May 4, 2016

Large Paleoeuropean DNA survey

An unprecedented survey of ancient DNA from Paleolithic Europe has been just published:

Qiaomei Fu et al., The genetic history of Ice Age Europe. Nature 2016. Pay per viewLINK [doi:10.1038/nature17993]

The supplemental materials (PDF) are freely accessible, as are the figures and tables (HTML). 

Quick highlights:
  1. Oldest Y-DNA R1b1 (and therefore R1b and R1) ever documented (Villabruna, Veneto, 14 Ka ago, Epigravettian cultural context). Also more Japan and La Braña related C1!
  2. Oldest mitochondrial DNA H (H7) may be in Gravettian Moravia, also oldest U6 may not be in Iberia or North Africa but in Gravettian Romania.
  3. Very important insights in autosomal DNA: a distinct Paleoeuropean population since Gravettian, two different late UP/Epipaleolithic populations. 
  4. Still very important gaps, notably SW France (the core of Paleolithic Europe) and most of Iberia. Also still missing West Asian sequences altogether, except for the rather anomalous Caucasus population and whatever may be inferred from Early European Farmers, whose ancestry was mostly (aprox. 3/4) West Asian.

A good synthesis of the scope and some of the findings of this study is in fig. 1:

(click to expand)


Y-DNA

The survey confirms (supp. materials 4) that haplogroup I used to be the most common patrilineage in Paleolithic Europe. But it was not the only one:

The oldest ones (pre-Villabruna, c. 14 Ka BP) were largely C1:
  • Kostenki 14 (Russia, Gravettian): C1b
  • Goyet Q116-1 (France, Aurignacian): C1a
  • Vestonice 16 (Moravia, Gravettian): C1a2
Also in this oldest group (arbitrarily defined as pre-Villabruna), there was some I* or maybe pre-I (some markers are missing in many individuals), including: Pavlov 1 (Gravettian, Moravia), Paglicci 133 (Gravettian, South Italy), Hohle Fels 49 (Magdalenian, Swabia), Goyet Q2 (Magdalenian, France) and Bukhardtshohle (Magdalenian, Swabia). Notice that its prevalence and clarity as "I proper" increases after the LGM; the Gravettian ones seem to be pre-I rather than true I.

Other oldest lineages are BT* (Vestonice 15), CT* (Ciclovina 1, Kostenki 12, Vestonice 13), F* (Vestonice 43). Notice that in most cases not all the ideal SNP testing was performed, so it is still possible and even probable, I'd think, that BT* and CT* are actually F*.

In the more recent "post-Villabruna" group:

The revelation of the group is of course Villabruna, which carried R1b1

There are also two I* (Cuiry Les Chardaudres 1 and Berry Au Bac), one I2 (Rochedane) and one F* (Falkenstein).

I must also mention that previous studies found mostly I2 in Epipaleolithic samples, excepted La Braña, which carried C* (maybe some sort of C1 but unconfirmed). R1a1* was found in Karelia as well.

Synthesis: I and R1b1, the most common lineages of Europe West of the Elbe, only show up after the Last Glacial Maximum, at least as far as we know. I probably coalesced in the subcontinent, the issue of where R1b, the most common modern patrlineage of Western Europe, coalesced and how it expanded remains open but the Villabruna data point defines a terminus ante quem for this haplogroup, which MUST be older than 14,000 years necessarily, discarding some of the most outrageous recentist chronologies altogether. The great initial diversity of CT-derived lineages suffered bottlenecks with the LGM and probably also later, pruning most of them (although rare instances of some of those lines such as F* or C1 are still found among modern Europeans).


Mitochondrial DNA

Lots of interesting stuff in this issue of the matrilineages, but also some strange issues in the data that do raise eyebrows quite a bit. The full dataset is in the supplemental materials section 2. 

However they do not provide clear data on how the tests were performed, just a generic listing. This is very problematic, notably when they state that El Mirón is U5b, when Hervella (with more clear methodology) classified her as H just a year ago. Another similar issue is the apparent H7 (H7a1?) in Vestonice 14, which is first classified as "damaged" (based apparently on X-chr contamination, the CI for H7 is 0.9-1) and then listed as "U" in the extended table 1, with no reasoning whatsoever for the change. 

Rumor is already around about a mysterious H-hater "black hand" being at play here. I can't neither confirm nor reject it but I do think that the authors should explain themselves more clearly on this most important matter, which is beginning to be more than just annoying, fueling conspiracy theories and what-not.

Another interesting issue is a possible U6 in Muierii (Gravettian Romania, CI 0.88-0.97), labeled as "damaged" again and refurbished as mere amorphous "U". This is a very important issue and is directly related with the presence of mtDNA H in Paleolithic Europe and the origin of these lineages in North Africa. 

