cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.95tv3/8
title: Mate choice data: Banded/striped, free-release trials
DOI: 10.5061/dryad.95tv3/9
title: Mate choice data: Spotted/striped, free-release trials
DOI: 10.5061/dryad.cf04g/1
title: Visual_Survey_Data

description: R data file of the visual survey data in distance format. R Code to open the file provided in readme.txt
DOI: 10.5061/dryad.cf04g/2
title: Digital_Survey_Data

description: R data file of the digital survey data in distance format. R Code to open the file provided in readme.txt
DOI: 10.5061/dryad.cf04g/3
title: Visual_vs_Digital_Comparison

description: Data used for bootstrap comparison of visual and digital DSM estimates to calculate the scaling factor for digital surveys.
DOI: 10.5061/dryad.cf04g/4
title: Acoustic_Data

description: Data used for comparison of acoustic indices to estimates of relative density from DSM of visual survey data.
DOI: 10.5061/dryad.d4841/1
title: Simulation and analysis code

description: Zipped archive of all data and scripts necessary to perform the analyses in Rabosky (2015), organized in order of the figures in the manuscript. Directory "fig_1_2_analyses" does the analysis of clade age and speciation rate, "fig_3" does analysis of phylogenetic tree balance, and "fig_4_5" does simulations and analysis of extinction rates when speciation rate heterogeneity is present.
DOI: 10.5061/dryad.dd3ph/3
title: seed size and beetle size means all sites

description: Variables:  site: 13 sites in North and South islands of New Zealand, two records per site as male and female beetles were treated separately. East Block (Lincoln, Canterbury), FF (Frost Flat, Waikato), Hanmer Pasture (Canterbury), Hanmer River (Hanmer Riverbed, Canterbury), Hanmer Forest (Canterbury), Jack’s Pass (Canterbury), Mangahao River (Manawatu - Wanganui), Masterton (Wellington), PN (Palmerston North, Manawatu – Wanganui), Poutu (Manawatu – Wanganui), Taitapu Alt (Canterbury), Waimakariri Forest (Canterbury), Wimakariri River Bed (Canterbury). 14 sites mentioned in main text but one of these had no beetles (Waiouru, Manawatu – Wanganui). seed_size_mg: mean of seed size from multiple plants per site. log_seed_size: natural log of seed_size_mg. elytra_area: mean of elytra area for beetles on multiple plants per site, mm2. beetle_sex: sex of beetles. Cases: each row represents the mean of one sex of beetles from multiple plants per site. One male and one female beetle per plant were measured. Two seeds (each containing a beetle) were measured per plant.
DOI: 10.5061/dryad.f851v/2
title: field data

description: Field data on predation, food abundance, and the intensity of male-male competition in Uta stansburiana
DOI: 10.5061/dryad.gs8r2/1
title: Microsatellite raw data
DOI: 10.5061/dryad.gs8r2/2
title: Fstat data
DOI: 10.5061/dryad.gs8r2/3
title: Structure data
DOI: 10.5061/dryad.gs8r2/4
title: GenAlEx
DOI: 10.5061/dryad.h4d22/1
title: classAandClassBEventStudy3_with_graphs2

description: For each stock ticker, this shows data from the Intensive Search period (length, peak, sum) followed by data about the financial event triggering the period (negative or positive; ISNEG = 1 is negative; absolute returns).
DOI: 10.5061/dryad.k7c3v/10
title: Actual annual female abundance for the 1994-1999 period (species = HAAM)

description: We fitted species-specific state-space models for annual abundance data over the 1987-2008 period outside the IPM, and used the 1994-1999 error-filtered female abundance as input to the IPM (data presented here).
DOI: 10.5061/dryad.k7c3v/11
title: Individual (adult) mark-recapture histories for the 1994-1999 period (species = HCRE)

description: Data used as input for the IPM, here in the MARK format.
DOI: 10.5061/dryad.k7c3v/12
title: Actual annual female abundance for the 1994-1999 period (species = HCRE)

