cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7215m/1
title: Genotype data used for genome scans and construction of genetic maps

description: The Excel sheet entitled "Genotype_genome_scan" contains the genotypes of 109 individuals at 436 microsatelitte markers used for genome scan analyses. The Excel sheet entitled "Genotype_genetic_map" contains genotype data at 343 polymorphic microsatelitte markers on a 3-generation pedigree that have been used to construct genetic maps.
DOI: 10.5061/dryad.vj35n/1
title: PAO1::mini-Tn7-pLAC-lux ancestral strain RNA-Seq

description: BAM files: RNA-Seq data for two biological replicates (BR) of the rifampin-sensitive PAO1::mini-Tn7-pLAC-lux ancestral strain.
DOI: 10.5061/dryad.vj35n/2
title: D521G rpoB mutant RNA-Seq

description: BAM files: RNA-Seq data for two biological replicates (BR) of the rifampin-resistant D521G rpoB mutant, which was evolved from the PAO1::mini-Tn7-pLAC-lux ancestral strain
DOI: 10.5061/dryad.vj35n/3
title: H531R rpoB mutant RNA-Seq

description: BAM files: RNA-Seq data for 2 biological replicates (BR) of the rifampin-resistant H531R rpoB mutant evolved from the PAO1::mini-Tn7-pLAC-lux ancestral strain
DOI: 10.5061/dryad.5n7p9/1
title: Protopopova et al. Raw Data

description: This is the raw data for all dogs across all days. Please contact the main author if any clarifications are required.
DOI: 10.5061/dryad.5n7p9/2
title: Protopopova et al. All Codes

description: All codes (STATA) used to analyze data. Please contact the first author for any clarifications.
DOI: 10.5061/dryad.hb558/1
title: Microsatellite genotype data for 3 aquatic insect species

description: The data set includes 3 text files, one for each of three aquatic insect species. Each is a GENEPOP input file. Loci are microsatellite markers. The order of the populations in each file is the same as in the manuscript.
DOI: 10.5061/dryad.hb558/2
title: Three-Species-LandGen_Data for R analysis_ABHE
DOI: 10.5061/dryad.hb558/3
title: Three-Species-LandGen_Data for R analysis_MLPE_MEAR_GR1
DOI: 10.5061/dryad.hb558/4
title: Three-Species-LandGen_Data for R analysis_MLPE_MEAR_GR2
DOI: 10.5061/dryad.hb558/5
title: Three-Species-LandGen_Data for R analysis_STAE
DOI: 10.5061/dryad.hb558/6
title: Stats in R_MLPE_VanStrien_ABHE

description: R scripts for running MLPE on Abedus herberti msat data.
DOI: 10.5061/dryad.hb558/7
title: Stats in R_MLPE_VanStrien_MEAR

description: R scripts for running MLPE on Mesocapnia arizonensis msat data.
DOI: 10.5061/dryad.hb558/8
title: Stats in R_MLPE_VanStrien_STAE

description: R scripts for running MLPE on Boreonectes aequinoctialis msat data.
DOI: 10.5061/dryad.587v1/1
title: Sex Ratio and SOI Data

description: CSV file containing individual and community-level data used in the analysis outlined in the article.
DOI: 10.5061/dryad.90835/1
title: All Structure Data

description: This is a structure input file containing allelic information for all individuals genotyped in this project including collections for Acropora digitifera and A. hyacinthus. These were the data used to determine which individuals to include within each species downstream using a K=3.
DOI: 10.5061/dryad.90835/2
title: Acropora digitifera structure

description: This file contains all data for 11 loci for individuals assigning to Acropora digitifera after initial clustering step.
DOI: 10.5061/dryad.90835/3
title: Acropora hyacinthus structure

description: This file contains all data for 12 loci for individuals assigned to Acropora hyacinthus after initial clustering step. Data are formatted as structure input files.
DOI: 10.5061/dryad.485qq/1
title: Avida Configuration Files for the Original Experiments

description: This compressed archive contains the configuration files required to perform the original experiments in full. Avida is available for free from https://github.com/devosoft/avida/. More information can be found about each of these files as part of the Avida documentation at https://github.com/devosoft/avida/wiki/Configuration-and-Command-Reference.
DOI: 10.5061/dryad.485qq/2
title: coevolving-complexity-original

