cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g0v6h003
title: Data from: The precopulatory function of male genital spines in Drosophila ananassae [Doleschall] (Diptera: Drosophilidae) revealed by laser surgery

description: That male genital morphology evolves via postcopulatory sexual selection
 is a widely held view. In contrast, the pre-copulatory sexual selection
 hypothesis for genital evolution has received less attention. Here, we
 test the hypothesis that male genital spines of Drosophila ananassae
 promote competitive male copulation success. Using laser surgery to
 manipulate trait size, we demonstrate that incremental reductions of spine
 length progressively reduce male copulation success: males without spines
 failed entirely to copulate because of an inability to couple the
 genitalia together, whereas males with halfway ablated and blunted spines
 suffered reductions in copulation success of 87% and 13%, respectively.
 The decrease in copulation success resulting from spine length reduction
 was markedly stronger in sexually competitive environments than in
 non-competitive environments, and females expressed resistance behaviors
 similarly toward competing male treatments, demonstrating directly the
 role of genital spines in promoting competitive copulation success.
 Because these spines are widespread within Drosophila, as are other
 genital traits with pre-copulatory functions among animals, pre-copulatory
 sexual selection may have a more pervasive role in genital evolution than
 previously recognized.
description: Grieshop &
 Polak_2012_Evolution
DOI: 10.5061/dryad.t56cn
title: Data from: Modeling effects of nonbreeders on population growth estimates

description: Adult individuals that do not breed in a given year occur in a wide range
 of natural populations. However, such nonbreeders are often ignored in
 theoretical and empirical population studies, limiting our knowledge of
 how nonbreeders affect realized and estimated population dynamics and
 potentially impeding projection of deterministic and stochastic population
 growth rates. We present and analyse a general modelling framework for
 systems where breeders and nonbreeders differ in key demographic rates,
 incorporating different forms of nonbreeding, different life histories and
 frequency-dependent effects of nonbreeders on demographic rates of
 breeders. Comparisons of estimates of deterministic population growth
 rate, λ, and demographic variance, math formula, from models with and
 without distinct nonbreeder classes show that models that do not
 explicitly incorporate nonbreeders give upwardly biased estimates of math
 formula, particularly when the equilibrium ratio of nonbreeders to
 breeders, math formula, is high. Estimates of λ from empirical
 observations of breeders only are substantially inflated when individuals
 frequently re-enter the breeding population after periods of nonbreeding.
 Sensitivity analyses of diverse parameterizations of our model framework,
 with and without negative frequency-dependent effects of nonbreeders on
 breeder demographic rates, show how changes in demographic rates of
 breeders vs. nonbreeders differentially affect λ. In particular, λ is most
 sensitive to nonbreeder parameters in long-lived species, when math
 formula, and when individuals are unlikely to breed at several consecutive
 time steps. Our results demonstrate that failing to account for
 nonbreeders in population studies can obscure low population growth rates
 that should cause management concern. Quantifying the size and demography
 of the nonbreeding section of populations and modelling appropriate
 demographic structuring is therefore essential to evaluate
 nonbreeders' influence on deterministic and stochastic population
 dynamics.
description: R code for constructing
 and analyzing matrices with nonbreedersR code to construct and
 analyze matrices in systems with pre- or post-breeding census, different
 types of nonbreeders, and with or without negative frequency dependence in
 breeder survival or fecundity. Analyses include growth rate, stable stage
 structure, reproductive value, demographic variance, comparison to
 equivalent Leslie matrix model, sensitivity analysis, effect of only
 observing breeders, and more.Lee_Nonbreeder_matrix_analysis_code.RR code for running sensitivity analyses in systems with nonbreedersR code for running sensitivity analyses on systems with different types of nonbreeders, with or without negative frequency dependence in breeder survival or reproduction.Lee_Nonbreeder_sensitivity_analysis_code.R
DOI: 10.5061/dryad.1mq2ts3
title: Data from: A Curated Cancer Clinical Outcomes Data Base (C3OD) for accelerating patient recruitment in cancer clinical trials

