The Y-DNA of Richard III

A skeleton excavated from beneath a car park Leicester in 2012 seems to be that of Richard III:

In 2012, a skeleton was excavated at the presumed site of the Grey Friars friary in Leicester, the last-known resting place of King Richard III. Archaeological, osteological and radiocarbon dating data were consistent with these being his remains. Here we report DNA analyses of both the skeletal remains and living relatives of Richard III. We find a perfect mitochondrial DNA match between the sequence obtained from the remains and one living relative, and a single-base substitution when compared with a second relative… DNA-predicted hair and eye colour are consistent with Richard’s appearance in an early portrait. We calculate likelihood ratios for the non-genetic and genetic data separately, and combined, and conclude that the evidence for the remains being those of Richard III is overwhelming.   

Since it exhibits signs that its owner suffered from severe scoliosis, a condition resulting in curvature of the spine, it backs up the Shakespearean portrait of the monarch. 

Our interest here is the mismatch there is between Y-DNA extracted from the skeleton and Y-DNA sampled from descendants of Henry Somerset the 5th Duke of Beaufort, who according to history descended from Richard's 2nd great grandfather Edward III (1312-1377). What do we mean when we say that there is a mismatch between these Y-Chromosomes? There are two complementary ways to look at the question of whether Edward III is a shared ancestor of Richard III and the Somersets. Assuming a mutation rate for STRs of 1 mutation per marker per 500 generations (0.002) this number of mismatched markers is too great for Richard and the Somersets to share an ancestor who lived as recently as Edward III: 

Assuming a mutation rate for SNPs of 1/10^9 per base pair per generation, Richard Y-DNA belongs to the wrong haplogroup - it is on the wrong branch of the Y-DNA tree- for he and the Somersets to share an ancestor who lived as recently as Edward III.

The implication according to geneticists, and the media, is that there is a 'false paternity event somewhere between Edward and the Somersets. The authors of the study maintain that this is unsurprising:

...the putative modern patrilinear relatives of Richard III are not genetically related to Skeleton 1 through the male line over the time period considered. However, this is not surprising, given an estimated average false- paternity rate of 1–2%. 

But the false paternity events don't end there, for only 4 of these 5 Somerset descendants actually match each other:

The Y-chromosome results also indicate one further false-paternity event between Henry Somerset and his five contemporary, presumed patrilinear descendants.

And it turns out that there is more, for although the patrilineal line of a Frenchman named Patrice de Warren links to Richard III through the illegitimate son of Edward III's 4th great grandfather, Geoffrey Plantagenet, Count of Anjou (1113 - 1151), de Warren's Y-DNA doesn't match that of Richard III or any of the Somersets:

Professor Kevin Schürer and I were approached by Patrice de Warren who could trace his male line to Richard through Geoffrey, the Count of Anjou.  This was very exciting and as a result of the research we are revealing new information at the Science Museum into the ancestry of Richard III.

If Patrice de Warren's Y chromosome matched that of Richard III, then this would mean that the break in the Y chromosome line occurred somewhere between Edward III and Henry Somerset.  If it matched the Somerset line, then it would mean the break occurred between Edward III and Richard III.  In short, it would help narrow down where the break in the line took place.

As it happens, it's revealed that another false paternity seems to have occurred in the tree as his Y chromosome type doesn't match either of them!  The hunt continues, and another mystery has arisen! 

