cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7tg18mb
title: Data from: REvoSim: organism-level simulation of macro and microevolution

description: Macroevolutionary processes dictate the generation and loss of
 biodiversity. Understanding them is a key challenge when interrogating the
 earth-life system in deep time. Model-based approaches can reveal
 important macroevolutionary patterns, and generate hypotheses on the
 underlying processes. Here we present and document a novel model called
 REvoSim (Rapid Evolutionary Simulator) coupled with a software
 implementation of this model. The latter is available here as both source
 code (C++/Qt, GNU General Public License), and as distributables for a
 variety of operating systems. REvoSim is an individual-based model with a
 strong focus on computational efficiency. It can simulate populations of
 105–107 digital organisms over geological timescales on a typical desktop
 computer, and incorporates spatial and temporal environmental variation,
 recombinant reproduction, mutation and dispersal. Whilst microevolutionary
 processes drive the model, macroevolutionary phenomena such as speciation
 and extinction emerge. We present results and analysis of the model
 focussing on validation, and note a number potential applications. REvoSim
 can serve as a multipurpose platform for studying both macro- and
 microevolution, and bridges this divide. It will be continually developed
 by the authors to expand its capabilities and hence its utility.
description: Supplementary
 videoAn HDMI MP4 video file
 showing the visualisations during several different REvoSim
 runs.Garwood_et_al_2018_SI_video.mp4Supplementary figuresA PDF file with supplementary figures: a graph of fitness using alternative error bars, and numerous visualisations captured during an exemplar REvoSim run.Garwood_et_al_REvoSim_SI_figures.pdfSource code - latest versionThis DOI resolves to the latest release of REvoSim which is automatically pushed through to Zenodo. The repository contains the source code for REvoSim and EnviroGen. Further details can be found within the readmes.Source code - version 2.0.0This DOI resolves to the release of REvoSim v2.0.0, which accompanies this paper. The repository contains the source code for REvoSim and EnviroGen. Further details can be found within the readmes.REvoSim GitHub release pageAt this URL are the releases of REvoSim. Each release contains the source code for REvoSim and EnviroGen. Further details can be found within the readmes. Releases also include redistrubtables for both pieces of software for numerous operating systems.
DOI: 10.5061/dryad.s6223
title: Data from: Mosquitoes rely on their gut microbiota for development

description: Field studies indicate adult mosquitoes (Culicidae) host low diversity
 communities of bacteria that vary greatly among individuals and species.
 In contrast, it remains unclear how adult mosquitoes acquire their
 microbiome, what influences community structure, and whether the
 microbiome is important for survival. Here we used pyrosequencing of 16S
 rRNA to characterize the bacterial communities of three mosquito species
 reared under identical conditions. Two of these species, Aedes aegypti and
 Anopheles gambiae, are anautogenous and must blood feed to produce eggs,
 while one, Georgecraigius atropalpus, is autogenous and produces eggs
 without blood feeding. Our results indicated each hosts a low diversity
 community comprised primarily of aerobic bacteria. However, the
 communities in Ae. aegypti and An. gambiae larvae were much more similar
 to one another than to Ge. atropalpus. Studies with Ae. aegypti indicated
 adults transstadially acquire many members of the larval bacterial
 community, whereas only four genera of bacteria in blood fed females were
 detected on eggs. Functional assays showed that axenic larvae of each
 species failed to develop beyond the first instar. Experiments with Ae.
 aegypti indicated several members of the microbial community and
 Escherichia coli successfully colonized axenic larvae and rescued
 development. Overall, our results provide new insights about the
 acquisition and structure of bacterial communities in mosquitoes. They
 also indicate three mosquito species spanning the breadth of the Culicidae
 depend on their gut microbiome for development, while suggesting the
 possibility the gut microbiome is an important factor in autogeny.
description: de-multiplexing
 scriptsEach demultiplexing
 script corresponds to a particular input dataset. demultiplex1.pl: Water,
 larvae, PBM and NBF Ae. agypti; demultiplex2.pl: Water (An. gambiae and
 Gr. atropalpus), sterilized and non-sterilized eggs (Ae. aegypti).
 demultiplex3.pl: Larvae (An. gambiae and Gr.
 atropalpus).scripts.tgzQIIME input fileFiltered and joined FASTA sequences for QIIME input.newbestseqs_redundant_abundant.fnadata_files_and_r_scriptData collected for larval survival, development and feeding assays, as well as R code used to perform statistical analyses.
DOI: 10.35079/hbm475.rvqm.799
title: Visium (no probes) data from the ovary (left) of a 30-year-old white female
DOI: 10.5061/dryad.6373nd6
title: Data from: Using satellite AIS to improve our understanding of shipping and fill gaps in ocean observation data to support marine spatial planning

