June 27, 2013

Revisiting the demographics of Northern and Central Europe in the Neolithic and Chalcolithic periods

Stimulated by the discussion at another entry, yesterday I made a little graph, almost a mnemonic, on the demographics of Northern European Neolithic and Chalcolithic, based on academic data which I discussed back in 2009.

This is the result:


The very simplified graph is nothing but a version of another one, used in 2009 (and reproduced below), which in turn is an annotated and composite version extracted from two different studies (references also below).

For convenience I have marked the millennia marks at the bottom (meaning 5000, 4000, 3000 and 2000 BCE, from left to right) while the unmarked vertical scale ranks from 0 to 100 (marked by the lowest and highest dots, not the frame, which is actually outside of the graph itself). The dots mark population level at any time as proportion of the maximum (100) in discrete intervals rounded up/down to 10 ppts and taken at intervals of 250 years. Notice that I ignored monuments in the case of Britain, only considering the habitation and other productive sites.

Not sure if it will result useful to you but it did help me to visualize the demographics of Northern Europe in these four millennia of surely dramatic population changes. If you don't like this version the more detailed original double graph is below, scroll down.

Something quite obvious is that while Danubian Neolithic first caused an important population expansion, it later declined to quite low population levels, maybe because of climatic cooling and the exhaustion of the lands because of poorly developed agricultural techniques. 

This late Danubian collapse lasted for about a millennium, when (1) Funnelbeaker (TRBK) in Denmark, (2) Megalithism in Britain and Denmark especially (later also in parts of Germany) and (3) Kurgan cultures in Poland (later also in Germany and Denmark) seem to have brought with them very notable demographic expansions.

But decline seems to set on again all around at the end of the Chalcolithic period, much more notably in the continent (in Poland the rate of archaeological findings decays to zero!) than in Britain and especially Denmark. 

And now indeed the original "verbose" graph:



And the sources:


Update (Sep 19): Dienekes mentions today a pay-per-view study by Nicky J. Whitehouse which deals with the same issues and finds similar patterns of apparent early Neolithic expansion and collapse in the case of Ireland. Relevant graph:


Plantago is a leafy weed or herb (depending on your viewpoint) that grows largely in prairies and plowed fields. 
Abstract
A multi-disciplinary study assessing the evidence for agriculture in Neolithic Ireland is presented, examining the timing, extent and nature of settlement and farming. Bayesian analyses of palaeoenvironmental and archaeological 14C data have allowed us to re-examine evidential strands within a strong chronological framework. While the nature and timing of the very beginning of the Neolithic in Ireland is still debated, our results – based on new Bayesian chronologies of plant macro-remains – are consistent with a rapid and abrupt transition to agriculture from c. 3750 cal BC, though there are hints of earlier Neolithic presence at a number of sites. We have emphatically confirmed the start of extensive Neolithic settlement in Ireland with the existence of a distinct ‘house horizon’, dating to 3720-3620 cal BC, lasting for up to a century. Cereals were being consumed at many sites during this period, with emmer wheat dominant, but also barley (naked and hulled), as well as occasional evidence for einkorn wheat, naked wheat and flax. The earliest farmers in Ireland, like farmers elsewhere across NW Europe, were not engaged in shifting cultivation, but practised longer-term fixed-plot agriculture. The association between early agriculture and the Elm Decline seen in many pollen diagrams shows that this latter event was not synchronous across all sites investigated, starting earlier in the north compared with the west, but that there is a strong coincidence with early agriculture at many sites. After this early boom, there are changes in the nature of settlement records; aside from passage tombs, the evidence for activity between 3400-3100 cal BC is limited. From 3400 cal BC, we see a decrease in the frequency of cereal evidence and an increase in some wild resources (e.g. fruits, but not nuts, in the records), alongside evidence for re-afforestation in pollen diagrams (3500–3000 cal BC). Changes occur at a time of worsening climatic conditions, as shown in Irish bog oak and reconstructed bog surface wetness records, although the links between the various records, and assessment of causes and effects, will require further investigation and may prove complex. This period seems to have been one of environmental, landscape, settlement and economic change. The later 4th millennium BC emerges as a period that would benefit from focused research attention, particularly as the observed changes in Ireland seem to have parallels in Britain and further afield.

June 26, 2013

Was the grove snail Epipaleolithic livestock in Western Europe?

Cepaea nemoralis
(CC by Papa Lima Whiskey 2)
The problem of disjunct distribution of Western European species or, in this case, subclades of a single species is nothing new and has been startling biologists for almost two centuries already, with particular interest of Irish-Iberian, Breton-Iberian or just general Irish-continental disjunct relationships of various species (the so called Lusitanian distribution). Among them is the iconic strawberry tree (madroño in Spanish, found in Ireland but not Great Britain) but also a number of small land animals: the Kerry slug (found in NW Iberia and SW Ireland only), the Quimper snail (found in NW Iberia and Western Brittany) or the Pyrenean glass snail (found in the Pyrenees and Ireland).