description: We fitted species-specific state-space models for annual abundance data over the 1987-2008 period outside the IPM, and used the 1994-1999 error-filtered female abundance as input to the IPM (data presented here).
DOI: 10.5061/dryad.k7c3v/13
title: Individual (adult) mark-recapture histories for the 1994-1999 period (species = IIWI)

description: Data used as input for the IPM, here in the MARK format.
DOI: 10.5061/dryad.k7c3v/14
title: Actual annual female abundance for the 1994-1999 period (species = IIWI)

description: We fitted species-specific state-space models for annual abundance data over the 1987-2008 period outside the IPM, and used the 1994-1999 error-filtered female abundance as input to the IPM (data presented here).
DOI: 10.5061/dryad.k7c3v/15
title: Individual (adult) mark-recapture histories for the 1994-1999 period (species = JAWE)

description: Data used as input for the IPM, here in the MARK format.
DOI: 10.5061/dryad.k7c3v/16
title: Actual annual female abundance for the 1994-1999 period (species = JAWE)

description: We fitted species-specific state-space models for annual abundance data over the 1987-2008 period outside the IPM, and used the 1994-1999 error-filtered female abundance as input to the IPM (data presented here).
DOI: 10.5061/dryad.k7c3v/9
title: Individual (adult) mark-recapture histories for the 1994-1999 period (species = HAAM)

description: Data used as input for the IPM, here in the MARK format.
DOI: 10.5061/dryad.kv686/1
title: Szymkowiak et al. data

description: Includes data worksheet that detail: 1. the abundance of wood warblers on experimental plots in pre-treatment and treatment years, 2. the temporal dynamics of floater abundance, 3. the song characteristics data used in acoustic analysis.
DOI: 10.5061/dryad.p9q57/1
title: Figure 2. B) Measurements of IFN-β gene induction in HeLa and MDCK cells via qPCR

description: This is the data corresponding to figure 2B, which describes the relative transcript levels of IFBN-beta in MDCK and HeLa cells after infection with VSV M51R.
DOI: 10.5061/dryad.p9q57/2
title: Fig 3. A-C) Quantification of IFN response in PC-3 and LNCaP cells

description: This file includes the data for Figure 3 A-C. Fig. 3A includes the data for IFN-b secretion by PC3 and LnCap cells after VSV infection, as measured by ELISA. Figure 3B-C) has the normalized transcript quantities for MXA and OAS1 after stimulation with IFN-b, as measured by RT-qPCR.
DOI: 10.5061/dryad.pq161/1
title: Individual soil mite data

description: Indiv is a data frame stored in "Individual soil mite data.Rdata" which contains the following columns relevant to the sampling experiment.
*trt* has levels that represent the food treatment: T1 (constant), T2 (famine), T3 (declining), T4 (fluctuating) 
*pop.ID* is a unique identifier for each of 2 replicate populations per treatment.
*date* is the date when a sampling event began
*stage* is the life stage of the individual at the beginning of the 24 hour sampling period.
*ind.ID* is a unique identifier of an individual observed for a sampling period.
*s24* is 1 if the individual was alive after 24 hours, 0 if it was dead, or NA if it was lost.
*t24* indicates transiton to either the same stage as the beginning of the sampling period (initial stage) the next, or in between stages (quiescent).
*f24* is the number of eggs laid in the 24 hour sampling period.
*l0* is the body length at the beginning of the sampling period (mm).
*l24* is the body length at the end of the sampling period (mm).
*density* is the approximate value of body lenghths summed over the population on the date of sampling (see apendix S2 from publication) (mm).
*supply* is food given divided by density on the date of sampling (mg/mm).
*food* is the amount of food given to the population on that date (mg).
*density.s* is the density scaled to have mean 0 and variance 1.
*supply.s* is the supply scaled to have mean 0 and variance 1.
*l0.s* is body length scaled to have mean 0 and variance 1.
*day* is the number of days since the start of the experiment.
DOI: 10.5061/dryad.pq161/2
title: Egg size from sampling

