Decoding human origins: Unveiling the secrets of ancient DNA


Does DNA hold all the answers? Image credit: U.S. Department of Energy, CC0.

This article is a runner-up for the Science Communication Competition organised by The Oxford Scientist, and supported by the Biochemical Society.

Imagine uncovering a long-buried secret of our ancient past, a riddle etched in time’s sands. Archaeologists have long been the custodians of these enigmatic tales, piecing together the puzzle of human history, artefact by artefact. Yet, a staggering revelation now emerges: the key to unravelling human history lies not within the dust-covered relics, but through the astonishing lens of ancient DNA. This biochemical marvel isn’t merely rewriting history; it’s unveiling a vibrant panorama of our ancestral heritage, offering an intimate glimpse into the lives of those who walked the earth long before us.

The DNA time machine

DNA, short for deoxyribonucleic acid, is the blueprint of life found in nearly every cell of every living organism. Comprised of four fundamental building blocks, or nucleotides—adenine (A), thymine (T), cytosine (C), and guanine (G)—its intricate sequence orchestrates the cell’s protein synthesis, governing cellular function and everything from eye colour to disease susceptibility. Through the prism of DNA, biochemists have come to understand the genetic underpinnings of what makes us human and indeed, the secrets of our ancestral heritage.

The key to unraveling human history lies not within the dust-covered relics, but through the astonishing lens of ancient DNA.

Most DNA resides in nuclei, inherited from both parents, while a smaller fraction exists in mitochondria, passed solely from mothers. The size of mitochondrial DNA (mtDNA) dwarves in comparison to nuclear DNA but is still rich in information, being present in numerous copies and clueing us in on maternal lineages. Being the very handbook of life itself, the integrity of both our nuclear DNA and mtDNA is maintained and protected by myriad cellular mechanisms. However, imperfections inevitably arise. Over time, this means that nucleotide-altering mutations occur in our DNA. While some mutations can be harmful or beneficial, many remain inconsequential, giving rise to variation within species. Geneticists scrutinise these mutations, comparing sequences to discern details of our lineage and to reveal the relevance of mutations and genes in health and disease.

mtDNA accumulates such mutations at an especially predictable rate. This means that the more differences there are between two samples of DNA, the longer the length of time between the two organisms and their last common ancestor. So, if a geneticist is given two random samples of mtDNA, they can compare how the samples differ and make a good guess for when their lineages diverged. In that way, mtDNA acts as a molecular clock.

The challenges and triumphs of ancient DNA

Knowing this now, it may seem like DNA has always been a cornerstone of archaeology, but it might surprise you to know that the field of archaeo-genetics has only really exploded in the last few decades. Whereas our interest in the material remains of the past goes back millennia, it took the completion of the Human Genome Project in 2003 for scientists to reliably make comparisons between modern and ancient DNA.

The survival of ancient DNA, spanning millennia or more, presents a Herculean obstacle. Once an organism has died, the enzymatic processes that maintain DNA cease to function, leaving it susceptible to the elements. Factors like temperature, humidity, pH, and their fluctuations heavily influence the quality of ancient DNA. Cold and dry environments like caves are the most conducive to preservation, but most hominin fossils come from equatorial regions, leaving few samples suitable for DNA analysis.

mtDNA acts as a molecular clock.

Contamination looms over all DNA analyses but is especially pertinent in ancient DNA analysis, where samples are exceptionally scarce. In archaeological digs, ancient samples pass through numerous hands. Each handler brings potential for contamination—be it through a sneeze, a cough, accidentally touching a sample with their bare hands, or with contaminated gloves—rendering the eradication of contamination near impossible. The challenge intensifies as differentiating between modern and ancient DNA is daunting. Researchers may be led astray in their unintentional analysis of contaminant DNA, culminating in misleading conclusions. 

In the face of these setbacks, archaeologists have forged ahead and found novel solutions. The refinement of techniques and equipment over the years has enhanced the retrieval and study of ancient DNA. Archaeologists have also capitalised on the fact that ancient DNA has characteristic degradation paterns to distinguish it from modern DNA contamination. Ancient DNA tends to fragment into pieces that end with A or G, have characteristic lesions at their ends, and have an unusually high frequency of C to T substitutions. These unique traits can allow the scientist to be certain that they have a true sample of ancient DNA.

How does a researcher access and analyse ancient DNA? It is primarily found in biological tissue like bone and teeth and, more rarely, in faecal mater or softer tissues. DNA extraction is unfortunately an inherently invasive process that necessitates drilling and powdering the artefact. Scientists then employ the polymerase chain reaction to replicate even a single fragment of DNA into millions of copies for ease of handling. The sample can then be sequenced and aligned against a reference genome.

Ancient DNA has revealed troves of information about ancient populations and their world. Through its analysis, complex migration patterns have been deciphered, shedding light on the introduction of Bronze Age technology into Britain. Ancient DNA has also illuminated the recent evolutionary history of modern humans, elucidating the emergence of traits like lactose tolerance, lighter skin and hair, and increased height. The oldest ancient DNA ever discovered, dating back a staggering 2 million years, has revealed an ancient forest in Greenland. These discoveries, among others, highlight the role of palaeo-genetics in enriching our understanding of the prehistoric world, with key figures like Svante Pääbo being honoured with the 2022 Nobel Prize in Physiology or Medicine.