There are also cases of subclades within an otherwise widespread species which show a similar pattern. In 2003, Masheretti et al. demonstrated that the Irish variant of the pygmy shrew had its greatest affinity with populations of Andorra, in the Eastern Pyrenees, from which they are descended.

This study illustrates a similar case but affecting the snail species Cepaea nemoralis (grove snail or brown lipped snail), whose Irish lineages are mostly derived from Iberian ones and in most cases from the Eastern Pyrenean haplogroup C.

Adele J. Grindon & Angus Davison, Irish Cepaea nemoralis Land Snails Have a Cryptic Franco-Iberian Origin That Is Most Easily Explained by the Movements of Mesolithic Humans. PLoS Genetics 2013. Open access LINK [doi:10.1371/journal.pone.0065792]

Abstract

The origins of flora and fauna that are only found in Ireland and Iberia, but which are absent from intervening countries, is one of the enduring questions of biogeography. As Southern French, Iberian and Irish populations of the land snail Cepaea nemoralis sometimes have a similar shell character, we used mitochondrial phylogenies to begin to understand if there is a shared “Lusitanian” history. Although much of Europe contains snails with A and D lineages, by far the majority of Irish individuals have a lineage, C, that in mainland Europe was only found in a restricted region of the Eastern Pyrenees. A past extinction of lineage C in the rest of Europe cannot be ruled out, but as there is a more than 8000 year continuous record of Cepaea fossils in Ireland, the species has long been a food source in the Pyrenees, and the Garonne river that flanks the Pyrenees is an ancient human route to the Atlantic, then we suggest that the unusual distribution of the C lineage is most easily explained by the movements of Mesolithic humans. If other Irish species have a similarly cryptic Lusitanian element, then this raises the possibility of a more widespread and significant pattern.

The evidence gathered by this study is most readily visible in fig. 2:


While it is not the focus of this study, we see here two other cases of probable disjunct distribution:
  • Hg D is found in Iberia, Ireland, small pockets in Britain and SW France but also in North and Central Europe.
  • Hg F shows also disjunct presence in Cornwall, far away from the main cluster around the Bay of Biscay.
The authors of this and previous studies have suggested that this distribution may have to do with intentional transport (as livestock) in the process of the colonization of the Atlantic Islands in the Epipaleolithic. In support of this claim, there is enough fossil evidence of the snail in the island:
Fossil material indicates that this species has been continuously present in Ireland for at least 8000 years (Newlands Cross, Co. Dublin: 7600+/−500 BP Cartronmacmanus, Co. Mayo: 8207+/−165) [7], [8].

In other cases, such as the inedible Kerry slug, we may suspect unintentional transport and therefore we would be justified to imagine a later time frame for their arrival to Ireland, possibly in the Chalcolithic-Megalithic period, but the evidence for C. nemoralis is highly suggestive of intentional transport in the Epipaleolithic. We can therefore say that the humble grove snail was one of the first domestic animals of Europe, possibly second after the dog.

June 22, 2013

The less homogeneous European "populations" are Italians and French

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] 
Abstract

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

Notes: 
  • 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.

New Maya city discovered

Archaeologists have discovered the ruins of a long lost Maya city in the jungle SE of Campeche state (Yucatan Peninsula, Mexico), in the historical Maya region of the central lowlands. 



The newly discovered city, Chaktún, occupies some 22 Ha. and is believed to have been an important local power between 600 and 900 CE. It was hidden in the northern area of the Biosphere Reserve of Calakmul, near the Guatemalan border.

Source: Paleorama[es].

Korean petroglyphs at risk by reservoir

A group of very beautiful South Korean petroglyphs that seem to represent whale hunting and are dated some 6000 years ago are being damaged by a water reservoir that provides water for the city of Ulsan. 



The Bangudae petroglyphs, discovered in 1971, are submerged under water seasonally, raising great controversy in the East Asian country. It seems that even President Park is greatly concerned about them, something not too usual in a politician, while the Cultural Heritage Administration is demanding measures to protect the ancient rock art, namely to keep water levels low enough. 

However water utilities claim that it is impossible to meet such demands while providing water to the seventh largest South Korean city. The Ulsan city government is proposing to build a wall around the petroglyphs in order to protect them while keeping the water levels, this however would cause environmental damage to the area, disqualifying the site for UNESCO World Heritage protection schemes.

