DNA, Identity, and the Amarna Royal Dead
One of the most debated questions in Amarna studies is the identity of Pharaoh Ankhkheperure Neferneferuaten, the female king who ruled briefly between Akhenaten's death and Tutankhamun's coronation. The scholarly consensus, championed most thoroughly by Aidan Dodson in Nefertiti, Queen and Pharaoh of Egypt, identifies this ruler as Nefertiti herself. It is a carefully constructed argument supported by significant evidence.
I should be clear about what I am and what I am not. I am not a professional Egyptologist. I am a writer of historical fiction who has read the scholarship as closely as I can, particularly the 2010 Hawass DNA study, the skeletal analyses of the KV55 mummy, and the titulary inscriptions, and who has made specific interpretive choices for The Amarna Mysteries based on that reading. Where the evidence is clear, I have followed it. Where it permits more than one reading, I have chosen the interpretation that I believe best fits the overall pattern. Professional scholars may well disagree with some of these choices, and they are far better qualified than I am to make that judgment. This is a popular-audience, authorial interpretation built on existing scholarship; where I take a position it is because it best serves the story and fits one defensible reading of the evidence.
This article explains the reasoning behind the interpretation adopted in the series. Readers of The Poisoner's Throne will recognize elements of it in the novel's Prologue, but this article goes into more detail about the reasoning behind those choices.
The case for identifying Nefertiti as Neferneferuaten is strong, and it deserves a fair hearing.
First, the shared name. From around Year 4/5 of Akhenaten's reign onward, Nefertiti's full cartouche name was Neferneferuaten-Nefertiti. The female pharaoh's nomen was Neferneferuaten. The overlap is striking and, for many scholars, compelling.
Second, Nefertiti's exceptional status during Akhenaten's reign. She was depicted smiting enemies, a pose traditionally reserved for the pharaoh, in imagery that was part of the broader Amarna artistic revolution. She wore crowns associated with kingship. Her titles and epithets went far beyond what was typical for a Great Royal Wife.
Third, the KV62 box fragment. A broken box lid from Tutankhamun's tomb (Cairo JE61500a) names Akhenaten, Neferneferuaten, and Queen Meryetaten in precisely the positions where one would expect Akhenaten, Nefertiti, and their eldest daughter. The absence of Smenkhkare despite the presence of his wife has been read as indicating that Meryetaten was now a widow.
Fourth, the epithet. Marc Gabolde's 1998 discovery that Neferneferuaten's nomen sometimes carried the epithet akhet-en-hi.es, meaning "beneficial for her husband," points to a woman who had been married to a king. This was reinforced by Allen and Gabolde's reassessment of the palimpsest inscriptions on the miniature gold coffins from KV62, which strengthened the case that the epithet pointed to Nefertiti. Nefertiti was unquestionably Akhenaten's principal wife.
These are substantial arguments. Dodson himself acknowledges that absolutely unequivocal evidence remains elusive, but he considers Nefertiti the overwhelmingly obvious candidate. I have great respect for his work, which has been one of the foundational sources for the entire series. The interpretation I have adopted differs from his, and what follows is my attempt to explain why.
The 2010 DNA study published in JAMA confirmed several relationships beyond reasonable doubt. Tutankhamun was the son of the KV55 male and the KV35 Younger Lady. Those two individuals were full siblings: both children of Amenhotep III and Queen Tiye. The Elder Lady from the same tomb was confirmed as Tiye herself.
These core findings are not in serious dispute, even among scholars who question aspects of the study's methodology.
What remains genuinely open is the identity of the KV55 male. The study's authors identified him as "most probably Akhenaten," but acknowledged this was a preferred interpretation rather than the only one consistent with the data. As Dodson has pointed out, the genetic profile identifying someone as "son of Amenhotep III and Tiye" and "father of Tutankhamun" would apply equally to any full brother of Akhenaten. Both brothers would have inherited their alleles from the same two parents, and the study's markers can identify whose children they were but cannot determine which son of that couple is being tested.
