cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8hk5r
title: Data from: Passively stuck: death does not affect gecko adhesion strength

description: Many geckos use adhesive toe pads on the bottom of their digits to attach
 to surfaces with remarkable strength. Although gecko adhesion has been
 studied for hundreds of years, gaps exist in our understanding at the
 whole-animal level. It remains unclear whether the strength and
 maintenance of adhesion are determined by the animal or are passively
 intrinsic to the system. Here we show, for the first time, that strong
 adhesion is produced passively at the whole-animal level. Experiments on
 both live and recently euthanized tokay geckos (Gekko gecko) revealed that
 death does not affect the dynamic adhesive force or motion of a gecko foot
 when pulled along a vertical surface. Using a novel device that applied
 repeatable and steady-increasing pulling forces to the foot in shear, we
 found that the adhesive force was similarly high and variable when the
 animal was alive (mean ± s.d. = 5.4 ± 1.7 N) and within 30 min after death
 (5.4 ± 2.1 N). However, kinematic analyses showed that live geckos are
 able to control the degree of toe pad engagement and can rapidly stop
 strong adhesion by hyperextending the toes. This study offers the first
 assessment of whole-animal adhesive force under extremely controlled
 conditions. Our findings reveal that dead geckos maintain the ability to
 adhere with the same force as living animals, disproving that strong
 adhesion requires active control.
description: SummaryTableThis is a table that summarizes the analyzed data for each of the 62 experiments that comprise the study. Experiments are in rows.mat filesThis zipped file contains 62 .mat data files, one corresponding to each experiment of the study. each mat file contains detailed data describing the kinematics and mechanics of a gecko foot during each pull.
DOI: 10.5061/dryad.s55f5
title: Data from: Using dense locality sampling resolves the subtle genetic population structure of the dispersive fish species Plecoglossus altivelis

description: In dispersive species with continuous distributions, genetic
 differentiation between local populations is often absent or subtle and
 thus difficult to detect. To incorporate such subtle differentiation into
 management plans, it may be essential to analyse many samples from many
 localities using adequate numbers of high-resolution genetic markers.
 Here, we evaluated the usefulness of dense locality sampling in resolving
 genetic population structure in the ayu (Plecoglossus altivelis), a
 dispersive fish important in Japanese inland fisheries. Genetic
 variability in, and differentiation between, ayu populations around the
 Japan–Ryukyu Archipelago were investigated in 4746 individuals collected
 from 120 localities by genotyping 12 microsatellite markers. These
 individuals represented the two subspecies of ayu, namely the Ryukyuan
 subspecies (Plecoglossus altivelis ryukyuensis) and both amphidromous and
 landlocked forms of the nominotypical subspecies (P. a. altivelis) along
 the archipelago. We successfully detected an absence of genetic
 differentiation within the landlocked form and subtle but significant
 differentiation and clear geographic patterns of genetic variation among
 populations of the amphidromous form, which had been considered
 genetically homogeneous. This suggests that dense locality sampling
 effectively resolves subtle differences in genetic population structure,
 reducing stochastic deviation in the detection of genetic differentiation
 and geographic patterns in local populations of this dispersive species.
 Resampling analyses based on empirical data sets clearly demonstrate the
 effectiveness of increasing the number of locality samples for stable and
 reliable estimations of genetic fixation indices. The genetic population
 structure observed within the amphidromous form provides useful
 information for identifying management or conservation units in ayu.
description: Microsatellite
 Genotypescustom Perl
 scripts
DOI: 10.5061/dryad.n8c22
title: Data from: The relative roles of cultural drift and acoustic adaptation in shaping syllable repertoires of island bird populations change with time since colonization

