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Systematic detection of brain protein-coding genes under positive selection during primate evolution and their roles in cognition

https://doi.org/10.1101/658658
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Mutational analysis of BARHL1 and BARX1 in three new patients with Joubert syndrome
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From Movement to Thought: Executive Function, Embodied Cognition, and the Cerebellum
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Influence of the choroid plexus on cerebellar development: analysis of retinoic acid synthesis
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Functional Gene Group Analysis Reveals a Role of Synaptic Heterotrimeric G Proteins in Cognitive Ability
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FAM111A Mutations Result in Hypoparathyroidism and Impaired Skeletal Development
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Accelerated Evolution of Nervous System Genes in the Origin of Homo sapiens
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A Humanized Version of Foxp2 Affects Cortico-Basal Ganglia Circuits in Mice
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Evolution of Human-Specific Neural SRGAP2 Genes by Incomplete Segmental Duplication
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Inhibition of SRGAP2 Function by Its Human-Specific Paralogs Induces Neoteny during Spine Maturation
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Human-Specific NOTCH2NL Genes Expand Cortical Neurogenesis through Delta/Notch Regulation
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A Single-Cell Transcriptional Atlas of the Developing Murine Cerebellum
inferredcites →https://doi.org/10.1016/j.gde.2016.08.001openalex-snapshot
Human adaptation and evolution by segmental duplication
inferredcites →https://doi.org/10.1016/j.neuroimage.2009.10.045openalex-snapshot
Evolution of the cerebellar cortex: The selective expansion of prefrontal-projecting cerebellar lobules
inferredcites →https://doi.org/10.1016/j.neuron.2015.09.016openalex-snapshot
Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci
inferredcites →https://doi.org/10.1016/j.tics.2017.01.004openalex-snapshot
Climbing Brain Levels of Organisation from Genes to Consciousness
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GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates
inferredcites →https://doi.org/10.1016/j.ygeno.2016.04.004openalex-snapshot
Insights into the dN/dS ratio heterogeneity between brain specific genes and widely expressed genes in species of different complexity
inferredcites →https://doi.org/10.1016/j.ygeno.2017.01.005openalex-snapshot
Improvements and impacts of GRCh38 human reference on high throughput sequencing data analysis
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Statistical methods for detecting molecular adaptation
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Roles of the mammalian subventricular zone in brain development
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A Calcium-Responsive Transcription Factor, CaRF, that Regulates Neuronal Activity-Dependent Expression of BDNF
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The role of the prefrontal cortex in higher cognitive functions
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Joubert syndrome may provide clues about human evolution
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Adaptive protein evolution at the Adh locus in Drosophila
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The evolution of brain activation during temporal processing
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Functional gene group analysis identifies synaptic gene groups as risk factor for schizophrenia
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Molecular evolution of FOXP2, a gene involved in speech and language
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An RNA gene expressed during cortical development evolved rapidly in humans
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Genome-wide atlas of gene expression in the adult mouse brain
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An anatomically comprehensive atlas of the adult human brain transcriptome
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Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility
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De novo nonsense mutations in ASXL1 cause Bohring-Opitz syndrome
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Abnormal cerebellar development and axonal decussation due to mutations in AHI1 in Joubert syndrome
inferredcites →https://doi.org/10.1038/nmeth.4050openalex-snapshot
The proteomes of excitatory and inhibitory synaptic clefts
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Prefrontal white matter volume is disproportionately larger in humans than in other primates
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Human uniqueness: genome interactions with environment, behaviour and culture
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The evolution and population diversity of human-specific segmental duplications
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Shared and distinct transcriptomic cell types across neocortical areas
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A map of constrained coding regions in the human genome
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A gene atlas of the mouse and human protein-encoding transcriptomes
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Role of BRCA1 in brain development
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Patterns of coding variation in the complete exomes of three Neandertals
inferredcites →https://doi.org/10.1073/pnas.1520760112openalex-snapshot
Human cerebral organoids recapitulate gene expression programs of fetal neocortex development
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A benchmark of gene expression tissue-specificity metrics
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BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks
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The Dyslexia-susceptibility Protein KIAA0319 Inhibits Axon Growth Through Smad2 Signaling
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The chromosome 6p22 haplotype associated with dyslexia reduces the expression of KIAA0319 , a novel gene involved in neuronal migration
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PAML 4: Phylogenetic Analysis by Maximum Likelihood
inferredcites →https://doi.org/10.1093/molbev/msp119openalex-snapshot
Estimating the Rate of Adaptive Molecular Evolution in the Presence of Slightly Deleterious Mutations and Population Size Change
inferredcites →https://doi.org/10.1093/molbev/msq249openalex-snapshot
Estimation of the Neutrality Index
inferredcites →https://doi.org/10.1093/molbev/msr279openalex-snapshot
The Role of GC-Biased Gene Conversion in Shaping the Fastest Evolving Regions of the Human Genome
inferredcites →https://doi.org/10.1093/molbev/msu046openalex-snapshot
Emergence and Evolutionary Analysis of the Human DDR Network: Implications in Comparative Genomics and Downstream Analyses
inferredcites →https://doi.org/10.1093/molbev/msx266openalex-snapshot
Mapping Selection within Drosophila melanogaster Embryo’s Anatomy
inferredcites →https://doi.org/10.1093/molbev/msx270openalex-snapshot
Faster Evolving Primate Genes Are More Likely to Duplicate
inferredcites →https://doi.org/10.1093/nar/gkn760openalex-snapshot
STRING 8--a global view on proteins and their functional interactions in 630 organisms
inferredcites →https://doi.org/10.1093/nar/gkq603openalex-snapshot
ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
inferredcites →https://doi.org/10.1093/nar/gky1105openalex-snapshot
Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources
inferredcites →https://doi.org/10.1098/rspb.2013.1743openalex-snapshot
ASPM and mammalian brain evolution: a case study in the difficulty in making macroevolutionary inferences about gene–phenotype associations
inferredcites →https://doi.org/10.1098/rstb.2016.0244openalex-snapshot
Why are there so many explanations for primate brain evolution?
