Rapid human genetic changes after the last Ice Age

Our hominin ancestors in Africa first fashioned tools about 3.5 Ma ago. Since then regular intake of animal protein through hunting, followed by the later discovery of fire and cooking, may progressively have encouraged the evolution of larger hominin brains. Both behavioural leaps would have reduced the length of the ‘working day’ needed to sustain hominin groups. That would have lengthened opportunities for cognitive reflection. social life and culture, and thus further evolution. They also expanded the opportunities for migration, beginning with Homo ergaster venturing beyond Africa at least 1.8 Ma ago. Hominins evolved to such an extent that several separate species occupied our home world at any one time until about 45 thousand years ago. After that only H. sapiens occupied Africa, Eurasia and Australasia.

Such protracted and meandering evolution and dispersal clearly involved episodic physiological and cultural changes, but all we have to go on are fragmentary fossil remains and artifacts of various kinds. DNA has yet to be extracted from hominin bones older than 400 ka (an early Neanderthal from northern Spain). Though H. sapiens first appeared in Morocco about 300 ka ago, DNA from our species dates back to only 45 ka (western and central Europe). What is today termed ‘ancient’ human DNA, is actually very young and restricted to climate zones where its decomposition has been slow. At present there is little point in analysing fossil material from tropical and subtropical latitudes; the DNA is degraded beyond recovery by even the most up-to-date techniques. Fascinating as discussion of human evolution is, in reality most is merely inferred from comparative anatomy and anthropological interpretation.

By 45 ka the heavy evolutionary lifting had been done, resulting in anatomically modern humans, but we have little, if any, chance of explaining in genetic terms how it was achieved. There has been much speculation about the conditions, particularly climatic ones, which may have driven the changes. During the last 2.6 Ma – the Quaternary Period – global climate has been the most changeable in the last 300 Ma. Ice ages have come and gone, first in 40 ka cycles and during the last million years every 100 ka. Much more rapid changes, such as millennial Dansgaard-Oeschger cycles, appeared during each glacial episode, the last being the Younger Dryas between 12.9 and 11.7 ka. For a long while ideas on the drivers of human evolution have been dominated by those concerning environmental stress. Unsurprisingly, genetic change has also been ascribed to such a Darwinian-ecological cause: adaptability to adversity. To test such a hypothesis requires genetic data, of course. But, except for the climatically more stable Holocene Epoch since 11.7 ka, ancient human genomes are in very short supply.

Renowned researcher into ancient human genetics David Reich of the Harvard Medical School in Boston, USA has collated more than 15 thousand ancient human genomes extracted from the remains of individuals who lived and died in Europe and parts of the Middle East during the last ten thousand years. These have been analysed statistically in the context of ‘directional selection’. This is a type of natural selection that occurs when one version of a gene – an allele – confers an extreme form of a trait. If it proves advantageous it rapidly gets passed on to more descendants than do less advantageous alleles, and thus rises in frequency across a population. This differs from other causes of gene frequency changes, such as human migration, population mixing, and random genetic fluctuations that occur in small populations. Well-known examples of directional selection are rapid changes among European Peppered moths, African cichlid fish, Alaskan Sockeye salmon and Big Cats which change over time in response to variations in their habitats. A human example is a genetic variant that maintains the ability to digest the sugar lactose in milk beyond infancy, which enables many modern Europeans to digest milk throughout their lives. The algorithm needed to separate signs of directional selection from other types of genetic change was developed by Ali Akbari, a computational geneticist also at Harvard Medical School. A recent paper by Akbari, Reich and colleagues in the US, Iran, Germany, and Austria (Akbari, A. and 15 others 2026. Ancient DNA reveals pervasive directional selection across West Eurasia. Nature, advance online publication; DOI: 10.1038/s41586-026-10358-1) seems set dramatically to change the research into recent human evolutionary genetics.

Akbari et al. discovered that directional selection has driven the spread or decline of hundreds of gene variants in human populations throughout Western Europe in the last ten millennia. In particular, selection accelerated with the adoption of farming rather than a hunter-gatherer lifestyle.  Among the gene variants are those connected with light skin, red hair, risk of celiac disease – linked to gluten in cereals –  susceptibility to gout, resistance to leprosy, baldness, rheumatoid arthritis and alcoholism. There are many more (see Figure 3 in the paper): the team identified 479 gene variants affected by directional selection, some that can be explained by changes in lifestyle, others less explicable and yet more that underlie complex traits such as mental illness and cognition. Some of the variants sprang up and were sustained in the population, others rose and then dwindled. The Neolithic began a period of fundamental life style changes in Europe, summed up as a shift from hunting and foraging to farming of cereals and livestock, as early as about 10 ka ago in what is now Türkiye. The pace of genetic changes of this kind reached a peak around the Bronze Age, perhaps because human activities in Europe became more complex then with the mass migration westwards of Yamnaya horse- and wagon-using people from the steppes to dominate Europe