description: In birds, song divergence often precedes and facilitates divergence of
 other traits. We assessed the relative roles of cultural drift, innovation
 and acoustic adaptation in divergence of island bird dialects, using
 silvereyes (Zosterops lateralis). In recently colonized populations,
 syllable diversity was not significantly lower than source populations,
 shared syllables between populations decreased with increasing number of
 founder events and dialect variation displayed contributions from both
 habitat features and drift. The breadth of multivariate space occupied by
 recently colonized Z. l. lateralis populations was comparable to
 evolutionarily old forms that have diverged over thousands to hundreds of
 thousands of years. In evolutionarily old subspecies, syllable diversity
 was comparable to the mainland and the amount of variation in syllable
 composition explained by habitat features increased by two- to three-fold
 compared to recently colonized populations. Together these results suggest
 that cultural drift influences syllable repertoires in recently colonized
 populations, but innovation likely counters syllable loss from
 colonization. In evolutionarily older populations, the influence of
 acoustic adaptation increases, possibly favoring a high diversity of
 syllables. These results suggest that the relative importance of cultural
 drift and acoustic adaptation changes with time since colonization in
 island bird populations, highlighting the value of considering multiple
 mechanisms and timescale of divergence when investigating island song
 divergence.
description: All syllables recorded
 and categorized from studyThis file contains
 acoustic details of all syllables recorded from all Zosterops lateralis
 individuals and populations included in the current study. Data was
 gathered by DAP, all acoustic measurements were made in RavenPro 1.4
 (Cornell Lab of Ornithology).Syllables2011TOTAL.xlsx
DOI: 10.5061/dryad.78vs2
title: Data from: Rapid species-level identification of vaginal and oral lactobacilli using MALDI-TOF MS analysis and 16S rDNA sequencing

description: Background: Lactobacillus represents a large genus with different
 implications for the human host. Specific lactobacilli are considered to
 maintain vaginal health and to protect from urogenital infection. The
 presence of Lactobacillus species in carious lesions on the other hand is
 associated with progressive caries. Despite their clinical significance,
 species-level identification of lactobacilli still poses difficulties and
 mostly involves a combination of different phenotypic and genotypic
 methods. This study evaluated rapid MALDI-TOF MS analysis of vaginal and
 oral Lactobacillus isolates in comparison to 16S rDNA analysis. Results:
 Both methods were used to analyze 77 vaginal and 21 oral Lactobacillus
 isolates. The concordance of both methods was at 96% with five samples
 discordantly identified. Fifteen different Lactobacillus species were
 found in the vaginal samples, primarily L. iners, L. crispatus, L.
 jensenii and L. gasseri. In the oral samples 11 different species were
 identified, mostly L. salivarius, L. gasseri, L. rhamnosus and L.
 paracasei. Overall, the species found belonged to six different
 phylogenetic groups. For several samples, MALDI-TOF MS analysis only
 yielded scores indicating genus-level identification. However, in most
 cases the species found agreed with the 16S rDNA analysis result.
 Conclusion: MALDI-TOF MS analysis proved to be a reliable and fast tool to
 identify lactobacilli to the species level. Even though some results were
 ambiguous while 16S rDNA sequencing yielded confident species
 identification, accuracy can be improved by extending reference databases.
 Thus, mass spectra analysis provides a suitable method to facilitate
 monitoring clinically relevant Lactobacillus species.
description: Phylogenetic tree based
 on the analysis of 16S rRNA gene sequences derived from oral and vaginal
 isolates16S rDNA sequences were
 aligned using the SINA plugin (ARB software package) and distances were
 calculated using the neighbor-joining method with Jukes-Cantor correction.
 Reference sequences with accession numbers are in regular type, sample
 sequences of vaginal isolates in bold type and of oral isolates in
 bold/italics type. Sample strains are named according to their
 identification by 16S rDNA sequencing results. Bootstrap values (from 1000
 replicates) greater than 40% are shown at the branch points. The bar
 indicates 5% sequence divergence.Lactobacilli-isolates-tree.pdf
DOI: 10.5061/dryad.6qs53
title: Data from: Statin use and cognitive function: population-based observational study with long-term follow-up