Source: cinabrio.over-blog[en/es] (incl. several pictures and press articles).

June 18, 2013

Mellars 2013: second round

As I mentioned before, I have already got copies of the controversial study by Paul Mellars et al., which argues for a very late colonization of Eurasia. It includes some aspects not dealt with in the first round, when I could only access the supplemental material. 

Paul Mellars et al., Genetic and archaeological perspectives on the initial modern human colonization of southern Asia. PNAS 2013. Pay per view (6-month embargo) → LINK [doi:10.1073/pnas.1306043110]

Maybe the most important is the very striking visual comparison between proto-LSA African microlithic industries and post-UP South Asian microlithic ones:



While it is maybe easy to dismiss the patterns drawn on ostrich shells in Africa and South Asia as not really looking the same at all and therefore likely coincidence, the visual comparison of the industries is much harder to reject. It does indeed pose a mysterious apparent link similar to others that are hard to explain like the similitude between Chatelperronian and Gravettian (not so long ago treated together as "Perigordian") or the hammering insistence by some rather marginal academics on the similitudes between the SW European Solutrean culture and the (much more recent) North American Clovis industry. 

Sure: impressive and intriguing. But when it comes to chronology the Mellars hypothesis seems to fail terribly. While the African microliths are pre-LSA and therefore from before ~49,000 years ago in all cases, the South Asian ones only show up mostly since c. 34-38,000 years ago, more than ten millennia later. Mellars makes this figure 40-35 Ka and then just 40 Ka for the following graph, which in fact misrepresents Petraglia's model and data in a key issue (see below):


It must be emphasized here that Petraglia's data and model, at least for what I know it, implies an hiatus between c. 110 Ka and c. 80 Ka BP, hiatus for which there is no archaeological data of any kind in South Asia. Therefore neither side graph should suggest continuity to the past before ~80 Ka, allowing at most for a highly hypothetical dotted line (as in Petraglia 2010):



Also there is nothing in Petraglia's work that could suggest discontinuity at the Toba ash layer, as suggested by Mellar's version, rather the opposite: continuity is very apparent in Jwalapuram:

Jwalapuram industries (from Petraglia 2007)

Quite conveniently Mellars ignores Petraglia's data again, which suggest continuity before and after microlithism in Jurreru Valley and then also finds a transition towards UP ("blade and bladelet", as well as "backed artifacts") technologies since c. 34 Ka BP. 

But regardless, I'm pretty sure that Prehistory-savvy readers have already noticed a major issue in all this chronology: we are talking of dates that are almost 20,000 years after the colonization of West Eurasian by H. sapiens with "Aurignacoid" technologies, which are dated to before 55 Ka BP in Palestine (OSL), to c. 49 Ka BP in Central Europe and to c. 47 Ka BP in Altai (C14 calibrated). 

And those who are also familiar with Eurasian population genetics are by now shaking their heads in disbelief and claiming to heaven and hell alike. Because West Eurasians derive, at a late relative date, from Tropical Asians and therefore, if our core ancestors were already separated before 55 Ka BP, there is just no room for the Tropical Asian (and Australasian) expansion that must have preceded the Sapiens colonization of the West Eurasian Neanderlands.

(Those unfamiliar with the basics of Eurasian population genetics, see here).

So there is no way that the Out of Africa migration could be dated to just c. 55 Ka BP, as Mellars does (after grabbing hard the burning nail of conjectural coastal sites now under the sea, which would have to account for some 15-20,000 years of Eurasian prehistory on their own).

In fact it is also impossible from the viewpoint of Australian chronology, which again needs to go after the settlement of Tropical Asia but surely before that of West Eurasia. 

So, regardless of the striking visual comparison between African and Indian industries, which is no doubt the "bunny in the hat" here, the Mellars hypothesis simply doesn't stand. 

Was there another cultural (surely not demic) flow from Africa to South Asia c. 40-35 Ka BP? Maybe. Or maybe it is just one of the many hard-to-explain coincidences in stone industry design. But whatever it is, it just cannot be the Out-of-Africa migration, unless one is ready to accept that Aurignacian and related European rock art, as well as Australian rock art, for example, are the product of archaic homo species (something that I am sure that Mellars won't admit to: it just goes against his "modern human behavior" prejudices). And, even then, it just doesn't add up either.


PS- Petraglia himself finds Mellar's alternative model untenable. From ABC Science (emphasis mine):

... Professor Michael Petraglia, an archaeologist from the University of Oxford disputes Richards' and Mellars' argument. 

Petraglia says there's not enough evidence to rule out an earlier colonisation before the eruption of Mount Toba. 

"The research reported by Mellars and colleagues is riddled with problems," he says. 

