Neanderthal DNA extraction

Modern human DNA reveals all sorts of unsuspected data: for example that humans are more closely related to mushrooms than sunflowers. Analysis of DNA of humans and mushrooms indicated the two groups split about 1.5 billion years ago. The split between humans and flowers was before that.

Elizabeth Kolbert wrote in The New Yorker: “DNA is often compared to a text, a comparison that’s apt as long as the definition of “text” encompasses writing that doesn’t make sense. DNA consists of molecules known as nucleotides knit together in the shape of a ladder—the famous double helix. Each nucleotide contains one of four bases: adenine, thymine, guanine, and cytosine, which are designated by the letters A, T, G, and C, so that a stretch of the human genome might be represented as ACCTCCTCTAATGTCA. (This is an actual sequence, from chromosome 10; the comparable sequence in an elephant is ACCTCCCCTAATGTCA.) The human genome is three billion bases—or, really, base pairs—long. As far as can be determined, most of it is junk. “Your mother and I are separating because I want what’s best for the country and your mother doesn’t.” [Source: Elizabeth Kolbert, The New Yorker, August 15, 2011 ]

“With the exception of red blood cells, every cell in an organism contains a complete copy of its DNA. It also contains many copies—hundreds to thousands—of an abridged form of DNA known as mitochondrial DNA, or mtDNA. But as soon as the organism dies the long chains of nucleotides begin to break down. Much of the damage is done in the first few hours, by enzymes inside the creature’s own body. After a while, all that remains is snippets, and after a longer while—how long seems to depend on the conditions of decomposition—these snippets, too, disintegrate. “Maybe in the permafrost you could go back five hundred thousand years,” geneticist Svante Pääbo, of the Max Planck Institute for Evolutionary Anthropology. “But it’s certainly on this side of a million.” Five hundred thousand years ago, the dinosaurs had been dead for more than sixty-four million years, so the whole “Jurassic Park” fantasy is, sadly, just that. On the other hand, five hundred thousand years ago modern humans did not yet exist.

Maddie Burakoff and Laura Ungar of Associated Press wrote: Many are hopeful that as DNA technology keeps advancing, we’ll be able to push further into the past and get ancient genomes from more parts of the world, adding more brushstrokes to our picture of human history. Because even though we were the only ones to survive, the other extinct groups played a key role in our history, and our present. They are part of a common humanity connecting every person, said Mary Prendergast, a Rice University archeologist. “If you look at the fossil record, the archeological record, the genetic record," she said, "you see that we share far more in common than what divides us.” [Source: Maddie Burakoff and Laura Ungar, Associated Press, September 24, 2023]

Websites and Resources on Hominins and Human Origins: Smithsonian Human Origins Program ; Institute of Human Origins ; Becoming Human University of Arizona site ; Hall of Human Origins American Museum of Natural History ; The Bradshaw Foundation ; Britannica Human Evolution ; Human Evolution ; University of California Museum of Anthropology; John Hawks' Anthropology Weblog ; New Scientist: Human Evolution; Archaeology Archaeology News Report ; : ; Archaeology in Europe ; Archaeology magazine ; HeritageDaily; Livescience

Book: “Human Origins: What Bones and Genomes Tell Us About Ourselves” by Rib DeSakke and Ian Tattersal (2008, Texas A&M University Press)

Human Genome

most of what we now about Denisovans comes from DNA extracted from this tooth

The human genetic code, or genome, is the blueprint of humankind that contains all the genetic codes to reproduce more humans. It is comprised of billions of sub-units call nucleotides, repeated in long, linear code that contain biological information on things like skin color, hair type, eye color, the ability to metabolize milk, facial features, brain structure and a host of things scientists have yet to figure out. Individuals get their DNA from their parents and they from their parents and so on to the beginning of the creation of life. Modern humans have DNA that can be traced back to ancestors that were early hominins, apes, mammals, reptiles, fish, and even plankton and bacteria.

The sequencing of human genome was completed in 2003. It found around 23,000 protein-coding genes in the human body (it was originally thought there were more than 100,000 and further studies may reduce the number to below 19,000). The relatively small number of genes has led scientists to look beyond them to amino acids sequences and the molecular switches that tell genes when to turn off and on to determine how human characteristics are constructed. Base pairs — the “letters” of the genetic alphabet — are the components of the genes behind mutations. There are 3 billion base pairs in the human genome.

The current conservative estimate is that about 10 percent of the human genome has underdone “positive selections” since modern humans emerged about 200,000 years ago. Scientists estimate that it takes about 200 generations for a specific “natural selection” to emerge from a mutation spread to a wide enough population to reveal itself. The rough genome of chimpanzees was completed in 2005, allowing comparison between humans and chimps.