description: We aimed to evaluate the association between statin use and cognitive
 function. Cognitive function was measured with the Ruff Figural Fluency
 Test (RFFT; worst score, 0; best score, 175 points) and the Visual
 Association Test (VAT; low performance, 0–10; high performance, 11–12
 points) in an observational study that included 4,095 community-dwelling
 participants aged 35–82 years. Data on statin use were obtained from a
 computerized pharmacy database. Analysis were done for the total cohort
 and subsamples matched on cardiovascular risk (N = 1232) or propensity
 score for statin use (N = 3609). We found that a total of 904 participants
 (10%) used a statin. Statin users were older than non-users: mean age (SD)
 61 (10) vs. 52 (11) years (p&lt;0.001). The median duration of statin
 use was 3.8 (interquartile range, 1.6–4.5) years. Unadjusted, statin users
 had worse cognitive performance than non-users. The mean RFFT score (SD)
 in statin users and non-users was 58 (23) and 72 (26) points, respectively
 (p&lt;0.001). VAT performance was high in 261 (29%) statin users and
 1351 (43%) non-users (p&lt;0.001). However, multiple regression
 analysis did not show a significant association of RFFT score with statin
 use (B, −0.82; 95%CI, −2.77 to 1.14; p = 0.41) nor with statin solubility,
 statin dose or duration of statin use. Statin users with high doses or
 long-term use had similar cognitive performance as non-users. This was
 found in persons with low as well as high cardiovascular risk, and in
 younger as well as older subjects. Also, the mean RFFT score per quintile
 of propensity score for statin use was comparable for statin users and
 non-users. Similar results were found for the VAT score as outcome
 measure. In conclusion, statin use was not associated with cognitive
 function. This was independent of statin dose or duration of statin use.
description: Cognition statin use
 Groningen the NetherlandsIBM SPSS Statistics 22
 file that includes the data on cognitive function (performance on the Ruff
 Figural Fluency Test and the Visual Association Test) and statin use of
 4,095 community-dwelling persons aged 35-82 years in the city of
 Groningen, the Netherlands.Cognition statin use
 Groningen the NetherlandsCSV file that includes
 the data on cognitive function (performance on the Ruff Figural Fluency
 Test and the Visual Association Test) and statin use of 4,095
 community-dwelling persons aged 35-82 years in the city of Groningen, the
 Netherlands.
DOI: 10.5061/dryad.d8810
title: Data from: A nanostructural basis for gloss of avian eggshells

description: The role of pigments in generating the colour and maculation of
 birds' eggs is well characterized, whereas the effects of the
 eggshell's nanostructure on the visual appearance of eggs are little
 studied. Here, we examined the nanostructural basis of glossiness of
 tinamou eggs. Tinamou eggs are well known for their glossy appearance, but
 the underlying mechanism responsible for this optical effect is unclear.
 Using experimental manipulations in conjunction with angle-resolved
 spectrophotometry, scanning electron microscopy, atomic force microscopy
 and chemical analyses, we show that the glossy appearance of tinamou
 eggshells is produced by an extremely smooth cuticle, composed of calcium
 carbonate, calcium phosphate and, potentially, organic compounds such as
 proteins and pigments. Optical calculations corroborate surface smoothness
 as the main factor producing gloss. Furthermore, we reveal the presence of
 weak iridescence on eggs of the great tinamou (Tinamus major), an optical
 effect never previously documented for bird eggs. These data highlight the
 need for further exploration into the nanostructural mechanisms for the
 production of colour and other optical effects of avian eggshells.
description: Contrast
 glossData for Hunter's
 contrast gloss measurements collected using a spectrophotometer.
 Spreadsheet contains specular and diffuse reflectance measurements for
 four tinamou species and an Araucana chicken.BluTin and Chicken
 specular angle spectraSpreadsheet containing
 specular reflectance measurements at different angles for three Tinamous
 major eggshells, a Gallus gallus eggshell, and a single T. major eggshell
 following cuticle removal using EDTA.Hue vs
 AngleData used in general
 linear models to test if there were relationships between the hue of
 specular measurements and specular angle. Spreadsheet contains data for
 three untreated Tinamus major eggs, a Gallus gallus egg, and a T. major
 egg following treatment with EDTA to remove the cuticle. Location ID
 designates the location at which a set of specular measurements at
 different angles were collected.
DOI: 10.5061/dryad.qk8fj
title: Data from: An SNP-based second-generation genetic map of Daphnia magna and its application to QTL analysis of phenotypic traits

