cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.31dj3/22
title: 3 Neurons
DOI: 10.5061/dryad.31dj3/23
title: 4 Neurons
DOI: 10.5061/dryad.31dj3/24
title: 7 Neurons
DOI: 10.5061/dryad.31dj3/25
title: 7 Neurons
DOI: 10.5061/dryad.31dj3/26
title: 7 Neurons
DOI: 10.5061/dryad.31dj3/27
title: 7 Neurons
DOI: 10.5061/dryad.4jk02/1
title: Terapontoidei Consensus Tree (Newick format)

description: Phylogeny for 88 Terapontoidei species
DOI: 10.5061/dryad.4jk02/2
title: Terapontoidei Trees (Nexus format)

description: 500 trees evenly sampled from the posterior BEAST distribution of 88 Terapontoidei species
DOI: 10.5061/dryad.4v52c/1
title: Database_Species_Iturralde-Pólit-BITR-16-251

description: Data base used for species modelling. Species id, geographic data and climatic data
DOI: 10.5061/dryad.72613/1
title: Datasets compiled for the analyses of species abundance and richness

description: Summary of the four datasets compiled for the analyses of species abundance and richness, including the study ID, the taxonomic group studied, the biome and the logarithm of the response ratio (Log(RR)). Log(RR) was not calculated (“NA”) when the abundance or richness was zero in any of the treatments under comparison. a) Studies comparing abundance between scattered trees and open areas. b) Studies comparing richness between scattered trees and open areas. c) Studies comparing abundance between habitat patches and scattered trees. d) Studies comparing richness between habitat patches and scattered trees.
DOI: 10.5061/dryad.72613/2
title: Datasets compiled for the analyses of community composition

description: Summary of the two datasets compiled for the analyses of community composition. a) Studies comparing abundance between scattered trees and open areas. b) Studies comparing abundance between scattered trees and habitat patches. c) Studies comparing abundance between habitat patches and open areas.
DOI: 10.5061/dryad.7dk42/1
title: 1717snps-203ind-gender.recode

description: American lobster SNP genotypes
DOI: 10.5061/dryad.7dk42/2
title: population-map-female-male

description: American lobster sex information samples.
DOI: 10.5061/dryad.7dk42/3
title: 290ind-6230snps-salmo.recode

description: Arctic char SNPs genotypes.
DOI: 10.5061/dryad.7dk42/4
title: SexPopDef

description: Arctic char sex information samples.
DOI: 10.5061/dryad.7k525/1
title: Relative times of onset and cessation of foraging

description: Data are shown for mornings (‘Dawn’ tab) and for evenings (‘Dusk’ tab)Site: experimental sites (N = 4). Numbers are used here and in the manuscript to designate the sitesTreatment: whether the morning (at dawn) or evening (at dusk) was experimentally lighted (‘light’) or not (‘dark’)Date: day of the experimental morning (at dawn) and evening (at dusk), with 1 = 1 January. Missing days are due to experimental mishap (experimental schedule file available on demand).Temperature: daily air temperature at sunrise (at dawn) and sunset (at dusk) in degrees Celsius (obtained using light/temperature loggers, used to calculate the residuals of temperature against date in the models)Weather: whether the weather in the morning (at dawn) or evening (at dusk) was clement or adverse (snow and/or strong wind was observed)Extraction: experimenter that extracted the data (ADS = Arnaud Da Silva or DAD = David Diez-Méndez)Next columns:Tab ‘Dawn’: Daily Onset of foraging” (in min relative to sunrise)Tab ‘Dusk’ “Daily Cessation of foraging” (in min relative to sunset) for:Blackbird, Great_tit, Blue_tit, Poecile, Nuthatch, and Jay (only at dawn for the latter)For ‘Dawn’Blackbird_outliers are data without the outliers after sunrise and Great_tit_outliers without 5 outliers &gt;40 min before sunrise and 2 outliers &gt;40 min after sunrise (for secondary analyses, see last paragraph of the methods)
DOI: 10.5061/dryad.83f17/2
title: Genotype calls and genetic divergence between parapatric populations.

