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.

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 access → LINK [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 view → LINK [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.

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.

>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.

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 access → LINK [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.

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).

Alert Iruña-Veleia: quite apparent new destruction of archaeological evidence

Tonight I got a most undesirable alert: the controversial archaeological site of Iruña-Veleia, has been again excavated with heavy machinery, with the very possible intent of destroying key evidence.

For background see here, here, here, here, here and here.

The area affected by the destructive excavation by the partisan director Julio Núñez is exactly within the bounds of the exceptional graffiti findings area that triggered all the controversy (conservative linguists and historians didn't like what was found, as it challenged their "theories", so they organized an Inquisition of sorts to condemn, hide and even destroy the evidence). The following map published at Ama Ata, shows the original situation of the ancient house upon the intervention by the institutions:

In red: the area of exceptional findings (texts)

Judging on J.M. Elexpuru's photos, the whole sector has been dug and then recovered with new earth, what is totally not what archaeologists usually do, much less with such a hurry:

The visual survey of the discard pile shows at least one piece of sigilata pottery and a broken millstone, as well as a common fossil. This is surely just the tip of the iceberg, as nobody by the perpetrators know where the rest of the materials extracted went and what they may have included.

The most likely motivation for this excavation is the throughout destruction of archaeological material, which is potential evidence in the languishing judiciary case against the previous archaeological team, based on nothing but made-up accusations. Not a single piece of actual evidence has been put against them, while their right to defense has been infringed once and again, with pitiful, if not crony, actuations on the side of all involved institutions: a powerless judge, police lab that wash their hands, governments that act in the hiding, manipulating evidence while reporting to no one, researchers that produce junk reports, and then this replacement "archaeologist" who took part in the inquisitorial "expert commission".

Dozens of studies support the authenticity of the findings precisely in this spot, now under destruction. Not a single paper other than those created ad hoc (and belatedly) for the inquisitorial commission, most of them linguists' opinions with zero probatory weight, support the hypothesis of falsehood. However an institutional conspiracy seems determined to do their worst, after all who cares about ancient archaeology and historical truth? Not the masses obviously.

Main responsible persons (currently), according to Euskararen Jatorria.
Left: Department of Archaeology (EHU-UPV), middle: Regional Government of Araba, right: top directors of EHU-UPV.

To the list above we must add all those who took part or impelled the inquisitorial commission, notably linguists Joseba Lakarra and Joaquín Gorrochategui and the former Deputy of Culture Lorena López de Lacalle, whose continuous presence (along with her Opus Dei patron R. Larreina and her sister) in the recent electoral lists of supposedly leftist and pro-transparency EH Bildu coalition is most worrisome. 

More details in the blogs linked in-text (Spanish and Basque languages).

Irish ancient DNA

This study was published just a few days ago but is already from the previous year, tricks of the calendar. It is a scheme-breaker in several aspects, so I hope to be able to reflect here the most important aspects of it.

Lara M. Cassidy, Rui Martiniano et al., Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome. PNAS 2015. Freely accessible → LINK [doi: 10.1073/pnas.1518445113]

Abstract

The Neolithic and Bronze Age transitions were profound cultural shifts catalyzed in parts of Europe by migrations, first of early farmers from the Near East and then Bronze Age herders from the Pontic Steppe. However, a decades-long, unresolved controversy is whether population change or cultural adoption occurred at the Atlantic edge, within the British Isles. We address this issue by using the first whole genome data from prehistoric Irish individuals. A Neolithic woman (3343–3020 cal BC) from a megalithic burial (10.3× coverage) possessed a genome of predominantly Near Eastern origin. She had some hunter–gatherer ancestry but belonged to a population of large effective size, suggesting a substantial influx of early farmers to the island. Three Bronze Age individuals from Rathlin Island (2026–1534 cal BC), including one high coverage (10.5×) genome, showed substantial Steppe genetic heritage indicating that the European population upheavals of the third millennium manifested all of the way from southern Siberia to the western ocean. This turnover invites the possibility of accompanying introduction of Indo-European, perhaps early Celtic, language. Irish Bronze Age haplotypic similarity is strongest within modern Irish, Scottish, and Welsh populations, and several important genetic variants that today show maximal or very high frequencies in Ireland appear at this horizon. These include those coding for lactase persistence, blue eye color, Y chromosome R1b haplotypes, and the hemochromatosis C282Y allele; to our knowledge, the first detection of a known Mendelian disease variant in prehistory. These findings together suggest the establishment of central attributes of the Irish genome 4,000 y ago.

