cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.65r63
title: Data from: Sexual selection has minimal impact on effective population sizes in species with high rates of random offspring mortality: an empirical demonstration using fitness distributions

description: The effective population size (Ne) is a fundamental parameter in
 population genetics that influences the rate of loss of genetic diversity.
 Sexual selection has the potential to reduce Ne by causing the
 sex-specific distributions of individuals that successfully reproduce to
 diverge. To empirically estimate the effect of sexual selection on Ne, we
 obtained fitness distributions for males and females from an outbred,
 laboratory-adapted population of Drosophila melanogaster. We observed
 strong sexual selection in this population (the variance in male
 reproductive success was ∼14 times higher than that for females), but
 found that sexual selection had only a modest effect on Ne, which was 75%
 of the census size. This occurs because the substantial random offspring
 mortality in this population diminishes the effects of sexual selection on
 Ne, a result that necessarily applies to other high fecundity species. The
 inclusion of this random offspring mortality creates a scaling effect that
 reduces the variance/mean ratios for male and female reproductive success
 and causes them to converge. Our results demonstrate that measuring
 reproductive success without considering offspring mortality can
 underestimate Ne and overestimate the genetic consequences of sexual
 selection. Similarly, comparing genetic diversity among different genomic
 components may fail to detect strong sexual selection.
description: Pischedda et al. 2015
 Evolution dataThis Excel Spreadsheet
 contains all of the fitness measurements used in the associated
 manuscript.
DOI: 10.5061/dryad.9095kg7
title: Data from: It's not just what you have, but how you use it: solar-positional and behavioral effects on hummingbird color appearance during courtship

description: Animals exhibit a diversity of colors that can play key roles in mating
 interactions. However, we presently lack an understanding of the relative
 importance of the environment, behavior, and natural reflective properties
 of colorful ornaments on an individual’s color appearance during
 mating-displays. We investigated interactions among structurally-based
 plumage, display environments, and courtship shuttle displays of male
 Costa's hummingbirds (Calypte costae) to test how these elements may
 differentially contribute to color appearance during shuttles. Male
 position relative to the sun was the strongest predictor of color
 appearance, with shuttle behaviors and feather reflectance playing smaller
 roles. Further, male solar orientation and shuttling behavior (e.g.
 shuttle width) were repeatable among displays, whereas male color
 appearance mostly was not. These results emphasize the contributions of
 behavior and environment to color-signaling and suggest that relying on
 reflectance measurements of colorful ornaments alone provides an
 incomplete picture of ecologically relevant visual phenotypes of
 displaying animals.
description: COHU_hummingbird_dataCO_hummingbird_data is an excel sheet with two tabs of data. The first tab - individual_data - contains information about each Costa's hummingbird male's morphology, display characteristics, plumage patch size, feather reflectance, display environment information, and chronological information. The second tab - display-color_data - contains information about each male's individual displays; specifically the angular distances he moved, the angles at which he oriented himself relative to the female, and the photometric variables (luminance, UV cone stimulation, SW cone stimulation, MW cone stimulation, and LW cone stimulation).
DOI: 10.5061/dryad.dh38s
title: Data from: Specialization of a polyphenism switch gene following serial duplications in Pristionchus nematodes

description: Polyphenism is an extreme manifestation of developmental plasticity,
 requiring distinct developmental programs and the addition of a switch
 mechanism. Because the genetic basis of polyphenism switches has only
 begun to be understood, how their mechanisms arise is unclear. In the
 nematode Pristionchus pacificus, which has a mouthpart polyphenism
 specialized for alternative diets, a gene (eud-1) executing the
 polyphenism switch was recently identified as the product of
 lineage-specific duplications. Here, we infer the role of gene
 duplications in producing a switch gene. Using reverse genetics and
 population genetic analyses, we examine evidence for competing scenarios
 of degeneration and complementation, neutral evolution, and functional
 specialization. Of the daughter genes, eud-1 alone has assumed switch-like
 regulation of the mouth polyphenism. Measurements of life-history traits
 in single, double, and triple sulfatase mutants did not, given a benign
 environment, identify alternative or complementary roles for eud-1
 paralogs. Although possible roles are still unknown, selection analyses of
 the sister species and 104 natural isolates of P. pacificus detected
 purifying selection on the genes, suggesting their functionality by their
 fixation and evolutionary maintenance. Our approach shows the tractability
 of reverse genetics in a nontraditional model system to study evolution by
 gene duplication.
description: Ragsdale_Ivers_dataOriginal data reported in Figures 3 and 4. Please note: The original sequences shown in Figure 2 of the associated publication (Ragsdale and Ivers. 2016. Evolution. doi:10.1111/evo.13011) are available at http://dx.doi.org/10.5061/dryad.34h7v
DOI: 10.5061/dryad.p31j8
title: Data from: The impact of library preparation protocols on the accuracy of allele frequency estimates in Pool-Seq data