Development of Ancient DNA Research

Andrew Curry wrote in National Geographic: In 2010, geneticists in Denmark passed a remarkable milestone. Extracting fragments of DNA from 4,000-year-old strands of hair from Greenland that had been stored in a Copenhagen museum for decades, they reconstructed the first complete ancient human genome. The study was the culmination of decades of work by researchers around the world, beginning with faltering attempts to get genetic material from Egyptian mummies in the 1980s. As recently as 2013, the number of ancient human genomes could still be counted on two hands. In the last five years, the numbers have increased exponentially: In April 2023, the 10,000th ancient human genome was published, with thousands more on their way. [Source: Andrew Curry, National Geographic, September 12, 2023]

The remarkable growth of ancient DNA research—the focus of an entirely new discipline called paleogenomics—may be the biggest thing to hit archaeology since the development of radiocarbon dating in the 1950s. Last year, pioneering researcher Svante Pääbo, a geneticist at the Max Planck Institute for Human Evolution in Leipzig, Germany, won a Nobel Prize for his work on the genes of extinct Neanderthals. Now, ancient DNA has become a tool to better understand where we came from—and a way to glimpse where we’re going.

To recover ancient DNA from ancient samples, researchers take a tiny bit of bone, tooth or hair from a skeleton using a dentist’s drill or similar tool and extract DNA fragments from them. By duplicating the DNA fragments multiple times and then using computers to match and reassemble the tiny strands, as if in a billion-piece puzzle, geneticists can reconstruct entire genomes.

The process took decades to perfect. The first attempts to get DNA from ancient bones in the 1980s were plagued by problems. The biggest was contamination: Every living organism has DNA, and early research struggled to separate ancient genetic material from modern DNA. Samples could be tainted by anything from soil bacteria that infiltrates buried bones to a lab technician’s stray dandruff. Early claims that dinosaur DNA could be recovered from Cretaceous-era amber proved to be overly optimistic, for example, and mostly the result of contamination—putting the entire field in doubt.

Pääbo and others persisted, developing ways to eliminate contamination and prove the DNA they were looking at indeed belonged to ancient specimens. As a result, today ancient DNA samples are taken under tightly controlled conditions, in clean rooms flooded with ultraviolet light, which is capable of destroying bacteria and their DNA. Results are compared to databases of DNA from modern species or other ancient samples, helping sort and isolate the genetic material from different sources.

Early on, the procedures were also wildly expensive—far more than most archaeologists and paleontologists could afford. But as costs have dropped and the number of samples increased, the method has become a powerful tool for understanding the past. Ancient DNA studies are shifting from headline-grabbing one-offs to a standard part of the archaeologist’s toolkit. That’s already led to better understandings of ancient migrations and how societies functioned in the distant past.

Information Derived from DNA

Clues about our genetic past are often unraveled using markers — tiny changes in our genetic code that occur infrequently but are copied and passed down in our DNA — which are use to unite and separate groups. If you share a marker with someone then you have a common ancestor with him or her sometime in the past. Carl Zimmer wrote in National Geographic: “A Human and a grain of rice may not, at first glance, look like cousins. And yet we share a quarter of our genes with that fine plant. The genes we share with rice—or rhinos or reef coral—are among the most striking signs of our common heritage. All animals, plants, and fungi share an ancestor that lived about 1.6 billion years ago. Every lineage that descended from that progenitor retains parts of its original genome, embodying one of evolution’s key principles: If it’s not broke, don’t fix it. Since evolution has conserved so many genes, exploring the genomes of other species can shed light on genes involved in human biology and disease. Even yeast has something to tell us about ourselves. [Source: Carl Zimmer, National Geographic, July 2013 ||+||]

“Of course, we aren’t really much like yeast at all. The genes we still share we use differently, in the same way you can use a clarinet to play the music of Mozart or Benny Goodman. And our catalogs of genes themselves have changed. Genes can disappear, and new ones can arise from mutations in DNA that previously served some other function or no function at all. Other novel genes have been delivered into our genomes by invading viruses. It’s hardly surprising that we share many more genes with chimpanzees than with yeast, because we’ve shared most of our evolutionary journey with those apes. And in the small portion of our genes with no counterpart in chimpanzees, we may be able to find additional clues to what makes us uniquely human.” ||+||

Andrew Curry wrote in National Geographic: By comparing the DNA of people buried in different time periods but the same geographic region, for example, geneticists and archaeologists can identify shifting populations. Dozens of studies in the last decade from all around the world show that migration and movement have always been part of the human story. We now know that Europe’s population has been dynamic for many millennia, with dramatically different populations entering the continent, mixing and mingling multiple times since the first modern humans arrived around 50,000 years ago. And ancient DNA has helped show when the first people arrived in the Americas and link them to ancestral populations in Asia. [Source: Andrew Curry, National Geographic, September 12, 2023]

Some discoveries go even further back. By comparing Neanderthal DNA to that of modern people, for instance, Pääbo and his team were able to show modern Europeans and Asians get a small fraction—up to 5 percent—of their ancestry from Neanderthals, suggesting that our distant ancestors encountered and mated with Neanderthals at some point in the distant past. DNA even makes it possible to figure out when: The genes of people in sub-Saharan Africa today contain no Neanderthal DNA. That suggests modern humans met our Neanderthal cousins after migrating out of Africa 50,000 years ago.

