cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8r6jp/2
title: GOT1p1_p2

description: Alignment of GOT1p1 and GOT1p2 paralogs from populations of the copepod Tigriopus californicus. All sequences are the result of direct sequencing off PCR products from genomic DNA isolated from single copepods. More details can be found in paper but each paralog was amplified by using primers that specifically amplified that paralog exclusively. Paralog is indicated by the p1 or p2 in the sequence and the population from which sequence was obtained is indicated by the AB, SD, SCN, or LJS label. The two alleles from a single individual are indicated with an A and B. In some cases two copies of each paralog were obtained from the same individual.
DOI: 10.5061/dryad.8r6jp/3
title: GOT1Sd_r_alignable_regions

description: This is a nexus file that provides a sequence alignment for the regions of the GOT1Sd and GOT1Sr that are alignable (and a region from 470 to 814 that does not align well in the middle). The 5-prime end of the alignment starts at position 1037 of the GOT1Sr alignment. The middle section of that is not alignable has been removed from this alignment. For the GOT1Sd gene after 539bp of sequence 282bp has been removed. For the GOT1Sr gene after 550bp a large fragment of this intron sequence has been removed (between 2271bp for the SD population and 3411 for the SCN population).
DOI: 10.5061/dryad.8r6jp/4
title: GOT1Sr_AB_SD_LJ

description: This file is an alignment of GOT1Sr from the SD, AB, and LJS populations. The SCN population is included as separate file because the large intron does not align well with the intron from these populations. Each sequence indicates the population with the AB, SD, or LJS labels. Sequences labeled with cDNA were sequenced from cDNA while sequences saying clone were sequenced from cloned PCR products from a single individual. The remaining sequences were from direct sequencing of PCR products from a single copepod. The two alleles are given the same label but the second allele is given an 'a' appendage. The phase of the mutations within an individual was not determined experimentally.
DOI: 10.5061/dryad.8r6jp/5
title: GOT1Sr_SCN

description: This file is an alignment of GOT1Sr from the SCN population. The SCN population is included as separate file because the large intron does not align well with the intron from these populations. The sequence labeled with cDNA was sequenced from cDNA while the sequence saying clone was sequenced from cloned PCR products from a single individual. The remaining sequences were from direct sequencing of PCR products from a single copepod. The two alleles are given the same label but the second allele is given an 'a' appendage. The phase of the mutations within an individual was not determined experimentally.
DOI: 10.5061/dryad.8r6jp/6
title: GOT1Sd_align

description: Alignment of GOT1Sd sequences from populations of the copepod Tigriopus californicus. This got1s_SDcomplete_m sequence is a cDNA sequence from the GOT1sr gene from the SD population that has been included for a reference. The population origin of the other sequences is indicated by the SD, SCN, AB, or LJS label. Sequences are from direct sequencing of PCR products obtained from a single individual. Two alleles from the same individual are indicated with the a or b labels (with the remainder of the label identical).
DOI: 10.5061/dryad.bp3g0/1
title: LaydateCS_12Mar13.xlsx

description: Excel file with data on changing phenology and population size of birds (N= 196 studies).  Variables are explained and sources given in the sheet titled "Variables & Sources"
DOI: 10.5061/dryad.c70gv/14
title: terfezia-peziz_ITS_algnmnt

description: Terfezia-peziza depress clade ITS alignment in FASTA format, Ambiguously aligned regions were excluded in GBlocks using the least stringent setting (Castresana, 2000; Talavera & Castresana, 2007), missing data is represented by "?" Sources of sequences include ascocarps, mitospore mats (taxon name preceded by "AM")and ectomycorrhizal roots (taxon name preceded by "EM").
DOI: 10.5061/dryad.c70gv/15
title: Tuber_ITS_alignment

