The less homogeneous European "populations" are Italians and French

22 Jun
This comes from a recent IBD study on Europe:
Peter Ralph & Graham Coop, The Geography of Recent Genetic Ancestry across Europe. PLoS Biology, 2013. Open accessLINK [doi:10.1371/journal.pbio.1001555] 


The recent genealogical history of human populations is a complex mosaic formed by individual migration, large-scale population movements, and other demographic events. Population genomics datasets can provide a window into this recent history, as rare traces of recent shared genetic ancestry are detectable due to long segments of shared genomic material. We make use of genomic data for 2,257 Europeans (in the Population Reference Sample [POPRES] dataset) to conduct one of the first surveys of recent genealogical ancestry over the past 3,000 years at a continental scale. We detected 1.9 million shared long genomic segments, and used the lengths of these to infer the distribution of shared ancestors across time and geography. We find that a pair of modern Europeans living in neighboring populations share around 2–12 genetic common ancestors from the last 1,500 years, and upwards of 100 genetic ancestors from the previous 1,000 years. These numbers drop off exponentially with geographic distance, but since these genetic ancestors are a tiny fraction of common genealogical ancestors, individuals from opposite ends of Europe are still expected to share millions of common genealogical ancestors over the last 1,000 years. There is also substantial regional variation in the number of shared genetic ancestors. For example, there are especially high numbers of common ancestors shared between many eastern populations that date roughly to the migration period (which includes the Slavic and Hunnic expansions into that region). Some of the lowest levels of common ancestry are seen in the Italian and Iberian peninsulas, which may indicate different effects of historical population expansions in these areas and/or more stably structured populations. Population genomic datasets have considerable power to uncover recent demographic history, and will allow a much fuller picture of the close genealogical kinship of individuals across the world.

Most interesting in my understanding is table 1 (right), which describes the IBD relation of the sampled populations within themselves and with other Europeans.
From this table it seems very apparent that Italians and French are not homogeneous at all and therefore, in my opinion, should not be treated as single populations in genetic studies but butchered at least a bit by regions (whose optimal dimensions are yet to be determined).
The degree of internal homogeneity of the samples (only n=5 or greater) can be simplified as follows:
  • Very low (<1): Italy, France.
  • Quite Low (1-1.4): Germany, UK, Belgium, England, Austria, French-Swiss, 
  • Somewhat low (1.5-1.9): Spain, German-Swiss, Greece, Portugal, Netherlands, Hungary.
  • Somewhat high (2-2.9): Czech R., Romania, Scotland, Ireland, Serbia, Croatia,
  • Quite high (3-3.9): Sweden, Poland
  • Very high (4-5): Bosnia, Russia*
  • Extremely high (>10): Albania
  • I ignored strangely labeled samples like “Switzerland” and “Yugoslavia”, which seem to mean actually “other” within these labels.  I retained the “United Kingdom” category for its large sample size, much larger than its obvious parts.
  • The level of relatedness of Russians may be exaggerated by the small sample: n=6, still above my cautionary threshold. 
  • I suspect that the extreme disparity of sample sizes may influence the results to some extent.
Eastern Europeans seem much more strongly related with others, especially other Eastern Europeans, than Western ones, while NW Europeans are more related with other groups (usually at regional level) than SW ones. In fact the Italian and Iberian peninsula show very low levels of “recent” relatedness with other populations, which is a bit perplexing, considering their non-negligible roles in Medieval and Modern European history. I guess that this may be partly caused by geographic barriers (mountains) and also by these areas having large populations since Antiquity or before. 

Figure 3. Geographic decay of recent relatedness.
In all figures, colors give categories based on the regional groupings of Table 1. (A–F) The area of the circle located on a particular population is proportional to the mean number of IBD blocks of length at least 1 cM shared between random individuals chosen from that population and the population named in the label (also marked with a star). Both regional variation of overall IBD rates and gradual geographic decay are apparent. (G–I) Mean number of IBD blocks of lengths 1–3 cM (oldest), 3–5 cM, and >5 cM (youngest), respectively, shared by a pair of individuals across all pairs of populations; the area of the point is proportional to sample size (number of distinct pairs), capped at a reasonable value; and lines show an exponential decay fit to each category (using a Poisson GLM weighted by sample size). Comparisons with no shared IBD are used in the fit but not shown in the figure (due to the log scale). “E–E,” “N–N,” and “W–W” denote any two populations both in the E, N, or W grouping, respectively; “TC-any” denotes any population paired with Turkey or Cyprus; “I-(I,E,N,W)” denotes Italy, Spain, or Portugal paired with any population except Turkey or Cyprus; and “between E,N,W” denotes the remaining pairs (when both populations are in E, N, or W, but the two are in different groups). The exponential fit for the N–N points is not shown due to the very small sample size. See Figure S8 for an SVG version of these plots where it is possible to identify individual points.
We can also see in the above figure (bottom) how most of the relatedness, especially along longer distances belongs to the oldest dates (1-3 cM).
The authors suggest that low heterogeneity within some of these groupings is influenced by regional variation, what makes good sense to me. This they illustrate with the examples of Italy and Great Britain:

