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Sunday, August 1, 2010

Ancient Danish mtDNA


There is a new paper with some potentially interesting information about hypothetical demographic changes in Northern Europe in recent prehistory.


Linea Melchior et al., Genetic Diversity among Ancient Nordic Populations. PLoS ONE 2010. Open access.

Most of the recovered data is from the last 2000 years and only three sequences are from earlier periods (two from Neolithic and one from Early Bronze). This limits somewhat the conclusions that can be reached from this paper alone but will be useful to complement the previous data and gradually draw a clearer picture of ancient genetics in Europe. Still they make some meaningful findings that I comment below.


Demographic replacement with Urnfield culture in Northern Europe?

The finding of haplogroup U4 and U5a among Neolithic Danes and yet another case of mtDNA U4 in the single Bronze Age successful sample, essentially discards the hypothesis of Neolithic replacement so far north (Bramanti 2009). It still remains as a possibility for Central Europe but this hypothesis is largely reliant on Epipaleolithic and Neolithic Era foragers' data from the Baltic area (essentially U5 and U4 as well) and a limited sample from Paleolithic Swabia.

The haplogroup frequencies for antique and historical Danes are very similar to present. What says that, if there was any replacement, this happened after the Early Bronze Age.

In this sense, I am considering more and more the possibility of a demic replacement in Northern Europe with the Urnfield culture expansion, because a similar situation is apparent in the Elbe basin, where the Corded Ware site of Eulau and previous Neolithic samples show mtDNA apportions quite different from modern (high K in Eulau, high N1a in Danubian Neolithic of East Germany, low H in all), while the nearby site of Liechtenstein, belonging to Urnfield culture (Late Bronze Age), already displays a very modern mtDNA pool, high in H and U.

Notice please that while this may apply to Northern Europe, it is certainly not the case in the South, specially in the Southwest, as well as in Morocco, where mtDNA H is found at modern frequencies more or less at all temporal layers since Late Upper Paleolithic. Sometimes partial data for Northern or Central Europe is happily extrapolated to the whole continent and this is very much incorrect.


The vanishing of haplogroup I

This is even more intriguing, specially because this paper findings (12.5% of haplogroup I) are highly consistent with previous data showing high apportions of mtDNA I in Denmark (all for the last two millennia), when now this haplogroup only amounts to 2.5%.

As I say, the rest of the samples for this period are totally modern but this identity is strangely broken when we consider haplogroup I, which has shrunk dramatically and nobody seems to understand why.

The authors notice that haplogroup diversity appears to have been higher in the past than today, which is surely related, but they are not able to propose a cause for this phenomenon other than drift.

25 comments:

aargiedude said...

I have a million things to say. I love this study. This is the revenge of paleolithic continuity. I'll put my thoughts together tomorrow. Don't believe any of this. It's beyond ridiculous. This study has finally broken the camel's back regarding the credibility of ancient mtdna studies. Not saying they're all wrong, but there must be some sort of technical or other issue with ancient mtdna testing that will produce, in some instances, artifacts. I don't know which is worse, the U4/U5 results or the mtdna I results. In both cases, even calculated by the authors for the former, the likelihood of such unusual frequencies occuring in a sample of modern danes is 1 in 500. That means mtdna I, in the last 1,000 years, must have undergone a serious change in its frequency. Either Denmark suffered 80%+ population replacement (!!!) in the last 1,000 years or mtdna I has strange phenotypic consequences that forced it to be weeded out. It's all ridiculous. The authors didn't seem terribly confident about the implications, unlike last year's study.

I was thinking about the possibility that certain mutations would tend to better protect the mtdna chain from breaking apart. They tested 24 very ancient samples, more than 3,000 years old, and 3 were succesful, a 13% frequency. The rate of U4/U5 in Denamrk today is around 12%. But, this wouldn't explain why other studies found instead strangely high levels of I or N1a, with very little U4/U5.

I'm going to look also at the individual mutations listed, to see if these samples also have an unsually high number of exceptionally rare mutations, as I found in the ancient mtdna study of Etruscans.

