Europeans Didn’t Evolve as One Population
Ancient DNA shows that ancestry influences traits, but evolutionary trajectories reshape them
Human evolution can move much faster than most people assume.
Ancient DNA findings still surprise people. When results show that prehistoric Europeans had darker skin than many Europeans today, someone inevitably asks: Why? Put bluntly: If modern Europeans look white, why didn’t their ancestors?
I’ve written before that the evolution of skin pigmentation, hair and eye colour in Europe over the last ~12,000 years was significant. Alleles associated with lighter features rose dramatically in frequency. That debate is largely settled.
But there is a subtler yet more persistent source of confusion that still shapes how people think about ancestry and traits.
Many assume that populations differ today because they inherited fixed trait profiles from ancestral groups. For example:
Northern Europeans are taller because they have more Steppe ancestry.
Middle Eastern ancestry implies darker pigmentation.
Hunter-gatherer ancestry implies shorter stature.
This assumes ancestral populations were fixed trait packages that just mixed but this is not how evolution works.
Lineages mix and evolve, and they do so at different speeds and in different directions.
I called one manifestation of this the Aryan paradox: many of the populations in Europe with the lightest skin and hair today derive a large fraction of their ancestry from groups like the Yamnaya, who likely had light-brown skin and dark hair. If ancestry alone determined traits, this shouldn’t happen. But traits changed within those lineages after they spread.
The real question is whether Europe’s ancestral components followed distinct evolutionary trajectories, not just different starting points but different directions and rates of change.
The answer turns out to be yes, and not in the way most people expect.
Methods
I analyzed ancient genomes from the Allen Ancient DNA Resource (AADR), restricting the sample to individuals within Europe dated between about 200 and 45,000 years before present and excluding modern individuals so the patterns reflect prehistoric processes rather than modern sampling.
For each individual I computed polygenic scores for educational attainment (averaging EA3 and EA4), cortical surface area, brain volume, height, and skin pigmentation. All scores were standardized across the dataset.
Ancient individuals were also assigned ancestry proportions from ADMIXTURE projections. Rather than treating ancestry as a static label, I modeled how polygenic scores changed through time as a function of ancestry background.
For each trait I estimated:
PGS ~ YearsBP × ancestry + coverage
YearsBP is measured in thousands of years and centered. Coverage is included as a technical control because sequencing depth affects PGS noise. The key quantity is the interaction between time and ancestry, which captures whether polygenic scores changed at different rates across ancestry backgrounds.
To make the results interpretable, I generated predicted evolutionary trajectories for populations dominated by a given ancestry while allowing small contributions from others. From these models I extracted ancestry-specific time slopes, which measure how quickly polygenic scores change per thousand years since that ancestry enters the record. Each slope corresponds to the time coefficient associated with that ancestry in the ancestry×time interaction, evaluated under the ancestry scenarios.
Europe’s 4+1 Deep Ancestries
Before looking at how traits changed within ancestries, it helps to see what those ancestries actually look like in the ancient record. These components are not arbitrary statistical constructs.; they correspond to recurring ancestry profiles that appear across archaeological populations. In earlier posts I emphasized four deep lineages shaping Europe: Anatolian farmer–related ancestry, Western hunter-gatherer ancestry, Steppe pastoralist ancestry, and an East Mediterranean lineage related to Levantine and Iranian populations.
In this dataset a fifth component also appears clearly: an Inner Asian ancestry associated mainly with Avar-period and some Hungarian samples. This doesn’t replace the four-lineage framework — outside of those populations the 4-way structure still describes variation well — but including the Inner Asian component prevents forcing those samples into the wrong ancestry bins and lets the models account for their distinct genetic background explicitly.
The figure below shows the average ancestry composition of ancient population groups with at least twenty individuals using this 4+1 framework. Population groups are ordered by the proportion of Steppe ancestry, highlighting how Steppe ancestry spreads across time and regions.
Figure 1. Mean ancestry composition of ancient European population groups (K=5 ADMIXTURE, Europe’s “4+1” ancestries).
The five ancestry components show clear geographic and temporal structure rather than being evenly distributed across European groups. Anatolian farmer ancestry is highest in Neolithic farming populations such as Austria_LBK (≈0.83), Germany_EN_LBK (≈0.81), Slovakia_N_LBK (≈0.80), and France_N (≈0.79), while it is much lower in hunter-gatherer groups like Serbia_IronGates_Mesolithic (≈0.10). Steppe ancestry peaks in Corded Ware and later northern European groups, reaching about 0.50 in Czechia_EBA_CordedWare and around 0.43 in Viking and Anglo-Saxon contexts, while remaining minimal in early farming populations. WHG ancestry is highest in Mesolithic hunter-gatherers such as Serbia_IronGates_Mesolithic (≈0.72) and remains elevated in northern European Neolithic contexts, but is low in Near Eastern–related populations. East Mediterranean ancestry is highest in Anatolia and Levant-proximal contexts such as Turkey_Hatay_Alalakh (≈0.41) and Turkey_Aegean_Mugla (≈0.34) and much lower across most central and northern European groups. Inner Asian ancestry is negligible across most European populations but rises sharply in Avar-period Hungary (≈0.35–0.47), where it becomes the dominant component.
Steppe ancestry characterizes Bronze and later northern Europeans, Anatolian ancestry dominates early farmers, WHG marks Mesolithic populations, East Mediterranean reflects southeastern Near Eastern input, and Inner Asian ancestry is localized to specific migration events.
Once you separate ancestry from evolutionary change, the results are not what most people expect.