inferredcites →https://doi.org/10.1101/gad.1606907openalex-snapshot
Global analysis of alternative splicing differences between humans and chimpanzees
inferredcites →https://doi.org/10.1101/gr.076554.108openalex-snapshot
Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs
inferredcites →https://doi.org/10.1101/gr.1239303openalex-snapshot
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
inferredcites →https://doi.org/10.1126/sciadv.aao5961openalex-snapshot
The evolution of modern human brain shape
inferredcites →https://doi.org/10.1126/science.1090005openalex-snapshot
Evolution at Two Levels in Humans and Chimpanzees
inferredcites →https://doi.org/10.1126/science.1113722openalex-snapshot
Microcephalin , a Gene Regulating Brain Size, Continues to Evolve Adaptively in Humans
inferredcites →https://doi.org/10.1126/science.1116815openalex-snapshot
Ongoing Adaptive Evolution of ASPM , a Brain Size Determinant in Homo sapiens
inferredcites →https://doi.org/10.1126/science.1137568openalex-snapshot
Comment on "Ongoing Adaptive Evolution of ASPM , a Brain Size Determinant in Homo sapiens "
inferredcites →https://doi.org/10.1126/science.1256780openalex-snapshot
Core and region-enriched networks of behaviorally regulated genes and the singing genome
inferredcites →https://doi.org/10.1126/science.1262110openalex-snapshot
The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans
inferredcites →https://doi.org/10.1126/science.aaa4788openalex-snapshot
Genomic signatures of evolutionary transitions from solitary to group living
inferredcites →https://doi.org/10.1126/science.aap8809openalex-snapshot
Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex
inferredcites →https://doi.org/10.1136/jmg.2004.028084openalex-snapshot
BRCA1 mutation and neuronal migration defect: implications for chemoprevention
inferredcites →https://doi.org/10.1182/blood.v128.22.5073.5073openalex-snapshot
A Homozygous Germ Line Nonsense Mutation in BRCA1 Leading Fanconi Anemia and Neuroblastoma
inferredcites →https://doi.org/10.1186/1471-2148-14-155openalex-snapshot
Rapid evolution of BRCA1 and BRCA2in humans and other primates
inferredcites →https://doi.org/10.1186/gb-2008-9-9-r142openalex-snapshot
Evolutionary rate and gene expression across different brain regions
inferredcites →https://doi.org/10.1242/dev.033498openalex-snapshot
Brca1 is required for embryonic development of the mouse cerebral cortex to normal size by preventing apoptosis of early neural progenitors
inferredcites →https://doi.org/10.1266/jjg.69.473openalex-snapshot
A possible link between molecular evolution and tissue evolution demonstrated by tissue specific genes.
inferredcites →https://doi.org/10.1371/journal.pbio.0030170openalex-snapshot
A Scan for Positively Selected Genes in the Genomes of Humans and Chimpanzees
inferredcites →https://doi.org/10.1371/journal.pbio.0050013openalex-snapshot
Rate of Evolution in Brain-Expressed Genes in Humans and Other Primates
inferredcites →https://doi.org/10.1371/journal.pone.0013984openalex-snapshot
Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation
inferredcites →https://doi.org/10.1371/journal.pone.0061280openalex-snapshot
Recent Adaptive Events in Human Brain Revealed by Meta-Analysis of Positively Selected Genes
inferredcites →https://doi.org/10.1523/jneurosci.4488-13.2014openalex-snapshot
Cell Type-Specific Expression Analysis to Identify Putative Cellular Mechanisms for Neurogenetic Disorders
inferredcites →https://doi.org/10.18637/jss.v061.i06openalex-snapshot
NbClust : An R Package for Determining the Relevant Number of Clusters in a Data Set
inferredcites →https://doi.org/10.2466/11.it.3.1openalex-snapshot
The Simple Difference Formula: An Approach to Teaching Nonparametric Correlation
inferredcites →https://doi.org/10.3389/fninf.2015.00008openalex-snapshot
NeuroVault.org: a web-based repository for collecting and sharing unthresholded statistical maps of the human brain
inferredcites →https://doi.org/10.3389/fnins.2015.00323openalex-snapshot
A FreeSurfer view of the cortical transcriptome generated from the Allen Human Brain Atlas

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Forkhead Transcription Factors in Health and Disease
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Epigenesis, Synapse Selection, Cultural Imprints, and Human Brain Development
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Reflection on the future of autism research: the neurodiversity hypothesis - Réflexion sur l'avenir de la recherche sur l'autisme : l'hypothèse de la neurodiversité
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