cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.73520/1
title: Robustness to link removal: data and computer codes

description: We implemented three interaction extinction sequences which intended to produce best-, worst- and intermediate case scenarios, as has been done in node extinction based scenarios. The first sequence always removed the interaction between the most connected species (hereafter, most connected first) and its most connected mutualistic partner. When more than one species had the same degree of connectivity, we randomly chose one of them. This process was repeated as many times as the number of interactions in the network until the last interaction (the least connected species and its least connected mutualistic partner) was removed. . Note that, contrary to NBRA, interaction removal did not follow a predefined sequence because the degree of species was updated after each interaction extinction. The second sequence always removed the interaction between the least connected species (hereafter, least connected first) and its least connected mutualistic partner, and then continued by removing the remaining interactions belonging to the least connected species and its least connected mutualistic partner at each iteration step. The third sequence, named random, removed interactions at random, to simulate an intermediate extinction scenario.
DOI: 10.5061/dryad.7dm4d/1
title: ReadMe

description: File containing detailed information about the different data files in this submission.
DOI: 10.5061/dryad.808p0/1
title: Life history parameters in parasitoid Hymenoptera

description: The dataset comprises an Excel file including the taxonomy, phylogeny, and life history parameters (along with the independent contrasts of their untransformed values) of 133 species of hymenopteran parasitoids.
DOI: 10.5061/dryad.867ts/1
title: Dargentetal.evolsexesJEB

description: File includes: individual identifier ("identifier"), names of populations used ("pop"), sex of individuals ("sex"), years of  field sample ("year"), individuals standard length in mm ("startsl"), type of treatment ("type", i.e. sham or infected=2 G. turnbulli), peak parasite load ("peakpara"), parasite rate of increase r0 ("ro0to10"), outlier status of the individual ("outlier"), relative condition index ("startkn"),  death during infection ("died"), and last day in which the individual was counted for parasites ("last count", i.e. day of death).
DOI: 10.5061/dryad.b28p8/1
title: Artificial test scenarios for TD indices

description: Those are artificial data (2-D, 3-D and 8-D) generated with the software R. Each row represents an individual organism, each column represents an hypothetical trait. Additional information can be found in the paragraph "Artificial test scenarios for TD indices" in the section "Materials and methods".
DOI: 10.5061/dryad.b28p8/2
title: Test scenarios for TD indices using real data

description: Those are real data (8-D) from 15 samples collected in Lake Zürich (Switzerland) during spring 2009 (Pomati et al. 2013). Each row represents an individual organism, each column represents a trait (principal component calculated using 46 descriptors of 3-D structure and fluorescence profile for each phytoplankton cell or colony). Additional information can be found in the paragraph "Test scenarios for TD indices using real data" in the section "Materials and methods".
DOI: 10.5061/dryad.cg40g/10
title: 6basalBC_bams.tar.gz.splitj

description: 6basalBC_bams.tar.gz, split, part j.
DOI: 10.5061/dryad.cg40g/11
title: 6basalBC_bams.tar.gz.splitk

description: 6basalBC_bams.tar.gz, split, part k.
DOI: 10.5061/dryad.cg40g/12
title: 6basalBC_bams.tar.gz.splitl

description: 6basalBC_bams.tar.gz, split, part L.
DOI: 10.5061/dryad.cg40g/13
title: 6basalBC_bams.tar.gz.splitm

description: 6basalBC_bams.tar.gz, split, part m.
DOI: 10.5061/dryad.cg40g/14
title: 6basalBC_bams.tar.gz.splitn

description: 6basalBC_bams.tar.gz, split, part n.
DOI: 10.5061/dryad.cg40g/15
title: 6basalBC_bams.tar.gz.splito

description: 6basalBC_bams.tar.gz, split, part o.
DOI: 10.5061/dryad.cg40g/7
title: 6basalBC_bams.tar.gz.splitg

description: 6basalBC_bams.tar.gz, split, part g.
DOI: 10.5061/dryad.cg40g/8
title: 6basalBC_bams.tar.gz.splith