This ambiguity is what opens the door to an alternative reading: that the KV55 male might be Smenkhkare rather than Akhenaten.
The KV55 skeleton has been studied repeatedly since its discovery in 1907, and the age at death has been a persistent source of disagreement. The majority of assessments place it in the early twenties. Grafton Elliot Smith estimated 25 to 26 years (with a margin of error of two to three years) in 1912. Douglas Derry revisited the remains in 1931 and concluded that they were too young to be Akhenaten. Harrison concluded a range of 17 to 25 years in 1966. Bob Brier, an anatomist who examined five separate skeletal indicators, arrived at an average of approximately 20.5 years.
The 2010 CT scan suggested a significantly older age, but this was met with rebuttals arguing for 18 to 23 years. The Spitalfields study of 18th and 19th century remains with known ages of death has shown that skeletal aging of pre-modern remains can involve systematic errors, with some younger individuals appearing considerably older by standard criteria. Dodson discusses this finding and considers it supportive of the lower age estimates.
Akhenaten reigned for 17 years. Even if he came to the throne as young as 15, he would have been at least 32 at death. If the majority of skeletal assessments are correct, the KV55 body is too young to be Akhenaten. Dodson himself concludes that if the majority view is correct, "the body cannot be that of Akhenaten, leaving Smenkhkare as the only candidate." Other studies, including CT-based work, have argued for an older age, so the matter is not settled; but Smenkhkare remains the most widely proposed alternative.
There is another piece of the puzzle that I found particularly significant when deciding how to construct the genealogy for the series.
The 2010 DNA study also examined the KV21A mummy and found her profile partially compatible with being the mother of the two stillborn fetuses (317a and 317b) found in Tutankhamun's tomb, whom the study identifies as Tutankhamun's daughters. The authors noted, however, that the data were "not statistically significant to define her as Ankhensenamun." If KV21A is nonetheless Ankhesenamun, as many scholars treat as likely given that she is Tutankhamun's only known wife, that identification has implications for the KV55 question.
However, KV21A's DNA does not match the KV55 skeleton as her father. This is a different kind of test from the one that cannot distinguish between brothers. While both Akhenaten and Smenkhkare inherited alleles from the same parents, each received a different combination at each locus. A paternity test checks whether a child carries one allele from the proposed father at every tested marker. If the numbers don't match at even one locus, paternity is excluded. The KV55 skeleton's specific alleles exclude him as KV21A's father, but Akhenaten, carrying a different combination from the same parents, could have had the right ones.
Historical records confirm that Ankhesenamun was Akhenaten's daughter. If KV21A is Ankhesenamun, then KV55 cannot be Akhenaten. If KV55 is Akhenaten, then KV21A cannot be Ankhesenamun. Both identifications cannot be correct simultaneously.
Mainstream scholarship generally treats the KV21A identification as tentative and retains KV55 as Akhenaten. For the series, I chose the opposite resolution: accepting KV21A as Ankhesenamun and KV55 as Smenkhkare. This is not because I believe the scholarly consensus is mistaken, but because this reading resolves more of the apparent contradictions in the evidence simultaneously, and because it provided the strongest foundation for the story I wanted to tell.
Two points of context. First, Dodson agrees that KV55 is most probably Smenkhkare but retains Akhenaten as Tutankhamun's biological father, arguing either that full brothers would share the genetic markers tested by the 2010 study, or that three generations of first-cousin marriages could produce an equivalent genetic signature in the final generation. The reconstruction in The Amarna Mysteries takes a different view on this parentage question, following the straightforward reading that the Younger Lady is Tutankhamun's biological mother. So far as I have been able to establish, Dodson has not considered the Younger Lady as a candidate for Neferneferuaten; the identification is a divergence from his reconstruction rather than a position he has examined and rejected.
If the KV55 male is Smenkhkare rather than Akhenaten, then Tutankhamun's mother, the Younger Lady, was the sister of both men: a daughter of Amenhotep III and Tiye.
