cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.28sm8/2
title: Linear correlation between relative CP size and ORG repertoire size was established and used to estimate likely ORG repertoire for the extinct sabertooth cat (Smilodon fatalis).

description: (a), Log-log regression plot of absolute CP surface area against body mass for 26 species (r2 = 0.83, P&lt;0.001).  Residuals from regression constitute relative CP size (RelCP) for each species and are used in all subsequent analyses.  (b), Strong positive linear correlation between RelCP and the number of functional ORG (log10) is shown in reduce major axis regression plot (r2 = 0.76, P&lt; 0.001, n=26).  (c), Linear correlation between RelCP and total ORG number (functional, pseudogenes) (log10).  (d), Axes from figure 2b plot are inverted and the RelCP value (green vertical line) for the sabertooth cat is applied to the regression equation.  This predicts Smilodon to have had ca. 600 (581,685) functional ORG.  Dotted lines: 95% confidence intervals around regression line. All work done in R.
DOI: 10.5061/dryad.28sm8/3
title: Nonlinear relationship between RelCP and OR pseudogene repertoires.

description: (a), Dual trends are evident in the relationship between RelCP and the absolute number of OR pseudogenes, as delineated here by the vertical line: in species with the largest pseudogene counts (&gt;~750), the correlation is robust (r2=0.744, P=0.026, PGLS-r2=0.723, P= 0.005); in the group of species with low pseudogene counts (
DOI: 10.5061/dryad.28sm8/4
title: Morphological disparity in CP seen in elephant, tarsier, platypus and dog skull models.

description: CP morphological disparity viewed in 3D models constructed with Mimics and 3-matic software from high-resolution CT scans. Yellow top center: CP of the African elephant (Loxodonta africana), viewed here from brain case, has the largest absolute and relative surface area and ~1,000 foramina for passage of olfactory nerves to the brain. Extreme reduction of complexity is evident in CPs of the tarsier (Tarsius syrichtus) (green, lower left) and platypus (Ornithorhynchus anatinus) (orange, bottom center) CPs. Dog (Canis familiaris) CP (blue, lower right).  The inset superimposed over elephant model shows tarsier, platypus and dog CPs to scale with the elephant’s CP.
DOI: 10.5061/dryad.2911p2v/1
title: DOM-Architecture data_raw
DOI: 10.5061/dryad.2911p2v/2
title: DOM-Architecture data_relative root volumes at different root diameters
DOI: 10.5061/dryad.2911p2v/3
title: DOM-Grass heights
DOI: 10.5061/dryad.2911p2v/4
title: DOM-Grass chemistry_strength_growth
DOI: 10.5061/dryad.31bp485/1
title: Heino & Tolonen_Ecography

description: This table includes information on species' regional occupancy (number of sites occupied), abundance (total abundance across 48 lakes), niche features, traits and taxonomic position.
DOI: 10.5061/dryad.3m8j0/1
title: EEG data from the right motor cortex during left-hand motor imagery, collected before, during and after contralateral tDCS

description: The present dataset includes the EEG data from twenty healthy volunteers, from the study described in our manuscript. The EEG data were acquired from 12 electrodes (Fcz, Fc2, Fc4, Fc6, Cz, C2, C4, C6, Cpz, Cp2, Cp4, Cp6) placed on the right motor cortex, during a left hand motor imagery task, and visually guided by neurofeedback. As the aim of the study was testing the effect of contralateral transcranial direct current stimulation (tDCS), the present dataset includes EEG recordings before, during and after stimulation. The EEG data were acquired by the LABVIEW-based neurofeedback software specifically implemented for this study, and stored in TAB-delimited .txt files. A "Readme.pdf" file is added to describe the organization of the dataset in detail.
DOI: 10.5061/dryad.477dp5c/1
title: comp females

description: Factors associated with competition among females
DOI: 10.5061/dryad.477dp5c/2
title: comp males

description: Factors associated with competition among males
DOI: 10.5061/dryad.477dp5c/3
title: reprod success females