description: Sequencing pools of individuals (Pool-Seq) is a cost-effective method to
 determine genome-wide allele frequency estimates. Given the importance of
 meta-analyses combining data sets, we determined the influence of
 different genomic library preparation protocols on the consistency of
 allele frequency estimates. We found that typically no more than 1% of the
 variation in allele frequency estimates could be attributed to differences
 in library preparation. Also read length had only a minor effect on the
 consistency of allele frequency estimates. By far, the most pronounced
 influence could be attributed to sequence coverage. Increasing the
 coverage from 30- to 50-fold improved the consistency of allele frequency
 estimates by at least 27%. We conclude that Pool-Seq data can be easily
 combined across different library preparation methods, but sufficient
 sequence coverage is key to reliable results.
description: Python scripts used for
 the analysisfor details about the
 script see the attached readmescripts-mre-koflernolteschlotc.zipset of high quality SNPs used in the analysisSNPs were identified by pooling the allele counts acrosss all libraries and requiring a minium base quality of 40 and a minimum allele count of 3; contains SNPs for D.melanogaster and D.simulans separatelysnps-kofnolschlot.zipallele counts for all sites, all libraries and all experiments (PoPoolation2 data)for detail see the attached readme fileallelelcounts.zip
DOI: 10.5061/dryad.5h45c
title: Data from: Temporal trends of predation resistance in Paleozoic crinoid arm branching morphologies

description: The rise of durophagous predators during the Paleozoic represents an
 ecological constraint imposed on sessile marine fauna. In crinoids, it has
 been suggested that increasing predation pressure drove the spread of
 adaptations against predation. Damage to a crinoid's arms from
 nonlethal predation varies as a function of arm branching pattern. Here,
 using a metric for resilience to predation (“expected arm loss,” EAL), we
 test the hypothesis that the increase in predation led to more
 predation-resistant arm branching patterns (lower EAL) among Paleozoic
 crinoids. EAL was computed for 230 genera of Paleozoic crinoids and
 analyzed with respect to taxonomy and time. The results show significant
 variability among taxa. Camerates, especially monobathrids, display a
 pattern of increasingly convergent and predation-resistant arm
 morphologies from the Ordovician through the Devonian, with no significant
 change during the Mississippian. In contrast, the mean EAL among cladids
 follows no overall trend through the Paleozoic. Regenerating arms are
 known to be significantly more common in camerates than in other Paleozoic
 taxa; if regeneration is taken as a proxy for nonlethal interactions with
 durophagous predators, this indicates that nonlethal predation occurred
 more often among camerates throughout the Early and Middle Paleozoic. In
 addition, frequency of injury among camerates is inversely correlated with
 EAL and positively correlated with infestation by parasitic snails. From
 this we conclude that decreasing EAL signals a selective pressure in favor
 of resistance to grazing predation in camerates but not in other
 subclasses before the Mississippian, with an apparent relaxation in this
 constraint after the late Devonian extinctions.
description: EALdataGenera used in analyses, with ranges from Webster (2003) and expected arm loss calculated here.infestation-regenerationData on genera found infested with parasitic platyceratid snails and those found with regenerating arms (compiled from papers by Baumiller and Gahn), along with EAL values calculated herein.
DOI: 10.5061/dryad.33m48
title: Data from: Dissecting molecular evolution in the highly diverse plant clade Caryophyllales using transcriptome sequencing