Reshaping human evolution

Though we Homo sapiens stand solitary among current human species, numerous other human species once thrived before and alongside us. Classical archaeological tools have been paramount in piecing together the puzzle of human evolution, using comparative anatomy to decipher the relationship between ancient hominins and us. However, it is through the lens of ancient DNA that we’ve unearthed elusive hominin species, piecing together a chronological timeline of our split from our closest kin: the Neanderthals and Denisovans.

Picture this: while inspecting Denisova Cave in Siberia, an unassuming fossilised fragment of a hominin finger is discovered. Just by looking at it, the tiny finger bone guards its secrets tightly. The fragment is too small to determine if it is a human bone, but genetic analysis uncovers an unexpected revelation: the sample belongs to a yet unidentified hominin species. Researchers compared the mtDNA of this sample to that of Neanderthals and modern humans, revealing twice as many genetic differences between the Siberian specimen’s mtDNA and modern humans as that of Neanderthals. Utilising the mitochondrial clock, this indicated that the Siberian ancestor branched off from the human evolutionary tree a million years ago, substantially earlier than the 500,000-year-old estimate for the last common ancestor of Neanderthals and modern humans. This enigmatic group of humans was termed the Denisovans, marking the first identification of a new hominin species through genetic analysis.

Through these genetic imprints, ancient DNA has allowed us to comprehend our intricately entangled hominin family tree.

In the same cave, another discovery emerged: a toe bone. Genetic sequencing revealed that the bone’s owner, a teen girl, had a Neanderthal father and a Denisovan mother. Additionally, her genome revealed that her parents were as closely related as half-siblings, hinting at frequent inbreeding between archaic humans. As it turns out, evidence for trysts between hominins simply cannot be ignored, with Homo sapiens DNA being found in ancient Neanderthal and Denisovan DNA and vice versa. Through these genetic imprints, ancient DNA has allowed us to comprehend our intricately entangled hominin family tree. 

Out of Africa

As early as Darwin, it was speculated that we Homo sapiens can find our origins in Africa. An ever-growing body of fossil evidence bolsters this theory, portraying the migration of modern humans from Africa and ultimately supplanting other hominins in the area. However, this “Out of Africa” narrative has always butted heads with the alternative theory that humans evolved in various places outside of Africa from separate populations of Homo erectus.

Through studies of modern genetics, scientists have largely come to a consensus. In a landmark 1987 paper, the mtDNA from several modern-day individuals were compared. Finding increased genetic diversity among Africans, the paper suggested that humans’ presence in Africa exceeds that of any other region of the globe. Combined with a growing body of other genetic, archaeological, and fossil evidence, it has become difficult to contest an African origin.

While not outright disputing this single-origin theory, ancient DNA has added an additional layer of complexity to the temptingly simple African migration story. Ancient DNA shows clear evidence of interbreeding between Homo sapiens and our hominin relatives outside of Africa. Furthermore, although Neanderthals are known to have evolved outside Africa, low levels of Neanderthal DNA found in modern African humans suggests that humans migrated in and out of Africa over time. While few can dispute a fundamentally African origin, ancient DNA has painted a multifaceted picture of human evolution and migration.

The moral landscape of ancient DNA research

The vast scientific potential of ancient DNA comes with some ethical quandaries. Consent cannot be obtained from individuals long dead, but there is no guideline for researchers to approach this issue. Given that the destructive nature of extracting ancient DNA may impact descendant communities, there is a need to respect the cultures and beliefs of these communities. Striking a balance between scientific inquiry and cultural sensitivity is imperative. Where possible, researchers must engage with and seek the input and consent of descendant communities. 

Balancing scientific advancement with cultural respect and ethical responsibility is essential to navigating the complexities of ancient DNA research.

Issues of data interpretation also present complex challenges. Researchers risk placing DNA evidence on a pedestal, side-lining other archaeological and anthropological data in what has been termed “molecular chauvinism”. For instance, the classification of Denisovans as a new species on the basis of a single mtDNA sample has been criticised, and similarly sweeping statements on migration and population changes built on just a few samples have been made. Historical precedents, like Gustaf Kossinna’s misinterpretation of Germanic artefacts leading to Nazi territorial claims, caution against speculative or culturally insensitive assertions. Establishing ethical guidelines is thus vital to ensuring responsible data interpretation and promoting accurate, respectful communication of research outcomes.

Balancing scientific advancement with cultural respect and ethical responsibility is essential to navigating the complexities of ancient DNA research. Archaeologists’ initial strides, proposing globally applicable guidelines and incorporating ethics statements in archaeogenetic studies, signal hope. Embracing these guiding principles signifies hope for the future of ancient DNA research – one that assures the unveiling of untold chapters of our ancient past while reinforcing a commitment to respect, sensitivity, and a profound understanding of our shared human narrative.