DNA STUDIES AND HOMININS | Facts and Details

DNA AND GENOMES

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.

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.

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,” Pääbo told me. “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.

Websites and Resources on Hominins and Human Origins: Smithsonian Human Origins Program humanorigins.si.edu ; Institute of Human Origins iho.asu.edu ; Becoming Human University of Arizona site becominghuman.org ; Talk Origins Index talkorigins.org/origins ; Last updated 2006. Hall of Human Origins American Museum of Natural History amnh.org/exhibitions ; Wikipedia article on Human Evolution Wikipedia ; Human Evolution Images evolution-textbook.org; Hominin Species talkorigins.org ; Paleoanthropology Links talkorigins.org ; Britannica Human Evolution britannica.com ; Human Evolution handprint.com ; National Geographic Map of Human Migrations genographic.nationalgeographic.com ; Humin Origins Washington State University wsu.edu/gened/learn-modules ; University of California Museum of Anthropology ucmp.berkeley.edu; BBC The evolution of man" bbc.co.uk/sn/prehistoric_life; "Bones, Stones and Genes: The Origin of Modern Humans" (Video lecture series). Howard Hughes Medical Institute.; Human Evolution Timeline ArchaeologyInfo.com ; Walking with Cavemen (BBC) bbc.co.uk/sn/prehistoric_life ; PBS Evolution: Humans pbs.org/wgbh/evolution/humans; PBS: Human Evolution Library www.pbs.org/wgbh/evolution/library; Human Evolution: you try it, from PBS pbs.org/wgbh/aso/tryit/evolution; John Hawks' Anthropology Weblog johnhawks.net/ ; New Scientist: Human Evolution newscientist.com/article-topic/human-evolution; Fossil Sites and Organizations: The Paleoanthropology Society paleoanthro.org; Institute of Human Origins (Don Johanson's organization) iho.asu.edu/; The Leakey Foundation leakeyfoundation.org; The Stone Age Institute stoneageinstitute.org; The Bradshaw Foundation bradshawfoundation.com ; Turkana Basin Institute turkanabasin.org; Koobi Fora Research Project kfrp.com; Maropeng Cradle of Humankind, South Africa maropeng.co.za ; Blombus Cave Project web.archive.org/web; Journals: Journal of Human Evolution journals.elsevier.com/; American Journal of Physical Anthropology onlinelibrary.wiley.com; Evolutionary Anthropology onlinelibrary.wiley.com; Comptes Rendus Palevol journals.elsevier.com/ ; PaleoAnthropology paleoanthro.org.

Archaeology News and Resources: Anthropology.net anthropology.net : serves the online community interested in anthropology and archaeology; archaeologica.org archaeologica.org is good source for archaeological news and information. Archaeology in Europe archeurope.com features educational resources, original material on many archaeological subjects and has information on archaeological events, study tours, field trips and archaeological courses, links to web sites and articles; Archaeology magazine archaeology.org has archaeology news and articles and is a publication of the Archaeological Institute of America; Archaeology News Network archaeologynewsnetwork is a non-profit, online open access, pro- community news website on archaeology; British Archaeology magazine british-archaeology-magazine is an excellent source published by the Council for British Archaeology; Current Archaeology magazine archaeology.co.uk is produced by the UK’s leading archaeology magazine; HeritageDaily heritagedaily.com is an online heritage and archaeology magazine, highlighting the latest news and new discoveries; Livescience livescience.com/ : general science website with plenty of archaeological content and news. Past Horizons, an online magazine site covering archaeology and heritage news as well as news on other science fields; The Archaeology Channel archaeologychannel.org explores archaeology and cultural heritage through streaming media; Ancient History Encyclopedia ancient.eu : is put out by a non-profit organization and includes articles on pre-history; Best of History Websites besthistorysites.net is a good source for links to other sites; Essential Humanities essential-humanities.net: provides information on History and Art History, including sections Prehistory.

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 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.

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.” ||+||

DNA Studies

chimpanzee chromosones

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, geneticist Svante Pääbo, of the Max Planck Institute for Evolutionary Anthropology, 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. |=|

“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 DNA Studies

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.”