Amenhotep III and Tiye had several daughters, most poorly attested in the historical record: Sitamun (elevated to Great Royal Wife), Iset, Henuttaneb, Nebetah, and possibly Beketaten. The Younger Lady was likely one of these princesses who became Akhenaten's sister-wife and bore Tutankhamun.
A statistical analysis by Juan Antonio Belmonte strengthens this reading. The genetics are not intuitive, but the logic is worth walking through.
At every tested locus, the Younger Lady has one allele that matches Amenhotep III and one that matches Tiye. This is exactly what you would expect from their daughter. The question is whether a granddaughter could show the same pattern.
Consider Meryetaten, the most commonly proposed granddaughter candidate. She was the daughter of Akhenaten and Nefertiti. Akhenaten was a son of Amenhotep III and Tiye, so at each locus he carried one allele from each of his parents. When he fathered a child, he passed along only one of his two alleles at each marker. For Meryetaten to look genetically identical to a direct daughter of Amenhotep III and Tiye, Akhenaten would have needed to pass along, at every single tested locus, only those alleles he had inherited from Amenhotep III and none of the ones he had inherited from Tiye, or vice versa. Each locus is an independent coin flip, and the odds of getting the "right" result at all eight tested markers are very low. Belmonte calculated the probability at less than 6%.
But there is a second problem. Nefertiti's contribution matters too. For a granddaughter to perfectly mimic the profile of a daughter of Amenhotep III and Tiye, Nefertiti's alleles would need to match Tiye's at every locus where Akhenaten's matched Amenhotep III's, or match Amenhotep III's at every locus where Akhenaten's matched Tiye's. The most straightforward way this could happen is if Nefertiti herself were also a child of Amenhotep III and Tiye, making Akhenaten and Nefertiti full siblings.
This is where the diploid alleles become relevant. At any given locus, each parent has two alleles and passes one to the child. When both parents are closely related, they are more likely to carry the same allele at a given locus. If both parents pass the same number, the child ends up with two identical copies: a diploid allele. This is not harmful in itself, but it is a detectable genetic signature of inbreeding.
The Younger Lady has no diploid alleles at any of the eight tested markers. This is consistent with parents who were related but not closely, which is what we know about Amenhotep III and Tiye. By contrast, Tutankhamun, whose parents were full siblings, shows diploid alleles at two of the eight loci. If the Younger Lady were the daughter of two siblings (as she would need to be in the Meryetaten scenario), we would expect to see at least some diploid alleles. Their absence fits a daughter of Amenhotep III and Tiye far better than it fits a granddaughter born to closely related parents.
Neither of these arguments is conclusive on its own. But taken together, the low probability and the absence of diploid alleles both point in the same direction: the Younger Lady's genetic profile is most naturally explained as that of a daughter of Amenhotep III and Tiye, not a granddaughter.
The DNA also rules out several other candidates. The Younger Lady cannot be Nefertiti, who never held the title "King's Daughter" and whose family background connects her to Ay's household rather than to the royal line of Amenhotep III. She cannot be Meryetaten, who was Akhenaten's daughter rather than his sister, nor Kiya, who was never titled as a king's daughter or sister.
Belmonte's position is similar. His statistical argument supports identifying the Younger Lady as a daughter of Amenhotep III and Tiye, married to KV55 (whom he also reads as Smenkhkare), and as the mother of Tutankhamun, a reconstruction the series follows directly. On Neferneferuaten's identity, Belmonte's preferred reading is Nefertiti, though he notes that Meritaten cannot a priori be ruled out. The further step I take, identifying the Younger Lady herself with Neferneferuaten, is one that Belmonte does not consider rather than one he has weighed and dismissed.
I think this distinction matters. Neither the Nefertiti identification nor the Younger Lady identification is established by direct inscriptional evidence. No text names any woman with the full pharaonic titulary of Ankhkheperure Neferneferuaten and an unambiguous personal name. Both identifications are inferences from circumstantial patterns, and the series' reading sits alongside the majority reconstruction rather than beneath it.
