February 13, 2015

Kurgan ancient DNA suggests major impact in North-Central Europe

After many rumors and pointless discussions based on them, finally the Haak et al. study on ancient Kurgan DNA is available only (pre-pub format):

W. Haak et al., Massive migration from the steppe is a source for Indo-European languages in Europe. bioRxiv 2015 (freely available pre-pub) → LINK [doi: http://dx.doi.org/10.1101/013433]

The study expands on previous work by Lazaridis 2014 by including a much larger array of ancient DNA from Germany and Hungary, as well as some key ancient DNA from Russia and also some complementary samples from Northern Iberia.


Autosomal DNA

Even if the authors admit it is difficult to properly quantify, there are clear tendencies that are outlined in fig. 2:

Figure 2: Population transformations in Europe. (a) PCA analysis, (b) ADMIXTURE
analysis. The full ADMIXTURE analysis including present-day humans is shown in
Extended Data Fig. 1.
Annotations in red by me.

The main inferred processes of demographic formation of the modern European genetic pool are outlined:
  1. A baseline of Epipaleolithic hunter-gatherers that pulls in the PC 1 towards the left (geographically would be the Atlantic). I call this layer Paleo-European (PE).
  2. A first replacement by Neolithic farmers of Thessalian origin (already discussed in depth in Lazaridis 2014), who were similar to modern Sardinians. I call this layer Neo-European (NE).
  3. A reflux of Paleo-European genetics that alters the Neo-European layer somewhat. This can be associated to Atlantic Neolithic flows (i.e. Megalithism, Funnelbeaker, etc.) We can call this stage Neo-European-2 (NE2).
  4. A second replacement wave by Steppe tribals, certainly bringing the Indoeuropean languages (IE).

Modern European populations align well along a IE-NE2 axis, whose midpoint seems to fall on North France, depending of course on which references you choose. I drew that axis as dotted red line. It is not substantively different from the Dimension 2 axis, although it is slightly slanted because the IE invaders obviously carried more PE than the NE layer. This new PE is not WHG (Magdalenian) but EHG (Eastern Epi-Gravettian) however - and hence its tendency towards Paleo-Siberian genetics (Ma1 or "ANE").

So Dimension 1 quite apparently contrasts the Paleo-European vs the West Asian components. What does Dimension 2 express? A quite apparent element is the Paleo-Siberian tendency. Alternatively it can also be considered to express the distinction between Lowland and Highland West Asians. Finally it can also be expressed as IE vs NE. All three are surely just variants of the same continental vs peripheral opposition, which is weaker than the PE vs West Asia one.

I must mention that fig. S5.2 offers a slightly different view:

Figure S5.2: PCA analysis with ancient individuals projected onto the variation of the
present-day ones.

Notable is that the NE-IE axis (not drawn) appears more slanted, with most modern populations showing greater excess of PE tendency and less "obviously" resolved by the late Chalcolithic populations (LNE/EBA in the authors terminology). 

As I said above, it seems very difficult to objectively measure the exact fractions of admixture (the tendencies are clear but the quantification not so much) and something that is becoming more and more painfully obvious is that Atlantic European ancient genomes are needed to explain the changes that happened prior to the arrival of Kurgans. Particularly it'd be most interesting to get ancient samples from: Portugal (Neolithic, Megalithic and Bronze Age), Basque Country and Gascony (Neolithic and Megalithic at the very least, preferably from the coastal regions), Brittany and West France (Neolithic, Megalithic 1 and Artenacian), Belgium (non-LBK Neolithic), Britain (several regions preferably, as the British Neolithic seems to have strong regional differences), West Germany (Michelsberg culture). This array or at least a sensible part of it could shed light on key processes taking place before and after the Kurgan migration. Bell Beaker samples from outside Central Europe would also be very interesting. 

I would also be interesting to see a PCA without West Asians, whose presence quite apparently does not add much to the analysis. It is known that when the PCA is European-only (or mostly), Basques and Sardinians display clearly different polarities (typically Sardinians vs Russians in PC1 and Basques vs Caucasians in PC2). It would be very interesting to observe how these ancient samples behave in a Europe-only PCA.


Y-DNA

A lot of the upheaval was around the fact of the finding of some R1b in Samara Valley. This is very interesting indeed but it is not the kind R1b that can be considered ancestral to modern European mainline R1b-M412. It is mostly of a different haplogroup whose modern distribution is unknown to me: R1b-Z2103.

*Update: some people have commented that R1b-Z2103 is found in West Asia and some Volga peoples.