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. +||+

“The revised clock also supports archaeological signs of modern human activity from more than 60,000 years ago at sites such as Jwalapuram, India (“Stone Age India,” January/February 2010), and Liujiang, China—evidence that has often been dismissed by geneticists as impossible. While more work is needed to confirm the findings, Scally says that archaeologists who work on such sites should be excited: “It can no longer be said that the genetic evidence is unequivocally against them.”“ +||+

Problems with Genetic Dating

Bridget Alex wrote in The Guardian: “For the past several years, there have been two main genetic methods to date evolutionary divergences - when our ancestors split from Neanderthals, chimpanzees, and other relatives. The problem was, the results of these methods differed by nearly two-fold. By one estimate, modern humans split from Neanderthals roughly 300,000 years ago. By the other, the split was closer to 600,000 years ago. Likewise, modern humans and chimps may have diverged around 6.5 or 13 million years ago. [Source: Bridget Alex, The Guardian, December 22, 2016. Bridget is a postdoctoral fellow in the department of human evolutionary biology at Harvard |=|]

“Puzzled by this wild disagreement, researchers with diverse expertise have been studying it from different angles. Their combined discoveries, recently reviewed here and here, have shed light on how genetic differences accumulate over time and have advanced methods of genetic dating. And if you’re in suspense, yes, they’ve also pinned down important events in our evolutionary timeline. Everyone alive today seems to share ancestors with each other just over 200,000 years ago and with Neanderthals between 765,000-550,000 years ago.”

human migrations and mitochondrial haplogroups

Key to Genetic Dating: You Need to Know the Rate

Bridget Alex wrote in The Guardian: “Go back in time and you’ll find a population of Homo sapiens who were the ancestors of everyone living today. Go back farther and our lineage meets up with Neanderthals, then chimps, and eventually all primates, mammals, and life. In order to date these evolutionary splits, geneticists have relied on the molecular clock - the idea that genetic mutations accumulate at a steady rate over time. Specifically this concerns mutations that become neutral substitutions, or lasting changes to letters of the genetic code that do not affect an organism’s chances of surviving and reproducing. |=| “If such mutations arise clocklike, then calculating the time since two organisms shared common ancestors should be as easy as dividing the number of genetic differences between them by the mutation rate - the same way that dividing distance by speed gives you travel time. [Source: Bridget Alex, The Guardian, December 22, 2016 |=|]

“For decades, anthropologists used fossil calibration to generate the so-called phylogenetic rate (a phylogeny is a tree showing evolutionary relationships). They took the geologic age of fossils from evolutionary branch points and calculated how fast mutations must have arisen along the resulting lineages. For example, the earliest fossils on the human branch after our split with chimps are identified by the fact that they seem to have walked on two legs; bipedalism is the first obvious difference that distinguishes our evolutionary lineage of hominins from that of chimps. These fossils are 7-6 million years old, and therefore the chimp-human split should be around that age. Dividing the number of genetic differences between living chimps and humans by 6.5 million years provides a mutation rate.

“Determined this way, the mutation rate is 0.000000001 (or 1x10-9) mutations per DNA base pair per year. Applied to genomes with 6 billion base pairs, that means, over millions of years of chimp and human evolution, there have been on average six changes to letters of the genetic This rate can be used to date evolutionary events that are not evident from fossils, such as the spread of modern humans out of Africa. |=|

“But genetic dating got messy in 2010, when improvements to DNA sequencing allowed researchers to determine the number of genetic differences between parents and their children. Known as pedigree analysis, this provides a more direct measurement of the current mutation rate within one generation, rather than an average over millions of years. Pedigree analysis counts 60-some mutations every generation; that converts to a rate approximately half the phylogenetic estimate—meaning evolutionary events would be twice as old.

Genetic Dating Rate Can Vary Based on Species, Sex and Mutation Type

Bridget Alex wrote in The Guardian: “Resolving this disagreement propelled researchers to reassess and revise their starting assumptions: How accurately were they counting the small number of differences between genomes of parents and children? Were fossils assigned to the correct branches of the evolutionary tree? And above all, how constant is the molecular clock? [Source: Bridget Alex, The Guardian, December 22, 2016 |=|]

“It turns out that among primates, the molecular clock varies significantly by species, sex, and mutation type. A recent study found that New World monkeys (i.e. monkeys of the Americas like marmosets and squirrel monkeys) have substitution rates about 64 percent higher than apes (including humans). Within apes, rates are about 7 percent higher in gorillas and 2 percent higher in chimpanzees, compared to humans. But even among humans, mutation rates differ, particularly between the sexes with age. As fathers get older, they gain about one additional mutation per year in the DNA they can pass on to children. Mothers, on the other hand, accumulate considerably fewer mutations with each passing year. |=|

“These species and sex differences make sense when you consider how mutations form. Most heritable mutations occur from mistakes when DNA copies itself in the germline, or cells leading to eggs and sperm. The number of times germline DNA has to copy itself depends on developmental and reproductive variables including age at puberty, age at reproduction, and the process of sperm production. |=|

“These traits vary across primates today, and certainly varied over primate evolution. For instance, average generation times are six years for New World monkeys, 19 years for gorillas, 25 years for chimps, and 29 years for humans. And those extra mutations as fathers get older? Sperm are produced continuously after puberty, so sperm made later in life are the result of more rounds of DNA replication and opportunities for replication errors. In contrast, a mother’s stock of eggs is formed by birth. The small increase with maternal age could be due to mutations from DNA damage, rather than replication errors.