In The Amarna Mysteries, the Younger Lady is an unnamed sister of Akhenaten: the biological mother of Tutankhamun and the woman who ruled briefly as Pharaoh Ankhkheperure Neferneferuaten. That identification is speculative — plausible and defensible, but not proven. I present it explicitly as the narrative choice underpinning the novels.
The strongest argument for the Nefertiti identification remains the shared name, and I want to be transparent about the limits of my counter-reading.
"Neferneferuaten" means "Beautiful are the Beauties of the Aten." In the context of Akhenaten's religious revolution, this functioned as a theological statement as much as a personal name. Nefertiti adopted it as a second cartouche name from Year 5 onward. It is at least possible that another royal woman could have received or adopted the same name when being elevated to pharaonic status within the same religious framework. I recognize that possibility is not the same as evidence, and that the name overlap remains a strong point in favor of the consensus view. It is circumstantial rather than conclusive, but it is the single strongest piece of circumstantial evidence in the debate.
The epithet "beneficial for her husband" is also cited as pointing specifically to Nefertiti. However, it would apply to any woman who had been married to a king. A sister-wife of Akhenaten would qualify.
One finding I consider particularly relevant is the Year 16 graffito from Dayr Abu Hinnis, discovered by the Dayr al-Barsha Project, which names Nefertiti as "Great Wife of the King" on the fifteenth day of the third month of the flooding season in Year 16 of Akhenaten's reign. She was still queen, still identified by her queenly titles, at the very end of Akhenaten's reign. No inscription has been found that explicitly names Nefertiti with pharaonic titles. The transition from queen to pharaoh is inferred from the shared name and the circumstantial evidence of her exceptional status, but it has not been directly documented.
The KV62 box fragment (Cairo JE61500a) is often cited in the scholarly discussion, and it deserves careful attention. The object is a broken box found in the entrance stair filling of Tutankhamun's tomb. What survives is the central strip of the vaulted lid; the rest of the box is lost.
The surviving strip names Akhenaten, King Ankhkheperure Neferneferuaten, and Queen Meryetaten. Dodson reads the absence of Smenkhkare as evidence that he was already dead. This is a reasonable reading, but it depends on the assumption that the surviving fragment represents the complete set of names that appeared on the object. Given that the box is broken and most of it is missing, Smenkhkare's name could have appeared on portions that did not survive. The fragmentary boxes provide suggestive evidence, but an argument from absence is only as strong as the completeness of the evidence, and in this case the evidence is genuinely fragmentary.
A second box from KV62 (Cairo JE61495) originally bore the cartouches of Neferneferuaten and Meryetaten, later overwritten with those of Tutankhamun and Ankhesenamun. This fits the well-documented pattern of Neferneferuaten's funerary goods being systematically appropriated for Tutankhamun's burial. The overwriting tells us that the equipment was recycled. It does not, by itself, tell us who Neferneferuaten was.
The Younger Lady's mummy shows severe trauma to the left side of the face. (The implications for the succession crisis are significant.) CT scans have confirmed this injury occurred around the time of death, not as post-mortem damage. This suggests a violent end rather than natural causes.
Dodson notes that Neferneferuaten's kingly burial goods were never used for her but were instead appropriated for Tutankhamun, indicating that she was not buried as a king. He observes that this strongly suggests her reign ended badly. The violent trauma on the Younger Lady's mummy is consistent with that assessment.
Nefertiti's ultimate fate is not demonstrably recorded in surviving inscriptions; any reconstruction is necessarily tentative. If she was not Pharaoh Neferneferuaten, then the question of her fate remains genuinely open. Her mummy has never been conclusively identified. No burial has been found. Her disappearance from the historical record after Year 16 is not necessarily evidence of death; it may be evidence of something else entirely.