description: We show results of the analysis of differentiation between parapatric pairs of parapatric populations as performed with the Popoolation2 software. RADseq genotypes were mapped the a genome draft. For each SNP (defined by the position along the genomic contig where it was mapped) and genomic comparison between two parapatric populations we show the identity and read counts for the major allele (maa) in the two populations (ie.. pop1 is the dune population and pop2 is the headland population). We also show the value of Fst, as calculated by Popoolation2, as well as the p-value of a fisher exact test of allelic differentiation (FET). Finally, in the last column we show if the SNPs had outlier Fst values (i.e. upper 5% tail of the distribution) and presented significantly different allelic frequencies in the FET (Bonferroni corrected p-value lower than 5%).
DOI: 10.5061/dryad.896r3/1
title: Dados_middens_SM_2011

description: Data on fungi from leafcutter middens, Viçosa, MG, SE Brazil
DOI: 10.5061/dryad.8f45n/1
title: Propithecus_perrieri_24loci_3pop

description: This file contains the microsatellite genotype data used in the current paper as well as in Salmona et al. 2015. The file is in .gtx format and can be opened and analyzed easily in Genetix, R, or with a common text editor. The file contains the data of 42 Propithecus perrieri individuals genotyped over 24 polymorphic microsatellites markers. The individuals are further classified in three "populations" that relates to sampling sites. Salmona et al. 2015 showed little differentiation between the three sampling sites, therefore the three "population" individuals can not be considered as belonging to the same population. A file containing the geographic coordinates of the samples is associated to this file. For further details on how the data was generated see Salmona, Jordi, et al. "Genetic Diversity, Population Size, and Conservation of the Critically Endangered Perrier’s Sifaka (Propithecus perrieri)." International Journal of Primatology 36.6 (2015): 1132-1153.
DOI: 10.5061/dryad.9g54r/4
title: devil_STDP

description: Structural images and outputs from BEDPOSTX and DTIFIT from Tasmanian devil brain (provided by the Save the Devil Project).
DOI: 10.5061/dryad.b3m45/1
title: Degree of melanziation raw data

description: To visually evaluate and quantify melanization in larvae attacked by aphid soldiers, we used double-blind observational assays. We quantified the melanization phenotype before and after attack by aphid soldiers by using a subjective visual assay of melanization. We collected P. obesinymphae galls in the vicinity of Nashville, TN in July 2013. To facilitate observation, galls were split in half, and we placed individual Drosophila larvae, a surrogate for common Dipertan predators of galling aphids, in galls with aphids or in galls in which the aphids had been removed. Larvae remained in galls for 1 hr. Each D. melanogaster larvae was photographed before attack, immediately following attack, after removing the attacking soldiers, and 1 hr following attack. Only Drosophila larvae being attacked by at least 10 aphid soldiers were included in the study. Additionally, as controls, Drosophila larvae were stabbed either once or multiple times with a sterile needle. Larvae were then placed in an empty gall for 1 hr. Using a double-blind assay, all Drosophila larvae were assigned a score based on the proportion of the body melanized: 1 (no observable melanization) to 4 (surface completely melaninized). The sample size for each group was greater than or equal to 10.
DOI: 10.5061/dryad.b3m45/2
title: Surviorship assay raw data

description: To examine if the over activation of the melanization pathway affected the survivorship of D. melanogaster following attack by aphid soldiers, we compared the survivorship of Drosophila mutants deficient in the melanization response to wild-type Drosophila. To measure survivorship, we introduced larvae to a gall, monitored the larvae every 20 minutes and noted the time to death, defined as when the larvae stopped moving.
DOI: 10.5061/dryad.b3m45/3
title: qPCR raw data