description: Factors associated with breeding success among females
DOI: 10.5061/dryad.477dp5c/4
title: reprod success males

description: Factors associated with breeding success among males
DOI: 10.5061/dryad.5r6d5kc/1
title: annotated assemblies

description: Assemblies automatically generated in GenBank flat file format.
DOI: 10.5061/dryad.632dn89/1
title: Paneveggio dataset

description: These are the data of the Paneveggio dataset. These are the data of the field measured trees. It is a table with five columns: 1) "PlotID": ID of the field plot; 2) "Height_m": field measured tree height in meters; 3) "CD_m": field measured crown diameter  in meters; 4) "DBH_cm": field measured DBH in centimeters; and 5) "AGB_kg": field estimated AGB in kilograms.
DOI: 10.5061/dryad.632dn89/2
title: Pellizzano dataset

description: These are the data of the Pellizzano dataset. These are the data of the detected ITCs. It is a table with six columns: 1) "PlotID": ID of the field plot; 2) "Height_m": ALS-derived height of the detected ITC in meters; 3) "CD_m": ALS-derived crown diameter of the detected ITC in meters; 4) "H_F_m": field measured tree height in meters of the tree associated to that ITC; 5) "DBH_F_cm": field measured tree DBH in centimeters of the tree associated to that ITC; and 6) "AGB_F_kg": field estimated tree AGB in kilograms of the tree associated to that ITC.
DOI: 10.5061/dryad.670m5n0/1
title: Densities OIKOS

description: Sea urchin densities per size class in two different habitats (macroalgal communities on rocky substrates and Posidonia oceanica seagrass meadows). Data were collected by SCUBA in the NW Mediterranean (Catalan Coast, NE Spain) in 8 different sites and 2 periods.
DOI: 10.5061/dryad.6vr0666/4
title: Reflectance data from semi-aridMed site

description: Summer (dry season) reflectance index data (WI, CHL, PRI) from semi-aridMed site
DOI: 10.5061/dryad.8463q13/1
title: Data used in paper Journal of Ecology-2017-0709.R2

description: Data collected in the field in southern France, at the La Fage experimental station (43°55N, 3°06E, 765-830 m a.s.l.). Analogues of demographic parameters are derived from changes in species abundance data in paddocks with intensified regime (increased fertilization and grazing pressure) over the 1978-2005 period, following Damgaard et al. (2011; Methods in Ecology and Evolution 2: 110-115). Plant traits were measured in 2006 and 2007. Column headings are: Species name (SpeciesName, following TaxRef, version 10); Botanical Family (BotanicalFamily); Life Cyle (LifeCycle); Raunkiaer life form (LifeForm); Population Growth Rate (PopGrowthRate, unitless); Elasticity of population growth rate to survival (Elast_s, unitless) and colonization (Elast_c, unitless); Reproductive Plant Height (RPH, in cm); Seed Mass (SeedMass, in mg); Onset of Flowering (OFL, in day of year); Area of an individual leaf (LeafArea, in cm2); Specific Leaf Area (SLA, in m2/kg); Leaf Dry Matter Content (LDMC, in mg/g); Mass-based Leaf Nitrogen Content (LNC, in mg/g); Mass-based Leaf Phosphorus Content (LPC, in mg/g); Leaf carbon isotopic fraction (LDelta13C, in ‰)
DOI: 10.5061/dryad.8ft948b/1
title: complete data set

description: complete data set from the laboratory experiment. the sheet entitled "measurements_bird level" contains all bird individual measurements. the sheet entitled "food consumption_cage level" contains all food consumption measurements at the cage level.
DOI: 10.5061/dryad.8p6m07g.1
title: Data from: Genomics of parallel ecological speciation in Lake Victoria cichlids
DOI: 10.5061/dryad.8p6m07g.2
title: Data from: Genomics of parallel ecological speciation in Lake Victoria cichlids
DOI: 10.5061/dryad.8p6m07g.2/1.2
title: Candidate regions of parallel selection on admixture variation