The two sample sites are from North Ireland, being the so-called Neolithic one from the interior (Co. Down, c. 3200 BCE) and the so-called Bronze Age ones are from a small island (Rathlin) north of the main island (Rathlin 1 and 2 from c. 1900 BCE, Rathlin 3 from c. 1600 BCE). 

I say "so-called" because I'm not really confident that the terms "Neolithic" and "Bronze Age" apply in fact to most of them (I'd rather use Chalcolithic, shorthand for "advanced Neolithic with social complexity, regardless of metals", for all but Rathlin 3). I think in any case that the divider here is not metallurgy as such but actually the Bell Beaker divide: before and after Bell Beaker.

Bell Beaker is becoming a key element to our understanding of the demographic changes in Northern Europe, more than I would have expected admittedly. In the case of Ireland (and to a lesser extent parts of Britain) the arrival of the Bell Beaker phenomenon is accompanied with striking demographic growth, which may (or not) imply new settlement from outside. For Ireland, it seems growingly clear now, it probably does, unless Rathlin is a very unusual site, what is not parsimonious as we will see. 

Enough with the intro, let's get to the substance.

 

Haploid genetics

Ballanyhatty (Co. Down), a woman, carried the mitochondrial haplogroup (matrilineage) HV0. Rathlin 1 carried U5a1b1e, Rathlin 2 U5b2a2 and Rathlin 3 carried J2b1a. The only thing remarkable here is the lack of haplogroup H, the most common one in Europe today and detected since the Magdalenian era in Iberia, but more commonly later on within Neolithic. It can be a fluke of course but the shallow impression is that the mtDNA pool is "pre-modern". However all the rest is very "modern" in Rathlin Island, so... let's assume it's a mere fluke.

The three Rathlin individuals are all men, and their Y-DNA haplogroup has been successfully sequenced: they all belong to R1b-M529, the most common patrilineage in Ireland (and much of Britain and also Brittany) to this day. There's some hints that some of them could belong to downstream subhaplogroups but, if you read the fine print (the supp. materials) this is quite unclear, so let's leave it at this. 

R1b-S116 structure per Valverde 2015

The implications of this data point are important: it clearly defines a terminus ante quem for all possible R1b-M529 and upstream haplogroups' chronologies. Whoever defended a shorter chronology was clearly wrong. Together with a German Bell Beaker individual, these are the oldest R1b-S116 known so far, what is hardly surprising considering the huge blank in aDNA sampling in Western Europe but also suggests that, at least in some areas, Bell Beaker was implicated in the expansion of this most important European patrilineage and in general in the formation of modern-like Western European populations.

There are many open questions here yet because we lack ancient DNA data from France, West Germany, Belgium, Britain, much of Iberia, etcetera. But, with these new data points, I am beginning to believe that Bell Beaker was, if not a general cause, at least a key pivot around which these demographic changes leading to modern populations took place. It was probably a cause in Ireland but it's truly hard to extrapolate to other regions, where aDNA information is missing and archaeological one suggests different patterns of change or continuity. 

Autosomal DNA

The most striking implication of the autosomal DNA of these two Irish sites is that Rathlin men are almost identical to modern Irish (also Scots, Welsh and Cornish), while the much older Ballanyhatty woman is only slightly similar to modern Irish (and Scots), being much more like Sardinians and some South Iberians (what is congruent with what happens to all other Neolithic samples through much of Europe). 

Selection from fig. 3

So we are before a clear-cut demographic change in Ireland (and maybe other regions) at some point in the third millennium BCE. The most plausible date for the beginning of this change is probably around 2500 BCE, when we see the start of significant demographic growth in Ireland and is also the approx. date for Bell Beaker arrival to the island and other parts of Northern Europe (several centuries older in the South however).

Putting these samples in the wider context the authors get this:

Fig. 1. Genetic affinities of ancient Irish individuals. (A and B) Genotypes from 82 ancient samples are projected onto the first two principal components defined by a set of 354,212 SNPs from Eurasian populations in the Human Origins dataset (29) (SI Appendix, Section S9.1 and S10). (A) This PCA projects ancient Eurasian Hunter–Gatherers and Neolithic Farmers, where they separate clearly into Early Neolithic, MN (including the Irish Ballynahatty genome), and several hunter–gatherer groups. (B) PCA projection of Late Neolithic, Copper, and Bronze Age individuals where the three Rathlin genomes adopt a central position within a large clustering of European Bronze Age individuals. (C) A plot of ADMIXTURE ancestry components (K = 11) of these same ancient genomes. In West and Central Europe, ancient individuals are composed almost entirely of two dominant strands of ancestry, linked to hunter–gatherer (red) and early farmer (orange) populations, until the Late Neolithic. At this point, a third (green) Caucasus component features. Previously, this component was only seen in ancient Steppe and Siberian populations such as the Yamnaya. The three Rathlin genomes each display this Caucasus strand of ancestry whereas the Irish Neolithic does not.