Schematically (following YSOGG), R1b-M343 and its sole relevant subclade R1b1-M415 are structured as follows:
  • R1b1a (L320)
    • R1b1a2a1 (L51/M412)
      • R1b1a2a1a (P311) 
        • R1b1a2a1a1 (U106) → NW Europe
        • R1b1a2a1a2 (P312/S116) → SW Europe with scatter elsewhere in the continent, including Ireland, Britain, Italy... Found in Kromsdorf (late Chalcolithic)
    • R1b1a2a2 (CTS1078/Z2103) → found in Samara culture
  • R1b1b (M335) → minor, West Asia
  • R1b1c (V88) → Mediterranean and Africa, particularly important in Sardinia and Central-East Africa.
Note: for further information on European R1b see HERE and HERE.
Otherwise all the spotted R1b in this study is R1b1*: in Samara culture and in Neolithic Aragon (NE Iberia), both of which are hard to relate to anything of modern relevance.  

Corded Ware is associated to R1a only at this time. So at least in Europe it makes good sense to associate Kurgan expansion with R1a expansion. 


Mitochondrial DNA

There is plenty of mtDNA data but most is recycled from previous studies so not really novel. An interesting detail is that there is no or nearly no mtDNA H within the Kurgan (IE) samples, strongly suggesting that their migration was largely male-biased, at least initially. As happens with Y-DNA R1b, Kurgan immigrants cannot be associated to any increase of mtDNA H, whose origins must therefore be sought in some other origin (namely: Atlantic Neolithic).


Note: my apologies for being so extremely passive in my blogging activity. I don't really know how to explain other than feeling OLD AND TIRED and needing LOTS of "me time". It's time for others to pick up the torch, I guess.

August 13, 2014

Chalcolithic mtDNA from Atapuerca still in the Neolithic range

Bell Beaker Blogger points me to this latest study on ancient mtDNA from the Center-North Iberian Peninsula, including 20 samples from a Chalcolithic site (without Bell Beaker apparently) that clearly shows continuity with mainline Neolithic (Cardium but also similar to Central European Linear Pottery Culture, both sharing the same Thessalian ultimate origins).

Daniel Gómez Sánchez, Iñigo Olalde et al., Mitochondrial DNA from El Mirador Cave (Atapuerca, Spain) Reveals the Heterogeneity of Chalcolithic Populations. PLoS ONE 2014. Open accessLINK [doi:10.1371/journal.pone.0105105]

Abstract

Previous mitochondrial DNA analyses on ancient European remains have suggested that the current distribution of haplogroup H was modeled by the expansion of the Bell Beaker culture (ca 4,500–4,050 years BP) out of Iberia during the Chalcolithic period. However, little is known on the genetic composition of contemporaneous Iberian populations that do not carry the archaeological tool kit defining this culture. Here we have retrieved mitochondrial DNA (mtDNA) sequences from 19 individuals from a Chalcolithic sample from El Mirador cave in Spain, dated to 4,760–4,200 years BP and we have analyzed the haplogroup composition in the context of modern and ancient populations. Regarding extant African, Asian and European populations, El Mirador shows affinities with Near Eastern groups. In different analyses with other ancient samples, El Mirador clusters with Middle and Late Neolithic populations from Germany, belonging to the Rössen, the Salzmünde and the Baalberge archaeological cultures but not with contemporaneous Bell Beakers. Our analyses support the existence of a common genetic signal between Western and Central Europe during the Middle and Late Neolithic and points to a heterogeneous genetic landscape among Chalcolithic groups.

The results show intense similitude with Catalan Neolithic and Languedoc's Chalcolithic but also with Central European Neolithic. They contrast instead with Portuguese and Basque Neolithic, as well as with Central European Bell Beaker, all them much higher in haplogroup H and, in the Basque case, also in U (being the most modern-like of all ancient mtDNA pools known before the Bronze Age in Europe).

Annotated version of fig. 2
Figure 2. Mitochondrial DNA haplogroup frequency for 21 ancient European samples.
This study: El Mirador (MIR). Published prehistoric cultures [21]: Hunter-gatherer central (HGC), Linear Pottery culture (LBK), Rössen culture (RSC), Schöningen group (SCG), Baalberge culture (BAC), Salzmünde culture (SMC), Bernburg culture (BEC), Corded Ware culture (CWC), Bell Beaker culture (BBC), Unetice culture (UC), Funnel Beaker culture (FBC), Pitted Ware culture (PWC), Hunter-Gatherer south (HGS), (Epi) Cardial (CAR), Neolithic Portugal (NPO), Neolithic Basque Country and Navarre (NBQ), Treilles culture (TRE), Hunter-gatherer east (HGE), Bronze Age Siberia (BAS), Bronze Age Kazakhstan (BAK).