Figure 2. Substructure in (A) Italian and (B) U.K. samples.
The leftmost plots of (A) show histograms of the numbers of IBD blocks that each Italian sample shares with any French-speaking Swiss (top) and anyone from the United Kingdom (bottom), overlaid with the expected distribution (Poisson) if there was no dependence between blocks. Next is shown a scatterplot of numbers of blocks shared with French-speaking Swiss and U.K. samples, for all samples from France, Italy, Greece, Turkey, and Cyprus. We see that the numbers of recent ancestors each Italian shares with the French-speaking Swiss and with the United Kingdom are both bimodal, and that these two are positively correlated, ranging continuously between values typical for Turkey/Cyprus and for France. Figure (B) is similar, showing that the substructure within the United Kingdom is part of a continuous trend ranging from Germany to Ireland. The outliers visible in the scatterplot of Figure 2B are easily explained as individuals with immigrant recent ancestors—the three outlying U.K. individuals in the lower left share many more blocks with Italians than all other U.K. samples, and the individual labeled “SK” is a clear outlier for the number of blocks shared with the Slovakian sample.
In the UK, there is a negative correlation between blocks shared with Ireland and those shared with Germany, what seems to imply a dual origin of Britons. 
Age estimates (double them?):
The authors also get to estimate ages, however it seems obvious from their own data that the results should be multiplied by 2.2 or something like that to make good sense:

Figure 4. Estimated average number of most recent genetic common ancestors per generation back through time.
Estimated average number of most recent genetic common ancestors per generation back through time shared by (A) pairs of individuals from “the Balkans” (former Yugoslavia, Bulgaria, Romania, Croatia, Bosnia, Montenegro, Macedonia, Serbia, and Slovenia, excluding Albanian speakers) and shared by one individual from the Balkans with one individual from (B) Albanian-speaking populations, (C) Italy, or (D) France. The black distribution is the maximum likelihood fit; shown in red is smoothest solution that still fits the data, as described in the Materials and Methods. (E) shows the observed IBD length distribution for pairs of individuals from the Balkans (red curve), along with the distribution predicted by the smooth (red) distribution in (A), as a stacked area plot partitioned by time period in which the common ancestor lived. The partitions with significant contribution are labeled on the left vertical axis (in generations ago), and the legend in (J) gives the same partitions, in years ago; the vertical scale is given on the right vertical axis. The second column of figures (F–J) is similar, except that comparisons are relative to samples from the United Kingdom.

I say that mainly because the shared ancestry between Balcans and both Italy and France is dated here to around 3000 or 3500 years ago, when it would fit much better to c. 7500 years ago (as much as 8000 BP for some parts of Italy), when the Neolithic expansion was ongoing. There is no particular reason why the Balcans would be related to France and Italy c. 3000 years ago specifically, unless one believes in undocumented massive Mycenaean migrations or something like that (and what about Albania then?)
However I am getting a headache with this issue because no correction, low or high seems good enough for all pairs, so, well, just take this part with your usual dose of healthy skepticism.
Some (annotated) excerpts:

In most cases, only pairs within the same population are likely to share genetic common ancestors within the last 500 years [i.e.: ~1100 years]. Exceptions are generally neighboring populations (e.g., United Kingdom and Ireland). During the period 500–1,500 ya [i.e. ~1100-3300 years ago: most of the Metal Ages], individuals typically share tens to hundreds of genetic common ancestors with others in the same or nearby populations, although some distant populations have very low rates. Longer ago than 1,500 ya [i.e. before ~3300 years ago: before the Late Bronze Age crisis], pairs of individuals from any part of Europe share hundreds of genetic ancestors in common, and some share significantly more.

On Italy:

There is relatively little common ancestry shared between the Italian peninsula and other locations, and what there is seems to derive mostly from longer ago than 2,500 ya [i.e. ~5500 y.a.: Megalithic era onwards]. An exception is that Italy and the neighboring Balkan populations share small but significant numbers of common ancestors in the last 1,500 years [i.e. after 3750 years: since the Mycenaean period]

On Iberia:

Patterns for the Iberian peninsula are similar, with both Spain and Portugal showing very few common ancestors with other populations over the last 2,500 years [i.e. 5500 years: Megalithic era onwards]. However, the rate of IBD sharing within the peninsula is much higher than within Italy… 

The low Iberian relationship with other populations seems to preclude this region as source for the conjectured re-expansion of mtDNA H and other Western lineages. I would suggest looking to (Western) France for an alternative source, as this state’s heterogeneous population shares more intense relations with other Western peoples around what could be c. 6200 BP, what is at the very beginning of Megalithic spread in Atlantic Europe, for which Armorica (Brittany and neighboring Western France) could well have been a major source (and definitely was in the case of Britain).
Of course, if you prefer to use the authors’ estimates, it would have no influence on the hypothesis because they simply can’t reach so far back in time, it seems. But I feel more comfortable overall reformulating the hypothesis towards Armorica.
For better reading of each pair of relationships through time, I include here fig. S16:

The maximum likelihood history (grey) and smoothest consistent history (red) for all pairs of population groupings of Figure S12 (including those of Figure 5). Each panel is analogous to a panel of Figure 4; time scale is given by vertical grey lines every 500 years. For these plots on a larger scale, see Figure S17.

As said before, I suggest to read each vertical grey line (counting from left) as meaning ~1100 years rather than just 500.

Update (Jun 23): on IBD-based molecular-clock-o-logy:

I have now and then found strange insistence on IBD-based chronological estimates being almost beyond reasonable doubt. I admittedly don’t know a great deal on the matter, so when Davidski (see comments) insisted again on that, I asked him for a reference, so I could learn something. He kindly suggested me to read Gusev et al. 2011, The Architecture of Long-Range Haplotypes Shared within and across Populations, which is indeed a good paper. However I could not find the clearly explained basis for the chronological estimates in general, probably buried deep in the bibliography. What I found instead was a clear example of these being short from historical reality by a lot.

This example corresponds to one of the best documented populations to have suffered a “recent” bottleneck event: Ashkenazi Jews (AJ). According to Gusev et al., these would have suffered a bottleneck (founder effect of some 400 nuclear families followed by expansion) around 20 generations ago (~600 years = 1400 CE) or, a few lines later more specifically: 23 generations ago (~1320 CE). So here we do have a clear case study.

