cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3t9k2
title: Data from: DNA barcoding reveals cryptic diversity in the peanut worm Sipunculus nudus

description: Peanut worm (Sipunculus nudus) is a cosmopolitan species mainly
 distributed in tropical and subtropical coastal waters. Analysis of the
 mitochondrial cytochrome c oxidase subunit I (COI) gene sequences among S.
 nudus from GenBank revealed high genetic variation (p-distance,
 0.115–0.235; k2p, 0.128–0.297) and paraphyletic relationships. These
 indicated misidentification and/or cryptic diversity may be present in the
 genus Sipunculus. To understand the genetic diversity and to manage the
 recourse of S. nudus, we collected specimens from coastal waters of
 southern China and Taiwan. In the phylogenetic topology, specimens can be
 separated into four distinct clades; three of these clades (clade A, B and
 C) were only represented from this region (southern China and Taiwan), but
 the clade D grouped with individuals from Central America (Atlantic
 coast). Furthermore, individuals of clades A and D were collected at the
 same location, which does not support the hypothesis that this genetic
 break reflects contemporary geographical isolation. The four distinct
 clades observed among coastal waters of southern China and Taiwan
 indicated underestimated diversity. It is noteworthy that the cryptic
 diversity is vulnerable under high pressure of human activity.
description: All_aliAll sequences for analysisBayesian phylogenetic analysisall_ali_haplotype_BEAST_final_new3haplotypeall_ali_haplotype.nextreefile (100 trees from BEAST)For bGMYC analysistreefile.tre
DOI: 10.5061/dryad.76hv890
title: Data from: No place like home? A test of the natal habitat-biased dispersal hypothesis in Scandinavian wolves

description: Natal dispersal is an important mechanism for the viability of
 populations. The influence of local conditions or experience gained in the
 natal habitat could improve fitness if dispersing individuals settle in an
 area with similar habitat characteristics. This process, defined as “natal
 habitat-biased dispersal” (NHBD), has been used to explain distribution
 patterns in large carnivores, but actual studies evaluating it are rare.
 We tested whether gray wolf Canis lupus territory establishment was
 influenced by the habitat characteristics of the natal territory using the
 long-term monitoring of the Scandinavian wolf population. We paired the
 locations of natal and established territories, accounted for available
 habitats along the dispersing route, and compared their habitat
 characteristics for 271 wolves during 1998-2012. Wolves with the shortest
 dispersal distances established in natal-like habitat types more than
 expected by chance, whereas wolves that dispersed longer distances did not
 show NHBD. The pattern was consistent for male and female wolves, with
 females showing more NHBD than males. Chances to detect NHBD increased
 with the size of habitat defined as available. This highlights the
 importance of considering the biological characteristics of the studied
 species when defining habitat availability. Our methodological approach
 can prove useful to inform conservation and management to identify
 habitats to be selected by reintroduced or naturally expanding
 populations.
description: Data_nhbdData allowing to reproduce the results of the conditional logistic regression to test the NHBD hypothesis. Each row correspond to an observation of a natal, established or available wolf territory. Variables describe the landscape characteristics of the territory, and the cluster/distance metric to which the territory was assigned in the different methods of defining habitat availability (i.e., clustering metods and distance metric). For further information on the variables refer to the README file attached to the excel document
DOI: 10.5061/dryad.166
title: Data from: The strength of phenotypic selection in natural populations

