February 2, 2016

Most Africans do not have significant Eurasian admixture

This is major news: the authors of the study on the ancient East African genome of Mota have recanted their conclusions. In a correction note echoed by Nature they say:

Erratum'to'Gallego'Llorente'et'al.'2015'

The results presented in the Report “Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent“ were affected by a bioinformatics error. A script necessary to convert the input produced by samtools v0.1.19 to be compatible with PLINK was not run when merging the ancient genome, Mota, with the contemporary populations SNP panel, leading to homozygote positions to the human reference genome being dropped as missing data (the analysis of admixture with Neanderthals and Denisovans was not affected). When those positions were included, 255,922 SNP out of 256,540 from the contemporary reference panel could be called in Mota. The conclusion of a large migration into East Africa from Western Eurasia, and more precisely from a source genetically close to the early Neolithic farmers, is not affected. However, the geographic extent of the genetic impact of this migration was overestimated: the Western Eurasian backflow mostly affected East Africa and only a few SubUSaharan populations; the Yoruba and Mbuti do not show higher levels of Western Eurasian ancestry compared to Mota.

We thank Pontus Skoglund and David Reich for letting us know about this problem.

This makes much better sense admittedly. I strongly appreciate the willingness of Gallego, Jones et al. for publicly amending their wrong as quickly as possible. It's said that erring is human but correcting is only for the wise.

January 24, 2016

Ancient mtDNA from a Megalithic tomb near Atapuerca

A new study has produced 22 mitochondrial sequences from a Megalithic tomb (dolmen) in Alto del Reinoso, some 7 Km NE of Atapuerca.

Kurt W. Alt, Stephanie Zech et al., A Community in Life and Death: The Late Neolithic Megalithic Tomb at Alto de Reinoso (Burgos, Spain). PLoS ONE 2016. Open access LINK [doi:10.1371/journal.pone.0146176]

Abstract

The analysis of the human remains from the megalithic tomb at Alto de Reinoso represents the widest integrative study of a Neolithic collective burial in Spain. Combining archaeology, osteology, molecular genetics and stable isotope analysis (87Sr/86Sr, δ15N, δ13C) it provides a wealth of information on the minimum number of individuals, age, sex, body height, pathologies, mitochondrial DNA profiles, kinship relations, mobility, and diet. The grave was in use for approximately one hundred years around 3700 cal BC, thus dating from the Late Neolithic of the Iberian chronology. At the bottom of the collective tomb, six complete and six partial skeletons lay in anatomically correct positions. Above them, further bodies represented a subsequent and different use of the tomb, with almost all of the skeletons exhibiting signs of manipulation such as missing skeletal parts, especially skulls. The megalithic monument comprised at least 47 individuals, including males, females, and subadults, although children aged 0–6 years were underrepresented. The skeletal remains exhibited a moderate number of pathologies, such as degenerative joint diseases, healed fractures, cranial trauma, and a low intensity of caries. The mitochondrial DNA profiles revealed a pattern pointing to a closely related local community with matrilineal kinship patterns. In some cases adjacent individuals in the bottom layer showed familial relationships. According to their strontium isotope ratios, only a few individuals were likely to have spent their early childhood in a different geological environment, whilst the majority of individuals grew up locally. Carbon and nitrogen isotope analysis, which was undertaken to reconstruct the dietary habits, indicated that this was a homogeneous group with egalitarian access to food. Cereals and small ruminants were the principal sources of nutrition. These data fit in well with a lifestyle typical of sedentary farming populations in the Spanish Meseta during this period of the Neolithic.

While the nutritional part has some interest, it is ultimately not too conclusive (high protein diet, similar to that of Dordogne Neolithic, high incidence of caries, three individuals who may have been raised outside the "closely knit" community), so I will focus my attention on the mitochondrial lineages.

These are:
  • U5b - 2
  • U5b2b3 - 4
  • U5b3 - 1*
  • U4 - 1*
  • V - 2
  • K - 4
  • K1a - 1
  • K1a1 - 3
  • X - 3
  • T2b - 3
  • T2a1b - 1*
  • H3 - 1
  • J - 1
The three individuals marked with an asterisk (*) might have been raised in other villages, two of them are adult men and the third one a teen-ager of unknown gender. While the possible immigration of men could suggest matrilocality, the reality is that most individuals buried whose gender could be discerned are men anyhow, and all the rest seem to share the same kind of diet (i.e. probably raised in the Alto del Reinoso community), so most unclear.