Sure: a key element here is the "teal" Caucasus-related component, which is a tell-tale signature of the Indoeuropean or Kurgan expansion into Europe. As exercise to get a rough estimate of how much Indoeuropean (Yamna-like) ancestry there is in each sample, I propose you to get a ruler and a calculator, measure it for each sample and find the resulting fraction. You can also do the same for the early Neolithic (EEF) ancestry, using the "orange" component. There is an interesting substantial leftover fraction that can only be extra "hunter-gatherer" (HG), wherever it comes from. 

My own estimates are as follows:

• Late Neolithic (LN) samples: 80% EEF + 20% extra HG.
• German LN (early Kurgans) = 23% IE + 40% EEF + 37% HG → 27% extra HG relative to LN
• Corded Ware = 64% IE + 21% EEF + 15 HG → 10% extra HG rel. to LN
• Elbe Bell Beaker (avg.) = 13% IE + 44% EEF + 43% HG} → 32% extra HG rel. to LN
• Irish BA = 25% IE + 34% EEF + 41% HG} → 32% extra HG rel. to LN

There is some data in the supp. materials (S12.2.2) which is roughly consistent with this, although their fraction of extra HG (using Lochsbour as reference) is smaller than mine, while their Yamna or IE one is larger instead (no idea why this lesser contradiction, honestly, although they almost overlap once we include error margins). 

Where does this extra HG fraction comes from? It is quite apparent that the currently available samples do not include its source. As I have mentioned many times, there is a huge "Atlantic" blank in the autosomal samples, including nearly all France and many areas around it: Switzerland, West Germany, Low Countries, Britain and about 3/4 of the Iberian Peninsula. 

In this study however we get a hint in the supp. materials: KO1, an Epi-Magdalenian sample from Hungary, stands out like a sore thumb in the f3 analyses of all three Rathlin samples:

Figure S12.1. Outgroup f3-Statistics for each ancient Irish Individual. Tests in the form f3(Mbuti; IA, X), where IA is an Irish ancient genome and X is any other ancient individual or population. Data points are coloured by archaeological context.

Obviously the origin of the extra HG cannot be KO1 as such but there must be one or several populations, as of yet unsampled, in which this extra HG (most akin to KO1) was notorious. My best candidates as of now are the following cultures:

• Michelsberg, which replaced LBK in most of Germany, North France, Belgium, Switzerland, etc. prior to the Corded Ware shockwave. It's part of the wider Funnelbeaker and Megalithic phenomena and one of the ancient cultures I really want to see sampled in some depth. 
• Artenac, which replaced previous layers in all West France and Belgium and is part of the wider Megalithic and Bell Beaker phenomena. It originated around Dordogne and is usually considered proto-Aquitanian, i.e. proto-Basque.
• The major civilization of Zambujal or Vila Nova de Sao Pedro in Portuguese Estremadura, which was a key pivot in the Megalithic and particularly the Bell Beaker phenomenon.

And in general I'd complement these with samples from all the Atlantic facade of Europe, including Britain, the Basque Country (a lot was going on in the Chalcolithic here in spite of the small size), West France, Belgium, the Rhône valley and Switzerland, etc. If we'd have data points for all these areas in the Chalcolithic period, we'd surely have a much more clear picture of what was going on in Europe in this critical period of demographic change. Definitely it's not just Corded Ware and the Elbe basin can only give us so much information anyhow. 

This is also important regarding the origins and spread of R1b-S116 and its "brother" haplogroup U106, no kidding. Let's sample the West, it's about time.

Caucasus and Swiss hunter-gatherer genomes

I know I'm late for the party but better late than never, right?

A recent study sequenced three hunter-gatherer genomes from Georgia and one from Switzerland, expanding our understanding of the pre-Neolithic genetic landscape of West Eurasia.

Eppie R. Jones et al., Upper Palaeolithic genomes reveal deep roots of modern Eurasians. Nature Communications 2015. Open access → LINK [doi:10.1038/ncomms9912]

Abstract

We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic–Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ~45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ~25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe ~3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.

Figure 1: Genetic structure of ancient Europe.

