There one can see the alleles at certain loci of various royal mummies, beginning with the oldest generation, Yuya and his wife, Thuya, down to two tiny little girls, who are nameless and could be the ill-fated children of Tutankhamun. Remember, one inherits one allele from each parent at a given locus.
No Matching Wedding Bands
Even though the mummy known as the Younger Lady from KV35 [KV35YL] and the remains from KV55 appear to be the parents of Tutankhamun, that is no guarantee that they were--or that they were even husband and wife. When it comes to females breeding with their full brothers--and because there is the potential of offspring inheriting one of four combinations of alleles at a given locus--we cannot rule out that the KV35YL was not married to another of her full brothers, instead, whose mummy we do not have. Such a brother cannot be ruled out precisely because we cannot see his alleles at the eight loci. [15 markers are normally looked at in a paternity test but, to distinguish between two brothers, even more may be necessary.] Things can get quite complicated where there is incest, but I'll try to explain. Because, epigraphically, Tut was the son of a king, there were three candidates for his father--and this used to include Amenhotep III. Amenhotep III is out of the running now, leaving Akhenaten and his ephemeral successor, Smenkhkare. But which of these two pharaohs is KV55? Many persons are of the opinion that the remains are too young at time of death to be those of Akhenaten due to pronouncements by those who examined the skeleton in the past. However, it was most recently subjected to a CT-scan whereas Egyptian radiologist, Ashraf Selim, opined that the young man to whom the bones belonged had to be at least 22 years old when he died, but the doctor could not pinpoint the age any nearer than 22-45. That could certainly fit to Akhenaten, as well. Historically, King Akhenaten was the son of the pharaoh Amenhotep III and Queen Tiye. If KV55 is not Akhenaten but King Smenkhkare, then Smenkhkare was definitely a full brother of Akhenaten and not a son of Akhenaten, as some believed.
The Problem of Queen Meritaten
Let's say, for the sake of argument, that the KV55 individual is Smenkhkare. The only king's daughter that we know of who was his wife was a child of Akhenaten and Queen Nefertiti. The KV35YL and KV55 are full sister and brother. Their parents were Amenhotep III and Queen Tiye. However, Meritaten cannot have been the full sister of Smenkhkare if he was the son of that couple. The same difficulty would apply to Meritaten's full sisters if Smenkhkare had married any of them, in addition. Therefore KV55 and the KV35YL are not Smenkhkare and Meritaten.
Was Nefertiti the Daughter of Amenhotep III?
Many people cannot believe in this possibility as Nefertiti is never styled "king's daughter" in any of the texts where she is represented. However, we know nothing of Nefertiti before she became the Chief Wife of Akhenaten--except one textual fact. Her nurse was Tey, the wife of Ay, and this is recorded in Ay's commoner tomb at El Amarna. A girl named Mutbeneret is also depicted in this tomb who seems to be Nefertiti's sister but, unfortunately, the term "snt" can mean both "sister" and "female cousin" in the Egyptian language. The fact that Mutbeneret is depicted in their tomb may make her the daughter of Ay and Tey but there is no way to know this for certain. While the daughters of Nefertiti are always called "king's daughter" while they are children, this changes when they married. Meritaten and Ankhesenamun are not depicted with their husbands very often, but when they are they are not styled "king's daughter" any longer but only "great royal wife"--just as was Nefertiti. Regardless of all this, the DNA seems to indicate that Nefertiti could have been the daughter of Amenhotep III--and he had many. They are depicted in the tomb of Kheruef, but they are not named there. Yet...even if Nefertiti was only a half-sister of Akhenaten or a cousin [but the descendant of kings] it would not have been so far-fetched to have her as the living incarnation of Tefnut to his Shu [twin deities who sprang from Re and were also husband and wife] than if Nefertiti was a mere commoner.
A Different Spouse for KV35YL?
There is nothing preventing the KV35YL from being the mother of Tutankhamun with another man who was a full brother of the KV55 individual and who had much the same alleles at the loci. If KV55 is not Akhenaten, the latter can still have sired King Tut. A brother of KV55 could have had, for instance, 6/15 at the second locus instead of the 15/15 of KV55, although at other loci they can have had the same numbers, as do KV55 and his sister, the KV35YL. But, if Akhenaten was the father of Tutankhamun, that still leaves us with the problem of "Who is the KV35YL?" Nefertiti is seen as the wife of Akhenaten quite early in his reign. The only other wife we know of for the pharaoh is the mysterious Kiya, no more styled "king's daughter" than Nefertiti. Beyond that, it would appear that Akhenaten, in later years, attempted to have offspring with his elder daughters. But Akhenaten would have had to sire Tutankhamun with his full sister.