description: Data used to determine patient eligibility for cancer clinical trials
 often come from disparate sources that are typically maintained by
 different groups within an institution, use differing technologies, and
 are stored in different formats. Collecting data and resolving
 inconsistencies across sources increase the time it takes to screen
 eligible patients, potentially delaying study completion. To address these
 challenges, the Biostatistics and Informatics Shared Resource at The
 University of Kansas Cancer Center developed the Cancer Curated Clinical
 Outcomes Database (C3OD). C3OD merges data from the electronic medical
 record (EMR), tumor registry, bio-specimen and data registry, and allows
 querying through a single unified platform. By centralizing access and
 maintaining appropriate controls, C3OD allows researchers to more rapidly
 obtain detailed information about each patient in order to accelerate
 eligibility screening. This paper describes the design of this informatics
 platform as well as initial assessments of its reliability and usability.
description: C30D usability survey
 dataThis data file contains
 the participant responses to the 21-item C3OD usability survey
 (Supplementary File 3) given to clinical research
 coordinators.
DOI: 10.5061/dryad.fg475
title: Data from: Evolution of antigenic diversity in the tick-transmitted bacterium Borrelia afzelii: a role for host specialization?

description: Antigenic diversity in pathogenic microbes can be a result of at least
 three different processes: diversifying selection by acquired immunity,
 host-pathogen coevolution, and/or host specialization. Here, we
 investigate if host specialization drives diversity at ospC (which encodes
 an immunodominant surface protein) in the tick-transmitted bacterium
 Borrelia afzelii. We determined prevalence and infection intensity of ospC
 strains in naturally infected wild mammals (rodents and shrews) by 454
 amplicon sequencing in combination with qPCR. Neither prevalence nor
 infection intensity of specific ospC strains varied in a species-specific
 manner (i.e. there were no significant ospC × host species interactions).
 Rankings of ospC prevalences were strongly positively correlated across
 host species. Rankings of ospC infection intensities were correlated more
 weakly, but only in one case significantly less than 1. ospC prevalences
 in the studied mammals were similar to those in ticks sampled at the study
 site, indicating that we did not miss any mammal species that are
 important hosts for specific ospC strains. Based on this we conclude that
 there is at best limited host specialization in B. afzelii, and that other
 processes are likely the main drivers of ospC diversity.
description: Raberg_HostSpecializationThis file contains qPCR and 454 amplicon sequencing data of Borrelia afzelii from tissue samples from mammals.
DOI: 10.5281/zenodo.18382433
title: TABLE. 4 in A revised infrageneric classification of Bellevalia Lapeyr. (Asparagaceae: Scilloideae) based on molecular analysis

description: TABLE. 4. Polymorphic positions of four chloroplast sequence alignment in the studied species of Bellevalia.
Species/nucleotide positionmat Krbc Ltrn L introntrn L- trn F spacer1 6 71 7 63 0 64 5 45 3 29 3 01 0 3 21 2 6 61 3 3 51 8 7 01 9 0 01 9 8 72 0 1 12 1 2 52 4 4 02 4 6 02 5 1 82 7 1 33 1 1 03 1 2 53 1 5 7B. dubiaACTCGACCGCAGAACGAAAGAB. glaucaACTCGACCGCAGAACGAAAGAB. heweriACTCGACCGCAGAACGAAAGAB. longistylaACTCGACCGCAGAACGAAAGAB. savicziiACTCGACCGCAGAACGAAAGAB. speciosaACTCGACCGCAGAACGAAAGAB. macrobotrysACGTGATCGTAGAACGAAAGGB. romanaCCGTTATCGTAAAAACAAAAGB. tabrizianaCTGTTGTTATCAGGACGGCAGB. tristisCTGTTGTTATCAGGACGGCAGB. assadiiCTGTTGTTATCAGGACGGCAGB. fominiiCTGTTGTTATCAGGACGGCAGB. paradoxaCTGTTGTTATCAGGACGGCAGB. wendelboiCTGTTGTTATCAGGACGGCAG
description: Published as part of Jafari, Azarnoosh, Vaezi, Jamil, Forghanifard, Mohammad Mahdi, Forest, Félix & Manning, John C., 2021, A revised infrageneric classification of Bellevalia Lapeyr. (Asparagaceae: Scilloideae) based on molecular analysis, pp. 80 in Phytotaxa 525 (1) on page 80, DOI: 10.11646/phytotaxa.525.1.9, http://zenodo.org/record/5681869
DOI: 10.5281/zenodo.18382432
title: TABLE. 4 in A revised infrageneric classification of Bellevalia Lapeyr. (Asparagaceae: Scilloideae) based on molecular analysis

