The King's Monologue

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Evaluating Population Genetics and Ancient DNA Interpretation in Africa: Addressing Methodological Bias and Eurocentric Historical Narratives in Modern Genomic Studies

Abstract: The field of ancient DNA and population genetics is a new field that has rapidly expanded over the past decade, offering new insights into human history. Innovations have advanced our ability to both collect and analyse DNA, and these innovations in public and academic use exposes the requirement for the field to undergo the kind of scrutiny and methodological protocols that we have become accustomed to in legacy fields of historiography.  This relatively novel field of study presents exciting possibilities for historians to corroborate historical evidences with genetic confirmations.  However, when applied to the African continent, particularly North and East Africa, there is a growing body of evidence suggesting the field suffers from systemic methodological inconsistencies and Eurocentric interpretive biases. This paper critiques five influential studies—Scheunemann et al. (2017), Llorente et al. (2015), Salem et al. (2025), Moubtahjj et al. (2024), and Morez et al. (2025)—through the lens of Lachance and Tishkoff’s (2013) seminal review on SNP ascertainment bias. By examining discrepancies in analytical weighting (e.g., fluctuating prioritisation of PCA, ADMIXTURE, and qpAdm), inconsistent reference population selection, and interpretive asymmetries in explaining African versus Eurasian ancestry, we reveal deep structural issues within the field which lead to biased reporting and a tendency for politically charged abstracts and conclusions.  These skewed narratives are then sensationalised in media headlines.  We argue for a paradigm shift towards more holistic African-centered methodologies, equitable genomic sampling, and historically contextualized interpretations.

“…it is imperative that researchers are aware of the effects of SNP ascertainment bias”

Lachance & Tishkoff (2013)

Introduction 

The interpretation of ancient DNA has revolutionized our understanding of human prehistory. Yet, in the case of Africa—the most genetically diverse continent and the cradle of humanity—studies often rely on analytical frameworks and genotyping tools that fail to reflect this diversity. This paper critically evaluates how methodological biases and historical narratives shape the conclusions of major ancient DNA studies focusing on African populations, with emphasis on North and East Africa.

The Novelty and Limitations of Genetics in Historiography 

Despite its growing influence, ancient DNA research is a relatively new scientific field. Its application to historiography is still in early stages, and the temptation to draw definitive conclusions from limited datasets remains problematic. Across most ancient populations—including those in Africa—the number of high-quality, securely dated genomes remains far too low to support sweeping historical generalizations. Interpretations based on a handful of individuals are frequently extrapolated into narratives that imply continental-level trends, when in reality, the genetic landscape of ancient Africa remains vastly underexplored. Without broad and diverse genomic sampling, and in the absence of interdisciplinary corroboration, genetic studies risk overreaching in their claims.

“One advantage of whole genome sequencing is that SNP ascertainment bias is reduced compared to alternative genotyping technologies. This lack of SNP ascertainment bias is critical for accurate population genetic analyses where allele frequency distributions are used to infer demographic history…”

Lachance & Tishkoff (2013)

Inconsistent & Fluctuating Methodological Weighting of PCA, ADMIXTURE, and qpAdm 

Across the five studies, there is notable inconsistency in the emphasis placed on different analytic tools:

• In Scheunemann et al. (2017), ADMIXTURE and f3-statistics are used to emphasize the “sub-Saharan” component of post-Roman Egyptian mummies, but PCA, which clusters these individuals closer to East Africans, is de-emphasized.
• Llorente et al. (2015) leans heavily on outgroup statistics and ADMIXTURE to highlight Eurasian input in a 4,500-year-old Ethiopian genome, while downplaying the African substrate and the limitations of the SNP panel.
• In Salem et al. (2025), the authors rely almost exclusively on outgroup statistics and qpAdm while minimizing the relevance of PCA, which shows affinities between the Takarkori individuals and modern Sahelian groups like the Fulani.
• Moubtahjj et al. (2024) focuses on isotopic evidence but draws genetic parallels without discussing ascertainment bias or PCA relationships with African groups.
• Morez et al. (2025) demonstrates similar issues, using qpAdm to infer Eurasian-related ancestry in an Old Kingdom Egyptian without fully reconciling these conclusions with ADMIXTURE or PCA signals clearly pointing to African affinity.

This selective use of methodology creates an inconsistent evidentiary hierarchy. Tools that support a Eurasian narrative are often elevated, while those suggesting African continuity are marginalized or treated as secondary. Morez (2025) entirely discarded the consistent outcomes of multiple PCA results and admixture clustering consistently relating Takarkori to the geographically and historically relevant Fulani and Kenyan Pastoralists of Africa, instead opting to elevate the importance of F(ST) Outgroup Analysis – which introduced substantial distance between Africans and the Takarkori samples.  No other study denigrates the outcomes of multiple PCA and Admixture clustering in this manner.