 (a). Principal component analysis. Ancient data from Bichon, Kotias and Satsurblia genomes were projected¹¹ onto the first two principal components defined by selected Eurasians from the Human Origins data set¹. The percentage of variance explained by each component accompanies the titles of the axes. For context we included data from published Eurasian ancient genomes sampled from the Late Pleistocene and Holocene where at least 200 000 SNPs were called^{1, 2, 3, 4, 5, 6, 7, 9} (Supplementary Table 1). Among ancients, the early farmer and western hunter-gatherer (including Bichon) clusters are clearly identifiable, and the influence of ancient north Eurasians is discernible in the separation of eastern hunter-gatherers and the Upper Palaeolithic Siberian sample MA1. The two Caucasus hunter-gatherers occupy a distinct region of the plot suggesting a Eurasian lineage distinct from previously described ancestral components. The Yamnaya are located in an intermediate position between CHG and EHG. (b). ADMIXTURE ancestry components¹² for ancient genomes (K=17) showing a CHG component (Kotias, Satsurblia) which also segregates in in the Yamnaya and later European populations.

The Swiss one (Bichon, Jura) is maybe less of a novelty, roughly falling within the already known parameters for Western European hunter-gatherers of Magdalenian tradition (WHG in the jargon) but the three samples from the Caucasus (CHG) are really a much needed new data-point, different from everything else that what we knew and surprisingly close to modern Caucasus populations. 

They are however very distant from all other known ancient West Eurasian samples. Fig. 2 shows an estimated divergence with early Neolithic Europeans (EEF, Stuttgart) dating from before the Last Glacial Maximum, to 24,000 years ago. The divergence of this composite West Asian macro-population (EEF's Paleoeuropean admixture is accounted for separately) with the pre-Neolithic Europeans seems to be of c. 46,000 years, what is consistent with early Upper Paleolithic (the large error margin allows for a secondary Gravettian genesis contact anyhow). On the other hand the divergence between Bichon and Lochsbour seems to fit with the Magdalenian time-frame as one would expect.

CHG are surprisingly close to modern Caucasus population, particularly to Georgians. CHG also appear to be an excellent candidate population for the formation of the early Indoeuropean Yamna people, which fit best as a mix of CHG and EHG (Eastern European hunter-gatherers). 

Figure 4: The relationship of Caucasus hunter-gatherers to modern populations.

a). Genomic affinity of modern populations¹ to Kotias, quantified by the outgroup f₃-statistics of the form f₃(Kotias, modern population; Yoruba). Kotias shares the most genetic drift with populations from the Caucasus with high values also found for northern Europe and central Asia. (b). Sources of admixture into modern populations: semicircles indicate those that provide the most negative outgroup f₃ statistic for that population. Populations for which a significantly negative statistic could not be determined are marked in white. Populations for which the ancient Caucasus genomes are best ancestral approximations include those of the Southern Caucasus and interestingly, South and Central Asia. Western Europe tends to be a mix of early farmers and western/eastern hunter-gatherers while Middle Eastern genomes are described as a mix of early farmers and Africans.

I find notable that the CHG component (do not confuse with the African one of similar color) is still apparent in the Indian subcontinent, something that was already detected in other analyses. The CHG component seems to be the core of the so called "ancient North Indian" (ANI) component, also known as "Gedrosian" or "Caucaso-Baloch". What they call in the above analysis "South Asian" would be approximately the also known as "ancient South Indian" (ASI) component, which is presumably pre-Neolithic. 

"Farmer" means European Early Farmer (EEF) and already implies some Paleolithic European admixture, until we have some Levant and Mesopotamian genuine first Neolithic samples, we should not assume that all the Fertile Crescent Neolithic people were just like that, although some may have been close. In fact, I tend to think that the CHG or a similar "highlander" component was probably important in the Zagros Neolithic and consequently in the Mesopotamian and Iranian one, reaching eventually to South Asia. See here for more details on how the Neolithic expansion in Europe and India were largely parallel but not identical at all in source populations. 

To illustrate this early Neolithic complexity, still apparent to some extent in West Asian genetics and, as I just said, in European and South Asian ones, the following archaeo-cultural map should help:

Source: Eleni Asouti 2006 (red color annotation is mine)

I strongly recommend to read the full source study, because it is very informative about what were some of our ancestors¹ doing when farming and herding were being developed in West Asia, but the map above alone gives a very good glimpse of the ethno-cultural complexity of these ancient West Asian populations. 

My understading is that the mainline (Thessalian or Aegean) European Neolithic founders must have originated within the PPNA/B complex, although uncertain about which specific culture within it (most likely not Harifian because that one is surely at the origin of Semitic languages but almost any other one would do, notably those close to the Mediterranean coast: Sultanian, Aswadian and Mureybetian). Instead the populations affecting Eastern European, Mesopotamian-Iranian (Sumer and Elam) and Indian Neolithic are most probably rather linked to what is here called as M'lafatian or Zagros Neolithic, which in turn were most likely linked one way or the other to Caucasus hunter-gatherers and in general to the "highlander" West Asian element apparent in other studies in contrast to a more EEF-like "lowlander" one. 