When we look at historical reality however, it is just impossible that AJ would have their founder effect bottleneck so late. Historical records document them often already in the Frankish period and they were definitely a vibrant expanding community by the time of the founding of Prague and Krakov c. 900 CE. A historical reasonable estimate for the AJ founder effect should be instead c. 700 CE, when they begin to appear in historical records, or maybe even a bit earlier, because of the lack of documentation in the Dark Ages.

That is not at all a mere 20-23 generations ago but almost double (counting generation time = 30 years, if gen-time would be 27 years, for example, the difference between estimates and reality would be even greater). Assuming a very reasonable AJ founder effect at 700 CE, then:

  • For gen-time = 30 years → 43 generations till now → 43/23 = 1.9 times for realistic correction
  • For gen-time = 27 years → 48 generations → 48/23 = 2.1 times for realistic correction
  • For gen-time = 25 years → 52 generations → 52/23 = 2.3 times for realistc correction

While it has become nowadays standard issue to assimilate generation time to 30 years, this is not any absolute measure because the actually observed generation time (i.e. the age difference between parental and child generations on average) varies in real life depending on cultural factors (such as marriage age), gender (female generation time is almost invariably shorter than male), life expectancy (mothers dead at birth at young age, for example, don’t have any more children), etc. So it is in the fine detail a somewhat blurry issue, with some significant variability among cultures and surely also through time.

Another issue is if this “short term” estimate correction is stable along time or does in fact vary somewhat. I can’t say.

Whatever the case, the approximate x2 correction proposed above, seems to stand in general terms.


66 responses to “The less homogeneous European "populations" are Italians and French

  1. Davidski

    June 23, 2013 at 3:18 am

    Well, if you think there's no reason why the French, Italians and Balkan populations should share post-Neolithic IBD, then what happened to the Oetzis of Europe? Why are they gone (except from Sardinia), and why do modern French and Italians appear genetically more northern, eastern and southeastern?Seems to me like there were massive population movements across Europe from the late Neolithic to the Medieval period. Only Sardinians and Basques weren't affected significantly.

  2. Davidski

    June 23, 2013 at 3:26 am

    Oh yeah, also, >2cM doesn't go back to the Copper Age, so this study doesn't preclude a massive expansion from Iberia during that time.

  3. Maju

    June 23, 2013 at 3:43 am

    I don't have too clear answers but what I have clear is that, with the archaeological record in hand, there was no migration from the Balcans ever after Neolithic, excepting the limited Greek colonization of Southern Italy and few other enclaves and the debated origins of the Etruscan elite in Anatolia maybe, all of which only could affect Italy, never France in any meaningful way (i.e. out of the walls of Massilia).For what I see of ancient DNA, even the Neolithic flow was not so impacting in the long term, although there was indeed a time (Early Neolithic) in which the Neolithic groups of (largely) Balcanic and West Asian origin were dominant in some areas (Catalonia-Languedoc, Germany at least) but not others (Portugal, Basque Country – here particularly the population seems stable since the earliest Neolithic). Then there was some sort of reverse flow around the time of Megalithic apogee (and Bell Beaker) and also E→W flow affecting Central and Norther Europe (Pitted Ware, Kurgans). Then the populations became stable or almost so until now. That is what I see in ancient mtDNA.

  4. Maju

    June 23, 2013 at 3:46 am

    How can you know that? I haven't yet investigated the molecular-clock-o-logy of IBD segments but, on first sight, I can only imagine it would be even more confusing than that of haploid lineages. Maybe I am wrong, so that's why I ask how can you feel so certain about the age estimate with this method? Which studies or other references support these chronological estimate claims?

  5. Davidski

    June 23, 2013 at 3:59 am

    What I see in ancient DNA is the replacement of early to mid Neolithic Near Eastern-like populations in Central Europe by genetically more European groups coming from the Atlantic Facade and Eastern Europe. Then I see an expansion of their mixed descendants back to the west and east in a series of movements from the Bronze Age to the Medieval period, which erased the Sardinian and Basque like populations from much of the continent, and East Eurasian-admixed populations from much of Eastern Europe. It's actually more complex than that, but this basic process that I describe fits modern DNA data very well, including ADMIXTURE and IBD analyses.

  6. Maju

    June 23, 2013 at 4:10 am

    We agree in the first part: "the replacement of early to mid Neolithic Near Eastern-like populations in Central Europe by genetically more European groups coming from the Atlantic Facade and Eastern Europe". I am not too much in agreement with the later part: "expansion of their mixed descendants back to the west and east in a series of movements from the Bronze Age to the Medieval period, which erased the Sardinian and Basque like populations from much of the continent", I don't make much sense of it, not so much of the process but of the concepts implied themselves: Which Basque-like populations? Where? How are these different from the "Atlantic populations" you admit to their importance? "Erased" or rather "slightly diluted"?. In any case, how do you fit the Balcans in this? They just do not fit in at all after the initial Neolithic expansion. Also, how do you fit into that the extremely low values of Italian relationship with any population after the Balcanic expansion?Have you tried to look at the issue from all the corners? If so, how is that you don't see the obvious contradictions pointed in the previous paragraphs of this comment?

  7. Maju

    June 23, 2013 at 4:12 am

    PS- I agree that Ötzi is a bit difficult to explain but he's just one sample, no matter how famous. Maybe he was not very representative of the mainstream populations of Italy already in his time.

  8. Davidski

    June 23, 2013 at 4:22 am

    Nah, it's not like haploid markers at all. Here's a good paper on IBD…

  9. Davidski

    June 23, 2013 at 4:27 am

    Oetzi isn't difficult to explain, and neither are the population turnovers and genetic shifts in Central Europe, and then in Southern and Eastern Europe. It all fits very well with what I said above, and with the IBD results.