Yeah right. In the words of Ian Fleming's Goldfinger,“Once is happenstance. Twice is coincidence. Three times is enemy action”

A similar case involving the comparison of ancient and modern Y-DNA concerns the presumed Y-DNA of Louis XVI (1754-1793) and that of living members of the House of Bourbon, and it supports a skeptical stance towards the received understanding of Y-DNA mutation rates. Y-DNA was extracted from a cloth supposedly bloodied at the time of Louis's beheading, and belongs -like that of Richard III- to haplogroup G, while the Y-DNA of 3 living members of the House of Bourbon belongs -like 4 of the 5 living Plantagenets- to R1b. Both Y-DNA and mtDNA were extracted from a mummified head presumed to be that of Louis's 5th great grandfather Henry IV (1553-1610). 5 Y-DNA markers were recovered—an insufficient number to determine a haplogroup—but Charlier et al. concluded that because 'the partial Y-chromosome profile is extremely rare in modern human databases... both males could be paternally related: 

The likelihood ratio of the two samples belonging to males separated by seven generations (as opposed to unrelated males) was estimated as 246.3, with a 95% confidence interval between 44.2 and 9729.  

If things are as they appear to be historically and genealogically, then in the light of the results of testing living members of the House of Bourbon, and the traditional view of DNA mutation rates, this implies that there are at least 2 false paternity events - Henry IV cannot have been the biological father of Louis XIII, and there is a false paternity event between Louis, le Grand Dauphin, and Louis XVI. The difficulty becomes even more pronounced when mtDNA extracted from the head is considered. This belongs to haplogroup U, but Henry IV was maternally related, through his mother Jeanne d'Albret to Marie-Antoinette, and tests performed on a lock of her hair and her son's heart show that Marie-Antoinette's mtDNA belongs to haplogroup H. If the mummified head belonged to Henry IV, then, assuming a traditional view of mtDNA mutation rates, this implies the existence of an exceptional false-maternity event somewhere between Henry IV and Marie-Antoinette. Interestingly, the Livingstons, the Plantagenets, and the Bourbons, all form part of the same family tree. 

The Richard III and Louis XVI cases present us with a  group of incompatible premises:   

1. uniform, simple-to-complex, Y-DNA mutations
2. accurate identification of ancient remains 
3. accurate genealogy   

In the Richard III case, it is (3) that is abandoned for the sake of consistency,  in the Louis XVI case, it is (2) that is abandoned. But no one is considering that the source of the inconsistency might be the presumption contained in (1).  If we were to give up (1), we would be giving up the presumption that SNPs mutate in the strictly one way—simple-to-complex—direction of the ISOGGY-DNA tree.   It doesn’t occur to anyone to challenge 1, but I don't see why not: how much confidence should we have in these mutation rates, and in the assumption that they were always thus? After all, they are based on observations made in the tiny window of the near-present, and extrapolated more or less on faith to the unobserved and vast window of the distant-past. Imagine a wheel that turns at a seemingly constant rate within the context of the present, but in fact turns ever more slowly in the direction of the past. The assumption that the wheel turned in the past as it turns in the present results in an overestimation of the total number of revolutions undergone by the wheel. If genealogy rather than genetics is right, then one way to account for the discrepancy between the two is with the idea that nature's clock is just such a wheel.   

In terms of mathematical physics, we are imagining that there is an asymmetrical relationship between the past and the future, so that time is not reversible, and experiments performed in the present will not necessarily yield the same results as these same experiments performed at an earlier or later time. We are very wary of casting doubt on the uniformity of nature in other parts of the universe because, whilst it is quite possible that nature is dis-uniform from place to place and from time to time, we depend on assumptions of uniformity to make predictions about these remote areas. But as Einstein's Theory of Relativity in particular teaches us, dis-uniformity is fine so long as there is an over-aching mathematical theory in whose context the dis-uniformity between two points of view can be understood and corrected for. If genealogy rather than genetics is right when it comes to the genetic-genealogical conflicts described above, one way to account for the discrepancy is with the idea of past-future asymmetry and the notion that time slows and mutation rates speed up in the direction of the past. If this is the way it works (and all the data I have seen leads me to think that this is the way it works), our clocks are surreptitiously spiralling rather than cycling. If this is the way it works, the assumption that they ticked over in the past as they do in the present results in an overestimation of the total number of hours that have elapsed on these clocks, and in a chronology of the universe, and of life on earth, that overestimates—potentially grossly overestimates—the age of things.