Ancient I-M253 samples list

[deadly77]

From the supplementary information file (page 30): 1.3 Norton on Tees - Two AngloSaxon cemeteries were excavated in the village of Norton, Teesside, north east England. They were located 200m apart and one of these, Norton East Mill, dated to the pagan AngloSaxon period (550650AD), while the adjacent cemetery, Norton Bishopsmill, dates to 650910AD and was Christian. The pagan cemetery contained 120 burials, many of which were furnished with grave goods, while the Christian burial ground contained the unfurnished burials of 100 skeletons. Analysis of the skeletal remains has revealed differences in the age and sex distributions as well as the pathology at the two sites 47,48. https://www.nature.com/articles/ncom...ry-information

From the manuscript of the paper (last sentence of Results - Archaeological samples, just before section on Sequencing results and sample contamination): Norton Bishopsmill, dates to 650–910 AD and was a Christian Anglo-Saxon cemetery excavated in the village of Norton, Teesside, northeast England14. We sampled 3 individuals from burials of 100 skeletons and selected the best preserved, NO3423, for the present study (Supplementary Notes 1 and 2 and Supplementary Fig. 1). https://www.nature.com/articles/ncomms10326

Ah - I see that Spruithean, JonikW and JMcB already had covered that. Cheers folks.

[deadly77]

I certainly agree that it makes it much easier to get a visual representation of the distribution of the ancient samples so far. Charts with data are good when just pure data is needed, but some of us like that visual for sure. It definitely looks like if we get more and more samples it will be easier to track via the map.



Ah, ok I see. I certainly agree with the choice to define the pre-TMRCA ancient I1 as pre-I1 or label them with question marks or skulls. I1 by definition to me is the haplogroup with 309 defining mutations and a rather young TMRCA, so everything prior to that can't literally be I1.



I don't think we may ever be sure whether those lineages are ancestral to modern I1, we don't even have any idea what the chronological order is for the SNPs that are phyloequivalent for M253. I'm also not sure we'll ever know considering soil in Scandinavia can be rather destructive to genetic material (same goes for parts of Britain, notably the new Saxon Tomb). I have seen the current I1 origin theory via Eupedia and some various comments on Eurogenes and elsewhere that it is believed I1 or pre-I1 was present in Mesolithic Central Europeans with the LBK culture which eventually led into the Funnelbeakers and Corded Ware and the eventual rise of Nordic Bronze Age and Germanic cultural development. However, I don't think we have enough to make assumptions yet.



That is actually quite reasonable and it would explain some of the diversity, distribution and the non-isolated finds. A hitched ride with the R1b folk would make sense indeed!

Admittedly I'm pretty chuffed to share a paternal lineage to some degree with some of those recent aDNA finds (Avar-era Hungarian, Conqueror-era Hungarian, Longobards, Icelanders, Baiuvarii, etc). It's definitely not something I'd anticipated back in the early genetic genealogy days, that's for sure.

The "hitched ride" theory I first heard while listening to The Insight podcast. It's a great regular podcast by Spencer Wells and Razib Khan of Insitome, often with guests and a variety of subjects related to genomics. This particular episode here: https://insitome.libsyn.com/y-chromosomal-stars specifically discussing I1 (albeit briefly) from 36.30min when Razib Khan brings it up. The more i've thought about it, it makes a lot of sense. Survived by assimilation and benefitted from being part of a succesful group of largely R1b.

Yes, I'm also pretty chuffed with what we have so far. Although I'm greedy for more

[deadly77]

I received an email from Hunter Provyn - he's the developer of the Phylogeographer/Mygrations webiste - he says he's keen to add more ancient DNA references to his portal ad he's been collaborating with Carlos Quiles of Indo-European.eu who has sent him 1600 dated, geolocated ancient Y-DNA samples he has been collecting. I looked through the spreadsheet and unfortunately there's several errors that we've discussed previously on this thread, including from taking misreported publication data at face value (eg. SVK-A1 I-Z131, CL63 I1-Z79, etc.) and misassignments due applying shorthand SNPs to the wrong version of the ISOGG tree in the ancient Iceland paper (eg. SSJ-A2 and HSJ-A1 listed as I-A8182 and SBT-A1 listed as I-S26062), SF11 being I1, etc. I've replied with a list of corrections and added samples that aren't in his spreadsheet.

It does however list three I1 samples that were not on my radar. Two of these were from the Sigtuna paper (Krzewi
nska 2018) where we've already discussed 84005 (I-CTS2208, I-Z74 in the paper) - the spreadsheet lists urm035 as I1 and DF29 (paper says haplogroup BDCDEF) and urm045 as I1 and Z60, Z61 (paper says haplogroup not determined) and lists Sylvester as responsible (who also lists 84005 as I-CTS2208 in the spreadsheet). I've got the BAM files and I'll take a look and see if I can verify this.