Notice also that, because of the limitations in haplogroup identification in ancient DNA, apparent "upstream" lineages such as U5b or K can perfectly be the same as "downstream" ones like U5b2b3 or K1a1 respectively. We just do not know for sure.

My preliminary diagnostic was that it looks a quite typical "mixed Neolithic" pool, much like the one of El Portalón in nearby Atapuerca, with dominance of "Neolithic" lineages (K, X, T, J - maybe also V and H3, not yet detected in Western hunter-gatherers) but also a high frequency of "Paleolithic" ones of the U typology (U5 and U4). It is almost absolutely "pre-modern", lacking the high frequencies (40-60%) of mtDNA H found today (and also found in the Neolithic of Paternabidea and Gurgy, in Navarre and Burgundy respectively) and therefore having great excess of both "Neolithic" and U frequencies.

It must be said that Northern Burgos is even today quite low in mtDNA H, with only 33% of this widespread lineage (half of it H3), being also unusually high (30%) in haplogroup U frequencies (ref.), but in any case the mtDNA pool is at the very least not standard for the wider geography and must have experienced some changes in the meantime therefore.

For that reason I considered comparing with the other nearby sites within this small Atapuerca-La Brújula mountain gates area that divides the Duero from the Ebro basins. The result (in percentages) is as follows:


Site date (BCE) n U5 U4 H* H1 H3 V J T2 X K U3
Reinoso ~3700 22 27 5 - - 5 9 5 18 14 18 -
Portalón ~3000 7 29 - - - 29 - 14 - 14 14 -
Mirador ~2500 20 - - 5 20 - - 10 20 20 20 5

[Ref. links for El Portalón and El Mirador (both in Atapuerca)].


The three sites provide jointly a most interesting sequence for the district. I would say that Reinoso and Portalón seem quite similar, especially considering that the latter sample is very small, allowing for some random fluctuations (decrease in V and T2, increase in H3 and J). However in El Mirador, some 500 years later, we just cannot ignore that there are notable changes.

While the main "Neolithic" lineages (J, T, X, K) remain pretty much the same, all the rest is completely different: U5 (and its faithful sidekick U4) has vanished, has happens with H3 and V, instead we see a sudden outburst of H1 (and H*) and also the less impressive appearance of U3.

What does this mean? Let's go back to the modern mtDNA pool in Northern Burgos Province (n=24) as per Behar 2012:
  • H1: 2 (8%)
  • H3: 4 (17%)
  • U: 8 (33%)
  • K: 2 (8%)
  • T: 2 (8%)
  • J: 2 (8%)
  • Singletons: H*, H4, V, L2
It seems to me that those ancient genetic pools are still very present: although there are greater frequencies of H and U than the average produced by merely admixing Reinoso and Mirador, the underlying typology that we can discern (within H most clearly) seems to conform to what those ancient populations already had. Instead the "Neolithic" lineages are less common.

Why?

My guess is that these ancient sites lay all in a key passage of a most strategic route, Spain's National Road 1, St. James' Way, Roman road Ab Asturica Burdigalam and surely much older trade and cultural routes went through that series of mountain passes. This may have attracted more immigrants from the Neolithic settler populations from the Mediterranean, who may have been surrounded by others of more "aboriginal" roots (mostly Paleolithic ascendancy) and rather low visibility for archaeologists.

It remains to be confirmed if Bell Beaker (associated with El Mirador site) may be directly blamed for the introduction of mtDNA H1 in the district. It is indeed possible but in any case the long term impact was limited.

It must also be understood that all this has very little to no relationship with what may have happened in the Basque Country, in spite of being not far away: the genetics involved, both ancient and modern, are quite different. It may be surprising how much the genetic pool can vary in just 200 Km but the rugged geography and diverse ecology seem to favor this kind of sharp distinctions. And, regardless of the causes and the surprise, it may cause, the data is there and is very clear.

January 23, 2016

Ancient DNA from England suggests strong impact of Germanic invasions

Recently sequenced Roman, Iron Age and Anglo-Saxon DNA sequences from England help to clarify the issue of the impact of Germanic migrations in Great Britain, which seems to have been significant.