description: To examine which genes were differential regulated following attack by aphid soldiers, we used quantitative PCR to assess expression levels of multiple immune genes in two experimental groups of D. melanogaster larvae: 1) Larvae attacked by P. obesinymphae for 1 hr; or 2) Larvae placed in an empty gall for 1 hr. One hour was chosen because it was prior to the average observed time of death caused by aphid soldiers (Lawson et al. 2014), but enough time to observe a melanization response. In order to provide a standardized reference and to establish whether our assays with aphids were sensitive enough to detect immunological activation, we also measured the expression of each these genes in Drosophila that were stabbed with sterile needles.
DOI: 10.5061/dryad.b3m45/4
title: Phenoloxidase assay raw data

description: Phenoloxidase levels in Drosophila tissues were measured using a simple procedure based on the transformation of L-dopa to dopachrome in the presence of phenoloxidase, measured as function of optical density, as described by Lario et al. (1993). Larvae were singly placed in freshly collected P. obesinymphae galls for 45 minutes, and subsequently removed with a small paintbrush. A control group of larvae of similar size was not exposed to the aphids and was labeled the “unattacked” group. In order to differentiate between phenoloxidase activation during mechanical wounding of the epithelia by aphid stylets, and circulating phenoloxidase activation in the hemolymph, Drosophila hemolymph was extracted from both the attacked larvae and the control group using fine needles. After hemolymph extraction, the larval midguts were removed using a pair of dissecting tweezers. The remaining cuticle was then placed in a 1.5 mL Eppendorf tube and ground by a pestle. The tubes were centrifuged briefly, and the liquid portion was removed by a pipette for use in the phenoloxidase assay, in addition to the extracted hemolymph.  Immediately after extraction, the hemolymph was transferred to ice-chilled ELISA wells containing 50 μL of 20 mM TRIS buffer, pH 7.0, with 1% sodium citrate. The cuticle fluids were transferred by pipette to ELISA wells containing the same mixture. After the hemolymph and cuticle fluids were collected, 50 μL of 3,4-dihydroxyphenyl-alanine (L-dopa), 5 mg/mL in TRIS buffer, were added to each well. Mixtures were incubated at 32°C for 45 min, and the wells were subsequently read in an ELISA spectrophotometer at a wavelength of 490 nm. Blank wells containing 50 μL TRIS buffer and 50 μL L-dopa in TRIS but no hemolymph or cuticle fluids were used as controls.
DOI: 10.5061/dryad.h21v2/1
title: Flowerheads photographed in UV

description: Zipped directory containing JPG files of Helianthus argophyllus flowerheads photographed with a Nikon D70s digital camera fitted with a Noflexar 35mm lens and a reverse-mounted 2 inch Baader U-Filter (restricting the transmission of light to 320–380 nm). Files are named according to the plant's location in the field and the photograph number (e.g. 'b1-11DSC_1586' is the plant from row 1, space 11, photograph 1586; exceptions are the F1 individuals which are labeled X3A-# or X3B-# instead of by field location). The archived data file with phenotypic measurements contains the key to translate field location to plant genotype.
DOI: 10.5061/dryad.h21v2/2
title: Custom Perl script for formatting paired-end GBS data for uneak pipeline

description: This script translates paired-end fastq sequencing files into two independent sets of individually barcoded reads with a custom Perl script, to be used in the uneak pipeline (which is built only for single-end reads, from TASSEL 3; Lu et al., 2013). usage: perl GBS_Fastq_BarcodeAdder.pl uneak_key_file.txt library_1.fq library_2.fq combined_library_out.fq
DOI: 10.5061/dryad.h21v2/3
title: Bash commands used to filter for final SNP matrix

