cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5pv83
title: Data from: The impact of geographic range, sampling, ecology, and time on extinction risk in the volatile clade Graptoloida

description: Although extinction risk has been found to have a consistent negative
 relationship with geographic range across wide temporal and taxonomic
 scales, the effect has been difficult to disentangle from factors such as
 sampling, ecological niche, or clade. In addition, studies of extinction
 risk have focused on benthic invertebrates with less work on planktic
 taxa. We employed a global set of 1114 planktic graptolite species from
 the Ordovician to lower Devonian to analyze the predictive power of
 species’ traits and abiotic factors on extinction risk, combining general
 linear models (GLMs), partial least-squares regression (PLSR), and
 permutation tests. Factors included measures of geographic range,
 sampling, and graptolite-specific factors such as clade, biofacies
 affiliation, shallow water tolerance, and age cohorts split at the base of
 the Katian and Rhuddanian stages. The percent variance in durations
 explained varied substantially between taxon subsets from 12% to 45%.
 Overall commonness, the correlated effects of geographic range and
 sampling, was the strongest, most consistent factor (12–30% variance
 explained), with clade and age cohort adding up to 18% and other factors
 &lt;10%. Surprisingly, geographic range alone contributed little
 explanatory power (&lt;5%). It is likely that this is a consequence of
 a nonlinear relationship between geographic range and extinction risk,
 wherein the largest reductions in extinction risk are gained from moderate
 expansion of small geographic ranges. Thus, even large differences in
 range size between graptolite species did not lead to a proportionate
 difference in extinction risk because of the large average ranges of these
 species. Finally, we emphasize that the common practice of determining the
 geographic range of taxa from the union of all occurrences over their
 duration poses a substantial risk of overestimating the geographic scope
 of the realized ecological niche and, thus, of further conflating sampling
 effects on observed duration with the biological effects of range size on
 extinction risk.
description: R Code for Running
 Analyses of Boyle et al. 2016This text file contains
 the R code used to perform the analyses detailed in Boyle et al. 2016
 "The Impact of Geographic Range, Sampling, and Time on Extinction
 Risk in the Volatile Clade Graptoloida" including general linear
 models and permutation tests. The file also contains details about data
 manipulation outside of the R environment.Boyle_et_al_SI_1.txtLoading Values for PLSR analysis from Boyle et al. 2016This excel file contains the loading values for the partial least squares regression analysis (PLSR) described in the text of Boyle et al. 2016 "The Impact of Geographic Range, Sampling, and Time on Extinction Risk in the Volatile Clade Graptoloida". Values are given for each taxon subset described in Table 2 of the article.Boyle_et_al_SI_2.xlsx
DOI: 10.5061/dryad.41r1q12
title: Data from: Running in circles in phylomorphospace: host environment constrains morphological diversification in parasitic wasps

description: Understanding phenotypic diversification and the conditions that spur
 morphological novelty or constraint is a major theme in evolutionary
 biology. Unequal morphological diversity between sister clades can result
 from either differences in the rate of morphological change or in the
 ability of clades to explore novel phenotype ranges. We combine an
 existing phylogenetic framework with new phylogenomic data and geometric
 morphometrics to explore the relative roles of rate versus mode of
 morphological evolution for a hyperdiverse group: cryptine ichneumonid
 wasps. Data from genomic ultraconserved elements (UCEs) confirm that
 cryptines are divided into two large clades: one specialized in the use of
 hosts that are deeply concealed under hard substrates, and another with a
 much more diversified host range. Using a phylomorphospace approach, we
 show that both clades have experienced similar rates of morphological
 evolution. Nonetheless, the more specialized group is much more restricted
 in morphospace occupation, indicating that it repeatedly evolved
 morphological change through the same morphospace regions. This is in
 agreement with our prediction that host use imposes constraints in the
 morphospace available to lineages, and reinforces an important distinction
 between evolutionary stasis as opposed to a scenario of continual
 morphological change restricted to a certain range of morphotypes.
description: Supplementary file
 S1List of taxa used in the
 phylogenomic analyses, including initial DNA concentrations; post-PCR
 library DNA concentration; general sequencing and assembly metrics; and
 number of UCE loci recovered for each sample.Supplementary_file_S1.xlsxSupplementary_file_S2Matrix of UCE data used in the phylogenetic analyses in RaxML.Supplementary material S3Whole set of images used for landmark capture for the geometric morphometrics analyses.Supplementary_File_S3.zipSupplementary file S4Landmark coordinates used in the geometric morphometrics analyses and spreadsheet with species names for each higher taxon.Supplementary_file_S4.zipSupplementary_file_S5UCE phylogenetic tree
DOI: 10.5061/dryad.11mq9
title: Data from: A novel molecular toolkit for rapid detection of the pathogen and primary vector of thousand cankers disease