description: Tuber ITS alignment in FASTA format, Ambiguously aligned regions were excluded in GBlocks using the least stringent setting (Castresana, 2000; Talavera & Castresana, 2007), missing data is represented by "?" Sources of sequences include ascocarps, mitospore mats (taxon name preceded by "AM")and ectomycorrhizal roots (taxon name preceded by "EM").
DOI: 10.5061/dryad.cc454m37/1
title: Leptolalax_2011

description: Nexus file with final alignment of 16S rDNA sequences used for phylogenetic analysis.
DOI: 10.5061/dryad.ct40s/23
title: Dumetella femur 242013
DOI: 10.5061/dryad.ct40s/24
title: Icterus 241804
DOI: 10.5061/dryad.ct40s/25
title: Larus femur 8771
DOI: 10.5061/dryad.ct40s/26
title: Meleagris R1718
DOI: 10.5061/dryad.ct40s/27
title: Otus 240864
DOI: 10.5061/dryad.ct40s/28
title: Otus 241793 femur
DOI: 10.5061/dryad.ct40s/29
title: Otus 241793 humerus
DOI: 10.5061/dryad.ct40s/30
title: Parus femur 241934
DOI: 10.5061/dryad.ct40s/31
title: Parus humerus 241963
DOI: 10.5061/dryad.ct40s/32
title: Parus femur 241963
DOI: 10.5061/dryad.f0824/1
title: Data for Van Buskirk (2013, JEB)

description: Two worksheets in a single Excel file. One contains results of the mesocosm experiment, and the other contains the original microsatellite data.
DOI: 10.5061/dryad.f660p/1
title: Harmonetal2010

description: Data files and r script.
DOI: 10.5061/dryad.hn1vn/1
title: Phylogenetic trees simulated under multi-process macroevolutionary models for analysis with BAMM

description: This file contains simulated datasets analyzed as part of Rabosky (2014). There are 6 general simulation scenarios, described at length in the manuscript. These include 500 phylogenetic trees simulated under each macroevolutionary scenario. Each batch of simulated datasets was analyzed with BAMM. This dataset contains the simulated datasets, and also the parameters underlying the simulations. For example, the subdirectory "constant" contains the 500 constant-rate birth-death process phylogenies that were analyzed with BAMM. These trees are stored in the fild "simtrees.txt". Another file in this directory, "cr_truerates.txt", contains the actual simulation parameters. For example, the first row of that file gives the speciation and extinction parameters that were used to simulate the first tree in the "simtrees.txt" file. The same general idea holds for the other subdirectories. dd_k1 for example is a pure-birth background process with a shift to a single diversity-dependent regime on one descendant lineage. The simulation scenarios are detailed in the master file "DESCRIPTION.txt".
DOI: 10.5061/dryad.hv4db/1
title: responses to seismic surveys

description: ZIP file containing 10 .txt data files as described in readme.txt
DOI: 10.5061/dryad.md545/1
title: Armadillidium_vulgare_454reads.fas

description: Fasta file containing 18511 reads from Armadillidium vulgare (Crustacea, Isopoda). The reads were generated by 454 pyrosequencing of a microsatellite-enriched genomic library derived from a pool of 8 individuals.
DOI: 10.5061/dryad.np597/6
title: Chlamydial cytotoxins tree

description: Phylogenetic tree of cytotoxins originating from Chlamydia species. Distances were calculated using a WAG+I+G substitution model and trees generated using MrBayes. File is in Newick tree file format.
DOI: 10.5061/dryad.pd383/2
title: Dryad_BahamasMales

description: The four life history variables used for males (SL, Lean Weight, Fat Content, and GSI).
DOI: 10.5061/dryad.pd383/3
title: Dryad_EnvrionmentalVariables

description: This file contains the environmental variables we measured for each site (phycocyanin, chlorophyll a, small phytoplankton, large phytoplankton, and zooplankton).
DOI: 10.5061/dryad.pq608/3
title: Gamble_Zarkower_Supp_File3

description: Supplementary File 3. RADtools output – sub-sampled datasets
DOI: 10.5061/dryad.q86rj/1
title: Bacterial communities on Agalychnis callidryas