Northwestern Africa (not counting Cyrenaica) did not experience any sort of Upper Paleolithic (UP) until c. 22 Ka BP, when a new culture of very likely Iberian Solutrean affinity, the Iberomaurusian or Oranian expanded from Taforalt (Arif, North Morocco). In my understanding this is the most likely origin of mtDNA H (H*, H1, H3, H4 and H7) in North Africa and maybe also of mtDNA V, and also should be related to the bicontinental distribution of mtDNA U6 (in North Africa but also and quite diversely in Iberia) and the surely related distribution of Y-DNA E1b-M81. 

While it's easy to imagine mtDNA H (and maybe also V) migrating from Europe to North Africa in this context, less clear has been so far the issue of U6 origins: as U-derived lineage it must ultimately derive from the early UP populations of West Asia but then again the first UP in the region must have arrived from SW Europe in the Last Glacial Maximum (LGM) period. So something I've been wondering all this time, particularly since the crucial, rare and basal, U6c lineage was discovered to exist not just in Morocco but also in Andalusia, is if U6 actually arrived to NW Africa from Europe and not, as is often assumed, vice-versa. 

So you will understand how this issue of properly identifying ancient mtDNA H and U6 lineages is important not only for the understanding of the roots of Europeans but also for those of North Africans. There are interests at play here because many geneticists have made a personal issue of "molecular clock" age estimates (whose actual scientific, empirical, value is often close to zero but are "sold" as "scientific" instead) and also of exaggerating the West Asian Neolithic influence in Europe beyond reason, leading to true quasi-ideological "DNA wars" that are totally out of place. 

Please, let's be serious: there is no room for childish games on these matters, you guys and gals are grown ups with a PhD!

Otherwise a lot of U (as usual: U*, U5, U2), notable is U8c (CI 0.91-1 but declared "damaged" in spite of extremely low X-chr contamination), which, if confirmed, could offer clues about the origins of the rare Italo-Jordanian U8c (and indirectly about Basque U8a and the quite common but surely Neolithic haplogroup K). Also discarded are several samples that initially produced lineages under macro-haplogroup M, however Goyet Q116-1 was labeled as "pass" with this lineage. So there is Paleoeuropean M, or at least there was once upon a time, this one beyond any doubt.


Autosomal DNA

This last part is most interesting as well. As you can see in the figure 1 above, the authors described three Paleoeuropean clusters: blue (aka Vestonice), green (aka El Mirón, however El Mirón is actually green-red admixed) and red (aka Villabruna, equivalent to the WHG grouping seen in some recent studies). Black-marked samples are out of any group and the Siberian (Mal'ta) and Caucasus (Satsurbilia) clusters are not too relevant here. 

Annotated by me: in green approx. dates for reference, in gray approx. reconstruction of the ancestry of late Paleoeuropeans

First of all it is clear that all or most Paleoeuropeans form a unique macro-cluster (orange shaded) to the exclusion of the Mal'ta and Satsurbilia clusters and also of Early Neolithic Stuttgart (~3/4 West Asian). This macro-cluster is comparable in affinity to that of Han-Dai-Karitiana, so even the word "race" can be used. Some people have argued that "there was no Europe" back then, because the Bosporus was an isthmus, but from the genetic data it seems clear that Europe was more distinctive then than it is now, after the Neolithic massive admixture event that spanned from Europe to India with West Asian centrality. 

Then we see an older "Gravettian" or blue or Vestonice cluster, that is clearly pre-LGM and that does not include however peripheral Gravettians such as Mal'ta, Kostenki or Goyet Q53-1.

But the most interesting feature is that two different populations existed at the end of the Paleolithic period: the green one (El Mirón) is strictly Magdalenian and vanishes with the Epipaleolithic (at least for this sample, which has mayor gaps), instead the red one (Villabruna or WHG) was initially less common in Magdalenian and spans beyond its cultural borders into Epigravettian Italy too, however it becomes the only thing around in the Epipaleolithic, suggesting the expansion of a single population in that late period, maybe with the geometric microlithism which precedes in most areas the arrival of Neolithic and may well have expanded from France. 

Looking at the orange range of less obvious affinities, I tried to pinpoint tentative origins for those two populations. The green one relates best with GoyetQ116-1 (Aurignacian), while the red one does with GoyetQ53-1 (Gravettian). This is also somewhat apparent in the PCA and I tried to indicate it with the annotated arrows. 

Especial thanks for his insights to Jean Lohizun.