description: 1. A key stage underpinning marine spatial planning (MSP) involves mapping
 the spatial distribution of ecological processes and biological features,
 as well the social and economic interests of different user groups. One
 sector, merchant shipping (vessels that transport cargo or passengers),
 however, is often poorly represented in MSP due to a perceived lack of
 fine-scale spatially explicit data to support decision making processes.
 2. Here, using the Republic of Congo as an example, we show how publicly
 accessible satellite derived Automatic Identification System (S-AIS) data
 can address gaps in ocean observation data for shipping at a national
 scale. We also demonstrate how fine-scale (0.05 km2 resolution) spatial
 data layers derived from S-AIS (intensity, occupancy) can be used to
 generate maps of vessel pressure to provide an indication of patterns of
 impact on the marine environment and potential for conflict with other
 ocean-user groups. 3. We reveal that passenger vessels, offshore service
 vessels, bulk carrier and cargo vessels and tankers account for 93.7% of
 all vessels and vessel traffic annually, and that these sectors operate in
 a combined area equivalent to 92% of Congo’s exclusive economic zone(EEZ)
 – far exceeding the areas allocated for other user-groups (conservation,
 fisheries and petrochemicals). We also show that the shallow coastal
 waters and habitats of the continental shelf are subject to more
 persistent pressure associated with shipping; and that the potential for
 conflict among user groups is likely to be greater with fisheries, whose
 zones are subject to the highest vessel pressure scores than with
 conservation or petrochemical sectors. 4. Synthesis and applications.
 Shipping dominates ocean use, and so excluding this sector from decision
 making could lead to increased conflict among user groups, poor compliance
 and negative environmental impacts. This study demonstrates how Satellite
 derived Automatic Identification System data can provide a comprehensive
 mechanism to fill gaps in ocean observation data and visualise patterns of
 vessel behaviour and potential threats to better support marine spatial
 planning at national scales.13-Feb-2018
description: AIS_spatial_data_filesSpatial data layers describing: (1) mean annual vessel intensity, occupancy and pressure for (A) bulk carrier and cargo vessels, (B) offshore service vessels, (C) passenger vessels, and (D) tankers in the Republic of Congo (Congo-Brazzaville) derived from Automatic Identification System (AIS) data from 2012 - 2014 obtained under commercial licence from © 2018 exactEarth Ltd; and (2) distribution of (A) broad-scale seabed habitats, (B) marine boundaries, (C) marine ecosystems and (D) legally defined zones within the Republic of Congo's waters. This file also includes all figures presented in the paper and supporting information.
DOI: 10.35079/hbm758.cfxq.932
title: Visium (no probes) data from the ovary (left) of a 30-year-old white female
DOI: 10.5061/dryad.c69n0
title: Data from: Gene expression patterns underlying parasite-induced alterations in host behaviour and life history

