cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f2313
title: Data from: Genomic footprints of speciation in Atlantic eels (Anguilla anguilla and A. rostrata)

description: The importance of speciation-with-gene-flow scenarios is increasingly
 appreciated. However, the specific processes and the resulting genomic
 footprints of selection are subject to much discussion. We studied the
 genomics of speciation between the two panmictic, sympatrically spawning
 sister-species; European (Anguilla anguilla) and American eel (A.
 rostrata). Divergence is assumed to have initiated more than 3 million
 years ago, and although low gene flow still occurs strong postzygotic
 barriers are present. Restriction-site Associated DNA (RAD) sequencing
 identified 328,300 SNPs for subsequent analysis. However, despite the
 presence of 3,757 strongly differentiated SNPs (FST &gt; 0.8), sliding
 window analyses of FST showed no larger genomic regions (i.e. hundreds of
 thousands to millions of bases) of elevated differentiation. Overall FST
 was 0.041 and linkage disequilibrium was virtually absent for SNPs
 separated by more than 1000 bp. We suggest this to reflect a case of
 genomic hitchhiking, where multiple regions are under directional
 selection between the species. However, low but biologically significant
 gene flow and high effective population sizes leading to very low genetic
 drift preclude accumulation of strong background differentiation. Genes
 containing candidate SNPs for positive selection showed significant
 enrichment for gene ontology (GO) terms relating to developmental
 processes and phosphorylation, which seems consistent with assumptions
 that differences in larval phase duration and migratory distances underlie
 speciation. Most SNPs under putative selection were found outside coding
 regions, lending support to emerging views that non-coding regions may be
 more functionally important than previously assumed. In total, the results
 demonstrate the necessity of interpreting genomic footprints of selection
 in the context of demographic parameters and life-history features of the
 studied species.
description: Genepop
 fileGenepop file for the
 analyzed individualsGenepop_MEC2014_FINALLoci_InformationSummary output (location, Fst, etc) from STACKS for each individual SNP
DOI: 10.5061/dryad.953hv
title: Data from: Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count?

description: A goal of many environmental DNA barcoding studies is to infer
 quantitative information about relative abundances of different taxa based
 on sequence read proportions generated by high-throughput sequencing.
 However, potential biases associated with this approach are only beginning
 to be examined. We sequenced DNA amplified from faeces (scats) of captive
 harbour seals (Phoca vitulina) to investigate whether sequence counts
 could be used to quantify the seals’ diet. Seals were fed fish in fixed
 proportions, a chordate-specific mitochondrial 16S marker was amplified
 from scat DNA and amplicons sequenced using an Ion Torrent PGM™. For a
 given set of bioinformatic parameters, there was generally low variability
 between scat samples in proportions of prey species sequences recovered.
 However, proportions varied substantially depending on sequencing
 direction, level of quality filtering (due to differences in sequence
 quality between species) and minimum read length considered. Short primer
 tags used to identify individual samples also influenced species
 proportions. In addition, there were complex interactions between factors;
 for example, the effect of quality filtering was influenced by the primer
 tag and sequencing direction. Resequencing of a subset of samples revealed
 some, but not all, biases were consistent between runs. Less stringent
 data filtering (based on quality scores or read length) generally produced
 more consistent proportional data, but overall proportions of sequences
 were very different than dietary mass proportions, indicating additional
 technical or biological biases are present. Our findings highlight that
 quantitative interpretations of sequence proportions generated via
 high-throughput sequencing will require careful experimental design and
 thoughtful data analysis.
description: Ion Torrent diet
 dataFASTQ sequence files and
 additional data described in the ReadMe file1 MER paper
 functionsFunctions needed to run
 R code2 MER R code
 databaseR
 code3 MER R code
 summaryR
 code
DOI: 10.5061/dryad.8m4r5
title: Data from: The identification of loci for immune traitsin chickens using a genome-wide association study

