• European Marine Science
• European Commission close
• Wellcome Trust close
• EU close
• GB close
• English close

Electrophysiological evidence suggested primarily the involvement of area MT in depth cue integration in macaques, as opposed to human imaging data pinpointing area V3B/KO. To clarify this conundrum, we decoded monkey fMRI responses evoked by stimuli signaling near or far depths defined by binocular disparity, relative motion and their combination, and we compared results with those from an identical experiment previously performed in humans.Responses in macaque area MT are more discriminable when two cues concurrently signal depth, and information provided by one cue is diagnostic of depth indicated by the other. This suggests that monkey area MT computes fusion of disparity and motion depth signals, exactly as shown for human area V3B/KO. Hence, these data reconcile previously reported discrepancies between depth processing in human and monkey by showing the involvement of the dorsal stream in depth cue integration using the same technique, despite the engagement of different regions. data describing fig 1-8 and sfig 1-12data.zip

We analyse new genomic data (0.05–2.95x) from 14 ancient individuals from Portugal distributed from the Middle Neolithic (4200–3500 BC) to the Middle Bronze Age (1740–1430 BC) and impute genomewide diploid genotypes in these together with published ancient Eurasians. While discontinuity is evident in the transition to agriculture across the region, sensitive haplotype-based analyses suggest a significant degree of local hunter-gatherer contribution to later Iberian Neolithic populations. A more subtle genetic influx is also apparent in the Bronze Age, detectable from analyses including haplotype sharing with both ancient and modern genomes, D-statistics and Y-chromosome lineages. However, the limited nature of this introgression contrasts with the major Steppe migration turnovers within third Millennium northern Europe and echoes the survival of non-Indo-European language in Iberia. Changes in genomic estimates of individual height across Europe are also associated with these major cultural transitions, and ancestral components continue to correlate with modern differences in stature. Index for VCF fileIndex for VCF filepost_imputation_Martiniano_et_al_2017_public.vcf.gz.tbiVCF file containing imputed genotype data belonging to 67 newly sequenced and publicly available ancient samples.VCF file containing imputed genotype data belonging to 67 newly sequenced and publicly available ancient samples which we analysed in Martiniano et al. (2017).post_imputation_Martiniano_et_al_2017_public.vcf.gzREADME_Martiniano_et_al_2017Description of the methods used for genotype imputation.

Genotype data of populations selected for virus resistanceColumns indicate the generation during selection, the Wolbachia infection status, the number of females with a given genotype (N_CC, N_CT, N_TT), the frequency of pastrel resistant allele (freq_C), the frequency of each genotype (freq_CC, freq_CT, freq_TT) and the number of individuals genotyped (N_individuals).Genotype_summary.txtGenotype data of control populations not exposed to the virusColumns indicate the generation during selection, the Wolbachia infection status, the number of females with a given genotype (N_CC, N_CT, N_TT), the frequency of pastrel resistant allele (freq_C), the frequency of each genotype (freq_CC, freq_CT, freq_TT) and the number of individuals genotyped (N_individuals).Genotype_summary_control.txtGenotype data of populations tested for DCV resistance after selectionColumns indicate the generation during selection, the Wolbachia infection status, the number of females with a given genotype (N_CC, N_CT, N_TT), the frequency of pastrel resistant allele (freq_C), the frequency of each genotype (freq_CC, freq_CT, freq_TT) and the number of individuals genotyped (N_individuals).Pastrel_Genotype_Phenotypic_assay.txtPhenotypic data on DCV resistance of populations after selectionColumns indicate the selection treatment, the Wolbachia infection status, the tetracycline treatment after selection, the infection treatment (stabbing with Ringer's solution or DCV), the replicate population, the replicate vial, the number of infected flies in a vial (N_flies) and the cumulative number of dead flies post-infection on a given day.Pastrel_phenotypic_assay.txtPhenotypic data on effect of infection procedure in control populationsColumns indicate the selection treatment, the Wolbachia infection status, the infection treatment (no stabbing, stabbing with Ringer's solution or DCV), the population, the replicate vial, the number of infected flies in a vial (N_flies) and the cumulative number of dead flies post-infection on a given day.pastrel_genotype_phenotype_survival.txtGenotype data of surviving flies 15 days post-infection in control populations (test of the infection procedure)Columns indicate the infection treatment, the Wolbachia infection status, the population, the number of females with a given genotype (N_CC, N_CT, N_TT), the frequency of pastrel resistant allele (freq_C), the frequency of each genotype (freq_CC, freq_CT, freq_TT) and the number of individuals genotyped (N_individuals).Genotype_summary_infection_procedure.txt Heritable symbionts that protect their hosts from pathogens have been described in a wide range of insect species. By reducing the incidence or severity of infection, these symbionts have the potential to reduce the strength of selection on genes in the insect genome that increase resistance. Therefore, the presence of such symbionts may slow down the evolution of resistance. Here we investigated this idea by exposing Drosophila melanogaster populations to infection with the pathogenic Drosophila C virus (DCV) in the presence or absence of Wolbachia, a heritable symbiont of arthropods that confers protection against viruses. After nine generations of selection, we found that resistance to DCV had increased in all populations. However, in the presence of Wolbachia the resistant allele of pastrel—a gene that has a major effect on resistance to DCV—was at a lower frequency than in the symbiont-free populations. This finding suggests that defensive symbionts have the potential to hamper the evolution of insect resistance genes, potentially leading to a state of evolutionary addiction where the genetically susceptible insect host mostly relies on its symbiont to fight pathogens.