description: 6basalBC_bams.tar.gz, split, part h.
DOI: 10.5061/dryad.cg40g/9
title: 6basalBC_bams.tar.gz.spliti

description: 6basalBC_bams.tar.gz, split, part i.
DOI: 10.5061/dryad.hj797/1
title: smolt-data

description: Offspring data is in ‘smolt-data.csv’ as follows:Column 1: PIT: Passive Integrated Transponder number used for individual IDColumn 2: FL: Fork length in mmColumn 3: mass: in gramsColumn 4: Sex: Male, Female, or NA (i.e. failed to assign)Column 5: cross: AA or BB (i.e. pure above-barrier cross or pure below-barrier cross)Column 6: Ma: Individual ID of motherColumn 7: MOM: A or B (origin of Ma)Column 8: Pa: Individual ID of fatherColumn 9: DAD: A or B (origin of Pa)Column 10: score: smolt condition: 1, 2, 3, 4, or NA (see explanation below)Column 11: smolt: 0 or 1 (non-smolt or smolt)
DOI: 10.5061/dryad.hj797/2
title: egg-data

description: Egg size and number data is in ‘egg-data.csv’ as follows:Column 2: MA: Individual ID of motherColumn 3: ORIGIN: A or B (i.e. Above- or Below-barrier)Column 4: EGG_NO: total number of eggs in clutchColumn 5: EGG_SIZE: in mm
DOI: 10.5061/dryad.hj797/3
title: movement-data

description: movement-data.csvColumn 1: PIT: Passive Integrated Transponder number used for individual IDColumn 2: cross: AxA, BxB, Hybrid, AxF1, BxF1, F1 (The latter four crosses are from a separate study not discussed in the corresponding manuscript. They were raised in the same manner as the AxA and BxB crosses discussed in the corresponding manuscript)Column 3: FL: Fork length in mmColumn 4: mass: in gramsColumn 5: score: 1, 2, 3, 4 or NA (see explanation below)Column 6: smolt: 0 or 1 (i.e. non-smolt or smolt)Column 7: detect: 0 or 1 (i.e. not detected or detected)
DOI: 10.5061/dryad.hj797/4
title: saltwater-challenge-data

description: Data from the seawater challenge experiment are in saltwater-challenge-data.csv as follows:Column 1: PIT: Passive Integrated Transponder number used for individual IDColumn 2: cross: AxA, BxB, Hybrid, AxF1, BxF1, F1 (The latter four crosses are from a separate study not discussed in the corresponding manuscript. They were raised in the same manner as the AxA and BxB crosses discussed in the corresponding manuscript)Column 3: FL: Fork length in mmColumn 4: mass: in gramsColumn 5: score: 1, 2, 3, 4 or NA (see explanation below)Column 6: smolt: 0 or 1 (non-smolt or smolt)Column 7: sex: Male, Female, or NA (i.e. failed to assign)Column 8: fate: 0 or 1: (i.e. dead or alive at the end of the experiment)Column 9: Date: date individual was declared deadColumn 10: Time: time individual was declared dead
DOI: 10.5061/dryad.hj797/5
title: README

description: README file for the four data files.
DOI: 10.5061/dryad.j5b8c/1
title: Taff_Data_ReadMe

description: Text file describing the contents of the data package and the meaning of column headers for the data files.
DOI: 10.5061/dryad.j5b8c/2
title: FemalePresent

description: Data file for the female presentation experiment.
DOI: 10.5061/dryad.k1c4j/2
title: Manual Cross Data

description: Data used to compute GI and HI.
DOI: 10.5061/dryad.k1c4j/3
title: Ecological Isolation Data

description: Habitat data used to compute EI.
DOI: 10.5061/dryad.k1c4j/4
title: Macroenvironmental Dataset

description: Data used to compute Macroenvironmental Differences.
DOI: 10.5061/dryad.k9c31/11
title: 11_Hoffmann_et_al_2001_Line_means

