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Genetics, Population

Gene deletions, duplications reveal our genetic storyline

By looking closely at DNA variation across a vast number of populations, researchers now have a better idea of how selection affects the human genome around the globe.

Counterclockwise from the top: The geographic coordinates of populations sampled are indicated on a world map (colored dots). The pie charts show the continental population allele frequency of a single ~225 kbp duplication polymorphism found exclusively among Oceanic populations and an archaic Denisova. The ancestral structure of this duplication locus (1) and the Denisova duplication structure (2) are shown in relation to their position on chromosome 16. We estimate that the duplication emerged ~440 thousand years ago (kya) in the Denisova and then introgressed into ancestral Papuan populations ~40 kya. Credit: Peter H. Sudmant

Counterclockwise from the top: The geographic coordinates of populations sampled are indicated on a world map (colored dots). The pie charts show the continental population allele frequency of a single ~225 kbp duplication polymorphism found exclusively among Oceanic populations and an archaic Denisova. The ancestral structure of this duplication locus (1) and the Denisova duplication structure (2) are shown in relation to their position on chromosome 16. We estimate that the duplication emerged ~440 thousand years ago (kya) in the Denisova and then introgressed into ancestral Papuan populations ~40 kya.
Credit: Peter H. Sudmant

Copy number variation is the structural difference between genomes when large portions of DNA are duplicated or deleted. It can involve genomic regions containing multiple genes or important regulatory regions. Because of this, it has been hypothesized that such changes are under selection (preferenntially surviving, or being eliminated), but the forces eliminating or maintaining them within our genomes have not been well understood.

To gain a better understanding of these patterns globally, Peter Sudmant and colleagues analyzed copy number variation across 236 individual genomes from 125 human populations.

Through this analysis, the researchers were able to identify patterns of ancestry as well as the maintenance of admixed genomes resulting from interbreeding of archaic hominids; Oceanic populations retain large duplications that originated in the Denisovan lineage. As expected, Africans were more likely to show evidence of ancestral genome sequences compared to non-African populations, as the latter have experienced more population bottlenecks, resulting in lower levels of diversity. These bottleneck events for non-African populations have also resulted in fewer deletions compared to African populations.

Surprisingly, the results suggest that DNA deletions are more reflective of selection, whereas duplications better highlight genetic subpopulations. This variation in our genomes tells a fascinating story of human movement and colonization around the world, and the demographic and selective pressures humans have faced over generations.

Reference: P. H. Sudmant, S. Mallick, B. J. Nelson, F. Hormozdiari, N. Krumm, J. Huddleston, B. P. Coe, C. Baker, S. Nordenfelt, M. Bamshad, L. B. Jorde, O. L. Posukh, H. Sahakyan, W. S. Watkins, L. Yepiskoposyan, M. S. Abdullah, C. M. Bravi, C. Capelli, T. Hervig, J. T. S. Wee, C. Tyler-Smith, G. van Driem, I. G. Romero, A. R. Jha, S. Karachanak-Yankova, D. Toncheva, D. Comas, B. Henn, T. Kivisild, A. Ruiz-Linares, A. Sajantila, E. Metspalu, J. Parik, R. Villems, E. B. Starikovskaya, G. Ayodo, C. M. Beall, A. Di Rienzo, M. Hammer, R. Khusainova, E. Khusnutdinova, W. Klitz, C. Winkler, D. Labuda, M. Metspalu, S. A. Tishkoff, S. Dryomov, R. Sukernik, N. Patterson, D. Reich, E. E. Eichler. Global diversity, population stratification, and selection of human copy number variation. Science, 2015; DOI: 10.1126/science.aab3761

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