description: Background: Although Daphnia is increasingly recognized as a model for
 ecological genomics and biomedical research, there is, as of yet, no
 high-resolution genetic map for the genus. Such a map would provide an
 important tool for mapping phenotypes and assembling the genome. Here we
 estimate the genome size of Daphnia magna and describe the construction of
 an SNP array based linkage map. We then test the suitability of the map
 for life history and behavioural trait mapping. The two parent genotypes
 used to produce the map derived from D. magna populations with and without
 fish predation, respectively and are therefore expected to show divergent
 behaviour and life-histories. Results: Using flow cytometry we estimated
 the genome size of D. magna to be about 238 mb. We developed an SNP array
 tailored to type SNPs in a D. magna F2 panel and used it to construct a D.
 magna linkage map, which included 1,324 informative markers. The map
 produced ten linkage groups ranging from 108.9 to 203.6 cM, with an
 average distance between markers of 1.13 cM and a total map length of
 1,483.6 cM (Kosambi corrected). The physical length per cM is estimated to
 be 160 kb. Mapping infertility genes, life history traits and behavioural
 traits on this map revealed several significant QTL peaks and showed a
 complex pattern of underlying genetics, with different traits showing
 strongly different genetic architectures. Conclusions: The new linkage map
 of D. magna constructed here allowed us to characterize genetic
 differences among parent genotypes from populations with ecological
 differences. The QTL effect plots are partially consistent with our
 expectation of local adaptation under contrasting predation regimes.
 Furthermore, the new genetic map will be an important tool for the Daphnia
 research community and will contribute to the physical map of the D. magna
 genome project and the further mapping of phenotypic traits. The clones
 used to produce the linkage map are maintained in a stock collection and
 can be used for mapping QTLs of traits that show variance among the F2
 clones.
description: Pheno and genotypes of
 Daphnia magna second-generation genetic mapPheno and genotypes in
 R/qtl format.routtu_bmc_genomics_2014.csv
DOI: 10.5061/dryad.404fh
title: Data from: "Identification of SNP markers for the endangered Ugandan red colobus (Procolobus rufomitratus tephrosceles) using RAD sequencing" in Genomic Resources Notes accepted 1 December 2014 to 31 January 2015

description: Despite dramatic growth in the field of primate genomics over the past
 decade, studies of primate population and conservation genomics in the
 wild have been hampered due to the difficulties inherent in studying
 non-model organisms and endangered species, such as lack of a reference
 genome and current challenges in de novo primate genome assembly. Here, we
 used Restriction-site Associated DNA (RAD) sequencing to develop a
 population-based SNP panel for the Ugandan red colobus (P. rufomitratus
 tephrosceles), which is a highly threatened monkey due to habitat loss. We
 analyzed blood samples from 24 individuals from Kibale National Park
 (Uganda) using single-end RAD sequencing. We obtained 70,773,857 reads, of
 which 58,814,906 passed the filtering steps. Using the program STACKS v.
 1.11 we identified 113,376 loci, of which 50,558 were polymorphic and had
 a mean observed heterozygosity of 0.25. These data will be used to study
 the effects of habitat fragmentation on genomic diversity, dispersal, and
 disease transmission in this species. Our approach provides a good example
 of the potential of RAD sequencing in studies of wild primate populations.
description: SNP information for loci
 identified using Restriction-site-associated DNA sequencing in the Ugandan
 red colobusThe file contains the
 SNP information for the loci identified using Restriction-site-associated
 DNA sequencing in the Ugandan red colobus. The text contains the following
 information: Locus (number assign to the locus by the program STACKS);
 Position (position of the SNP); SNP (identifies the change of the base in
 the SNP position); Consensus sequence (consensus sequence for the locus);
 number of individuals (number of individuals where the locus has been
 genotyped). It also includes the genotypes for all the individuals. If the
 individual could not be genotyped a "-" will appear. Some loci
 present more than one SNP, in those cases, the SNP information will appear
 in consecutive rows. For example locus 4 has SNPs in positions 86 (row
 number 2 in the table) and 89 (row number 3 in the table). In those cases
 the genotypes for the individuals always show the complete genotype.
 Heterozygotes are indicated with a "/". For example A/G is
 heterozygote for 1 SNP, CA/GG is heterozygote for 2 SNPs, GA/GG is
 heterozygote for 1 SNP out of 2.RedcolobuslociSNPinformation.xlsx
DOI: 10.5061/dryad.78k38
title: Data from: Demographic inferences using short-read genomic data in an Approximate Bayesian Computation framework: in silico evaluation of power, biases, and proof of concept in Atlantic walrus