description: TABLE. 4. Polymorphic positions of four chloroplast sequence alignment in the studied species of Bellevalia.
Species/nucleotide positionmat Krbc Ltrn L introntrn L- trn F spacer1 6 71 7 63 0 64 5 45 3 29 3 01 0 3 21 2 6 61 3 3 51 8 7 01 9 0 01 9 8 72 0 1 12 1 2 52 4 4 02 4 6 02 5 1 82 7 1 33 1 1 03 1 2 53 1 5 7B. dubiaACTCGACCGCAGAACGAAAGAB. glaucaACTCGACCGCAGAACGAAAGAB. heweriACTCGACCGCAGAACGAAAGAB. longistylaACTCGACCGCAGAACGAAAGAB. savicziiACTCGACCGCAGAACGAAAGAB. speciosaACTCGACCGCAGAACGAAAGAB. macrobotrysACGTGATCGTAGAACGAAAGGB. romanaCCGTTATCGTAAAAACAAAAGB. tabrizianaCTGTTGTTATCAGGACGGCAGB. tristisCTGTTGTTATCAGGACGGCAGB. assadiiCTGTTGTTATCAGGACGGCAGB. fominiiCTGTTGTTATCAGGACGGCAGB. paradoxaCTGTTGTTATCAGGACGGCAGB. wendelboiCTGTTGTTATCAGGACGGCAG
description: Published as part of Jafari, Azarnoosh, Vaezi, Jamil, Forghanifard, Mohammad Mahdi, Forest, Félix & Manning, John C., 2021, A revised infrageneric classification of Bellevalia Lapeyr. (Asparagaceae: Scilloideae) based on molecular analysis, pp. 80 in Phytotaxa 525 (1) on page 80, DOI: 10.11646/phytotaxa.525.1.9, http://zenodo.org/record/5681869
DOI: 10.5061/dryad.3g280
title: Data from: Surrogate modelling for the prediction of spatial fields based on simultaneous dimensionality reduction of high-dimensional input/output spaces

description: Time-consuming numerical simulators for solving groundwater flow and
 dissolution models of physico-chemical processes in deep aquifers normally
 require some of the model inputs to be defined in high-dimensional spaces
 in order to return realistic results. Sometimes, the outputs of interest
 are spatial fields leading also to high-dimensional output spaces.
 Although Gaussian process emulation has been satisfactorily used for
 computing faithful and inexpensive approximations of complex simulators,
 these have been mostly applied to problems defined in low-dimensional
 input spaces. In this paper, we propose a method for simultaneously
 reducing the dimensionality of very high-dimensional input and output
 spaces in Gaussian process emulators for stochastic partial differential
 equation models while retaining the qualitative features of the original
 models. This allows us to build a surrogate model for the prediction of
 spatial fields in such time-consuming simulators. We apply the methodology
 to a model of convection and dissolution processes occurring during carbon
 capture and storage.
description: Supporting data for the
 figures showed in the manuscriptSupporting
 dataRSOS-171933.rar
DOI: 10.5061/dryad.bv9247d
title: Data from: On dangerous ground: the evolution of body armour in cordyline lizards

description: Animal body armour is often considered an adaptation that protects prey
 against predatory attacks, yet comparative studies that link the
 diversification of these allegedly protective coverings to differential
 predation risk or pressure are scarce. Here, we examine the evolution of
 body armour, including spines and osteoderms, in Cordylinae, a radiation
 of southern African lizards. Using phylogenetic comparative methods, we
 attempt to identify the ecological and environmental correlates of body
 armour that may hint at the selective pressures responsible for defensive
 trait diversification. Our results show that species inhabiting arid
 environments are more likely to possess elaborated body armour,
 specifically osteoderms. We did not find any effect of estimated predation
 pressure or risk on the degree of body armour. These findings suggest that
 body armour might not necessarily evolve in response to direct
 interactions with predators, but rather as a result of increased
 habitat-mediated predation risk. Furthermore, we discuss the possibility
 that osteoderms might have been shaped by factors unrelated to predation.
description: Data predation
 indicesData used to calculate
 terrestrial and aerial predation pressure/risk.Data environmental
 variablesClimatic and
 environmental variables for each species of cordyline
 lizard.
DOI: 10.5061/dryad.3nd75
title: Data from: AFLPs and mitochondrial haplotypes reveal local adaptation to extreme thermal environments in a freshwater gastropod

