What now appears to be certain is that Neanderthals, Homo sapiens (as modern humans are classified taxonomically), and Denisovans all shared and descended from a common ancestor a million years or so ago.58 The divergence of the Neanderthal line from the modern human line began at least 430,000 years ago, and perhaps as early as 765,000 years ago.59 The divergence of the Neanderthal line from the Denisovan line occurred between 381,000 and 473,000 years ago.60 Humans today are therefore, to a greater or lesser degree, hybrids who have inherited genes from Neanderthals, Denisovans, and archaic Homo sapiens.
CROSSING THE LINE
THE MODERN INHABITANTS OF THE Altai are notable in that they have inherited virtually no Denisovan DNA at all—just a tiny fraction of a single percent.61 By contrast, the human populations with the highest percentage of Denisovan DNA today are found among “geographically isolated New Guinean and Australian aborigines (in the range of 3–4%).”62
The first detailed investigation went a little higher than this in some cases, concluding, for example, that the archaic Denisovan population “contributed 4–6% of its genetic material to the genomes of present-day Melanesians.”63 Subsequently, varying levels of Denisovan admixture have also been identified in populations from eastern Indonesia, the Philippines, Near and Remote Oceania, and the Americas.64
At first this widespread heritage seems strange in view of the location of Denisova Cave itself, deep in the Altai Mountains of southern Siberia, thousands of miles from New Guinea and Australia and even farther from the Americas. But tens of millennia have passed since the Denisovans occupied the cave, occasionally interbreeding with Neanderthals and anatomically modern humans and passing on their genes through all kinds of convoluted liaisons and migrations. We don’t even know—on the most recent evidence it seems unlikely—that the cave was in any way central to the Denisovan range. It could equally well have been some peripheral outpost and indeed a number of scientists, notable among them Alan Cooper of the University of Adelaide and Christopher Stringer of London’s Natural History Museum, have made a case that the ancient Denisovan homeland was not in Siberia, or indeed in Asia at all, but instead lay “east of Wallace’s Line.”65
A deep oceanic trough, notorious for its fast-flowing currents, Wallace’s Line divides Asia to its west from Australia to its east. It is rightly recognized as “one of the world’s biggest biogeographic disjunctions”66 and even during the lowered sea levels of the last Ice Age it would always have confronted migrants seeking to travel in either direction with a challenging maritime crossing. Any who undertook it must not only have been intrepid explorers of unknown realms and lands, but must also have possessed sufficient sailing and navigational skills to cross 30 kilometers of deep and sometimes turbulent open water between Bali and Lombok and, in the case of those who reached Papua New Guinea and Australia, to cross again the wider gulf of the Timor Straits—a formidable barrier of 90 kilometers of open water even at times of lowest sea level.
Coupled with the presence very far to the west in Siberia of Denisovan artifacts as well as Denisovan physical remains yielding a fully sequenced genome, the prominent Denisovan genetic signal among Australian aborigines and Melanesians cannot be explained without invoking these open-water crossings. In remote antiquity somebody was certainly undertaking them, and in the process spreading Denisovan genes. What we don’t know yet is whether this gene flow was the result of direct interbreeding with the Denisovans themselves, or with some perhaps as yet unidentified people whose own heritage included a significant admixture of Denisovan genes.
We also don’t know, and can only guess, at the location of the lost homeland of the Denisovans. Was it east of Wallace’s Line, as Cooper and Stringer have argued? Or might it not just as well have been west of the Line on the plains and savannas of the exposed Sunda Shelf during the lowered sea levels of the last Ice Age when the Malaysian peninsula and the islands of Sumatra, Java, and Borneo all formed one continuous landmass?67
Wherever it was, we know that 90 kilometers of open water was no barrier to these people—so why not farther? Why should they not even have crossed to the other side of the Pacific Ocean, making landfall in the Americas?
THE STRANGE AND MYSTERIOUS GENETIC HERITAGE OF NATIVE AMERICANS
BY NO MEANS FULLY UNDERSTOOD yet despite the best efforts of Darwin and his successors, the process we call “evolution” combines continuous change with continuous conservation in an endless, swirling, bewildering dance of almost unbelievable intricacy. Zoom in at sufficiently high resolution to the DNA that choreographs this dance, however, and certain distinct and identifiable patterns begin to emerge. Because we are all members of a single human family, these patterns can then be used to establish the degree of relatedness—and thus to track the prehistoric migrations and liaisons—of seemingly disparate populations, even if they now reside on opposite sides of the globe. It’s an endeavor of great technical complexity, deploying the latest advances in twenty-first-century genomic science, but it reveals previously hidden clues to the lost story of our past and—potentially—offers us a way out of the cultural amnesia that has erased tens of thousands of years of ancestral experiences from our collective memory.