description: How strong is phenotypic selection on quantitative traits in the wild? We
 reviewed the literature from 1984 through 1997 for studies that estimated
 the strength of linear and quadratic selection in terms of standardized
 selection gradients or differentials on natural variation in quantitative
 traits for field populations. We tabulated 63 published studies of 62
 species that reported over 2,500 estimates of linear or quadratic
 selection. More than 80% of the estimates were for morphological traits;
 there is very little data for behavioral or physiological traits. Most
 published selection studies were unreplicated and had sample sizes below
 135 individuals, resulting in low statistical power to detect selection of
 the magnitude typically reported for natural populations. The absolute
 values of linear selection gradients |β| were exponentially distributed
 with an overall median of 0.16, suggesting that strong directional
 selection was uncommon. The values of |β| for selection on morphological
 and on life-history/phenological traits were significantly different: on
 average, selection on morphology was stronger than selection on
 phenology/life history. Similarly, the values of |β| for selection via
 aspects of survival, fecundity, and mating success were significantly
 different: on average, selection on mating success was stronger than on
 survival. Comparisons of estimated linear selection gradients and
 differentials suggest that indirect components of phenotypic selection
 were usually modest relative to direct components. The absolute values of
 quadratic selection gradients |γ| were exponentially distributed with an
 overall median of only 0.10, suggesting that quadratic selection is
 typically quite weak. The distribution of γ values was symmetric about 0,
 providing no evidence that stabilizing selection is stronger or more
 common than disruptive selection in nature.
description: Selection
 DatabaseThe excel file has both
 the data, and a worksheet explaining each of the columns/fields. We would
 appreciate it if you would bring to our attention any errors or
 ambiguities that you find in the database (no doubt there are some). We
 will periodically update the database as needed. In addition, we are very
 interested in new insights you may have about selection from your own
 analyses of this database and relate sources. We’d appreciate it if you
 would tell us what you are finding, or papers that have resulted from it.
 Any questions or comments may be directed to: Joel Kingsolver, Department
 of Biology, CB-3280, University of North Carolina, Chapel Hill, NC
 27599-3280, 919 843-6291 (phone) 919 962-1625 (fax)
 jgking@bio.unc.eduKingsolveretal.SelnDatabase.norepdur.3.2001.xls
DOI: 10.5061/dryad.gr38v6r
title: Data from: An Ishihara-style test of animal colour vision

description: Colour vision mediates ecologically relevant tasks for many animals, such
 as mate choice, foraging and predator avoidance. However, our
 understanding of animal colour perception is largely derived from human
 psychophysics, even though animal visual systems differ from our own.
 Behavioural tests of non-human animals are required to understand how
 colour signals are perceived by them. Here we introduce a novel test of
 colour vision in animals inspired by the Ishihara colour charts, which are
 widely used to identify human colour deficiencies. These charts consist of
 dots that vary in colour, brightness and size, and are designed so that a
 numeral or letter is distinguishable from distractor dots for humans with
 normal colour vision. In our method, distractor dots have a fixed
 chromaticity (hue and saturation) but vary in luminance. Animals can be
 trained to find single target dots that differ from distractor dots in
 chromaticity. We provide Matlab code for creating these stimuli, which can
 be modified for use with different animals. We demonstrate the success of
 this method with triggerfish, Rhinecanthus aculeatus, and highlight
 behavioural parameters that can be measured, including success of finding
 the target dot, time to detect dot and error rate. Triggerfish quickly
 learnt to select target dots that differed from distractors dots
 regardless of the particular hue or saturation, and proved to use acute
 colour vision. We measured discrimination thresholds by testing the
 detection of target colours that were of increasing colour distances (∆S)
 from distractor dots in different directions of colour space. At least for
 some colours, thresholds indicated better discrimination than expected
 from the Receptor Noise Limited (RNL) model assuming 5% Weber fraction for
 the long-wavelength cone. This methodology seems to be highly effective
 because it resembles natural foraging behavior for the triggerfish and may
 well be adaptable to a range of other animals, including mammals, birds,
 bees and freshwater fish. Other questions may be addressed using this
 methodology, including luminance thresholds, sensory bias, effects of
 sensory noise in detection tasks, colour categorization and saliency
description: BackgroundDiskDataCircleGetRGBcombinationsIshiharaoidAndStimuliReadParamsIshiharaoidDiskGenerationIshiParametersAchromaticMakeStimuliOnGrayBackgroundReadme
DOI: 10.5061/dryad.dm57j
title: Data from: A collection of non-human primate computed tomography scans housed in MorphoSource, a repository for 3D data