Ancient DNA has even revealed the existence of entirely new species of human ancestors. In 2008, archaeologists recovered a fragment of knuckle bone from a cave in western Siberia. They estimated it was more than 50,000 years old, but the fragment was too small to say much more using traditional archaeological methods. Thanks to cool conditions in the Siberian cave, researchers were able to extract DNA from the bone—revealing it was neither Neanderthal nor modern human, but something else entirely: a previously unknown ancestral human species now referred to as Denisovans, after the cave in which their remains were initially discovered. Human DNA is just the tip of the iceberg. The same techniques used to investigate long-gone humans have also allowed researchers to sequence the DNA of extinct species. The genes of wooly mammoths, cave bears and dodo birds have offering unprecedented glimpses into the past—and a better understanding of the biology of their living relatives.

Meanwhile millennia-old bacterial DNA make it possible to track the origins and evolution of diseases like tuberculosis and yersinia pestis, better known as the Black Plague. And scientists have isolated and identified bacteria trapped in plaque on the teeth of ancient skeletons, showing what people ate, what diseases they had, and how the modern microbiome differs from that of our ancestors.

DNA Studies

Robin McKie wrote in The Guardian: “Ancient DNA studies are overturning our oversimplified vision of our past and are the outcome of a late 20th-century revolution in molecular biology that gave scientists the power to study DNA, the material from which our genes are made, with startling precision. For the first time, the exact structure and makeup of a gene could be determined and the detailed origins of many inherited illnesses and cancers outlined, setting in motion the slow, ongoing task of developing new treatments. [Source: Robin McKie, The Guardian, April 7, 2018]

“By contrast, the study of ancient DNA, which uses the same basic technology, began late but has since flowered far more dramatically. “It is in the area of shedding light on human migrations – rather than in explaining human biology – that the genome revolution has been a runaway success,” says Harvard geneticist David Reich. The field’s hesitant start is understandable. In samples from living animals, DNA exists in long, healthy, easily analysed strands. However, DNA starts to decay the moment an organism dies and those strands quickly fragment. And the longer the passage of time, the shorter the fragments become.

“Nevertheless, scientists have persevered and in 2007, Pääbo decided to assemble a team of experts to sequence a Neanderthal genome that would be billions of DNA units in length. Reich, an innovator in the field of studying population mixtures, was asked to join and has since played a key role in the fledgling field’s remarkable development. |=|

chimpanzee chromosones

“Clean rooms were built, advanced gene sequencers purchased and DNA extracted from Neanderthal bones that had been found in Vindija cave in Croatia. A Neanderthal genome was slowly spliced together from pieces of DNA only a few dozen units in length. It was a brilliant achievement though Reich makes clear progress was halting. “The Neanderthal sequences we were working with had a mistake approximately every 200 DNA letters,” he reveals in his book. |=|

“These errors were not due to differences between humans and Neanderthals, it should be pointed out, but to errors made in analysing DNA. It was Reich’s task to get round these problems and help create a meaningful genome of a Neanderthal. From that, scientists could assess just how closely we were related to these ancient people. His tests succeeded and subsequently showed, to everyone’s surprise, that many modern humans carry small amounts of Neanderthal DNA in their genomes. “Non-African genomes today are around 1.5 to 2.1 percent Neanderthal in origin,” he says.” |=|

““There’s nothing unique about most of science,” Ed Green, a professor of biomolecular engineering at the University of California at Santa Cruz who works on the Neanderthal Genome Project, said. “If you don’t do it, somebody else is going to do it a few months later. Svante is one of the rare people in science for whom that is not true. There wouldn’t even be a field of ancient DNA as we know it without him. It’s a nice rarity in science when people take not only unique but also productive paths,” Craig Venter, who led a rival effort to the Human Genome Project, told me. “And Svante has clearly done both. I have immense respect for him and what he’s done.”

Book: “Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past” by David Reich, Oxford University Press 2018.