Rui Martiniano et al., Genomic signals of migration and continuity in Britain before the Anglo-Saxons. Nature 2016. Open accessLINK [doi:10.1038/ncomms10326]

Abstract

The purported migrations that have formed the peoples of Britain have been the focus of generations of scholarly controversy. However, this has not benefited from direct analyses of ancient genomes. Here we report nine ancient genomes (~1 ×) of individuals from northern Britain: seven from a Roman era York cemetery, bookended by earlier Iron-Age and later Anglo-Saxon burials. Six of the Roman genomes show affinity with modern British Celtic populations, particularly Welsh, but significantly diverge from populations from Yorkshire and other eastern English samples. They also show similarity with the earlier Iron-Age genome, suggesting population continuity, but differ from the later Anglo-Saxon genome. This pattern concords with profound impact of migrations in the Anglo-Saxon period. Strikingly, one Roman skeleton shows a clear signal of exogenous origin, with affinities pointing towards the Middle East, confirming the cosmopolitan character of the Empire, even at its northernmost fringes.

Notice that I say Germanic rather than Anglo-Saxon because I'm not sure how much can be attributed to these and how much to Vikings, whose genomes were similar. A recent study on British genetics seemed to indicate that the Danish (Viking) origins were clearly more important than the Saxon ones from Low Germany. However... were the original Angles more akin to Saxons or to Danes?

Anyway, the ancient samples are mostly Romano-Briton, from burials at Driffield Terrace, near York (Eboracum), dating to c. 200 BCE and including many decapitated remains. Another sample is from the Iron Age of Melton (East Yorkshire), dated between 200 and 40 CE. Finally a Christian Anglo-Saxon individual from Norton (Teesside, 70 Km north of York), dated sometime between the 7th to 10th centuries. 

Excepted one Roman era outlier (3DRIF-26), who seems an immigrant from the Eastern Mediterranean (autosomal DNA strongly suggests the Levant or Arabia), the rest all fit well with the autosomal genetics of the Iron Age one and modern Welsh. Modern English seem to have, in most cases, at least some Germanic admixture:

Figure 3 - Principal Component Analysis
(a) PCA of the Roman samples from Driffield Terrace (excluding one outlier), one Iron-Age individual and one Anglo-Saxon merged with modern Irish, British and Dutch genotype data. (b) Boxplot of PC1 broken down by subregion. The symbols on the left represent the significance of a Mann–Whitney test performed to compare the Roman population with all other populations in the data set. There were no significant differences between the Roman sample and the present-day Welsh, Northern and North Western English samples included in this analysis; all other regions had significantly different median values for PC1. Population key: Du, Dutch; En, English; Ir, Irish; NS, not significant; Sc, Scottish; Wa, Wales. NS-P>0.05; *0.05>P>0.01; **0.01>P>0.0001; ***P<0.0001.

Using the Dutch average as proxy for continental Germanics and the Welsh average for Romano-Britons, it would seem that modern English are on average, about 1/3 drifted towards Germanics, while the ancient Anglosaxon from Teesside was a bit more than half drifted in that direction. He was still within modern English variance, although rather towards the Germanic extreme of it.


Haploid lineages

The Iron Age sample was a woman with mtDNA haplogroup U2e1e.

The Romano-Brithons (all men), excluding the Eastern Mediterranean outlier, carried all variants of Y-DNA haplogroup R1b1a2a1-M412. It is notable that M405/U106 ("North Sea" subclade) was found in two of them, so it cannot be attributed to Germanic immigration. Another carried a sublineage of the M529 ("Irish") subclade (common also in Great Britain) and two others of the S28/U152 ("Alpine") sublineage (less common in Britain). The remaining two carried upstream L52* (generic "West European") paragroup lineages. See this entry for overall distribution details.

Their matrilineages were all subclades of H1, H2, H6 and J1. Details can be found in table 1

The outlier carried Y-DNA J2-L228 and mtDNA H5. The patrilineage fits well with a West Asian origin (an Italian one also fits) but the matrilineage is much more common in SE Europe, although it also reaches high frequencies in Wales. However the ADMIXTURE analysis strongly negates the possibility that he was European and very clearly supports a West Asian origin instead.

Finally the Anglo-Saxon man carried Y-DNA lineage I1 (most common in Sweden but scattered at low frequencies through Europe) and mtDNA H1.


