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brimcmike
12-30-2015, 12:29 AM
Cross-posted from R1b-L21:
While not DF49, I figured it was noteworthy to DF49ers because of the just-upstream DF13 and parallel downstream DF21 SNPs.

Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome.
http://www.pnas.org/content/early/2015/12/22/1518445113.full.pdf

Abstract: The Neolithic and Bronze Age transitions were profound cultural shifts catalyzed in parts of Europe by migrations, first of early farmers from the Near East and then Bronze Age herders from the Pontic Steppe. However, a decades-long, unresolved controversy is whether population change or cultural adoption occurred at the Atlantic edge, within the British Isles. We address this issue by using the first whole genome data from prehistoric Irish individuals. A Neolithic woman (3343–3020 cal BC) from a megalithic burial (10.3× coverage) possessed a genome of predominantly Near Eastern origin. She had some hunter–gatherer ancestry but belonged to a population of large effective size, suggesting a substantial influx of early farmers to the island. Three Bronze Age individuals from Rathlin Island (2026–1534 cal BC), including one high coverage (10.5×) genome, showed substantial Steppe genetic heritage indicating that the European population upheavals of the third millennium manifested all of the way from southern Siberia to the western ocean. This turnover invites the possibility of accompanying introduction of Indo-European, perhaps early Celtic, language. Irish Bronze Age haplotypic similarity is strongest within modern Irish, Scottish, and Welsh populations, and several important genetic variants that today show maximal or very high frequencies in Ireland appear at this horizon. These include those coding for lactase persistence, blue eye color, Y chromosome R1b haplotypes, and the hemochromatosis C282Y allele; to our knowledge, the first detection of a known Mendelian disease variant in prehistory. These findings together suggest the establishment of central attributes of the Irish genome 4,000 y ago.

Pretty cool.
B)

brimcmike
03-20-2016, 05:18 AM
Nosing around the appendix, it appears to me that there was in fact some very interesting downstream SNP signal detected
(even as far downstream as M222!, which I might add implies DF49 :beerchug: DF23 ), but that the noise to signal-strength ratio was too high to call.

"S8: Y Chromosome Analysis," appears on pgs 28-31 of the Supplemental Information Appendix (http://www.pnas.org/content/suppl/2015/12/23/1518445113.DCSupplemental/pnas.1518445113.sapp.pdf). In particular, see the bottom of pg 28 et seq, "One particular subclade of M529 [L21], defined by the mutation M222 (52 [Myres NM, et al. (2011) A major Y-chromosome haplogroup R1b Holocene era founder effect in Central and Western Europe. Eur J Hum Genet 19(1):95–101.]), has a distribution which in the present day is considerably restricted to Ireland. Rathlin1, however, the only sample with reads covering SNP M222, presents the ancestral allele at this position....

brimcmike
03-20-2016, 05:37 AM
However, just noticed that they called Rathlin1 as DF21, which doesn't make sense to me that there was valid downstream M222 signal detected from the same body. Could this represent investigator contamination?

brimcmike
03-20-2016, 01:42 PM
I was very kindly and gently schooled over in the Ancestral DNA Forum:


Scientists never like talking in plain English and 'ancestral allele' means Rathlin1 was negative for M222.


Indeed the two relevant terms to watch out for is "ancestral" and "derived"

Never mind.

Rory Cain
03-31-2016, 09:53 PM
However, just noticed that they called Rathlin1 as DF21, which doesn't make sense to me that there was valid downstream M222 signal detected from the same body. Could this represent investigator contamination?

The M222 guys were the big winners from FTDNA's Deep Clade test in 2006. Nothing in it for the DF21+ guys who had to work hard over the following 5 years to get to the same pint as the M222 guys and find their SNP. Walk The Y failed to deliver it, despite the cost. Eventually DNA Forums announced that DF21 had been found in the 1K Genomes database. As DF21 united a number of SNPs found through Walk The Y, this produced a small pay-off for the faithful who purchased Walk The Y.