description: Thousand Cankers Disease (TCD) of Juglans and Pterocarya (Juglandaceae)
 involves a fungal pathogen, Geosmithia morbida, and a primary insect
 vector, Pityophthorus juglandis. TCD was described originally from dying
 Juglans nigra trees in the western United States (USA), but it was
 reported subsequently from the eastern USA and northern Italy. The disease
 is often difficult to diagnose due to the absence of symptoms or signs on
 the bark surface of the host. Furthermore, disease symptoms can be
 confused with those caused by other biotic and abiotic agents. Thus, there
 is a critical need for a method for rapid detection of the pathogen and
 vector of TCD. Using species-specific microsatellite DNA markers, we
 developed a molecular protocol for the detection of G. morbida and P.
 juglandis. To demonstrate the utility of the method for delineating TCD
 quarantine zones, we tested whether geographical occurrence of symptoms
 and signs of TCD was correlated with molecular evidence for the presence
 of the cryptic TCD organisms. A total of 1600 drill cores were taken from
 branch sections collected from three regions (n=40 trees for each
 location): California-J. hindsii (heavy disease incidence); Tennessee-J.
 nigra (mild disease incidence); and outside the known TCD zone
 (Missouri-J. nigra, no record of the disease). California samples had the
 highest incidence of the TCD organisms (85%, 34/40). Tennessee had
 intermediate incidence (42.5%, 17/40), whereas neither organism was
 detected in samples from Missouri. The low cost molecular protocol
 developed here has a high degree of sensitivity and specificity, and it
 significantly reduces sample-processing time, making the protocol a
 powerful tool for rapid detection of TCD.
description: Molecular detection of
 Thousand Cankers DiseaseData for TCD RMD-Oren et
 al_PlosOne 2017.xlsx
DOI: 10.5061/dryad.7182c
title: Data from: Outlier analyses to test for local adaptation to breeding grounds in a migratory arctic seabird

description: Investigating the extent (or the existence) of local adaptation is crucial
 to understanding how populations adapt. When experiments or fitness
 measurements are difficult or impossible to perform in natural
 populations, genomic techniques allow us to investigate local adaptation
 through the comparison of allele frequencies and outlier loci along
 environmental clines. The thick-billed murre (Uria lomvia) is a highly
 philopatric colonial arctic seabird that occupies a significant
 environmental gradient, shows marked phenotypic differences among
 colonies, and has large effective population sizes. To test whether
 thick-billed murres from five colonies along the eastern Canadian Arctic
 coast show genomic signatures of local adaptation to their breeding
 grounds, we analyzed geographic variation in genome-wide markers mapped to
 a newly assembled thick-billed murre reference genome. We used outlier
 analyses to detect loci putatively under selection, and clustering
 analyses to investigate patterns of differentiation based on 2220
 genomewide single nucleotide polymorphisms (SNPs) and 137 outlier SNPs. We
 found no evidence of population structure among colonies using all loci
 but found population structure based on outliers only, where birds from
 the two northernmost colonies (Minarets and Prince Leopold) grouped with
 birds from the southernmost colony (Gannet), and birds from Coats and
 Akpatok were distinct from all other colonies. Although results from our
 analyses did not support local adaptation along the latitudinal cline of
 breeding colonies, outlier loci grouped birds from different colonies
 according to their non-breeding distributions, suggesting that outliers
 may be informative about adaptation and/or demographic connectivity
 associated with their migration patterns or nonbreeding grounds.
description: Structure_files_RAD_TBMUThe folder contains four genotype filesUria_lomvia_genome_raysscapeWhole genome sequence of a female thick-billed murre (Uria lomvia) from Coats Island, Nunavut, Canada. The assembly was performed using Ray and SScape.
DOI: 10.5061/dryad.jk4r6
title: Data from: Effects of partial selfing on the equilibrium genetic variance, mutation load and inbreeding depression under stabilizing selection