description: The 41 shared highly divergent regions (SHDRs) that group the species by male nuptial coloration and are thus candidates of parallel selection. The genes in the vicinity of the regions are shown above. The Fst values between the older species at Makobe Island and between the younger species at Python Island are shown in windows of 15 SNPs. Windows that the HMM approach assigned to the high differentiation state are shown with red or orange color. The next row shows excess allele sharing (fd) in windows of 20 kb. Windows that have a TWISST weight of the color topology &gt;0.66 are indicated in black. The next rows show the mean nucleotide diversity, dxy, difference in nucleotide diversity, extended haplotype length (EHL) statistics, Tajima's D and the recombination rate.
DOI: 10.5061/dryad.8p6m07g.2/2.2
title: Candidate regions of parallel selection on admixture variation

description: bed file indicating the locations of the candidate regions of parallel selection on admixture variation
DOI: 10.5061/dryad.8s20p92/1
title: The mean value of functional traits including CO2 assimilation rate per unit area (Aarea; μmol s-1), instantaneous water use efficiency (WUEi; μmol mol-1), stomatal conductance per unit area (gsa; mmol m-2 s-1), phosphorus concentration per leaf mass (Pmass; mg kg-1), sapwood specific hydraulic conductivity (Ks; kg m-1 s-1 MPa-1), leaf water potential at turgor loss point (ψtlp; MPa), leaf chlorophyll concentration (Chl; g/m2), leaf size (Ls; cm2), leaf lamina thickness (Thk; cm), specific leaf area (SLA; cm2/g), leaf dry matter content (LDMC; %), and wood density (WD; g/m3) for the 112 study species in dinghu moutain in southern China.
DOI: 10.5061/dryad.8s20p92/2
title: The mean DBH (in cm) of the 112 study species in the plot and DBH values (in cm) of the sampled individuals (n) for each study species in dinghu moutain in southern China.
DOI: 10.5061/dryad.8s20p92/3
title: Species abundance (the total number of all living stems; N) for each of the 208 species found in the 20-ha subtropical forest plot in dinghu moutain in southern China.
DOI: 10.5061/dryad.cc3n6j5/1
title: amph_shl_new_Backbone

description: Species chosen from the 4,061-species matrix for representation in the 175-species backbone tree.
DOI: 10.5061/dryad.d5p86fp/1
title: Keating-Bitonti&Payne_FigureS1

description: Figure S1. (A) Results of L1-regularized regression analysis assessing the correlations between environmental predictors and log adult/proloculus size ratios for Atlantic endemic species. Plots B-E show the relationship between Atlantic endemic species’ log adult/proloculus size ratios to local temperature, oxygen, calcite saturation, and oxygen, respectively, with solid black lines representing the linear regression of these data. The L1-regularized regression analysis identified that temperature alone best predicts the log adult/proloculus size ratios of Atlantic endemics and the plot B supports this result with the largest R2 value compared to the other environmental variables (see Table S1).
DOI: 10.5061/dryad.d5p86fp/2
title: Keating-Bitonti-SITables-05.01.18

description: Supplemental Tables S1 and S2
DOI: 10.5061/dryad.db40gj8/1
title: losapio_etal_2018oikos

description: This .RData file contains both the raw data from Pugnaire et al. 1996 and Pugnaire & Lazaro 2000 as well as the processed data, as the ecological networks and null models. The relative R code is attached in README.
DOI: 10.5061/dryad.df2jt/3
title: nuclear RNA of the Sericostoma genome assembly

description: Nuclear RNA sequences were identified in the draft genome assembly. tRNA genes were identified using tRNAscan-SE with default parameters. miRNA and snRNA were identified using the INFERNAL software by searching against the Rfam database (release 9.1) with default parameters. rRNA genes were identified by BLASTn (cutoff: 10-5) searches against conserved invertebrate rRNA sequences. Separate files are provided for each type of RNA.
DOI: 10.5061/dryad.ds0h5pq/1
title: Microsatellite genotypic data for Cimex adjunctus