Tweeking and Improving Genetic Dating

Bridget Alex wrote in The Guardian: “It’s now clear that one mutation rate cannot determine the dates for all divergences relevant to human evolution. However, researchers can secure the timeline for important evolutionary events by combining new methods of genetic dating with fossils and geologic ages. Innovative computational methods have incorporated reproductive variables into calculations. By taking into account ages of reproduction in both sexes, age of male puberty, and sperm production rates, researchers have estimated split times that accord with the fossil record. [Source: Bridget Alex, The Guardian, December 22, 2016|=|]

“Another new approach has analysed mutations that are mainly independent of DNA replication. It seems that certain classes of mutations, related to DNA damage, do behave more clocklike. And some researchers have focused on ancient DNA. Comparing human fossils from the past 50,000 years to humans today, suggests a mutation rate that agrees with pedigree analysis. |=|

“At least one evolutionary split was pinned down in 2016, after ancient DNA was extracted from 430,000 year-old hominin fossils from Sima de los Huesos, Spain. The Sima hominins looked like early members of the Neanderthal lineage based on morphological similarities. This hypothesis fit the timing of the split between Neanderthals and modern humans based on pedigree analysis (765,000-550,000 years ago), but did not work with the phylogenetic estimate (383,000-275,000 years ago). |=|

“Where do the Sima hominins belong on our family tree? Were they ancestors of both Neanderthals and modern humans, just Neanderthals, or neither? DNA answered this definitively. The Sima hominins belong to the Neanderthal branch after it split with modern humans. Moreover, the result provides a firm time point in our family tree, suggesting that the pedigree rate works for this period of human evolution. |=|

“Neanderthals and modern humans likely diverged between 765,000-550,000 years ago. Other evolutionary splits may soon be clarified as well, thanks to advances brought about by the mutation rate debates. Someday soon, when you see a chimp, you may be able to salute your great, great… great grandparent, with the correct number of “greats.” |=|

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./~/

“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. /~/

DNA Study Related to a Large Population: in This Case Sub-Saharan Africans

In 2017, Harvard Medical School reported: “The first large-scale study of ancient human DNA from sub-Saharan Africa opens 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. 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, phys.org ~]

“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.” ~

Difficulty in Obtaining Ancient Human DNA in Africa

Ben Panko wrote in smithsonian.com: “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, smithsonian.com, 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.” ***

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

The genome of Otzi, the iceman found in the Alps near the Italian-Austrian border in 1991,, 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 Reuter. “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]

Tia Ghose wrote in Live Science: “The researchers sequenced only part of the genome, and the 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,” Sikora 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 ||*||]

“To answer that question, Sikora’s team sequenced Ötzi’s entire genome and compared it with those from hundreds of modern-day Europeans, as well as the genomes of a Stone Age hunter-gatherer found in Sweden, a farmer from Sweden, a 7,000-year-old hunter-gatherer iceman found in Iberia, and an Iron Age man found in Bulgaria. The team confirmed that, of modern people, Sardinians are Ötzi’s closest relatives. But among the prehistoric quartet, Ötzi most closely resembled the farmers found in Bulgaria and Sweden, while the Swedish and Iberian hunter-gatherers looked more like present-day Northern Europeans.” ||*||

The findings, reported at the American Society of Human Genetics conference in 2012, “support the theory that farmers, and not just the technology of farming, spread during prehistoric times from the Middle East all the way to Finland. “The idea is that the spread of farming and agriculture, right now we have good evidence that it was also associated with a movement of people and not only technology,” said study co-author Martin Sikora, a geneticist at Stanford University.

“The findings support the notion that people migrating from the Middle East all the way to Northern Europe brought agriculture with them and mixed with the native hunter-gatherers, enabling the population to explode, Sikora said. While the traces of these ancient migrations are largely lost in most of Europe, Sardinian islanders remained more isolated and therefore retain larger genetic traces of those first Neolithic farmers, Sikora said. ||*||

“The findings add to a growing body of evidence showing that farming played a major role in shaping the people of Europe, said Chris Gignoux, a geneticist at the University of California San Francisco, who was not involved in the study. I think it’s really intriguing,” Gignoux said. “The more that people are sequencing these ancient genomes from Europe, that we’re really starting to see the impact of farmers moving into Europe.”“||*||

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 September 2018