Notice please that the above column for Central European Bell Beaker (BBC) includes the more than dubiously attributed Kromsdorft site, which has a totally different genetic signature. In my previous analysis of European ancient DNA evolution, I treated them separately and I still think that it is much more correct to do it that way.

Notice also that one sample from Mirador was sequenced for autosomal DNA by Evangelia Dasakali, producing an Italian-like sequence, roughly in line with other early European farmers, excepted the Atlantic ones. See here.

So what we see is a "wedge" of Mediterranean or Neolithic ancestry probably penetrating along the Ebro river up to Atapuerca and contrasting with Atlantic Iberian (Basque and Portuguese) ancestry, more modern-like or even "hyper-modern" (by contrast with mainline farmers) in the case of Portugal. This same contrast exists with Central European Bell Beaker sites and also (in the autosomal DNA aspect) with Megalithic farmers from Southern Sweden. 

None of those "modernizing" tendencies can be found instead among Eastern European Neolithic peoples nor among early Indoeuropeans of Central Europe such as those of the Unetice culture. So the overall conclusion can only be that there was in the Chalcolithic (and to some extent Neolithic) a duality of ancestries between the Mainline or Mediterranean (but also Danubian) Neolithic and a more "modern" Atlantic Neolithic, which is related to the Megalithic and Bell Beaker cultural phenomena (and in North-Central Europe also to Funnelbeaker). 

There are still a lot of dark spots in our understanding of how this "modernization" or "Westernization" of the genetic pool happened but, in general terms, it seems to imply a sizable (albeit somewhat irregular) demographic flow from Atlantic Europe into the areas previously occupied by Mainline Neolithic populations of partial West Asian affinity. This is apparent in both mtDNA as in autosomal DNA. 

These sequences from El Mirador (Atapuerca) only underline this phenomenon and the fact that in the Chalcolithic, some 4500 years ago, this process of "modernization" of the European genetic pool was still incomplete.

July 30, 2014

Bell Beaker of Estremadura (Portugal)

This is a very interesting read for everyone interested in the Chalcolithic Era and particularly in the Bell Beaker phenomenon in one of its most crucial areas: the Lisbon Peninsula of Portugal:

João Luís Cardoso. Absolute chronology of the Beaker phenomenon North of the Tagus estuary: demographic and social implications. Trabajos de Prehistoria 2014. Open accessLINK [doi: 10.3989/tp.2014.12124]

Abstract

The complexity of the Beaker phenomenon in the Tagus estuary does not fit well with the model of three successive groups (International, Palmela and Incised Groups). The above seems to result from the nature of the settlements rather than from its chronology, as all three groups are present during the second half of the 3rd millennium BC. Therefore while artefacts of the International Group predominate in the fortified sites, the Incised Group appears almost exclusively in open sites. The Palmela Group seems of minor importance, at least in the north region of the Tagus River estuary. The remarkable antiquity of Beaker pottery found in the FM hut at Leceia (which dates from the 2nd quarter of the 3rd millennium BC, re-confirmed by AMS dating) has parallels both in the North and South of Portugal, as well as in Spain. Thus we conclude that in the Lower Estremadura (one of the most important regions in Europe for the discussion of the origin and diffusion of Beaker “phenomenon”), the Beaker social formation with its own distinct cultural characteristics, coexisted with local Chalcolithic cultures, although never merged with them.


Fig. 2. Leceia. Plan of the fortified settlement, with the
location of the two Bell Beaker huts identified outside the walls.
One of the important findings of this study is that the Incised Bell Beaker style is strictly contemporary of the International style and not a later development. The difference is that, while the International (or Maritime) high quality pottery style dominated the fortified settlements, their rural hinterland used the more modest Incised style pottery or, in some cases, no Bell Beaker pottery at all. 

The author questions the traditional tripartite division between Early, Full and Late Chalcolithic (with Bell Beaker only present in the late stage) and claims a simpler division between Early and Full/Late Chalcolithic based not only on Bell Beaker presence but also of the more widespread local pottery styles (channeled and acacia-leaf decoration). 