description: Genotypic data at 9 microsatellite markers for 117 Cimex adjunctus individuals. The first three digits in each string describe the length (in base pairs) of the first allele, and the last three describe the length of the second allele. Missing data is identified with “000000”.
DOI: 10.5061/dryad.h3m2jf7/1
title: Data- Soil microbial processes and resource limitation in karst and non-karst forests
DOI: 10.5061/dryad.j6k6112/1
title: Appendix 2
DOI: 10.5061/dryad.j6k6112/2
title: Appendix 1
DOI: 10.5061/dryad.k0v636g/1
title: Data from:Multidimensional analyses of physical performance reveal a size dependent trade-off between suites of traits.

description: Morphology and performance data.
DOI: 10.5061/dryad.kr8t0/1
title: Seawater uptake, mechanical strength, wear rate of PEEK composites in seawater under hydrostatic pressure
DOI: 10.5061/dryad.m6dn0g8/3
title: Isopod_trait_data

description: Trait values for Isopoda species
DOI: 10.5061/dryad.q4f4ns6/12
title: Pamlico_Waters_Extended_wgs
DOI: 10.5061/dryad.qm1n85p/1
title: Field observations of Plethodon climbing behavior

description: Data was collected in the field and the file was created using Microsoft Excel. The column headings are as follows: site initials (DCA = Dismal Creek A, DCB = Dismal Creek B, HB = Hunter's Branch, WR = Wind Rock, and WSP = War Spur Trail); transect (identifier for each 15x3m survey transect), survey (survey number, 1-3), date (date of survey), start_time (time of survey initiation), stop_time (time of survey completion), species (Plethodon species name), count (total individuals observed on a given survey), count_climbing (number of individuals found climbing on a given survey), count_ground (number of individuals found not climbing or on the ground on a given survey), community (denotes whether P. montanus was native, introduced, or absent at the specified site), trees (total number of trees &gt; 3cm dbh in the transect), understory_mean (mean % understory cover in the transect).
DOI: 10.5061/dryad.sc30g/3
title: Nest sizes of daughters and their foster mothers during a cross-fostering experiment

description: Nest sizes (recorded as fraction of standardised nest box filled) of daughters and their foster mothers, as recorded by SCG in Wytham Woods, UK during 2001-2003 breeding seasons. Rear_depth is the size of the nest in which the chick was reared in, recruit_av_depth is the average depth of the recruits nest in future seasons in 2002-3
DOI: 10.5061/dryad.sc30g/4
title: R code for all of the analysis of blue tit nest sizes

description: The R code that I wrote to analyse different factors controlling the nest size of blue tits in Wytham Woods, UK during the 2001-2003 breeding seasons using the data files attached
DOI: 10.5061/dryad.t8v2gg7/1
title: README
DOI: 10.5061/dryad.t8v2gg7/2
title: restricted ctap
DOI: 10.5061/dryad.v8cp134/1
title: SNP dataset retrieved from 176 whole-genome sequences (117 A. m. iberiensis, 28 A. m. carnica and 31 A. m. ligustica)

description: The dataset contains a total of 2,366,382 SNPs detected between 117 A. m. iberiensis, 28 A. m. carnica and 31 A. m. ligustica. SNP calling was performed using three different variant calling tools: GATK's, SAMtools’ mpileup 1.1 and PLATYPUS 0.8.1 Details for SNP processing and quality control is provided in the paper and its supplementary information.
DOI: 10.17632/hst99x5393.1
title: Data for: A Coupled CFD-PBM and Thermodynamic Analysis of Continuous Supercritical Hydrothermal Synthesis of Nanoparticles

description: We have provided the detailed boundary conditions for all the variables, model parameters, and user-defined functions for mass averaged density, nucleation rate, diffusional growth rate, and coagulation kernels etc.
DOI: 10.5061/dryad.1hn0951/1
title: VCF_file
DOI: 10.5061/dryad.28sm8/10
title: Cribriform plate surface area data for individual specimens, .csv format