description: eggdat is a data frame stored in "Egg size from sampling.Rdata" contianing measurments of individual eggs from sampled females.
*egg.ID* is a unique identifier for an egg.
*pop.ID*, *date*, *trt*, *s24*, *f24*, *l0*, *l0.s*, *density*, *density.s*, *supply*, and *supply.s* are the same as in the individual data in another file.
*fem.ID*  is the same as indiv.ID above for the mother of the eggs.
*esize* is the size of the sampled egg (mm).
DOI: 10.5061/dryad.rc63v/1
title: Chemotaxis Middle Chamber

description: Holograms of Malene Bay brine sample exposed to a bottom-to-top serine gradient (data file 2015.03.30 06-28) Data for Fig. 9 B, C in paper and Video S9.
DOI: 10.5061/dryad.rc63v/2
title: Chemotaxis Side Chamber

description: Brine sample exposed to a right-to-left serine gradient. Data file 2015.03.30 06-14. Data for Fig. 9 A in paper.
DOI: 10.5061/dryad.rc63v/3
title: Seawater at +4C

description: Malene Bay seawater kept overnight at +4 C with the addition of 1/2 strength 2216 marine medium. File 2015.03.30 05-58. Data for Figures 7 and 8E in paper and Videos 4 and 7.
DOI: 10.5061/dryad.t297p/1
title: Data and code for polyfreqs manuscript

description: This folder contains all of the code and data for the simulation study conducted to evaluate polyfreqs. It also contains the empirical data for the potato data set analyzed in the manuscript and the supplemental walk through. The code for producing all of the figures is also provided. These are all in the 'code', 'example' or 'supplement' folders. Each folder has it's own README file.
DOI: 10.5061/dryad.tm680/1
title: alignment fasta file for 18S rRNA, 28S rRNA and COI

description: This file contains the alignments of the 18S rRNA, 28S rRNA, and COI datasets used in the paper, respectively.  The file is in fasta-format.
DOI: 10.5061/dryad.tp0d0/3
title: Farm plant data 2012

description: 2012 grassland plant survey data (species level) across 10 farms (20 fields). Transect monitoring.
DOI: 10.5061/dryad.tp0d0/4
title: Farm plant-pollinator data 2013

description: 2013 pollinator survey data (species level) across 10 farms (one field per farm). Each row represents a plant-pollinator interaction.
DOI: 10.5061/dryad.tp0d0/5
title: Farm plant survey data 2013

description: 2013 grassland plant survey data (species level) across 10 farms (one field per farm). Transect monitoring.
DOI: 10.5061/dryad.tp0d0/6
title: Vicia faba seed count and weight (phytometer experiment)

description: Phytometer experiment measuring pollination of bean plants via seed set in relation to the adjacent grassland.
DOI: 10.5061/dryad.tp0d0/7
title: Fragaria × ananassa fruit class and weight (phytometer experiment)

description: Phytometer experiment measuring pollination of Fragaria × ananassa plants via fruit class and weight in relation to the adjacent grassland.
DOI: 10.5061/dryad.tp0d0/8
title: Silene dioica seed count (phytometer experiment)

description: Phytometer experiment measuring pollination of Silene dioica plants via seed set in relation to the adjacent grassland.
DOI: 10.5061/dryad.ts183/1
title: CRT_optimal_DRYAD

description: Data collected during study period at the different phases (i.e. baseline, 3 months, and 6 months.) Questionnaires are SF-36 and LIfHE, each "@-number" corresponds to standard question. "Ventrikulaer_aktivitet" means ventricular activity.
DOI: 10.5061/dryad.248vp/1
title: schluter speciation ecological opportunity and latitude

description: Data files from the literature used in calculations of speciation and diversification when not provided in text by sources.
DOI: 10.5061/dryad.2qb35/1
title: mtDNA_simple

description: This is a nexus file that includes alignments of mitochondrial DNA sequences that were analyzed in this study
DOI: 10.5061/dryad.2qb35/10
title: Male vocalization of X. kobeli; field ID number BJE3073

description: Male vocalization of X. kobeli; field ID number BJE3073
DOI: 10.5061/dryad.2qb35/2
title: mtDNA_simple.nxs

description: This is an input file for BEAST that was generated from the nexus file and that was used to analyze the mitochondrial DNA sequence alignment
DOI: 10.5061/dryad.2qb35/5
title: R1R2_pileup_simple.nxs