Perception adapts to mismatching multisensory information, both when different cues appear simultaneously and when they appear sequentially. While both multisensory integration and adaptive trial-by-trial recalibration are central for behavior, it remains unknown whether they are mechanistically linked and arise from a common neural substrate. To relate the neural underpinnings of sensory integration and recalibration, we measured whole-brain magnetoencephalography while human participants performed an audio-visual ventriloquist task. Using single-trial multivariate analysis, we localized the perceptually-relevant encoding of multisensory information within and between trials. While we found neural signatures of multisensory integration within temporal and parietal regions, only medial superior parietal activity encoded past and current sensory information and mediated the perceptual recalibration within and between trials. These results highlight a common neural substrate of sensory integration and perceptual recalibration, and reveal a role of medial parietal regions in linking present and previous multisensory evidence to guide adaptive behavior. PARK_KAYSER_RecalMEG_2019Please see README file.

Dogs were present in the Americas prior to the arrival of European colonists, but the origin and fate of these pre-contact dogs are largely unknown. We sequenced 71 mitochondrial and seven nuclear genomes from ancient North American and Siberian dogs spanning ~9,000 years. Our analysis indicates that American dogs were not domesticated from North American wolves. Instead, American dogs form a monophyletic lineage that likely originated in Siberia and dispersed into the Americas alongside people. After the arrival of Europeans, native American dogs almost completely disappeared, leaving a minimal genetic legacy in modern dog populations. Remarkably, the closest detectable extant lineage to pre-contact American dogs is the canine transmissible venereal tumor, a contagious cancer clone derived from an individual dog that lived up to 8,000 years ago. Mitochondrial DNA FASTA fileFASTA file containing 1166 dog mtDNA genomes used in this studyfull_mtDNA_alignment.fastaNEXUS treeMaximum likelihood tree (RAxML) of 1166 dogs mtDNA genomes used in this studyfull_mtDNA_alignment.treExcel sheetPublication source of the 1166 mtDNA genomes used in this studyfull_mtDNA_alignment.xlsxPlink (bed) fileContains genotype for dogs 54 dogsfull_data.bedPlink file (bim)Contains genotype for 54 dogsfull_data.bimPlink file (fam)Contains genotype for 54 dogsfull_data.famNJ tree in Figure 2bNJ tree in Figure 2b (see Table S2 for more info)Figure_b.treNexus fileNexus file used for producing Figure S12 (MKV model in MrBayes)Binary_char_MKV.nexNEXUS treeBayesian tree in Figure S12 (see Table S2 for more info)Figure_S12.tre

In previous papers, we introduced a normative scheme for scene construction and epistemic (visual) searches based upon active inference. This scheme provides a principled account of how people decide where to look, when categorising a visual scene based on its contents. In this paper, we use active inference to explain the visual searches of normal human subjects; enabling us to answer some key questions about visual foraging and salience attribution. First, we asked whether there is any evidence for 'epistemic foraging'; i.e. exploration that resolves uncertainty about a scene. In brief, we used Bayesian model comparison to compare Markov decision process (MDP) models of scan-paths that did - and did not - contain the epistemic, uncertainty-resolving imperatives for action selection. In the course of this model comparison, we discovered that it was necessary to include non-epistemic (heuristic) policies to explain observed behaviour (e.g., a reading-like strategy that involved scanning from left to right). Despite this use of heuristic policies, model comparison showed that there is substantial evidence for epistemic foraging in the visual exploration of even simple scenes. Second, we compared MDP models that did - and did not - allow for changes in prior expectations over successive blocks of the visual search paradigm. We found that implicit prior beliefs about the speed and accuracy of visual searches changed systematically with experience. Finally, we characterised intersubject variability in terms of subject-specific prior beliefs. Specifically, we used canonical correlation analysis to see if there were any mixtures of prior expectations that could predict between-subject differences in performance; thereby establishing a quantitative link between different behavioural phenotypes and Bayesian belief updating. We demonstrated that better scene categorisation performance is consistently associated with lower reliance on heuristics; i.e., a greater use of a generative model of the scene to direct its exploration. Scan-path dataThis file contains the scan-paths of the subjects that performed the "Scene construction task" described in the paper "Human visual exploration reduces uncertainty about the sensed world". There are some additional files that can be used to regenerate the figures and results in this paper.