description: The mating system of a species is expected to have important effects on
 its genetic diversity. In this paper, we explore the effects of partial
 selfing on the equilibrium genetic variance Vg, mutation load L and
 inbreeding depression δ under stabilizing selection acting on a arbitrary
 number n of quantitative traits coded by biallelic loci with additive
 effects. When the U/n ratio is low (where U is the total haploid mutation
 rate on selected traits) and effective recombination rates are
 sufficiently high, genetic associations between loci are negligible and
 the genetic variance, mutation load and inbreeding depression are well
 predicted by approximations based on single-locus models. For higher
 values of U/n and/or lower effective recombination, moderate genetic
 associations generated by epistasis tend to increase Vg, L and δ, this
 regime being well predicted by approximations including the effects of
 pairwise associations between loci. For yet higher values of U/n and/or
 lower effective recombination, a different regime is reached under which
 the maintenance of coadapted gene complexes reduces Vg, L and δ.
 Simulations indicate that the values of Vg, L and δ are little affected by
 assumptions regarding the number of possible alleles per locus.
description: C++ simulation
 programSimulates a population
 of N diploid individuals undergoing partial selfing, under Gaussian
 stabilizing selection on n phenotypic traits coded by biallelic loci,
 equally spaced along a single linear chromosome.program.tar
DOI: 10.5061/dryad.jv0gh
title: Data from: Humans exploit the biomechanics of bipedal gait during visually guided walking over complex terrain

description: How do humans achieve such remarkable energetic efficiency when walking
 over complex terrain such as a rocky trail? Recent research in
 biomechanics suggests that the efficiency of human walking over flat,
 obstacle-free terrain derives from the ability to exploit the physical
 dynamics of our bodies. In this study, we investigated whether this
 principle also applies to visually guided walking over complex terrain. We
 found that when humans can see the immediate foreground as little as two
 step lengths ahead, they are able to choose footholds that allow them to
 exploit their biomechanical structure as efficiently as they can with
 unlimited visual information. We conclude that when humans walk over
 complex terrain, they use visual information from two step lengths ahead
 to choose footholds that allow them to approximate the energetic
 efficiency of walking in flat, obstacle-free environments.
description: subjectData_1of2Data from subjects 1-6subjectData_2of2Data from subjects 7-12
DOI: 10.5061/dryad.dr4s8
title: Data from: Genetic and ecological data reveal species boundaries between viviparous and oviparous lizard lineages

description: Identification of cryptic species is an essential aim for conservation
 biologists to avoid premature extinctions of ‘unrecognized’ species.
 Integrating different types of data can undoubtedly aid in resolving the
 issue of species delimitation. We studied here two lineages of the common
 lizard Zootoca vivipara that display different reproductive mode (the
 viviparous Z. v. vivipara and the oviparous Z. v. carniolica) and that
 overlap their distributional ranges in the European Alps. With the purpose
 of delimiting species’ boundaries, we analyzed their ecological, genetic
 and natural history features. More than 300 samples were collected and
 analyzed at cytochrome b and 11 microsatellites loci for investigating
 genetic variation, population structure, individual relatedness and
 evolutionary histories of the two lineages. Additionally, we compared
 their ecological niches using eight ecological variables. Genetic data
 showed contrasting patterns of genetic structure between the two lineages,
 different demographic dynamics and no hybridization events. Also strong
 ecological differences (such as temperature) emerged between the two
 lineages, and niche overlap was limited. Taken together, these results
 indicate that Z. v. vivipara and Z. v. carniolica should be recognized as
 two separate species, and particular conservation consideration should be
 given to the oviparous lineage that tends to live in areas threatened by
 increasing impact of human activities. However, recent and rapid climate
 warming might determine an increasing risk for the persistence of the
 viviparous lineage, being adapted to cold environments.
description: intraspecies
 genepopGenepop file of 304
 genotyped Z. vivipara individualsvivipara 9
 lociGenepop file of
 genotyped Z. vivipara vivipara individualscarniolica 8 loci
 genepopGenepop file of
 genotyped Z. vivipara carniolica individuals
DOI: 10.5281/zenodo.18379716
title: Supplemental material for the paper "Untangling the Tapestry: 𝑘-bounded Problems and Local Optima Networks"

