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deadly77
07-08-2019, 10:56 PM
I'm putting up a new thread that has a link the Haplogroup I1 Ancient Samples Map that I put together on Google Maps so that it's easier to find than being buried in the middle of the Ancient I-M253 samples thread. This isn't intended to replace or compete with the Ancient I-M253 samples thread.

Link to the Google map is here: https://www.google.com/maps/d/viewer?mid=1znTXv7qpl4_2T4u9068jOaLzpsjNf62F&ll=55.53882686743272%2C-26.647114350000038&z=3

But please go back to the original Ancient I-M253 samples thread to talk about the samples (where a lot of the original discussions and results are) and continue to use the original thread for new discussions and samples as they come in.

Link to original Ancient I-M253 samples thread here: https://anthrogenica.com/showthread.php?13783-Ancient-I-M253-samples-list

deadly77
08-13-2019, 10:09 PM
The map is receiving a lot of attention, which is great - up to over 3000 views as of today. And that's not just every time I go in and update the map. Also, a shorter shareable link at https://bit.ly/2Z3CJk7 - the original one is a bit long and sometimes gets truncated during sharing.

Now that there are a lot more samples on there (more than 120!), I'm thinking about perhaps better way to visualize the data rather than mostly blue upside down teardrops (which is the default). I had already differentiated the I*/pre-I1 in black with a skull and crossbones for samples which predate the I1 TMRCA and have several confirmed ancestral I1 SNPs (SF11 and BAL051), as well as brown with question mark for the low quality samples which only have a small number of the I1 SNPs and a lot of no calls.

Two main ways I've been considering - different colours for haplogroup subclades or by time period. I get the feeling that the latter may be easier to categorize via carbon 14 dating or graveyard context (although that's not without error - for example the Salme ship burial samples of the four brothers who have rather differing age estimates). However, I the visual distribution of subclades could be quite interesting to see, although some of the samples don't always have enough data to reliably assign a subclade.

Any thoughts?

JonikW
08-14-2019, 10:03 AM
The map is receiving a lot of attention, which is great - up to over 3000 views as of today. And that's not just every time I go in and update the map. Also, a shorter shareable link at https://bit.ly/2Z3CJk7 - the original one is a bit long and sometimes gets truncated during sharing.

Now that there are a lot more samples on there (more than 120!), I'm thinking about perhaps better way to visualize the data rather than mostly blue upside down teardrops (which is the default). I had already differentiated the I*/pre-I1 in black with a skull and crossbones for samples which predate the I1 TMRCA and have several confirmed ancestral I1 SNPs (SF11 and BAL051), as well as brown with question mark for the low quality samples which only have a small number of the I1 SNPs and a lot of no calls.

Two main ways I've been considering - different colours for haplogroup subclades or by time period. I get the feeling that the latter may be easier to categorize via carbon 14 dating or graveyard context (although that's not without error - for example the Salme ship burial samples of the four brothers who have rather differing age estimates). However, I the visual distribution of subclades could be quite interesting to see, although some of the samples don't always have enough data to reliably assign a subclade.

Any thoughts?

I'd find a limited number of subclades most useful because a given date in itself could encompass several discrete cultures. I can see that this is worth tackling in case the hoped for flood materialises, making your task even more difficult. The map looks great by the way.

deadly77
08-14-2019, 09:47 PM
I'd find a limited number of subclades most useful because a given date in itself could encompass several discrete cultures. I can see that this is worth tackling in case the hoped for flood materialises, making your task even more difficult. The map looks great by the way.

I may give that a try in a limited fashion - I'll see how it looks if I split them into the largest subclades of I1 - I-Z58, I-Z2336, I-Z63 and then the last category as everything else (other subclades of I-DF29, the xDF29 branches). One thing I'm looking to avoid is having too many colours which then need to be explained in a description.

Perhaps I can use icons for different groups - longships for Vikings (probably more appropriate than a helmet with horns...)

spruithean
08-14-2019, 09:53 PM
I'd find a limited number of subclades most useful because a given date in itself could encompass several discrete cultures. I can see that this is worth tackling in case the hoped for flood materialises, making your task even more difficult. The map looks great by the way.

Agreed.


I may give that a try in a limited fashion - I'll see how it looks if I split them into the largest subclades of I1 - I-Z58, I-Z2336, I-Z63 and then the last category as everything else (other subclades of I-DF29, the xDF29 branches). One thing I'm looking to avoid is having too many colours which then need to be explained in a description.

Perhaps I can use icons for different groups - longships for Vikings (probably more appropriate than a helmet with horns...)