In The Amarna Mysteries, I explore one possibility: that Nefertiti's disappearance was deliberate. But that is fiction, built upon the gaps in the evidence. What matters is that the evidence permits, though it does not require, an interpretation in which Nefertiti and Neferneferuaten are different women.
Every reconstruction of this period involves choices about which evidence to prioritize and which ambiguities to resolve in which direction. What I have tried to do is adopt interpretations that are consistent with the published evidence, that resolve as many contradictions as possible, and that provide the strongest foundation for the story.
The interpretation I adopted is this:
The Younger Lady (KV35YL) is an unnamed sister of Akhenaten, daughter of Amenhotep III and Tiye, and the biological mother of Tutankhamun. She ruled briefly as Pharaoh Ankhkheperure Neferneferuaten before being murdered. Her violent death is preserved in the trauma visible on her mummy. Her funerary equipment was appropriated for her son Tutankhamun's burial.
The KV55 skeleton is Smenkhkare, not Akhenaten, consistent with the majority of skeletal age assessments and with Dodson's own conclusion that the body is more likely a brother of Akhenaten than Akhenaten himself.
KV21A is Ankhesenamun, mother of Tutankhamun's stillborn daughters, consistent with the DNA evidence and free of the incompatibility that arises from identifying KV55 as her father.
Nefertiti was Tutankhamun's stepmother, never his birth mother, and never pharaoh. Her fate remains an open question, as it should.
Where the DNA evidence is clear, I have followed it. Where it permits multiple interpretations, I have chosen the reading that best resolves the contradictions while preserving the genuine mysteries. The enduring question of what happened to Nefertiti is one of those mysteries, and I believe it deserves to remain one.
The Royal Women of the Amarna Period — Nefertiti, Kiya, and the daughters at the centre of the succession debate.
Succession and Aftermath — The broader crisis between Akhenaten's death and Tutankhamun's coronation.
Akhenaten and the Aten Revolution — The reign that created the political conditions for Neferneferuaten's rule.
Evidence and Power in the Amarna Period — How the archaeological record shapes what we know and what remains debated.
The Amarna Period: Overview — The broader historical context of the identity debate.
The Amarna Mysteries — The four-book series built on this history.
How The Amarna Mysteries Are Made — The creative and research process behind the series.
Belmonte, J.A., DNA, Wine & Eclipses: the Dakhamunzu Affaire (2013)
Brier, B., The Murder of Tutankhamen (1998)
Derry, D.E., Note on the Skeleton Hitherto Believed to Be That of King Akhenaten (1931)
Dodson, A., Nefertiti, Queen and Pharaoh of Egypt: Lives and Afterlives (2020)
Dodson, A., Amarna Sunrise: Egypt from Golden Age to Age of Heresy (2014)
Dodson, A., Amarna Sunset: Nefertiti, Tutankhamun, Ay, Horemheb, and the Egyptian Counter-Reformation (2009)
Gabolde, M., D'Akhenaton à Toutânkhamon (1998)
Gabolde, M., L'ADN de la famille royale amarnienne et les sources égyptiennes (2013)
Harrison, R.G., An Anatomical Examination of the Pharaonic Remains Purported to Be Akhenaten (1966)
Hawass, Z. et al., Ancestry and Pathology in King Tutankhamun's Family (2010)
Kloska, M., The Role of Nefertiti in the Religion and the Politics of the Amarna Period (2016)
Smith, G.E., The Royal Mummies (1912)
Van der Perre, A., The Year 16 Graffito of Akhenaten in Dayr Abū Ḥinnis (2014)
A.J. Tilke is the author of The Amarna Mysteries, a four-book historical fiction series set in ancient Egypt's 18th Dynasty. The Poisoner's Throne (Book 1) publishes June 2026, followed by The Restoration Trilogy — The Hittite Reckoning, The Restoration Murders, and The Dakhamunzu Affair — later in 2026. A short-story anthology, The Twelve Hours of Night, is planned for 2027.