description: Many parasites manipulate their hosts’ phenotype. In particular, parasites
 with complex life cycles take control of their intermediate hosts’
 behaviour and life history to increase transmission to their definitive
 host. The proximate mechanisms underlying these parasite-induced
 alterations are poorly understood. The cestode Anomotaenia brevis affects
 the behaviour, life history and morphology of parasitized Temnothorax
 nylanderi ants and indirectly of their unparasitized nestmates. To gain
 insights on how parasites alter host phenotypes, we contrast brain gene
 expression patterns of T. nylanderi workers parasitized with the cestode,
 their unparasitized nestmates and unparasitized workers from unparasitized
 colonies. Over 400 differentially expressed genes between the three groups
 were identified, with most uniquely expressed genes detected in
 parasitized workers. Among these are genes that can be linked to the
 increased lifespan of parasitized workers. Furthermore, many muscle
 (functionality) genes are downregulated in these workers, potentially
 causing the observed muscular deformations and their inactive behaviour.
 Alterations in lifespan and activity could be adaptive for the parasite by
 increasing the likelihood that infected workers residing in acorns are
 eaten by their definitive host, a woodpecker. Our transcriptome analysis
 reveals numerous gene expression changes in parasitized workers and their
 uninfected nestmates and indicates possible routes of parasite
 manipulation. Although causality still needs to be established,
 parasite-induced alterations in lifespan and host behaviour appear to be
 partly explained by morphological muscle atrophy instead of central
 nervous system interference, which is often the core of behavioural
 regulation. Results of this study will shed light upon the molecular basis
 of antagonistic species interactions.
description: T.nylanderi
 contigsde novo assembled
 contigs. Trimmed reads were assembled to contigs for each of the worker
 groups in CLC workbench. A meta-assembly on these contigs was conducted in
 MIRA.Tnyl-contigs-MIRAclcws45_all.fastaTnyl_read-countsnormalized read counts as obtained from eXpress.Tnylanderi_morphological_measurementsMorphological measures as well as number of parasites for parasitized and unparasitized workers.
DOI: 10.5061/dryad.69sq3
title: Data from: Density dependence in demography and dispersal generates fluctuating invasion speeds

description: Density dependence plays an important role in population regulation and is
 known to generate temporal fluctuations in population density. However,
 the ways in which density dependence affects spatial population processes,
 such as species invasions, are less understood. Although classical
 ecological theory suggests that invasions should advance at a constant
 speed, empirical work is illuminating the highly variable nature of
 biological invasions, which often exhibit nonconstant spreading speeds,
 even in simple, controlled settings. Here, we explore endogenous density
 dependence as a mechanism for inducing variability in biological invasions
 with a set of population models that incorporate density dependence in
 demographic and dispersal parameters. We show that density dependence in
 demography at low population densities—i.e., an Allee effect—combined with
 spatiotemporal variability in population density behind the invasion front
 can produce fluctuations in spreading speed. The density fluctuations
 behind the front can arise from either overcompensatory population growth
 or density-dependent dispersal, both of which are common in nature. Our
 results show that simple rules can generate complex spread dynamics and
 highlight a source of variability in biological invasions that may aid in
 ecological forecasting.
description: Figure
 1Code
 to run models and plot Figure 1Fig1.zipFigure 2Code to run the models and plot Figure 2Fig2.zipFigure 3Code to run model and plot Figure 3Fig3.zip
DOI: 10.35079/hbm594.pdtt.492
title: Visium (no probes) data from the ovary (left) of a 30-year-old white female
DOI: 10.5061/dryad.rn617
title: Data from: Anatomical atlas of the quail's ear (Coturnix coturnix)

description: This study aims to enhance the anatomical knowledge of the ear of the
 adult quail (Coturnix coturnix) through the creation of a scaled 3D model
 utilizing data from micro-CT images. In addition, 17 annotated
 histological sections of the quail's ear are aligned to their 3D
 position in the model. The resulting anatomical atlas provides an
 intuitive insight into the 3D anatomy and can be used for medical
 education. The model also allows measuring anatomical structures and can
 thus serve as reference for the quail's auricular anatomy and as a
 basis to evaluate clinical diagnostic imaging results.
description: 3D PDF of the
 quail's skull and earAmira 5.4 (FEI
 Visualization Sciences Group, FEI Corporate, Burlington, Massachusetts,
 USA) was used for the construction of a 3D-model of the avian skull. The
 3D PDF was created following the supplementary 3D PDF-protocol of De Boer
 et al. (2011) using Adobe Acrobat Pro Extended 9.1 and Adobe Illustrator
 CS4.3DPDF_quail.pdfAnatomical atlas of the quail's ear (Coturnix coturnix)17 histological sections were aligned manually to reference-microCT data and a 3D model of the quails skull and ear. Pictures were arranged using Adobe Illustrator.anatomiacalatlas_quail_ear.pdfAnatomical measurements on the quail's earMeasurements were taken on microCT data. Measurements of anatomical structures were taken with the software Amira 5.4, using the measurement-module of ‘3D line’, ‘3D angle’ and ‘SplineProbe’. For surface measurements, a picture (‘CreateImage’) of the appropriate plane was taken and the area was measured with the module ‘MaterialStatistics’.measurements_quail_ear.pdf
DOI: 10.35079/hbm778.pjqw.538
title: Visium (no probes) data from the ovary (left) of a 30-year-old white female
DOI: 10.5281/zenodo.8364950
title: Economically Based Product Process Patent Dataset (EPP)