Back to work

My apologies to readers for being for so long in "lazy mode". Actually I got interrupted largely by a request to provide a quality article on Basque, Sardinian and European origins for a soon to be published collective book in Basque language. This took me a lot of time and energies in late March and early April, so basically I put everything else on hold. The last weeks I've been resting indeed, what may be aggravated by a declining health that makes me sleep irregularly and often for much longer than most of you do. Being fed up with Internet information feeds and a quite active political reality also drain my energies to other endeavors, not to mention paperwork.

In this sense I want to announce that I have begun recently a new multi-purpose blog in Spanish language: Bagauda. Most of it is politics, I warn you, but I have also included the unedited raw article for that book I mention in the previous paragraph (prior to translation to Basque and corrections). I'm reasonably sure that those of you who have Spanish as primary or even secondary language will be interested in having a look (→ here).

Another relevant entry was the announcement of the upcoming congress on Iruña-Veleia to be held on May 7 in Vitoria-Gasteiz. You can still register but hurry up.

I will now proceed to comment in a separate entry on the news of the week, the Fu et al. study of a large array of Paleoeuropean ancient DNA. But, before I get to that, I must mention some interesting studies that I have not been able to get time to even properly read, let alone discuss:

  • K. Voskarides, S. Mazières et al., Y-chromosome phylogeographic analysis of the Greek-Cypriot population reveals elements consistent with Neolithic and Bronze Age settlements. Investigative Genetics 2016. Open accessLINK [doi:10.1186/s13323-016-0032-8]
  • B. Vernot et al., Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals. Science 2016. Freely accessible (with registration?)LINK [doi:10.1126/science.aad9416]
  • Y.Y. Waldman, A. Biddanda et al., The Genetics of Bene Israel from India Reveals Both Substantial Jewish and Indian Ancestry. PLoS ONE 2016. Open access → LINK [doi: 10.1371/journal.pone.0152056]

Another intriguing new independent paper by a regular visitor and commenter to this blog, Olympus Mons, that I have not yet read is:

→ R1b from Sulaweri-Shomu to Bell Beaker, available as PDF or in blog format.

He seems to argue for a Caucasus origin of both the lineage and Bell Beaker phenomenon. I have no opinion as of yet, because, simply put, I have not been able to read it in full.

Another regular visitor here to have put an independent paper online, also on the issue of R1b origins, is Paul Conroy:

→ Anatole A. Klyosov and Paul M. Conroy, Origins of the Irish, Scottish, Welsh and English R1b-M222 population. Available at Paul's Academia.edu account.

Again I have not yet got the opportunity to read it, so no opinion. 

Feel free to use this entry to comment on any of the aforementioned studies or articles or to provide info about stuff I may have missed.

March 16, 2016

South Asian autosomal structure

A recent study finds "five" components, although in practice they can be reduced to three.

Analabha Basu et al., Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structure. PNAS 2015. Freely accessibleLINK [doi: 10.1073/pnas.1513197113]

Abstract

India, occupying the center stage of Paleolithic and Neolithic migrations, has been underrepresented in genome-wide studies of variation. Systematic analysis of genome-wide data, using multiple robust statistical methods, on (i) 367 unrelated individuals drawn from 18 mainland and 2 island (Andaman and Nicobar Islands) populations selected to represent geographic, linguistic, and ethnic diversities, and (ii) individuals from populations represented in the Human Genome Diversity Panel (HGDP), reveal four major ancestries in mainland India. This contrasts with an earlier inference of two ancestries based on limited population sampling. A distinct ancestry of the populations of Andaman archipelago was identified and found to be coancestral to Oceanic populations. Analysis of ancestral haplotype blocks revealed that extant mainland populations (i) admixed widely irrespective of ancestry, although admixtures between populations was not always symmetric, and (ii) this practice was rapidly replaced by endogamy about 70 generations ago, among upper castes and Indo-European speakers predominantly. This estimated time coincides with the historical period of formulation and adoption of sociocultural norms restricting intermarriage in large social strata. A similar replacement observed among tribal populations was temporally less uniform.


One of the components, very distant from the rest, is the Andamanese one (Jarawa, Onge), but the isolated islands are not really in South Asia, rather in SE Asia (south of Myanmar, belonging to India only because of historical accident), what reduces the structure of South Asia to what we can see in the following graph:


Fig. 2.
(A) Scatterplot of 331 individuals from 18 mainland Indian populations by the first two PCs extracted from genome-wide genotype data. Four distinct clines and clusters were noted; these are encircled using four colors. (B) Estimates of ancestral components of 331 individuals from 18 mainland Indian populations. A model with four ancestral components (K = 4) was the most parsimonious to explain the variation and similarities of the genome-wide genotype data on the 331 individuals. Each individual is represented by a vertical line partitioned into colored segments whose lengths are proportional to the contributions of the ancestral components to the genome of the individual. Population labels were added only after each individual’s ancestry had been estimated. We have used green and red to represent ANI and ASI ancestries; and cyan and blue with the inferred AAA and ATB ancestries. These colors correspond to the colors used to encircle clusters of individuals in A. (Also see SI Appendix, Figs. S2 and S3.)

