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Journal Article

The evolution and functional impact of human deletion variants shared with archaic hominin genomes

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http://pubman.mpdl.mpg.de/cone/persons/resource/persons138350

Karakoc,  Emre
Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society;

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Citation

Lin, Y.-L., Pavlidis, P., Karakoc, E., Ajay, J., & Gokcumen, O. (2015). The evolution and functional impact of human deletion variants shared with archaic hominin genomes. Molecular Biology and Evolution, 32(1): msu405v2. doi:10.1093/molbev/msu405.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0024-91EC-C
Abstract
Allele sharing between modern and archaic hominin genomes has been variously interpreted to have originated from ancestral genetic structure or through non-African introgression from archaic hominins. However, evolution of polymorphic human deletions that are shared with archaic hominin genomes have yet to be studied. We identified 427 polymorphic human deletions that are shared with archaic hominin genomes, ~87% of which originated before the Human-Neandertal divergence (ancient) and only ~9% of which have been introgressed from Neandertals (introgressed). Recurrence, incomplete lineage sorting between human and chimp lineages, and hominid-specific insertions constitute the remaining ~4% of allele sharing between humans and archaic hominins. We observed that ancient deletions correspond to more than 13% of all common (>5% allele frequency) deletion variation among modern humans. Our analyses indicate that the genomic landscapes of both ancient and introgressed deletion variants were primarily shaped by purifying selection, eliminating large and exonic variants. We found 17 exonic deletions that are shared with archaic hominin genomes, including those leading to 3 fusion transcripts. The affected genes are involved in metabolism of external and internal compounds, growth and sperm formation, as well as susceptibility to psoriasis and Crohn's disease. Our analyses suggest that these exonic deletion variants have evolved through different adaptive forces, including balancing and population specific positive selection. Our findings reveal that genomic structural variants that are shared between humans and archaic hominin genomes are common among modern humans and can influence biomedically and evolutionarily important phenotypes.