________________________________________

¹ Sure: I'm thinking mostly of Euro-Mediterranean and Central-South Asian peoples but even if you are East Asian or Tropical African it's still very probable that some random ancestor comes from this crucial paleo-historical knot (or almost from anywhere else: admixture never ends and we are all related, even if thinly, within the last millennium or so).

Basque R1b-DF27

Jean sent me a copy of this study (many weeks ago, admittedly), which is an update on the maybe more interesting previous paper by the same UPV-EHU team of June 2015, discussed in this entry.

Patricia Villaescusa et al., Dissection of the DF27 paternal lineage. FSI Genetics 2015. Freely accessible → LINK [doi: http://dx.doi.org/10.1016/j.fsigss.2015.09.172]

Abstract

The genetic evidence provided by the analysis of the Y chromosome is a valuable tool for the study of the evolution of paternal lineages. The dissection of S116, the major M269 subhaplogroup in Western and South-Western Europe uncovered an outstanding frequency of DF27 sublineage in the Basque region. In this study, a dissection of DF27 haplogroup was performed to the highest resolution to date in 340 individuals from the Basque Country. Our results describe frequency distribution patterns for some DF27 sublineages for the first time, and reveal a possible substructure of its paragroups.

And that's basically what it is. They found that Basque R1b-DF27 (70%) mostly belong to two categories: DF27* (31%) and S356 (28%), which are neatly distinct in the neighbor-joining haplotype structure, suggesting to the authors that the remaining DF27* may constitute a yet undescribed subhaplogroup.

Fig. 1. MJN of the DF27 haplogroup in the autochthonous Basque population sample. Two phylogenetic splits into DF27* and S356* paragroups can be observed.

Table 1 lists the frequencies in their Basque sample for a variety of markers under DF27, which includes 70% of Basque Y-DNA lineages. However there's also a significant fraction of R1b-S116* which they only mention by passing:

The high frequencies of DF27* and S116* paragroups indicate a probable existence of new subhaplogroups supporting the subdivision of both of them.

To understand this we have to go back to Valverde 2015, which detected high frequencies of paragroup R1b-S116* among Basques and Irish (but not other Iberians nor Bretons). There is a blank of knowledge about the exact details of R1b-S116 in France but otherwise we have a pretty good idea of the phylogenetic and geographic structure (what I call the "geostructure") of this most important European patrilineage. 

I won't repeat everything (please check the provided link and other links stemming from there for full details) but I will again synthesize what it means here because there is still some people who seems oblivious to factual reality about this haplogroup. An image is worth a thousand words:

My reconstruction of the origins of R1b-S116 based on known 'geostructure'

The three ovals represent very generically the distribution of the three major subclades of R1b-S116 (check the Valverde 2015 maps for full details), the two green stars represent confirmed areas of high R1b-S116* frequencies and the pale green star with the question mark represent possible other such areas in France, particularly an unconfirmed (unsourced) claim on this paragroup being very important at the Massif Central. If you know something more on this fine detail of R1b-S116 in France (or other relevant areas such as Britain, Germany), please share (with references). 

It has been recently known that some Bell Beaker period Irish already carried R1b-M529, what forces the origins of the overall S116 haplogroup to an older date necessarily, at the very least Early Chalcolithic, more likely Neolithic. I'll discuss those findings in an upcoming entry.

Personally I'm tempted for a Dordogne or Greater Aquitaine area of origin, i.e. rather to the West than to the East of the pink delimited region, but cannot be sure with the data we have as of now, particularly the many blanks in France's coverage. 

The claims about this major European lineage being original from Central Europe or even Eastern Europe are totally inconsistent with the data we have: they are nothing but wishful Indoeuropeanist thinking and totally within the realm of pseudoscience.

Happy new Roman year

Yeah, for some odd reason Romans were the ones to establish that the year began in a day like today, minor calendar corrections excepted. I still don't understand why the year "begins" in winter rather than in spring but that's how things are customarily. So happy new year to all. 

My goal for the new year is to get this blog back into activity, doing the most important work I left "to do" in the past two months. With a bit of luck and patience I may be able to do that today. If I wait, most likely it'll happen as with all other new year commitments: that it's left for the next year and so on, and so on...

So my goal is to do my new year commitment in a single day. Cross fingers, take deep breath, go!