Colours could be one way, a longship would be a nice touch!

deadly77
08-16-2019, 12:59 PM
Experimented with some colours to categorise into the three largest subclade groups (I-Z2336, I-Z58, I-Z63) and default blue for everything else, including those which are not in the aforementioned three based on the available data, so I-DF29 and minor subclades, I-Z17925 (xDF29) and those that are just I1 - mostly due to not enough coverage to make a reliable subclade assignment. The pre-I1/I* are also marked separately (and have been for a while before) - ones with very low coverage and a small number of derived I1 SNPs are brown with a "?" icon as well as BAB5 (since there's only data on one I1 SNP); then ones with confirmed ancestral calls for several I1 SNPs are black with skull and crossbones.

spruithean
08-17-2019, 05:43 PM
Experimented with some colours to categorise into the three largest subclade groups (I-Z2336, I-Z58, I-Z63) and default blue for everything else, including those which are not in the aforementioned three based on the available data, so I-DF29 and minor subclades, I-Z17925 (xDF29) and those that are just I1 - mostly due to not enough coverage to make a reliable subclade assignment. The pre-I1/I* are also marked separately (and have been for a while before) - ones with very low coverage and a small number of derived I1 SNPs are brown with a "?" icon as well as BAB5 (since there's only data on one I1 SNP); then ones with confirmed ancestral calls for several I1 SNPs are black with skull and crossbones.

Looks good! The colour coding certainly helps differentiate Z2336, Z58 and Z63 when taking a quick glance, especially with subclades one isn't totally familiar with.

deadly77
08-17-2019, 11:40 PM
Looks good! The colour coding certainly helps differentiate Z2336, Z58 and Z63 when taking a quick glance, especially with subclades one isn't totally familiar with.

I thought this would be easier to view rather than breaking down each subclade - otherwise the explanantion of becomes longer than the map itself - I'm trying to keep this from tl,dr territory. Plus there are only a limited number of colours. The standard icons are mostly lame. There is an option for layers - I may experiment with the time periods for that.

deadly77
12-18-2019, 07:58 AM
Hi folks - JonikW says he's not able to access the Ancient I1 Samples Map by the link in my signature. It works fine on my end, but that could be because I'm the creator. I'd appreciate it if anyone else could check and see if the link is broken from their end. Cheers.

spruithean
12-18-2019, 02:52 PM
Hi folks - JonikW says he's not able to access the Ancient I1 Samples Map by the link in my signature. It works fine on my end, but that could be because I'm the creator. I'd appreciate it if anyone else could check and see if the link is broken from their end. Cheers.

It works for me. Perhaps a browser issue?

JonikW
12-18-2019, 03:02 PM
It works for me. Perhaps a browser issue?

Thanks spruithean. Deadly77 sent me the long link and that works fine. Oh well, great that this excellent resource is still accessible. As always, I'm hoping for some new additions soon.

spruithean
12-18-2019, 03:04 PM
Thanks spruithean. Deadly77 sent me the long link and that works fine. Oh well, great that this excellent resource is still accessible. As always, I'm hoping for some new additions soon.

I'm hoping the paper that Cat Jarman talked about on twitter provides some more ancient I1.

mwauthy
12-18-2019, 03:56 PM
Works fine for me too.

deadly77
12-18-2019, 11:20 PM
Thanks spruithean. Deadly77 sent me the long link and that works fine. Oh well, great that this excellent resource is still accessible. As always, I'm hoping for some new additions soon.

Cheers to spruithean and mwauthy for checking the link. JonikW - perhaps clear cache, etc. But thanks that you like the map - I think it's a good way of summarizing the data. But any new data, I think you will see on this forum first before it makes it onto the map. Map gets updated as and when I'm aware of a new sample (and if I can verify it).

I'm also collaborating with Hunter Provyn to get some of these on his Phylogeographer tool. More when we've resolved a few things.

deadly77
12-18-2019, 11:31 PM
I'm hoping the paper that Cat Jarman talked about on twitter provides some more ancient I1.

Well, you've got a 32% chance of the main Repton burials being I1. If I recall, they were also sampling the charnel pit, but a lot of the main focus was on the elaborate double grave. I am a bit surprised that this hasn't been published yet. The only thing I can think of is that Cat Jarman is planning to publish a book in 2020 and perhaps they are holding for that.

But then again, publications take time. Around the time that the Repton documentary was broadcast, my former colleagues and I submitted a (completely unrelated) research paper for publication to a journal and it was rejected. Submitted to a different journal and rejected from that one too.

deadly77
12-18-2019, 11:32 PM
I'll add that 32% is better odds than the Buffalo Bills winning the Superbowl...