The utility of using evolutionary and ecological frameworks to understand the dynamics of infectious diseases is gaining increasing recognition. However, integrating evolutionary ecology and infectious disease epidemiology is challenging because within-host dynamics can have counterintuitive consequences for between-host transmission, especially for vector-borne parasites. A major obstacle to linking within- and between-host processes is that the drivers of the relationships between the density, virulence, and fitness of parasites are poorly understood. By experimentally manipulating the intensity of rodent malaria (Plasmodium berghei) infections in Anopheles stephensi mosquitoes under different environmental conditions, we show that parasites experience substantial density-dependent fitness costs because crowding reduces both parasite proliferation and vector survival. We then use our data to predict how interactions between parasite density and vector environmental conditions shape within-vector processes and onward disease transmission. Our model predicts that density-dependent processes can have substantial and unexpected effects on the transmission potential of vector-borne disease, which should be considered in the development and evaluation of transmission-blocking interventions. data for dryadDensity data from individual mosquito dissections. For further information please contact Laura Pollitt (laura.pollitt@googlemail.com).

chicken.all_samples.galGal3.tpm.refgene.oscData for the analysis of the chicken chromosome Z. FANTOM5 chicken libraries consisted of 25 CAGE libraries including: chicken aortic smooth muscles, hepatocytes, mesenchymal stem cells, leg buds, wing buds, embryo extra-embryonic tissue (day 7 and day 15), and whole body developmental time course (from 5 hours 30 minutes to 20 days). The number of available datapoints to which TPM was normalized was limited by the number of annotated chicken RefSeq transcripts (which was approximately six times smaller than human, N = 4,426 on autosomes, and N = 241 on chromosome Z). Consequently, the cutoff for a gene to be classified as “on” was adjusted six times higher to 60 TPM.human.primary_cell.hCAGE.hg19.tpm.refgene.oscThe FANTOM5 dataset for human primary cells.human.cell_line.hCAGE.hg19.tpm.refgene.oscThe FANTOM5 dataset for human cancer cell-lines.human.tissue.hCAGE.hg19.tpm.refgene.oscThe FANTOM5 dataset for human tissue. CAGE tags were mapped to RefSeq transcripts +/-500 base pairs (bps) from their TSSes and normalized to tags per million (TPM), as previously described [37,45]. The signal of ten TPM was chosen as the cutoff for a gene to be classified as “on” (this cutoff was accepted as the standard for human data throughout the consortium). FANTOM5 is the most comprehensive expression dataset ever generated, including 952 human and 396 mouse tissues, primary cells and cancer cell-lines. FANTOM5 is based on cap analysis of gene expression (CAGE) a unique technology that characterizes TSSes across the entire genome in an unbiased fashion and at a single-base resolution level [21]. CAGE automatically sums expression levels of all transcripts beginning at a given transcription start site.raw_Z_Exp_Anc_LData for Fig 2 "The comparison of change in gene expression (Z) since the human-Chimpanzee common ancestor for five somatic tissues."SUPPLEMENTARY TABLESData in Table S3 underlies Figure 4. Data in Table S7 partially underlies Fig 1. Data in Tables S4 underlies Fig 3. Data in Tables S10-12 underlies Fig S1.data for Fig1R environment containing data underlying Fig1. The environment contains the following variables sorted identically as the gene list in refSeqs: chromosome (chromosomal location), chromosome_short (location on autosomes,chrX, or chrY?), data_matrix (F5 data matrix in TPM for human tissues)‚ MAX (maximal expression for each RefSeq)‚ max (maximal expression for each tissue)‚ strata_classification (strata classification for genes on chromosome X)‚ refSeqs_2entrezIDs (entrez ids mapped to refseqs)‚ boe (the breadth of expression)env_fig1GC-contents data for for Fig S6 and S7This R environment contains GC-contents data for either proximal promoters or isochore around the TSS (marked as big). The data is calculated for either masked or unmasked genome seqeuence.env_gc_contentsdata for Fig S3numbers of ENCODE transcription factor binding sites mapped to TSSes of RefSeq genes in symmetrical windows of different sizes (from 250 to 20000 bps) and depending on ENCODE quality cut-off (strict or all).FigS3_data.txtdata underlying Fig S8Breadth of expression and maximal expression is compared in three groups of observations: (1) autosomal paralogs of X-linked genes, (2) other autosomal paralogs matched by age, (3) X-linked paralogs. Newly formed paralogs are defined as those mapped by phylogenetic timing to taxa Theria or younger. Pre-existing duplications are defined as those descending from duplication notes mapped by phylogenetic timing to taxa Amniota or older.FigS8_data.txtdata underlying Fig7Fig7_data.txtTreeFam data for timing of gene duplications in R environmentsThese files are R environments. Use load() to load them into your R session! You ls() to view contents. You may use attach() syntax to load the namespace or access data members of the environment using the "$" reference operator. There is no warranty for this softwareenv_duplicator_baseAdditional TreeFam gene duplication data with duplication timingenv_duplicator_vectors X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X’s gene content, gene expression, and evolution.