Developmental Loci Harbor Clusters of Accelerated Regions That Evolved Independently in Ape Lineages
| Autor: | Alisha K. Holloway, Katherine S. Pollard, Dennis Kostka |
|---|---|
| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
primates Gene Conversion Gorilla biased gene conversion Human accelerated regions Genome Evolution Molecular 03 medical and health sciences positive selection biology.animal Genetics Animals Humans Computer Simulation Gene conversion Selection Genetic Enhancer development Molecular Biology Gene Discoveries Ecology Evolution Behavior and Systematics Regulator gene Models Genetic biology Hominidae likelihood ratio test 030104 developmental biology Evolutionary biology Human genome enhancer Algorithms |
| Zdroj: | Molecular Biology and Evolution |
| ISSN: | 1537-1719 0737-4038 |
| DOI: | 10.1093/molbev/msy109 |
| Popis: | Some of the fastest evolving regions of the human genome are conserved noncoding elements with many human-specific DNA substitutions. These human accelerated regions (HARs) are enriched nearby regulatory genes, and several HARs function as developmental enhancers. To investigate if this evolutionary signature is unique to humans, we quantified evidence of accelerated substitutions in conserved genomic elements across multiple lineages and applied this approach simultaneously to the genomes of five apes: human, chimpanzee, gorilla, orangutan, and gibbon. We find roughly similar numbers and genomic distributions of lineage-specific accelerated regions (linARs) in all five apes. In particular, apes share an enrichment of linARs in regulatory DNA nearby genes involved in development, especially transcription factors and other regulators. Many developmental loci harbor clusters of nonoverlapping linARs from multiple apes, suggesting that accelerated evolution in each species affected distinct regulatory elements that control a shared set of developmental pathways. Our statistical tests distinguish between GC-biased and unbiased accelerated substitution rates, allowing us to quantify the roles of different evolutionary forces in creating linARs. We find evidence of GC-biased gene conversion in each ape, but unbiased acceleration consistent with positive selection or loss of constraint is more common in all five lineages. It therefore appears that similar evolutionary processes created independent accelerated regions in the genomes of different apes, and that these lineage-specific changes to conserved noncoding sequences may have differentially altered expression of a core set of developmental genes across ape evolution. |
| Databáze: | OpenAIRE |
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