I'm becoming more and more convinced there's a fundamental problem with the validity of (some) ancient mtdna testing.

Maju said...

Hmmm... maybe you're right.

Why does the mtDNA I keep showing up in Viking Age Denmark and only there? Drift definitively explains nothing because numbers must have been large already and time short, and we KNOW there's been NO population replacement in that time. Maybe the haplogroup is highly susceptible to some disease because of some mtDNA-specific reason? But then how it became so frequent to begin with?

Maju said...

Another possibility is that they keep digging the wrong tombs, i.e. those of a minority rather than the mainstream group. I got this idea when I realized haplogroup I is only really common among some minor groups of the Carpaths.

Maju said...

What I see is that haplogroup I only appears in ancient mtDNA (see Jean Manco's excellent reference page) in Denmark and Kurgan contexts (both in Europe and Asia). There is one notable exception: one early Chalcolithic individual from Catalonia, which pre-dates all others (1000-500 years older than the second oldest one: Eulau, East Germany).

Wilhelm von E. said...

Would it be possible that mtDNA haplogroup I was associated to phenotypical disadvantages against the Black Death?

Maju said...

Might be, Wilhelm. Impossible to say without further experimentation. I find it kind of unlikely but the survival of the lineage among Carpathian peoples (an area unaffected by the black death), can well suggest that.

Maybe it represents the temporary high visibility of a missionary, mercenary or slave group coming from elsewhere. If you'd sampled slave tombs in America, you'd see that the haplogroups varied because they had very high mortality and their ranks had to be renewed all the time with new blood which might or not come from the same specific areas. The same was surely the case for slaves in ancient Rome or in the Middle Ages in many cases.

People, specially young people without much reading of history and too exposed to medieval fantasy stories, have this idea that the Middle Ages were "noble and chivalrous" but in fact they were a gigantic slave trading ruse, specially east of the Rhine, where most people were slaves (N.J.Pounds 1974).

The more I look at it, the more it looks to me something like that. Anyhow the epidemic hypothesis can be tested in vitro. I'd test also other harmful "modern" illnesses like syphilis, btw.

Maju said...

PS - notice in table S1, that most of the people with haplogroup I were females:

1. "Roman" Iron Age (Antiquity):

Borbjegaard (South Sjaelland): 2/3 women.

Skovgaarde (South Sjaelland, near the previous one): 0/8 or 9 women.

Simonsborg (South Sjaelland): 1/4 women yielding genetic data (one did not).

2. "Viking Age" (Early Middle Ages):

Galgedil (North Fyn): 1/5 man, 0/5 women.

Kongemarken (North Sjaelland): 2/6 women yielding genetic data (one did not).

3. Medieval Age (High Middle Ages):

Riisby (South Sjaelland): 1/7 men yielding genetic data, 0/3 women.

To me this pattern does suggest two ideas:

1. It may be a haplogroup still particularly common in some areas of rural Denmark, specially in South Sjaelland but not overall.

2. Alternatively, it may be a case of imported slave women who had gradually less and less reproductive success because of their lower social status (or maybe because of sexual selection??).

There can be other explanations such as the epidemic susceptibility, the random fluke in the data, the random drift (you see less women with it and more men as time passes, what can "kill" a female lineage) in reality and who knows what.

Maju said...

I'm trying to find out now where mtDNA is particularly common.

The classical McDonalds' haplogroups map shows relatively high levels (less than 5% in any case) for Iceland and Kurdistan but Europe is only shown on regional basis, what does not help much.

Per the data at FTDNA, I find the following areas with some notable concentration of haplogroup I:

- Lithuania
- Norway (rather inland)
- Formerly Finish St. Petersburg area, near Lake Ladoga.
- North Germany (?)
- Ireland (possibly related to Icelandic "high" frequencies)

Then also some frequency by Hungary, Swabia, an specific locality in SE France (La Vallette), some Scots, and some Iberians (specially in Azores). No or very few and unclear mentions to Denmark nor England.