description: The way environmental variation shapes neutral and adaptive genetic
 variation in natural populations is a key issue in evolutionary biology.
 Genome scans allow the identification of the genetic basis of local
 adaptation without previous knowledge of genetic variation or traits under
 selection. Candidate loci for divergent adaptation are expected to show
 higher FST than neutral loci influenced solely by random genetic drift,
 migration and mutation. The comparison of spatial patterns of neutral
 markers and loci under selection may help disentangle the effects of gene
 flow, genetic drift and selection among populations living in contrasting
 environments. Using the gastropod Radix balthica as a system, we analyzed
 376 AFLP markers and 25 mtDNA COI haplotypes for candidate loci and
 associations with local adaptation among contrasting thermal environments
 in Lake Mývatn, a volcanic lake in northern Iceland. We found that 2% of
 the analysed AFLP markers were under directional selection and 12% of the
 mitochondrial haplotypes correlated with differing thermal habitats. The
 genetic networks were concordant for AFLP markers and mitochondrial
 haplotypes, depicting distinct topologies at neutral and candidate loci.
 Neutral topologies were characterized by intense gene flow revealed by
 dense nets with edges connecting contrasting thermal habitats, whereas the
 connections at candidate loci were mostly restricted to populations within
 each thermal habitat and the number of edges decreased with temperature.
 Our results suggest microgeographic adaptation within Lake Mývatn and
 highlight the utility of genome scans in detecting adaptive divergence.
description: Lake Mývatn_Radix
 balthica AFLPs
DOI: 10.5061/dryad.8vn5d
title: Data from: Genetic architecture of isolation between two species of Silene with sex chromosomes and Haldane's rule

description: Examination of the genetic architecture of hybrid breakdown can provide
 insight into the genetic mechanisms of commonly observed isolating
 phenomena such as Haldane’s rule. We used line-cross analysis to dissect
 the genetic architecture of divergence between two plant species that
 exhibit Haldane’s rule for male sterility and rarity, Silene latifolia and
 Silene diclinis. We made 15 types of crosses, including reciprocal F1, F2,
 backcrosses, and later-generation crosses, grew the seeds to flowering,
 and measured the number of viable ovules, proportion of viable pollen, and
 sex ratio. Typically, Haldane’s rule for male rarity in XY animal hybrids
 is explained by interactions involving recessive X-linked alleles that are
 deleterious when hemizygous (dominance theory), while sterility is
 explained by rapid evolution of spermatogenesis genes (faster-male
 evolution). In contrast, we found that the genetic mechanisms underlying
 Haldane’s rule between the two Silene species did not follow these
 conventions. Dominance theory was sufficient to explain male sterility,
 but male rarity likely involved faster-male evolution. We also found an
 effect of the neo-sex chromosomes of S. diclinis on the extreme rarity of
 some hybrid males. Our findings suggest that the genetic architecture of
 Haldane’s rule in dioecious plants may differ from those commonly found in
 animals.
description: Ovule number, pollen
 viability, and sex ratio by cross typeThe data are counts of
 ovule number, pollen viability, and sex ratio (by family) for 15 different
 crosses between Silene latifolia and Silene diclinis used to investigate
 the genetic basis of Haldane's rule between these two flowering plant
 species. Cross type is as in Table 1 of the paper these data are
 associated with.Silene data for
 Dryad.xlsx
DOI: 10.5061/dryad.55304br
title: Data from: Age, condition and dominance-related sexual ornament size before and during the breeding season in the black grouse Lyrurus tetrix

description: Male ornaments function as honest cues of male quality in many species and
 are subject to intra- and intersexual selection. These ornaments are
 generally studied during peak expression, however their size outside the
 breeding season may determine ultimate ornament size and costliness, and
 as such reproductive success. We investigated whether male black grouse
 Lyrurus tetrix eye comb size was related to age, condition and measures of
 male dominance before and during the breeding season. Total combined eye
 comb size began to increase ~70 days before the start of the breeding
 season. Adult males (aged ≥ 2 years old) had consistently larger eye combs
 than younger males (1 year old) both before and during the breeding
 season. Heavier and more dominant adult males (attending the lek more
 frequently and successfully reproducing) had larger eye combs. For younger
 males, those that were heavier had larger eye combs. Additionally, males
 that spent more time on the lek showed increased eye comb size as the
 breeding season approached. Overall we find that ornament size is
 positively related to dominance and condition before and during the
 breeding season. Since dominance is accrued through year-round
 interactions in many species, the ability to maintain larger signals over
 prolonged periods,
description: Harris et al. 2018 -
 age, condition, dominance and eye comb size dataData collected in the
 field from 5 protected lek sites in central Finland (centred around
 Petäjävesi: lat. 62°25′N, long. 25°18′E) from January-May, 2001-13 and
 2015. Behavioural measures were then calculated at a later date. Legend
 included within database.Harris et al. 2018 -
 data.xlsx
DOI: 10.5061/dryad.jc2pj
title: Data from: A comparison of single nucleotide polymorphism and microsatellite markers for analysis of parentage and kinship in a cooperatively breeding bird