description: A dataset of high-resolution microCT scans of primate skulls (crania and
 mandibles) and certain postcranial elements was collected to address
 questions about primate skull morphology. The sample consists of 489 scans
 taken from 431 specimens, representing 53 species of most Primate
 families. These data have transformative reuse potential as such datasets
 are necessary for conducting high power research into primate evolution,
 but require significant time and funding to collect. Similar datasets were
 previously only available to select research groups across the world. The
 physical specimens are vouchered at Harvard's Museum of Comparative
 Zoology. The data collection took place at the Center for Nanoscale
 Systems at Harvard. The dataset is archived on MorphoSource.org. Though
 this is the largest high fidelity comparative dataset yet available, its
 provisioning on a web archive that allows unlimited researcher
 contributions promises a future with vastly increased digital collections
 available at researchers' finger tips.
description: Copes et al. Dryad
 submissionThe zipped folder
 contains the original Excel spreadsheet with 3D digitized points from ~400
 non-human primate skulls. It also contains "cleaned up" versions
 of the points split into separate files by infraorder (strepsirrhines,
 catarrhines, platyrrines) and R code for importing the files. Many thanks
 to Randi Griffin for her assistance in reformatting the original data to
 make it more useful/accessible for analysis.
DOI: 10.5061/dryad.bt72k
title: Data from: Evaluation of Argos telemetry accuracy in the High-Arctic and implications for the estimation of home-range size

description: Animal tracking through Argos satellite telemetry has enormous potential
 to test hypotheses in animal behavior, evolutionary ecology, or
 conservation biology. Yet the applicability of this technique cannot be
 fully assessed because no clear picture exists as to the conditions
 influencing the accuracy of Argos locations. Latitude, type of
 environment, and transmitter movement are among the main candidate factors
 affecting accuracy. A posteriori data filtering can remove “bad”
 locations, but again testing is still needed to refine filters. First, we
 evaluate experimentally the accuracy of Argos locations in a polar
 terrestrial environment (Nunavut, Canada), with both static and mobile
 transmitters transported by humans and coupled to GPS transmitters. We
 report static errors among the lowest published. However, the 68th error
 percentiles of mobile transmitters were 1.7 to 3.8 times greater than
 those of static transmitters. Second, we test how different filtering
 methods influence the quality of Argos location datasets. Accuracy of
 location datasets was best improved when filtering in locations of the
 best classes (LC3 and 2), while the Douglas Argos filter and a homemade
 speed filter yielded similar performance while retaining more locations.
 All filters effectively reduced the 68th error percentiles. Finally, we
 assess how location error impacted, at six spatial scales, two common
 estimators of home-range size (a proxy of animal space use behavior
 synthetizing movements), the minimum convex polygon and the fixed kernel
 estimator. Location error led to a sometimes dramatic overestimation of
 home-range size, especially at very local scales. We conclude that Argos
 telemetry is appropriate to study medium-size terrestrial animals in polar
 environments, but recommend that location errors are always measured and
 evaluated against research hypotheses, and that data are always filtered
 before analysis. How movement speed of transmitters affects location error
 needs additional research.
description: Raw data_Christin et
 al_PLoS OneThese datasets are the
 GPS and Argos locations of static and mobile tests conducted in the
 High-Arctic; experiments were replicated several times, and the files are
 organized in different folders according to the experiment type. All files
 are provided in csv format. More information is provided in the joined
 ReadMe file.
DOI: 10.5061/dryad.0618v
title: Data from: PSMC (pairwise sequentially Markovian coalescent) analysis of RAD (restriction site associated DNA) sequencing data