It is quite apparent that the AAA (Ancient Austroasiatic) component behaves as the ASI (Ancient South Indian) one but with a tendency towards the ATB (Ancient Tibeto-Burman) one, strongly suggesting it is basically product of admixture and not a truly autonomous ancestral component. 

This may be more apparent in the wider pan-Asian context:

Fig. 3.
Approximate “mirroring” of genes and geography. Genomic variation of individuals, represented by the first two PCs, sampled from 18 mainland Indians combined with the CS-Asians) and E-Asians from HGDP, compared with the map of the Indian subcontinent showing the approximate locations from which the individuals and populations were sampled.

In this wider mapping (would be even more clear if West Asian populations were included), we see that:
  1. ANI (Ancient North Indian) strongly tends to the West. In other analyses it is very similar to the Caucasus modal component and therefore a logical conclusion is that we are before a Neolithic immigrant element, much as happens in Europe.
  2. ATB (Ancient Tibeto-Burman) strongly tends to the East, more specifically SE Asia, and is therefore the reverse to ANI, although much less influential.
  3. ASI (Ancient South Indian) is the true aboriginal (pre-Neolithic) component of India, better preserved in southern populations but more clinal than the sample choice allows us to perceive.
  4. AAA (Ancient Austroasiatic) is very similar to ASI but has some SE Asian admixture, as is logical to expect, being Austroasiatic a SE Asian language of likely Neolithic expansiveness. 
So ASI and AAA are basically the same thing and that's why I say that the "five" components can be simplified to just three. Said that, it is indeed possible that there is underlying complexity within the ASI+AAA component but this study does not help us to clarify that. 

It is true that the K=4 (after exclusion of Andamanese, K=5 with them) fits the parsimony criterion best but the K=3 is also a good fit and shows AAA exactly as I describe them: largely ASI ("aboriginal") with a significant ATB (Eastern) component. The AAA component can therefore be perceived as consolidated, homogenized, ancient admixture. Prove me wrong on this and I'll eat my words. 


Caste apartheid stopped genetic flow

Quite interestingly, the authors also dwell on how the admixture process was stopped by the Gupta laws (Middle Ages) that imposed apartheid (caste system) enforced endogamy and caused the now apparent genetic isolation of the multiple groups.

We have provided evidence that gene flow ended abruptly with the defining imposition of some social values and norms. The reign of the ardent Hindu Gupta rulers, known as the age of Vedic Brahminism, was marked by strictures laid down in Dharmaśāstra—the ancient compendium of moral laws and principles for religious duty and righteous conduct to be followed by a Hindu—and enforced through the powerful state machinery of a developing political economy (15). These strictures and enforcements resulted in a shift to endogamy. The evidence of more recent admixture among the Maratha (MRT) is in agreement with the known history of the post-Gupta Chalukya (543–753 CE) and the Rashtrakuta empires (753–982 CE) of western India, which established a clan of warriors (Kshatriyas) drawn from the local peasantry (15). In eastern and northeastern India, populations such as the West Bengal Brahmins (WBR) and the TB populations continued to admix until the emergence of the Buddhist Pala dynasty during the 8th to 12th centuries CE. The asymmetry of admixture, with ANI populations providing genomic inputs to tribal populations (AA, Dravidian tribe, and TB) but not vice versa, is consistent with elite dominance and patriarchy. Males from dominant populations, possibly upper castes, with high ANI component, mated outside of their caste, but their offspring were not allowed to be inducted into the caste. This phenomenon has been previously observed as asymmetry in homogeneity of mtDNA and heterogeneity of Y-chromosomal haplotypes in tribal populations of India (6) as well as the African Americans in United States (34). In this study, we noted that, although there are subtle sex-specific differences in admixture proportions, there are no major differences in inferences about population relationships and peopling whether X-chromosomal or autosomal data are used. We have also found our inferences to become more robust when our data are jointly analyzed with HGDP data.

I can't but find quite curious how, once again, Indian and European histories behave so similarly: in Europe also a simpler but also "god-sanctioned" caste system (designed by Agustin of Hippo) was imposed upon the collapse of the Roman Empire (very similar dates). However popular revolutions gradually but systematically destroyed it. The same is happening in India now but with a delayed timeline. Instead Muslim West Asia (and surroundings) had no caste system and that's probably why it was so successful back in the day: because it allowed relatively more freedom and intellectual pursuit than other neighboring social systems. Of course, this stopped being the case after the Mongol conquests, roughly coincident with European Renaissance, when Islam cocooned itself into reactionary mode, leading to stagnation and eventually to colonial subservience.

