Most of us, non-Africans, carry tiny snippets of Neanderthal DNA inside of us, as part of our genome. This is because our ancestors had sex with Neanderthals as they moved across Eurasia, the children born from this admixture carried both Homo sapiens and Neanderthal DNA. Selection weeded out the nasty genes and dilution after countless generations of intra-human breeding watered down the Neanderthal DNA in our genomes, but we still carry roughly 1 to 3% of their DNA in us.
Humans also interbred with the mysterious Denisovans (in Asia), and Melanesians carry roughly 3 to 5% Denisovan DNA with them.
A paper by Ping Hsun Hsieh et al. published today, (Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes Science - 18 Oct 2019 Vol. 366, Issue 6463, eaax2083 DOI: 10.1126/science.aax2083) took a closer look at this admixture in Melanesians.
We usually carry small snippets of archaic DNA, moswt of these are merely single nucleotide changes, which is a switch in a "letter" of our genetic code, where one molecule (nucleotides are molecules that contain a phosphate group, a sugar group and a nitrogen base) changes for another, for instance an adenine nucleotide (A) changes for a thymine nucleotide (T) altering the genetic sequence.
These single nucleotide changes don't have much of an evolutionary impact, they are therefore immune to selection.
This paper looked for more significant changes: deletions and duplications, formally known as "Copy Number Variants" or CNVs.
And they found that Melanesians carry long strands of archaic DNA in their genes.
The images below are from the paper:
Deletions are parts of a DNA molecule that have been lost during replication. In general deletions are more deleterious than duplications.
Duplications are sections of DNA that are duplicated, as if they were copied and pasted. They are four times more common than deletions. They can be pasted adjacent to the original chunk, and this is known as "tandem duplication" -which are quite rare in humans- or somewhere else ("displaced duplication").
A duplicated section of DNA will of course be passed on to the descent of the mutant carrying it, and will be subjected to the forces of natural selection. If the mutation is beneficial, it will be conserved, but if it alters the metabolism of the person carrying it, selection will weed it out (the person may die or not have viable offspring).
This paper reported 37 CNVs in Melanesians, of which 19 came from Neanderthals and Denisovans. For instance two large chunks of archaich DNA: in chromosome 8, which came from Neanderthals, and in chromosome 16, inherited from Denisovans.
- Chr. 8: Neanderthal with a duplication (38,000 base pairs -bp- long, carried by 44% of Melanesians), and a deletion (6,000 bp long.
- Chr. 16: Denisovan, with two duplications. The first is 380,000 bp long and is found in 79% of the Melanesians that were sampled.
As a point of interest, the first Denisovan duplication lies next to DNA sequences linked to autism (Chromosome 16p11.2 critical region, are associated to roughly 1% of human autism cases).
Also, related to autism, is the region in chromosome 8 (8p21.3) affected by the Neanderthal CNVs. (see more).
The fact that these CNVs have survived tens of thousands of years means that they have contributed some positive trait, that helped those carrying it survive beter than those lacking it. Selective pressure therefore retained these changes as they provided an advantage to the "mutants".
As the paper is behind a paywall I have not been able to read the particulars, but I wonder why do Melanesians carry such large snippets of archaic DNA? Do we all carry long snippets of Neanderthal DNA and it hasn't yet been detected in Eurasians because nobody has looked for it or, on the other hand we don't carry any?
Did Melanesia have specific conditions that favored keeping these duplications while the rest of the world didn't? (certain diseases for instance which can be averted thanks to these CNVs).
The medical significance of these mutations will have to be investigated.
One of the images from the paper suggest that these particular mutations are very rare among non-Melanesians:
The CNVs had first been studied in a paper Global diversity, population stratification, and selection of human copy-number variation, by Peter H. Sudmant et al., (2015) published in Science 11 Sep 2015: Vol. 349, Issue 6253, aab3761 DOI: 10.1126/science.aab3761. It too noticed the high level of Denisovan CNVs, in Melanesians, but not in Australian Aboriginals. They calculated its origin 440 kya among the Denisovans. They mention a chr 16 duplicaton:
"a duplication polymorphism restricted to modern Oceanic populations yet also present in the genome of the archaic Denisova hominin. This 225–kilo–base pair (kbp) duplication includes two microRNA genes and is almost fixed among human Papuan-Bougainville genomes".
This paper (Sudmat el al.,) also studied CNVs among modern humans and were surprised to find that when comparing the difference between Africans and non-Africans regarding deletions and duplications using a parameter they named "Deletion load", "... Africans exhibited an apparent higher deletion load than non-African populations ... Duplications showed no such effect."
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