description: The pairwise sequentially Markovian coalescent (PSMC) method uses the
 genome sequence of a single individual to estimate demographic history
 covering a time span of thousands of generations. Although originally
 designed for whole-genome data, we here use simulations to investigate its
 applicability to reference genome-aligned restriction site associated DNA
 (RAD) data. We find that RAD data can potentially be used for PSMC
 analysis, but at present with limitations. The key factor is the
 proportion (p) of the genome that the RAD data covers. In our simulations,
 a proportion of 10% can still retain a substantial amount of coalescent
 information, whereas for 1% estimation becomes unreliable. The performance
 depends strongly on mutation rate (μ) and recombination rate (r) and is
 proportional to μ*p/r. When the value of this term is low, increasing the
 amount of data and number of iterations helps restoring the power of the
 estimation. We subsequently analyse one whole-genome-sequenced and 17
 RAD-sequenced three-spined sticklebacks (Gasterosteus aculeatus) from a
 lake in Greenland. The whole-genome sequence suggests a relatively recent
 expansion and decline within ca. 4000–40 000 generations ago, possibly
 reflecting postglacial expansion and founding of the lake population. RAD
 data, where chromosomes from 10 individuals are combined, identify a
 similar pattern. Our study provides guidance about the use of PSMC
 analysis and suggests measures that can improve its utility for RAD data.
 Finally, the study shows that RAD loci in general contain coalescent
 information that can be used for developing more targeted methods.
description: empirical data(psmcfa
 files)The zip file contains
 the input files for PSMC from the empirical data of threespine
 sticklebacks in the study. Seventeen of them are from RAD data, and one of
 them is from whole genome sequencing data.Generating PSMC input
 files from simulated dataThe file contains a
 function written in R. This function randomly samples RAD loci from
 chromosomes simulated by ms (Hudson 2002), and transforms the RAD data
 into a ".psmcfa" file for PSMC analysis.ms2psmcfa.rGenerating PSMC input files from empirical RAD dataThe files contains a script written in R. The script creates input files for PSMC from empirical RAD data using tag files and allele files. Tag files and allele files are generated through pstacks in Stacks v1.13.stacks2psmcfa.rPlot PSMC resultsThe file contains functions written in R. The functions are used to visualize the results from PSMC.plotPsmc.r
DOI: 10.5061/dryad.rb66j52h
title: Data from: Applying plant DNA barcodes to identify species of Parnassia (Parnassiaceae)

description: DNA barcoding is a technique to identity species by using standardized DNA
 sequences. In the present study, a total of 105 samples, representing 30
 Parnassia species were collected to test the effectiveness of four
 proposed DNA barcodes (rbcL, matK, trnH-psbA and ITS) for species
 identification. Our results demonstrated that all four candidate DNA
 markers have a maximum level of primer universality and sequencing
 success. As single DNA marker, ITS region provided the highest species
 resolution with 86.7%, followed by trnH-psbA with 73.3%. The combination
 of the core barcode, matK + rbcL, gave the lowest species identification
 success (63.3%) among any combination of multiple markers, and was found
 unsuitable as DNA barcode for Parnassia. The combination of ITS +
 trnH-psbA achieved the highest species discrimination with 90.0%
 resolution (27 out of 30 sampled species), equal to the four-marker
 combination; ITS combined with matK, rbcL or matK + rbcL did not improve
 species discrimination. Therefore, matK and rbcL should not be used as DNA
 barcode for species identification of Parnassia. Based on the overall
 performance, the combination of ITS + trnH-psbA, is proposed as the most
 suitable DNA barcode for identifying Parnassia species. DNA barcoding is a
 useful technique to providing a reliable and effective mean for the
 discrimination of Parnassia species, and in combination with morphology
 based taxonomy can be a robust approach for tackling taxonomically complex
 groups. In the light of our findings, we found among the three species not
 identified a possible cryptic speciation event in Parnassia.
description: rbcLThis is the matrix of
 rbcL gene barcodes used in this article.matKThis is the matrix of
 matK gene barcodes used in the article.trnH-psbAThis is the matrix of trnH-psbA gene barcoded used in the article.ITSThis is the matrix of ITS gene barcodeds used in the article.Table 1 Parnassia species____ sampledParnassia species sampled, voucher information and GenBank accession number
DOI: 10.5061/dryad.1cg26
title: Data from: Environmental variability counteracts priority effects to facilitate species coexistence: evidence from nectar microbes