Other details

The authors estimate that Iron Age and Romano-British samples were typically brunette with brown eyes. There is one exception though, 6DRIF-18, who was probably blond and blue-eyed, as was surely the Anglo-Saxon.

Blood type O was inferred for all Iron Age and Roman era samples, except 6DRIF-22 who was A. The Anglo-Saxon one may have carried type B or A (or AB?)

Evidence of human presence in the Arctic 45,000 years ago

Quickies

Pre- and post-mortem injuries in a mammoth carcass found at 72°N in the Yenisei River basin and a separate finding of a killed wolf of similar age indicate that some humans were hunting in the Far North, 10,000 years before any other evidence known before (Mousterian implements from Komi Republic, surely made by H. neanderthalensis).

My first hunch is that the authors of these killings were also Neanderthals of the same Arctic population as the one living in Komi Republic, across the Urals. Another possibility could be that they were related to Ust'-Ishim man, a H. sapiens specimen from c. 45 Ka BP from further south-west, in the Ob-Irtish rivers' basin or to people established in Altai, who belonged to various human species (H. heidelbergensis, neanderthalensis and sapiens), depending on period and specific site.

Vladimir V. Pitulko et al., Early human presence in the Arctic: Evidence from 45,000-year-old mammoth remains. Science 2016. Pay per viewLINK [doi:10.1126/science.aad0554]

Abstract

Archaeological evidence for human dispersal through northern Eurasia before 40,000 years ago is rare. In west Siberia, the northernmost find of that age is located at 57°N. Elsewhere, the earliest presence of humans in the Arctic is commonly thought to be circa 35,000 to 30,000 years before the present. A mammoth kill site in the central Siberian Arctic, dated to 45,000 years before the present, expands the populated area to almost 72°N. The advancement of mammoth hunting probably allowed people to survive and spread widely across northernmost Arctic Siberia.

January 21, 2016

New planet in the solar system

Description of the orbit of the new planet and associated objects (Batygin & Brown)
This kind of stuff does not happen every day: a new planet 10 times the mass of Earth has been inferred to exist in the outer reaches of the solar system, but has not yet been directly observed. Or has it?

Konstantin Batygin and Mike Brown have deduced (press release, study) the existence of this object from the trajectory of several anomalous transneptunian bodies of the type of Sedna, whose trajectories seem to orbit both the sun and a distant "super-earth" type planet, so remote that it takes 20,000 years to complete an orbit. 

The Caltech team has not directly eyed the object. However...

A Swedish-Mexican team led by R. Liseau pre-published last month a study where they claimed to have directly spotted a possible outer solar system planet. After some controversy the second version of the pre-pub was withdrawn until further data was collected but the first version is still available online. Another pre-pub paper on the same issue was also authored by W. Vlemmings et al., co-authors of the previous one. 

Direct observation of an object that might be a new planet (Liseau et al.)

I do not know yet if the two studies are convergent or rather they refer to different objects. Neither is fully confirmed as of now in any case but something is almost certainly out there lurking in the depths of the Oort cloud.

January 16, 2016

>100 Ka old tools found in Sulawesi

Quickies

Flake type tools dated to approx. 118,000 years ago have been found in Sulawesi (Indonesia). They imply that some species of human was making them but it is unclear which one. Homo floresiensis (alias The Hobbit) is maybe the first one that comes to mind but actually there are other possibilities: on one hand the significant H. heidelbergensis (alias Denisovan) admixture found in Australasian aboriginals would be consistent with its presence somewhere in SE Asia, Wallacea even, but another serious possibility is that they are in fact made by H. sapiens, whose presence in other parts of Asia soon after this date (or even before in the case of West Asia) is well known by now.

January 10, 2016

Goat domestication took place in the Zagros

Quickies

Genetic data seems to support the archaeological notion of domestication of the goat (also appliable to several other animals) in the Zagros mountains, roughly what we now call Kurdistan.

L. Colli, K. Lancioni et al., Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability. BMC Genomics 2015. Open accessLINK [doi:10.1186/s12864-015-2342-2]

Abstract

Background

The current extensive use of the domestic goat (Capra hircus) is the result of its medium size and high adaptability as multiple breeds. The extent to which its genetic variability was influenced by early domestication practices is largely unknown. A common standard by which to analyze maternally-inherited variability of livestock species is through complete sequencing of the entire mitogenome (mitochondrial DNA, mtDNA).