  10. Davidski

    June 23, 2013 at 4:39 am

    Yes, I've looked at the issue from all angles.The re-expansion of the mixed populations from Central Europe, as per above, had to happen. Your people are good evidence of that. Iberians and even most French would be Basque-like and many Italians Sardinian-like if not for these back migrations.The relative isolation of Italy and Iberia in terms of the >1cM IBD is easy to explain. Both were quickly filled up to capacity for those times and then maintained high effective population sizes. Moreover, they were blocked off from the rest of Europe by the Pyrenees and Alps, while Italy also experienced maritime migrations, which increased its IBD diversity and differentiation from Europe, and even between many Italian populations.

  11. Maju

    June 23, 2013 at 5:00 pm

    This comment has been removed by the author.

  12. Maju

    June 23, 2013 at 5:02 pm

    Thanks for the link, David. The paper is interesting no doubt but I am having a hard time finding why they estimate X cM values to correspond to Y time, measured in generations. However I found the following regarding Ashkenazi Jews:"… the observed exponential decay of 0.671 per cM (SD 0.055) is consistent with a bottleneck event around 20 generations before present, followed by a rapid expansion"…The bottleneck model seems indeed demonstrated (fig. 4a) but… 20 gen x 30 years = 600 years ago, i.e. ~1400 CE. By this time the Ashkenazi Jewish population was very much consolidated, being the real historical bottleneck dated to the Frankish period, arguably at Marseilles, surely before 700 CE in any case, when historical records already mention Jews often North of the Alps. Also, around the time of the foundation of Prague and Krakow, c. 900 CE, Ashkenazim were already a vibrant community with widespread presence in most of Europe.So the AJ bottleneck MUST about twice the age claimed by the authors, not 20 but around 40-45 generations ago (maybe even a bit older if we consider the fact that almost no documentation exists from the Dark Ages: c. 500-800 CE, allowing for some two centuries of great uncertainty).A few lines later they talk of "23 generations ago" (= ~690 years = ~1300 CE), what fixes nothing.See for example: research by Gil Atzmon is mentioned, suggesting that AJs "went through a 'severe bottleneck' as they dispersed, reducing a population of several million to just 400 families who left Northern Italy around the year 1000 for Central and eventually Eastern Europe". Gusev's study suggests "950 diploid indivdiuals", what is very close, but not in the age estimate, which gets quite farther from historical reality than Atzmon.So, even against my own expectations, I rather feel vindicated by this paper's obvious inability to estimate on IBD counts alone, the actual historical events of one of the best researched and historically documented "bottlenecked" populations on Earth. The actual age estimates should be (pending more research) around double than what Gusev et al. claim (which, for what I understand, is the standard in IBD molecular-clock-o-logy).

  13. Maju

    June 23, 2013 at 5:15 pm

    "Oetzi isn't difficult to explain"…His mtDNA isn't maybe (although his particular K1 subhaplogroup is extinct apparently) but the autosomal genetics are: 1. Apparent excess (double) of Neanderthal ancestry (per Hawks), compared with every modern West Eurasian (or just Eurasian) population, including Sardinians. 2. If, as you and others assume, he represents the Chalcolithic populations of Italy (or at least North Italy), we have a major issue here because there does not seem to be any major "replacement" in the later prehistory of Italy, which, according to this paper's chronological estimates, the IBD sharing of Italians with whatever other Europeans or West Asians is very low for the last 4000 years, i.e. since the time of Bell Beaker apogee (~ double that time with my corrections). So there does not seem to have been any "replacement" in Italy since Late Chalcolithic (or since around Neolithic). So I'm suspecting that Ötzi does not properly represents average (North) Italians of his time but maybe some anomalous isolate population of the Alps. It is quite plausible that, especially in the Alpine valleys (as is still the case now to a large extent) genetically isolated populations existed with only general cultural links to the mainstream ones of the lowlands.

  14. Maju

    June 23, 2013 at 5:58 pm

    Updated in order to reflect this discussion (from my viewpoint, of course).

  15. Grey

    June 23, 2013 at 8:17 pm

    "Some of the lowest levels of common ancestry are seen in the Italian and Iberian peninsulas"I'd have thought the way the mountain ranges divide Spain and Italy into regions might mean IBD testing there could give very high results if comparing just one region with itself but very low compared with anywhere else e.g. testing Catalonia just with Catalonia or Calabria just with Calabria.I think that would be interesting to see.///"The low Iberian relationship with other populations seems to preclude this region as source for the conjectured re-expansion of mtDNA H and other Western lineages."I'm surprised to see this as i thought there'd be more connection along the Atlantic fringe from c. Galicia onwards. Although perhaps if the previous point about mountain-delimited regions is correct the source for the Iberian expansion may not be sampled?Or maybe it is France instead? I thought the critical dividing line would be the boundary between ecozones.This post has maps of estimated ecozones on those maps Armorica *is* the ecozone dividing line so it does fit the original idea just much further along the coast than i previously thought it would be.///"While it has become nowadays standard issue to assimilate generation time to 30 years, this is not any absolute measure because the actually observed generation time (i.e. the age difference between parental and child generations on average) varies in real life depending on cultural factors (such as marriage age), gender (female generation time is almost invariably shorter than male), life expectancy (mothers dead at birth at young age, for example, don't have any more children), etc. So it is in the fine detail a somewhat blurry issue, with some significant variability among cultures and surely also through time."Yes, i think generation times will have varied over time and place and that may be significant sometimes.