description: Identification, source, sex and morphological data for sample species.  Abbreviations, AMNH: American Museum of Natural History.  CMNH: Cleveland Museum of Natural History. DLC: Duke Lemur Center. DUPC: Duke University Primate Center. IZCAS: Institute of Zoology of the Chinese Academy of Sciences. LACM: Natural History Museum of Los Angeles County. LACMRLP: Rancho La Brea Tar Pits. MVZ: Museum of Vertebrate Zoology. SDSNH: San Diego Society of Natural History. UCLA: Dickey Collection at the University of California Los Angeles. UCLAEEB: UCLA Department of Ecology and Evolutionary Biology. USNM: National Museum of Natural History. UTO: University of Texas Austin. TMM: Texas Memorial Museum. *The presence of a cribriform plate in the ethmoid bone of the bottlenose dolphin (Tursiops truncatus) could not be established in this study.
DOI: 10.5061/dryad.28sm8/11
title: Digitally quantifying CP surface area.

description: (a), Three-dimensional CP model from the French bulldog (Canis familiaris) is reconstructed from CT scan data in Mimics imaging program.  (b), CP foramina are digitally filled to create a generalized continuous surface within the perforate region of the bone. (c), Surface area is isolated and calculated with imaging software 3-matic.
DOI: 10.5061/dryad.28sm8/12
title: Strong linear correlation between cribriform plate (CP) surface area (perforate area) and cumulative cross-sectional area of the CP foramina (log-log) (r2 = 0.91, P &lt; 0.0001, n = 19).

description: The more exacting metric of total CP foramina area, representing the imprint of olfactory axon bundles in the ethmoid bone, serves to validate CP surface area as a metric of relative olfactory innervation. CP surface area is the preferable metric for future studies, as it is easily quantifiable, even in skulls with some CP damage, such as fossils.  CP surface area was measurable here in 26 sample species, while foramina area was measurable in only 19 species. Image on y axis: taken from figure S3. Images on the x axis: left, section of CP bone (red) with splines, (rings of coordinate points), assigned to the perimeters of several foramina in Mimics; right, imaging software Rhinoceros creates non-planar surfaces from the splines, and surface areas of foramina are calculated and tallied.
DOI: 10.5061/dryad.28sm8/13
title: 3D skull models showing marked reduction in CP morphology in taxa heavily reliant on non-olfactory sensory modalities.

description: (a), CP loss viewed in nasal morphology of bottlenose dolphin (Tursiops truncatus), which uses echolocation. Pink: Single pair of foramina connecting ethmoid area of the nasal passage to the cranium. Inset, magnification of foramina. (b-c), Impact of orbit size on CP size constraints, contrasting the tarsier (Tarsius syrichta) and armadillo (Dasypus novemcinctus). (b), Tarsier, a visually-specialized nocturnal primate with enlarged, forward facing orbits, has reduced olfactory anatomy. Red: CP squeezed between convergent orbits. (c), By contrast, the armadillo’s large CP (red) fills the space between small, laterally oriented, wide set orbits. 3D models constructed with Mimics and 3-matic software from high-resolution CT scans.
DOI: 10.5061/dryad.28sm8/5
title: Movie of cribriform plate and nasal anatomy within skull.

description: Animated 3D model of an arctic fox (Vulpes lagopus) skull featuring the cribriform plate and general nasal anatomy.The cribriform plate (red) model clearly displays the perforations, or foramina, through which axon bundles from olfactory sensory neurons pass en route to the olfactory bulb of the brain.  Sensory neurons in the olfactory epithelium are located primarily on the ethmoturbinal (green) and nasoturbinal (yellow) bones. Maxillary turbinals, which carry respiratory epithelium are shown in blue. The arctic fox is not among the sample species but its model is used here because of its particular clarity. 3D models were constructed with Mimics and 3-matic software from high-resolution CT scans. Animations was constructed with ParaView software.
DOI: 10.5061/dryad.28sm8/7
title: Key resource table, Excel format