So maybe we are looking to an "imported" haplogroup in the sense I mentioned before, as it seems more common around Denmark than in Denmark itself.

Maju said...

Another group "high" in mtDNA I are Mordvins, a Volga-Finnic ethnicity, among whom it reaches almost 6% (Bermisheva 2002).

I can't find much more but the slavery or minority hypothesis should be considered along with any biological/medical one.

aargiedude said...

Hmmm... maybe you're right.

It's a very difficult situation: it seems very hard to justify the change in mtdna I from just 1000 years ago, but if the results aren't accurate and the problem is the testing itself, it seems just as hard to come up with some explanation of what that problem could possibly be.

Another possibility is that they keep digging the wrong tombs, i.e. those of a minority rather than the mainstream group.

But they showed a map of the sites and they were all over the place: in the peninsula and in the 2 main islands.

What I see is that haplogroup I only appears in ancient mtDNA (see Jean Manco's excellent reference page) in Denmark and Kurgan contexts

But if the Danish mtdna I results are some sort of artifact, who's to say all those other results aren't also the product of the same problem? The famous duo of U4/U5 has a remarkable ability to appear in many places at rates way in excess of its current frequency in the same region. Dienekes even postulated that perhaps U4/U5 were under some negative selection pressure. What I remember, though, is that the study that found 3 mtdna samples from Italy from 20,000 years ago noted that mutations 16356 and 16270 were the most common to suffer false positives in their amplifications of ancient mtdna, especially the latter. They define, respectively, U4 and U5. That doesn't explain, though, that many of these current U4/U5 results are also positive for the coding mutation 12208 (I know, I got it wrong, whatever), which defines haplogroup U. The Italian study included the actual spreadsheet with all the results and I was able to see for myself that indeed 16270 was by far the most common mutation that suffered false positives. I dunno... The other kid in this drama is N1a. It's not just the Haak study of Central Europe; N1a has been found quite a few other times, including this very study we're discussing! Yup, there's 1 N1a out of 56 total samples, or 2%. The modern rate of N1a anywhere in Europe is 0,3%. No wonder Dienekes postulates negative selection to explain these anomalies: it's just an impossible riddle, otherwise.

aargiedude said...

Looking at some data from neighboring countries, I'd say Denmark's population was around 100,000 in 0 AD and 200,000 or 300,000 in 1000 AD.

----------------------------------------------

Here are some stats on mtdna I in Europe, from Richards (2000):
Iraq.....................................0%
Levant................................0,4%
Anatolia..............................2,6%
Caucasus...........................1,8%
Greece to Romania..............2,8%
Italy....................................2,0%
Alps...................................1,8%
Germany to Poland..............2,1%
Iberia (exc. Basques)...........0,9%
France and Britain................3,1%
Sweden to Norway...............1,3%
Finland? Russia? Baltics?.....2,7%

In a graph, it shows clearly that mtdna I has a rather uniform rate throughout Europe, hovering between 2% and 3%. The authors state the modern rate of mtdna I in Denmark is precisely 2,5%. This is another problem. Mtdna I looks like yet another haplogroup that is uniformly diffused throughout Europe. If it used to be 13% just 1000 years ago, it's a remarkable coincidence that whatever changed that stopped precisely at the same rate that mtdna I was found in the rest of Europe. Unless mtdna I was also found at high rates everywhere, and they were all affected by some mysterious phenomenon.

----------------------------------------------

I redid the calculations of how unlikely the mtdna I coincidence truly is. The likelihood that a sample of 53, taken from a population in which mtdna I is found at a frequency of 2,5%, will contain 7 or more samples of mtdna I is 1 in 3,000. I previously said it was 1 in 500. Ergo, we got a problem here. The one thing we can't say about these results is that they could be just a wild longshot oddity. Nope, 1 in 3000 chance, can't be. Add to that the results from the previous study of Denmark also finding mtdna I at a strangely high frequency and we now know that something is definitely going on here, period. Randomness and luck don't play a part in this saga.