H. heidelbergensis is Neanderthal ancestor and not 'Denisovan' cousin

Quickies

The unprecedented sequencing of a small fraction of the autosomal DNA of Homo heidelbergensis from the Sima de los Huesos of Atapuerca proves that they are in direct ancestral line to H. neanderthalensis and not particularly related to Denisovans.

Matthias Meyer et al., Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins. Nature 2015. Pay per viewLINK [doi:10.1038/nature17405]

Abstract

A unique assemblage of 28 hominin individuals, found in Sima de los Huesos in the Sierra de Atapuerca in Spain, has recently been dated to approximately 430,000 years ago1. An interesting question is how these Middle Pleistocene hominins were related to those who lived in the Late Pleistocene epoch, in particular to Neanderthals in western Eurasia and to Denisovans, a sister group of Neanderthals so far known only from southern Siberia. While the Sima de los Huesos hominins share some derived morphological features with Neanderthals, the mitochondrial genome retrieved from one individual from Sima de los Huesos is more closely related to the mitochondrial DNA of Denisovans than to that of Neanderthals2. However, since the mitochondrial DNA does not reveal the full picture of relationships among populations, we have investigated DNA preservation in several individuals found at Sima de los Huesos. Here we recover nuclear DNA sequences from two specimens, which show that the Sima de los Huesos hominins were related to Neanderthals rather than to Denisovans, indicating that the population divergence between Neanderthals and Denisovans predates 430,000 years ago. A mitochondrial DNA recovered from one of the specimens shares the previously described relationship to Denisovan mitochondrial DNAs, suggesting, among other possibilities, that the mitochondrial DNA gene pool of Neanderthals turned over later in their history.


Some articles that describe the findings:
at Público (in Spanish)

Matthieson also found that the Sima de los Huesos hominids were closer to Denisovans and Neanderthals in mtDNA two years ago. But this sequencing of their nuclear DNA puts them much closer to Neanderthals instead.

Prüffer et al. found in 2013 that Neanderthals form a cline with "Denisovans" in nuclear DNA but not in mtDNA, in which they are closer to us. This one is a very interesting read for background, as it explores in great detail the various possible scenarios.

That "Denisovans" could be closely related to H. erectus (a catch-all term for most archaic populations, particularly in Asia) has been considered as very possible before (Waddell et al. 2012) but there is no genetic confirmation so far, neither strong rejection. Getting DNA from such ancient specimens is considered a breakthrough and this partial sequencing of 400,000 years ago is believed to be within the very limits of absolute possibility.

[Conclusions edited on Mar 19th because I got it all wrong and don't wish to keep confusing anybody else. Instead I listed several relevant background studies, judge yourself].

February 14, 2016

Neolithic East Asians tamed leopard cats

Quickies

Leopard cat
(CC: F. Spangenberg - Der Irbis)
It's hard to say that cats are domestic at all, tamed is probably a better concept. Some would of course argue that it is cats who have tamed us humans, debatable I guess.

In any case this relationship has not been restricted to the common cat (Felis silvestris catus) but it has been known now that ancient East Asians managed to establish the same kind of relationship with a local feline of similar characteristics: the leopard cat (Prionailurus bengalensis). However at some point the Western cat took over and nothing remains of that ancient domestication event.

Jean-Denis Vigne et al., Earliest “Domestic” Cats in China Identified as Leopard Cat (Prionailurus bengalensis). PLoS ONE 2015. Open access → LINK [doi:10.1371/journal.pone.0147295]

Abstract

The ancestor of all modern domestic cats is the wildcat, Felis silvestris lybica, with archaeological evidence indicating it was domesticated as early as 10,000 years ago in South-West Asia. A recent study, however, claims that cat domestication also occurred in China some 5,000 years ago and involved the same wildcat ancestor (F. silvestris). The application of geometric morphometric analyses to ancient small felid bones from China dating between 5,500 to 4,900 BP, instead reveal these and other remains to be that of the leopard cat (Prionailurus bengalensis). These data clearly indicate that the origins of a human-cat ‘domestic’ relationship in Neolithic China began independently from South-West Asia and involved a different wild felid species altogether. The leopard cat’s ‘domestic’ status, however, appears to have been short-lived—its apparent subsequent replacement shown by the fact that today all domestic cats in China are genetically related to F. silvestris.

Goat genetics suggest that two populations were domesticated

Quickies


Licia Colli, Hovirang 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.