description: Bacterial counts from swab cultures of captive Agalychnis callidryas grown on R2A media. Frogs were fed on carotenoid enriched or normal diets. Data are divided by gender.
DOI: 10.5061/dryad.rf18s/1
title: Crotalinae_Tree

description: Phylogeny containing 104 ingroup species. Reconstructed using simultaneous tree and date estimation in BEAST. Calibration points are detailed in the Methods section of the paper. Corresponding sequence alignment is included in the Dryad package.
DOI: 10.5061/dryad.rf18s/2
title: Crotalinae_Seq_Nexus

description: DNA sequence alignment in Nexus format. Up to 8 genes for 104 species. Range = 528bp (8%) - 6342bp (95%) complete. GenBank Accession numbers are provided in online suppl. info Appendix S1.
DOI: 10.5061/dryad.s147c/1
title: Miller&Rudgers_Dryad_data_submission_18Nov2013
DOI: 10.5061/dryad.v3p3j/1
title: Concat12

description: Concatenated alignment of the two ribosomal subunit rDNA genes (18S and 28S) and six protein coding genes: actin, elongation factor 1 alpha (EF1 alpha), alpha and beta tubulins, and the heat shock proteins 70 (hsp 70) and 90 (hsp 90)
DOI: 10.5061/dryad.v60r7/1
title: Simulation code in C for stigmergic avoiding animals

description: The C code contained here simulates the collective movement and interaction of animals in a 2D lattice as follows. Each individual moves as a random walker (with different type of movement statistics) and deposits a mark over each of the lattice location it visits. The deposited mark remains present only for a finite amount of time, T, after which it disappears. When another individual encounters a foreign mark, it retreats towards the centroid of its own active marked area with a probability that decreases as a function of the age of the mark. The functional form with which it decays is controlled by the response decay exponent. For more details read the Material and Methods and Supplementary Information of the article.
DOI: 10.5061/dryad.vk67d/1
title: Microsatellite_and_MITE_data
DOI: 10.5061/dryad.vr157/1
title: Fossil Occurrence Data

description: Fossil occurrence data compiled from the MIOMAP and FAUNMAP databases (http://www.ucmp.berkeley.edu/neomap/). Each locality is identified by the combination of database name (“MM” for MIOMAP, “FM” for FAUNMAP), Machine Number, and Analysis Unit. Included in the data table are: Max_age, maximum age of locality in million years; Min_age, minimum age of locality in million years; Genus_accepted, standardized genus designation; Species_accepted, standardized species designation; Genus_NEOMAP, genus designation in MIOMAP/FAUNMAP; Species_NEOMAP, species designation in MIOMAP/FAUNMAP; ID_conf_NEOMAP, level of confidence in the original species identification.
DOI: 10.5061/dryad.vr157/2
title: Cladogram

description: Composite cladogram for 276 North American fossil genera. See article and Online Appendix B for complete sources of information.
DOI: 10.5061/dryad.vr157/3
title: Body Mass Data

description: Skeletal measurements and estimated body masses of 901 taxa. Refer to Online Appendix B for additional information. Included in the data table are: LnMass, natural-log transformed body mass (originally in grams); m1L, anteroposterior length of the lower first molar; m1W, transverse width of the lower first molar; otherL, anteroposterior length of a skeletal element other than m1 (reported under Remarks); otherW, transverse width of a skeletal element other than m1 (reported under Remarks). See Body Mass References for a list of literature sources of measurements. Measurement data in the Paleobiology Database were obtained from: http://paleodb.org/cgi-bin/bridge.pl.
DOI: 10.5061/dryad.vt642/1
title: EE-Aythya ferina

description: Microsatellite genotype table including geographic coordinates of each sample
DOI: 10.5061/dryad.13kr7/1
title: Sphagnum fallax microsatellite data