description: This file contains the series of bash commands used to filter uneak output to call genotypes using more stringent filters. Starting with the HapMapCount file (for each individual at each tag pair: minimum of 10 tags, heterozygote if the ratio of the two tags &lt; 10, homozygote if the ratio of the two tags &gt; 50, otherwise N), filter the resulting file for sites with alternate homozygous genotypes in the two parent individuals (7,875 sites), filter those sites for a minimum coverage of 50% across all individuals and observed heterozygousity of 0.3–0.7, and then format these genotypes for import into R/qtl.
DOI: 10.5061/dryad.h21v2/4
title: Phenotype and genotype matrix for QTL mapping

description: Data matrix formatted for R/qtl, for QTL mapping in F2 population of Helianthus argophyllus. Column headers are: GBS_name (sample identifier in sequence files), name (field location, e.g. R1-11 is row 1, space 11), id (numeric identifier unique to individual), fam (F2 family), row (row location), , place (place within row location), mom (identity of F1 maternal parent), uvR (proportional UV pigmentation), uvD (absolute UV bullseye diameter, cm), total.d.cm (total flowerhead diameter, cm), disc.d (disc diameter, cm), petal.d.cm (mean ligule length, cm), FHage (binned maturity score of flowerhead). The following columns are marker genotypes, with the map location of those markers on rows 2 (linkage group) and 3 (centiMorgan).
DOI: 10.5061/dryad.h781v/1
title: Microbial community and network of meadow alpine soil by Illumina sequencing

description: The Qinghai-Tibet Plateau is the highest and the largest low-latitude plateau in the world, and also it is an extremely sensitive region to the impact of global warming and environmental changes. The alpine meadow, widely distributed on the Tibetan Plateau, occupies over 40% of the Qinghai-Tibetan Plateau area and plays a critical role in regional sustainable development, biodiversity and water resource conservation. The alpine meadow also was a large soil organic-carbon pool.In recently decades, succession and degradation were gradually occurring between different alpine meadow types, such as alpine meadow might appear in the alpine steppe meadow region according to years of field investigation which could be the consequences of the climate warming and anthropogenic activities. The aims of our study were to determine the effect of degenerated succession from alpine meadow (AM) to alpine steppe meadow (ASM) on soil organic carbon and soil microbial community structure.The archived files included one OTU table generated from the 16S rRNA gene sequencing data, as well as the input and output files for the network analyses.
DOI: 10.5061/dryad.h7kn8/1
title: Answers to AQ, ASRS, PDI questionnaires

description: This Excel file contains the answers to every item of each of the 3 questionnaires (AQ, ASRS, PDI), for all the participants (n=925). This is the raw data, so no score has been computed. The answers of each questionnaire are presented separately, on individual spreadsheets (3 in total). The questionnaire items are also presented on individual spreadsheets (3 in total).
DOI: 10.5061/dryad.j555d/1
title: Interaction data, phylogenies, and analysis code for paco

description: Data on the Mendoza pollination network analysed with paco. Phylogenies of both plants and pollinators as well as their interaction network are included. There is also an R script for the analyses. Please note that the interaction network was originally published by Arroyo, M. T. K., Primack, R. B. & Armesto, J. J. (Community studies in pollination ecology in the high temperate Andes of central Chile. I. Pollination mechanisms and altitudinal variation, 1982). The version here has been cleaned to remove unidentified species and to confirm species names are correct.
DOI: 10.5061/dryad.m7m23/1
title: monthly summary of frog calling intensity

description: This file gives the total calling intensity of frogs per month (i.e. the sum of all records per month, on a four point logarithmic scale). Variable names are as explained in the paper
DOI: 10.5061/dryad.mn3g7/1
title: Table_Genotype_phenotype_data

description: This file is an excel file containing the individual genotype of each plants, and its phenotype assess during two years (see article for more details).This dataset was used to performed association studies of wild pearl millet populations.
DOI: 10.5061/dryad.n54g4/4
title: structure_primarydata

description: Shows the data collected for close call structural analysis of individual meerkats. IPI: Interpulse Interval, F0: Fundamental Frequency
DOI: 10.5061/dryad.n54g4/5
title: summarized_glucocorticoid_rate_primary_data