Note: "Southeastern Anatolia" should read Northern Kurdistan, as the Turkish official concept of Anatolia wildly goes beyond the actual Anatolia or Asia Minor peninsula into Upper Mesopotamia. Also Anatolia Peninsula was not involved, as far as we know, in the Early Neolithic and only cow domestication, which is of a later date, can be tracked to that region. The oldest known goats are from the M'lafatian culture of the Zagros (Jarmo and such). The same happens with sheep and pigs.

An archaic human population surviving in SW China until at least 14,000 years ago

Quickies

Just a femur but looks like it. Homo heidelbergensis (Denisovan)?

Darren Curnoe, Xueping Li et al. A Hominin Femur with Archaic Affinities from the Late Pleistocene of Southwest China. PLoS ONE 2015. Open accessLINK [doi:10.1371/journal.pone.0143332]

Abstract

The number of Late Pleistocene hominin species and the timing of their extinction are issues receiving renewed attention following genomic evidence for interbreeding between the ancestors of some living humans and archaic taxa. Yet, major gaps in the fossil record and uncertainties surrounding the age of key fossils have meant that these questions remain poorly understood. Here we describe and compare a highly unusual femur from Late Pleistocene sediments at Maludong (Yunnan), Southwest China, recovered along with cranial remains that exhibit a mixture of anatomically modern human and archaic traits. Our studies show that the Maludong femur has affinities to archaic hominins, especially Lower Pleistocene femora. However, the scarcity of later Middle and Late Pleistocene archaic remains in East Asia makes an assessment of systematically relevant character states difficult, warranting caution in assigning the specimen to a species at this time. The Maludong fossil probably samples an archaic population that survived until around 14,000 years ago in the biogeographically complex region of Southwest China.

Ancient DNA confirms that dogs were first domesticated in Southeast Asia

Quickies

I have already argued for this scenario several times (as opposed to the Neolithic West Asian one, which just makes no sense and rather seems to represent a secondary layer of dog genetics), so I'm very glad that ancient DNA research can confirm it even further.

Guo-Dong Wang, Out of southern East Asia: the natural history of domestic dogs across the world. Cell Research 2015. Open accessLINK [doi:10.1038/cr.2015.147]

Abstract

The origin and evolution of the domestic dog remains a controversial question for the scientific community, with basic aspects such as the place and date of origin, and the number of times dogs were domesticated, open to dispute. Using whole genome sequences from a total of 58 canids (12 gray wolves, 27 primitive dogs from Asia and Africa, and a collection of 19 diverse breeds from across the world), we find that dogs from southern East Asia have significantly higher genetic diversity compared to other populations, and are the most basal group relating to gray wolves, indicating an ancient origin of domestic dogs in southern East Asia 33 000 years ago. Around 15 000 years ago, a subset of ancestral dogs started migrating to the Middle East, Africa and Europe, arriving in Europe at about 10 000 years ago. One of the out of Asia lineages also migrated back to the east, creating a series of admixed populations with the endemic Asian lineages in northern China before migrating to the New World. For the first time, our study unravels an extraordinary journey that the domestic dog has traveled on earth.

I will dare, once again, to challenge the age guesstimates and suggest that they are in fact notably older, maybe even double the proposed age. Notice that I tentatively associate the domestication of dogs with the massive secondary "out of SE Asia" expansion led by Y-DNA haplogroup K2 and mtDNA haplogroup R, which probably took place, at least in my understanding, at some point between the Toba catastrophe (c. 74 Ka BP) and the beginnings of the Upper Paleolithic in Western Eurasia (c. 50 Ka BP), so, yeah, c. 65 or 60 Ka BP is a good age estimate for me, more so considering that we already know of domesticated dogs far from SE Asia, in 33,000 BP.


See also:

Genetic structure of pearl millet, an African cereal

Quickies

Zhenbin Hu et al., Population genomics of pearl millet (Pennisetum glaucum (L.) R. Br.): Comparative analysis of global accessions and Senegalese landraces. BMC genomics 2015. Open accessLINK [doi:10.1186/s12864-015-2255-0]

Abstract

Background

Pearl millet is a staple food for people in arid and semi-arid regions of Africa and South Asia due to its high drought tolerance and nutritional qualities. A better understanding of the genomic diversity and population structure of pearl millet germplasm is needed to support germplasm conservation and genetic improvement of this crop. Here we characterized two pearl millet diversity panels, (i) a set of global accessions from Africa, Asia, and the America, and (ii) a collection of landraces from multiple agro-ecological zones in Senegal.