  16. Maju

    June 23, 2013 at 11:51 pm

    "I'd have thought the way the mountain ranges divide Spain and Italy into regions"…At least in Iberia mountain ranges have not much to do with actual regional divisions, especially if we see them historically. For example, modern Asturias or Cantabria may be partly defined by mountain ranges but ancient Astures and Cantabri, as well as the roughly corresponding medieval realms of Asturias-León and Castile respectively, existed across the mountain range, which was much more of a backbone than a divide. Basques also live across mountain ranges, again acting as backbone, etc. Even further East ancient Ligurians lived at both sides of the Alps…Anyhow the population samples should indeed be more regionally focused because in all these cases we hardly know what they mean when they say "French", "Italians", etc. Still in the Iberian case there are two different samples: "Spain" and "Portugal", granting at least a modicum of regional diversity in it. About the econiches, I am not really keen of how the study you mention differentiates them. In reality there are three ecological zones: Mediterranean, Continental and Atlantic, not two. The Atlantic one is defined for being quite more humid than the others (also colder than the Mediterranean but warmer than the Continental area). For example there are no olives (other than in a few gardens with a merely decorative role) in Biscay and the crops that would fare better are often closer to those doing well in Denmark than those successful in Sicily, although there's of course a temperature gradient between Atlantic Iberia and Western Scandinavia and all that is in between. Also the actual distribution of Cardium (senso lato) does not fit too well with the proposed econiche because there was a clear penetration along the Rhone and further North into Germany, etc. (La Hoguette and other transitional cultures), while instead in the Atlantic North of central Portugal we cannot talk at all of Cardium or anything clearly related (with maybe some pocket exceptions in SW France, which are again very peculiar local variants). Whatever the case the probable demic flows in the Chalcolithic may have been more motivated by political than purely ecological motivations. In those time there must have already been some quite notable political entities of some sort, social complexity was already quite high and we cannot anymore talk of mere tribal organization, although this one probably coexisted with wider political interaction.

  17. Davidski

    June 24, 2013 at 6:08 am

    Maju if you still think that Europe wasn't the scene of major continental migrations and genetic shifts during the late Neolithic/early Bronze Age, then you're seriously behind the times.Here's another article which shows that the same thing happened on the North Pontic Steppe at exactly the same time as in Central Europe. not only did the Oetzis of Italy go the way of the dodo, but also whoever was living on the steppe prior to the Catacomb Culture moving in. Interestingly, the Catacomb Culture is related to the Corded Ware and Unetice groups which replaced the descendant of the LBK farmers in Central Europe.The really interesting question now is where did they come from exactly, because I'd say they came from the same place.

  18. Grey

    June 24, 2013 at 9:20 am

    "In reality there are three ecological zones: Mediterranean, Continental and Atlantic, not two."Yes that is what i was thinking but either way it is the *border* between ecozones where people will seek to adapt a farming package designed for one ecozone to work in another.Looking at it another way i wonder if the most accurate way of describing it might be two core ecozones: Continental and Mediterranean (with the border in Armorica?) along with a coastal overlay ecozone creating the Atlantic Coast Continental and Atlantic Coast Mediterranean sub-ecozones.The reason why i think it might be important is that if you look at it in food-getting terms it seems to me the people most likely to *fully* adapt the mediterranean package to the continental ecozone are people living at the border between the two in a hybrid ecozone but especially if they have a secondary food source to fall back on.So they go:fish + mediterranean package -> fish + continental package.I think that would explain why you could get an expansion from the Atlantic. The people there were in the best spot to adapt the mediterranean package to the continental ecozone.(Expansion into the continental ecozone along large rivers might have a similar dynamic assuming supplemental food sources were also easier to find along rivers?)."Whatever the case the probable demic flows in the Chalcolithic may have been more motivated by political than purely ecological motivations. In those time there must have already been some quite notable political entities of some sort"Yes, i'm talking about earlier and the initial creation of a modified food-getting package that eventually spread along the Atlantic facade which then supported the population density which led to those political entities.

  19. Grey

    June 24, 2013 at 9:31 am

    Basically i was thinking adding the extent of the Atlantic Coastal and Continental ecozones togetehr would more or less map onto the same area as the Celtic expansion.

  20. Maju

    June 24, 2013 at 3:44 pm

    I wrote a comment at your blog that I hope you find informative. Somehow I missed that entry (maybe because the beginning was in German?)AFAIK Catacomb derives from Maikop, even if it does indeed have contacts with Afanasevo (proto-Tocharians) and Corded Ware (early Western-IEs), as well as other groups.AFAIK it was Catacomb who influenced the genesis of Corded Ware in Cuyavia (out of Globular Amphorae otherwise) and not the other way around. It seems that some early Catacomb raiders settled in your country (conquered it?, just mercenaries?) and may have been decisive in the very genesis of Corded Ware."… whoever was living on the steppe prior to the Catacomb Culture moving in."The proto-Indo-Iranians of Yamnaya? No. They continued existing in the IE urheimat around Samara, East of the Volga, from where they would retake the Northern Pontic Steppe later on (Srubna: proto-Cimmerians). Anyhow it is possible that only elite burials are being examined and that the bulk of the people is not really being analyzed at all. You are not even considering real data here, just some ambiguous references from a German language magazine. Neither you nor I can properly evaluate the extent of the (apparent) genetic shift without looking first at the data in some detail. Maybe they were not as different as the article suggests or maybe we can track the most plausible origins and other relations of those haplogroups – but first we have to know which they are. One thing seems clear: Catacomb burials appear to have got darker eyes than Yamnaya ones, what is consistent with a North Caucasus (Maikop) origin. If so, they may have spoken a language related to Hittite and Luvian. …