description: This is the xml file that was generated from the RAG1 and RAG2 concatenated nexus file that was used as input for the BEAST analysis.
DOI: 10.5061/dryad.2qb35/6
title: R1R2con

description: This is the consensus tree from the BEAST analysis of the concatenated sequence data from RAG1 and RAG2.
DOI: 10.5061/dryad.2qb35/7
title: Male vocalization of X. allofraseri specimen MCZ A-148176

description: Male vocalization of X. allofraseri specimen MCZ A-148176
DOI: 10.5061/dryad.2qb35/8
title: Male vocalization of X. eysoole; specimen MCZ A-148129 or MCZ A-148130

description: Male vocalization of X. eysoole; specimen MCZ A-148129 or MCZ A-148130 (we are not sure which of these individuals was recorded)
DOI: 10.5061/dryad.2qb35/9
title: Male vocalization of X. fischbergi.

description: Male vocalization of X. fischbergi.  No specimen ID is associated with this recording.
DOI: 10.5061/dryad.343nd/1
title: Raw labeled reads from Insect trap samples

description: Collected on daily basis using three emergence traps and one Malaise trap. DNA extracted from bulk samples using a modified salt-extraction method. Sequenced using Ion Torrent PGM. FASTQ file header stands for: @READNUMBER;barcodelabel=TRAPTYPE-DAY_MONTH.
DOI: 10.5061/dryad.343nd/2
title: Raw labeled reads from faecal samples of Myotis daubentonii

description: Collected on daily basis one single location. DNA extracted from individual pellets using Qiagen Stool Mini Kit. Sequenced using Ion Torrent PGM. FASTQ file header stands for: @READNUMBER;barcodelabel=SAMPLEID-DAY_MONTH.
DOI: 10.5061/dryad.343nd/3
title: OTU sequences

description: Clustered to OTUs using USEARCH algorithm with default (97%) similarity. This way there is a little bit of oversplitting, and OTUs belonging to same biological species are clustered subsequently.
DOI: 10.5061/dryad.343nd/4
title: Readmap linking trimmed reads and samples

description: The readmap shows read count for each sample. The readmap is constructed using USEARCH software.
DOI: 10.5061/dryad.343nd/5
title: Technical data sheet for IonTorrent PGM runs

description: The data generated by Ion Torrent PGM for each run in hte study.
DOI: 10.5061/dryad.343nd/6
title: Command pipeline used for bioinformatics

description: The file contains all the commandds used in this study to generate the final data. The bioinformatics was carried out at servers on CSC - IT Center for SCience in Finland .
DOI: 10.5061/dryad.343nd/7
title: The final readmap

description: This readmap contains the final read counts for each sample. The difference to raw readmap is that some OTU's in this version have been clumped together.
DOI: 10.5061/dryad.38c1g.2
title: Data from: Evolutionary processes driving spatial patterns of intra-specific genetic diversity in river ecosystems
DOI: 10.5061/dryad.38c1g.2/1.2
title: Simulated data from the gene-flow model

description: Parameter values and summary statistics for simulations generated under the gene-flow model
DOI: 10.5061/dryad.38c1g.2/2.2
title: Simulated data from the habitat availability model

description: Parameter values and summary statistics for simulations generated under the habitat availability model
DOI: 10.5061/dryad.3pf61/1
title: Data for Pace of life, predators and parasites: Stephenson et al. Biology Letters

description: These data are from guppies, Poecilia reticulata, from several sample sites across Trinidad. For each fish, we recorded the sex, weight, condition (using the scaled mass index), and the presence and number of Gyrodactylus spp. parasites infecting the fish. We provide the drainage, river, course and site, as well as the nested terms where appropriate, where each fish was collected.
DOI: 10.5061/dryad.4902q/1
title: 1_Aargenteus_D-loop_YSuzuki

description: The sequences of the mitochondrial control region of Apodemus argenteus used for the construction of the phylogenetic tree and network.
DOI: 10.5061/dryad.4902q/2
title: 2_Aargenteus_Cytb_YSuzuki

