive nodes, that with a lower rate, activate and start
 propagating. Adjusting the ratio of the rates controls the expected tree
 balance. We present several theoretical results under the dual-birth
 model, introduce parameter estimation techniques, and study the properties
 of the model in simulations. We then use the dual-birth model to estimate
 the number of active Alu elements and their rates of propagation and
 activation in the human genome based on a large phylogenetic tree that we
 build from close to one million Alu sequences.
description: Online-Only
 Supplementary MaterialsThe online-only
 supplement of the manuscriptalu-paper-systematic-supplement.pdfHuman Alu FilesFiles related to the Human Alu dataset used in the manuscripthuman-alu-files.zipTree Simulation FilesTree simulation files used to test the properties of the dual-birth model as well as to study the inference of trees generated by the modeltree-simulations.zipREADMEREADME file describing the contents of the supplementary materials
DOI: 10.5061/dryad.1922
title: Data from: Exploring the universe of protein structures beyond the Protein Data Bank

description: It is currently believed that the atlas of existing protein structures is
 faithfully represented in the Protein Data Bank. However, whether this
 atlas covers the full universe of all possible protein structures is still
 a highly debated issue. By using a sophisticated numerical approach, we
 performed an exhaustive exploration of the conformational space of a 60
 amino acid polypeptide chain described with an accurate all-atom
 interaction potential. We generated a database of around 30,000 compact
 folds with at least 30% of secondary structure corresponding to local
 minima of the potential energy. This ensemble plausibly represents the
 universe of protein folds of similar length; indeed, all the known folds
 are represented in the set with good accuracy. However, we discover that
 the known folds form a rather small subset, which cannot be reproduced by
 choosing random structures in the database. Rather, natural and possible
 folds differ by the contact order, on average significantly smaller in the
 former. This suggests the presence of an evolutionary bias, possibly
 related to kinetic accessibility, towards structures with shorter loops
 between contacting residues. Beside their conceptual relevance, the new
 structures open a range of practical applications such as the development
 of accurate structure prediction strategies, the optimization of force
 fields, and the identification and design of novel folds.
description: VAL60Collection of 30063
 files in PDB-format, each containing all-atom structural data for the
 conformation of a polyvaline molecule with 60 residues. All conformations
 where computer-generated by means of meta-dynamics.
DOI: 10.5061/dryad.rv801
title: Data from: Predatory behavior of the cave shrimp Creaseria morleyi (Creaser, 1936) (Caridea: Palaemonidae), the blind hunter of the Yucatán cenotes, Mexico

description: Recent studies of the trophic structure of the underwater cave ecosystems
 in the Yucatán Peninsula have regarded the largest crustacean inhabitant,
 the blind palaemonid shrimp Creaseria morleyi (Creaser, 1936), as a
 scavenger and predator without any evidence on the behavior of the shrimp.
 The predatory behavior of C. morleyi is here described for the first time,
 verifying its classification as a predator. A variety of prey targets,
 including the atyid shrimp Typhlatya sp., were used to demonstrate
 predation and saprophagous feeding behavior in C. morleyi using in vitro
 and in situ observations. Scanning electron microscope images show the
 structures of the antennules and antennae that could be responsible for
 prey detection. Findings show that C. morleyi is capable of hunting a
 variety of prey, most likely depending on their relative size.
 Observations on the feeding strategy of C. morleyi suggest any animal
 within a particular size range is a potential prey, including its own
 species, which suggests the hypothesis that growth may be favored in early
 stages of life in order to reach a size refuge from predation. These
 observations provide information of some of the adaptations necessary for
 a predator to thrive in an aphotic and oligotrophic environment.
description: Creaseria_morleyi_Blind_Huntershort video (less than 5min) with laboratory predation-interaction between two cave dwelling blind shrimps from the Yucatan peninsula innundated caves (cenotes), plus film-takes in the wild of predation bouts.