Ancient Humans Had A Lot More DNA Than We Do

Colored dots indicate geographic coordinates of populations sampled. Oceanic populations (purple) retain large duplications that originated in the Denisovan lineage (black), as shown with pie charts. Peter H. Sudmant.
Janet Fang 11 Aug 2015, 18:43

Researchers have analyzed variations in the DNA of hundreds of people living around the planet to see how selection affects the human genome. "The take-home message is that we continue to find a lot more genetic variation between humans than we appreciated previously," University of Washington’s Evan Eichler tells The Scientist. The findings were published in Science last week.

Structural differences called “copy number variants” (CNVs) are when large portions of DNA are duplicated or deleted. Sometimes this involves parts of the genome that contain multiple genes or important regulatory regions. Researchers think that these sorts of changes are under adaptive selection pressures; that is, they’re either surviving preferentially or they’re being eliminated. But these maintaining and eliminating forces within our genomes aren’t well understood. 
 
Now, Eichler and a huge international team analyzed CNVs in the genomes of 236 individuals from 125 populations spanning six continents. They also compared these modern genomes to three ancient human genomes as well as two extinct lineages: Neanderthal and Denisova. This allowed the researchers to reconstruct the structure and content of the ancestral human genome before our species migrated out of Africa. Then, to identify ancestral sequences that may have been lost through deletion, they compared this to chimpanzee and orangutan genomes. The ancestral human genome, they discovered, contains 40.7 million base pairs that aren’t found in today’s human reference genome. (Base pairs are made up of those familiar letters, A, T, G, and C.) As Eichler tells Science News, that’s enough DNA to build a small chromosome. 

People living in Africa today show more evidence of ancestral genome sequences. This is because non-Africans have experienced more population reductions called genetic bottlenecks, which resulted in lower levels of diversity. These same bottleneck events also resulted in fewer deletions compared to African populations.

Additionally, the team identified “admixed” genomes that resulted from interbreeding among archaic human ancestors: Populations in Oceania today (in purple, above) have retained large duplications that originated in the Denisovan lineage (in black). Their findings suggest that while DNA deletions reflect selection, duplications seem to highlight genetic subpopulations. 

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