This is not a genetics textbook and I don’t want us to get bogged down in superfluous details, but here are some essentials we’ll need going forward:
DNA is the genetic mechanism of inheritance, and the various types of DNA present in our cells have, as a result of scientific advances in the late twentieth and early twenty-first centuries, been subject to close investigation by a range of highly sophisticated techniques.1 The results of these investigations have shed light on the degree of genetic relatedness that exists between individuals and, on a larger scale, between entire populations.2
Located in the fluid surrounding the nucleus of every cell in our bodies, mtDNA (mitochondrial DNA) is inherited by both males and females but is passed on to offspring only by females.3 MtDNA can identify lines of descent from shared maternal, but not paternal, ancestors.4 What geneticists like about mtDNA is its abundance, being present in multiple copies per cell, giving plenty of material to work with.5
The same cannot be said of nuclear DNA, inherited equally from both parents, which has only two copies per cell but which encodes far more genetic information than mtDNA, allowing for far more robust and precise analyses of genetic relatedness.6
Within the cell nucleus are also located the chromosomes—segments of DNA that determine sex. If you have two X chromosomes you’re a female; if you have an X and a Y you’re male. Y-DNA is passed on only by males, thus facilitating the determination only of shared paternal ancestry, whereas X-DNA is inherited both through the maternal and paternal lines (since males and females both have X chromosomes) and can therefore be useful in isolating shared common ancestors along particular branches of inheritance.7
Is it important to understand the technicalities of DNA and DNA analysis as a means of establishing degrees of relatedness?
By all means dig deeper if you wish to, for this whole area of science is a fascinating one. But don’t feel you have to—any more, for example, than you might feel you must master plumbing in order to run water from a tap, or the intricacies of mechanical engineering in order to drive a car, or medical studies before undergoing surgery.
In other words, genetics, unlike archaeology, is a hard science where the pronouncements of experts are based on facts, measurements, and replicable experimentation rather than inferences or preconceived opinions. Mistakes are made by geneticists, of course, and profound disagreements are routinely thrashed out between colleagues in the professional journals. By and large, however, just as we trust the engineer, or the plumber, or the surgeon for their specialized knowledge (even though they sometimes get things wrong), it will streamline matters greatly here if we trust the conclusions of specialists working with the latest high-tech tools at the cutting edge of analysis of ancient DNA.
TWO SITES, TWO FAMILIES, ONE HUMA
N RACE
MIND YOU, “SHOTGUN SEQUENCING” OF long strands of DNA and other similarly esoteric technologies are not required for us to connect—at a basic human level—with the story of our ancestors. Particularly poignant examples of what I mean here are provided at two ancient sites, one in Siberia and one in Montana.
The Siberian site lies to the west of Lake Baikal near the village of Mal’ta on the banks of the Bolshaya Belaya River. As the crow flies (and a great deal farther on foot through winding valleys and over high passes) this is a location more than 1,000 kilometers east of Denisova Cave. Its reach back into the human past does not extend as far as Denisova’s. Still it has been recognized for many years as the home of an Upper Paleolithic culture—archaeologists call it the Mal’ta-Buret culture—that left behind many beautiful and mysterious works of art thought to be more than 20,000 years old.8 Among them, done in bone and mammoth ivory, are carvings of elegant, long-necked water fowl and a collection of thirty human Venus figures that are “rare for Siberia but found at a number of Upper Paleolithic sites across western Eurasia.”9
The primary excavations at Mal’ta, which took place between 1928 and 1958,10 also uncovered two burials, both of young children interred with curious and beautiful grave goods including pendants, badges, and ornamental beads.11 One of these children, a boy aged 3–4 years and now known to archaeologists as MA-I, had been buried beneath a stone slab, there was a Venus figurine beside him,12 and he was “wearing an ivory diadem, a bead necklace and a bird-shaped pendant.”13 Traces of pigmentation were found on his bones,14 which presently reside in the Hermitage State Museum in St. Petersburg, where a high-level international team of investigators, prominently featuring geneticists and evolutionary biologists, paid them a visit in 2009. The scientists drilled out a number of small samples from the bones and subjected them to accelerator mass spectrometry C-14 dating that showed them, give or take a few hundred years, to be 24,000 years old.15 Detailed tests were then carried out on the samples and in due course the investigators announced that they had successfully sequenced MA-1’s entire genome—making it, when a full account of the investigation was published in Nature in 2014, “the oldest anatomically modern human genome reported to date.”16
We’ll consider the implications of what was found in context also of the second site I mentioned above—located in Montana. Known to archaeologists as the Anzick-1 burial site and dated to 12,600 years ago (which makes it 11,400 years younger than MA-1), it is also a child’s grave—in this case a boy aged 1–2 years who was interred with more than 100 tools of stone and antler, all sprinkled with red ochre.17
One thing we see for sure in both these ancient burials, separated by thousands of miles and thousands of years, is that the human capacity to love and cherish family members, and to regret and mourn those who pass prematurely, is not diminished by time; indeed, we instantly recognize and identify with it today because we share it. For convenience we’ll continue to use the rather dehumanizing archaeological labels “MA-1” and “Anzick-1” here. But let’s not forget the bereaved parents and family members as they gathered around those gravesides 24,000 years ago in Siberia and 12,600 years ago in Montana, and the care and thought, the symbolism and emotions, the love and the aching sense of loss that went into the careful preparation of the graves and the choice and placing of the grave goods in both cases.