description: Many phylogenomic studies based on transcriptomes have been limited to
 “single-copy” genes due to methodological challenges in homology and
 orthology inferences. Only a relatively small number of studies have
 explored analyses beyond reconstructing species relationships. We sampled
 69 transcriptomes in the hyperdiverse plant clade Caryophyllales and 27
 outgroups from annotated genomes across eudicots. Using a combined
 similarity- and phylogenetic tree-based approach, we recovered 10,960
 homolog groups, where each was represented by at least eight ingroup taxa.
 By decomposing these homolog trees, and taking gene duplications into
 account, we obtained 17,273 ortholog groups, where each was represented by
 at least ten ingroup taxa. We reconstructed the species phylogeny using a
 1,122-gene data set with a gene occupancy of 92.1%. From the homolog
 trees, we found that both synonymous and nonsynonymous substitution rates
 in herbaceous lineages are up to three times as fast as in their woody
 relatives. This is the first time such a pattern has been shown across
 thousands of nuclear genes with dense taxon sampling. We also pinpointed
 regions of the Caryophyllales tree that were characterized by relatively
 high frequencies of gene duplication, including three previously
 unrecognized whole-genome duplications. By further combining information
 from homolog tree topology and synonymous distance between paralog pairs,
 phylogenetic locations for 13 putative genome duplication events were
 identified. Genes that experienced the greatest gene family expansion were
 concentrated among those involved in signal transduction and
 oxidoreduction, including a cytochrome P450 gene that encodes a key enzyme
 in the betalain synthesis pathway. Our approach demonstrates a new
 approach for functional phylogenomic analysis in nonmodel species that is
 based on homolog groups in addition to inferred ortholog groups.
description: cary_dryad.tar
DOI: 10.5061/dryad.n8v973b
title: Data from: Genetic decline, restoration and rescue of an isolated ungulate population

description: Isolation of small populations is expected to reduce fitness through
 inbreeding and loss of genetic variation, impeding population growth and
 compromising population persistence. Species with long generation time are
 the least likely to be rescued by evolution alone. Management
 interventions that maintain or restore genetic variation to assure
 population viability are consequently of significant importance. We
 investigated, over 27 years, the genetic and demographic consequences of a
 demographic bottleneck followed by artificial supplementation in an
 isolated population of bighorn sheep (Ovis canadensis). Based on a
 long-term pedigree and individual monitoring, we documented the genetic
 decline, restoration and rescue of the population. Microsatellite analyses
 revealed that the demographic bottleneck reduced expected heterozygosity
 and allelic diversity by 6.2 and 11.3%, respectively, over two
 generations. Following supplementation, first-generation admixed lambs
 were 6.4% heavier at weaning and had 28.3% higher survival to 1 year
 compared to lambs of endemic ancestry. Expected heterozygosity and allelic
 diversity increased by 4.6 and 14.3% after two generations through new
 alleles contributed by translocated individuals. We found no evidence for
 outbreeding depression and did not see immediate evidence of swamping of
 local genes. Rapid intervention following the demographic bottleneck
 allowed the genetic restoration and rescue of this bighorn sheep
 population, likely preventing further losses at both the genetic and
 demographic levels. Our results provide further empirical evidence that
 translocation can be used to reduce inbreeding depression in nature and
 has the potential to mitigate the effect of human-driven environmental
 changes on wild population.
description: Poirier2018_RcodesContains all R codes and a Read.me file providing a short description of included files.Poirier2018_DataFilesContains all data files. See README.txt file for a description of files and variables.
DOI: 10.5061/dryad.5fj1310p
title: Data from: QTL linkage mapping of wing length in zebra finch using genome-wide single nucleotide polymorphisms markers