Results

We present the first extensive survey of goat mitogenomic variability based on 84 complete sequences selected from an initial collection of 758 samples that represent 60 different breeds of C. hircus, as well as its wild sister species, bezoar (Capra aegagrus) from Iran. Our phylogenetic analyses dated the most recent common ancestor of C. hircus to ~460,000 years (ka) ago and identified five distinctive domestic haplogroups (A, B1, C1a, D1 and G). More than 90 % of goats examined were in haplogroup A. These domestic lineages are predominantly nested within C. aegagrus branches, diverged concomitantly at the interface between the Epipaleolithic and early Neolithic periods, and underwent a dramatic expansion starting from ~12–10 ka ago.

Conclusions

Domestic goat mitogenomes descended from a small number of founding haplotypes that underwent domestication after surviving the last glacial maximum in the Near Eastern refuges. All modern haplotypes A probably descended from a single (or at most a few closely related) female C. aegagrus. Zooarchaelogical data indicate that domestication first occurred in Southeastern Anatolia. Goats accompanying the first Neolithic migration waves into the Mediterranean were already characterized by two ancestral A and C variants. The ancient separation of the C branch (~130 ka ago) suggests a genetically distinct population that could have been involved in a second event of domestication. The novel diagnostic mutational motifs defined here, which distinguish wild and domestic haplogroups, could be used to understand phylogenetic relationships among modern breeds and ancient remains and to evaluate whether selection differentially affected mitochondrial genome variants during the development of economically important breeds.


Fig. 4
Spatial frequency distributions of goat mtDNA haplogroups in different geographic areas based on different datasets: modern breeds (C. hircus) a ; wild goats (C. aegagrus) b; and ancient goat remains c. See Additional file 2 (Table S5) for more information


Notice that the term "Southeastern Anatolia" is clearly being used in the Turkish imperialist ideological frame and actually must be read as Northern Kurdistan, not at all in the Anatolian Peninsula but rather Upper Mesopotamia.

January 9, 2016

Good documentaries on human Prehistory

I just watched the documentary "First Peoples - Asia" (by NOVA) and found it quite good, discussing many of the issues that I and the readers of this blog have been following and discussing the last years on the settling of Asia (and geographical dependencies): the Zhirendong jaw, the Nubian points of Arabia, the archaic admixture events... 

The only issue is that for some odd reason (copyright masking?) interviewed people voices often have a too high pitch.

I hope the other four documentaries of the series are similarly good. I haven't watched them yet but the full playlist is embedded below beginning with the Asian colonization movie. For many readers it won't be that interesting personally (they already know all or most of it, maybe even better than what the movie explains) but it is still a promising tool to share your hobby with family and friends, so watch it in good company. 

Enjoy!





Update (Jan 9):

I've watched already four of them (Africa, Asia, Australia and Europe) and the European one is no doubt the worst: a superficial Neanderthal hybridization neo-myth spearheaded by John Hawks. Also the only map or description of the route followed by modern humans to Europe is absolute nonsense: directly from Africa via Palestine, when in fact it's extremely clear that at least most of the lineages went all the way to SE Asia and back before ever entering Europe. What happened to the spear in the rib of Zawi Chemi Shanidar man? What happened to the very fast replacement in the early Aurignacian, coincident with the Campanian Ignimbrite eruption? What about dogs? Not a word! Just whitewashing of the probably quite violent Sapiens-Neanderthal interaction. You can skip that one, really, it's pretty much nonsense.

Some hyper-hybridationism permeates all the documentaries but the others seem much better: the Asia one is quite good, the Africa one is not bad either (although could be much better if they paid more attention to archaeology, also Africa deserves 50% of the documentary space probably), the Australia one is OK but it simply ignores Papua and Wallacea altogether, what is a bit perplexing to say the least. The Europe one is just horrible: it has some facts but half of it its John Hawks' preaching his particular ideology about people being oh-so-nice that they probably used spears as toothpicks, Paabo making a lot of extra work for the cleaning crew (spectacular admittedly but should be in a separate Neanderthal docu, not in one dedicated to H. sapiens) and some real archaeology scattered around (but definitely not enough at all).