The 1K Genomes database was racially exclusive, and excluded arguably the two most Celtic countries in the Isles, Ireland and Wales. So 1K Genomes understated the strength of DF21 until it started to emerge in
Irish samples. A more representative picture began to emerge.

The a ancient DNA of Hinxton4, a Z246+ man was used to make DF21 the Belgae tribe Catauvellauni, among the most recent Celts to reach Britain just ahead of the Roman legions. But this claim ignored the large DF21 band in Scotland at the northern extent of Halstatt culture. And the DF21 band in Ireland as the southern extent of La Tene culture. Both events thoroughly pre-dated the arrival of the Catauvellauni. It was always more likely that Hinxton4 was a straggler left behind as DF21 moved north some centuries earlier.

That much is largely confirmed by the Rathlin burials. It appears far more likely that DF21 arrived with the first beaker folk. How times change! It wasn't that long ago that an English DF21+ guy, uncomfortable that DF21 included Irish and Scots, tried to tell me that I couldn't be Irish, only Anglo-Norman at best. How wrong can one be when one allows racial preferences to dictate.

No doubt sone more re-thinking is still to come as new discoveries are made. All good.

JamesKane
03-31-2016, 10:38 PM
I think the thread has got back on track, so I'll just reiterate. Rathlin-1 is indisputably DF21. Rathlin-2 has three derived reads for DF21 in the b38 aligned BAM created from the raw FASTQ files. Rathlin-3's status is unknown as there are no reads aligned to the region, but he wasn't derived for anything else downstream of DF13 either.

I would not be surprised if all three men were DF21.

oneillabu
04-01-2016, 07:24 PM
The M222 guys were the big winners from FTDNA's Deep Clade test in 2006. Nothing in it for the DF21+ guys who had to work hard over the following 5 years to get to the same pint as the M222 guys and find their SNP. Walk The Y failed to deliver it, despite the cost. Eventually DNA Forums announced that DF21 had been found in the 1K Genomes database. As DF21 united a number of SNPs found through Walk The Y, this produced a small pay-off for the faithful who purchased Walk The Y.

The 1K Genomes database was racially exclusive, and excluded arguably the two most Celtic countries in the Isles, Ireland and Wales. So 1K Genomes understated the strength of DF21 until it started to emerge in
Irish samples. A more representative picture began to emerge.

The a ancient DNA of Hinxton4, a Z246+ man was used to make DF21 the Belgae tribe Catauvellauni, among the most recent Celts to reach Britain just ahead of the Roman legions. But this claim ignored the large DF21 band in Scotland at the northern extent of Halstatt culture. And the DF21 band in Ireland as the southern extent of La Tene culture. Both events thoroughly pre-dated the arrival of the Catauvellauni. It was always more likely that Hinxton4 was a straggler left behind as DF21 moved north some centuries earlier.

That much is largely confirmed by the Rathlin burials. It appears far more likely that DF21 arrived with the first beaker folk. How times change! It wasn't that long ago that an English DF21+ guy, uncomfortable that DF21 included Irish and Scots, tried to tell me that I couldn't be Irish, only Anglo-Norman at best. How wrong can one be when one allows racial preferences to dictate.

No doubt sone more re-thinking is still to come as new discoveries are made. All good.

Speaking as the only person who actually was correct on both the age and origin of DF21 and likewise S5488 there is a lesson to be learned here and that is GENETIC DISTANCES BETWEEN PEOPLE OF THE SAME PARENT CLADE ARE OF PARAMOUNT IMPORTANCE.

When you have surnames of Irish origin showing very large GD's between them then the penny should drop that we are looking at an old Irish clade, likewise for instance if we want to track the Irish migration to Scotland as reflected in the pedigrees you should look for an older Irish upstream clade which becomes predominantly Scottish at a given point reflected by an SNP and matched by Genetic distances that reflect the correct timeframe.

