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Thread: Ancient I-M253 samples list

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    Quote Originally Posted by JonikW View Post
    Thanks again for your wonderful work deadly77. I see now this comment from David in his Nordic thread:

    "The high frequencies of U106 and I1 in Scandinavia are best explained by extreme local founder effects during the Bronze Age.

    Not migrations of U106 and I1 rich populations into Scandinavia from, say, the Carpathian Basin.

    It's unlikely that anyone will find the relevant, ancestral I1 in the ancient DNA before the founder effect. That is, dating to the TRB, Battle Axe or BB periods."
    I'm intrigued by this extreme founder effect that would have expanded I1 in Scandinavia. What do you think caused it? Plague, invasion, the emergence of a dominant social class? When should anything such have happened and how is it supported by genetic and archeological evidence? I have tried to formulate some ideas but find myself more confused the more I think about it.

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    Quote Originally Posted by janan View Post
    I'm intrigued by this extreme founder effect that would have expanded I1 in Scandinavia. What do you think caused it? Plague, invasion, the emergence of a dominant social class? When should anything such have happened and how is it supported by genetic and archeological evidence? I have tried to formulate some ideas but find myself more confused the more I think about it.
    I've wondered this too and I suspect it could be an environmental thing that kept I-M253 bottlenecked until it finally expanded, obviously plague or conflict could also be the cause if not happening in tandem with an environmental scenario. Scandinavia didn't exactly lend itself to agriculture and other means at that time. Mr. Khan and a few others think maybe I-M253 hitched a ride with R-U106 and benefitted by association. I don't take this to mean they literally migrated with them, I interpret it to mean that whatever advances came with the cultures that were high in U106 (and the "Germanic" branches of R1a) directly benefitted the populations with I-M253 lineages. Obviously one of M253's descendants was successful since the majority of I1 descendants are I-DF29 subclades. There was definitely a preoccupation with boats leading up to the pre-Roman Iron Age, which obviously remained a focal point for the coastal populations along the North Sea and the Baltic. So the sea was definitely an important resource in this time considering farming would have been more difficult than other places.

    Judging by the ancient I1 map and other data, it seems like I1 really expanded and diversified in Northern Europe, whether it originated there I don't know. We can't totally rely on BAB5 from Hungary or BAL051 from Spain.

    This isn't gospel by any means, just my own ramblings at the moment...

    Hopefully we get some more I1 aDNA from the Repton study and others!
    Last edited by spruithean; 05-28-2019 at 01:41 AM.

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    Indeed, fully agree that we can't totally rely on BAB5 from Hungary or BAL051 from Spain, but by the same token can't totally rely on SF11 or the RISE samples either.

    Regarding plague, this is an interesting paper titled "Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline" that was published last year in Cell: https://www.cell.com/action/showPdf?...2818%2931464-8 - unfortunately, it's behind a paywall, but you can read the summary and the graphical abstract: Cell 2018 Y pestis plague graphical abstract.jpg and and article about the paper with quotes from one of the authors here: https://www.sciencedaily.com/release...1206120035.htm

    Around 4900 years ago, a series of plagues hit Northern Europe, noted in the graphical abstract by skulls and dates. At that point we have the first large settlements becoming common in Europe with people, animals, and stored food close together, and, likely, very poor sanitation - breeding ground for plague and disease. Throw in active trade with horses and wheeled carts migrating along trade routes: just the thing to ignite and spread the plague.

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  6. #324
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    Quote Originally Posted by spruithean View Post
    I've wondered this too and I suspect it could be an environmental thing that kept I-M253 bottlenecked until it finally expanded, obviously plague or conflict could also be the cause if not happening in tandem with an environmental scenario. Scandinavia didn't exactly lend itself to agriculture and other means at that time. Mr. Khan and a few others think maybe I-M253 hitched a ride with R-U106 and benefitted by association. I don't take this to mean they literally migrated with them, I interpret it to mean that whatever advances came with the cultures that were high in U106 (and the "Germanic" branches of R1a) directly benefitted the populations with I-M253 lineages. Obviously one of M253's descendants was successful since the majority of I1 descendants are I-DF29 subclades. There was definitely a preoccupation with boats leading up to the pre-Roman Iron Age, which obviously remained a focal point for the coastal populations along the North Sea and the Baltic. So the sea was definitely an important resource in this time considering farming would have been more difficult than other places.