Problems with Studying DNA

Maddie Burakoff and Laura Ungar of Associated Press wrote: Scientists can’t get useful genetic information out of every fossil they find, especially if it’s really old or in the wrong climate. They haven't been able to gather much ancient DNA from Africa, where Homo sapiens first evolved, because it has been degraded by heat and moisture. [Source: Maddie Burakoff and Laura Ungar, Associated Press, September 24, 2023]

One obstacle that had to be overcome in the examination of DNA from ancient samples is the fact that DNA degrades over time, breaking down into pieces or disintegrating completely. In recent years, using a technique called polymerase chain reaction (PCR), researchers have been able to “unzip” minute fragments of surviving DNA and duplicate them millions of times until they have a sample large enough to test. Then, by comparing differences between ancient material and modern samples of known provenance they can analyze a long-extinct animal’s genome.

Monte Morin wrote in the Los Angeles Times: “Ancient genetic information has been extremely difficult to sequence, for at least two reasons. First, DNA strands disintegrate into smaller and smaller pieces over time, making it tricky to determine their original order. The second issue is one of contamination. DNA from archaeologists and lab workers can get mixed up with the sample, confusing analysis. Older DNA samples have been obtained for other animals — scientists recently sequenced the genome of a 700,000-year-old horse — but those specimens are usually found in permafrost conditions, far from early human remains.” [Source: Monte Morin, Los Angeles Times, December 6, 2013]

Robin McKie wrote in The Guardian: “This disintegration poses problems. If, for example, you want to study Neanderthals, who dominated Europe for around 400,000 years and who were close in evolutionary terms to Homo sapiens, DNA from their fossils is going to be in minuscule pieces. The last member of this doomed species died more than 40,000 years ago, after all. Genetic material taken from Neanderthal fossils is also likely to be contaminated with large amounts of DNA from bacteria and vegetation – and sometimes from researchers. Trying to create a genome from these sullied scraps has been likened, by writer Elizabeth Kolbert, to reassembling “a Manhattan telephone book from pages that have been put through a shredder, mixed with yesterday’s trash and left to rot in a landfill”. [Source: Robin McKie, The Guardian, April 7, 2018]

DNA Contamination Issue

Pääbo Svante is the man credited with using genetics to glean information from the distant past Elizabeth Kolbert wrote in The New Yorker: “When Pääbo arrived in California, he was still interested in finding a way to use genetics to study human history. He’d discovered, however, a big problem with trying to locate fragments of ancient Egyptian DNA: they look an awful lot like—indeed, identical to—fragments of contemporary human DNA. Thus a single microscopic particle of his own skin, or of someone else’s, even some long-dead museum curator’s, could nullify months of work. [Source: Elizabeth Kolbert, The New Yorker, August 15, 2011 ]

““It became clear that human contamination was a huge problem,” he explained. (Eventually, Pääbo concluded that the sequences he had obtained for his original mummy paper had probably been corrupted in this way.) As a sort of warmup exercise, he began working on extinct animals. He analyzed scraps of mtDNA from giant ground sloths, which disappeared about twelve thousand years ago, and from mammoths, which vanished around the same time, and from Tasmanian tigers, which were hunted to extinction by the nineteen-thirties. He extracted mtDNA from moas, the giant flightless birds that populated New Zealand before the arrival of the Maori, and found that moas were more closely related to birds from Australia than to kiwis, the flightless birds that inhabit New Zealand today. “That was a blow to New Zealand self-esteem,” he recalled. He also probed plenty of remains that yielded no usable DNA, including bones from the La Brea tar pits and fossilized insects preserved in amber. In the process of this work, Pääbo more or less invented the field of paleogenetics.

““Frankly, it was a problem that I wouldn’t have tackled myself, because I thought it was too difficult,” Maynard Olson, an emeritus professor at the University of Washington and one of the founders of the Human Genome Project, told me. “Pääbo brought very high standards to this area, and took the field of ancient DNA study from its ‘Jurassic Park’ origins to a real science, which is a major accomplishment.”

Difficulty in Obtaining Ancient Human DNA in Africa

Ben Panko wrote in “Africa may be the continent where humans first arose, but compared to Europe, relatively little ancient DNA has been sequenced from there. This hasn’t been for lack of trying, says Jessica Thompson, an archaeologist at Emory University who focuses on ancient Africa, but rather due to the differences in environment between the continents. [Source: Ben Panko,, September 21, 2017 ***]

DNA can be a resilient molecule, surviving hundreds of thousands of years under the right conditions. But it can also be very fragile, subject to degrading in the presence of heat or moisture. Both of these are found in abundance in much of Africa, making it far more difficult to extract usable DNA to sequence. In contrast, scientists have sequenced DNA from Neanderthals in Europe that date back to more than 400,000 years, thanks to a climate that is generally cooler, drier and therefore better suited for preserving DNA. “For an Africanist, it’s frustrating, because we don’t have access to the same kinds of data that people who are studying the prehistory of say ancient Europe has,” Thompson says, “and I’ll admit I’ve been kind of jealous about that.” ***