  21. Maju

    June 24, 2013 at 4:06 pm

    …"… if you still think that Europe wasn't the scene of major continental migrations and genetic shifts during the late Neolithic/early Bronze Age, then you're seriously behind the times"."Behind the times"? I generally tend to be ahead (mostly because I'm quite critical of fashions, unlike so many others). But who knows? Time goes through all us and age can be a handicap. All I can say is that I do my best not to get stagnated. Whatever the case what you say sound in this quote more like one of those vacuous cliché political discourses than anything with substance: different regions may well have undergone different processes (they surely did), even if somewhat loosely related by the technological and social period they were immersed in. In the Chalcolithic period there were indeed many changes in Central, North, East and SE Europe. Only in this last case (Balcans) we can talk of Bronze Age before 2000 BCE (or some centuries later) but then again the beginning of Bronze means relative stability in the area, excepted, at a later stage, the migration of the early Greeks into the country that now bears their name and their later "Viking era" of sorts in the Mediterranean. Eastern Europe suffered more cultural (and possibly demic, at least to some extent) changes in the Bronze (Srubna) and Iron ages (Scythians). Central and Western Europe were instead essentially stable for a whole millennium until the Urnfields era, already approaching the Iron Age. The only exception I know of is SW Iberia where the various successive "horizons", of mysterious origin (proto-Tartessian?), replaced the pre-existent cities in an expansive process in northward direction. Italy is a more complex case because there was some Mycenaean colonization, Etruscans (their elites) were probably also exotic and Italics may have invaded a couple of centuries (?) before Urnfields proper. But still there was stability in the BB period as well. But even one such archaeologically strong influence as that of Urnfields in Catalonia appears to have been shallow enough, as the peoples of that area quickly swifted to Iberian allegiance soon after the foundation of Massilia, being clearly Iberian by ethnicity (and not anymore Celtic or otherwise IE) in the proto-historical period, even if they retained Urnfields burial customs. So in this late period around the Late Bronze and the Iron Age there were indeed migrations but these seem to have been mostly elite groups in search of conquests: i.e. land worked by local enslaved peoples rather than land to work with their own hands. They were culturally and linguistically influential but genetically not so much. …

  22. Maju

    June 24, 2013 at 4:10 pm

    Whatever the case, the key issue is not what I or you "believe" but whether the age estimates derived of IBD methodology, as we know it, is reliable or not. I say it is not because there is at least one very clear case of huge error of about x2 the alleged estimate. This is hard to challenge and all you did was to divert the discussion. Interesting, sure, but not what I was pointing to: the unreliability of molecular clock estimates also by this method, always producing way too low ages.

  23. Maju

    June 24, 2013 at 4:44 pm

    … "Atlantic Coast Continental and Atlantic Coast Mediterranean sub-ecozones".Try using Köppen climate classification system maybe, where Oceanic (Atlantic) is approximated by Cfa, although the maps I am familiar with for Iberia, extend the Oceanic climate to all Galicia (where it always rains, or so they claim) and all the rest of Iberia (mountains excepted) would be Mediterranean, Mediterranean-Continental (interior zones) and transitional Oceanic-Mediterranean (northern Portuguese half). Climate is not rocket science, you know. Continental climate in those maps (for Europe) is approximated by the Dfb zone, which begins in the middle of Germany. Transitional Med-Oceanic zones could be Northern Portugal, SE France or Northern Italy. There are no substantial differences between the climate in Biscay and that of Scotland, being all mild-temperate (C) areas where it rains in all seasons (f), the last "c" reflects the avg. temperature range but it's less important, and apparently not too variable between the Bay of Biscay and Scotland. "fish + mediterranean package -> fish + continental package".The Mediterranean package was already quite "fishy". In fact Impressed-Cardium Pottery peoples seem to be the first Europeans ever to have practiced deep sea fishing, what also explains their expansion speed, especially along the coasts. The Atlantic Neolithic (diverse but later largely homogenized by Megalithism) was surely also quite intensely related to fishing, it has even been argued that Megalithism may have expanded first with cod fishing campaigns over long distances. Instead the Danubian Neolithic was totally oblivious to fishing and specially sea activities, being a clearly ground-based culture. "I think that would explain why you could get an expansion from the Atlantic. The people there were in the best spot to adapt the mediterranean package to the continental ecozone".Apart from naval skills and maybe specific breeds of the same general crops, the Mediterranean package was not too different from the Continental one. If it has anything to do with climate and ecology, I'd rather relate it with the Oceanic climate area, where first we see a flourishing of many different cultures (from Portugal to Belgium and Germany), more or less related to either macro-zone (or both), and later the formation of an specifically Atlantic cultural area (Megalithism especially). But in any case I think you are abusing the possibilities of ecological influences, whose generic relevance I do not reject but are not absolute determinants but rather just another factor.

  24. Anders Pålsen

    June 24, 2013 at 7:15 pm

    In small size hunter gatheres IBD analysis "cousin" relationships should considered "overestimated" as in Siberians, Native Americans, Greenlanders and Saamis, or mesolitic European hunter gatheres.

  25. Maju

    June 24, 2013 at 8:44 pm

    Why? If there is a (stochastic but mid-term quasi-regular) pattern of fragmentation, fragments should be about the same in all cases depending on ancestor's distance in time (measured in generations). Whatever the case, how does that matter? In any case this study only covers from Neolithic onwards (my reading) or from the Chalcolithic onwards (authors' interpretation).