description: This file contains the time series data used to generate Figure 2 and Figure 3, as well as some additional details recorded over time. These data were summarized from several individual output files generated by Avida experiments. 1. update - The update (point in time) when this row of data was collected2. parasite_treatment - Were parasites included in these experiments? (0/1)3. remove_parasites - Were parasites experimentally removed? (0/1)4. replicate - The replicate within a group of runs the data are from5. num_parasites - The density of parasites6. num_hosts - The density of hosts7. average_host_nands - Number of NANDs required to perform the hosts average function, averaged across all hosts8. host_max_task_nands - Number of NANDs required to perform the most complex host function, averaged across all hosts9. average_number_of_host_tasks - Average number of tasks hosts perform10. average_number_of_parasite_tasks - Average number of tasks parasites perform11. lost_parasites - Were parasites driven extinct in this replicate? (0/1)12. treatment - Number id that identifies the treatment (0 - Evolved, 1 - Coevolved, 2 - Cured)
DOI: 10.5061/dryad.485qq/3
title: coevolving-complexity-equ_ancestors
DOI: 10.5061/dryad.fc4vf/1
title: Supplementary Tables

description: CT derived volume, buoyancy, and hydrostatic data for a Cadoceras and reconstructed Spirula hatchling.
DOI: 10.5061/dryad.485qq/10
title: coevolving-complexity-details_and_phenotype_grids.tar

description: This compressed archive contains raw data output from Avida that was used to generate the MRCA data above as well as part of the raw data summarized in coevolving-complexity-original.csv. The detail files were used to generate Figure 7, the phylogenetic tree of example populations, as described above. The GridDump files were used to generate the data panels of Figure 4 (E-H). A more detailed description of these data files can be found with the Avida documentation:https://github.com/devosoft/avida/wiki/PrintData-Optionshttps://github.com/devosoft/avida/wiki/List-of-actions#DumpParasiteTaskGridhttps://github.com/devosoft/avida/wiki/List-of-actions#DumpHostTaskGrid
DOI: 10.5061/dryad.485qq/12
title: coevolving-complexity-replay_parasites

description: These two files contain the same data columns as the original experiments, but here the parasite genotypes were replayed exactly from a coevolving population while hosts evolved anew to the changing but non-coevolving parasites (replay treatment). Along with coevolving-complexity-original.csv, these data were used to make Figure 5.
DOI: 10.5061/dryad.485qq/13
title: coevolving-complexity-freeze_parasites

description: These two files contain the same data columns as the original experiments, but here the parasite genotypes were either kept constant (freeze treatment) while hosts evolved anew to the changing but non-coevolving parasites (replay treatment). Along with coevolving-complexity-original.csv, these data were used to make Figure 5.
DOI: 10.5061/dryad.485qq/14
title: coevolving-complexity-challenge-data-nands

description: These data were generated through the challenge experiment, where host and parasite lineages were coevolved through successive "challenge" bouts. The following columns are contained in the csv:1. replicate - The replicate challenge experiment 2. completed - Were all 50 rounds of challenges complete?3. step - The round that the data row is from4. host_phenotype - The integer phenotype for the host - computed by considering the phenotype bitstring (e.g., 10100000 = 4)5. parasite_phenotype - The integer phenotype for the parasite6. host_iterations - The number of iterations of generating random host populations that were required to find a succesful mutant7. parasite_iterations - The number of iterations of generating random parasite populations that were required to find a successful mutant8. host_sequence - The genetic sequence of the successful host9. parasite_sequence - The genetic sequence of the successful parasite 10. host_avg_task_nands - The number of NANDs required to compute the hosts average task11. host_max_task_nands - The number of NANDs required to compute the hosts most complex task
DOI: 10.5061/dryad.485qq/4
title: coevolving-complexity-equ-distribution_detail

description: This file contains a breakdown of the frequency at which hosts's most complex functions require 1, 2, 3, 4, or 5 NANDs (Column named N.nand). These data are recorded much more frequently, but for an overall shorter length of time. These data were used to generate Figure S1.
DOI: 10.5061/dryad.485qq/7
title: coevolving-complexity-dominant_genotype_landscaping

description: These data are used to make Figure 9 in the manuscript. It contains data generated by systematically mutating the most abundant genotype from each replicate population. Every possible point mutation is made and run through Avida to identify which tasks it now performs. That data is then summarized into the following columns:1. Treatment - The name of the treatment genotypes came from (Evolved/Coevolved)3. Replicate - The replicate within the treatment these data are about4. Point_Decrease - The number of point mutations that decrease the number of tasks this genotype performs5. Point_Increase - The number of point mutations that increase the number of tasks this genotype performs6. Point_Neutral - The number of point mutations that change the identity of the tasks performed while keeping the number of tasks the same7. Point_Viable - The number of point mutations that produce a viable genotype regardless of changes to phenotype8. Point_Inviable - The number of point mutations that produce inviable genotypes9. Dominant_Genotype - The sequence of the genotype being analyzed
DOI: 10.5061/dryad.485qq/8
title: coevolving-complexity-matching_phenotype_genetic_landscaping