“In Thompson’s field work in the southeastern country of Malawi, she recalled visiting sites that were at relatively high elevations that were noticeably cold, where skeletons had been found in the mid-20th century. Thompson’s efforts to track down these skeletons put her in touch with an already nascent effort by anthropologists and other researchers to fill the void of ancient African DNA by harnessing scientific advances. Thompson found two ancient human samples in another lab, but analyzing them produced inconsistent results. So she decided to return to the Malawi sites where they were dug up to look for more clues. She ended up uncovering three more sets of human remains, which contained DNA dating back as far as 8,000 years ago; she collected other samples from scientific archives in Malawi. ***

“Other researchers also sequenced eight more ancient samples from southern Malwai, which Thompson’s group included in a study published in the journal Cell. Time had degraded the samples, says Pontus Skoglund, a geneticist at Harvard Medical School who led the study. However, with persistence and advancing genetic technology, researchers were able to obtain at least 30,000 DNA base pairs from each sample—“more than enough to do powerful statistical analyses,” Skoglund says.” ***

Neanderthal DNA comparison

Genetic Dating and the DNA Clock

Katherine Sharpe wrote in Archaeology: For years, archaeologists and geneticists have been troubled by the fact that their time lines for key events in human evolution don’t always match up. While archaeologists rely on the dating of physical remains to determine when and how human beings spread across the globe, geneticists use a DNA “clock” based on the assumption that the human genome mutates at a constant rate. By comparing differences between modern and ancient DNA, geneticists then calculate when early humans diverged from other species and when human populations formed different genetic groups. [Source: Katherine Sharpe, Archaeology, December 17, 2012 +||+]

“The DNA clock is a powerful tool, but its conclusions—for example, that modern humans first emerged from Africa about 60,000 years ago—can disagree with archaeological evidence that shows signs of modern human activity well before that date at sites in regions as far-flung as Arabia, India, and China. +||+

“Now, new work, based on observation of the genetic differences between present-day parents and children, suggests that the genetic clock may actually run about twice as slowly as previously believed, at least for the last million years or so of primate history. In their review paper in the journal Nature Reviews Genetics, Aylwyn Scally and Richard Durbin of the Wellcome Trust Sanger Institute in Hinxton, England, propose much earlier dates for watershed events in human evolution, which could help bring the genetic and archaeological records in line. For instance, a slower clock places the migration of modern humans out of Africa at around 120,000 years ago, which is more consistent with archaeological evidence. +||+

No Bones? No Problem! DNA from Dirt

In 2017, in a study published in the journal Science, scientists said they’d figured out a way to extract tiny traces of ancient human DNA from dirt in caves that lack skeletal remains. Associated Press reported: “The technique could be valuable for reconstructing human evolutionary history. That’s because fossilized bones, currently the main source of ancient DNA, are scarce even at sites where circumstantial evidence points to a prehistoric human presence. “There are many caves where stone tools are found but no bones,” said Matthias Meyer, a geneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, who co-authored the study. [Source: Associated Press, April 28, 2017 /~/]

“The researchers collected 85 sediment samples from seven caves in Europe and Russia that humans are known to have entered or even lived in between 14,000 and 550,000 years ago. Neanderthal microbes reveal surprises about what they ate — and whom they kissed Skulls found in China were part modern human, part Neanderthal — and could be a new species By refining a method previously used to find plant and animal DNA, they were able to search specifically for genetic material belonging to ancient humans and other mammals./~/

human migrations and mitochondrial haplogroups

“Scientists focused on mitochondrial DNA, which is passed down the maternal line, because it is particularly suited to telling apart closely related species. And by analyzing damaged molecules they were able to separate ancient genetic material from any contamination left behind by modern visitors. The researchers found evidence of 12 mammal families including extinct species such as woolly mammoth, woolly rhinoceros, cave bear and cave hyena. /~/

“By further enriching the samples for human-like DNA, however, the scientists were able to detect genetic traces of Denisovans — a mysterious lineage of ancient humans first discovered in a cave in Siberia — and Neanderthals from samples taken at four sites. Crucially, one of the sites where they discovered Neanderthal DNA was a cave in Belgium, known as Trou Al’Wesse, where no human bones had ever been found, though stone artefacts and animal bones with cut marks strongly suggested people had visited it. /~/

“Eske Willerslev, who helped pioneer the search for DNA in sediment but wasn’t involved in the latest research, said the new study was an interesting step, but cautioned that it’s difficult to determine how old sediment samples found in caves are. “In general (it) is very disturbed and unless you can show that’s not the case you have no idea of the date of the findings,” said Willerslev, an evolutionary geneticist at the University of Copenhagen, Denmark. /~/