description: Shows the data collected for close call rate and glucocorticoid metabolite levels of individual meerkats.
DOI: 10.5061/dryad.n77r3/10
title: CpG_CTOB_lane1_34_TGACCACT_L001_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txt

description: DNA methylation data embryo #34
DOI: 10.5061/dryad.n77r3/11
title: CpG_CTOT_lane1_34_TGACCACT_L001_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txt

description: DNA methylation data embryo #34_2
DOI: 10.5061/dryad.n77r3/12
title: CpG_CTOB_lane1_35_CGATGTTT_L001_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txt

description: DNA methylation data embryo #35
DOI: 10.5061/dryad.n77r3/6
title: lane3277_ATCACGTT_190re_L007_trimmed_tophat

description: RNA-Seq data embryo #190
DOI: 10.5061/dryad.n77r3/7
title: lane3277_CAGATCTG_189re_L007_trimmed_tophat

description: RNA-Seq data embry #189
DOI: 10.5061/dryad.n77r3/8
title: lane3277_GCCAATGT_96re_L007_trimmed_tophat

description: RNA-Seq data embryo #96
DOI: 10.5061/dryad.n77r3/9
title: lane3276_ATCACGTT_27re_L006_trimmed_tophat

description: RNA-Seq data embro #27
DOI: 10.5061/dryad.qb29h/1
title: Limborg et al. 2017_MEC-16-1473

description: This file contains three sheets with data for PolyFreqs based allele frequency estimates for all non-duplicated and all duplicated SNPs as well as co-dominant genotype data for all 4,077 non-duplicated SNPs. In this data file population samples are also named according to their location so that: Copper River resident = COPPL08, Copper River anadromous = TANA09, Columbia River resident = MEAD00, Columbia River anadromous = WENAT06.Copper River resident = COPPL08, Copper River anadromous = TANA09, Columbia River resident = MEAD00, Columbia River anadromous = WENAT06.
DOI: 10.5061/dryad.r1072/1
title: human_participant_data

description: Behavioral data for human participants for each session. Analysis code available at https://github.com/jbonaiuto/perceptual-choice-hysteresis
DOI: 10.5061/dryad.s612j/1
title: Liow_sp_interaction_size_16.1.2017

description: Data used for Liow et al. 2017 (Ecology Letters)
DOI: 10.5061/dryad.s612j/2
title: FormationAges

description: Formation data for Liow et al. 2017 (Ecology Letters)
DOI: 10.5061/dryad.s612j/3
title: Measured for Fig. 4

description: Zooid size measurements for Liow et al. 2017 (Ecology Letters)
DOI: 10.5061/dryad.s8n05/3
title: DGPS measurements of bathymetric height

description: DGPS measurements on Balgzand intertidal area, on 20 May 2012. These measurements were performed to verify the accuracy of the bathymetric maps, and to determine the height at which pressure loggers to measure tidal height were deployed in the Balgzand study area.
DOI: 10.5061/dryad.s8n05/4
title: GPS tracking and accelerometer data of individual Eurasian Oystercatchers foraging in the intertidal

description: This file contains GPS tracking data and accelerometer data of 10 individually tracked Eurasian Oystercatchers. GPS fixes have been linked to metadata on weather, sun/moon position, bathymetry and tidal information. Covers the period 1 August 2011 - 1 Mar 2012.
DOI: 10.5061/dryad.s8n05/5
title: Kriging interpolation estimates of intertidal bivalve densities and biomass

description: Kriging interpolation estimates for Cockle and Razor clam densities, lengths, and fresh weights, based on benthic survey data of the intertidal food stock of Eurasian Oystercatchers
DOI: 10.5061/dryad.s8n05/6
title: tidal height measurements based on diving pressure logger data

description: pressure logger data for four locations in the Balgzand intertidal area, used to measure the local water height in the study area
DOI: 10.5061/dryad.s8n05/7
title: R code to fit Oystercatcher distribution models, using MCMC sampling