What the Alleles Say
You will see at the National Geographic website, that a badly-treated mummy is thought to be the best candidate for the mother of the two little babies found in the tomb of Tutankhamun. This female mummy is called KV21A, after the tomb in which her remains were discovered. One of the most interesting aspects of this mummy's DNA profile is that she has the allele 35 at D21S11, not seen there since the profile of Thuya. Allele 35 is rather rare at the locus, but makes the biggest showing in Africa, not so much Egypt where it is shown at 0.0110. Elsewhere in Africa it is definitely higher at the locus. Otherwise, in the Middle East, there is only Turkey, the So. Adana Area having the highest at 0.0070. These numbers come from the DNA of modern populations, but this may be indicative of the distant past, as well.
Also, KV21A has an extremly rare allele, 16, at the first locus, which she shares with Amenhotep III. In fact, her numbers at the locus are 10/16, exactly the same as the king. Since 16 is a much rarer allele at the first locus than 35 is at the fourth, this is most interesting. The important question is--since Tutankhamun *could* be the father of the babies and his Chief Wife was Ankhesenamun--is KV21A actually Ankhesenamun? Although Tut makes a good candidate for the father, that does not rule out other males of his family according to the 8-locus profile.
For the sake of argument, let us say Akhenaten isn't KV55 and did not have 10/12 at the first locus like KV55--but the combination of 11/16 instead [which is very possible given his known parentage]. Then where does KV21A, as Ankhesenamun, get the 10 at the first locus? Even if KV55 *is* Akhenaten, then where does KV21A get the 16? None of those numbers are present at the first locus in Yuya, Thuya, or their daughter Tiye. They only show up in the first locus with Amenhotep III. My suggestion for the best solution to the problem is this: I think it's most likely that KV21A is the offspring of a union between a daughter of Amenhotep III [and an unknown female] and a son of Amenhotep III and Queen Tiye [probably Akhenaten]. That way, whether Akhenaten had 10/12 or 11/16 at the first locus, the number required to make up the 10/16 of KV21A will be provided by the daughter of Amenhotep III, who got it from his side of the family. I suppose one might say that KV21A seems to be related to Amenhotep III any way you cut it. Even if she is merely the offspring of one of Amenhotep III's brothers. Without this connection of Nefertiti to Amenhotep III, discussed above, it is unlikely that KV21A can be Ankhesenamun and another identity would need to be sought for this mummy.
Now the allele of KV21A at the fourth locus, which is 35, may just coincidentally be the same as Thuya there. The reason I think so is the 10 of KV21A at the 6th locus. Nobody has it there in the entire family tree until KV21A and the next generation. That's why I think the grandmother of KV21A is someone unrelated to the family as represented in the tree we have so far. But further test results from these mummies, such as mitochondrial DNA, might help answer the questions.
It would have been helpful to include Thutmose IV, the father of Amenhotep III, in this family tree. Since the parents of Queen Tiye were tested, another generation from the patrilineal side would have aided in showing what "royal DNA" of the 18th Dynasty looks like. Or, rather, which alleles Amenhotep III got from his father. That way we might get a better idea of how someone like the lady, KV21A, was related to the royal line. There can be little question, however, that Yuya was a relative of Amenhotep III. They share alleles at five of the eight markers, too many for it to be coincidental. This goes a long way toward explaining why the young pharaoh was married to Tiye, Yuya's daughter. But, again, without the DNA profile of Thutmose IV, we cannot tell if Yuya was related to Amenhotep's mother or his father. My guess is--and this is mere speculation--that allele 10 that Amenhotep III introduces into the presently-known family tree at the marker D13S317 is non-Egyptian and may have been contributed to the gene pool via a foreign female. 10 at this locus does not make a very good showing in north Africa [Egypt, pooled, has only .0631 and central Egypt, el-Minia, does slightly better with .0830] or in Africa in general. However, the farther east of Egypt the higher the numbers, from Anatolia to India and best of all, the Far East. In other words, it is an Asiatic allele, with numbers as low in Europe as in most of Africa.