Maju said...

I find difficult not to believe this careful research is not for real, they have used the best methods available, it seems (see previous paper) and even checked the methods successfully against an Inuit sample 500 years old. The results are not based only on the control region but also on the coding region.

There are two possibilities: (1) that the haplogroup is intrinsically much more susceptible to some disease such as the plague or (2) that there is a bias in the sampling that we cannot discern easily.

This last includes my hypothesis of minorities of foreign origin such as Finnic or Central European slaves. A few populations in these areas have higher apportions of mtDNA I and it's possible that there were others with even higher apportions that have just gone effectively extinct precisely because of overexploitation in the Medieval slave trade maybe, which was brutal in Eastern Europe.

Notice anyhow that it may be also accidental. Even if it's unlikely to throw five dices and get all sixes, it sometimes happen anyhow. In the previous paper, they did not detect any mtDNA I in Galgedil cemetery (Fyn) for instance, however now they did find one case (different individuals).

Anyhow, for me much more intriguing is the possibility of a demic replacement from Rhineland with the Urnfield culture, as suggested by the growing apportion of mtDNA H precisely since that time. The why of mtDNA I apparent decline does not seem as important, as only affects one haplogroup, while the rest are found at "normal" apportions. But the apparent replacement of mostly "Paleolithic" (U) and "Neolithic" (K, T, J) populations by H-dominated ones in the late Bronze Age is quite curious and most unexpected because it does not fit with any of the usual scenarios such as the Neolithic replacement model or the Indoeuropean (Kurgan) replacement hypothesis. Things thou shall see...

Is this the "revenge" of indeuropeanized "Paleolithics"? Maybe.

Va_Highlander said...

Weren't the Saami disproportionally spared the Black Death due to their lifestyle? And weren't the more populated ares of the Scandinavia devestated by plague?

If this is true, then to my mind that does imply at least some population replacement in the past 1,000 years. Whether or not this might account for the decline of mtDNA I, is a different story.

Maju said...

A demographic crisis such as the Black Death is not by any means a population replacement, just a mild narrowing of the demographic pattern.

In order to have population replacement you need first of all a migration from place A to place B, and that migration to have enough strength to become dominant in place B.

I see nothing of that except very arguably between short distances sometimes in all the Middle Ages. Even the great colonization of the period, the Drang Nach Östen was largely a Germanization and Christianization of Slavic peoples East of the Elbe, even if interspersed with effective colonization from West Germany.

However some localized groups may well have been exterminated, deported and/or enslaved altogether now and then.

Nothing of that can be attributed to any known Finnic expansion, much less Sami.

What the Black Death and other plague epidemics might have implied maybe can only be that mitochondria of haplogroup I was particularly susceptible to the disease, gradually dying off nearly all of them. This can be an explanation but something that should be confirmed by experimentation in vitro before we can be sure.

As said before I'd also check with other diseases such as syphilis (an import from America, it seems).

But if this would be true, then there would have been no population replacement at all, just negative selection against unfit genotypes.

Va_Highlander said...

According to Wiki, northern Norway was substantially depopulated during the plague years and the Saami were still resettling abandoned farms as late as the 1700s. The fishing industry was so badly affected that the monarchy actively encouraged the Saami to relocate and take up fishing.

I'm not that familiar with Northern European history and thought maybe someone with better knowledge of what transpired in Denemark could say if plague could have had a similar impact and consequence there, as well.

Maju said...

I can only say one thing: there have never been any Samis in Denmark. Even extrapolating anything of what you mention to Southern Scandinavia Peninsula seems plainly impossible.

It's like discussing New York's demographic history and suddenly you mention the Inuit in North Labrador... I can only look around perplex. ;)

"I'm not that familiar with Northern European history and thought maybe someone with better knowledge of what transpired in Denemark could say if plague could have had a similar impact and consequence there, as well".