There was also an additional I1 in the spreasheet with sample AE 1154, referenicing Bavaria, Rott2018 and Altenerding-Klettham cemetery. I figured this would be from the same paper AED 249, STR 486, STR 241. However, I can't find any sample AE 1154 in the paper.

[JonikW]

The "hitched ride" theory I first heard while listening to The Insight podcast. It's a great regular podcast by Spencer Wells and Razib Khan of Insitome, often with guests and a variety of subjects related to genomics. This particular episode here: https://insitome.libsyn.com/y-chromosomal-stars specifically discussing I1 (albeit briefly) from 36.30min when Razib Khan brings it up. The more i've thought about it, it makes a lot of sense. Survived by assimilation and benefitted from being part of a succesful group of largely R1b.

Yes, I'm also pretty chuffed with what we have so far. Although I'm greedy for more

It's worth trying to pinpoint the potential location of the massive Stone Age bottleneck that led to the explosion of modern I1 and how this ties in with the expansion of R1a and R1b folk and eventual formation of a Germanic culture. The Battle Axe/Single Grave/Corded Ware Culture’s entry into Scandinavia and blending with the people that were already there seems a good place to start and the dates look right.
Perhaps the indigenous I1 were seen by the incomers as holding some knowledge, skill, power or authority that was worth incorporating.
This passage in an early chapter of “The Spoils of Victory” published by the national museum in Copenhagen is interesting. It shows clues in the artefact assemblages that could illustrate the bottleneck and subsequent events. The text below was written by Kaul Flemming: “Throughout the Neolithic period one notes a number of important changes, some of which took place during the Middle Neolithic Funnel Beaker Culture. At an early stage of this culture the number of bog finds of earthenware vessels drops radically, so that around 3000 BC the custom of placing them in bogs has by and large stopped. Around the same time the number of Funnel Beaker Culture battle-axes in the bogs also declines, as do the large depositions of amber. By contrast the deposition of flint axes in bogs continues, now in the form of among other things thick-butted and thin-bladed axes. Another find category shows the same picture - the sacrificial layers in front of the megalithic tomb facades. Here too the number of deposited earthenware vessels declines drastically at the same time, but axes, now even in increasing numbers, continue to be deposited throughout the remainder of the Funnel Beaker Culture.
During the transition to the Single Grave Culture (the period is also called MN b) several cultural changes took place, for instance other burial types and other pottery forms came into use. But as far as the depositions in the bogs are concerned, the Danish area in general seems to display a certain continuity; for the changes in the deposition customs had already taken place during the period of the Middle Neolithic Funnel Beaker Culture (also called MN A), and the general features that are found in depositions at the end of Funnel Beaker Culture seem to continue into the Single Grave Culture.”
So there may be mixed evidence of disruption and continuity, just as occurred in Britain during what we now know were periods of population replacement. Most archaeologists had simply missed the implications

[spruithean]

The "hitched ride" theory I first heard while listening to The Insight podcast. It's a great regular podcast by Spencer Wells and Razib Khan of Insitome, often with guests and a variety of subjects related to genomics. This particular episode here: https://insitome.libsyn.com/y-chromosomal-stars specifically discussing I1 (albeit briefly) from 36.30min when Razib Khan brings it up. The more i've thought about it, it makes a lot of sense. Survived by assimilation and benefitted from being part of a succesful group of largely R1b.

Yes, I'm also pretty chuffed with what we have so far. Although I'm greedy for more

Thanks for sharing that link, I'll give it a listen, any discussion mentioning I1, even if briefly, is probably important. I don't see very much discussion of I1 on most of the big blogs such as Eurogenes or Quiles Indo-European blog.

I received an email from Hunter Provyn - he's the developer of the Phylogeographer/Mygrations webiste - he says he's keen to add more ancient DNA references to his portal ad he's been collaborating with Carlos Quiles of Indo-European.eu who has sent him 1600 dated, geolocated ancient Y-DNA samples he has been collecting. I looked through the spreadsheet and unfortunately there's several errors that we've discussed previously on this thread, including from taking misreported publication data at face value (eg. SVK-A1 I-Z131, CL63 I1-Z79, etc.) and misassignments due applying shorthand SNPs to the wrong version of the ISOGG tree in the ancient Iceland paper (eg. SSJ-A2 and HSJ-A1 listed as I-A8182 and SBT-A1 listed as I-S26062), SF11 being I1, etc. I've replied with a list of corrections and added samples that aren't in his spreadsheet.

Don't tell anyone at Eurogenes about this collaboration! I know there is some rivalry between the two camps in terms of what ancient people brought R1a or R1b and spoke this or that language

I hope that Mr. Provyn is willing to go through with corrections of the aDNA samples that you've examined. It is certainly a bit strange that these papers used old forms of ISOGG when most of us have moved on and refer to haplogroups with the main root and terminal SNP method.