description: These data specifically pair genotypes from coevolved and evolved populations performing the same exact set of tasks. These data are used to generate Figure 10. 1. ReplicateEvo - The replicate population which the evolved genotype came from2. ReplicateCoevo - The replicate population which the coevolved genotype came from3. MatchingPhenotype - The phenotype that was matched between the evolved and coevolved treatments4. Point_Decrease.Evo - The number of point mutations that decrease the number of tasks this evolved genotype performs 5. Point_Increase.Evo - The number of point mutations that increase the number of tasks this evolved genotype performs 6. Point_Neutral.Evo- The number of point mutations that change the identity of the tasks performed while keeping the number of tasks the same in the evolved genotype7. Point_Viable.Evo - The number of point mutations that produce a viable genotype regardless of changes to phenotype for the evolved genotype8. Point_Inviable.Evo - The number of point mutations that produce an inviable genotype for the evolved genotype9. NumUniqueReachable.Evo - The number of unique phenotypes reachable by only single point mutations from the evolved genotype10. Point_Decrease.Coevo - The number of point mutations that decrease the number of tasks this coevolved genotype performs 11. Point_Increase.Coevo - The number of point mutations that increase the number of tasks this coevolved genotype performs 12. Point_Neutral.Coevo - The number of point mutations that change the identity of the tasks performed while keeping the number of tasks the same in the coevolved genotype13. Point_Viable.Coevo - The number of point mutations that produce a viable genotype regardless of changes to phenotype for the coevolved genotype14. Point_Inviable.Coevo - The number of point mutations that produce an inviable genotype for the coevolved genotype15. NumUniqueReachable.Coevo - The number of unique phenotypes reachable by only single point mutations from the coevolved genotype
DOI: 10.5061/dryad.485qq/9
title: coevolving-complexity-time_to_MRCA

description: These data are used to generate Figure 8 in the manuscript. The MRCA is identified by essentially building the phylogenetic tree of all living Avida programs at the end of each run and identifying the first branching event. The tree is constructed using data included in the  **detail** files, which are provided in the compressed files coevolving-complexity-details_and_phenotype_grids.tar.gz. These detail files record the parent/offspring relationship for every genotype alive as well as their entire line of decent. The summarized data are summarized with the following columns: 1. Treatment - Name of the treatment where these data are from (Coevolved/Evolved)2. Replicate - The replicate population within the treatment3. UpdateLCABorn - The update that the last common ancestor of all the organisms present at the end of the experiment  (MRCA) was born4. lost_parasites - Did this population drive parasites extinct? (0/1)
DOI: 10.5061/dryad.1fq87/1
title: Images & landmarks

description: Microscopic images of the tail fins of 20 rainbow trout specimens (Oncorhynchus mykiss). The fish were collected from one hatchery in the year 2000. Specimens were euthanized by overdose of MS222, fixed in buffered formalin, and stored in 70% ethanol. Seven of them were fixed at 21 days post fertilization (dpf), eight at 40 dpf, and five at 56 dpf. In 2013, the specimens were transferred into distilled water before they were stained with Mayer’s hematoxylin for 10 minutes. All images were taken under identical light conditions and standardized specimen orientation with a 5x magnification.

Four anatomical landmarks and 95 semilandmarks were recorded on each of the 20 images using the software TPSdig (James Rohlf). The resulting raw landmark coordinates are given in the file "landmarks.tps".
DOI: 10.5061/dryad.63t28/1
title: Data from: Spatial analysis of gene regulation reveals new insights into the molecular basis of upper thermal limits.