description: Approximate Bayesian Computation (ABC) is a powerful tool for model-based
 inference of demographic population histories from large genetic data
 sets. For most organisms its implementation has been hampered by the lack
 of sufficient genetic data. Genotyping-by-sequencing (GBS) provides cheap
 genome-scale data to fill this gap, but its potential has not fully been
 exploited. Here, we explored power, precision and biases of a
 coalescent-based ABC approach where GBS data were modeled with either a
 population mutation parameter (θ) or with a fixed sites (FS) approach,
 allowing single or several segregating sites per locus. With simulated
 data ranging from 500 to 50,000 loci a variety of demographic models could
 be reliably inferred across a range of timescales and migration scenarios.
 Posterior estimates were informative with 1,000 loci for migration and
 split time in simple population divergence models. In more complex models
 posterior distributions were wide and almost reverted to the uninformative
 prior even with 50,000 loci. ABC parameter estimates, however, were
 generally more accurate than an alternative composite-likelihood method.
 Bottleneck scenarios proved particularly difficult and only recent
 bottlenecks without recovery could be reliably detected and dated.
 Notably, minor allele frequency filters – usual practice for GBS data –
 negatively affected nearly all estimates. With this in mind, we used a
 combination of FS and θ approaches on empirical GBS data generated from
 the Atlantic walrus (Odobenus rosmarus rosmarus), collectively providing
 support for a population split before the last glacial maximum followed by
 asymmetrical migration and a range-wide bottleneck. Overall, this study
 evaluates the potential and limitations of GBS data in an ABC-coalescence
 framework and proposes a best-practice approach.
description: Walrus ms
 dataWalrus GBS data in ms
 formatWalrus.msWalrus VCFWalrus GBS data in vcf formatWalrus.vcf
DOI: 10.5061/dryad.j678b
title: Data from: Quantifying realized inbreeding in wild and captive animal populations

description: Most molecular measures of inbreeding do not measure inbreeding at the
 scale that is most relevant for understanding inbreeding depression—namely
 the proportion of the genome that is identical-by-descent (IBD). The
 inbreeding coefficient FPed obtained from pedigrees is a valuable
 estimator of IBD, but pedigrees are not always available, and cannot
 capture inbreeding loops that reach back in time further than the
 pedigree. We here propose a molecular approach to quantify the realized
 proportion of the genome that is IBD (propIBD), and we apply this method
 to a wild and a captive population of zebra finches (Taeniopygia guttata).
 In each of 948 wild and 1057 captive individuals we analyzed available
 single-nucleotide polymorphism (SNP) data (260 SNPs) spread over four
 different genomic regions in each population. This allowed us to determine
 whether any of these four regions was completely homozygous within an
 individual, which indicates IBD with high confidence. In the highly
 nomadic wild population, we did not find a single case of IBD, implying
 that inbreeding must be extremely rare (propIBD=0–0.00094, 95% CI). In the
 captive population, a five-generation pedigree strongly underestimated the
 average amount of realized inbreeding (FPed=0.013
description: data.genotypesThe file contains the genotypes of all 948 individuals studied. Each row represents one individual.The first column gives the individual ID followed by the genotypes of all SNPs. Alleles are coded as 0, 1 or 2 representing 0, 1 or 2 copies of the A-Allele, respectively.data.genesThe file contains all SNP names and their location within a gene.
DOI: 10.15468/dl.syrdb9
title: Occurrence Download

description: A dataset containing 31039 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-104.33376 19.03367,-104.34018 19.029,-104.34224 19.0178,-104.3334 19.01379,-104.32086 19.01584,-104.20755 18.97522,-104.1722 18.96196,-104.11454 18.93855,-104.05991 18.9051,-104.03114 18.88835,-104.00031 18.87869,-103.9997 18.8863,-103.99692 18.9088,-103.99939 18.92093,-104.01686 18.93809,-104.0325 18.97366,-104.05459 18.98424,-104.09066 19.00089,-104.11742 19.02181,-104.13345 19.02695,-104.16234 19.04277,-104.19175 19.04292,-104.20973 19.05145,-104.2274 19.0608,-104.26409 19.06912,-104.28176 19.06738,-104.29245 19.06553,-104.2943 19.05833,-104.29728 19.05751,-104.29933 19.0607,-104.30262 19.0607,-104.30529 19.05782,-104.31094 19.05484,-104.31475 19.05607,-104.31927 19.05731,-104.32328 19.05638,-104.32584 19.05515,-104.32944 19.05186,-104.33037 19.04826,-104.33191 19.04683,-104.33242 19.04456,-104.3315 19.04271,-104.33109 19.03902,-104.33139 19.03593,-104.33324 19.03562,-104.33376 19.03367))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 31039 records from 180 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016022-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.