M222 and DF21 have two completely different origins, with M222 you can have over a thousand different unrelated surnames showing a match at 67 markers within a timeframe of 800 years which points to a large scale influx of M222 into Ireland who adopted Irish surnames, compare this with DF21 where there are ancient Irish clusters with the same SNP that have very large Genetic Distances between them for example your own BY3384 cluster that is share by an O'Byrne BY3384 cluster with the common ancestor over two thousand years ago.

Regarding the Latta result that was hailed as proof of the Belgic origin of DF21 I argued at the time that this was not borne out by the Genetic distances (not to mention the Ulster and Scottish other Latta surname matches) to the other Irish and sure enough we now have an Irish (James McKusker) match who is also Z16281+ and the Genetic distance indicates that Latta's prescence in Belgium is due to Viking slaving raids in Ireland. What is interesting is that there are Nordic surnames that are also R-Z16294+ together with other Irish surnames which may point to the capture and subjugation from an area that was predominantly R-Z16294+ so this could be a very interesting cluster.

Rory Cain
04-01-2016, 09:36 PM
You were quite right to point out that Latta, despite ending in a vowel, is not Continental but Scots. In a farming community settled by Scots, I went to school with a Latta. In Scotland the Latta surname is a mirror image of the main distribution of DF21 in a band across Central
Scotland. One can but smile at the mythology of a Norman ancestor resulting in someone from a braw Scots clan and clade entering Belgium or France as thier country of origin. Amusing.

Rory Cain
04-02-2016, 12:11 AM
I think the thread has got back on track, so I'll just reiterate. Rathlin-1 is indisputably DF21. Rathlin-2 has three derived reads for DF21 in the b38 aligned BAM created from the raw FASTQ files. Rathlin-3's status is unknown as there are no reads aligned to the region, but he wasn't derived for anything else downstream of DF13 either.

I would not be surprised if all three men were DF21.

As I read it then, there have been some subtle shifts. Build 37 had Rathlin 1 as Z30233, Rathlin 2 as DF21 with some ambiguous S5488 reads, and Rathlin 3 was L 21. Using build 38, has Rathlin 3 now progressed from L21 to DF13, and Rathlin 1 regressed from Z30233 back to DF21?

JamesKane
04-02-2016, 01:07 AM
Rathlin-1 remains Z30233 with 7 reads. Rathlin-2 has DF21+ reads, and I haven't looked downstream for him yet.

Rathlin-3 remains Z260 (an L21 equivalent.) For some reason I was thinking this was DF13 level not L21.

MacUalraig
04-03-2016, 07:56 AM
The M222 guys were the big winners from FTDNA's Deep Clade test in 2006. Nothing in it for the DF21+ guys ...

Just on a historical note M222 was found in 1999 and commercialised first by Jim Wilson and David Faux of Ethnoancestry in March 2006. Only after that did ftdna start selling it.

For further fascinating historical titbits see http://www.kennedydna.com/HistoryOfM222.pdf

Rory Cain
04-05-2016, 02:51 AM
Just on a historical note M222 was found in 1999 and commercialised first by Jim Wilson and David Faux of Ethnoancestry in March 2006. Only after that did ftdna start selling it.

For further fascinating historical titbits see http://www.kennedydna.com/HistoryOfM222.pdf

Which would be consistent with what I stated about M222 being part of FTDNA's Deep Clade test in 2006. Just one year before, in 2005, the late Roy Cain & I did a haplogroup test that gave R1b males just one SNP, and that was P25. FTDNA's marketing almost discouraged customers from taking that test- a curious stance for a commercial company! It apparently reflected their own lack of interest in SNPs.

Rory Cain
05-04-2016, 06:19 AM
Regarding the Latta result that was hailed as proof of the Belgic origin of DF21 ...

The same Continental theorists were sucked in by a Montgomery who listed his country of origin as France, based on one of the numerous Montgomery lines traditionally being descended from a Norman. Of the numerous haplogroups found in persons bearing the surname Montgomery, DF21 would be amongst the least likely to be winner of the Norman lottery.

In fact that particular Montgomery should perhaps look at how many kinsfolk he has who bear the Scots surname of Jameson. But he fooled a few folks who should have known better with his listing of France as his supposed place of origin.