Tutankhamun's immediate family are interesting not just because Tutankhamun's tomb was found "recently" and was intact when discovered. Tutankhamun was Pharaoh towards the end of the 18th Dynasty, a dynasty that ruled Egypt from c.1550BC to c.1295BC at the start of the New Kingdom period. The Pharaohs before him are known to be Amenhotep III, Akhenaten (initially known as Amenhotep IV), Smenkhare (a very enigmatic figure) then Tutankhamun. Akhenaten has attracted a lot of interest because during his reign he changed the religion of Egypt from a polytheistic one where the priests were the intermediaries with the gods to a monotheistic one where the Pharaoh was the only intermediary, all blessings flowed through him. He also moved the capital of Egypt from Thebes (where the great temples to Amun were) to Amarna where he constructed a new city with only temples to the Aten, his one god. This new religion & capital did not long survive Akhenaten - during Tutankhamun's reign the old ways were gradually reinstated and the capital moved back to Thebes.
Because of the religious changes Akhenaten, Smenkhare & Tutankhamun were fairly thoroughly removed from the historical record of the Egyptian people - some things survive, particularly at Amarna and in Tutankhamun's tomb, but their names are generally not in the King Lists of later Pharaohs or other documents. This means that things like the family relationships between them are not well documented. What is known is that Amenhotep III was married to Tiye, the daughter of Thuya and Yuya. Akhenaten is attested as their son. After that the relationships are more murky - was Tutankhamun a younger brother of Akhenaten? or his son? if his son, then by which wife? I think it's accepted that he's not the son of Nefertiti (Akhenaten's senior wife) but there are multiple other candidates. And who Smenkhare is and if he really existed is even more obscured - one theory is even that this could be a name (and male persona) that Nefertiti took to be Pharaoh after Akhenaten's death, other than that he could be a younger brother of Akhenaten or an older brother of Tutankhamun (and both of them sons of Akhenaten). Or he may not exist, he's mentioned so rarely that this might be misunderstanding of the texts available.
And there is a lot of speculation around Tutankhamun's state of health & cause of death. The art style of the Amarna era is odd - the royal family are represented with odd looking bodies, which has lead to speculation that they had various genetic disorders. And Tutankhamun died young (age 19), so was he ill? was he murdered? was it an accident?
So this paper presents three strands of evidence to look at all these questions. First they present genetic data on 11 mummies, including Tutankhamun and putative members of his immediate family, and use these to construct a 5 generation tree of relationships. This confirms the identity of some of mummies that were less well attested (and some previously totally unidentified), and puts Tutankhamun into context with his predecessor Pharaohs. He is shown to be the grandchild of Amenhotep III and Tiye, via two of their children - his parents were full siblings. Because of the existence in the historical record of Smenkhare it isn't really possible to say if Akhenaten is his father or not (although the paper states that in their opinion this is most plausible). The two fetuses found buried in Tutankhamun's tomb may be his daughters (rather than ceremonial offerings), but the identity of their mother isn't clear. The previously well identified mummies were Tutankhamun, Thuya and Yuya. It is now possible to be sure that the mummy of Amenhotep III is indeed correctly identified, and a previously unidentified mummy (known as K35EL) is his wife Tiye. Mummy KV55 may be Akhenaten (tho may also be Smenkhare or a different son of Amenhotep III as I note above), and KV35YL is Tutankhamun's mother and a full sibling of his father.
They then present an anatomical examination of those same mummies and dismiss any possibility of a diagnosis of a feminising genetic disorder, but show that clubfeet and cleft palates (amongst other things) ran in the family - unsurprising in some ways due to the level of inbreeding that both the historic record and the genetic analysis demonstrate.
And finally they look for evidence of a selection of diseases including Black Death, tuberculosis, leprosy, malaria. The only one present was malaria, with both Tutankhamun and his great-grandparents showing evidence of multiple infections with the parasite. They then speculate that Tutankhamun's death was really due to a multitude of things which then overwhelmed him - he was weak due to his congenital defects and repeated malaria infections, then a severe fracture to his leg would combine with those to lead to his death.
I pretty much have to take the anatomical data, and the egyptological discussion, on faith - I have insufficient knowledge in either of those fields to examine the data critically. The genetic analysis on the other hand is closer to my own field, so I can poke at it with a more professional & critical eye. Though you should bear in mind that I'm 5 years out of date and this wasn't quite my field when I was current. So before I go through the actual data, here's some thoughts on the methods/presentation.
They don't discuss the details of the extraction of the DNA from the bones of the mummies - they do however cite 4 papers (only 2 of which have overlapping authors with this paper) for the method they use, so I'm inclined to think (without reading those papers) that this is a known and tried method in the field of ancient DNA extraction.
They use commercially available kits to do the genetic fingerprinting, from a quick glance through the company's website they're used for more modern forensic applications too. I was, though, concerned that although they use 16 markers on the Y-chromosome analysis they only use 8 markers for the autosomal DNA (the rest of the DNA in the nucleus that is not sex chromosomes). The kit seemed to allow you to test more markers than that - but they don't mention why only 8. Was it that they had good data for those 8? or is this an accepted practice? (as I said, this isn't quite my field). Some note of that might have been nice.