description: The genetic improvement of disease resistance in poultry continues to be a
 challenge. To identify candidate genes and loci responsible for these
 traits, genome-wide association studies using the chicken 60k high density
 single nucleotide polymorphism (SNP) array for six immune traits, total
 serum immunoglobulin Y (IgY) level, numbers of, and the ratio of
 heterophils and lymphocytes, and antibody responses against Avian
 Influenza Virus (AIV) and Sheep Red Blood Cell (SRBC), were performed.
 RT-qPCR was used to quantify the relative expression of the identified
 candidate genes. Nine significantly associated SNPs (P &lt; 2.81E-06)
 and 30 SNPs reaching the suggestively significant level (P &lt;
 5.62E-05) were identified. Five of the 10 SNPs that were suggestively
 associated with the antibody response to SRBC were located within or close
 to previously reported QTL regions. Fifteen SNPs reached a suggestive
 significance level for AIV antibody titer and seven were found on the sex
 chromosome Z. Seven suggestive markers involving five different SNPs were
 identified for the numbers of heterophils and lymphocytes, and the
 heterophil/lymphocyte ratio. Nine significant SNPs, all on chromosome 16,
 were significantly associated with serum total IgY concentration, and the
 five most significant were located within a narrow region spanning 6.4kb
 to 253.4kb (P = 1.20E-14 to 5.33E-08). After testing expression of five
 candidate genes (IL4I1, CD1b, GNB2L1, TRIM27 and ZNF692) located in this
 region, changes in IL4I1, CD1b transcripts were consistent with the
 concentrations of IgY, while abundances of TRIM27 and ZNF692 showed
 reciprocal changes to those of IgY concentrations. This study has revealed
 39 SNPs associated with six immune traits (total serum IgY level, numbers
 of, and the ratio of heterophils and lymphocytes, and antibody responses
 against AIV and SRBC) in Beijing-You chickens. The narrow region spanning
 247kb on chromosome 16 is an important QTL for serum total IgY
 concentration. Five candidate genes related to IgY level validated here
 are novel and may play critical roles in the modulation of immune
 responses. Potentially useful candidate SNPs for marker-assisted selection
 for disease resistance are identified. It is highly likely that these
 candidate genes play roles in various aspects of the immune response in
 chickens.
description: Genotypes for the
 association panel10-234_Full Data Table_728
 samples.xlsx
DOI: 10.5061/dryad.rq2r7
title: Data from: Magnetic resonance imaging and tensor-based morphometry in the MPTP non-human primate model of Parkinson’s disease

description: Parkinson’s disease (PD) is the second most common neurodegenerative
 disorder producing a variety of motor and cognitive deficits with the
 causes remaining largely unknown. The gradual loss of the nigrostriatal
 pathway is currently considered the pivotal pathological event. To better
 understand the progression of PD and improve treatment management,
 defining the disease on a structural basis and expanding brain analysis to
 extra-nigral structures is indispensable. The anatomical complexity and
 the presence of neuromelanin, make the use of non-human primates an
 essential element in developing putative imaging biomarkers of PD. To this
 end, ex vivo T2-weighted magnetic resonance images were acquired from
 control and 1-methyl-4 phenyl-1,2,3,6-tetrahydropyridine (MPTP)-treated
 marmosets. Volume measurements of the caudate, putamen, and substantia
 nigra indicated significant atrophy and cortical thinning. Tensor-based
 morphometry provided a more extensive and hypothesis free assessment of
 widespread changes caused by the toxin insult to the brain, especially
 highlighting regional cortical atrophy. The results highlight the
 importance of developing imaging biomarkers of PD in non-human primate
 models considering their distinct neuroanatomy. It is essential to further
 develop these biomarkers in vivo to provide non-invasive tools to detect
 pre-symptomatic PD and to monitor potential disease altering therapeutics.
description: MRI Data
 PLOS1T2-weighted MR images of
 control and MPTP-treated marmosets
DOI: 10.5061/dryad.93h33
title: Data from: Applications of random forest feature selection for fine-scale genetic population assignment