  26. Grey

    June 24, 2013 at 10:18 pm

    "Try using Köppen climate classification system maybe"Ah very useful, ty."But in any case I think you are abusing the possibilities of ecological influences, whose generic relevance I do not reject but are not absolute determinants but rather just another factor."I like speculating for fun so it is quite possible. I think the development of a cattle-centric culture was key and once that was developed it allowed expansion from the coast away from the umbilical cord of seafood. If that speculation is correct then somewhere along the Atlantic coast there would need to be a culture that showed an archaeological transition from coastal only settlements to inland settlements. If that doesn't exist then the idea would be wrong – but that's okay as i find it entertaining.

  27. Maju

    June 24, 2013 at 10:52 pm

    There were very few "cattle-centric" or otherwise pastoralist cultures in Europe, other than the Kurgan phenomenon at its beginnings (and later on but only in the steppes). It was not certainly any Atlantic-focused phenomenon. Bow and arrow on the other hand…

  28. Grey

    June 25, 2013 at 12:24 am

    "There were very few "cattle-centric" or otherwise pastoralist cultures in Europe"Cattle-centric may be too strong. What i mean is a transition from using oxen as primarily draft animals to them becoming a major part of the food package.

  29. Anders Pålsen

    June 25, 2013 at 6:12 am

    This comment has been removed by the author.

  30. Anders Pålsen

    June 25, 2013 at 6:23 am

    Why? It is because of initial foundereffect and genetic drift. It gives an initial similarity that keep the IBD sizes longer.

  31. Maju

    June 25, 2013 at 12:15 pm

    I think that you speculate a lot and present no data to support your speculations, not even some circumstantial or localized evidence. I have some data for Iberia but it does not surely apply to your speculative scenarios. Whatever the case, it seems that in Iberia the horse was very important since the beginning of Chalcolithic, accompanied by ovicaprids (sheep, goats), bovine cattle and pigs (in this order probably but with variants). In the transition from the Middle to the Late Bronze Age, apparent environmental deterioration took place and, after a bout of massive horse-slaughter in some sites at least, ovicaprids and bovines became dominant for the first time (but together instead of separated: the real opposition seems to be horses vs the rest).

  32. Maju

    June 25, 2013 at 12:17 pm

    Are you saying that recombination somehow "rebuilds" the IBD chunks from its fragments? I would like any academic support for that claim before I can believe it.

  33. Anders Pålsen

    June 25, 2013 at 1:33 pm

    In a isolated population with a few initial founders IBD's overestimate the actual cousin relationship. This is well known. This gives more identical haplotypes in circulation and then of course give more IBD's.Example Jews.

  34. Maju

    June 25, 2013 at 2:13 pm

    I don't read what you read: IBD actually helps to discern when a SNP-reconstructed affinity is caused by recent endogamy or not (and details about it). Also the only case of hunter-gatherers in your second link, the Biaka, show no apparent sign of endogamy (fig. 3b).

  35. Grey

    June 25, 2013 at 10:01 pm

    It's deductive.1. There's no reason to expect the neolithic farming package to be as productive outside a latitude/climate range similar to where it was developed.2. If it was as productive outside the mediterranean ecozone there would have been a rapid range expansion.It seems to me the lack of a rapid and dense range expansion means the story outside the mediterranean ecozone must revolve around how and where a modified method of food-getting that worked better was developed out of the neolithic package."I think that you speculate a lot and present no data to support your speculations, not even some circumstantial or localized evidence."There is some, Ertobolle etc but that's much further along the coast than i was expecting. If the idea was correct I was assuming any switch to using cattle as more of a food animal than a draft animal to have taken place somewhere between Gallicia and Franco-Cantabria but wiki has gaps. I'm still looking though.

  36. Grey

    June 25, 2013 at 10:12 pm

    I appreciate science is supposed to be data-first but i'm an amateur.

  37. Maju

    June 25, 2013 at 11:41 pm

    Let's see: the Neolithic Continental wave was essentially contemporary to the Mediterranean one (and both have roughly the same origins, although there are important differences in their manifestations: pottery style and the issue of mariner orientation, proper of the Mediterranean wave – also this seems to have been much more clearly assimilative of pre-existing HG populations). Was there a crop and cattle (generic: all kind of domestic-productive animals) adaption as the Balcano-Danubian Neolithic peoples marched Northwards? Surely but we only know so much about it. It seems it was not any major problem because their advance was relatively fast and steady. There are two reasons I can think that supported that adaption: (1) it was the Neolithic Climate Optimum (the warmest post-glacial period before the last decades) and (2) Continental climate is rather dry, and in this similar to what we find in West Asia and the Balcans.On the contrary, the Oceanic climate is much more humid, what can indeed be a serious problem for dry land crops (rot). This probably acted as buffer, relatively dissuading further advance of both waves and allowing the development of autonomous local Neolithic cultures instead, which surely relied first heavily on hunt, fishing and other foraging. Is it possible that in North-Central Europe especially (Funnelbeaker for example, which is rooted in the same area as Ertebølle) some kind of re-expansion of these Oceanic Neolithic peoples took place after the Climate Optimum? Yes it is: TRBK (Funnelbeaker) actually began in Denmark in synchrony with that cooling, showing soon a clear demographic expansion, associated intensely with Megalithism (see: Has all this something to do with cattle, sheep or whatever? I do not know. Only data can confirm or reject your speculations. But, on the little I know, I'd think it has to do with fish primarily because that's the kind of the stuff the Danes (and many other Megalithic peoples) would rely on primarily in those times. LBK shows a clear demographic explosion between 5500 and 5000 BCE, soon after the best of the Climate Optimum, then they quickly declined in numbers (maybe they exhausted the land with their burn-and-slash techniques?) Long after that, the first region to recover, c. 4000 BCE, was Denmark (TRBK-Megalithism), with the mentioned sharp demographic explosion, followed by Poland (late Baalberge, since c. 3600 BCE), the last one being Germany (Globular Amphorae period, since c. 3100 BCE). The demographic recovery of Germany is coincident with declines in the other regions (however Denmark stayed relatively populated even after Germany's population declined again twice, first after GA and then after Bell Beaker). What seems clear from these demographic reconstructions is that the population of Central Europe fluctuated a lot up and down in both Neolithic and Chalcolithic and hence we cannot expect it to be referential for other (probably) more stable regions of Europe. These fluctuations alone (rather than appealing only to the magic of migrations) can well have been the main cause behind the demographic changes in those areas after Neolithic: peoples grew and declined fast and acutely enough to allow very important composition changes. …