description: This data file contains line mean starvation resistance (LT50 in hours), desiccation resistance (LT50 in hours), cold resistance (mortality out of 10), lipid content (proportion of body weight) and thorax length (mm) for four Queensland and three Tasmanian Drosophila melanogaster populations collected in 1997 (Fig. 2). Note longitudes in data are approximate. When using this data, please cite the original publication:Hoffmann, A. A., Hallas, R., Sinclair, C., and Mitrovski, P. (2001). Levels of variation in stress resistance in Drosophila among strains, local populations, and geographic regions: Patterns for desiccation, starvation, cold resistance, and associated traits. Evolution 55: 1621-1630
DOI: 10.5061/dryad.k9c31/14
title: 14_Hoffmann_et_al_2002_Heat_knockdown_time

description: This data contains raw heat knockdown time (minutes) for female Drosophila melanogaster from 176 isofemale lines and originating from 24 populations collected in 1999-2000 (Fig. 1a). Note longitudes in data are approximate. When using this data, please cite the original publication:Hoffmann, Ary A., Anderson, Alisha and Hallas, Rebecca (2002). Opposing clines for high and low temperature resistance in Drosophila melanogaster. Ecology Letters 5: 614-618
DOI: 10.5061/dryad.k9c31/15
title: 15_Hoffmann_et_al_2003_Overwinter_fecundity

description: This data set contains means, standard deviation (SD) and standard error (SE) of fecundity rate (daily per female egg output), midpoint of egg output (time to produce half the eggs in a cage over the time interval tested) and mortality (number of flies alive out of 34 at the end of the experiment) for seven D. melanogaster populations. Note longitudes in data are approximate. When using this data, please cite the original publication:Hoffmann, A. A., Scott, M., Partridge, L. and Hallas, R. (2003). Overwintering in Drosophila melanogaster: outdoor field cage experiments on clinal and laboratory selected populations help to elucidate traits under selection. Journal of Evolutionary Biology 16: 614-623
DOI: 10.5061/dryad.k9c31/16
title: 16_Hoffmann_et_al_2012_Frost_locusA

description: This data file contains Frost 6P and 10P allele frequencies (%) of 17 Drosophila melanogaster populations collected in 2005 and genotyped by acrylamide gel electrophoresis (Fig. 3A). Note longitudes in data are approximate. When using this data, please cite the original publication:
Hoffmann, A. A., Blacket, M. J., McKechnie, S. W., Rako, L., Schiffer, M., Rane, R. V., Good, R. T., Robin, C., and Lee, S. F. (2012). A proline repeat polymorphism of the Frost gene of Drosophila melanogaster showing clinal variation but not associated with cold resistance. Insect Molecular Biology 21: 437-445
DOI: 10.5061/dryad.k9c31/17
title: 17_Hoffmann_et_al_2012_Frost_locusB

description: This data file contains Frost 6P allele frequencies (%) of 20 Drosophila melanogaster populations
collected independently in 2005-2006 and genotyped by Roche/454-amplicon sequencing (Fig. 3B). Note longitudes in data are approximate. When using this data, please cite the original publication:
Hoffmann, A. A., Blacket, M. J., McKechnie, S. W., Rako, L., Schiffer, M., Rane, R. V., Good, R. T., Robin, C., and Lee, S. F. (2012). A proline repeat polymorphism of the Frost gene of Drosophila melanogaster showing clinal variation but not associated with cold resistance. Insect Molecular Biology 21: 437-445
DOI: 10.5061/dryad.k9c31/4
title: 04 Gockel et al. 2001, Wing area

description: This data set contains means and standard deviations (SD) of wing area (mm2) for females and males of 19 Drosophila melanogaster locations collected at 11 latitudes in 2000 (extracted from Fig.1).When using this data, please cite the original publication:Gockel, Julia, Kennington, W. Jason, Hoffmann, Ary, Goldstein, David B., and Partridge, Linda (2001). Nonclinality of Molecular Variation Implicates Selection in Maintaining a Morphological Cline of Drosophila melanogaster. Genetics 158: 319-323
DOI: 10.5061/dryad.k9c31/5
title: 05 Griffiths et al. 2005, Development time