description: This dataset provides the share of a patent's independent publication claims which are classified as process innovations as described in: “Product and Process Innovation in the U.S. from 1980-2015 and Over the Firm’s Life Cycle”.  The measurement is available for all patents granted to U.S. publicly traded manufacturing firms that appear in the DISCERN database.
DOI: 10.5281/zenodo.8364951
title: Economically Based Product Process Patent Dataset (EPP)

description: This dataset provides the share of a patent's independent publication claims which are classified as process innovations as described in: “Product and Process Innovation in the U.S. from 1980-2015 and Over the Firm’s Life Cycle”.  The measurement is available for all patents granted to U.S. publicly traded manufacturing firms that appear in the DISCERN database.
DOI: 10.35079/hbm238.vhfn.453
title: Visium (no probes) data from the fallopian tube (right) of a 30-year-old white female
DOI: 10.5061/dryad.p88q8
title: Data from: Introgression and the fate of domesticated genes in a wild mammal population

description: When domesticated species are not reproductively isolated from their wild
 relatives, the opportunity arises for artificially selected variants to be
 re-introduced into the wild. However, the evolutionary consequences of
 introgression of domesticated genes back into the wild are poorly
 understood. By combining high-throughput genotyping with 25 years of
 long-term ecological field data, we describe the occurrence and
 consequences of admixture between a primitive sheep breed, the free-living
 Soay sheep of St Kilda, and more modern breeds. Utilizing data from a 50 K
 ovine SNP chip, together with forward simulations of demographic
 scenarios, we show that admixture occurred between Soay sheep and a more
 modern breed, consistent with historical accounts, approximately 150 years
 ago. Haplotype-sharing analyses with other breeds revealed that
 polymorphisms in coat colour and pattern in Soay sheep arose as a result
 of introgression of genetic variants favoured by artificial selection.
 Because the haplotypes carrying the causative mutations are known to be
 under natural selection in free-living Soay sheep, the admixture event
 created an opportunity to observe the outcome of a ‘natural laboratory’
 experiment where ancestral and domesticated genes competed with each
 other. The haplotype carrying the domesticated light coat colour allele
 was favoured by natural selection, while the haplotype associated with the
 domesticated self coat pattern allele was associated with decreased
 survival. Therefore, we demonstrate that introgression of domesticated
 alleles into wild populations can provide a novel source of variation
 capable of generating rapid evolutionary changes.
description: 29564HighQualitySNPsplink map file to extract the high quality SNPs used for analysis from ISGC11405PrunedSNPsplink map file for LD pruned marker setSOA_OAR2plink map file of marker set on OAR2 (TYRP1)SOA_OAR13plink map file for marker set on OAR13 (ASIP)QMsimScriptQMsim parameter file to simulate genome-wide data with and without admixturesimad50Ksimulated genom-wide SNP data under an admixture scenarion (plink ped file)simad50Ksimulated genom-wide SNP data under an admixture scenarion (plink map file)simnoad50Ksimulated genom-wide SNP data under a no admixture scenarion (plink ped file)simnoad50Ksimulated genom-wide SNP data under a no admixture scenarion (plink map file)sim50Kqc_pruneplink map file for quality filtered and pruned marker set for simulated data setsplink2fastPHASER script for converting from plink (.ped) to fastPHASE (.inp) input formatfastPHASE2haplotypesR script for converting fastPHASE output into a list of phased haplotypes with duplicated IDsHSR script to calculate haplotype sharing (HS) between Soays and other breeds
DOI: 10.35079/hbm253.pjkb.347
title: Visium (no probes) data from the fallopian tube (right) of a 30-year-old white female
DOI: 10.5061/dryad.3vd6k
title: Data from: Heterogeneity and concordance in locus-specific differentiation and introgression between species of towhees