    Judging by the ancient I1 map and other data, it seems like I1 really expanded and diversified in Northern Europe, whether it originated there I don't know. We can't totally rely on BAB5 from Hungary or BAL051 from Spain.

    This isn't gospel by any means, just my own ramblings at the moment...

    Hopefully we get some more I1 aDNA from the Repton study and others!
    I'll join your rambling :-)

    "Environmental thing"? Are you thinking of climate change? Scandinavia up until and including the bronze age was as warm as northern France is today. You could grow grapes here then. Archeological evidence show the bronze age was a quite expansive time. Population growth, amassing riches, develping a specific culture. There was a climate change, but that was at the end of the bronze age when weather got colder and wetter. That might also be what helped end the bronze age, with its stratified society where an elite controlled resources and metal through long range trading networks. Iron were available everywhere (ores were picked up from the bottom of shallow lakes), so no need anymore for the elite's network of international business associates.

    But that means the population bottle neck we're looking for happened in the break bronze/iron age. Why not.
    Last edited by janan; 05-28-2019 at 09:27 AM.

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    deadly77, thanks for that link, that'll be a good read.

    janan, I was most definitely confusing my time periods for the environment thing! Perhaps indeed it was a mixture of warfare and plague (see deadly's post). It is definitely bizarre in the case of I1, however I think things aren't very clear considering the oldest samples of I1 are found in the Migration Period leading up to the later Medieval eras. Everything older than that seems to be pre-I1 unless those samples are suddenly retested for more accuracy.

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    Quote Originally Posted by deadly77 View Post
    Indeed, fully agree that we can't totally rely on BAB5 from Hungary or BAL051 from Spain, but by the same token can't totally rely on SF11 or the RISE samples either.

    Regarding plague, this is an interesting paper titled "Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline" that was published last year in Cell: https://www.cell.com/action/showPdf?...2818%2931464-8 - unfortunately, it's behind a paywall, but you can read the summary and the graphical abstract: Cell 2018 Y pestis plague graphical abstract.jpg and and article about the paper with quotes from one of the authors here: https://www.sciencedaily.com/release...1206120035.htm

    Around 4900 years ago, a series of plagues hit Northern Europe, noted in the graphical abstract by skulls and dates. At that point we have the first large settlements becoming common in Europe with people, animals, and stored food close together, and, likely, very poor sanitation - breeding ground for plague and disease. Throw in active trade with horses and wheeled carts migrating along trade routes: just the thing to ignite and spread the plague.
    Ah yes the plague. The two individuals found to carry Yersinia pestis come from the Gökhem grave and belong to the funnel beaker culture, thus early European farmers. So these were killed off by the plague, and left the country open for the Yamna invasion who might have come to a largely abandonded country. If the farmers had been gone for say 100 years, there wouldn't have been much traces after them in the countryside. Also, pitted-ware culture expanded into earlier farmer's country at the same time.

    On the other hand, there is a whole lot of EEF ancestry in present-day Swedes, around 20-30 %, which at least means that the farmers weren't eradicated. Same with SWG, still present in our DNA with 10-20 %. So there are no obvious evidence for a bottleneck or close-to-complete population replacement at these times, as there are e.g. in Great Britain where 90 % of the DNA was replaced when the Bell Beakers arrived.

    There's just nothing clear with this case.

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    Quote Originally Posted by janan View Post
    Ah yes the plague. The two individuals found to carry Yersinia pestis come from the Gökhem grave and belong to the funnel beaker culture, thus early European farmers. So these were killed off by the plague, and left the country open for the Yamna invasion who might have come to a largely abandonded country. If the farmers had been gone for say 100 years, there wouldn't have been much traces after them in the countryside. Also, pitted-ware culture expanded into earlier farmer's country at the same time.