Petraglia says that the similarity between tools used in Africa 60,000 years ago and those from Asia dating to around 35,000 years ago is not a consequence of direct migration.

"These toolkits are separated in time by more than 20,000 years and distances exceeding several thousand miles." 

He questions the evidence supporting a migration along the coast. He says that surveys of ancient shorelines have not revealed any evidence for human settlements anywhere along the Indian Ocean shore between 55,000 and 50,000 years ago.

He also says genetic dating should be treated cautiously. 

"Most geneticists will admit that genetic dating of the out-of-Africa event is tenuous, at best. Published genetic ages for out-of-Africa range anywhere between 45,000 to 130,000 years ago.

Petraglia says his team is currently conducting archaeological fieldwork in Arabia, India and Sri Lanka they expect will show that the story of human dispersal from Africa is complex.

"What we can agree on is that little research in these key geographic regions has been conducted and much more evidence needs to be collected to support or refute the different theories," says Petraglia.

June 11, 2013

Mellars challenges the 'early out of Africa' model

I do not have yet access to this potentially key paper, so first of all I want to make an appeal here to share a copy with me (→ email address). Thanks in advance. Update: got it (thanks to all who shared, you people are just great!) I will review it again as soon as possible.

Update (Jun 18): complementary review of the full paper now available here.

Paul Mellars et al., Genetic and archaeological perspectives on the initial modern human colonization of southern Asia. PNAS 2013. Pay per view (6-month embargo) → LINK [doi:10.1073/pnas.1306043110]

Abstract

It has been argued recently that the initial dispersal of anatomically modern humans from Africa to southern Asia occurred before the volcanic “supereruption” of the Mount Toba volcano (Sumatra) at ∼74,000 y before present (B.P.)—possibly as early as 120,000 y B.P. We show here that this “pre-Toba” dispersal model is in serious conflict with both the most recent genetic evidence from both Africa and Asia and the archaeological evidence from South Asian sites. We present an alternative model based on a combination of genetic analyses and recent archaeological evidence from South Asia and Africa. These data support a coastally oriented dispersal of modern humans from eastern Africa to southern Asia ∼60–50 thousand years ago (ka). This was associated with distinctively African microlithic and “backed-segment” technologies analogous to the African “Howiesons Poort” and related technologies, together with a range of distinctively “modern” cultural and symbolic features (highly shaped bone tools, personal ornaments, abstract artistic motifs, microblade technology, etc.), similar to those that accompanied the replacement of “archaic” Neanderthal by anatomically modern human populations in other regions of western Eurasia at a broadly similar date.

A review has been published at Live Science.

South Asian artifacts from ~30-50 Ka BP.

By "genetic evidence" they obviously mean "molecular clock" nonsense, so it is not evidence at all but mere speculation. However I am indeed very interested in knowing in detail what they mean by "archaeological evidence", because they seem to get into direct confrontation with much accumulated evidence, first and foremost all of Petraglia's research in both India and Arabia but also with the quite strong evidence for pre-60 Ka human presence in Australia and growing evidence for pre-60 Ka modern humans in SE Asia (in some cases even as old as 100 Ka). 

It must be said that Paul Mellars has been criticized before a lot for several reasons but very especially for his adherence to the quite speculative "modern human behavior" conjecture and, relatedly, bigotric attitudes against Neanderthal intellectual capabilities, based on nothing too solid. Therefore I'm generally skeptic about what Mellars has to say on this matter because this kind of conclusion is what one would expect from him. 

However Mellars is certainly a distinguished academic and, even if prejudiced and stuck to his own old-school and somewhat Eurocentric interpretations, he knows his trade as archaeologist and prehistorian. So he may be onto something, even if it is not exactly what he wants us to believe. 

For example, it is not impossible that this research may have, unbeknown to the authors, found evidence of a secondary OoA wave (maybe related to the spread of Y-DNA D and mtDNA N?) or even a distinctive evolution in Southern Asian technology prior to the expansion of Western Eurasia. 

It is interesting that they suggest that the 80-60/50 Ka toolkits of India would have been made by Neanderthals, when they are not describing them at all as Mousterian, the almost exclusively Neanderthal techno-culture, or Mousterian-related.