description: This data file contains means and standard errors of development times (days) of female and male Drosophila birchii originating from 11 populations collected in 2002 (Fig. 2). Note longitudes in data are approximate. When using this data, please cite the original publication:Griffiths, J. A., Schiffer, M., and Hoffmann, A. A. (2005). Clinal variation and laboratory adaptation in the rainforest species Drosophila birchii for stress resistance, wing size, wing shape and development time. Journal of Evolutionary Biology 18: 213-222
DOI: 10.5061/dryad.k9c31/8
title: 08 Hoffmann & Shirriffs 2002, Wing traits

description: This data file contains x and y coordinates of nine landmarks for wings and different traits related to wing shape for 19 Drosophila serrata populations collected in 2001. Measurements were taken for up to 10 isofemale lines per population. Wing_aspect was defined as wing length (the linear distance between landmarks 3 and 6) divided by the square root of wing area (here taken to be centroid size). Angle (outer-wing aspect) was defined as the angle between the vectors from landmarks 2 and 8 and the vector between landmarks 4 and 8. Wing proportion (outer_wing aspect) was defined as the linear distance between landmarks 2 and 4 divided by wing length (Fig. 2). Note longitudes in data are approximate. When using this data, please cite the original publication:Hoffmann, Ary A. and Shirriffs, Jennifer (2002). Geographic variation for wing shape in Drosophila serrata. Evolution 56: 1068-1073
DOI: 10.5061/dryad.k9c31/9
title: 09 Hoffmann et al. 2001, Desiccation resistance

description: This data file contains desiccation resistance (hours to death) of female and male Drosophila melanogaster of two types of lines (isofemale lines and F1s of a cross between two isofemale lines from the same population) and originating from 18 populations collected in 2000 (Fig. 4). Note longitudes in data are approximate. When using this data, please cite the original publication:Hoffmann, A. A., Hallas, R., Sinclair, C., and Mitrovski, P. (2001). Levels of variation in stress resistance in Drosophila among strains, local populations, and geographic regions: Patterns for desiccation, starvation, cold resistance, and associated traits. Evolution 55: 1621-1630
DOI: 10.5061/dryad.mv185/3
title: Amino acid sequence of reconstructed archaeal ancestral NDK, Arc6

description: Amino acid sequence of Arc6, a last archaeal common ancestor of nucleoside diphosphate kinase inferred from a dataset without hyperthermophilic sequences.
DOI: 10.5061/dryad.mv185/4
title: Amino acid sequence of reconstructed archaeal and bacterial ancestral NDK, ArcBac7

description: Amino acid sequence of ArcBac7, a last archaeal and bacterial ancestor of nucleoside diphosphate kinase inferred from a dataset without hyperthermophilic sequences.
DOI: 10.5061/dryad.mv185/5
title: Amino acid sequence of reconstructed bacterial ancestral NDK, Bac3nh

description: Amino acid sequence of Bac3nh, a last bacterial common ancestor of nucleoside diphosphate kinase inferred using a non-homogeneous evolution model.
DOI: 10.5061/dryad.mv185/6
title: Amino acid sequence of reconstructed bacterial ancestral NDK, Bac4nh

description: Amino acid sequence of Bac4nh, a last bacterial common ancestor of nucleoside diphosphate kinase inferred using a non-homogeneous evolution model.
DOI: 10.5061/dryad.mv185/7
title: Amino acid sequence of reconstructed bacterial ancestral NDK, Bac6

description: Amino acid sequence of Bac6, a last bacterial common ancestor of nucleoside diphosphate kinase inferred from a dataset without hyperthermophilic sequences.
DOI: 10.5061/dryad.mv185/8
title: Amino acid sequence of reconstructed last universal common ancestral NDK, Com3nh

description: Amino acid sequence of Com3nh, a last universal common ancestor of nucleoside diphosphate kinase inferred using a non-homogeneous evolution model.
DOI: 10.5061/dryad.mv185/9
title: Amino acid sequence of reconstructed last universal common ancestral NDK, Com4nh