description: Genetic population assignment used to inform wildlife management and
 conservation efforts requires panels of highly informative genetic markers
 and sensitive assignment tests. We explored the utility of
 machine-learning algorithms (random forest, regularized random forest, and
 guided regularized random forest) compared with FST ranking for selection
 of single nucleotide polymorphisms (SNP) for fine-scale population
 assignment. We applied these methods to an unpublished SNP dataset for
 Atlantic salmon (Salmo salar) and a published SNP data set for Alaskan
 Chinook salmon (Oncorhynchus tshawytscha). In each species, we identified
 the minimum panel size required to obtain a self-assignment accuracy of at
 least 90% using each method to create panels of 50-700 markers Panels of
 SNPs identified using random forest-based methods performed up to 7.8 and
 11.2 percentage points better than FST-selected panels of similar size for
 the Atlantic salmon and Chinook salmon data, respectively. Self-assignment
 accuracy ≥90% was obtained with panels of 670 and 384 SNPs for each
 dataset, respectively, a level of accuracy never reached for these species
 using FST-selected panels. Our results demonstrate a role for
 machine-learning approaches in marker selection across large genomic
 datasets to improve assignment for management and conservation of
 exploited populations.
description: AtlanticSalmon_93KGenepopGenepop file containing 93,703 SNPs from Labrador Atlantic salmon, filtered from original 220K SNP chip.format_dataframe_for_RFR script to convert data in adjusted PLINK format to format suitable for RF analyses. Example run of RF included in script.
DOI: 10.5061/dryad.mb2tj
title: Data from: Experimental evidence of genome-wide impact of ecological selection during early stages of speciation-with-gene-flow

description: Theory predicts that speciation-with-gene-flow is more likely when the
 consequences of selection for population divergence transitions from
 mainly direct effects of selection acting on individual genes to a
 collective property of all selected genes in the genome. Thus,
 understanding the direct impacts of ecologically based selection, as well
 as the indirect effects due to correlations among loci, is critical to
 understanding speciation. Here, we measure the genome-wide impacts of
 host-associated selection between hawthorn and apple host races of
 Rhagoletis pomonella (Diptera: Tephritidae), a model for contemporary
 speciation-with-gene-flow. Allele frequency shifts of 32 455 SNPs induced
 in a selection experiment based on host phenology were genome wide and
 highly concordant with genetic divergence between co-occurring apple and
 hawthorn flies in nature. This striking genome-wide similarity between
 experimental and natural populations of R. pomonella underscores the
 importance of ecological selection at early stages of divergence and calls
 for further integration of studies of eco-evolutionary dynamics and genome
 divergence.
description: VCF file for
 experimental and natural populationsThis is the VCF file for
 the experimental and natural population comparisons. To test for
 differentiation genome wide among sympatric populations, we contrasted our
 apple7 and haw7 groups; for a response to selection in our experiment, we
 compared haw7 and haw30. Haw or apple represents the host plant from which
 the flies were collected; the number - 7 or 30 - represents the pre-winter
 warm period experienced by larvae/pupae prior to overwintering to match
 that found in nature on haw or apple plants. See txt file to match
 individual MID labels in the VCF file with the experimental group they
 were part of.snps.ScottSelection.05-400-20.filteredHwe0.05.wOutApple30.cleaned.vcfR_pomonella_denovo_assemblyThis file is the de novo assembly of Illumina sequence reads (20 million reads; 3% of total data) generated by Seqman NGen 4.0.0 (DNASTAR) using parameter values described in Gompert et al. 2012. See methods for more details.LatestRadFakeGenome.cut.fa.txtR. pomonella Linkage MapLinkage map giving the linear order of SNPs on each of the five chromosomes/linkage groups. Column labels: chromosome (1 to 5), Sn = SNP number ID (1-N by chromosome), locus = location of SNP in our de novo assembly by contig, then by location along contig, separated by an underscore, Position = distance along each linkage group/chromosome in centiMorgans.MapLinearOrderAllChrom.txt
DOI: 10.5061/dryad.65q64
title: Data from: Short-term activity cycles impede information transmission in ant colonies