description: This compressed folder contains three data files comprising the raw phenotype data (heat knockdown), the raw real time PCR data for the stv isoforms and reference gene RPL11, and the normalised real-time PCR data for the stv isoforms
DOI: 10.5061/dryad.6vd4v/1
title: SNPs and sperm length data
DOI: 10.5061/dryad.6vd4v/2
title: COI sequences
DOI: 10.5061/dryad.6vd4v/3
title: SNAPP 2000SNPs input file
DOI: 10.5061/dryad.6vd4v/4
title: SNAPP Libya input file
DOI: 10.5061/dryad.6vd4v/5
title: Structure 7500 SNPs input file
DOI: 10.5061/dryad.6vd4v/6
title: Structure input data (Libyan set)
DOI: 10.5061/dryad.p631f/1
title: monkey_LFP_V1_stimulus_contrast_example_data

description: Example LFP data from one contact point of a laminar probe inserted in macaque V1 (superficial cortex)
DOI: 10.5061/dryad.p631f/2
title: PING_HH_increasing_drive

description: Simulaiton of a Hodgkin-Huxley pramidal-interneuron gamma (PING) network with different input drive conditions (corresponds to Figure 1).
DOI: 10.5061/dryad.p631f/3
title: ring_PING_HH_data

description: Simulation of a ring-shaped PING network with spatial-defined connectivity and input drive to E-cells                                                                                                                                                                                   Fig3 = the network used for figure 3 in the main manuscripthighEE= high interconnecitons strength between E-cellshighII = high interconnection strength between I-cellsnoII = no interconnection strength between I-cellsnoEE= no interconnecitons strength between E-cellsnoiselevel1 = low noise level in the input AMPA train to E-cell noiselevel2 = higher noise level in the input AMPA train to E-cell
DOI: 10.5061/dryad.p631f/5
title: two_interacting_PING_HH_data

description: It includes the simulation of two interacting Hodgkin-Huxley pryramidal-interneuron gamma (PING) networks with different coupling conditions and input drive conditions. The coupling value is indicated in the folder name and the mean excitatory drive to each network is saved as input variables in the folder.
DOI: 10.5061/dryad.p631f/10
title: code_phase_oscillator_ring_network

description: Matlab Code of a ring-shaped phase-oscillator model (Fig.6)
DOI: 10.5061/dryad.p631f/4
title: phase_oscillator_lattice_data_part1

description: simulation data from lattice phase-oscillator model part 1
DOI: 10.5061/dryad.p631f/6
title: overview

description: If any questions arise, please contact e.lowet@fcdonders.ru.nl The sharing folder consists of:1. monkey_LFP_V1_stimulus_contrast_example_data (Fig.1A-B)Example monkey data (one contact of a laminar probe inserted in parafoveal V1 , see Roberts et al.,2013 in Neuron)with 8 different contrast conditons. A square-wave grating is shown with different constrasts that stimulated the V1 receptive field.The monkey is engaged in a passive fixation task.2. PING_HH_increasing_driveHere a single PING- network receive different level of excitatory input. This corresponds to Fig.1 C-F. This simulation to show that aPING network react with increasing gamma frequency with increasing input drive. The relates to the experimental observation in themonkey experiment where it is known that visual contrast increase the input drive to V1.8 input level conditions are inlcuded here. The neuronal spiking data (spikes) as well as different network signals (signals) areincluded.3. two_interacting_PING_HH_dataThis relates to Fig.2. Here two interacting PING networks are simulated. The coupling strength as well as the input level difference is manipulated systematicallyto be able to reconstruct the Arnold tongue. In each folder the spikes, network signals as well the inputs to the both PING networks are included.The coupling values are in the folder names. 4.  ring_PING_HH_dataHere different simulaiton with the ring-PING network is included. Simulations realted to Fig.3 as well as Suppl.Fig 1-2 are included. Only the relevant spiking data are included.5. phase_oscillator_lattice_dataIt includes the simulation output data from the lattice phase-oscillator model for each of 80 input natural contrast images used. The natural contrast imageswere used to set the intrinisc freuqency of the phase-osicllators. This relates to Fig.7-8. 6. code_phase_oscillator_ring_network.m (MATLAB code)This simulation code corresponds to Fig.6. The simulation code reproduces the output data of the ring-phase-oscillator model. 7. code_izhi_ring_network.m(MATLAB code)This simulation code corresponds to Suppl.Fig.3. The simulation code reproduces the output data of the ring-PING network with Izhikevih-type neurons.
DOI: 10.5061/dryad.p631f/7
title: read_phaseoscillator_data
DOI: 10.5061/dryad.p631f/8
title: read_HH_data
DOI: 10.5061/dryad.p631f/9
title: code_izhi_ring_network

description: Matlab Code of a ring-shaped pryramidal-interneuron gamma (PING) network with Izhikevich-type model neurons (Suppl. Fig.3).
DOI: 10.5061/dryad.3k506/1
title: Input for Fdash for Dipteryx odorata