They did analysis on 30 samples for each mummy, taken from different biopsies - it might've been nice to have seen a figure with the biopsy locations marked on it (in the supplemental data perhaps). And it would've been nice to see the numbers - the data given is noted as the "majority", but I think I would've liked to see the actual figures. It makes a difference if something came up in 16 of the samples or in 29 of the samples.
I would also have liked to see some controls! In the Y-chromosome analysis they do compare the three male mummies with another unrelated one. But in the bulk of the data they don't show the control data. It's not even clear if it's been done, although there is a line in the methods section about using 4 mummies from earlier in the 18th dynasty (not just royal family mummies) as a genetic control group. I would have liked to see this data (in the supplemental data again, maybe, not the main paper). They do, however, make it clear that everyone involved in the handling of the DNA was also analysed, and they state none of them had the same profile. It's unlikely anyone who handled the mummies prior to this study could have contaminated the data as the sample were taken from within the bone.
The mummies tested were:
- Thuya (female)
- Yuya (male)
- Amenhotep III (almost certainly identified, but less sure than other named ones, male)
- KV55 (an unknown male mummy thought to be maybe Akhenaten)
- KV35EL (an unknown older female mummy)
- KV35YL (an unknown younger female mummy)
- Fetus 1 (from Tutankhamun's tomb, female)
- Fetus 2 (from Tutankhamun's tomb, female)
- KV21A (unknown female)
- KV21B (unknown female)
The last 4 have very patchy data and this means it's very hard to draw any conclusions about them and their relationships.
The Y-chromosome analysis data isn't shown in a table or figure, but is just stated in the text. The three male mummies tested (Amenhotep III, KV55, Tutankhamun) share the same profile, so are in the same paternal line. You can't draw any other conclusions about precise relationships from that. They also didn't match modern people involved in the work, didn't match an older mummy thought to be unrelated, and no Y chromosomes were found in mummies thought to be female (a good cross check, and confirms the sex of them).
The fingerprinting they've done is short tandem repeat (STR) analysis - there are sections of DNA that are repeats of short sequences. It doesn't appear to do anything, and as a result these regions mutate more than functional sections of the genome, so can be used to trace familial relationships (unless of course you get a mutation right between two generations of the family you're looking at, but that is still a rare occurrence). For any given marker what they do is look at how many repeats the sample has - there will be 2 numbers of repeats, as chromosomes come in pairs. Brief explanation - the DNA in a person is organised into 46 chromosomes, 22 pairs of non-sex chromosomes normally known by numbers and 2 sex chromosomes (XX for women, XY for men). You inherit one of each pair of chromosomes from your father and one from your mother, and this is randomly organised. So if your mother's chromosomes are labelled A & B, and your Dad's are C & D, you could inherit chromosome 1 as A (from your mother) & C (from your father), chromosome 2 as A&D, chromosome 3 as B&D, chromosome 4 as A&D and so on; a full sibling of yours would get a different random selection, ie 1 B&D, 2 A&D, 3 B&C, 4 A&C. And importantly you MUST get one in each pair from each parent, you'll never have 1 A&B for instance.
So with the STR analysis you get a bunch of numbers for repeats of the short section for each marker, and you use markers spread across the chromosomes so that they are independently inherited. To look at one of the markers for Tutankhamun's family (a marker called FGA), Tutankhamun has 23 repeats on both chromosomes. Amenhotep III has 23/31, KV35EL (Tiye) has 20/26. So Tutankhamun cannot be the child of those two people - where would he get the second 23 from? KV55 has 20/23 - so you see he can be son of Amenhotep III/Tiye, and KV35YL has 20/23 as well (so she can be a daughter). And Tutankhamun can be the son of KV55/KV35YL because he can get one 23 from each of them.
Basically you do this sort of comparison across all the markers you look at - 8 in this case. And calculate probabilities for each trio (mother/father/child), they say 99.73% is the accepted standard for "practical proving" the relationship. The data they have in excess of this figure in all cases (tho as I said above I would've liked to see n numbers for the samples, and possibly more markers) so seems very solid.
The data shows:
KV35EL is the daughter of Thuya and Yuya.
KV35EL and Amenhotep III are the parents of KV55 and KV35YL.
KV55 and KV35YL are the parents of Tutankhamun.
Taking these three together with the historical record allows definite identification of KV35EL as Tiye (daughter of Thuya and Yuya known to have married Amenhotep III), and solidifies the identification of Amenhotep III's mummy.
They also state that they think KV55 is most plausibly Akhenaten - but just seem to dismiss Smenkhare out of hand, and I'm not sure the data support that. If KV55 is indeed Akhenaten, then KV35YL being a full sibling is interesting - why's she not the senior wife, being higher status than Nefertiti (who is not King's Daughter in the historical record, so not KV35YL)?
They do speculate on the data from the fetuses, that it isn't ruled out that they are daughters of Tutankhamun, and possibly KV21A but the data is so patchy that no firm conclusions can be drawn (and indeed they don't try to).
Dear lord that got long :)