    On the other hand, there is a whole lot of EEF ancestry in present-day Swedes, around 20-30 %, which at least means that the farmers weren't eradicated. Same with SWG, still present in our DNA with 10-20 %. So there are no obvious evidence for a bottleneck or close-to-complete population replacement at these times, as there are e.g. in Great Britain where 90 % of the DNA was replaced when the Bell Beakers arrived.

    There's just nothing clear with this case.
    I wasn't implying that plague was the sole or primary reason for a Y-DNA bottleneck or founder event, my intention was that it was likely a contributing factor along with others that Spruithean suggested. But I though the premise of the paper was interesting given the quoted dates, although I haven't read the actual paper fully because it's not open access.

    I also wasn't implying that there was a close-to-complete population replacement in the region at these times, more that the Y-DNA ancestry derives from a relatively recent founder effect. I think you're equating a Y-DNA bottleneck with a close-to-complete population eradication as the same thing, but for me there they aren't exactly the same. Apologies if I am misunderstanding your intention.

    Statistically, throughout most of recorded history, only about 10% of all male lines have survived more than 30 generations (~1000 years). We don’t always need volcanoes or plagues or slaughtering clan lords to cause Y-DNA lineage extinctions. For almost all of history, and certainly prehistory, when population growth was very slow, simple chance - the throw of the dice on how many sons or daughters you have (or if any) - assures that most lineages will go extinct. A Y-DNA bottleneck isn't inexorably indicative of a total or close-to-complete population replacement. Of course thousands of other men survived at the time we are discussing and had descendants, but not neccesarily their strict patrilineage in the form of Y-DNA survived to these descendants (or without the same following massive expansion as the TMRCA of I1, R1a and R1b Y-DNA descendants in Europe). Ancestors outside of the Y-chromosome patrilineal line can contribute to the autosomal DNA makeup (to your point of percentage EEF or SWG (SHG?) ancestry of modern Swedes) but not be reflected in the Y-DNA haplogroup distribution of modern population. Likewise, the Y-DNA of ancient samples in Scandinavia prior to the founder effect - lots of samples of Y-DNA haplogroup I2 in Hum2, I0012, I0013, I0015, I0016, I0017, Steigen, SBj, Ansarve 8, Ansarve 14, Ansarve 17, Ansarve 16, etc. (which outstrip current known ancient samples of I1, R1a, R1b in this region prior to the founder effect) aren't well represented in the modern population (Y-DNA I2 appears to be less than 6% in Scandinavian countries).

    Y-DNA bottleneck is from a single paternal line surviving and a founder effect after which we see all of the expansion of subclades from the SNP data of modern testers. This is also reflected in the STR variation signatures observed in modern I1 descendants as the relatively late TMRCA has the effect of resetting the odometer in terms of STR divergence from the modal or "convergence". R-U106 also observe these phenomena from a similarly recent TMRCA and expansion of SNP subclades that isn't observed in say, haplogroup E which has a point of diversity and TMRCA further back in time. We don't see bottlenecks of this nature in the same time period for mtDNA lineages - subclades of mtDNA branch off on a continuous basis expected from a simple model of steady birth/offspring/death so not close-to-complete population replacement at these times. Same with autosomal DNA ancestry. Y-DNA bottlenecks, founder events and expansions don't necessarily have to completely replace or eradicate the previous population.

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    Quote Originally Posted by spruithean View Post

    Keep us posted on those urm guys, they could get really interesting and even a tentative placement as simply I-DF29 for both is a hell of lot better than "ND" and "BCDEF". I was reading (yet again) the Sigtuna paper yesterday, quite an interesting read in terms of where some of these people likely came from in relation to Sigtuna.
    Just quickly on these ones - I was having another look at the Sigtuna paper, and the genome coverage for these two was really low - Table 1 has urm035 at genome coverage x0.26 and urm045 as x0.09 - that's the second worst male in the dataset. By comparison, the I1 sample 84005 was x1.03 and the only sample from this paper that's made it onto the YFull tree was 84001 which had genome coverage x3.7 on branch N-Y4339. My feeling is that the amount of info that we get from urm035 and urm045 may not be very much.

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    I'm just trying to get my head around this. I type faster than I think so please consider these posts of mine as "work in progress".