description: The maintenance or breakdown of reproductive isolation are observable
 outcomes of secondary contact between species. In cases where hybrids
 beyond the F1 are formed, the representation of each species’ ancestry can
 vary dramatically among genomic regions. This genomic heterogeneity in
 ancestry and introgression can offer insight into evolutionary processes,
 particularly if introgression is compared in multiple hybrid zones.
 Similarly, considerable heterogeneity exists across the genome in the
 extent to which populations and species have diverged, reflecting the
 combined effects of different evolutionary processes on genetic variation.
 We studied hybridization across two hybrid zones of two phenotypically
 well-differentiated bird species in Mexico (Pipilo maculatus and P. ocai),
 to investigate genomic heterogeneity in differentiation and introgression.
 Using genotyping by sequencing (GBS) and hierarchical Bayesian models, we
 genotyped 460 birds at over 41,000 single nucleotide polymorphism (SNP)
 loci. We identified loci exhibiting extreme introgression relative to the
 genome-wide expectation using a Bayesian genomic cline model. We also
 estimated locus-specific FST and identified loci with exceptionally high
 genetic divergence between the parental species. We found some concordance
 of locus-specific introgression in the two independent hybrid zones (6-20%
 of extreme loci shared across zones), reflecting areas of the genome that
 experience similar gene flow when the species interact. Additionally,
 heterogeneity in introgression and divergence across the genome revealed
 another subset of loci under the influence of locally specific factors.
 These results are consistent with a history in which reproductive
 isolation has been influenced by a common set of loci in both hybrid
 zones, but where local environmental and stochastic factors also lead to
 genomic differentiation.
description: Pipilo genotype
 probability matrixSNP genotype
 probabilities across 41,324 loci for 460 Pipilo
 individualsKingston_etal_Pipilo_genotype_probability.txtPipilo plumage and metadataPlumage scores and voucher, tissue, field, population, and genotype ID numbers associated with 460 Pipilo individualsKingston_etal_Pipilo_plumage_and_metadataDRYAD.txtPipilo short read assemblyBAM (alignment) file of short reads associated with the 460 Pipilo individualsKingston_etal_Pipilo_assembly.bam
DOI: 10.5061/dryad.494j5
title: Data from: Environmental enrichment normalizes hippocampal timing coding in a malformed hippocampus

description: Neurodevelopmental insults leading to malformations of cortical
 development (MCD) are a common cause of psychiatric disorders, learning
 impairments and epilepsy. In the methylazoxymethanol (MAM) model of MCDs,
 animals have impairments in spatial cognition that, remarkably, are
 improved by post-weaning environmental enrichment (EE). To establish how
 EE impacts network-level mechanisms of spatial cognition, hippocampal in
 vivo single unit recordings were performed in freely moving animals in an
 open arena. We took a generalized linear modeling approach to extract fine
 spike timing (FST) characteristics and related these to place cell
 fidelity used as a surrogate of spatial cognition. We find that MAM
 disrupts FST and place-modulated rate coding in hippocampal CA1 and that
 EE improves many FST parameters towards normal. Moreover, FST parameters
 predict spatial coherence of neurons, suggesting that mechanisms
 determining altered FST are responsible for impaired cognition in MCDs.
 This suggests that FST parameters could represent a therapeutic target to
 improve cognition even in the context of a brain that develops with a
 structural abnormality.  
description: Supplemental Model
 DataMatlab binary data files
 containing: 1) place field information for every cell, 2) fitted
 generalized linear models, and 3) a text file with a key for each analyzed
 cell. Rasters of clustered units are contained within GLM data
 files.SuppModelData.zip
DOI: 10.35079/hbm344.jnfc.652
title: Visium (no probes) data from the fallopian tube (right) of a 30-year-old white female