description: Please see the README.txt for information and instructions.
DOI: 10.5281/zenodo.18379717
title: Supplemental material for the paper "Untangling the Tapestry: 𝑘-bounded Problems and Local Optima Networks"

description: Please see the README.txt for information and instructions.
DOI: 10.5061/dryad.j57k3
title: Data from: Multiple mating but not recombination causes quantitative increase in offspring genetic diversity for varying genetic architectures

description: Explaining the evolution of sex and recombination is particularly
 intriguing for some species of eusocial insects because they display
 exceptionally high mating frequencies and genomic recombination rates.
 Explanations for both phenomena are based on the notion that both increase
 colony genetic diversity, with demonstrated benefits for colony disease
 resistance and division of labor. However, the relative contributions of
 mating number and recombination rate to colony genetic diversity have
 never been simultaneously assessed. Our study simulates colonies, assuming
 different mating numbers, recombination rates, and genetic architectures,
 to assess their worker genotypic diversity. The number of loci has a
 strong negative effect on genotypic diversity when the allelic effects are
 inversely scaled to locus number. In contrast, dominance, epistasis,
 lethal effects, or limiting the allelic diversity at each locus does not
 significantly affect the model outcomes. Mating number increases colony
 genotypic variance and lowers variation among colonies with quickly
 diminishing returns. Genomic recombination rate does not affect intra- and
 inter-colonial genotypic variance, regardless of mating frequency and
 genetic architecture. Recombination slightly increases the genotypic range
 of colonies and more strongly the number of workers with unique allele
 combinations across all loci. Overall, our study contradicts the argument
 that the exceptionally high recombination rates cause a quantitative
 increase in offspring genotypic diversity across one generation.
 Alternative explanations for the evolution of high recombination rates in
 social insects are therefore needed. Short-term benefits are central to
 most explanations of the evolution of multiple mating and high
 recombination rates in social insects but our results also apply to other
 species.
description: R-code for colony model
 and simulationsThis title contains two
 "R" code modules. The first can be used to generate the worker
 genotypes of a colony of haplodiploid social insects from one mother and a
 specified number of males, assuming a certain number of loci and a certain
 recombination rate. The second module uses this colony algorithm to
 evaluate colony genetic diversity across varying numbers of males,
 recombination rates, and loci numbers.S1_R_code.doc
DOI: 10.5061/dryad.c3k48j0
title: Data from: Modelling the co-evolution of indirect genetic effects and inherited variability