I have some difficulties judging before reading the whole study. However the supplemental material (quite extensive) is freely accessible and for what I can see there:
  1. They dedicate much text to attempt to justify a particular version of mainstream "molecular clock" hypothesis, which are clearly broke in my understanding. The kind of arguments "rebated" are more or less what I have been putting forward since many years ago. Ironically their "molecular clock" estimates make N and R much older than M, what I absolutely oppose (just count mutations downstream of the L3 node).
  2. No real attention is given instead to the geographical structure/distribution of major mtDNA haplogroups, only mentioned in relation to "molecular clock" speculations.
  3. The criticism of the African affinity of the Jwalapuram (Jurreru Valley) cores (Petraglia 2007) focuses on dismissal of any possibility of comparison, rather than on alternative comparisons. 
  4. Another "criticism" is that there is no apparent connection between Jwalapuram and the Nubian Complex (why there should be any?, it is not the only East African techno-culture, nor the only group that shows indications of traveling to Arabia in the Abbassia Pluvial).
  5. Also it is "criticized" that the most comparable African culture, Howiesons Poort) is not recorded before c. 71 Ka BP (what IMO may indicate late cultural dispersals to Southern Africa from East Africa, for example, but, hey!, Mellars is fencing off balls like crazy at his conservative goal). 
  6. They find clear similitudes between Indian and African microlithic industries (apparently related to the development of "mode 4" in both areas, as well as in West Eurasia). Indian industries are dated to c. 38-40 Ka BP, while African ones are dated to c. 49 Ka BP (Kenya) or later. However West Eurasian ones have dates as old as 55 Ka BP (not for Mellars, who remains stuck in older date references which he describes as ∼40–45 ka [calibrated (cal.) before present (B.P.)]), what really suggest that we are talking here not of the "out of Africa" but of the West Eurasian colonization process (necessarily from further into Asia, genetic phylo-geographic structure demands) with offshoots to the nearby regions. 
  7. Another element of late Africa-India "similitude" they find is "the remarkable, double bounded criss-cross design incised on ostrich eggshell", dated in India (Patne) to at least ∼30 ka (cal. B.P.), much earlier in South Africa. For Mellars this is beyond the range of either pure coincidence or entirely independent and remarkably convergent cultural evolutionary processes. Hmmm, really? Or are we before a clear case of wishful thinking as happens with the Solutrean-Clovis relationship hypothesis? Isn't it 30 Ka BP anyhow well beyond any reasonable expectations for the OoA time frame, including Mellar's own conjectures?
  8. Mellars accepts the paradox that the geographical limits of these highly distinctive microblade and geometric microlithic technologies are confined to the Indian subcontinent, with no currently documented traces of these technologies in regions farther to the east. And then makes up excuses for it, such as biological and cultural bottlenecks caused by "founder effects", mysteriously leading to a loss or simplification of cultural and technological know-how, as well as fininding new and contrasting environments (in the same latitudes?!)
  9. Even in the case of Arabian colonization, Mellars shows to be in a very defensive attitude, admitting only to the reality of the Palestinian sites with clearly modern skulls, as well as to the area of Nubian Complex colonization (on whose peculiarities he insists a lot, as if it would be the only expression of the wider MSA techno-complex), disdaining all the other MSA colonization areas and, often ill-defined, variants.

In brief, for what I could see in the supplemental material, along with some potentially interesting references to the relative cultural community spanning from East Africa to South Asia at the time of emergence of "mode 4" industries, it seems that Mellars and allies are essentially putting the cart (their models) before the horses (the facts), what is bad science. 

In 2008, Zilhao and d'Errico angrily accused Mellars of being an obsolete armchair prehistorian (different words maybe, same idea). Back in the day I was tempted to support Mellars but nowadays I must agree that he is clearly stuck in a one-sided interpretation of prehistory whose time is long gone. Whatever the case I welcome the debate and can only hope that will help to produce even more evidence to further clarify the actual facts of the Prehistory of Humankind.

June 10, 2013

55 million years old evolved primate fossil

A small early Tarsiiforme specimen, named Archicebus achilles, lived some 55 million years ago in what is now Central China, it has been known from a recently discovered fossil (right).

This primate was already an ancestor of modern tarsiers, then just diverged from the line leading to us Anthropoidea, what comes to support the theories that suggest an old origin of the primate lineage, possibly c. 85 Ma ago, still in the Cretaceous era, when T. rex and all the famous Hollywood dinosaurs still roamed the Earth.

And this has of course implications as well for the origin of mammals, popularly believed to be in a very early stage of their evolution in that period... but maybe much more diversified than some pop documentaries want us believe. 

Until now the oldest known primate was Plesiadapsis, a proto-lemur that may look maybe more like a squirrel than a primate (at least to my eyes). Plesiadapsis is from the same time as Achicebus, c. 55-58 Ma ago. 

Primate phylogenetic tree (from Wikipedia) with the aprox. placement of Archicebus

Ref. X. Ni et al. The oldest known primate skeleton and early haplorhine evolution. Nature. Vol. 498, June 6, 2013, p. 60. doi:10.1038/nature12200.