description: Source of information: Genotypes from lab experiments, here is the input for Fdash software for genetic diversity of polyploid analysis. Input contains genotypes of pre- and post-logging adults, pre- and post-logging progenies. First column contains id of population, second column onwards contains genotypes of Do03, Do17, Do18, Do25, Do08, Do19 and Do20  loci. abbreviations: adultos corresponds to pre-logging adults sample, adultospos (post-logging adults sample), filhotespre (pre-logging progenies sample) and filhotespos (post-logging progenies sample).
DOI: 10.5061/dryad.3k506/2
title: Input for Spagedi for Dipteryx odorata

description: Source of information: Genotypes from lab experiments. Here is the input for Spagedi software for spatial genetic diversity analysis, divide into two parts, first part contains pre-logging adult input and second part contains post-logging adult input.  First column contains id of sample, second and third column contains x and y coordinates, forth column onwards contains genotypes of Do03, Do17, Do18, Do25, Do08, Do19 and Do20  loci.
DOI: 10.5061/dryad.3k506/3
title: Input for paternity software for pre-logging Dipteryx odorata

description: Source of information: Genotypes from lab experiments. Here is the input for Orchard software for paternity analysis, divide into two parts, first part contains pre-logging progenies input and second part contains pre-logging candidate father input.  Pre-logging progenies input contains first column contains id of progeny, second column onwards contains genotypes of Do03, Do17, Do18, Do25, Do08, Do19 and Do20  loci and last column contains name of known mother. Pre-logging candidate father input contains first column contains id of individual, second column onwards contains genotypes of Do03, Do17, Do18, Do25, Do08, Do19 and Do20  loci and last two columns contains X and Y coordinates.
DOI: 10.5061/dryad.3k506/4
title: Input for paternity software for post-logging Dipteryx odorata

description: Source of information: Genotypes from lab experiments. Here is the input for Orchard software for paternity analysis, divide into two parts, first part contains post-logging progenies input and second part contains post-logging candidate father input.  Post-logging progenies input contains first column contains id of progeny, second column onwards contains genotypes of Do03, Do17, Do18, Do25, Do08, Do19 and Do20  loci and last column contains name of known mother. Post-logging candidate father input contains first column contains id of individual, second column onwards contains genotypes of Do03, Do17, Do18, Do25, Do08, Do19 and Do20  loci and last two columns contains X and Y coordinates.
DOI: 10.5061/dryad.3k506/5
title: Input for MLTR software for Jacaranda copaia

description: Source of information: Genotypes from lab experiments. Here is the input for MLTR software for mating system analysis. Input contains genotypes of pre- and post-logging progenies. First column contains id of known mother, second column contains group id (a=pre-logging, b=post-logging), third column onwards contains genotypes of the progeny of JC03, JC09, JC21, JC05, JC28 loci.
DOI: 10.5061/dryad.3k506/6
title: Input for Spagedi software for Jacaranda copaia

description: Source of information: Genotypes from lab experiments. Here is the input for Spagedi software for spatial genetic diversity analysis, divide into two parts, first part contains pre-logging adults input and second part contains post-logging adults input.  First column contains id of individual, second column contains field id, third column contains measure of diameter at breast height (DBH) in cm, and fifth column onwards contains genotypes of JC03, JC09, JC21, JC05, JC28 loci.
DOI: 10.5061/dryad.3k506/7
title: Input for Cervus software for Jacaranda copaia

description: Source of information: Genotypes from lab experiments. Here is the input for Cervus software for paternity analysis, divide into three parts. First part contains pre-logging progenies and pre-logging adults genotypes first column contains id of individual, second column onwards contains genotypes of JC03, JC09, JC21, JC05, JC28 loci. Second part contains list of progenies with known mother and third part is the list of candidate fathers.
DOI: 10.5061/dryad.3k506/8
title: Input for Cervus software for Jacaranda copaia

description: Source of information: Genotypes from lab experiments. Here is the input for Cervus software for paternity analysis, divide into three parts. First part contains post-logging progenies and post-logging adults genotypes first column contains id of individual, second column onwards contains genotypes of JC03, JC09, JC21, JC05, JC28 loci. Second part contains list of progenies with known mother and third part is the list of candidate fathers.
DOI: 10.5061/dryad.p631f/11
title: phase_oscillator_lattice_data_part2

description: simulation data from lattice phase-oscillator model part 2
DOI: 10.5061/dryad.p631f/12
title: phase_oscillator_lattice_data_part3

description: simulation data from lattice phase-oscillator model part 3