He also argues that, somehow, there was a "cultural" (or is it "class"?) division between the fortified cities and their rural hinterland, division that would reappear later in the Bronze Age. This division is largely defined by certain pottery styles and particularly quality. A possible interpretation I do is that this reflects a division between a cosmopolitan urban "elite" and a rural society that was not immersed in this cosmopolitanism of the fortified towns. The author finds no sign of conflict between the two areas.
On a more global approximation to the socio-cultural reality during the 2nd half of the 3rd millennium BC in Lower Estremadura, we may consider that if Beaker society was segmented with two clearly differentiated components, it may have corresponded nevertheless to a cultural entity as a whole with its own characteristics, at least in the region under appreciation.

The absolute chronology for the earliest bell beakers in Estremadura is 2700-2600 BCE, prior to the transition between the two Chalcolithic phases (c. 2600-2700 BCE in Leceia).

I find the following particularly interesting:
The comparison of chronometric and archaeological results described above suggests that the first Beaker productions in the region of Lower Estremadura (between about 2700 and 2600 BC) coexisted, with lower interaction, with Chalcolithic populations that lived in some fortified sites, as shown by the chronology of the FM hut at Leceia. This is the same period in which fluted pottery typical of the Early Chalcolithic of Estremadura was still used inside this fortified settlement. But in other cases this coexistence was followed by interaction with the inhabitants of those already-existing fortified sites (as found in the fortified Chalcolithic settlement of Zambujal).

This interaction persisted throughout the whole Full Chalcolithic (represented by the characteristic “acacia-leaf” ceramic pattern) until the end of the 3rd millennium BC, as can be seen in almost all the fortified settlements of Lower Estremadura.

Does this support the formation of Bell Beaker as some sort of "sect" or distinctive "ethnic group", which only in a second phase became inserted in the wider local society? One possible interpretation might be that Bell Beaker users could have arrived from elsewhere as some sort of colonists, maybe a colony of specialist traders or metallurgists or even a religious community, but, if so, where from?, because Iberia seems to have the oldest Bell Beaker dates?

Estremadura is today one of the most likely candidates for the formation of the Bell Beaker phenomenon but this paper also mentions similarly older dates in other parts of Portugal, and the same seems true for other parts of Iberia and SE France. Whatever its exact origin, it seems likely that the vibrant and often ill-understood Chalcolithic civilization of Estremadura was surely a trampoline from which the important cultural phenomenon reached other areas of Atlantic (and maybe even inland) Europe.

July 2, 2014

Altitude-adaption in Tibetans is "Denisovan-like"

It seems that archaic humans left a small but critical legacy among us:

Emilia Huerta Sánchez et al., Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. Nature 2014. Pay per viewLINK [doi:10.1038/nature13408] 
Abstract

As modern humans migrated out of Africa, they encountered many new environmental conditions, including greater temperature extremes, different pathogens and higher altitudes. These diverse environments are likely to have acted as agents of natural selection and to have led to local adaptations. One of the most celebrated examples in humans is the adaptation of Tibetans to the hypoxic environment of the high-altitude Tibetan plateau1, 2, 3. A hypoxia pathway gene, EPAS1, was previously identified as having the most extreme signature of positive selection in Tibetans4, 5, 6, 7, 8, 9, 10, and was shown to be associated with differences in haemoglobin concentration at high altitude. Re-sequencing the region around EPAS1 in 40 Tibetan and 40 Han individuals, we find that this gene has a highly unusual haplotype structure that can only be convincingly explained by introgression of DNA from Denisovan or Denisovan-related individuals into humans. Scanning a larger set of worldwide populations, we find that the selected haplotype is only found in Denisovans and in Tibetans, and at very low frequency among Han Chinese. Furthermore, the length of the haplotype, and the fact that it is not found in any other populations, makes it unlikely that the haplotype sharing between Tibetans and Denisovans was caused by incomplete ancestral lineage sorting rather than introgression. Our findings illustrate that admixture with other hominin species has provided genetic variation that helped humans to adapt to new environments.