“Meyer said the new method greatly increases the number of sites where archaeologists will be able to find genetic evidence to help fill gaps in the history of human evolution and migration, such as how widespread Neanderthal populations were and which stone tools they were able to make. Scientists may also be able to greatly expand their limited knowledge of the Denisovans, whose DNA can still be found in Melanesians and Aboriginal Australians today, by using the new procedure. “In principle, every cave where there’s evidence of human activity now offers this possibility,” Meyer told The Associated Press. /~/

Using the DNA from Dirt Technique To Locate Neanderthals

Daniel Weiss wrote in Archaeology magazine: “Remains of early humans such as Neanderthals and Denisovans have been discovered at just a limited number of sites in Europe and Asia. This has long frustrated archaeologists, who are confident that many more locations were occupied throughout these regions. This year, however, researchers announced a new way of detecting the hominins’ presence — through genetic traces in cave sediments. [Source: Daniel Weiss, Archaeology magazine, January-February 2018]

A team led by Viviane Slon of the Max Planck Institute for Evolutionary Anthropology analyzed sediments from seven sites in France, Belgium, Spain, Croatia, and Russia, and found Neanderthal DNA at three sites dating to up to 60,000 years ago, and Neanderthal and Denisovan DNA in Russia’s Denisova Cave dating to around 100,000 years ago. In a number of cases, the genetic evidence was located at stratigraphic levels where no hominin remains have been found. “It was really exciting,” says Slon, “to see that even without the bones, we can still find the DNA of these people.”

“The technique worked even with sediments that had been collected a number of years ago and stored in labs, Slon notes, “so we’re not only restricted to active excavations.” The researchers hypothesize that the DNA in the sediments comes from body fluids left behind by hominins as well as decomposition of their remains. So far, they have focused on mitochondrial DNA, but hope to be able to find nuclear DNA as well, which would provide additional genetic information about the hominins.

Paleoproteomics — Studying Ancient Proteins to Learn About Ancient DNA

In recent years scientists have started using a method called paleoproteomics — literally, the study of ancient proteins — to get genetic information from fossils. By examining proteins in organic artifacts like teeth and bones, scientists can now learn details of the DNA that created them—but without having to analyze any actual DNA that may have survived. Studying ancient proteins has certain advantages over DNA analysis. DNA degrades relatively quickly, becoming unreadable within several hundred thousand years. To date, the oldest human DNA ever sequenced are about 800,000 and 430,000 years old. Proteins, on the other hand can survive in fossils for millions of years. Scientists have used protein sequencing methods to study the genetic code of a 1.77-million-year-old rhino found in Dmanisi, Georgia, and a 1.9-million-year-old extinct ape in China. [Source: Brandon Specktor, Live Science, April 4, 2020]

Brandon Specktor wrote in Live Science: Using mass spectrometry, which displays the masses of all the molecules in a sample, scientists can identify the specific proteins in a given fossil. Our cells build proteins according to instructions contained in our DNA, with three nucleotides, or letters, in a string of DNA coding for a specific amino acid. Strings of amino acids form a protein. So, the amino acid chains that form each person's unique protein sequence reveal the patterns of nucleotides that form that person's genetic code, lead study author Frido Welker, a molecular anthropologist at the University of Copenhagen, told

While protein analysis allows researchers to look much further into the past than other genetic-sequencing methods, the findings are still limited by the quality and number of specimens available to study. Because the present research is based only on a single tooth from a single Homo antecessor individual, the results provide only a "best guess" as to where the species lands on the human evolutionary tree, the authors wrote. Different types of cells produce many different kinds of proteins, so this enamel proteome is far from a complete genetic profile. More fossil evidence is needed to flesh out these results.

Of course, the quality of those fossil samples matters, too. As part of this study, the researchers also examined a 1.77-million-year-old molar taken from a fossil Homo erectus (an ancient human ancestor that lived 2 million years ago) previously discovered in Georgia; however, the protein sequence was too short and damaged to offer any new insights about the specimen's DNA. Our human family tree will have to remain, for now, a tangled messy bush.

Uses of Paleoproteomics

Paleoproteomics is a cheaper and easier method of extracting DNA information than conventional DNA analysis and as been used to work a variety of things from the distant past such sex, animal type and disease. Tom Metcalfe wrote in National Geographic: A study published in July 2023 in Scientific Reports describes the discovery of the tomb in 2008 at Valencina de Concepción, a town near Seville in southern Spain. It lies within a vast burial ground dated to Iberia’s Copper Age, between 4,200 and 5,200 years ago; and it was one of the richest tombs ever found in Spain, with lavish grave goods that included an entire elephant’s tusk, a dagger with a crystal blade, and dozens of mother-of-pearl beads. Archaeologists at the time suggested the person buried there was a man aged between 17 and 25, based on their assessment of the skeletal remains; the grave goods indicated “he” had held an elite position in society. But a new examination of the tooth enamel from the individual’s remains shows the presence of proteins made by genes on an X chromosome—but no equivalent proteins made by genes on a Y chromosome. That suggests the person in the tomb was biologically female (XX), and not male (XY). [Source: Tom Metcalfe, National Geographic, July 07, 2023]

Cintas-Peña and study senior author Leonardo García Sanjuán, also at the University of Seville, say their new discovery challenges models of prehistoric societies in Iberia that suggest they were led by charismatic men. But “our study shows this was not necessarily the case,” the researchers say; instead, it seems that women could also be leaders—forcing a rethink of the societal roles of women in Copper Age Iberia and elsewhere.