description: When individuals interact, their phenotypes may be affected by genes in
 their social partners, a phenomenon known as Indirect Genetic Effects
 (IGEs). In aquaculture species and some plants, competition not only
 affects trait levels of individuals, but also inflates variation of trait
 values among individuals. Variability of trait values has been studied as
 a quantitative trait in itself, and is often referred to as inherited
 variability. Although the observed phenotypic relationship between
 competition and variability suggests an underlying genetic relationship,
 models of IGE and inherited variability do not allow for such
 relationship. Models of trait levels show IGEs may considerably change
 heritable variation in trait values. Currently, we lack the tools to
 investigate whether this result extends to inherited variability. Here we
 present a model that integrates IGEs and inherited variability. In this
 model, the target phenotype, say growth rate, is a function of genetic and
 environmental effects of the focal individual and of the difference in
 trait values between the social partner and the focal individual,
 multiplied by a regression coefficient. The regression coefficient is a
 genetic trait which is measure of cooperation; a negative value indicates
 competition, a positive value cooperation, and an increasing value due to
 selection indicates the evolution of cooperation. Our simulations show
 that the model results in increased variability of body weight with
 increase of competition. When competition decreases, variability becomes
 significantly smaller. Our findings suggest we may have been overlooking
 an entire level of genetic variation in variability, the one due to IGEs.
description: Simulated data sets for
 each of the five scenariosThe zip file contains 5
 folders, each corresponding to one of the five scenarios presented in the
 manuscript. Folders contain 100 simulated data frames, i.e., replicates.
 In S1, simulated b_average equals - 0.08, in S2, b_average = - 0.05, in
 S3, b_average = 0, in S4, b_average = + 0.05, and in S5, b_average = +
 0.08. Column names are explained in the file which is uploaded
 separately.data_sets.7zColumn_names_explainedThe file explains column names of data sets in S1-S5
DOI: 10.5061/dryad.j6g1c
title: Data from: Structural alterations of the social brain: a comparison between schizophrenia and autism

description: Autism spectrum disorder and schizophrenia share a substantial number of
 etiologic and phenotypic characteristics. Still, no direct comparison of
 both disorders has been performed to identify differences and
 commonalities in brain structure. In this voxel based morphometry study,
 34 patients with autism spectrum disorder, 21 patients with schizophrenia
 and 26 typically developed control subjects were included to identify
 global and regional brain volume alterations. No global gray matter or
 white matter differences were found between groups. In regional data,
 patients with autism spectrum disorder compared to typically developed
 control subjects showed smaller gray matter volume in the amygdala,
 insula, and anterior medial prefrontal cortex. Compared to patients with
 schizophrenia, patients with autism spectrum disorder displayed smaller
 gray matter volume in the left insula. Disorder specific positive
 correlations were found between mentalizing ability and left amygdala
 volume in autism spectrum disorder, and hallucinatory behavior and insula
 volume in schizophrenia. Results suggest the involvement of social brain
 areas in both disorders. Further studies are needed to replicate these
 findings and to quantify the amount of distinct and overlapping neural
 correlates in autism spectrum disorder and schizophrenia.
description: epidemiological,
 behavioral and MRI dataepidemiological,
 behavioral and MRI data by each subjectData
 Dryad_07_2014_final.xls
DOI: 10.5061/dryad.gk1g3
title: Data from: A three-dimensionally preserved lobopodian from the Herefordshire (Silurian) Lagerstätte, UK

description: The Herefordshire (Silurian) Lagerstätte (c. 430 MYr BP) has yielded,
 amongst many exceptionally preserved invertebrates, a wide range of new
 genera belonging to crown-group Panarthropoda. Here we increase this
 panarthropod diversity with the lobopodian Thanahita distos, a new
 total-group panarthropod genus and species. This new lobopodian preserves
 at least nine paired, long, slender appendages, the anterior two in the
 head region and the posterior seven representing trunk lobopods. The body
 ends in a short post-appendicular extension. Some of the trunk lobopods
 bear two claws, others a single claw. The body is covered by paired,
 tuft-like papillae. T. distos joins only seven other known
 three-dimensionally preserved lobopodian or onychophoran (velvet worm)
 fossil specimens and is the first lobopodian to be formally described from
 the Silurian. Phylogenetic analysis recovered it, together with all
 described Hallucigenia species, in a sister-clade to crown-group
 panarthropods. Its placement in a redefined Hallucigeniidae, an iconic
 Cambrian clade, indicates the survival of this clade to Silurian times.
description: Thanahita distos
 holotype - VAXML model and raw serial-grinding dataContains: A) the model
 of the holotype used in the publication, in VAXML format. This format
 comprises and XML descriptor and STL-format geometry. See
 www.spiers-software.org for a free VAXML viewer and details of the
 specification. B) BMP format raw images from physical-optical tomography
 (serial grinding). See readme file within appropriate ZIP for more
 details.Thanahita.zip