Figure 3: A haplotype network based on the number of pairwise differences between the 40 most common haplotypes.
The haplotypes were defined from all the SNPs present in the combined 1000 Genomes and Tibetan samples: 515 SNPs in total within the 32.7-kb EPAS1 region. The Denisovan haplotypes were added to the set of the common haplotypes. The R software package pegas23 was used to generate the figure, using pairwise differences as distances. Each pie chart represents one unique haplotype, labelled with Roman numerals, and the radius of the pie chart is proportional to the log2(number of chromosomes with that haplotype) plus a minimum size so that it is easier to see the Denisovan haplotype. The sections in the pie provide the breakdown of the haplotype representation amongst populations. The width of the edges is proportional to the number of pairwise differences between the joined haplotypes; the thinnest edge represents a difference of one mutation. The legend shows all the possible haplotypes among these populations. The numbers (1, 9, 35 and 40) next to an edge (the line connecting two haplotypes) in the bottom right are the number of pairwise differences between the corresponding haplotypes. We added an edge afterwards between the Tibetan haplotype XXXIII and its closest non-Denisovan haplotype (XXI) to indicate its divergence from the other modern human groups. Extended Data Fig. 5a contains all the pairwise differences between the haplotypes presented in this figure. ASW, African Americans from the south western United States; CEU, Utah residents with northern and western European ancestry; GBR, British; FIN, Finnish; JPT, Japanese; LWK, Luhya; CHS, southern Han Chinese; CHB, Han Chinese from Beijing; MXL, Mexican; PUR, Puerto Rican; CLM, Colombian; TSI, Toscani; YRI, Yoruban. Where there is only one line within a pie chart, this indicates that only one population contains the haplotype.


See also this entry on Neanderthal introgression being subject to positive and negative selection.

Sino-Basque is not for real

Unmistakable evidence: beret-wearing Chinese!
(humorously borrowed from Zubia-Qiao blog,
which is about real Basque-China relations)
Linguistic speculation haunts us and today I stumbled on this paper, which has an interesting introduction but ends up claiming the extremely unlikely Sino-Caucasian family (including Basque and what-not):

Murray Gell-Mann, Ilia Peiros & George Starostin, Distant Language Relationships: The Current Perspective. Available at academia.eduLINK

I admit I have been skeptic of the Sino-Caucasian hypothesis since I tried once to learn some Chinese and was surprised of how little this language actually resembles Basque. Probably a random African or Australian language is not more different than Chinese is to Basque, or so I thought without having performed until now any formal test of the hypothesis.

There are a lot of reasons: the general skepticism of most linguists but also the lack of any apparent archaeological or meaningful genetic relationship since maybe 60 Ka ago (or, if Sino-Tibetan is related to Amerind and other Native American languages, since c. 45 Ka ago at the latest).

But the hypothesis continues to have some currency and today I finally decided to test it following the Swadesh-100 method suggested in the paper. The result:

Sino-Tibetan/Basque/English Swadesh-100 comparison (open office ODT format, similar to Excel - if anyone has a problem, please ask and I will upload an Excel version of it). 

Conclusion: Basque is not more related to Sino-Tibetan (either Mandarin or Burmese) than English is. If anything, the opposite is true, although the low level of plausible cognates for both languages (5-7%) seems merely stochastic noise, or maybe in some case wanderworts. Of course, the exact number of similar words (possible cognates) depends on one's permisivity but the pattern is so similar for the three possible pairings that, if there is any relationship at all, it must include English and therefore Indoeuropean.

Check it yourself, of course.

June 29, 2014

Pan-Homo split: 11-17 million years ago

Chimpanzee mutation rate is largely determined by fathers' age and, overall, implies a Pan-Homo divergence rate of ~13 million years (95% CI: 11-17 Ma), about double than usually assumed by conservative scholastic inertia.

Oliver Venn et al., Strong male bias drives germline mutation in chimpanzees. Science 2014. Pay per viewLINK [doi:10.1126/science.344.6189.1272]

cc Matthew Hoelscher
The focus of this study are the important differences between patrilineal and matrilineal mutation rate depending on the father's age among chimpanzees, notably more biased than among humans. However the resulting estimate for Pan-Homo divergence is not less important because it radically challenges the usual assumptions of 5-7 Ma, repeated once and again in molecular clock estimates, which are based on studies that are already quite obsolete.

In the studied captive population of Western chimpanzees 30 out of 35 mutations happened in the paternal lineage, and these increase with the father's age. No effect could be attributed to maternal age or familiar peculiarities.

Interestingly most of these patrilineal mutations happen near the telomeres, an effect not seen in female line mutations.

Owing to this gender bias, the mutation rate of the X chromosome among chimpanzees is 74% that of autosomal DNA (in humans: 85%). 

The gender bias in mutation rate and its differential with humans is attributed to differences in mating systems among great apes, with chimpanzees having the greatest competition among males, what is reflected in testicle size. They predict that gorillas (who experience less competition between males) will show less patrilineal mutation rate bias than humans and chimpanzees.

