Recent adaptive events in human brain revealed by meta-analysis of positively selected genes

PLoS One. 2013 Apr 9;8(4):e61280. doi: 10.1371/journal.pone.0061280. Print 2013.


Background and objectives: Analysis of positively-selected genes can help us understand how human evolved, especially the evolution of highly developed cognitive functions. However, previous works have reached conflicting conclusions regarding whether human neuronal genes are over-represented among genes under positive selection.

Methods and results: We divided positively-selected genes into four groups according to the identification approaches, compiling a comprehensive list from 27 previous studies. We showed that genes that are highly expressed in the central nervous system are enriched in recent positive selection events in human history identified by intra-species genomic scan, especially in brain regions related to cognitive functions. This pattern holds when different datasets, parameters and analysis pipelines were used. Functional category enrichment analysis supported these findings, showing that synapse-related functions are enriched in genes under recent positive selection. In contrast, immune-related functions, for instance, are enriched in genes under ancient positive selection revealed by inter-species coding region comparison. We further demonstrated that most of these patterns still hold even after controlling for genomic characteristics that might bias genome-wide identification of positively-selected genes including gene length, gene density, GC composition, and intensity of negative selection.

Conclusion: Our rigorous analysis resolved previous conflicting conclusions and revealed recent adaptation of human brain functions.

Publication types

  • Meta-Analysis
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptation, Biological / genetics*
  • Brain / physiology*
  • Computational Biology
  • Databases, Nucleic Acid
  • Gene Expression Profiling
  • Gene Expression Regulation
  • Genomics
  • Humans
  • Molecular Sequence Annotation
  • Organ Specificity / genetics
  • Selection, Genetic*

Grant support

Funding was provided by the "National Outstanding Young Investigator" award from the Natural Science Foundation of China (31025014) and Johnson and Johnson (scholarship). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.