Update (Jan 2015): Purgatorius, an even older primate-like mammal, dated to c. 65 Ma ago, was already tree adapted in ways unique to primates (i.e. it was an early primate and not related to rodents anymore in spite of its squirrel-like appearance), new research has found. This is concordant with the placing of Archicebus early in the tarsier branch as shown above.

June 9, 2013

HERC2 haplotypes, phylogeny and frequencies

Palisto at Kurdish DNA has a most interesting report of his own production on the eye color gene HERC2, its variant haplotypes, their phylogeny and their frequency in West Eurasian and Pakistani populations.

Based on Kurdish haplotypes, he developed the following phylogeny:



All branches produce dark eye color, excepted the two colored in blue, which are associated with light eye color. 

The defining transitions from branch#3 to branch#1 are rs1129038 and rs12913832 (demonstrated to cause blue eyes in 99% of cases) while the transition to branch#2 is found at rs11636232

He also produced haplotype frequency tables for the two light eye color haplotypes (here the one sorted by branch#1 frequencies):


Branch#1 Branch#2
Brahui 2% 2%
Balochi 8% 2%
Balochi 12% 6%
Kalash 12% 16%
Sardinian 16% 4%
Palestinian 18% 3%
Burusho 18% 12%
Basque 19% 21%
Italians 25% 19%
Adygei 26% 6%
Orcadian 28% 41%
Galician 30% 17%
French 32% 30%
Russians 36% 46%
Italians 42% 27%
Swedes 42% 54%
Germans 46% 33%
Danes 52% 32%
Austrian 55% 28%
Swiss 69% 25%


In West Asia and Pakistan (the most plausible ancient origin of the trait), we see how the ancestral #1 variant is generally dominant, with the only exception of the Kalash, reaching the highest frequencies (18%) among the Burusho and Palestinians, among the studied populations. 

This pattern is continued (at overall quite higher frequencies) in Central Europe, Denmark, Italy and Galicia, with peak among the Swiss (69%). Instead the derived haplotype #2 seems dominant among Swedes, Russians and Orcadians. French and Basques are balanced for both types.


Update (Jun 25): map:


Includes also Kurdish data from Palisto's update.

The two Balochi samples are pooled in one (same weight for each), instead the two Italian samples were retained separated and assumed to be from South and North Italy respectively (not sure but makes sense). 



See also:



Update (Jun 27): Kurdish DNA just published the HERC2 data a much wider sample of populations from all Eurasia and not anymore focusing only on the blue eye haplotypes but all them instead.

It is very interesting that ht3, ancestral to blue eyes' haplotypes ht1 and, through this one, also ht2 , is widespread through the continent with very few exceptions: Russians, Belorussians, Lithuanians and a Mordvin tribe in Europe, as well as the Kurmi, Nihali, Chenchu and Puliyar in India.

Ht5 and ht6 are also very common in Eurasia, ht7 is rare in most groups but dominant in a few (Kurmi, Melanesians) while ht4 (ancestral to ht3) is rather rare as well (highest in South and Central Asia, as well as Lebanon). Other (undetermined) haplotypes are also concentrated in some populations like the Chenchu and have some importance across Asia.

June 8, 2013

Breatsfeeding vastly improves brain development in early infancy

Nature vs nurture? Where genetics often fail to explain most differences in cognitive development in a satisfactory manner, environmental causes instead show outstanding importance. 

A very clear case is breastfeeding, which not only provides the best nutrition for babies but also key emotional support. And new research only emphasizes this.


The research found that by age 2, babies who had been breastfed exclusively for at least three months had enhanced development in key parts of the brain compared to children who were fed formula exclusively or who were fed a combination of formula and breastmilk. The extra growth was most pronounced in parts of the brain associated with language, emotional function, and cognition, the research showed.
(...)

The study showed that the exclusively breastfed group had the fastest growth in myelinated white matter of the three groups, with the increase in white matter volume becoming substantial by age 2. The group fed both breastmilk and formula had more growth than the exclusively formula-fed group, but less than the breastmilk-only group.

"We're finding the difference [in white matter growth] is on the order of 20 to 30 percent, comparing the breastfed and the non-breastfed kids," said [lead researcher Sean] Deoni. "I think it's astounding that you could have that much difference so early."

Ref. (pay per view): Sean C.L. Deoni, Douglas C. Dean, Irene Piryatinksy, Jonathan O'Muircheartaigh, Nicole Waskiewicz, Katie Lehman, Michelle Han, Holly Dirks. Breastfeeding and early white matter development: A cross-sectional study. NeuroImage, 2013; DOI: 10.1016/j.neuroimage.2013.05.090

Caribbean autosomal ancestry

Battle of Vertières (Haiti 1803)
A very interesting study on Caribbean populations' autosomal ancestry is in the oven (pre-publication at arXiv).