It does however list three I1 samples that were not on my radar. Two of these were from the Sigtuna paper (Krzewinska 2018) where we've already discussed 84005 (I-CTS2208, I-Z74 in the paper) - the spreadsheet lists urm035 as I1 and DF29 (paper says haplogroup BDCDEF) and urm045 as I1 and Z60, Z61 (paper says haplogroup not determined) and lists Sylvester as responsible (who also lists 84005 as I-CTS2208 in the spreadsheet). I've got the BAM files and I'll take a look and see if I can verify this.

There was also an additional I1 in the spreasheet with sample AE 1154, referenicing Bavaria, Rott2018 and Altenerding-Klettham cemetery. I figured this would be from the same paper AED 249, STR 486, STR 241. However, I can't find any sample AE 1154 in the paper.

I'm not familiar with URM035 and URM045, however if there were errors and broad haplogroup designations in the paper such as "BCDEF" that seems a bit suspect and warrants deeper investigation, interesting that it is designated I-Z60/Z61 in the spreadsheet. That could be very interesting if confirmed. I think most ancient I1 we'll find will be Migration Period and within the Medieval period (and of course the higher middle ages up to colonial eras). Obvious places to look are already being looked at as of late.

I suspect that AE 1154 may be a error, I've not seen that sample anywhere in that paper and I've scoured it a few times. However perhaps it is referencing something else that may flown under the radar that was picked up recently. Perhaps time will tell.

[Paul333]

Was it really a pagan burial? Should we really consider it an Anglo-Saxon then? Would it possibly be a Viking burial then?

Here is part of the supplementary data for the burial:



I seem to remember NO3423 being from Bishopsmill.

Appologies, you are correct. The earlier Norton pagan cemetery, was discovered by children playing in the bankside, of Mill Lane, in 1982, and excavated, between 1983-1985. The later nearby Bishopsmill,'christian cemetery', was found during later building work.

I confused the two separate cemeterys as one, despite owning the 1992,Sherlock & Welch research Report 82, regarding the first of these, the Mill Lane cemetery.

[JonikW]

I wonder whether deadly77 and other well versed experts on ancient I1 see any implications for us here. Very interesting.

Edit: it kind of goes with what I posted earlier today on Scandinavia but I don't know what to make of any of it. I'm sure someone sees the bigger picture. I guess a small population of I1 got involved early on with the invaders, got lucky and expanded quite rapidly.

http://eurogenes.blogspot.com/2019/0...e-age.html?m=1

[spruithean]

I wonder whether deadly77 and other well versed experts on ancient I1 see any implications for us here. Very interesting.

Edit: it kind of goes with what I posted earlier today on Scandinavia but I don't know what to make of any of it. I'm sure someone sees the bigger picture.

http://eurogenes.blogspot.com/2019/0...e-age.html?m=1

I had been hoping some comments about I1 would appear in that thread. A commenter under the name "Angantyr" claims that Nordic_LN II RISE179 is I1. That sample is on deadly's ancient I1 map as a pre-I1. Which I believe is appropriate as it is a low coverage sample and it was no call for ">99%" of the defining I1 SNPs.

I think we can't be too lenient (but can't be too strict either) on what we define as I1. We already know I1 has a young TMRCA so true I1 will be in that timeframe.

EDIT: keep your eye on this Eurogenes post, the comments are getting quite interesting!

[deadly77]

It's worth trying to pinpoint the potential location of the massive Stone Age bottleneck that led to the explosion of modern I1 and how this ties in with the expansion of R1a and R1b folk and eventual formation of a Germanic culture. The Battle Axe/Single Grave/Corded Ware Culture’s entry into Scandinavia and blending with the people that were already there seems a good place to start and the dates look right.
Perhaps the indigenous I1 were seen by the incomers as holding some knowledge, skill, power or authority that was worth incorporating.
This passage in an early chapter of “The Spoils of Victory” published by the national museum in Copenhagen is interesting. It shows clues in the artefact assemblages that could illustrate the bottleneck and subsequent events. The text below was written by Kaul Flemming: “Throughout the Neolithic period one notes a number of important changes, some of which took place during the Middle Neolithic Funnel Beaker Culture. At an early stage of this culture the number of bog finds of earthenware vessels drops radically, so that around 3000 BC the custom of placing them in bogs has by and large stopped. Around the same time the number of Funnel Beaker Culture battle-axes in the bogs also declines, as do the large depositions of amber. By contrast the deposition of flint axes in bogs continues, now in the form of among other things thick-butted and thin-bladed axes. Another find category shows the same picture - the sacrificial layers in front of the megalithic tomb facades. Here too the number of deposited earthenware vessels declines drastically at the same time, but axes, now even in increasing numbers, continue to be deposited throughout the remainder of the Funnel Beaker Culture.
During the transition to the Single Grave Culture (the period is also called MN b) several cultural changes took place, for instance other burial types and other pottery forms came into use. But as far as the depositions in the bogs are concerned, the Danish area in general seems to display a certain continuity; for the changes in the deposition customs had already taken place during the period of the Middle Neolithic Funnel Beaker Culture (also called MN A), and the general features that are found in depositions at the end of Funnel Beaker Culture seem to continue into the Single Grave Culture.”
So there may be mixed evidence of disruption and continuity, just as occurred in Britain during what we now know were periods of population replacement. Most archaeologists had simply missed the implications