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Narrative Asymmetry and Historical Framing 

The interpretive framework of these studies often mirrors outdated colonial narratives:

• In Scheunemann et al. (2017), the appearance of African ancestry is almost exclusively attributed to trans-Saharan slave trade, while Eurasian admixture is left unexplained, normalized, or attributed to migration.
• No mention is made of well-documented historical slave trades from the Eurasian steppe, Anatolia, or southern Europe into Egypt, despite ample archaeological and textual support.
• Llorente et al. (2015) presents Eurasian admixture in East Africa as evidence of a massive back-to-Africa event without fully addressing the potential for deep shared ancestry or the limitations of the SNP panel used.

This pattern of over-explaining African components as recent, invasive, or disruptive while treating Eurasian elements as normative or ancestral creates an imbalance in historical interpretation.

“SNP ascertainment bias is the systematic deviation of population genetic statistics from theoretical expectations, and it can be caused by sampling a nonrandom set of individuals or by biased SNP discovery protocols. Unless the whole genome of every individual in a population is sequenced there will always be some form of SNP ascertainment bias.”

Lachance & Tishkoff (2013)

Exploitation of Sensationalist and Racially Charged Narratives 

In several studies, scientific interpretations are undermined by sensationalist or politically charged language that appears disconnected from the actual data. For example, Scheunemann et al. (2017) was widely publicized with headlines implying that ancient Egyptians were genetically European and only became “Sub-Saharan” due to slavery. This headline narrative, unsupported by archaeological or genetic evidence, reflects a broader trend of weaponizing genetic data to reinforce anti-African sentiment. Similarly, Morez et al. (2025) disproportionately emphasized Eurasian admixture while virtually ignoring Africa’s relevance to the subject individual’s ancestry, despite clustering analyses and geographic context pointing toward strong African connections.

The framing and public communication of these studies often do more to confuse than clarify, reinforcing racially biased interpretations while presenting them as objective scientific fact.

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The Eurocentric Genomic Pipeline – From Data Collection to Interpretation 

The issues highlighted above are not merely analytical; they are embedded in the entire data pipeline:

• Data collection: Many African regions remain vastly under-sampled, especially in the Sahel, Nile Valley, and Central Africa.  This remains the case in spite of the significant excess in genomic diversity seen on the African continent which geneticists consistently agree requires more, not less sampling on the continent to compensate for.
• Genotyping arrays: Panels continue to be biased toward Eurasian SNPs.
• Reference populations: Key African groups are often missing from qpAdm or f-stat models, leading to substitution by Eurasian proxies.
• Analytic tools: Tools like qpAdm and outgroup f3/f4 are sensitive to reference panel completeness and SNP coverage—a fact often unacknowledged.
• Narrative framing: Conclusions frequently lean toward a Eurasian-centric storyline, reinforced by methodological and reference limitations.

Recommendations for Reform

To resolve these issues and promote scientific integrity in African ancient DNA studies, we propose:

• Development and use of African-specific SNP panels.
• Prioritization of whole-genome sequencing over sparse SNP arrays.
• Inclusion of broader and more relevant African reference populations in all models.
• Methodological transparency and consistency across studies.
• Critical engagement with historical narratives, avoiding over-simplistic or Eurocentric explanations.
• Greater editorial oversight in the framing and promotion of findings, particularly to avoid racial sensationalism in public discourse.

“The value of population genetic data is maximized when researchers are aware of existing biases… whole genome sequencing reduces the amount of ascertainment bias, we encourage researchers to use high-coverage sequencing data whenever it is feasible.”

Lachance & Tishkoff (2013)

Conclusion 

The studies examined here represent important milestones in ancient African genomics, but they also illustrate deep methodological and narrative flaws that require urgent correction. Without reform, the field risks perpetuating a skewed vision of African history rooted not in evidence, but in the legacy of biased scientific frameworks – continuing a dying legacy of the deliberate European misrepresentation of history.

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References:

• Lachance, J., & Tishkoff, S.A. (2013). SNP ascertainment bias in population genetic analyses: Why it is important, and how to correct it. Bioessays, 35(9), 780–786.
• Scheunemann, V. et al. (2017). Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods. Nature Communications.
• Llorente, M.G. et al. (2015). Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa. Science.
• Salem, R. et al. (2025). Ancient DNA from the Green Sahara reveals ancestral North African lineage. Nature.
• Kittles, R. A. & Keita S. O. Y (1999). Interpreting African Genetic Diversity. African Archeological Review.
• Shriner, D. & Keita, S. O. Migration route out of Africa unresolved by 225 Egyptian and Ethiopian whole genome sequences. Front. (2016).
• Henn, B. M. et al. Genomic ancestry of North Africans supports back-to-Africa migrations. PLoS Genet. 8, e1002397 (2012)