Results

We identified 83,875 single nucleotide polymorphisms (SNPs) in 500 pearl millet accessions, comprised of 252 global accessions and 248 Senegalese landraces, using genotyping by sequencing (GBS) of PstI-MspI reduced representation libraries. We used these SNPs to characterize genomic diversity and population structure among the accessions. The Senegalese landraces had the highest levels of genetic diversity (π), while accessions from southern Africa and Asia showed lower diversity levels. Principal component analyses and ancestry estimation indicated clear population structure between the Senegalese landraces and the global accessions, and among countries in the global accessions. In contrast, little population structure was observed across in the Senegalese landraces collections. We ordered SNPs on the pearl millet genetic map and observed much faster linkage disequilibrium (LD) decay in Senegalese landraces compared to global accessions. A comparison of pearl millet GBS linkage map with the foxtail millet (Setaria italica) and sorghum (Sorghum bicolor) genomes indicated extensive regions of synteny, as well as some large-scale rearrangements in the pearl millet lineage.

Conclusions

We identified 83,875 SNPs as a genomic resource for pearl millet improvement. The high genetic diversity in Senegal relative to other regions of Africa and Asia supports a West African origin of this crop, followed by wide diffusion. The rapid LD decay and lack of confounding population structure along agro-ecological zones in Senegalese pearl millet will facilitate future association mapping studies. Comparative population genomics will provide insights into panicoid crop evolution and support improvement of these climate-resilient crops.



Fig. 4

The genetic relatedness of pearl millet accessions. a F-statistic (F ST ) between populations with different origins. The circles indicate the countries of origin, and the values represent the F ST between accessions from the two countries. The thickness of the lines is proportional to the value of F ST . b Genetic relatedness among 500 accessions assessed with the neighbor joining method. Global accessions are colored by countries of origin, and Senegalese landraces are colored by regions of origin


See also: Review of Tropical Neolithic flows (a most important agricultural development in the African and Asian Tropics).

Patrilineages of Panama

Quickies

Viola Grugni et al., Exploring the Y Chromosomal Ancestry of Modern Panamanians. PLoS ONE 2015. Open access → LINK [doi:10.1371/journal.pone.0144223]

Abstract

Geologically, Panama belongs to the Central American land-bridge between North and South America crossed by Homo sapiens >14 ka ago. Archaeologically, it belongs to a wider Isthmo-Colombian Area. Today, seven indigenous ethnic groups account for 12.3% of Panama’s population. Five speak Chibchan languages and are characterized by low genetic diversity and a high level of differentiation. In addition, no evidence of differential structuring between maternally and paternally inherited genes has been reported in isthmian Chibchan cultural groups. Recent data have shown that 83% of the Panamanian general population harbour mitochondrial DNAs (mtDNAs) of Native American ancestry. Considering differential male/female mortality at European contact and multiple degrees of geographical and genetic isolation over the subsequent five centuries, the Y-chromosome Native American component is expected to vary across different geographic regions and communities in Panama. To address this issue, we investigated Y-chromosome variation in 408 modern males from the nine provinces of Panama and one indigenous territory (the comarca of Kuna Yala). In contrast to mtDNA data, the Y-chromosome Native American component (haplogroup Q) exceeds 50% only in three populations facing the Caribbean Sea: the comarca of Kuna Yala and Bocas del Toro province where Chibchan languages are spoken by the majority, and the province of Colón where many Kuna and people of mixed indigenous-African-and-European descent live. Elsewhere the Old World component is dominant and mostly represented by western Eurasian haplogroups, which signal the strong male genetic impact of invaders. Sub-Saharan African input accounts for 5.9% of male haplotypes. This reflects the consequences of the colonial Atlantic slave trade and more recent influxes of West Indians of African heritage. Overall, our findings reveal a local evolution of the male Native American ancestral gene pool, and a strong but geographically differentiated unidirectional sex bias in the formation of local modern Panamanian populations.


Fig 1. Spatial distributions of Y-chromosome components in Panama.
Bars show Native American (violet), West Eurasian/North African (green), sub-Saharan African (yellow) and South Asian (light blue) components in each province or comarca. In grey the Y-chromosome portion with discordant haplogroup predictions.

How different is Howieson Port Middle Paleolithic tech from its neighbors and successors?

Quickies

That's what a recently published paper discusses. Oh, by the way, context for the casual reader: Howieson Port and related industries are among the oldest ones in South Africa, yet they are very advanced for their time, suggesting that our species was innovating in ways that our (now essentially extinct) cousins were not doing. See also: this entry on African Middle Paleolithic.