description: The order of species arrival during community assembly can greatly affect
 species coexistence, but the strength of these effects, known as priority
 effects, appears highly variable across species and ecosystems.
 Furthermore, the causes of this variation remain unclear despite their
 fundamental importance in understanding species coexistence. Here, we show
 that one potential cause is environmental variability. In laboratory
 experiments using nectar-inhabiting microorganisms as a model system, we
 manipulated spatial and temporal variability of temperature, and examined
 consequences for priority effects. If species arrived sequentially,
 multiple species coexisted under variable temperature, but not under
 constant temperature. Temperature variability prevented extinction of
 late-arriving species that would have been excluded owing to priority
 effects if temperature had been constant. By contrast, if species arrived
 simultaneously, species coexisted under both variable and constant
 temperatures. We propose possible mechanisms underlying these results
 using a mathematical model that incorporates contrasting effects of
 microbial species on nectar pH and amino acids. Overall, our findings
 suggest that understanding consequences of priority effects for species
 coexistence requires explicit consideration of environmental variability.
description: Results from a microcosm
 experiment using nectar microbesPopulation sizes of four
 species--Gluconobacter sp., Asaia sp., Metschnikowia reukaufii, and
 Starmarella bombicola--over 32 days. Experimental treatments were order of
 species arrival and temperature variability treatment. Additional
 experiments of changes in pH and amino acid composition of the media over
 the experiment also included.dryad
 data.xlsx
DOI: 10.5061/dryad.dh546
title: Data from: A new oviraptorid (Dinosauria: Theropoda) from the Upper Cretaceous of southern China

description: This paper describes a new oviraptorid dinosaur taxon, Ganzhousaurus
 nankangensis gen. et sp. nov., based on a specimen collected from the
 Upper Cretaceous Nanxiong Formation of Nankang County, Ganzhou City,
 Jiangxi Province, southern China. This new taxon is distinguishable from
 other oviraptorids based on the following unique combination of primitive
 and derived features: relatively shallow dentary; absence of fossa or
 pneumatopore on lateral surface of dentary; weakly downturned anterior
 mandibular end; shallow depression immediately surrounding anterior margin
 of external mandibular fenestra; external mandibular fenestra subdivided
 by anterior process of surangular; dentary posteroventral process
 slight-ly twisted and positioned on mandibular ventrolateral surface;
 shallow longitudinal groove along medial surface of den-tary
 posteroventral process; angular anterior process wider transversely than
 deep dorsoventrally; sharp groove along ventrolateral surface of angular
 anterior process; ventral border of external mandibular fenestra formed
 mainly by angular; ventral flange along distal half of metatarsal II; and
 arctometatarsal condition absent. Phylogenetic analysis places
 Ganzhousaurus nankangensis gen. et sp. nov. in the clade Oviraptoridae,
 together with Oviraptor, Citipati, Rinchenia and the unnamed Zamyn Khondt
 oviraptorid.
description: Newly added characters
 and data matrix for oviraptorids phylogenyThis character
 description was modified from Longrich et al. (Longrich, N. R., Currie, P.
 J. & Dong, Z. M. 2010 A new oviraptorid (Dinosauria: Theropoda) from
 the Upper Cretaceous of Bayan Mandahu, Inner Mongolia. Palaeontology, 53,
 945–960). The matrix was expanded by adding four characters and two taxa
 (Banji long and Ganzhousaurus nankangensis; for a total of 185 characters
 and 19 taxa).Appendix --easily readable
 format.doc
DOI: 10.7910/dvn/rwzll9
title: Efficacy and Safety of Treatments for Multicentric Reticulohistiocytosis: An Evidence Based Review

description: Multicentric reticulohistiocytosis (MRH) is a rare non-Langerhans cell histiocytosis characterized by papulonodular cutaneous lesions and a rapidly progressive, symmetric erosive arthritis. There is currently no standardized treatment approach for MRH or approved therapies. This systematic review investigates evidence surrounding treatment outcomes for MRH.