description: The mitochondrial cytochrome b gene sequences of Apodemus argenteus used for the construction of the phylogenetic tree and network.
DOI: 10.5061/dryad.4dd3s/2
title: Source code to replicate all results and figures

description: Unzip then read "README.md" for instructions
DOI: 10.5061/dryad.6v79q/3
title: Mitonuclear line male data

description: This file has data on male ejaculate weight and lifespan, and reference female lifespan, fecundity, fertility and offspring hatching success
DOI: 10.5061/dryad.6v79q/4
title: Mitonuclear line ref female egg size

description: This file has data on mitonuclear line male mates' egg size.
DOI: 10.5061/dryad.88589/1
title: Ornelas_et al_IMa_AMETvsBLUE_mt+micros

description: Amethyst-throated (Sierra Madre Oriental and Trans-Mexican Volcanic Belt) versus blue-throated (Sierra Madre del Sur) populations of Lampornis amethystinus for mitochondrial markers  (ND2 and cytochrome b) and microsatellites.
DOI: 10.5061/dryad.88589/2
title: Ornelas_et al_IMa_SMOSvsTMVB_mt+micros

description: Amethyst-throated populations from the Sierra Madre Oriental versus amethyst-throated populations along the Trans-Mexican Volcanic Belt of Lampornis amethystinus for mitochondrial markers  (ND2 and cytochrome b) and microsatellites.
DOI: 10.5061/dryad.88589/3
title: Ornelas_et al_IMa_WESTvsEAST_mt+micros

description: Amethyst-throated (incl. blue-throated) populations west of the Istmus of Tehuantepec versus amethyst-throated populations east of the Isthmus of Tehuantepec of Lampornis amethystinus for mitochondrial markers  (ND2 and cytochrome b) and microsatellites.
DOI: 10.5061/dryad.88589/4
title: Ornelas_et al_DIYABC_Genotypes_mito

description: Ornelas_et al_DIYABC_Genotypes_mito text-formatted DIYABC data file containing microsatellite genotypes and mitochondrial ND2 and cytochrome b concatenated sequences of populations of Lampornis amethystinus.
DOI: 10.5061/dryad.88589/5
title: Ornelas_et al_DIYABC_models_header

description: Ornelas_et al_DIYABC_models_header text-formatted DIYABC reftableHeader file containing scenarios, priors and summary statistics used in the DIYABC analysis.
DOI: 10.5061/dryad.88589/6
title: Ornelas_et al_microsatellites_info

description: Microsatellite sizing for 126 samples of Lampornis amethystinus hummingbirds genotyped at eigth autosomal microsatellite loci previously designed for Campylopterus curvipennis (Cacu16-1 and Cacu17-2; Molecular Ecology Resources Primer Development Consortium et al. 2010; GenBank accession nos. GQ294539–GQ294550) and Selasphorus platycercus (HUMB2, HUMB3, HUMB9, HUMB10, HUMBB11 and HUMB15Oyler-McCance et al. 2011; HQ316946–HQ316955). Microsatellite sizing for each loci consists in 3 digits (e.g. 216  for L32 Malinche, Tlax. at loci Cacu 16-1).
DOI: 10.5061/dryad.88589/7
title: Ornelas_et al_MAXENT_Lampornis_amethystinus

description: Lampornis amethystinus_MAXENT_File: coordinates longitude and latitude of Lampornis amethystinus.
DOI: 10.5061/dryad.gs8r2/5
title: mtDNA sequences
DOI: 10.5061/dryad.k7c3v/17
title: Individual (adult) mark-recapture histories for the 1994-1999 period (species = OMAO)

description: Data used as input for the IPM, here in the MARK format.
DOI: 10.5061/dryad.k7c3v/18
title: Actual annual female abundance for the 1994-1999 period (species = OMAO)

description: We fitted species-specific state-space models for annual abundance data over the 1987-2008 period outside the IPM, and used the 1994-1999 error-filtered female abundance as input to the IPM (data presented here).
DOI: 10.5061/dryad.k7c3v/19
title: Individual (adult) mark-recapture histories for the 1994-1999 period (species = RBLE)

description: Data used as input for the IPM, here in the MARK format.
DOI: 10.5061/dryad.k7c3v/20
title: Actual annual female abundance for the 1994-1999 period (species = RBLE)

description: We fitted species-specific state-space models for annual abundance data over the 1987-2008 period outside the IPM, and used the 1994-1999 error-filtered female abundance as input to the IPM (data presented here).
DOI: 10.5061/dryad.mk556/1
title: Fig 1. Characterization of primary cell culture derived from placenta for MSC origin.