While breakthroughs in the study of ancient DNA are enabling archaeologists to extract detailed information from archaeological remains, from sex down to eye color, the process can be expensive and time-consuming, with samples prone to contamination—when there’s actually enough DNA to recover. Proteomics, on the other hand, can be used to create a partial genetic profile from remains regardless of the presence of DNA in the sample: “It allows you to get a very small genotype from DNA, even when the DNA in a sample is degraded and gone,” says Glendon Parker at the University of California Davis, a pioneer in proteomics who has spent more than a decade researching forensic and archaeological applications. Parker’s studies also show proteins are often more stable and better preserved in ancient bones and teeth than DNA: “It is always the case that if you have DNA you will have protein,” he says. “But if you have protein, you may not have DNA.”

Using proteomics to determine the sex of human remains is “more effective, cheaper, and faster” than ancient DNA analysis, agree Cintas-Peña and García Sanjuán. Besides providing genetic information from animal and human remains, proteomics can also be used to investigate microorganisms that caused ancient diseases such as leprosy or plagues; to identify food residues on ancient pottery; and to determine sources of fibers used in ancient textiles, which could provide insight into ancient trading networks.

Biomolecular archaeologist Michael Buckley at the University of Manchester in the United Kingdom has developed the proteomics of collagen—the main protein in bones—into the Zooarchaeology by Mass Spectrometry (ZooMS) method of determining which animal species a particular bone from an archaeological site came from. The technique was recently used to show that ivory in a fifth or sixth century English grave came from an African elephant, which implies a previously unknown trade route across the ancient world at that time.

DNA Extracted from a Pendant of a 20,000-Year-Old Woman Using the Laundry Method

A study published in the journal Nature in May 2023 reported that scientists have extracted human DNA from a deer-tooth pendant likely worn by a woman about 20,000 years ago. This was the first time ancient human DNA has been recovered from an artifact made from another animal, opening the way the glean information on thingslik how ancient humans divided tasks between sexes, such as sewing hides or making bone spear points. This new DNA extraction technique can also date bone artifacts without damaging them—an advantage over radiocarbon dating, which destroys a small sample of the material. “This is a proof of principle study,” says a study senior author, geneticist Matthias Meyer at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. “It will take some time until this translates into new insights… but it will be huge.” [Source: Tom Metcalfe, National Geographic, May 4, 2023]

Tom Metcalfe wrote in National Geographic: Meyer and his colleagues studied a pendant made from a deer tooth found in Siberia’s Denisova cave in 2021. The cave was occupied by different hominin groups for about 50,000 years and became famous in 2010 with the discovery there of a previously unknown human species called Denisovans. The pendant, however, comes from a sediment layer about 20,000 years old, when the cave was inhabited by Homo sapiens. It’s not been possible before now to extract ancient human DNA from such an artifact; usually a sample would be drilled from the tooth and ground up, hopefully revealing the DNA of the deer it came from. But the new technique, which involves washing the artifact in a sodium phosphate solution, has recovered both sets of ancient DNA—from the deer as well as the human who made or wore it—and without damaging the pendant.

Molecular biologist Elena Essel, the study’s lead author and a doctoral student at the Max Planck Institute for Evolutionary Anthropology, says the researchers tried different chemicals until they hit on using sodium phosphate, which is also used in washing powders for clothes. The method of extracting DNA is also similar to doing laundry: the pendant was bathed in a fresh batch of the solution several times, at increasing temperatures up to almost 200 degrees Fahrenheit. The researchers used their knowledge of human and deer genetics to distinguish one (Homo sapiens) from the other (wapiti, a type of elk), and to determine both the sex and ancestry of the human, showing she descended from ancient North Eurasians, an ancient population that until now has only been recorded further east. The researchers also dated the pendant by calculating the number of mutations in the ancient DNA and comparing them to modern genomes. Both the deer and the human DNA yielded a date of between 19,000 and 25,000 years ago, which is a larger time range than that provided by radiocarbon dating (which can provide dates to within a few decades in some cases) but was done without damaging the pendant—while the radiocarbon method would, Essel says.