    Quote Originally Posted by deadly77 View Post
    Y-DNA bottlenecks, founder events and expansions don't necessarily have to completely replace or eradicate the previous population.
    Yes true. The SHG and EEF in us suggest no population replacement. And I also agree with:

    Quote Originally Posted by deadly77 View Post
    We don't see bottlenecks of this nature in the same time period for mtDNA lineages
    So why is there an "extreme founder effect" for a male lineage but not for female dittos? That some guy just got lucky might be true but should be a last resort as an explanation. So I think about male domination. Perhaps when the steppe herders arrived. The problem with that alternative is that I1 has not been found in any such related population so why would they be the source at all. An alternative is the formation and expansion of the Nordic bronze age. This is thought to be a time when an elite formed and enriched itself through control of trading networks. My guess is that this elite could be the founders that spread I1 through their domination of the society. If so, the origin of I1 might just as well be local.

    Just rambling, of course.

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    Quote Originally Posted by deadly77 View Post
    Just quickly on these ones - I was having another look at the Sigtuna paper, and the genome coverage for these two was really low - Table 1 has urm035 at genome coverage x0.26 and urm045 as x0.09 - that's the second worst male in the dataset. By comparison, the I1 sample 84005 was x1.03 and the only sample from this paper that's made it onto the YFull tree was 84001 which had genome coverage x3.7 on branch N-Y4339. My feeling is that the amount of info that we get from urm035 and urm045 may not be very much.
    Darn, that's too bad. Well at least we got some I1 from that Sigtuna paper, better than nothing. I'm sure we'll keep finding more I1 throughout the Migration Period and later eras, whether we'll find the puzzle piece I1 I'm not sure. I still think it is a bit misleading for a lot of these papers to a haplogroup call for sample "BCDEF", or some such.

    Quote Originally Posted by janan View Post
    I'm just trying to get my head around this. I type faster than I think so please consider these posts of mine as "work in progress".



    Yes true. The SHG and EEF in us suggest no population replacement. And I also agree with:



    So why is there an "extreme founder effect" for a male lineage but not for female dittos? That some guy just got lucky might be true but should be a last resort as an explanation. So I think about male domination. Perhaps when the steppe herders arrived. The problem with that alternative is that I1 has not been found in any such related population so why would they be the source at all. An alternative is the formation and expansion of the Nordic bronze age. This is thought to be a time when an elite formed and enriched itself through control of trading networks. My guess is that this elite could be the founders that spread I1 through their domination of the society. If so, the origin of I1 might just as well be local.

    Just rambling, of course.
    I'll ramble too...

    That could be a possibility, I mean Allentoft et al (2015) did find "I1" and "I1a" in the Nordic Bronze Age, so perhaps there is something to that however Allentoft et al dubbed them I1/I1a, however here it has been decided that due to lower coverage, or few important SNPs tested, etc we call them pre-I1. However it wouldn't be a surprise if they were legitimate I1 lineages as they are dated to within that 4,600 YBP TMRCA timeframe. So perhaps you're on to something here, as you say an elite formed during the Nordic BA and perhaps in some part of Scandinavia the founder of modern I1 managed to take hold of that elite status in his area. I'm not sure we could say I1 arrived with Steppe descended cultures as no I1 has been found in the Yamnaya areas (those areas are fairly well tested at this point). I've thought on the off chance that the BAB5 in Hungary was a legitimate I1 that perhaps I1 was present in the LBK sphere (through absorption of hunter gatherers by the farmers) and some group of them ended up in Scandinavia and remained during the Funnelbeakers period and eventual rise of the the Corded Ware groups such as Single Grave or Battle-Axe cultures in Denmark and Norway/Sweden respectively, and perhaps it wasn't until the Bronze Age that I1 began to expand.

    Perhaps one day they'll take another crack at some Nordic BA remains and grab a better sample.

    I1 is really a sort of strange haplogroup in all seriousness, it's somewhat common or dominant in a certain range of Europe, yet it doesn't appear in aDNA as often as R1b, R1a, G, E, etc perhaps due to where these people lived and their funerary practices be that burying their dead in soil that doesn't preserve genetic material or cremating their dead.
    Last edited by spruithean; 05-29-2019 at 11:00 AM.

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