description: (A) RT-PCR analysis for expression of typical MSC markers: cells provide a signal for CD90, CD73, and CD105 MSC while being negative for CD34 hematopoietic marker. (B) Minus RT control for RT-PCR. (C,D) Cells display strong signals for CD73 and CD105 in flow cytometry analysis.
DOI: 10.5061/dryad.mk556/2
title: Fig 2. Differentiation potential of primary cell culture derived from placenta into lineages of MSC origin.

description: MSCs were differentiated into (A) adipogenic (Oil Red O staining), (B) osteogenic (Von Kossa staining), and (C) chondrogenic (Alcian blue staining) lineages as a proof of principle for plasticity of MSCs. Cells expanded in regular MSC culture medium represent the negative control (bar = 50 µm).
DOI: 10.5061/dryad.mk556/3
title: Fig 3. MSCs of placenta after storage at +20°C (A,B) and 4°C (C,D).

description: Trypan blue staining, (A,C); phase contrast microscopy (B,D). Scale bar is 200 µm.
DOI: 10.5061/dryad.mk556/4
title: Fig. 4. Parameters of placental MSCs after cryopreservation with different cooling rates.

description: (A) - cell number in the sample; (B) - viable cells according to Trypan blue and 7 AAD staining; (C) - functional activity of cells in studied samples; (D) – adherence to plastic.*- significance to positive control p&lt;0.05.
DOI: 10.5061/dryad.mk556/5
title: Fig. 4. Parameters of placental MSCs after cryopreservation with different cooling rates:

description: Data set for Fig.4
DOI: 10.5061/dryad.n41nk/1
title: Allelic Richness Analysis
DOI: 10.5061/dryad.n41nk/2
title: Allelic Richness Analysis
DOI: 10.5061/dryad.n41nk/3
title: IBD and GLM Data
DOI: 10.5061/dryad.n41nk/4
title: IBD and GLM Data
DOI: 10.5061/dryad.n41nk/5
title: Microsatellite
DOI: 10.5061/dryad.n41nk/6
title: Microsatellite
DOI: 10.5061/dryad.nf61t/1
title: Krug & Patzkowsky 2015 Stages and Superfamilies copy

description: Data for data binned into stages temporally. Analysis is for extinction and origination of genera within superfamilies. M-tax files designate genera within the same family in each interval. M_ext files designate genera within each interval that go extinct simultaneously within the interval. M_orig files designate genera that originate simultaneously within the interval. The number at the ned of the file designates the interval in question.
DOI: 10.5061/dryad.nf61t/2
title: Krug & Patzkowsky 2015 Stages and Families copy

description: Data for data binned into stages temporally. Analysis is for extinction and origination of genera within families. M-tax files designate genera within the same family in each interval. M_ext files designate genera within each interval that go extinct simultaneously within the interval. M_orig files designate genera that originate simultaneously within the interval. The number at the ned of the file designates the interval in question.
DOI: 10.5061/dryad.nf61t/3
title: Krug & Patzkowsky 2015 Substages and Families copy

description: Data for data binned into substages temporally. Analysis is for extinction and origination of genera within families. M-tax files designate genera within the same family in each interval. M_ext files designate genera within each interval that go extinct simultaneously within the interval. M_orig files designate genera that originate simultaneously within the interval. The number at the ned of the file designates the interval in question.
DOI: 10.5061/dryad.p9q57/3
title: Figure 5. Selection in temporally heterogeneous innate immune environments leads to VSV strains with differential capacities to block IFN-β production.

description: This data corresponds to the graph in Figure 5. It describes the secretion of IFN-b in PC3 cells (as measured by ELISA) after infection with different strains of VSV experimentally evolved in heterogeneous innate immune environments.