DNA Studies of Large Populations

In 2017, the first large-scale study of ancient human DNA from sub-Saharan Africa was published, opening a long-awaited window into the identity of prehistoric populations in the region and how they moved around and replaced one another over the past 8,000 years. Harvard Medical School reported: . The findings, published in Cell by an international research team led by Harvard Medical School, answer several longstanding mysteries and uncover surprising details about sub-Saharan African ancestry—including genetic adaptations for a hunter-gatherer lifestyle and the first glimpses of population distribution before farmers and animal herders swept across the continent about 3,000 years ago."The last few thousand years were an incredibly rich and formative period that is key to understanding how populations in Africa got to where they are today," said David Reich, professor of genetics at HMS and a senior associate member of the Broad Institute of MIT and Harvard. "Ancestry during this time period is such an unexplored landscape that everything we learned was new." [Source: Harvard Medical School, September 21, 2017, ~]

“Reich shares senior authorship of the study with Ron Pinhasi of the University of Vienna and Johannes Krause of the Max Planck Institute for the Science of Human History and the University of Tübingen in Germany. "Ancient DNA is the only tool we have for characterizing past genomic diversity. It teaches us things we don't know about history from archaeology and linguistics and can help us better understand present-day populations," said Pontus Skoglund, a postdoctoral researcher in the Reich lab and the study's first author. "We need to ensure we use it for the benefit of all populations around the world, perhaps especially Africa, which contains the greatest human genetic diversity in the world but has been underserved by the genomics community." ~

“Although ancient-DNA research has revealed insights into the population histories of many areas of the world, delving into the deep ancestry of African groups wasn't possible until recently because genetic material degrades too rapidly in warm, humid climates. Technological advances—including the discovery by Pinhasi and colleagues that DNA persists longer in small, dense ear bones—are now beginning to break the climate barrier. Last year, Reich and colleagues used the new techniques to generate the first genome-wide data from the earliest farmers in the Near East, who lived between 8,000 and 12,000 years ago. ~

“In the new study, Skoglund and team, including colleagues from South Africa, Malawi, Tanzania and Kenya, coaxed DNA from the remains of 15 ancient sub-Saharan Africans. The individuals came from a variety of geographic regions and ranged in age from about 500 to 8,500 years old. The researchers compared these ancient genomes—along with the only other known ancient genome from the region, previously published in 2015—against those of nearly 600 present-day people from 59 African populations and 300 people from 142 non-African groups. Almost half of the team's samples came from Malawi, providing a series of genomic snapshots from the same location across thousands of years.” ~

DNA Study of Otzi, the Iceman, Provide Insights in European Migration Patterns

Ötzi’s genome was sequenced in 2012 and produced a surprising result: he was more closely related to present-day Sardinians than he was to present-day Central Europeans that live close to where he was found.. Angela Graefen, a human genetics researcher at the Eurac Institute for the Mummies and the Iceman in Bolzano, Italy, told Reuters. “He is more closely related to modern Sardinian or Corsican populations than, for instance, mainland Italy further to the south. But that doesn’t mean he comes from Sardinia or Corsica. His ancestors were more plausibly from the first wave of migrants from the Near East. The genome group stuck in the isolated regions which were less affected by human migrations, Mediterranean islands but also remote Alpine valleys.” [Source: Michel Rose, Reuters, March 2, 2012]

Thanks to Y-chromosome DNA found in Otzi’s left hip, scientists found that Otzi belonged to a particular so-called Y-chromosome haplogroup that is quite rare among today's Europeans, suggesting his ancestors probably originated in the Middle East, and migrated to Europe as cattle-breeding became more widespread. Today, this genetic heritage is most likely to be found in the inhabitants of islands in the Tyrrhenian Sea, such as Sardinia and Corsica. [Source: Catharine Paddock PhD, Medical News Today, March 1, 2012]

Tia Ghose wrote in Live Science: The initial results didn’t resolve an underlying question: Did most of the Neolithic people in Central Europe have genetic profiles more characteristic of Sardinia, or had Ötzi’s family recently emigrated from Southern Europe? “Maybe Ötzi was just a tourist, maybe his parents were Sardinian and he decided to move to the Alps,” Martin Sikora, a geneticist at Stanford University, said. That would have required Ötzi’s family to travel hundreds of miles, an unlikely prospect, Sikora said. “Five thousand years ago, it’s not really expected that our populations were so mobile,” Sikora told LiveScience. [Source: Tia Ghose, Live Science, November 9, 2012 ||*||]

Image Sources: Wikimedia Commons

Text Sources: National Geographic, New York Times, Washington Post, Los Angeles Times, Smithsonian magazine, Nature, Scientific American. Live Science, Discover magazine, Discovery News, Natural History magazine, Archaeology magazine, The New Yorker, Time, BBC, The Guardian, Reuters, AP, AFP and various books and other publications.

Last updated June 2024

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