Across the ages and regardless of geography, in everything that really matters, it bears repeating that we are all members of a SINGLE human family—a family of intrepid adventurers who have been exploring the world in one form or another for the best part of a million years.18 In the course of this long odyssey we’ve moved so far apart, across oceans, over mountains, and to the opposite ends of jungles, deserts, and ice caps that we’ve forgotten how closely related we in fact are. In this sense, like the simple human message of the burials, the message of genetics also speaks to a hidden unity within our apparent diversity—and sometimes in ways that defy our expectations.
ANCIENT EUROPEAN GENES
FEW HAVE COMMENTED ON THE obvious cultural similarities in burial practices, but as to genetics, all authorities agree that MA-1 and Anzick-1 are closely related, sharing large sequences of DNA.19 Anzick-1, however, “belonged to a population directly ancestral to many contemporary Native Americans” and thus, unsurprisingly—despite his proximity to MA-1—is “more closely related to all indigenous American populations than to any other group.”20
Just as it was for so long an article of faith that the Americas were peopled exclusively by migrations from Siberia across the Bering land bridge, so, too, it was held to be self-evident that those Siberian migrants must have been most closely related to east Asians.21 What did the Bering land bridge do, after all, if not connect the far northeast of Asia with the far northwest of North America?
But a surprise awaited the investigative team led by Maanasa Raghavan of the Centre for GeoGenetics at Denmark’s Natural History Museum and Pontus Skoglund of Harvard Medical School’s Department of Genetics. Instead of confirming the anticipated connection to east Asia, MA-1’s Y chromosome (the male sex chromosome) turned out to be “basal to modern-day western Eurasians.”22 We have mentioned the limitations of Y-chromosome analysis already, so it is good—and raises the confidence level all around—that this unanticipated and potentially boat-rocking finding was subsequently confirmed with autosomal evidence23 (the best kind of DNA evidence, derived from the nucleus of the cell). “MA-1,” the investigators repeat and reemphasize, “is basal to modern-day western Eurasians … with no close affinity to east Asians.”24
Moreover—and most intriguingly—the investigators discovered that MA-1 also stands “near the root of most Native American lineages,”25 and “14 to 38% of Native American ancestry may originate through gene flow from this ancient population [the population from which MA-1 stemmed]. This is likely to have occurred after the divergence of Native American ancestors from east Asian ancestors, but before the diversification of Native American populations in the New World.”26
The final link in the chain of evidence emerged when MA-1’s mitochondrial genome was sequenced, revealing the Siberian infant to be a member of “haplogroup U, which has also been found at high frequency among Upper Paleolithic and Mesolithic European hunter-gatherers.”27
“Our result,” the investigators conclude, “therefore suggests a connection between pre-agricultural Europe and Upper Paleolithic Siberia.”28
A genetic consequence of this previously unsuspected European/Siberian nexus, since as much as 38 percent of Native American ancestry is attributable to gene flow from MA-1’s people, is that Native American DNA carries a strong and very ancient “European” signal.29
HIDDEN SOUTH AMERICAN ORIGINS OF CLOVIS REVEALED
SOMETHING I HAVEN’T MENTIONED YET—the ochre-dusted stone and antler tools found buried with Anzick-1 were unmistakably Clovis artifacts.30
There are two reasons why this “Clovis connection” is particularly noteworthy and relevant to our quest.
First, the Anzick-1 burial was originally dated to around 12,600 years ago—or, more exactly, within the limits of resolution of C-14, to between 12,707 and 12,556 years ago.31 This suggested that the grave was dug and the grave goods placed with the remains of the deceased infant a century or two after the abrupt and mysterious disappearance of the Clovis culture from the archaeological record around 12,800 years ago.
That disappearance testifies to a sudden cessation of previously widespread cultural activities, suggestive of interruption by some far-reaching cataclysmic event. What it does not mean, however, is that every member of the Clovis population died out overnight. Even if most did there would, undoubtedly, have been survivors—small groups coalescing into scattered, wandering tribes, whose members might have looked back on the achievements of their ancestors with awe.
One possibility that has been considered is that Anzick-1 himself may have belonged to just such a remnant group. This poss
ibility was raised after a small but significant discrepancy was found between the dates of Anzick-1’s bones and the dates of certain artifacts buried with him.
The artifacts, known as “foreshafts,” are specially cut, shaped, and hollowed sections of red deer antler, each designed to hold a projectile point at one end and to clamp onto the tip of a wooden spear shaft at the other. As we’ve seen, Anzick-1’s bones were initially dated between 12,707 and 12,556 years ago. The antler foreshafts among his grave goods are a century or two older than that—in the range of 12,800 to 13,000 years ago32—“a much more typical and acceptable age for Clovis,” as archaeologist Stuart J. Fiedel observes, than the “age attributed to the infant’s bones.”33
To resolve the discrepancy, Fiedel offers a simple but insightful reading of the evidence. The discordant data, he speculates in a paper published in Quaternary International in June 2017, would be reconciled if “the foreshafts were 100 to 200-year-old antique heirlooms interred with the infant by the very last Clovis folks in the region.”34
Alternatively he suggests that due to contamination of the sample, “the infant bone dates may be slightly too young.”35
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