Ancient Dna And The Neanderthal Genome

When the preservation conditions are right, it is possible to extract DNA from ancient—even fossilized—animal and plant remains. Cold dry environments or wet anaerobic ones are usually the best for preserving ancient DNA, or aDNA.

Because the survival of old molecules of DNA is rare, and because those that survive actually degrade over time, there is a general rule that specimens older than 100,000 years old are not viable candidates for aDNA extraction. (A potential exception maybe 400,000-year-old plants frozen in Siberian ice that may have preserved aDNA.)

Degraded aDNA sequences can be compared to closely related modern species to correct for sequencing errors that occur when nucleotides degrade to "look" like different nucleotides. Cloning an organism from aDNA to bring it to life could only be possible if the entire DNA is preserved and the chances of this occurring are very slim.

So far aDNA has been extracted from at least six Neanderthals (from Germany, Croatia, Georgia, Belgium, France, and Spain) and at least five modern human fossils (from Czech Republic, France, and Italy). MtDNA is useful for aDNA studies because there are thousands of mitochondria containing mtDNA in a cell as opposed to just one nucleus with DNA per cell. After degradation, mtDNA has a much better chance at preserving than nuclear DNA. Small portions of the bones or teeth must be drilled out and ground up in order to be analyzed, but fortunately casting technology is at the point where high-quality replicas of the specimens can be crafted prior to aDNA extraction. It is a destructive process so paleoanthropologists are constantly weighing the merits of preserving the fossils and their morphology on one hand versus extracting the precious genetic information they possess.

ANCIENt DNA MEthODs

Before aDNA can be sequenced it must be cloned and amplified using a technique called PCR (polymerase chain reaction), which is the same technique used in paternity testing. Thousands of copies of the aDNA are needed to perform the laboratory techniques used in sequencing and PCR provides those copies. All aDNA analyses must take place in a physically isolated work area to avoid human contamination, which can result in the amplification of DNA that is not the aDNA being investigated. In order to detect sparse aDNA, multiple extractions from the fossil and multiple PCR procedures must be performed. An act as simple as handling a fossil without gloves can contaminate a specimen, so aDNA analyses of fossils that have been handled for many years in museum collections are treated with extra care. Because of all the chances for human contamination and because it may be very difficult to determine whether or not the aDNA or the geneticist's DNA is being amplified and sequenced, extra precautions are necessary. For instance, results should be repeatable from the same, and different aDNA extractions of a fossil specimen and separate samples of a specimen should be extracted and sequenced in independent laboratories.

Based on ancient mtDNA analyses we know that Neanderthals are three to four times more different from modern humans than modern humans are from one another. Plus, the genetic variation between Neanderthals and modern humans is much greater than that within modern humans alone. The variation among Neanderthal aDNA from fossils at distant sites is similar to that among modern human populations.

Neanderthals fall between chimps and humans and outside living and fossil modern human range. Based on molecular clock rates of mito-chondrial aDNA, the Neanderthal lineage diverged about 500 Kya from the lineage that led to modern humans. Neanderthals, according to their genes, are distinct from modern humans and they are not more closely related to modern Europeans than any other modern human (which is a strike against the Multiregional hypothesis for human origins, see Chapter 6). It is therefore unlikely we are descended from Neanderthals and unlikely we shared genes with them (i.e., interbred with them). We should probably consider Neanderthals our distant cousins.

Methods of aDNA analysis have advanced far enough to allow scientists, like Svante Paabo, to extract nuclear DNA from Neanderthals. With enough aDNA from enough specimens, eventually large portions of the Neanderthal genome will be reconstructed. So far, the 38 Kya male found in Vindija Cave, Croatia, produced a sequence of around a million base pairs of nuclear DNA, which is around 0.03 percent of the genome.

With nuclear DNA, the functional genes and the sex chromosomes can be analyzed. So for instance, the Y chromosome of Neanderthals is vastly different from those of humans and chimpanzees compared to other chromosomes, suggesting that little interbreeding occurred at least by the latest Neanderthal times.

Neanderthals share an estimated 99.5 percent of their genome with humans, but humans are only 0.1 percent different from each other. So since variation does not overlap, the separate species designation of Neanderthals and humans is supported. Like the mtDNA studies, the nuclear genome of Neanderthals shares no derived alleles that are special to European populations, meaning that Neanderthals did not contribute to European human evolution.

It will soon be possible to study functional and diseased genes in the extinct species. It will also be possible to test whether Neanderthals contributed to the human genome as some scientists have hypothesized is the case with the microcephalin gene (see Chapter 5).

The most promising aspect of the Neanderthal genome project is the opportunity to look for special genes in the human genome for language and art—traits and behaviors that are unique to humans and are not always considered to have existed in Neanderthals. Candidates for these genes would be those shared by chimpanzees and Neanderthals to the exclusion of humans. What's more, genes that are shared by Neanderthals and modern humans, but not chimpanzees, may point to genetic changes that occurred earlier in hominin evolution.

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