Interesting - I think there's definitely something in that worth thinking about. It might be difficult to verify from DNA of any ancient remains that are found, given that I1 was likely down to a single lineage (or at least a very small groups of lineages among a population). Talk about a needle in a haystack. Within a few generations, the I1 individual would not have been overtly outwardly distinguishable from the R1b group that they became assimilated into. Perhaps "hiding in plain sight" is a better analogy than hitching a ride.

[deadly77]

Thanks for sharing that link, I'll give it a listen, any discussion mentioning I1, even if briefly, is probably important. I don't see very much discussion of I1 on most of the big blogs such as Eurogenes or Quiles Indo-European blog.



Don't tell anyone at Eurogenes about this collaboration! I know there is some rivalry between the two camps in terms of what ancient people brought R1a or R1b and spoke this or that language

I hope that Mr. Provyn is willing to go through with corrections of the aDNA samples that you've examined. It is certainly a bit strange that these papers used old forms of ISOGG when most of us have moved on and refer to haplogroups with the main root and terminal SNP method.




I'm not familiar with URM035 and URM045, however if there were errors and broad haplogroup designations in the paper such as "BCDEF" that seems a bit suspect and warrants deeper investigation, interesting that it is designated I-Z60/Z61 in the spreadsheet. That could be very interesting if confirmed. I think most ancient I1 we'll find will be Migration Period and within the Medieval period (and of course the higher middle ages up to colonial eras). Obvious places to look are already being looked at as of late.

I suspect that AE 1154 may be a error, I've not seen that sample anywhere in that paper and I've scoured it a few times. However perhaps it is referencing something else that may flown under the radar that was picked up recently. Perhaps time will tell.

I've found the Insitome podcast really interesting as a series - they also cover a lot of different areas in other blog posts. Really worth listening to.

Yes, Hunter says thanks and he will update the spreadsheet with corrections. I've discussed a few things with him before and I think he's keen to have accuracy. He's put a short video on YouTube discussing the collaboration on these ancient samples with Carlos Quiles and Vadim Urasin from YFull here https://www.youtube.com/watch?v=zjQa...NCMshz5F5PNTeU his main goal appears to be getting the data into a format that's compatible with his Phylogeographer tool.

I think the longhand nomenclature for persists due to familiarity of those who have likely used that nomenclature for years. As a relative latecomer, I often have to look those up and translate the alphabet soup. I much prefer I-L338 rather than I1a2a1a1a1a1 (as defined by 2019 ISOGG tree). The longhand nomenclature also changes from year to year on the ISOGG tree, which is where I think Carlos Quiles is making mistakes in I1 subclades in his spreadsheet regarding the ancient Iceland genomes. The supplementary information in that Science 2018 paper defines that the authors are using the 2016 version of the ISOGG tree - as long as you follow that, there's no conflict - SSJ-A2 is I1a1b3 which is I-Z74, HSJ-A1 is I1a1b3b which is I-L813, SBT-A1 is I1a2a1a2 which is I-F2642. All fine. Problem comes when Carlos Quiles takes the longhand data of these samples and then looks at a later version of the ISOGG tree and incorrectly interprets SSJ-A2 and HSJ-A1 as I-A8182 and SBT-A1 as I-S26062. It's another arguement for moving on from this obsolete nomenclature to avoid the confusion.

I haven't done full analysis of urm035 and urm 045 yet, but the assignments are matching up with the BAM files - urm035 has derived calls for DF29 and Z2892/CTS9848 but an ancestral call for Z2893 among the I-DF29 branch. Also one read ancestral for Z59 and Z140 so far. urm045 has derived calls for Z2893 and Z2892/CTS9848 among the I-DF29 branch and derived for S439/Z61. All these are one read SNPs so not solid yet and I'll dig a bit deeper and see if there's a bit more evidence. Probably not reported in paper as any indentifying Y-SNPs were below threshold for reporting or they weren't looking in the right places. They did get 84005 as I1a1b3/I-Z74 in the paper though.

Yeah, I havent found AE 1154 either - in the paper or at ENA (where the other three I1 from that paper are). It could be a mis-transcription of AED249 that we already know about.