description: Microsatellite allele sizes for Sphagnum fallax.
DOI: 10.5061/dryad.13kr7/2
title: Sphagnum fimbriatum microsatellite data

description: Microsatellite allele sizes for Sphagnum fimbriatum.
DOI: 10.5061/dryad.13kr7/3
title: Sphagnum palustre microsatellite data

description: Microsatellite data for Sphagnum palustre.
DOI: 10.5061/dryad.1d60p/1
title: nc_pottsetal_online_data

description: Data on distances between successive locations of Caribou, the habitats at the start and end of the steps, and the probabilities that we would expect each step to end in each habitat if there is no selection.
DOI: 10.5061/dryad.1rs10/1
title: expt12_female_survival_data

description: This file contains data on the survival of adult female mosquitoes from Experiments 1 and 2.
DOI: 10.5061/dryad.1rs10/2
title: expt1_fecundity_blood_data

description: The file 'expt1_fecundity_blood_data' contains data from the Experiment 1 related to female fecundity and blood feeding.
DOI: 10.5061/dryad.32665/1
title: Remate

description: Sperm numbers in space and time after second mating.  Variables:  Cross - Species identity of first and second male to mate with a D. simulans female, where "s" indicates D. simulans and "m" indicates D. mauritiana, such that "ss" indicates that both males were D. simulans, "ms" indicates that the first male was D. mauritiana and the second male was D. simulans, etc. MinASM – time after the start of mating at which female was frozen, in minutes. Remate – day after first mating (day 0) on which female remated. Cop1 – duration in minutes of the first copulation. Cop2 – duration in minutes of the second copulation. PriorProg – number of progeny produced by female before remating. Matings - number of successful matings by that female. ThoraxF - female thorax length, in arbitrary units. ThoraxM1 - thorax length of the first male, in arbitrary units. ThoraxM2 - thorax length of the second male, in arbitrary units. Bursa1 – number of first-male sperm in the bursa. Bursa2 – number of second-male sperm in the bursa. SR1 – number of first-male sperm in the SR. SR2 – number of second-male sperm in the SR. Sp1 – number of first-male sperm in the spermathecae. Sp2 – number of second-male sperm in the spermathecae
DOI: 10.5061/dryad.32665/2
title: Virgin

description: Data on sperm transfer and storage after single mating of D. simulans female with D. mauritiana male. Variables: Treat – treatment, storage or transfer. Cop – copulation duration in minutes. ThoraxF - female thorax length, in arbitrary units. ThoraxM - thorax length of the second male, in arbitrary units. Bursa – number of sperm in the bursa. SR – number of sperm in the seminal receptacle. Sp – number of sperm in the spermathecae
DOI: 10.5061/dryad.32665/3
title: Ejection1

description: Timing and number of sperm ejected after a single mating of a D. simulans female with a D. mauritiana male. Variables: CopDur - copulation duration in minutes. EjTime - minutes after start of copulation when female ejected sperm mass. Sperm – number of sperm in the ejected sperm mass
DOI: 10.5061/dryad.3801d/1
title: Lepais et al Plos ONE North African alder microsatellite data

description: Microsatellite genotype file including individuals mane (ID), country and population of origin, and allele names at 11 microsatellites.
DOI: 10.5061/dryad.39jb0/1
title: genotype_age_location_Dryad2012