JonikW
12-18-2019, 11:59 PM
I'll add that 32% is better odds than the Buffalo Bills winning the Superbowl...

Perhaps our odds are considerably over 50 percent given that I1 accounted for the bulk of the Viking paper. Repton is of great interest to me given it's only a few miles from the Peak District. I'm looking for any clues that could help me solve my Angle or Dane conundrum regarding my first Y forefather to arrive on these shores. From my matches so far, a relatively late sixth century migration (I'm a step downstream of people who I think arrived via the Wash) or the year 865 look equally likely possibilities.

deadly77
12-19-2019, 12:32 AM
Perhaps our odds are considerably over 50 percent given that I1 accounted for the bulk of the Viking paper. Repton is of great interest to me given it's only a few miles from the Peak District. I'm looking for any clues that could help me solve my Angle or Dane conundrum regarding my first Y forefather to arrive on these shores. From my matches so far, a relatively late sixth century migration (I'm a step downstream of people who I think arrived via the Wash) or the year 865 look equally likely possibilities.

I'm basing the 32% I1 on the Y-DNA distribution of the 442 Viking preprint samples. Also a 29% chance of R1b and 21% chance of R1a. For the samples in the UK in that preprint, there were 11 I1 out of 32, so that's a similar ratio. I think we're considerably below 50%. Of course if the father at Repton is I1, the chances of the son being I1 go up to 100%...
35487
But there are more studies planned, and most of them will be analyzed better than before. I do have fingers crossed for VK327 (the I-YSC261 sample from the Viking preprint).

On a slightly unrelated note, if you're looking for some historical fiction of that time period, I've been enjoying Matthew Harffy's Bernica Chronicles series recently.

JonikW
12-19-2019, 01:00 AM
I'm basing the 32% I1 on the Y-DNA distribution of the 442 Viking preprint samples. Also a 29% chance of R1b and 21% chance of R1a. For the samples in the UK in that preprint, there were 11 I1 out of 32, so that's a similar ratio. I think we're considerably below 50%. Of course if the father at Repton is I1, the chances of the son being I1 go up to 100%...
35487
But there are more studies planned, and most of them will be analyzed better than before. I do have fingers crossed for VK327 (the I-YSC261 sample from the Viking preprint).

On a slightly unrelated note, if you're looking for some historical fiction of that time period, I've been enjoying Matthew Harffy's Bernica Chronicles series recently.

My maths was out there. It's been a long day... Sealand VK532 is another one (among several) I'm particularly interested in given his Roman Iron Age dating. Thanks for the book tip and I'm glad the link problem was specific to me.

Stone Meadow
12-19-2019, 09:57 PM
Works for me, too. Eagerly awaiting more info on VK327 (AKA Denmark_Ribe_6). He and I share a common male antecedent a few thousand years before he lived and died. Keep up the good work, Simon!

Kamo
07-11-2020, 08:27 PM
This is a truly fascinating part of the Ydna subject for me. I had no idea until 3-4 years ago that dna could still be extracted from such old remains. One issue I have questions about when it comes to burials is why do we never see any BME(Body Mass Estimate) being done or info shared when it comes to these remains? It can in fact be done so just wonder why they don't seem to do any of that, or if they do why not share it with the public? As an example, one of the burials in Denmark lists as a description of the man's remains as being 'robust'. In general terms we all know what that implies but it is still rather vague. Was he fat? Short and fat? Just a very big guy? What are they saying exactly? I am one who likes facts and figures/statistics etc. Something within the scientific realm that creates a clear and unambiguous picture. Maybe I have missed it somewhere but I have viewed archaeological records of many of these digs and have yet to ever see a BME listed on any of them. The police today(and for a long time) have used this BME technique whenever they have found remains with no flesh left on them, i.e. a skeleton just like what are being found in these graves. One can tell that for instance the Viking man found in grave 511 in Repton was 'robust' simply by the fact that he has noticeably large/heavy limb bones, particularly his legs and he was just under 6 ft tall. But that in itself tells us nothing as to an actual body mass estimate. It is my understanding though I could be wrong, that BMEs are pretty easy for them to do. Doesn't involve any drawn out or costly measures to do one.