  38. Maju

    June 25, 2013 at 11:42 pm

    …The relative demographic values (measured from density of archaeological findings) were for each region (peaks enhanced):·Germany: 10→100→20→40→30→70→50→20·Poland: 10→90→40→30→100→60→10→0·Denmark: 30→20→10→90→100→80→50→30·Britain: 10→10→20→40→90→40→50*→60*Sequence (for Germany-Poland): Latest Epipaleolithic → Early Neol. → Middle Neol. → Late Neol. → Early Copper → Mid. Copper → Late Copper → Latest CopperFor Britain and Denmark the Epipaleolithic is longer, it seems, up to the continental Middle Neolithic (included) but otherwise it is the same timeline. In Britain I counted the monuments, what is maybe not too correct, otherwise the differences are smaller and the late apogee (asterisks) does not exist at all (rather a decline). In any case we do see that the demographic recoveries after the collapse of the early Neolithic was led by Megalithism (earliest in time but affecting mostly Denmark and Britain) and then, with ups and downs, by the Kurgan peoples, with a minor role for Bell Beaker at best.

  39. Anders Pålsen

    June 26, 2013 at 12:53 pm

    I just did this experiment now using BEAGLE fastibd using all of the HGDP Native American populations to show what I already know from practical experience doing analysis.Tell me then why a Maya (HGDP00876) share 21 cM or 2525 SNPs of total 289k SNP (assuming 1 cM = 1 mill BP) with a Columbian (HGDP00704). If we in addition include a segment that at one edge overlap with the centromere its 37 cM or 3655 SNPs.If sharing 21 cM it should qualify for somewhere between 2rd and 3rd cousin if assuming initial total unrelatedness in the autosomes. It doesnt make sense when considering the space in time, geography and etnicity between these individuals. However it make sense if assuming the a small isolated founder population and following genetic drift.

  40. Maju

    June 26, 2013 at 2:38 pm

    I don't know what it means: it is clear that Colombians (correct spelling) and Mayas have not been TOGETHER a single tiny population in many many centuries, surely millennia. So it does not matter how tiny they were on their own (they were not "tiny" either before European arrival: both peoples were agricultural and largely civilized) what matters the most is that they have not been the same population in a very long time. However, if you are right, your own argumentation would trample down the whole IBD theory, right?

  41. Anders Pålsen

    June 26, 2013 at 4:45 pm

    Its still IBD but far older than "recent endagomy". This is my point. The fouding of the native american population was from a tiny group. They later spread out of the rest of the continent, however they are still similar to each other and even still appears as "cousins" in IBD analysis compared to well mixed cosmopolition populations.

  42. Maju

    June 26, 2013 at 5:31 pm

    I don't think that what you say makes much sense: sure the founding population of Native Americans some 17,000 years ago (!!!) was surely small but so was the founder population of Ashkenazim just 1300 years ago and they do not show such extreme coincidences. Something is wrong, although I can't say what.

  43. Maju

    June 26, 2013 at 6:01 pm

    What I mean is that you may well be onto something but, the way you explain it, makes no sense. Why don't we find similar phenomena elsewhere? Sardinians, for example are not much more cosmopolitan than Mayas, nor are most Finnic peoples either.

  44. Grey

    June 26, 2013 at 10:25 pm

    Very interesting, ty."(1) it was the Neolithic Climate Optimum (the warmest post-glacial period before the last decades) and (2) Continental climate is rather dry, and in this similar to what we find in West Asia and the Balcans."I do need to remember that bit.

  45. Maju

    June 27, 2013 at 12:40 am

    Seems I forgot a link somewhere. In any case I made yesterday an overlapping graph for direct comparison of the four regions and I have just posted an entry on the matter.

  46. mikej2

    June 27, 2013 at 9:24 am

    Shared IBD's and IBS's inside recent populational boundaries, like linguistically regions or later built states (like France and UK) are influenced by many factors, like internal migrations, life style, I.e. the time of founding first national states. I see many factors that make evaluating of thousands years' old history uncertain. We all have same amount of ancestors in our family tree and the result in IBD blocks depends on above-mentioned matters.

  47. Anders Pålsen

    June 27, 2013 at 10:07 am

    If you in addition do a Plink –genome run on the HGDP dataset you will find that HGDP00876 and HGDP00704 share a PI HAT of 0.1612. PI HAT = 1 is identical twins or duplicate samples. PI HAT 0.5 is paret-offspring, PI HAT 0.25 are full siblings. So again using a differnt method than IBD these distant individuals fall into the "cousin" category.

  48. Anders Pålsen

    June 27, 2013 at 10:12 am

    Jews do more recent endagomy as they have not experienced the same total isolations as some other populations. Thats why Jews in Europe, China or Ethiopia looks very much like the local population.

  49. mikej2

    June 27, 2013 at 10:45 am

    Although I dont fully understand the issue Anders is figuring, because I am not familiar with his examples, I do back his idea of the rebuilt IBD's. Sure it happens in certain history and not so seldom at all. No doubt about it. In these cases age estimates fail and are show too young age and point to some younger event in history. The question is whether we know this history or still try to infer the history.


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