description: American glass eels recruitment begins in Florida around December and progresses northward to Newfoundland–Labrador until June/July (Helfman et al. 1987). The first waves of glass eels at each location were sampled in 2008 following this latitudinal trend at 17 sites evenly distributed along eastern North America up to the St. Lawrence estuary. For each location, 50 individuals were measured and preserved in 95% ethanol. Yellow eels were also collected between May and September 2008 at 15 locations ranging from the upper St. Lawrence River to the Atlantic coast of Canada. The emphasis on yellow eel sampling in this region was motivated by the occurrence of strikingly different recruitment trends reported between Atlantic Canada versus the upper St. Lawrence River and Lake Ontario (Cairns et al. 2008). Sample size varied from 69 to 100 yellow eels per location. Fin clips were preserved in 95% ethanol for DNA extraction and genotyping, and heads were kept for otolith extraction. Yellow Eels collected in 2007 were finally rejected since they were frozen before being preserved in ethanol, wich caused a bias in microsattelits amplification. AGE DETERMINATION: Age was determined for 946 yellow eels, which allowed us to subdivide them into annual cohorts. Sagittal otoliths were extracted, stored in glass vials in a 95% ethanol: glycerine solution (1 : 1 ratio), and cleaned with successive baths of bleach, water, and 95% ethanol. Once dried, otoliths were embedded in a mix of epoxy resin and hardener (4:1 ratio) inside gelatine capsules for 24 h, ground to the core on the sagittal plane, and polished with alumina powder on a polishing disc. Sections were etched, decalcified in 5% EDTA for annuli enhancing, stained in 0.01% toluidine blue solution, and digitally photographed (e.g., Tremblay 2009). The first annulus after the dark central nucleus was considered as the elver check (metamorphosis from leptochephalus larva to glass eel) and subsequent annuli as winter checks (e.g., ICES 2011). Eels were considered by convention to be of age 0 + in their year of arrival in continental waters, and their “cohort year” was thus defined as so. Each otolith was aged twice by two eel experts to confirm aging. A total of 946 yellow eel otoliths were readable, representing 17 different cohorts, each comprising 1 to 127 individuals.
DOI: 10.5061/dryad.39jb0/2
title: Abondance index variation and North Atlantic Oscillation Index

description: We tested for statistical associations among several combinations of the NAO time series and temporal fluctuations of three variables used as proxies of relative abundance. Variation in Nb was used as a proxy for relative variation in the number of breeders. Allelic richness (Ar), measured for each cohort, was used as a proxy for the relative abundance of recruits since it has previously been proposed to correlate with offspring recruitment (McCusker & Bentzen 2010). YCSI was used as a second proxy of recruit abundance. We first tested for pairwise correlations between Nb, Ar, and YCSI, and time series of these three parameters were then compared with the monthly normalized NAO (http://www.cgd.ucar.edu). The “corresponding year” between time series represented the year when glass eels reached the continent for the Ar, Nb, and YCSI time series. To test environmental influence on previous life stages, +2 to -2 year lags were also tested. To assess the statistical significance of climate influence on eel abundance, multivariate models were run where the explanatory variables considered were the NAO time series. Stepwise regressions of the three relative abundance variables (Nb, Ar, and YCSI) were fitted to the explanatory variables to determine which ones were significant. The Akaike Information Criterion (AIC) was used to select models. Cross-validation R2 was computed to determine the prediction strength of the selected model and semi-partial R2 were computed to assess the relative importance of each selected variable. Analyses were performed using SAS 9.2 software.
DOI: 10.5061/dryad.3h3f3380/2
title: Phylogeny_data

description: Multiple sequence alignment in Nexus format
DOI: 10.5061/dryad.3h3f3380/3
title: Complete_tree

description: ML phylogenetic tree obtained with PAUP* under the GTR+G+I model of sequence evolution using 5 nuclear gene and 52 species mainly rodents
DOI: 10.5061/dryad.3h3f3380/4
title: Tree_used_in_trait_analyses

description: Phylogenetic tree used in trait analysis, branch length were derived from the complete tree
DOI: 10.5061/dryad.3j07n/1
title: Raw data

description: Excel file with raw data for all surfaces (univariate and multivariate). Measurements are retrodeformed, after mathematically removing tectonic bed-parallel shortening (see Clapham et al., 2003; Wood et al., 2003). Only complete measurements are used; measurements from incomplete/broken specimens are excluded.
DOI: 10.5061/dryad.3v0n3/1
title: Comp assays, lasR, PAO1
DOI: 10.5061/dryad.3v0n3/2
title: OD600 monocultures strain A,B,C
DOI: 10.5061/dryad.3v0n3/3
title: OD600, RFU, strains A,B,C
DOI: 10.5061/dryad.3v0n3/4
title: W values of strains A,B,C
DOI: 10.5061/dryad.4k24d37q/2
title: Only file for Salinas et al 2012
DOI: 10.5061/dryad.5g2s0/1
title: pollen_datadryad