JonikW
07-11-2020, 09:35 PM
This is a truly fascinating part of the Ydna subject for me. I had no idea until 3-4 years ago that dna could still be extracted from such old remains. One issue I have questions about when it comes to burials is why do we never see any BME(Body Mass Estimate) being done or info shared when it comes to these remains? It can in fact be done so just wonder why they don't seem to do any of that, or if they do why not share it with the public? As an example, one of the burials in Denmark lists as a description of the man's remains as being 'robust'. In general terms we all know what that implies but it is still rather vague. Was he fat? Short and fat? Just a very big guy? What are they saying exactly? I am one who likes facts and figures/statistics etc. Something within the scientific realm that creates a clear and unambiguous picture. Maybe I have missed it somewhere but I have viewed archaeological records of many of these digs and have yet to ever see a BME listed on any of them. The police today(and for a long time) have used this BME technique whenever they have found remains with no flesh left on them, i.e. a skeleton just like what are being found in these graves. One can tell that for instance the Viking man found in grave 511 in Repton was 'robust' simply by the fact that he has noticeably large/heavy limb bones, particularly his legs and he was just under 6 ft tall. But that in itself tells us nothing as to an actual body mass estimate. It is my understanding though I could be wrong, that BMEs are pretty easy for them to do. Doesn't involve any drawn out or costly measures to do one.

It's possible to tell that an individual was well muscled by assessing the robustness of arm and other bones. For example those of gladiators or practised warriors are not those of your average guy. But body fat isn't calculable from skeletal remains as far as I know. That's why many modern facial reconstructions of unidentified but recently dead individuals have been found to be so inaccurate once they were actually identified. It's also one of the reasons why you should take facial reconstructions of ancient individuals with a hefty pinch of salt, in my view.

If you're interested in this you should start a thread in the Anatomy and Physiology section, or see whether there are already posts on it there. This isn't the best place.

Kamo
07-11-2020, 10:26 PM
I am aware of some of the methods used such as the depth of groove on shoulder created by shoulder muscle tendons(deeper the groove, larger/stronger muscle likely to have been). 6-8 years ago skeletal remains of what turned out to be a 47 year old woman were found in tall grass beside a highway entrance ramp several miles from my town. They had of course constructed an artists rendition of her face and also stated she would have been 135-155 lbs in weight. Well, they found out who she was some months later. You are right, the face did not look at all the same, but they had her estimated weight nearly right on. It turned out from records she weighed 146 lbs which falls into the range they estimated. With that in mind, there must be some method that is commonly used for this purpose. Was just a point of curiosity for me that's all. I thought this thread was a good place since it refers to burials and remains. I won't belabor it but thanks for the info just the same as always JonikW.

deadly77
07-11-2020, 10:44 PM
To be honest, it's not something that I see mentioned a lot in the papers that describe the genetic analysis, although there is sometimes an approximate age and more rarely a description of wounds/deformities - see Birger Magnusson and his son Erik. Although as JonikW says there may be some conjecture in such interpretations, as opposed to reporting actual data - ie, SNPs that are positive or negative (Y, mt, autosomal); calibrated radiocarbon dates; genome coverage, etc.

However, several of these samples were excavated many years or even decades before DNA analysis was available, so such descriptions that you're looking for may be in an earlier report.

Oh, and JonikW - congratulations on the moderator appointment - just noticed that. Well done and a good choice by the AG team.

Kamo
07-12-2020, 03:54 AM
As far as the samples map goes, is that map added to at any time(more marker locations) or does it remain the same until an entirely new map is created with new samples?(and then a new URL)

deadly77
07-12-2020, 06:17 AM
As far as the samples map goes, is that map added to at any time(more marker locations) or does it remain the same until an entirely new map is created with new samples?(and then a new URL)

Yes, new ancient I1 (and pre-I1) samples are added to the map is as I become aware of them, and in the case of more detailed SNP analysis, when the BAM files become available so I can dig into the raw data. The list on the left of the map is in (semi) historical order, so the last one added was BES1248, the iron age sample from South of France. That came from this paper https://www.pnas.org/content/117/23/12791 that was published online 26 May 2020. If there's a lack of data such as BAM files not being available to analyze or there's missing information information, then I may hold off adding it to the map until that data becomes available.

Discussion of ancient I1 samples, as and when they become known or analyzed further is in the Ancient I-M253 samples thread which is here https://anthrogenica.com/showthread.php?13783-Ancient-I-M253-samples-list but at 73 pages and 730 posts, it's not the easiest to find information quickly. So the map is more of an attempt to summarize and organize a lot of data that's in the big ancient I1 thread.

No, the url doesn't change when new samples are updated - stays the same - link in my signature. There's usually a discussion of any new samples that get added in the big ancient I1 thread.