Andrés Moreno Estrada et al., Reconstructing the Population Genetic History of the Caribbean. arXiv 2013 (pre-pub). Freely accessibleLINK [ref. arXiv:1306.0558v1]


Update (Nov 15): formally published at PLoS Genetics (open accessLINK). No apparent major changes.

Abstract

The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations. Here, by making use of genome-wide SNP array data, we characterize ancestral components of Caribbean populations on a sub-continental level and unveil fine-scale patterns of population structure distinguishing insular from mainland Caribbean populations as well as from other Hispanic/Latino groups. We provide genetic evidence for an inland South American origin of the Native American component in island populations and for extensive pre-Columbian gene flow across the Caribbean basin. The Caribbean-derived European component shows significant differentiation from parental Iberian populations, presumably as a result of founder effects during the colonization of the New World. Based on demographic models, we reconstruct the complex population history of the Caribbean since the onset of continental admixture. We find that insular populations are best modeled as mixtures absorbing two pulses of African migrants, coinciding with early and maximum activity stages of the transatlantic slave trade. These two pulses appear to have originated in different regions within West Africa, imprinting two distinguishable signatures in present day Afro-Caribbean genomes and shedding light on the genetic impact of the dynamics occurring during the slave trade in the Caribbean.

The most synthetic graph is the following one:
Figure 1: Population structure of Caribbean and neighboring populations. A) On the map, areas in red indicate countries of origin of newly genotyped admixed population samples and blue circles indicate new Venezuelan (underlined) and other previously published Native American samples. B) Principal Component Analysis and C) ADMIXTURE [12] clustering analysis using the high-density dataset containing approximately 390K autosomal SNP loci in common across admixed and reference panel populations. Unsupervised models assuming K= 3 and K=8 ancestral clusters are shown. At K=3, Caribbean admixed populations show extensive variation in continental ancestry proportions among and within groups. At K=8, sub-continental components show differential proportions in recently admixed individuals. A Latino-specific European component accounts for the majority of the European ancestry among Caribbean Latinos and is exclusively shared with Iberian populations within Europe. Notably, this component is different from the two main gradients of ancestry differentiating southern from northern Europeans. Native Venezuelan components are present in higher proportions in admixed Colombians, Hondurans, and native Mayans.

As expected, Mexicans and most Colombians and Hondurans cluster mostly between Europeans and Native Americans, while Cuban, Dominicans and Haitians do between Europeans and Africans instead, with Puerto Ricans and some Colombians and Hondurans showing tripartite ancestry. 

A most notable issue is that the bulk of Caribbean Latin American ancestry from Europe forms a distinctive component that the authors suggest is a founder effect from the early colonization almost 500 years ago but that I feel that deserves a closer look.

The authors provide also the full ADMIXTURE results for up to K=15, with cross-validation data, what is certainly appreciated by this blogger.

Figure S3:
ADMIXTURE metrics at increasing K values
based on Log-likelihoods (A)
and cross-validation errors (B)
for results shown in Figure S2.

Using table B, the best fit is K=7:

From Fig. S2 (ADMIXTURE results)


Here we see a generic Mediterranean presence in Europe of the "black" component. Would it be just a simple reflection of European structure, then we should expect that the European component in Latin Americans would be c. 70% "red" and just 30% "black". But nope, not even in Cubans, who are the ones with the most recent European input overall (because it was a colony until a century ago). 

This may indeed have the explanation that the authors suggest: that it is the result of a "recent" founder effect some 500 years ago in the early moments of the Castilian conquest and colonization of America. But still something does not ring correct. At the very least I have some doubts. 

An alternative possibility that should be eventually tested could be that what we identify as "European" ancestry is in fact something European-like but not exactly European, for example North African and/or Jewish ancestry. There could be various sources for this trans-Mediterranean flow into America: on one side it has often been speculated (but never really proven) that a lot of Muslim and Jewish converts migrated to the colonies in the hope to escape the Inquisition. A major problem here is that most Muslim Iberians should be identical or nearly identical in ancestry other Iberians (Jews were not numerous enough probably anyhow).

But another interesting possibility is that many North Africans (including Canarian Aborigines or Guanches) may have been enslaved early on to supply the plantations of the Caribbean. Initially the excuse for slavery was not "racial" (an Illustration development in fact) but "religious". There are known many Papal edicts insisting that Canarian converts would not be enslaved, something that the Portuguese (first colonial power in the archipelago) did anyhow again and again. It is plausible (but ill-documented) that North African conquest campaigns and raids by Portugal first and Castile later would also capture many slaves in those areas, slaves that would probably end up in America in many cases, where they may have been emancipated eventually, becoming part of the Mestizo backbone of the Castilian colonial empire. 