Paloma de la Peña, Refining Our Understanding of Howiesons Poort Lithic Technology: The Evidence from Grey Rocky Layer in Sibudu Cave (KwaZulu-Natal, South Africa). Open accessLINK [doi:10.1371/journal.pone.0143451]

Abstract

The detailed technological analysis of the youngest Howiesons Poort occupation in Sibudu Cave, layer Grey Rocky, has shown the importance of blade production (with different knapping methods involved), but also of flaking methods in coarse grained rock types. Moreover, new strategies of bifacial production and microlithism were important. Grey Rocky lithic technology shows a really versatile example of reduction strategies that were highly influenced by the characteristics of the rock types. This lithic assemblage is another example of the technological variability linked to the Howiesons Poort technocomplex. The reasons for this variability are still difficult to elucidate. Discrepancies between sites might be for different reasons: diachronic variations, functional variations, organizational variations or maybe different regional variations within what has been recognized traditionally and typologically as Howiesons Poort. The technological comparison of the Grey Rocky assemblage with assemblages from other Howiesons Poort sites demonstrates that there are common technological trends during the late Pleistocene, but they still need to be properly circumscribed chronologically. On the one hand, Howiesons Poort characteristics such as the bifacial production in quartz are reminiscent of production in some Still Bay or pre-Still Bay industries and the flake production or the prismatic blade production described here could be a point in common with pre-Still Bay and post-Howiesons Poort industries. On the other hand, the detailed analysis of the Grey Rocky lithics reinforces the particular character of this Howiesons Poort technocomplex, yet it also shows clear technological links with other Middle Stone Age assemblages.

A Magdalenian campsite map from Catalonia

Quickies


A neat curiosity from the Ice Age:

Marcos García Díez & Manuel Vaquero, Looking at the Camp: Paleolithic Depiction of a Hunter-Gatherer Campsite. PLoS ONE 2015. Open access → LINK [doi:10.1371/journal.pone.0143002]


Abstract

Landscapes and features of the everyday world were scarcely represented in Paleolithic art, especially those features associated with the human landscape (huts and campsites). On the contrary, other figurative motifs (especially animals) and signs, traditionally linked to the magic or religious conceptions of these hunter-gatherer societies, are the predominant themes of Upper Paleolithic art. This paper seeks to present an engraved schist slab recently found in the Molí del Salt site (North-eastern Iberia) and dated at the end of the Upper Paleolithic, ca. 13,800 years ago. This slab displays seven semicircular motifs that may be interpreted as the representation of dome-shaped huts. The analysis of individual motifs and the composition, as well as the ethnographic and archeological contextualization, suggests that this engraving is a naturalistic depiction of a hunter-gatherer campsite. Campsites can be considered the first human landscape, the first area of land whose visible features were entirely constructed by humans. Given the social meaning of campsites in hunter-gatherer life-styles, this engraving may be considered one of the first representations of the domestic and social space of a human group.

Archaeologists studying Monte Verde claim an age of 18 Ka BP and add some detail

Quickies

I'm going in this and upcoming short entries through my backlog. You are warned.

New archaeology from Monte Verde (Chile) suggests a date of 18 Ka BP (slightly older than the oldest known North American site) and also that it was a transiting site for highly mobile peoples and not a main base, as they were not using superior local lithics but bringing their own.

Tom D. Dillehay et al. New Archaeological Evidence for an Early Human Presence at Monte Verde, Chile. PLoS ONE 2015. Open accessLINK [doi:10.1371/journal.pone.0141923]

Abstract

Questions surrounding the chronology, place, and character of the initial human colonization of the Americas are a long-standing focus of debate. Interdisciplinary debate continues over the timing of entry, the rapidity and direction of dispersion, the variety of human responses to diverse habitats, the criteria for evaluating the validity of early sites, and the differences and similarities between colonization in North and South America. Despite recent advances in our understanding of these issues, archaeology still faces challenges in defining interdisciplinary research problems, assessing the reliability of the data, and applying new interpretative models. As the debates and challenges continue, new studies take place and previous research reexamined. Here we discuss recent exploratory excavation at and interdisciplinary data from the Monte Verde area in Chile to further our understanding of the first peopling of the Americas. New evidence of stone artifacts, faunal remains, and burned areas suggests discrete horizons of ephemeral human activity in a sandur plain setting radiocarbon and luminescence dated between at least ~18,500 and 14,500 cal BP. Based on multiple lines of evidence, including sedimentary proxies and artifact analysis, we present the probable anthropogenic origins and wider implications of this evidence. In a non-glacial cold climate environment of the south-central Andes, which is challenging for human occupation and for the preservation of hunter-gatherer sites, these horizons provide insight into an earlier context of late Pleistocene human behavior in northern Patagonia.

Notice that Monte Verde is quite towards the south and, in Ice Age contexts, it was a rather extreme environment, barely outside of the glaciers. I wonder what they looked for in such a remote place, even if they probably only went there in summer.

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.