The shift from small wandering bands to living in settlements was a drastic change from a lifestyle that had continued throughout all previous human history. So, it is hardly surprising that there was a major shift in humans’ genetic makeup. But such a change in human labour was not unique to Europe and is known to have occurred on all inhabited continents, with the exception of Australia, at different times during the Holocene. Other regional genetic databases can be analysed in much the same way, once sufficient ancient DNA is collected in Asia, Africa and the Americas. Yet not much is available. The authors comment: ‘A variant that now correlates to household income or years of schooling [remarkably, there are some!] had to have meant something different in the Stone Age. So these results do not mean that Europeans evolved to be smarter or healthier.’  Moreover, the research results in the paper seem likely to be amplified as the data set is so large and complex.

See also: Dutchen, S. et al. 2026. Massive Ancient-DNA Study Reveals Natural Selection Has Accelerated in Recent Human Evolution. Harvard Medical School: News & Events. 15 April 2026; Callaway, E. 2026. Landmark ancient-genome study shows surprise acceleration of human evolution. Nature, v. 652, News, 15 April 2026

CSI and detecting the presence of ancient humans

Enter a room, even for a few minutes, and dead skin cells will follow you like an invisible cloud to settle on exposed surfaces. Live there and a greyish white, fluffy dust builds up in every room. Even the most obsessive cleaning will not remove it, especially under a bed or on the bathroom floor. Consider a cave as a home, but one without vacuum cleaners, any kind of sanitation, paper tissues, panty liners, nappies or wet wipes. For pre-modern human dwellings can be added snot, fecal matter, sweat, urine, menstrual blood and semen among all the other detritus of living. A modern crime-scene investigator would be overwhelmed by the sheer abundance of DNA from the host of people who had once dwelt there. CSI works today as much because most homes are pretty clean and most people are fastidious about personal hygene as because of the rapidly shrinking lower limit of DNA detection of the tools at its disposal. Except, that is, when someone from outside the home commits a criminal offence: burglary, GBH, rape, murder. We have all eagerly watched ‘police operas’ and in the absence of other evidence the forensic team generally gets its perpetrator, unless they did the deed wearing a hazmat suit, mask, bootees and latex gloves.

Artistic impression of Neanderthal extended-family life in a cave (credit: Tyler B. Tretsven)

Since 2015 analysis of environmental DNA from soils has begun to revolutionise the analysis of ancient ecosystems, including the living spaces of ancient humans (see: Detecting the presence of hominins in ancient soil samples, April 2017). It is no longer necessary to find tools or skeletal remains of humans to detect their former presence and work out their ancestry. DNA sequencing of soil samples, formerly discarded from archaeological sites, can now detect former human presence in a particular layer, as well as that of other animals. In many cases the ‘signal’ pervades the layer rather than occurring in a particular spot, as expected from shed skin cells and bodily fluids. The first results were promising but only revealed mitochondrial DNA. Now the technique has extended to nuclear DNA: the genome (Vernot, B. and 33 others 2021. Unearthing Neanderthal population history using nuclear and mitochondrial DNA from cave sediments. Science, v. 372, article eabf1667; DOI: 10.1126/science.abf1667). Benjamin Vernot and colleagues from 7 countries collected and analysed cave soils from three promising sites with tangible signs of ancient human occupation. Two of them were in Siberia and had previously yielded Neanderthal and Denisovan genomes from bones. The other is part of the Atapuerca cave complex of NW Spain that had not. The Russian caves yielded DNA from more than 60 samples, 30 being nuclear DNA consistent with that from actual Neanderthal and Denisovan bones found in the caves. Galería de las Estatuas cave in Spain presented a soil profile spanning about 40 thousand years from 112 to 70 ka.

Teasing-out nuclear DNA from soil is complicated, from both technical and theoretical standpoints. So being able to match genomes from soil and bone samples in the Russian caves validated the methodology. The Spanish samples could then be treated with confidence. Galería de las Estatuas revealed the presence of Neanderthals throughout its 40 ka soil profile, but also a surprise. The older DNA was sufficiently distinct from that from later levels to suggest that two different populations had used the cave as a home, the original occupants being replaced by another genetically different group around 100 to 115 ka ago. The earlier affinity was with the ancestors of sequenced Neanderthal remains from Belgium, the later with those from Croatia. That time is at the end of the last (Eemian) interglacial episode, so one possibility is a population change driven by climatic deterioration. This success is sure to encourage other re-examinations of caves all over the place. That is, if there is the analyical capacity to perform such painstaking work in greater volume and at greater pace. Like many other palaeo-genomic studies, this one has relied heavily on the analytical facilities pioneered and developed by Svante Paäbo at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. Covid has forced genetics to the front page for a year and more. And it has led to many advances in anlytical techniques, particularly in their speed. It would nice to think that a dreadful experience may end-up with positive benefits for understanding the full history of humanity.