description: Avian wing length is an important trait that covaries with the ecology and
 migratory behaviour of a species and tends to change rapidly when the
 conditions are altered. Long-distance migrants typically have longer wings
 than short-distance migrants and sedentary species, and long-winged
 species also tend to be more dispersive. Although the substantial
 heritability of avian wing length is well established, the identification
 of causal genes has remained elusive. Based on large-scale genotyping of
 1404 informative single nucleotide polymorphisms (SNP) in a captive
 population of 1067 zebra finches, we here show that the within-population
 variation of relative wing length (h2 = 0.74 ± 0.05) is associated with
 standing genetic variation in at least six genomic regions (one
 genome-wide significant and five suggestive). The variance explained by
 these six quantitative trait loci (QTL) sums to 36.8% of the phenotypic
 variance (half of the additive genetic variance), although this likely is
 an overestimate attributable to the Beavis effect. As avian wing length is
 primarily determined by the length of the primary feathers, we then
 searched for candidate genes that are related to feather growth.
 Interestingly, all of the QTL signals co-locate with Wnt growth factors
 and closely interacting genes (Wnt3a, Wnt5a, Wnt6, Wnt7a, Wnt9a, RhoU and
 RhoV). Our findings therefore suggest that standing genetic variation in
 the Wnt genes might be linked to avian wing morphology, although there are
 many other genes that also fall within the confidence regions.
description: data_phenotypesThe table contains data on phenotypes for all individuals (IndID). Columns Tarsus and Wing give tarsus and wing length in mm. F_Gen, FBroodID and Wline are the identifiers for the mother, the brood of rearing, the maternal line and the measuring session, respectively. Age280 is an age identifier that separates individuals below 280 days of age (Age280=0) and those above 280 days of age (Age280=1) at the time of measuring. F is the inbreeding coefficient. Sex is the sex of the subject (0=females, 1=males).
DOI: 10.5061/dryad.hk14j
title: Data from: Factors affecting GEBV accuracy with single-step Bayesian models

description: A single-step approach to obtain genomic prediction was firstly proposed
 in 2009. Many studies have investigated the components of GEBV accuracy in
 genomic selection. However, it is still unclear how the population
 structure and the relationships between training and validation
 populations influence GEBV accuracy in term of single-step analysis. Here,
 we explored the components of GEBV accuracy in single-step Bayesian
 analysis with a simulation study. Three scenarios with various numbers of
 QTL (5, 50 and 500) were simulated. Three models were implemented to
 analyze the simulated data: single-step GBLUP (SSGBLUP), single-step
 BayesA (SS-BayesA) and single-step BayesB (SS-BayesB). According to our
 results, GEBV accuracy was influenced by the relationships between the
 training and validation populations more significantly for ungenotyped
 animals than that for genotyped animals. SS-BayesA/BayesB showed an
 obvious advantage over SSGBLUP with the scenarios of 5 and 50 QT L.
 SS-BayesB model obtained the lowest accuracy with the 500 QTL in the
 simulation. SS-BayesA model was the most efficient and robust considering
 all QTL scenarios. Generally, both the relationships between training and
 validation populations and LD between markers and QTL contributed to GEBV
 accuracy in the single-step analysis, and the advantages of single-step
 Bayesian models were more apparent when the trait is controlled by fewer
 QTL.
description: data
DOI: 10.5061/dryad.cn667
title: Data from: Food vibrations: Asian spice sets lips trembling

description: Szechuan pepper, a widely used ingredient in the cuisine of many Asian
 countries, is known for the tingling sensation it induces on the tongue
 and lips. While the molecular mechanism by which Szechuan pepper activates
 tactile afferent fibres has been clarified, the tingling sensation itself
 has been less studied, and it remains unclear which fibres are
 responsible. We investigated the somatosensory perception of tingling in
 humans to identify the characteristic temporal frequency and compare this
 to the established selectivity of tactile afferents. Szechuan pepper was
 applied to the lower lip of participants. Participants judged the
 frequency of the tingling sensation on the lips by comparing this with the
 frequencies of mechanical vibrations applied to their right index finger.
 The perceived frequency of the tingling was consistently at around 50 Hz,
 corresponding to the range of tactile RA1 afferent fibres. Furthermore,
 adaptation of the RA1 channel by prolonged mechanical vibration reliably
 reduced the tingling frequency induced by Szechuan pepper, confirming that
 the frequency-specific tactile channel is shared between Szechuan pepper
 and mechanical vibration. Combining information about molecular reactions
 at peripheral receptors with quantitative psychophysical measurement may
 provide a unique method for characterizing unusual experiences by
 decomposing them into identifiable minimal units of sensation.
description: raw_dataThis is the raw data associated with the the paper accepted in Proceedings of Royal Society: Biological Sciences, entitled; "Food vibrations: Asian spice sets lips trembling". It is a human psychophysical data about tactile frequency perception. Please see the README.txt for the detail of the data structure, as well as the summary of the data acquisition.
DOI: 10.5061/dryad.12pn2
title: Data from: Buoyancy mechanisms limit preservation of coleoid cephalopod soft tissues in Mesozoic Lagerstätten