This is probably the more synthetic paragraph from the study:
Under a model in which the mutation rate increases linearly with parental age, the rate of neutral substitution is the ratio of the average number of mutations inherited per generation to the average parental age. We predict the neutral substitution rate to be ~0.46 × 10−9 per base pair (bp) per year in chimpanzees, compared to estimates in humans of ~0.51 × 10−9 bp−1 year−1 (9). These results are consistent with near-identical levels of lineage-specific sequence divergence (12) but surprising given the differences in paternal age effect. In the intersection of the autosomal genome accessible in this study and regions where human and chimpanzee genomes can be aligned with high confidence, the rate is slightly lower (0.45 × 10−9 bp−1 year−1) and the level of divergence is 1.2% (13), implying an average time to the most common ancestor of 13 million years, assuming uniformity of the mutation rate over this time (95% ETPI 11 to 17 million years; table S11).


13 million years of the hominid line

This is not at all the first study to highlight the extreme dubiousness of the usual scholastic assumptions regarding the Pan-Homo divergence, which taint so many genetic studies, turning their chronological estimates totally worthless.

In 2010, Wilkinson et al. estimated a Pan-Homo divergence rate of 8-10 Ma. In 2012 Langergraber et al. recalibrated previous studies getting a Pan-Homo divergence bracket of 6.78-13.45 Ma (fig.2), while the divergence from Gorilla would be significantly older: 8.31-20.0.

Fig. 1 from Langergraber 2012. Legend: Diagram illustrating the branching pattern and timing of the splits between humans, chimpanzees, bonobos, western gorillas, and eastern gorillas. The paler shading indicates the range of split times inferred in this study. Cartoon skulls indicate approximate age of the indicated fossil remains, but do not imply that these fossils were necessarily on those ancestral lineages or that entire crania actually exist for these forms.


A key fossil affecting this controversy is Sahelanthropus tchadiensis (Toumaï), which has been recently confirmed to be in the human line on several hardly questionable traits and is dated to c. 7 Ma.

A related debate is whether primates in general are much older than usually claimed and lived already in the Jurassic, something suggested by the already mentioned Wilkinson study and also by Heads 2010. Here a major issue is that mainline conservative estimates would have the ancestors of New World monkeys swimming (island hoping) to South America, something that those monkeys (and most other primates) simply will not do. The radiation of primates to South America and possibly also Madagascar is much better explained if these animals could just tree-hop, rather than island-hop to their destinations. However this would demand a radical revision of the usual age estimate for vertebrate radiation, what so far lacks fossil support (but lack of evidence is not evidence of lack, you know: fossil ages can only be taken as terminus ante quem dates and not absolute direct references).

But this is a side question, what really matters to us is that our ancestors split from the chimpanzee line c. 13 Ma (according to this study) and not after 8 Ma in any case (weighting all the evidence). This not just renders most "molecular clock" estimates useless and effectively false (wrong, erroneous, inadequate, misleading, junk, pseudoscientific...) but also help us to rethink our ancestral history in the African savannas since long before we became humans (Homo sp.)

Looking for some ecological context clues, I found this 1996 study by Jean Maley, which shows that Africa was largely humid in the early Miocene (smectite: evidence of water) but that it became increasingly arid towards the middle Miocene (kaolinite: evidence of sand). Up to this key ecological change of the Middle Miocene, the rainforest extended all the way to Egypt and East Africa. This kind of ecology allows for the common ancestor of African great apes to have arrived and first diverged in a jungle-dominated ecology and, later, for the speciation event leading to humans (bipedalism) to have happened as this once widespread jungle became scarcer, yielding to deserts and savanna.

Sahelanthropus (from fossilized.org)
It just makes all sense that the evolution of bipedalism was coincident with the vanishing of that originally widespread jungle environment whose dating is of approx. 13 Ma ago. However it must be said that the consolidation of the Sahara only happened much later, c. 7 Ma ago, already approaching the Pliocene.

Regardless of the exact split-time, a big question I have on hominid evolution is how on Earth did our small-brained and small-toothed precursors like Toumaï survive in the open savannas and grasslands without fire nor weapons. Even if they resorted to trees (isolated or in patches) for refuge, there were already felines of the saber-toothed family roaming in Africa and these big cats were no doubt be able  to climb on trees and in some cases they have been shown to predate on australopithecines. How could our precursors in the hominin line be able to face this menace without the advantage of speed (as ruminants have) or good defenses? Were their strong forelimbs, together with team action enough to confront the threat of predators? Did they use primitive weapons such as branches and stone throwing?

June 21, 2014

Claim of 13 Ma Pan-Homo split

[Update (Jun 29): new entry on this issue available].

