Who We Are and How We Got Here

1. Ancient DNA has revolutionized our understanding of human prehistory.

In just five years the study of ancient DNA has transformed our understanding of world prehistory.

A new lens. The ability to extract and sequence DNA from ancient bones has fundamentally changed how we see the human past. Before this "ancient DNA revolution," our understanding relied primarily on archaeology, linguistics, and limited genetic data from living people (like mitochondrial DNA or Y-chromosomes). These older methods provided valuable insights but often painted a static or overly simplistic picture.

Beyond the surface. Ancient DNA allows us to directly analyze the genetic makeup of people who lived thousands of years ago. This provides a level of detail and certainty about population movements, relationships, and mixtures that was previously impossible. It's like moving from blurry outlines to high-resolution images of the past.

Overturning consensus. This new data has already overturned long-held theories, such as the idea that present-day population structures directly reflect ancient ones or that major cultural shifts were solely due to the spread of ideas rather than people. Ancient DNA has become a more definitive source of information for past population movements.

2. Human history is a story of repeated, large-scale population mixture.

A great surprise that emerges from the genome revolution is that in the relatively recent past, human populations were just as different from each other as they are today, but that the fault lines across populations were almost unrecognizably different from today.

Not a simple tree. The traditional metaphor of a branching tree of human populations, where groups split and remain separate, is fundamentally wrong. The reality revealed by genetics is more like a trellis, with branches repeatedly coming back together through mixture.

Mixture is the norm. Major mixtures between highly divergent populations have occurred repeatedly throughout human history, not just in recent times like the European colonization of the Americas. These mixtures have reshaped the genetic landscape of continents.

Past vs. Present. Populations that were highly distinct thousands of years ago have mixed to form the populations we see today. This means that today's genetic clusters do not represent ancient, "pure" groups, but are themselves the products of complex histories of comingling.

3. Archaic humans like Neanderthals and Denisovans interbred with modern humans.

The proof was in the picture.

Beyond replacement. While modern humans expanding out of Africa largely replaced archaic groups like Neanderthals and Denisovans, they also interbred with them. This is evident in the DNA of people living today outside of Africa.

Genetic legacy. Non-Africans today carry about 1.5-2.1% Neanderthal ancestry, while some populations in Oceania and East Asia also carry 3-6% Denisovan ancestry. This archaic DNA is not evenly distributed across our genomes, suggesting natural selection has removed some parts (like those affecting male fertility) while preserving others (like those related to immunity or adaptation to new environments).

Direct evidence. Ancient DNA from individuals like the Oase man in Romania, who lived ~40,000 years ago, shows much higher proportions of Neanderthal ancestry (~6-9%), indicating a very recent Neanderthal ancestor (within 4-6 generations). This provides direct proof of interbreeding events.

4. "Ghost populations," now extinct in pure form, are major ancestors of people today.

I think of this group as “superarchaic” humans, as they represent a more deeply splitting lineage than Denisovans.

Statistical detection. The existence of ancient populations that no longer exist in unmixed form can be inferred statistically from the DNA of living people. These "ghost populations" left genetic traces through mixture events.

Major contributors. Examples include the Ancient North Eurasians, who contributed significantly to both Europeans and Native Americans, and the Basal Eurasians, a deeply divergent lineage that contributed substantially to populations in the Near East, Europe, and South Asia.

Revealed by ancient DNA. While some ghosts can be inferred from modern DNA, ancient DNA samples from individuals like the Mal'ta boy (~24,000 years ago) directly represent these ghost populations (Ancient North Eurasians), allowing for much clearer reconstruction of past mixtures.

5. Europe's modern population formed from three highly distinct ancient groups.

The extraordinary fact that emerges from ancient DNA is that just five thousand years ago, the people who are now the primary ancestors of all extant northern Europeans had not yet arrived.

Multiple layers. Present-day Europeans are primarily a mix of three ancient populations that were as different from each other as Europeans and East Asians are today:

• Western European Hunter-Gatherers (indigenous to Europe)
• Early European Farmers (migrated from Anatolia ~9,000 years ago)
• Steppe Pastoralists (migrated from the Pontic-Caspian steppe ~5,000 years ago)

Dramatic shifts. The arrival of farmers from Anatolia largely replaced the indigenous hunter-gatherers across much of Europe. Later, the migration of steppe pastoralists, associated with the Yamnaya culture, caused another massive population replacement, particularly in northern Europe.

Bronze Age transformation. The Bronze Age (~5,000 years ago) was a period of profound change, marked by the spread of the Yamnaya culture, horses, and wheeled vehicles. This migration had a massive genetic impact, especially on the male line, and is strongly linked to the spread of Indo-European languages across Europe.

6. India's population is a recent mix of deeply divergent ancestral groups.

The result is that everyone in mainland India today is a mix, albeit in different proportions, of ancestry related to West Eurasians, and ancestry more closely related to diverse East Asian and South Asian populations.

A collision of ancestries. The vast majority of groups in mainland India today are the product of mixture between two primary ancestral populations: the Ancestral North Indians (ANI) and the Ancestral South Indians (ASI). These groups were as genetically different from each other as Europeans and East Asians are today.

Timing and context. This mixture occurred relatively recently, between 4,000 and 2,000 years ago, coinciding with the decline of the Indus Valley Civilization and the composition of the Rig Veda. The mixture was often sex-biased, with more ANI male ancestry, suggesting social stratification.