description: Coleoid cephalopods are characterized by internalization of their shell,
 and are divided into the ten-armed Decabrachia (squids and cuttlefish) and
 the eight-armed Vampyropoda (octopuses and vampire squid). They have a
 rich fossil record predominantly of the limited biomineralized skeletal
 elements they possess: arm hooks, statoliths, mouthparts (the buccal mass)
 and internal shell (gladius or pen), although exquisitely preserved soft
 tissue coleoids are known from several Lagerstätten worldwide. Recent
 studies have shown that although morphological similarities between extant
 decabrachian gladii and fossil examples exist, no known examples of fossil
 decabrachians are currently known. However, molecular clock data and
 phylogenetic bracketing suggest that they should be present in
 Lagerstätten that are rich in vampyropod soft tissue fossils (i.e. Hâkel
 and Hâdjoula Lagerstätten, Cretaceous, Lebanon). We propose that a
 hitherto unknown taphonomic bias pertaining to the differing methods of
 buoyancy control within coleoid groups limits preservation potential. Both
 negatively and neutrally buoyant decabrachians use chemical buoyancy
 control (ammonia) whereas vampyropods do not. In the event of rapid burial
 in an environment conducive to exceptional preservation, ammonia
 dramatically decreases the ability of the decabrachian carcass to generate
 the required pH for authigenic calcium phosphate replacement, limiting its
 preservation potential. Moreover, the greater surface area and
 comparatively fragile dermis further decrease the potential for
 fossilization. This taphonomic bias may have contributed to the lack of
 preserved labile soft-tissues in other cephalopods groups such as the
 ammonoids.
description: Experimental data of
 coleoid decaypH recordings over 14
 day periods for octopus and squid carcasses and body parts. Ammonia
 readings for each experimental run.TC_Ceph_Taph_data.xlsx
DOI: 10.5061/dryad.km728
title: Data from: Morphometric analysis and taxonomic revision of Anisopteromalus Ruschka (Hymenoptera: Chalcidoidea: Pteromalidae) – an integrative approach

description: We use an integrative taxonomic approach to revise the genus
 Anisopteromalus. In particular, we apply multivariate ratio analysis
 (MRA), a rather new statistical method based on principal component
 analysis (PCA) and linear discriminant analysis (LDA), to numerous body
 measurements and combine the data with those from our molecular analysis
 of Cytb and ITS2 genetic markers (on a subset of species) and all
 available published data on morphology, karyology, behavior, host
 associations, and geographic distribution. We demonstrate that the
 analysis of quantitative characters using MRA plays a major role for the
 integration of name-bearing types and thus for the association of taxa
 with names. Six species are recognized, of which two are new: A. cornis
 Baur sp. n. and A. quinarius Gokhman & Baur sp. n. For
 Anisopteromalus calandrae (Howard), a well-known, cosmopolitan parasitoid
 of stored-product pests, we have selected a neotype to foster continuity
 and stability in the application of this important name. The species was
 sometimes confused with the related A. quinarius sp. n., another
 cosmopolitan species that is frequently encountered in similar
 environments. We also show that several species originally described or
 later put under Anisopteromalus actually belong to different genera:
 Cyrtoptyx camerunus (Risbec) comb. n.; Meraporus glaber (Szelényi) comb.
 n.; Dinarmus schwenkei (Roomi, Khan & Khan) comb. n. Neocatolaccus
 indicus Ayyar & Mani is confirmed as a junior synonym of Oxysychus
 sphenopterae (Ferrière) syn. n. and Anisopteromalus calandrae brasiliensis
 (Domenichini) stat. rev. must be considered as a valid but doubtful taxon.
description: Baur_et_al_2014_Anisopteromalus_raw_data_files_and_images