description: Amino acid sequence of Com4nh, a last universal common ancestor of nucleoside diphosphate kinase inferred using a non-homogeneous evolution model.
DOI: 10.5061/dryad.n85m5/1
title: Legume plastid gene alignment

description: A 71 plastid gene alignment including 36 species of legumes. Phylip format.
DOI: 10.5061/dryad.p093c/1
title: Marie-Orleach.et.al_Evolution 2016

description: Complete dataset of the associated manuscript. Please see manuscript for abbreviations.
DOI: 10.5061/dryad.q20p3/1
title: soil-N cycling rates and soil chemical characteristics data

description: Please see ReadMe file.
DOI: 10.5061/dryad.rn745/4
title: Eulemur flavifrons fastq file for PSMC

description: This fastq file was generated from the all-sites vcf file for Harlow (the E. flavifrons individual used for the de novo assembly), and was used to infer historic Ne using PSMC (Li and Durbin 2011). The vcf was generated by running GATK (McKenna et al. 2010; DePristo et al. 2011) on the filtered bam file (mapping quality 20 or above, PE reads aligned to the same scaffold with correctly oriented read pairs mapping within three standard deviations of the mean, duplicates removed), with the EMIT_ALL_SITES option and a minimum base quality of 20. The fastq was generated from this all-sites vcf using the vcf2fq function within the vcfutils.pl script, using a minimum depth of 26 and a maximum depth of 104 (0.5 and 2x the mean depth, respectively), and a minimum quality (QUAL*GQ) of 20.
DOI: 10.5061/dryad.rn745/5
title: Eulemur macaco fastq files for PSMC

description: These two files should be combined into one fastq representing the whole genome. The combined fastq file was generated from the all-sites vcf file for Harmonia (the E. macaco individual used for the de novo assembly), and was used to infer historic Ne using PSMC (Li and Durbin 2011). The vcf was generated by running GATK (McKenna et al. 2010; DePristo et al. 2011) on the filtered bam file (mapping quality 10 or above, duplicates removed), with the EMIT_ALL_SITES option and a minimum base quality of 20. The fastq was generated from this all-sites vcf using a modification of the vcf2fq function within the vcfutils.pl script (vcf2fqnonref, in https://github.com/sorrywm/genome_analysis/vcfutils_mod.pl), using a minimum depth of 10 and a maximum depth of 41 (0.5 and 2x the mean depth, respectively), and a minimum quality (QUAL*GQ) of 20.
DOI: 10.5061/dryad.rn745/6
title: Eulemur macaco fastq files for PSMC

description: These two files should be combined into one fastq representing the whole genome. The combined fastq file was generated from the all-sites vcf file for Harmonia (the E. macaco individual used for the de novo assembly), and was used to infer historic Ne using PSMC (Li and Durbin 2011). The vcf was generated by running GATK (McKenna et al. 2010; DePristo et al. 2011) on the filtered bam file (mapping quality 10 or above, duplicates removed), with the EMIT_ALL_SITES option and a minimum base quality of 20. The fastq was generated from this all-sites vcf using a modification of the vcf2fq function within the vcfutils.pl script (vcf2fqnonref, in https://github.com/sorrywm/genome_analysis/vcfutils_mod.pl), using a minimum depth of 10 and a maximum depth of 41 (0.5 and 2x the mean depth, respectively), and a minimum quality (QUAL*GQ) of 20.
DOI: 10.5061/dryad.rn745/7
title: Dataset S1: Annotated transcripts in the 1% FST tail