[Update: the origin of this news is Venn 2014 but I could not find the mention of the 13 Ma split initially, as it was not something they underlined at all. I will write something as soon as possible. Thanks to all the people who helped my confused mind].

Live Science reports this week that the divergence of the human and chimpanzee lines may be as old as 13 million years. This is the oldest range of what Langergraber 2012 suggested (8-13 Ma in Fig.1, although in text they wrote "6.8-11.6 Ma") and older than the Wilkinson 2010 estimates (8-10 Ma), and would totally break all the usual "molecular clocks" so extremely abused in human genetics because it is double of the usual scholastic mindless parroting (5-7 Ma, which are necessarily too recent because they do not allow for Sahelanthropus' evolution and not even for bonobo evolution under the protection of the mighty Congo river).

Sadly the article includes no reference to the source, not even the name of the scientists involved, and I could not find it any reference online. For a moment I thought it could be another new study on gender bias in chimpanzee mutation rate (Venn et al. 2014 (ppv)) but after getting a copy it does not seem to have any direct relation.

So I would appreciate if someone can give me a lead on where this claim may come from.

Atapuerca skulls show "intermediate" features

H. heidelbergensis from Atapuerca
Cranium 5 "Miguelón"
(CC by José Manuel Benito)
This has been in the news all around this week with various emphasis, but probably the most important highlight is that, according to Atapuerca researchers, Homo heidelbergensis may well be a diffuse category with varied degrees of affinity to their Neanderthal successors.

J.L. Arsuaga et al., Neandertal roots: Cranial and chronological evidence from Sima de los Huesos. Science 2014. Pay per viewLINK [doi:10.1126/science.1253958]


Months ago, it was found that Atapuerca's H. heidelbergensis and the Denisova hominins formed a single mitochondrial DNA clade to the exclusion of Neanderthals and us. However Arsuaga et al. find that facial traits in the hominins of Sima de los Huesos seem to be already much closer to those of Neanderthals than to the local precursors. Instead other cranial traits such as brain size do not seem to change yet. 

There seems to be some uncertain speculation by the researchers on what this partial "neanderthalization" process in Atapuerca hominins could signify. 
"We think based on the morphology that the Sima people were part of the Neanderthal clade," Arsuaga said, "although not necessarily direct ancestors to the classic Neanderthals."

This, I guess, could indicate some sort of convergent evolution or be caused by some Neanderthal admixture on the male side.
 
Another important finding is that, contrasting with the similitude of the various specimens from Sima de los Huesos ("Chasm of the Bones", a key subsite of Atapuerca), other contemporary European specimens look quite different, suggesting that H. heidelbergensis was a quite diverse human species.

The study includes seven new specimens, as well as ten other previously reported ones.

Atlas of Inuit trails

An anthropological and geographical resource that may be of interest:


The atlas seems so far mostly limited to Nunavut and other parts of Northern Canada.

From the Introduction:
The Atlas provides a synoptic view (although certainly incomplete) of Inuit mobility and occupancy of Arctic waters, coasts and lands, including its icescapes, as documented in written historical records (maps of trails and place names). 

The documents that form the foundation of this Atlas consist of both published and unpublished accounts of Inuit engagement with cartography during the 19th and 20th centuries. All documents are held in public libraries or archives. The focus of the Atlas in this initial project is on material from the Eastern and Central Canadian Arctic. It is hoped that the Atlas can be further developed in subsequent phases to present material of other Inuit groups such as the Inupiat, Inuvialuit, and peoples of Nunatsiavut (Labrador) and Nunavik. 

Delineations of trails and place names play a critical role in documenting the Inuit spatial narratives about their homelands. To show where these trails lead and connect to other trails, the historical records used in making this Atlas are being relationally linked, referenced geospatially, and displayed on a base map.


Partial image of the atlas

June 15, 2014

Mexico's Native American diversity

Interesting study on Mexico's Native American diversity:

Andrés Moreno Estrada et al., The genetics of Mexico recapitulates Native American substructure and affects biomedical traits. Science 2014. Freely available with registrationLINK [doi:10.1126/science.1251688]
Abstract

Mexico harbors great cultural and ethnic diversity, yet fine-scale patterns of human genome-wide variation from this region remain largely uncharacterized. We studied genomic variation within Mexico from over 1000 individuals representing 20 indigenous and 11 mestizo populations. We found striking genetic stratification among indigenous populations within Mexico at varying degrees of geographic isolation. Some groups were as differentiated as Europeans are from East Asians. Pre-Columbian genetic substructure is recapitulated in the indigenous ancestry of admixed mestizo individuals across the country. Furthermore, two independently phenotyped cohorts of Mexicans and Mexican Americans showed a significant association between subcontinental ancestry and lung function. Thus, accounting for fine-scale ancestry patterns is critical for medical and population genetic studies within Mexico, in Mexican-descent populations, and likely in many other populations worldwide.