description: Rhythmical activity patterns are ubiquitous in nature. We study an
 oscillatory biological system: collective activity cycles in ant colonies.
 Ant colonies have become model systems for research on biological networks
 because the interactions between the component parts are visible to the
 naked eye, and because the time-ordered contact network formed by these
 interactions serves as the substrate for the distribution of information
 and other resources throughout the colony. To understand how the
 collective activity cycles influence the contact network transport
 properties, we used an automated tracking system to record the movement of
 all the individuals within nine different ant colonies. From these
 trajectories we extracted over two million ant-to-ant interactions.
 Time-series analysis of the temporal fluctuations of the overall colony
 interaction and movement rates revealed that both the period and amplitude
 of the activity cycles exhibit a diurnal cycle, in which daytime cycles
 are faster and of greater amplitude than night cycles. Using
 epidemiology-derived models of transmission over networks, we compared the
 transmission properties of the observed periodic contact networks with
 those of synthetic aperiodic networks. These simulations revealed that
 contrary to some predictions, regularly-oscillating contact networks
 should impede information transmission. Further, we provide a mechanistic
 explanation for this effect, and present evidence in support of it.
description: Contacts.tarArchive contains 16 .txt files. Each file represents a time-ordered edgelist representing pairwise physical contacts between ants. Files are named according to the identity of the colony ('col2' represents colony number 2), and the replicate number ('Rep_1' is the first replicate). See Readme.txt for description of the file contents.
DOI: 10.5061/dryad.hf11rb4
title: Data from: The leading-edge vortex on a rotating wing changes markedly beyond a certain central body size

description: Stable attachment of a leading-edge vortex (LEV) plays a key role in
 generating the high lift on rotating wings with a central body. The
 central body-size can affect the LEV structure broadly in two ways. First,
 an overall change in the size changes the Reynolds number, which is known
 to have an influence on the LEV structure. Second, it may affect the
 Coriolis acceleration acting across the wing, depending on the wing-offset
 from the axis of rotation. To investigate this, the effects of Reynolds
 number and the wing-offset are independently studied for a rotating wing.
 The three-dimensional LEV structure is mapped using a scanning PIV
 technique. The rapid acquisition of images and their correlation are
 carefully validated. The results presented in this paper show that the LEV
 structure changes mainly with the Reynolds number. The LEV-split is found
 to be only minimally affected by changing the central body radius in the
 range of small offsets, which interestingly includes the range for most
 insects. However, beyond this small offset range, the LEV-split is found
 to change dramatically.
description: Data from: The
 leading-edge vortex on a rotating wing changes markedly beyond a certain
 central body sizeStable attachment of a
 leading-edge vortex (LEV) plays a key role in generating the high lift on
 rotating wings with a central body. The central body-size can affect the
 LEV structure broadly in two ways. First, an overall change in the size
 changes the Reynolds number, which is known to have an influence on the
 LEV structure. Second, it may affect the Coriolis acceleration acting
 across the wing, depending on the wing-offset from the axis of rotation.
 To investigate this, the effects of Reynolds number and the wing-offset
 are independently studied for a rotating wing. The three-dimensional LEV
 structure is mapped using a scanning PIV technique. The rapid acquisition
 of images and their correlation are carefully validated. The results
 presented in this paper show that the LEV structure changes mainly with
 the Reynolds number. The LEV-split is found to be only minimally affected
 by changing the central body radius in the range of small offsets, which
 interestingly includes the range for most insects. However, beyond this
 small offset range, the LEV-split is found to change
 dramatically.supporting_material_RSOS172197.zip
DOI: 10.5061/dryad.10nh8
title: Data from: The relationship of recombination rate, genome structure, and patterns of molecular evolution across angiosperms