description: This list contains all transcripts mapped to regions in the 1% tail of FST from the full dataset in either species. Columns represent Ensembl transcript ID, region of high FST where the transcript was annotated, start position of the transcript within the region, end position of the transcript within the region, proportion of the transcript mapped to the region, mean percent identity for parts of the transcript that mapped, Ensembl gene ID, and gene symbol. We annotated genes in the 1% tail of all 20 kb non-overlapping windows by aligning human protein sequences to the blue-eyed black lemur genome. We obtained protein sequences for human genome build hg18 and used TBLASTN version 2.2.22+ (Altschul et al. 1990, 1997), with an e-value threshold of 5 x 10-5 to identify orthologs within the regions of the blue-eyed black lemur reference genome corresponding to the 1% FST tail. We then took the list of all human proteins with hits within candidate regions and performed TBLASTN for these proteins against the entire lemur genome. We retained proteins whose best genome-wide match (containing the lowest e-value or maximum mean percent identity) for any subset of the protein sequence overlapped the candidate region. In cases in which multiple proteins mapped to the same location (&gt;50% protein length overlapping, presumably representing multiple transcripts of the same gene or multiple genes in the same family), we retained the protein with the largest total length spanned by initial TBLASTN hits or the largest mean percent identity.
DOI: 10.5061/dryad.11cv0/1
title: Supplementary Figures-Caribbean Plate

description: Molecular phylogenies and Ancestral area estimates of Poeciliidae and Cichlidae
DOI: 10.5061/dryad.17pp3/1
title: Ballantyne et al 2015 visitation and pollen deposition data file
DOI: 10.5061/dryad.18v6q/1
title: Aggression data

description: The table shows the number of aggressive events by focal Hypsophrys nicaraguensis territory owners. The ID of the territory, sex of each focal individual, stimulus type, order of presentation, stimulus species (when not P. managuensis), depth at the focal territory and breeding season (by year) are also given.
DOI: 10.5061/dryad.18v6q/2
title: Nearest neighbour distribution: A. sagittae

description: The table shows the nearest neighbours of the focal Amphilophus sagittae territory owners. The ID of each focal territory, focal pair colour type, and breeding season (year) are also given.
DOI: 10.5061/dryad.18v6q/3
title: Nearest neighbour distribution: H. nicaraguensis

description: The table shows the nearest neighbours of the focal H. nicaraguensis territories by species. The ID of each focal territory, neighbouring pair colour type (when relevant) and breeding season (by year) are also given.
DOI: 10.5061/dryad.1h46d/1
title: All acoustic sound files of killer whale vocalisations analyzed for this manuscript

description: All vocalisations analysed for this manuscript are included in this zip folder as .wav files. There are a total of 142 whistles and burst-pulse vocalisations that were analysed and categorized accordingly. There are also 2 echolocation clicks that are discussed in this manuscript. Acoustic recordings were obtained with two devices. Primarily recordings were undertaken with a High Tech Inc. HTI-96-MIN hydrophone with built-in pre-amplifier (flat frequency response of 2 Hz to 30 kHz; sensitivity -164.1 dB re 1 V/µPa), fitted to a Sound Devices 722 digital recorder sampling at 96 kHz, 24-bit. Secondary to this, a SoundTrap (Ocean Instruments, New Zealand) —a self-contained  underwater sound recorder—was rigged to a tow-line and deployed overside during an encounter when the vessel was travelling less than 5 knots. The SoundTrap sampled at 192 kHz, 16-bit.
DOI: 10.5061/dryad.1kh77/1
title: Multiple paternity in Dalechampia scandens
DOI: 10.5061/dryad.1v42d/1
title: Pouch fluid oxygen levels during brooding in male broad-nosed pipefish

description: The file BragaGoncalvesetalJExpB_datafile1.csv contains the data used for the analysis of the effects of male size, oxygen treatment and brood pouch section on pouch fluid oxygen levels (%) and on average embryo length in the pipefish Syngnathus typhle.
DOI: 10.5061/dryad.2503h/1
title: Vole monitoring data

description: Vole data for each trapping occasion, inlcuding individual characterisitcs, population density, haematological indices and survival.
DOI: 10.5061/dryad.2503h/2
title: Vole infection data

description: Vole data for euthanised individuals. Inlcudes infection and co-infection status, and pathological changes.
DOI: 10.5061/dryad.2k6nr/1
title: JHB MS Data

description: Data from the LCMS chromatography of M. producens JHB and pure compound MS2 spectra from direct injection; in both .RAW and .mzXML format compressed in a .zip archive.