I know I am speculating a bit here but it is an interesting alternative to explore. In this regard I really miss North African control populations, because they would shed light on this intriguing matter.

Another issue the paper explores is the origin of African ancestry, finding that the oldest ancestry is mostly from westernmost Africa (Mandenka, Brong as reference populations), while more recent ancestry is mostly from the Nigeria-Angola arc (Yoruba, Igbo, Bamoun, Fang and Kongo). 

The study also tries to reconstruct population history but some of their results are perplexing and highly unlikely.

Figure 3: Demographic reconstruction since the onset of admixture in the Caribbean. We used the length distribution of ancestry tracts within each population from A) insular and B) [not shown] mainland Caribbean countries of origin. Scatter data points represent the observed distribution of ancestry tracts, and solid-colored lines represent the distribution from the model, with shaded areas indicating 68.3% confidence intervals. We used Markov models implemented in Tracts to test different demographic models for best fitting the observed data. Insular populations are best modeled when allowing for a second pulse of African ancestry, and mainland populations when a second pulse of European ancestry is allowed. Admixture time estimates (in number of generations ago), migration events, volume of migrants, and ancestry proportions over time are given for each population under the best-fitting model. The estimated age for the onset of admixture among insular populations is consistently older (i.e., 16-17) compared to that among mainland populations (i.e., 14).

The really perplexing issue here is that in Haiti and Cuba particularly, the latest and quite notable arrival of African ancestors corresponds to a mere four generations ago, what means (as the approx. generation length is of c. 30 years, not longer because then the earliest European arrival would be before Columbus' feat) a mere 120 years ago, i.e. around 1890. 

The reality is that Haiti became independent in 1791-1804 and no relevant demographic inflow has happened since then. Similarly the last major batch of slaves to Cuba (from Spain, where slavery was being outlawed, as well as from Haiti itself) was in the earliest 19th century (however slavery would not be abolished in Cuba until 1884, although human trade was declared illegal in 1835 under British pressure). 

Therefore there must be an error of some sort in these reconstructions, which generate more recent African inflows that are realistically possible.


Update (3 Nov): Canary Islands were a major source of Caribbean "white" ancestry.

A very interesting and informative discussion with a Puerto Rican in search of his ancestry arose recently at my old blog Leherensuge. Charles provided very useful information on this matter and told me about aspects of the history of the colonization of America, and very especially the strategical (but economically less important) islands of the Greater Antilles.

A very unknown historical element is that Castile (not as much as Portugal but still) lacked great amounts of willing settlers in its free (non-serf) population and that therefore it had to look for assimilated colonists in odd places like the Canary Islands, where the clannish Guanches (the distinctive aboriginal islander Berbers) seem to have served that purpose by grade or force.

For example, in 1678 the Castilian Government issued a decree (cédula) that has become popularly known as Tributo de Sangre[es] (Blood Tribute) by which the Canarian oligarchs were imposed a "tax" of nine families to be moved to the Caribbean for each 1000 tons of local exports to America. There are some historians who criticize[es] this concept as "a myth" but what seems very clear is that, either way, Canarian Aborigines contributed heavily to the settlement of "Spanish America", very especially the Dominican Republic, Puerto Rico and Cuba.

So it seems I was correct in imagining a North African origin of this "black" component of Caribbean European-like ancestry. Of course, it still awaits a formal test of comparison with North Africans but I am pretty much persuaded now.

This is an interesting example of settlement with a culture (Castilian/Spanish in this case) different from the genetic roots of the population (largely Aboriginal Canarian). A similar example can well be that of the Irish (partly forced) settlement of Australia, carrying an "English" language and identity but effectively being from a different origin. In the case of Quebec it is also very probable that most original settlers came from some specific region of the French state and surely not from the "core France" around Paris (Southwest? - still untested but there is a very clear founder effect in any case).

I wonder how many other such cases have happened also in prehistory. For example: how genuinely "Indoeuropean" (by blood) were the Celts or other invaders of the Metal Ages. The likely answer is: probably not much. This has probably happened a lot but is in most cases undocumented. Only careful and dispassionate genetic research can give us some answers.


Update (Feb 16 2014): Charles has found another very interesting study, with plenty of data, which illustrates the continuous flow of Canarians to the Spanish possessions in the Caribbean. It is in Spanish language however:

Juan Manuel Santana Pérez, Isleños en Cuba y Puerto Rico (del siglo XVIII a mediados del XIX). Cuadernos Americanos nº 126, 2008 → LINK (freely accessible PDF).