Biology

Neanderthal and unknown human ancestor DNA found in the "dark heart" of chromosomes

Neanderthal and unknown human ...
Geneticists have discovered some of the most ancient pieces of human DNA hiding in the centromere, the middle section of the chromosome
Geneticists have discovered some of the most ancient pieces of human DNA hiding in the centromere, the middle section of the chromosome
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Geneticists have discovered some of the most ancient pieces of human DNA hiding in the centromere, the middle section of the chromosome
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Geneticists have discovered some of the most ancient pieces of human DNA hiding in the centromere, the middle section of the chromosome

Genes get shuffled and re-dealt with every new generation, meaning many are relatively recent. But while exploring the "dark heart" of the human genome, geneticists have now found some of the most ancient pieces of DNA, inherited from Neanderthals and an as-yet-unknown human relative, which may be affecting our sense of smell to this day.

Although the human genome was fully sequenced in 2003, we still don't understand what everything in there does. One particular dark spot is the centromere – the skinny bit in the middle of the chromosome's X or Y shape – which is full of repeating sequences.

This difficult-to-decipher region could be hiding some of the most ancient sections of human DNA, giving new evolutionary clues to where specific traits came from. That's because the centromere stays more intact through the generations, as opposed to DNA further down the "arms" of the chromosomes which is split and shuffled when forming sperm or eggs.

Researchers from the University of California Davis, the University of California Santa Cruz and Berkeley Lab set out to map the haplotypes – clusters of genes that are usually inherited as a group – located in the centromere. To find out if it was even possible to identify these, they examined the genome of fruit flies, in search of changes to a single DNA letter. Sure enough, they managed to spot these centromeric haplotypes (cenhaps) in fruit fly DNA.

Next, they brought the search over to the human genome, scouring through the 1000 Genomes Project, which is an open database of different genomes designed to showcase human genetic variation. The team examined the centromere sequences in this data, and found haplotypes in the hearts of all the chromosomes on show.

And they uncovered some fascinating clues hiding in there, with some haplotypes dating back half a million years. One of the oldest lineages was found to be absent on the genomes of people descended from a more recent emigration of humans out of Africa.

The centromere of chromosome 11 was particularly interesting. Non-African genomes were found to house very different haplotypes of Neanderthal DNA, which appeared to have diverged as long as a million years ago. And it seems that these Neanderthals are still influencing our senses of smell and taste today – about 34 of our 400 genes related to odorant receptors were found within the chromosome 11 cenhap. Exactly what effects the differences in these genes may have is still unclear, but the link is there.

Perhaps more mysterious is what was found in the centromere of chromosome 12. The team discovered gene sequences that seem to be inherited from even older, more primitive human relatives that remain unknown to science. While we have plenty of evidence of interbreeding between hominin species like modern humans, Neanderthals and Denisovans, there are others that we apparently haven't discovered yet, like the "ghost species" that turned up during studies into human saliva proteins.

Further research will help fill out our understanding of human evolutionary history, as well as diseases like cancer that spring from cell division gone wrong.

The study was published in the journal eLife.

Source: UC Davis

7 comments
Wolf0579
I find this highly interesting as it seems large primates also communicate with odors... so scent perception would be required to receive these scent messages. This is particularly interesting when applied to the Sasquatch, which also seems to be able to generate a variety of different odors according to credible witnesses. Another interesting facet of this story is the unknown ancestor. Almost all of the genetic samples known to be from Sasquatch, when tested, show results consistent with heavy human "contamination". Some of these samples were collected by people with medical backgrounds, who used sterile gloves, and anti-contamination procedures when collecting these samples. I'm wondering if Sasquatch doesn't have a human ancestor somewhere back up the time line.
amazed W1
Does this finding suggest why species undergo such radical and swift changes during times of stress? It looks as if only what were described as the outer parts of the genome need to change to cause quite radical differences in the new being, and over a relatively small number of generations.... Sub question, does this also explain why mammals but only a few dinosaurs survived whatever it was that destroyed the rest? Does the incomplete dinosaur DNA that we were told had been extracted, or even bird DNA use less of these outer parts in their genome and so restrict the speed of change?
BlueCat49
Scientists continue to be amazed at all this stuff because they start with false assumptions. Until a few years ago most DNA was "junk". Now there is so MUCH DNA they don't have a clue what to think and their assumptions are no help. Time to rethink their most BASIC assumptions.
ljaques
Yesterday's junk genes are today's unknown early investors. Is it any wonder CRISPR had failed so miserably in splicing? (or why this terrifies most of the public to let people try this) P.S: Stop calling Chewbacca's people "Sasquatch. They're wookies, and most are hermitic by nature. Leave them alone.
Hildie
Little by little we are going to discover that we are the Neanderthals! Well not really, but at least we are going to discover that they did not go extinct by any other reason than breeding. A small number of Neanderthal breeding with a greater number of Homo Sapiens got assimilated into the greater population. In South America except the high Andes or the Amazon there is almost not "pure blood" indigenous population due to mixing with Europeans. The population of indigenous males was decimated by wars or hard work, then indigenous female mixed with Europeans immigrants. sciencemag.org/news/2015/11/inca-child-mummy-reveals-lost-genetic-history-south-america
Kpar
Bluecat49 has an excellent point. Quite recently, this talk of "junk" DNA (comprising almost 95% of human DNA) has been replaced by talk of the relatively new science of "epigenetics", which finds functionality of the so-called "junk" DNA- particularly as it controls protein folding, and influenced by environmental factors. And Wolf0579? Where are the genetic samples "known" to be from Sasquatch? Inquiring minds want to know...
RangerJones
IOW the more we know, the less we know. Perhaps there is nothing to know...Possibly it has all been wrong...Probably we will never know.