Fig. 1-D
First of all it has to be highlighted that the sentence "some groups were as differentiated as Europeans are from East Asians" is a bit misleading. It refers to the raw FST parameter (Fixation Index) which in these cases is caused by extreme drift, product of isolation and small number endogamy.

Otherwise the Seris (Comcaac), who are the only population affected by the claim, are clearly derived not only from the same root as the rest of Native Americans but more specifically from the ancestor population of the Tarahumaras (Rarámuri), as fig.1-D reflects (right). 

The Seris are a small population of coastal Sonora who add up to less than one thousand people and have remained proudly distinct, not only from the colonial population but also from other fellow Native Americans. In spite of this long extreme isolation that makes the appear "as differentiated as Europeans are from East Asians", it is apparent that they must derive from the Uto-Aztecan populations of NW Mexico (and maybe also across the border). 

K=9 (fig. 2-B-part)
Other very isolated and heavily drifted populations are the Lacandon and Tojolabal Mayas. Again, in spite of their radical isolation, they seem related to other Mayas by origin. In these cases their languages are recognized as members of the Maya family, while the Seri language is considered an isolate. 

Actually the extreme FST scores only apply between these extremely drifted populations: FST{Seri-Lacandon}=0.136, FST{Seri-Tojolabal}=0.121. 

This reference is interesting because it explains how subcontinental levels of differentiation can happen in relatively short time if the founder populations are small and isolated for some 20 Ka. It is a warning call against reaching to too many conclusions based only on populations with a long history of isolation.

Otherwise the Seri FST scores are high but more normal: 0.087 to 0.096.  See table S-4 for further details. 

The tree is interesting also because it suggest a main division separating the Nahuas from the rest of the Uto-Aztecan meta-population (Saris included). The Nahuas, who approximately correspond to the the ancient Aztecs, are actually divided in several groups, which seem rather akin to their immediate neighbors and not so much among them or their linguistic relatives. 

This implies that, as the ancestors of the Nahuas migrated southwards, they assimilated so many locales that they largely lost their distinctiveness. In the ADMIXTURE graph to the left, we see that they do keep a variably small fraction of Uto-Aztecan affinity (not just them, also the Purepecha and Totonac, whose languages are distinct). 

Otherwise Mexican Natives have two main components at K=9: the main Mexican one (blue) and the Maya one (orange). The Maya division is also apparent in the tree. 

However it must be mentioned that the ADMIXTURE run available in the supp. materials (fig. S-10) reaches down to K=20, showing further differentiation between the various Mesoamerican populations dominated by the blue components at K=9. 

For comparison, in the European segment only the Basque component shows up as distinct in all those runs (since K=10). So we are talking about a fairly diverse population compared with European relative homogeneity.

Sequence of further components or distinctions showing at depths greater than K=9:
  • K=12: Tarahumara
  • K=14: Nahua-Purepecha-Totonac
  • K=15: Tepehuan
  • K=16: Purepecha + Jalisco-Nahua
  • K=18: Triqui
  • K=20 Totonac



Mestizo ancestries

An issue worth mentioning, particularly in relation to the so far unconfirmed but quite plausible Canarian origin of a large share of the "European" ancestry in the Caribbean region, is that the European ancestry of Mexicans seems essentially Iberian, as shown in fig. S-14:


I am anyhow awaiting for a sensible geneticist to address this question properly. When dealing with Mexicans and other Latin American populations of complex colonial ancestry, it seems quite apparent that so diverse European samples are in excess and that instead a North African control is surely missing instead.

A more regionalized approach to Iberian ancestry could also be interesting.

Regarding the Native American share of the ancestry, a finding of this study is that there is important regional variation: Yucatan and Campeche Mexicans have clearly strong Maya ancestry, while in Sonora it is something more like Tarahumara and in the core of Mexico it seems Nahua-like or from other "central" populations like the Zapotec or Totonac. See fig. 2A for details.

There is also very minor Tropical African ancestry across the board, somewhat more relevant in Guerrero and Veracruz, states which historically hosted the main port cities of New Spain and still have some small Afrodescendant populations.