description: Background: Although homologous recombination affects the efficacy of
 selection in populations, the pattern of recombination rate evolution and
 its effects on genome evolution across plants are largely unknown.
 Recombination can reduce genome size by enabling the removal of LTR
 retrotransposons, alter codon usage by GC biased gene conversion,
 contribute to complex histories of gene duplication and loss through
 tandem duplication, and enhance purifying selection on genes. Therefore,
 variation in recombination rate across species may explain some of the
 variation in genomic architecture as well as rates of molecular evolution.
 We used phylogenetic comparative methods to investigate the evolution of
 global meiotic recombination rate in angiosperms and its effects on genome
 architecture and selection at the molecular level using genetic maps and
 genome sequences from thirty angiosperm species. Results: Recombination
 rate is negatively correlated with genome size, which is likely caused by
 the removal of LTR retrotransposons. After correcting recombination rates
 for euchromatin content, we also found an association between global
 recombination rate and average gene family size. This suggests a role for
 recombination in the preservation of duplicate genes or expansion of gene
 families. An analysis of the correlation between the ratio of
 nonsynonymous to synonymous substitution rates (dN/dS) and recombination
 rate in 3748 genes indicates that higher recombination rates are
 associated with an increased efficacy of purifying selection, suggesting
 that global recombination rates affect variation in rates of molecular
 evolution across distantly related angiosperm species, not just between
 populations. We also identified shifts in dN/dS for recombination proteins
 that are associated with shifts in global recombination rate across our
 sample of angiosperms. Conclusions: Although our analyses only reveal
 correlations, not mechanisms, and do not include potential covariates of
 recombination rate, like effective population size, they suggest that
 global recombination rates may play an important role in shaping the
 macroevolutionary patterns of gene and genome evolution in plants.
 Interspecific recombination rate variation is tightly correlated with
 genome size as well as variation in overall LTR retrotransposon
 abundances. Recombination may shape gene-to-gene variation in dN/dS
 between species, which might impact the overall gene duplication and loss
 rates.
description: Codon
 AlignmentsCodon alignments used in
 study.CodonAlignments.zipmatK alignmentThe matK alignment was used for obtaining ultrametric branch lengths on the species tree.matK_opt.mf.fastaSpecies treeThis is the species tree used for all comparative analyses.RRsTree.tre
DOI: 10.5061/dryad.3bv80
title: Data from: Analysis of bacterial genomes from an evolution experiment with horizontal gene transfer shows that recombination can sometimes overwhelm selection

description: Few experimental studies have examined the role that sexual recombination
 plays in bacterial evolution, including the effects of horizontal gene
 transfer on genome structure. To address this limitation, we analyzed
 genomes from an experiment in which Escherichia coli K-12 Hfr (high
 frequency recombination) donors were periodically introduced into 12
 evolving populations of E. coli B and allowed to conjugate repeatedly over
 the course of 1000 generations. Previous analyses of the evolved strains
 from this experiment showed that recombination did not accelerate
 adaptation, despite increasing genetic variation relative to asexual
 controls. However, the resolution in that previous work was limited to
 only a few genetic markers. We sought to clarify and understand these
 puzzling results by sequencing complete genomes from each population. The
 effects of recombination were highly variable: one lineage was mostly
 derived from the donors, while another acquired almost no donor DNA. In
 most lineages, some regions showed repeated introgression and others
 almost none. Regions with high introgression tended to be near the donors’
 origin of transfer sites. To determine whether introgressed alleles
 imposed a genetic load, we extended the experiment for 200 generations
 without recombination and sequenced whole-population samples. Beneficial
 alleles in the recipient populations were occasionally driven extinct by
 maladaptive donor-derived alleles. On balance, our analyses indicate that
 the plasmid-mediated recombination was sufficiently frequent to drive
 donor alleles to fixation without providing much, if any, selective
 advantage.
description: DRYAD-STLE-analysisData files and scripts for all analyses and figures in Maddamsetti and Lenski (2018).