description: Data were collected at field sites in Baja California Sur, Mexico by Winifred F. Frick. Geographic locations for SiteIDs can be obtained by author upon request. Species codes are LEYE: Leptonycteris yerbabuenae; ANPA: Antrozous pallidus. Time = time visit occurred; Sunset = time of local sunset; MinSunset= minutes after local sunset of when visit occurred; Pollen Grains = number of pollen grains of Pachycereus pringlei found on stigma after single visit by identified bat species.
DOI: 10.5061/dryad.61f07/1
title: survival data

description: We measured larval mortality for S. droebachiensis at 3 different temperatures (3, 10 and 21 °C) reared in 4-l culture jars (n = 3). Temperatures in the jars were maintained either by placing them in a water bath (3 and 21 °C) or in a temperature-controlled room (10 °C). These temperatures encompass ambient and the extreme temperatures used in the experimental thermoclines. Six-day old larvae (each replicate was from a single parental pair, and reared at 10 °C) were used for this experiment. To quantify mortality, 30 larvae from every treatment for each replicate were transferred to a Petri dish at 0, 24 and 48 h, and categorized as live if swimming was observed using a Nikon SMZ 1500 dissecting microscope. Data set includes jar (replicate 4-l cuture jars), temperature (°C), time (h), and the number of live and dead larvae from a sample of 30 larvae
DOI: 10.5061/dryad.61f07/2
title: vertical distribution

description: We manipulated both the temperature in the bottom water layer (B) and the temperature difference between layers (ΔT) in an orthogonal design. We used, for S. droebachiensis (n = 5): 4 levels of ΔT (0, 3, 6 and 12 °C) and 3 levels of B (3, 6 and 9 °C); for A. rubens (n = 4): 3 levels ΔT (0, 6 and 12 °C) and 2 levels of B (6 and 12 °C); and for A. irradians (n = 4): 3 levels of ΔT (0, 5 and 11 °C) and 2 levels of B (5 and 11 °C). These combinations of factors were chosen to represent the conditions in the local environment. Since there were up to 12 treatment combinations for a particular species and we only had 4 thermocline chambers, not all replicates could be run simultaneously. For S. droebachiensis, different cohorts (from unique parental pairs) were blocked in time and all treatments were completed in 3 randomized groups of 4 within 26 h. For the other species, all replicates of all treatments were conducted in randomized order with a single larval cohort (from multiple parental pairs) within 48 h. Due to limitations of the seawater system at the time, the surface water was ~ 20 °C rather than 21 °C in the treatment combination of ΔT = 12 °C and B = 9 °C for S. droebachiensis.Once the thermoclines were established, 50 ml of seawater containing 250–350 larvae were introduced to each chamber within 1 cm from the bottom of the observation compartment (filled with 0.45 μm-filtered seawater) by gently pouring into a funnel attached to a small tube (2-mm inner diameter). Before being introduced to the experimental chamber, larvae were acclimated to the respective bottom temperature for 15 min. Larval position was visually determined to the nearest cm at 5, 15, 30, 45, 60 and 90 min after introduction for S. droebachiensis and A. irradians, and at 10, 30, 60 and 90 min for A. rubens. Larvae in the entire 50 cm water columns were counted in &lt; 2 min, making repeat counts of individual larvae highly unlikely. Data set includes experimental species, date, temperature of the top and bottom layers of the water column (°C), the temperature difference between layers (°C), time (min), and the number of larvae counted at each depth (cm)
DOI: 10.5061/dryad.66r6s/1
title: Life-history traits in Callosobruchus maculatus