description: The development of genetic markers has revolutionized molecular studies
 within and among populations. Although poly-allelic microsatellites are
 the most commonly used genetic marker for within-population studies of
 free-living animals, biallelic single nucleotide polymorphisms, or SNPs,
 have also emerged as a viable option for use in nonmodel systems. We
 describe a robust method of SNP discovery from the transcriptome of a
 nonmodel organism that resulted in more than 99% of the markers working
 successfully during genotyping. We then compare the use of 102 novel SNPs
 with 15 previously developed microsatellites for studies of parentage and
 kinship in cooperatively breeding superb starlings (Lamprotornis superbus)
 that live in highly kin-structured groups. For 95% of the offspring
 surveyed, SNPs and microsatellites identified the same genetic father, but
 only when behavioural information about the likely parents at a nest was
 included to aid in assignment. Moreover, when such behavioural information
 was available, the number of SNPs necessary for successful parentage
 assignment was reduced by half. However, in a few cases where candidate
 fathers were highly related, SNPs did a better job at assigning fathers
 than microsatellites. Despite high variation between individual pairwise
 relatedness values, microsatellites and SNPs performed equally well in
 kinship analyses. This study is the first to compare SNPs and
 microsatellites for analyses of parentage and relatedness in a species
 that lives in groups with a complex social and kin structure. It should
 also prove informative for those interested in developing SNP loci from
 transcriptome data when published genomes are unavailable.
description: SNP
 GenotypesSNP genotypes for 224
 individualsWeinman et
 al_SNPgenotypes.csvMicrosatellite
 genotypesMicrosatellite genotypes
 for 225 individualsWeinman et al_Microsatgenotypes
 .csvWeinman et al. Social
 ParentsSummary of behavioral
 focal observations of social parentsWeinman et
 al_SocialParents.csv
DOI: 10.5061/dryad.1122
title: Data from: Fine-scale spatial and temporal population genetics of Aedes japonicus, a new US mosquito, reveal multiple introductions

description: The newly introduced mosquito Aedes japonicus has expanded from its
 original range in Northeastern Asia to twenty-two US states (including
 Hawaii) plus Canada and northern Europe. Our objectives were to test an
 earlier hypothesis of multiple introductions of this species to the
 Northeastern US, and evaluate putative temporal changes in genetic makeup.
 Using a panel of seven microsatellite loci, we confirmed the existence of
 two abundant genetic forms in specimens originally collected in 1999-2000
 (FST value based on microsatellite data = 0.26) that matches the
 disjunctive distribution of mitochondrial haplotypes. To examine the
 distribution of the two genetic â typesâ across Pennsylvania we created a
 fine-scale genetic map of Ae. japonicus using 439 specimens collected from
 54 Pennsylvania counties in 2002-03. We also made direct comparisons
 between collections in 1999-2000 and new collections made in 2004-2005
 obtained from the same areas in the northeastern US. We observed that the
 strong association between mtDNA haplotype and microsatellite signature
 seen in 1999-2000 had weakened significantly by 2002 across Pennsylvania,
 a trend continued to some extent in 2004-2005 in PA, NJ, and NY,
 indicating that once easily distinguishable separate introductions are
 merging. The two expanding genetic forms create a complex correlation
 between spatial and genetic distances. The existence of multiple
 introductions would be obscured without sampling early and across time
 with highly polymorphic molecular markers. Our results provide a
 high-resolution analysis of the spatial and temporal dynamics of a newly
 introduced disease vector and argue that successive introductions may be a
 common pattern for invasive mosquitoes.
description: Aej-OldNew.txtMicrosatellite alleles for a comparison over timeAej-PA.txtMicrosatellite alleles for fine resolution analysis across Pennsylvania (allele sizes)Aej-PA2.txtMicrosatellite alleles for fine resolution analysis across Pennsylvania (for Phylip)
DOI: 10.5281/zenodo.18382354
title: Tetanic Stimulation and Carbachol Modulation: Robust Strategies for Enhancing Recognition in Homogeneous and Modular Biological Neural Networks

description: Code and Data for the Manuscript.