Probably the records are limited for the North in that period. Even in the better documented areas of France or Italy we get only a fragmented picture. It's most unlikely that overall the Black Death killed more than 20% of the people, though it hit particularly badly to young people. Some areas, like Poland/Hungary or the Bearn were almost totally spared, while in other localities maybe up to 50% of the people died.

The Black Death had some advantages in the mid run, because people gained some choice and land for several generations, weakening the feudal system somewhat. In general anyhow, you can expect the gradual repopulation to have drawn from the local genetic pool, and I see absolutely no reason for Denmark to be different at all.

If the plague had anything to do with the vanishing of mtDNA I, it must have meant not any repopulation but an specific susceptibility of the mtDNA haplogroup. It's not the first time that mtDNA has been suggested to be differentially fit, after all mitochodria are not there just for decoration: they are central to our metabolism. Some mutations may be perfectly neutral... until conditions change and this may be one of those cases.

Because you see mtDNA I going down but you see all other haplogroups perfectly stable, so there should not be any population change - and we know from history there was not.

midnightravenmoon said...

I am researching to day .My mtdna is HgI1a.My blood type is O neg.I am seeking to try and locate my first mother .So to speak.The blood type is ,some say ,down to 3 per cent.I see the Hg is dying off as well.I just want to find my first mother's tribe.Why we I am as I am .I have found many weird things about my own ancestry ,everyone does .Things which do not seem likely
So ,she is a part of me ,not everything .But ,the root of it .I do not know my father's blood type .He is dead and there are no male heirs.

I do not understand much of this dna talk,one would almost have to be a scientist in this field .Thank you.Ter

Maju said...

You're welcome. If you have specific questions feel free to ask (though I'm not sure if I will be able to answer, I'll try).

Bombix said...

Although this falls squarely in the anecdotal camp, I have done extensive research on my female to female line back to 1803 -- I am mtDNA haplogroup I1a. Although my research covers only 200 years, I can tell you that even though the families I researched had many children, I have been hard pressed to find many maternal line descendants left. I don't know why this is, exactly. Even if women didn't marry or died young, there should still be more descendants, not less. If my sister's daughter doesn't have a daughter, that will end the mtDNA haplogroup I succession in our family. Maybe someone should do a study on percentage of population in the past 200 years and see if the decline ratio is persistent.

Maju said...

Evidently that's a case of random drift (I can only imagine that the haplogroup does NOT affect specifically number of female offspring or offspring in general). But in the big picture what happens in one line should be the reverse in another, so statistically everything should remain the same.

However it did not, it seems. And that is quite puzzling.

If at least we could pinpoint a trait that made the lineage successful in the past and now quite less so... be it biological or sociological... but nope! Nothing apparent.

midnightravenmoon said...

I wish I could finish my maternal line most of all.I1a.Have they now dropped the a?I got back for certain to my gg grandmother.Israel Boone's wife ,found on the internet is I1a.I mean ,what if we are remnants from Atlantis ?A large city has been found off the coast of Cuba.These stone structures and pyramids,all over the world .I think it points to a world before this one .Maybe our mt dna is off world .
I thought I read that the Visigoths and Danes had this mtdna hg.Did our people undergo genicide at one time ?I cant give up .Just slowed down ,a lot.Good hunting yall.Teri

Maju said...

Uh?

If Atlantis or something similar existed it was in modern day Portugal (look up Castro de Zambujal) and it probably has nothing to do with mtDNA I1(a).

Nope they have not dropped the a but the phyologenies and nomenclatures get reworked now and then anyhow: http://www.phylotree.org/

midnightravenmoon said...

Is everyone here have mtdna hg Iia or I ?Is anyone else o neg ?

midnightravenmoon said...

If we all have the same maternal line ,are we not the people of the same people of that mother line ?Sorry ,tornado in progress.ned to get off here.Just found this blog again.

Maju said...

@midnightravenmoon: most probably not. I have never checked my DNA as I'm only interested in its collective and not personal information, but, being Basque by both purely paternal and maternal lines, probably not. Can't say about the rest.