description: Key resource table for sample specimens, CT scanning machines and facilities, and digital imaging software.
DOI: 10.5061/dryad.28sm8/8
title: Key resource table, .csv format

description: Key resource table for sample specimens, CT scanning machines and facilities, and digital imaging software.
DOI: 10.5061/dryad.28sm8/9
title: Cribriform plate surface area data for individual specimens, Excel format

description: Identification, source, sex and morphological data for sample species.  Abbreviations, AMNH: American Museum of Natural History.  CMNH: Cleveland Museum of Natural History. DLC: Duke Lemur Center. DUPC: Duke University Primate Center. IZCAS: Institute of Zoology of the Chinese Academy of Sciences. LACM: Natural History Museum of Los Angeles County. LACMRLP: Rancho La Brea Tar Pits. MVZ: Museum of Vertebrate Zoology. SDSNH: San Diego Society of Natural History. UCLA: Dickey Collection at the University of California Los Angeles. UCLAEEB: UCLA Department of Ecology and Evolutionary Biology. USNM: National Museum of Natural History. UTO: University of Texas Austin. TMM: Texas Memorial Museum. *The presence of a cribriform plate in the ethmoid bone of the bottlenose dolphin (Tursiops truncatus) could not be established in this study.
DOI: 10.5061/dryad.34kb373/1
title: Serengeti_Thomsons_Gazelle_Application_Data

description: Data for the manuscript "Identifying Drivers of Spatial Variation in Occupancy with Limited Replication Camera Trap Data", by Hepler, Staci; Erhardt, Robert; Anderson, T. Michael. Contains data from the Snapshot Serengeti camera trap study. The response variable 'Thomson's Gazelle' is a binary indicator of presence/absence based on the camera trap images. The variable information came from field work, with the exception of NDVI which is based on NASA's MODIS satellite.
DOI: 10.5061/dryad.35tv6rs/1
title: Data files of capture histories used in E-Surge software

description: Data files “histories_males” and “histories_females” include capture histories (column 'H:') of males and females respectively, for European Blackbird from the Żeromski Park in Szczecin. For both dataset, the capture history is followed by the column 'S:' (denotes number of individuals with the capture history), the column '$COV:Mgp' (covariate coding for age, Ad = adult birds older than 2 years, Juv = immature birds in their second year, Juv2 = new adults; immatures in their second year of live capture in the second part of season). These capture histories were used to model pair fidelity and survival in E-Surge software. The life histories are coded using 6 different codes events, and each code shows the observed event for each individual on each capture occasion. For details see Method from Jankowiak et al. 2018.
DOI: 10.5061/dryad.5r6d5kc/2
title: Concatenated alignment used in phylogeny inference

description: 251 concatenated genes (introns and low coverage areas removed).
DOI: 10.5061/dryad.5r6d5kc/3
title: Alignments
DOI: 10.5061/dryad.5r6d5kc/4
title: Tree from Bayesian inference with posterior probability support
DOI: 10.5061/dryad.5r6d5kc/5
title: Tree from Bayesian inference with ML bootstrap support

description: Tree inferred with Exabayes with node support taken from a analyses of bootstrapped alignment with trees estimated using  Maximum Likelihood
DOI: 10.5061/dryad.5r6d5kc/6
title: custom scripts used

description: Scripts used in sequence preparation. This contains one bash script "master_raw_to_alignment.sh" which undertakes simple bash commands which acts as a wrapper for various pieces of software and custom scripts. The rest of the files are specific python 3 scripts to complete specific tasks.
DOI: 10.5061/dryad.82541dc/1
title: Biedrzycka_etal_MHC_parasites

description: This file contains data on prevalence and infection intensity of Haemoproteus strains detected in sedge warbler. For every individual the number of alleles in each supertype is given. The age and sex for every individual is also given.
DOI: 10.5061/dryad.82541dc/2
title: Sedge_warbler_MHCI_genotypes

description: The file contains the results of genotyping of analysed individuals with use of AmpliSAS pipeline. The supertypes assigned for each allele are also given.