description: Contains R code to fit all spatial distribution models for Oystercatchers based on generalised functional responses, using MCMC sampling. Also contains all required benthos, bathymetric and GPS data in the form of R data frames to run the models.
DOI: 10.5061/dryad.s8n05/8
title: bathymetric map of Balgzand intertidal area in the Dutch Wadden Sea

description: Based on the cycle 5 bathymetric map for the Dutch Wadden Sea at 20 meter resolution, prepared by Rijkswaterstaat, Ministry of Infrastructure and the Environment, the Netherlands, with a few improvements and patches.
DOI: 10.5061/dryad.t3q41/1
title: Population size data

description: Population sizes, treatment variables, and extinction data for experimentally observed populations of Tribolium castaneum.
DOI: 10.5061/dryad.073gb/1
title: Data_HomeRangeScale

description: Data used in the home-range scale analysis.
DOI: 10.5061/dryad.073gb/2
title: Data_WithinHomeRangeScale

description: Data used in the within-home-range scale analysis.
DOI: 10.5061/dryad.073gb/3
title: Data_WithinHomeRangeScale_Windchill

description: Data used in the within-home-range scale analysis describing wind-chill data
DOI: 10.5061/dryad.073gb/4
title: Data_ForagingTrackScale

description: Data used in the foraging track scale analysis.
DOI: 10.5061/dryad.0b63g/1
title: Behavioural and morphological measurements of great tits Parus major

description: Behavioural (problem-solving, learning and neophobia) and morphological (age, body condition and colour variables-see the associated manuscript for details on the colour variables used) measurements of wild great tits in Gotland (Sweden) in 2010 and 2011.
DOI: 10.5061/dryad.18nh4/1
title: Data from wolf predation studies carried out in Scandinavia (2001-2015) and Yellowstone National Park (2008-2015).

description: Excel file of data from wolf predation studies carried out in Scandinavia (2002-2015) and Yellowstone National Park (2008-2015). Data include: study system (Scandinavia or Yellowstone), study season (spring or summer), study year, pack ID (pack name/territory), wolf ID (identity of each wolf followed – Yellowstone only), unique kill ID (identity number associated with each wolf killed carcass – Yellowstone only), kill interval (time to next kill in days), bear presence (Scandinavia – absent or present in the study system; Yellowstone – absent or present at carcass site), Julian date (date of wolf kill), prey type (Scandinavia spring study – adult (i.e., &gt; 1 year) or calf (i.e., &lt; 1 year) moose; Scandinavia summer study – neonate or non-neonate moose (i.e., newborn calf or adult/yearling); Yellowstone summer study – large (i.e., elk, bison, or moose ≥11 months) or small (i.e., any neonate, or adult deer, bighorn sheep, or pronghorn) ungulate), pack size, road (distance from wolf kill to the nearest road in kilometers), scavenge (the number of carcasses wolves visited between kills – Yellowstone only), moose density (number of moose harvested/km2 averaged over the territory – Scandinavia only), and snow depth (snow depth on date of kill, measured in meters, recorded at the meteorological station closest to each territory – Scandinavia spring study only).
DOI: 10.5061/dryad.1cb8j/1
title: Cricket-full data Proc R Soc B
DOI: 10.5061/dryad.31dj3/28
title: 7 Neurons
DOI: 10.5061/dryad.31dj3/29
title: 4 Neurons
DOI: 10.5061/dryad.31dj3/30
title: 4 Neurons
DOI: 10.5061/dryad.31dj3/31
title: 4 Neurons
DOI: 10.5061/dryad.31dj3/32
title: 3 Neurons
DOI: 10.5061/dryad.31dj3/33
title: 5 Neurons
DOI: 10.5061/dryad.31dj3/34
title: 3 Neurons
DOI: 10.5061/dryad.31dj3/35
title: 4 Neurons
DOI: 10.5061/dryad.31dj3/36
title: 3 Neurons