Multiple sources. Further analysis shows both ANI and ASI are themselves mixed. ANI are a mix of Iranian farmer-related and Steppe pastoralist-related ancestry. ASI are a mix of Iranian farmer-related and a deeply divergent South Asian hunter-gatherer ancestry (related to Andaman Islanders).

7. The Americas were peopled by multiple waves of migration from Asia.

Three years later, I found out I was wrong.

Beyond "Clovis First". The long-held model that the Americas were first peopled by a single group associated with the Clovis culture (~13,000 years ago) is incorrect. Archaeological evidence (like Monte Verde) and genetic data show humans were south of the ice sheets earlier.

Multiple founding lineages. Genetic studies reveal at least two major founding lineages contributed to Native Americans: the "First Americans" (ancestral to most groups from Mexico south) and "Population Y" (with affinity to Australasians, found primarily in Amazonia).

Later migrations. Additional migrations from Asia contributed to populations in northern North America, including the ancestors of Na-Dene speakers and Paleo-Eskimos. These later groups also carry significant amounts of First American ancestry, showing subsequent mixture within the Americas.

8. Agricultural expansions drove massive population shifts and mixtures globally.

The fusion of these highly different populations into today’s West Eurasians is vividly evident in what might be considered the classic northern European look: blue eyes, light skin, and blond hair.

Transformative technology. The invention and spread of agriculture, independently in places like the Near East and China, supported much higher population densities and led to major migrations. These movements often resulted in the displacement or mixture with pre-existing hunter-gatherer populations.

Global impact.

• Near East farmers spread to Europe and India.
• Chinese farmers spread throughout East Asia and to islands in Southeast Asia and the Pacific.
• Bantu farmers expanded across sub-Saharan Africa.
• Pastoralists from the steppe, leveraging new technologies like the wheel and horse, expanded into Europe and India.

Cultural and genetic change. These agricultural expansions were often associated with the spread of language families (like Indo-European, Sino-Tibetan, Bantu) and profound cultural transformations, demonstrating how technology, migration, and culture are intertwined.

9. Genetic data reveals ancient social structures and inequality, including sex bias.

It is amazing that genetic data can reveal such profound information about the social nature of past events.

Unequal contributions. Genetic patterns, particularly on the Y-chromosome (passed father-to-son) and mitochondrial DNA (passed mother-to-daughter), can reveal sex-biased population mixture. This often reflects social inequality where males from one group had greater reproductive success with females from another.

Examples of sex bias:

• European male bias in admixture with African and Native American females in the Americas.
• Steppe male bias in admixture with European and Indian females during Bronze Age expansions.
• Bantu male bias in admixture with Pygmy females in Central Africa.

Star Clusters. The Y-chromosome shows evidence of "Star Clusters," where a small number of males had an extraordinarily large number of descendants, particularly prominent around 5,000 years ago during the rise of socially stratified Bronze Age societies. This reflects extreme inequality in male reproductive success.

10. Biological differences exist across populations, challenging old orthodoxies.

But whether we like it or not, there is no stopping the genome revolution.

Beyond skin deep. While most genetic variation is within populations, the genome revolution shows there are undeniable average genetic differences across populations in traits beyond just appearance. These include differences in:

• Bodily dimensions (e.g., height)
• Metabolic abilities (e.g., digesting milk, starch)
• Adaptation to environment (e.g., high altitude)
• Disease susceptibility

Polygenic traits. Traits influenced by many genes (polygenic traits), including behavioral and cognitive ones, are also subject to natural selection and can differ on average across populations. Studies are beginning to find genetic variations associated with traits like educational attainment and intelligence test performance.

Orthodoxy challenged. The previous consensus that biological differences across populations are too modest to be significant is becoming untenable in the face of accumulating genetic data. Denying these differences is scientifically unsustainable and leaves a vacuum for pseudoscience.

11. "Ancestry" offers a new, more accurate framework for understanding human variation than "race."

Mixture is fundamental to who we are, and we need to embrace it, not deny that it occurred.

Race is a poor fit. Traditional concepts of "race" are inconsistent and do not align with the complex history of human populations revealed by genetics. The idea of "pure" races is a myth debunked by the pervasive evidence of mixture.

Ancestry reflects history. The term "ancestry" is a more precise way to describe the proportions of genetic material inherited from different historical populations. It acknowledges that modern groups are blends of ancient, often highly divergent, source populations.

Shared heritage. The history of repeated mixture highlights the deep interconnectedness of all human populations. Understanding this shared history can provide a new basis for identity, moving beyond narrow, often inaccurate, notions of biological purity and promoting a sense of shared human heritage.

12. Ancient DNA is a revolutionary tool transforming our view of the human past.

The measure of a revolutionary technology is the rate at which it reveals surprises, and in this sense, ancient DNA is more revolutionary than any previous scientific technology for studying the past, including radiocarbon dating.

Unprecedented insights. Like the microscope revealing the microbial world, ancient DNA is opening up a previously unseen dimension of human history. It provides definitive answers about population movements and mixtures that were previously debated based on indirect evidence.

Building an atlas. The field is rapidly expanding beyond its initial focus on Europe to build a global ancient DNA atlas, densely sampling human history across time and space. This resource will provide a fundamental framework for understanding human population history worldwide.

Future potential. Beyond population movements, ancient DNA promises insights into:

• Changes in human population size over time.
• The rate and nature of human biological adaptation and natural selection.
• The history and evolution of ancient pathogens and human microbiomes.

Last updated: May 8, 2025