On Sunday, August 27, 2017 at 2:54:20 PM UTC-5, taf wrote: > On Sunday, August 27, 2017 at 10:38:10 AM UTC-7, Stewart Baldwin wrote: > > On 8/26/2017 4:03 PM, taf wrote: > > > In fact, the smallest divisible segments are probably in the 10s to > > > 100s of thousands of bases, which is what puts a definite limit on the > > > number of generations over which autosomal is likely to be informative > > > without a huge amount of luck (for every ancestor from 1600 from whom > > > you have a detectable preserved block, you have many more ancestors > > > from whom you inherit no DNA whatsoever). These blocks pass intact for > > > an incredibly long time, the block that includes the gene determining > > > the most common form of blue eyes is about 150,000bp long and to have > > > passed largely intact for more than 12,000 years. This presents a > > > problem on two sides - relatively close relative may not share the > > > block at all. If two people do share the block, it shows they are > > > related, but perhaps too distantly to be genealogically relevant. > > > > Doesn't the "centimorgan" (cM) measurement take this partially into > > account?  If I understand the method correctly, one cM will sometimes > > contain a huge number of base pairs, and sometimes a relatively small > > number (if it is contained in a "hot spot").  So, wouldn't a long > > segment that passed on intact (or essentially intact) over thousands of > > years have a centimorgan measurement close to zero?  Do I have this right? > > A centimorgan is very much a term of traditional, pre-genomic genetics, so to a degree we are using rotary-phone terminology to describe smartphones, but there are, on average, with very large error bars, about 750,000 bp per cM in humans. If there was a hotspot, this would produce a smaller number of bp per centimorgan in the immediate proximity, while a region devoid of crossing-over would be part of a larger-than-average sized centimorgan (it would take more total sequence to generate a 1% chance of crossing over, since you would have this long stretch with no crossing over whatsoever). > > > > With regard to Richard's Y-DNA, have STR-tests been done for enough > > markers that one could do a global search to see what surnames pop up > > among his closest matches?  I know that the noise to information ration > > can be too large if not enough markers have been tested, but it seems > > like it would be worth a shot. > > They did a 23-marker analysis, which is pretty superficial, and gave thm just one step beyond the basal haplogroup. G2 arose well before 7000 years ago, at which time is is found in Spain, France and Germany, in burials associated with the first agriculturalist populations that spread from Anatolia to largely displace the native hunter-gatherers. It was already highly divergent by that time, so it probably is quite ancient. The 23-marker testing done on Richard does not allow his subclade to be determined, so a surname analysis on this level would be largely uninformative. To say that Alans included Gs so Richard's came from the Alans is completely unsupportable in light of this history. > > For their specific results, see Supplementary Table 2, on p. 8 of their Data Supplement: > https://images.nature.com/original/nature-assets/ncomms/2014/141202/ncomms6631/extref/ncomms6631-s1.pdf > > They have an ongoing project to do whole genome sequencing, from which further markers may be determined that would allow the subclade to be determined, but as far as I know, this information is not public yet, and until it is, such a surname study can only serve to exclude those who are not G2, but will not provide genealogically-relevant information. > > taf Amazing. Posted this thread--left for a little while--and came back to a fascinating discussion. Why did they even bother with such a superficial test when so many people worldwide must be interested in the details of Richard's DNA? Just wondering if politics and funding weigh into what seems to be an academic "walking on eggshells." Is there a question of embarrassing the monarchy with the truth about Richard's male line or are funds just limited?

On Thursday, August 31, 2017 at 12:06:22 PM UTC-7, gets...@gmail.com wrote: > On Sunday, August 27, 2017 at 2:54:20 PM UTC-5, taf wrote: > > They did a 23-marker analysis, which is pretty superficial, and gave thm just one step beyond the basal haplogroup. G2 arose well before 7000 years ago, at which time is is found in Spain, France and Germany, in burials associated with the first agriculturalist populations that spread from Anatolia to largely displace the native hunter-gatherers. It was already highly divergent by that time, so it probably is quite ancient. The 23-marker testing done on Richard does not allow his subclade to be determined, so a surname analysis on this level would be largely uninformative. To say that Alans included Gs so Richard's came from the Alans is completely unsupportable in light of this history. > > > > For their specific results, see Supplementary Table 2, on p. 8 of their Data Supplement: > > https://images.nature.com/original/nature-assets/ncomms/2014/141202/ncomms6631/extref/ncomms6631-s1.pdf > > > > They have an ongoing project to do whole genome sequencing, from which further markers may be determined that would allow the subclade to be determined, but as far as I know, this information is not public yet, and until it is, such a surname study can only serve to exclude those who are not G2, but will not provide genealogically-relevant information. > > > > Amazing. Posted this thread--left for a little while--and came back to > a fascinating discussion. Why did they even bother with such a superficial > test when so many people worldwide must be interested in the details of > Richard's DNA? Just wondering if politics and funding weigh into what > seems to be an academic "walking on eggshells." Is there a question of > embarrassing the monarchy with the truth about Richard's male line or are > funds just limited? I suspect that the answer is much more mundane. These are scientists doing genetic anthropology, not genealogists going genealogy. The 23 marker test is standard 'first-pass' analysis for anthropological samples, as indicated by the fact that the biotech company Promega markets a 23-marker kit. Likewise, the test accomplished what they needed it to - their goal was not to identify modern kin of the Plangtagenets, as a genealogist might set out to do. Their goal was to see whether Richard's matched the Beaufort/Somerset type. The 23-marker test was fully sufficient to allow an unambiguous conclusion that negated a Y-chromosome match. This is standard scientific process - come up with a hypothesis, ask a discreet question, preferably one that produces a yes-or-no answer, and perform a test that answers that question to see it it confirms the hypothesis. The alternative, what a genealogist would do, determine a detailed haplotype and then, vaguely, 'see if you can find anyone anywhere that matches it - to cast a wide net and see what you catch, is disparaged in science as a so-called fishing expedition (a term misused earlier in this thread), and is unfundable. They had a definitive, publishable result, and so they published it. The next question is whether they will pursue it further. Bearing in mind that their audience is one of scientists and not genealogists, they may well conclude that the take isn't worth the chase. No funding agency would fund such an investigation, since in addition to being a fishing expedition, there is a distinct possibility they would fail to find any matches, meaning the money would be wasted. Even if they did, such a result may be unpublishable - if they were to find someone named Smith who matches Richard's Y, what do you say about it that would appeal to a scientific journal? That is why they told of the Patrice de Warren result in an interview with The Guardian, because they saw no prospects of the result ever being part of a scientific paper. If they got the money to sequence the genome, then they may spin off a little bit of money to do a more detailed Y-typing, but if they didn't get the money, they are likely to turn their sights to a different question entirely - they intend to investigate Jack the Ripper's victims. This is actually a hopeful sign, as there is no purely scientific or historic reason for doing this. There is no question of the identity of the skeletons, and nothing that makes their genetics 'special'. They are clearly chasing headlines, so they may be more willing to do experiments that have poor justification on a purely scientific basis, if they think it will get them in the papers, and 'is Bob Smith from Ipswich the true heir of the Plantagenets?' just might do the trick. taf