June 26, 2016

Ancient genomes from Neolithic West Asia

This week we got to know a lot more about the genetics of ancient West Asians, from the Mesolithic, Neolithic and later times. All in a single major study:

Iosif Lazaridis et al., The genetic structure of the world's first farmers. BioRxiv 2016. Freely accessible (pre-pub)LINK [doi: http://dx.doi.org/10.1101/059311]

Abstract

We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000-1,400 BCE, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a 'Basal Eurasian' lineage that had little if any Neanderthal admixture and that separated from other non-African lineages prior to their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to drastically reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those from Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.

Highlights:

  • There were (at least) two clearly distinct populations in West Asia in the Mesolithic and Early Neolithic times.
  • Both populations contributed to the West Anatolian farmers that are precursors of the settlers of Neolithic Europe.
  • The so-called "Basal Eurasian" component is not yet clarified if it is something local or admixture with Africans or both. However it is clear that it is associated with reduced Neanderthal admixture.
  • West Eurasian genetic composition can be now understood quite well as the mixture from four sources: two West Asian ones, favored by the Neolithic revolution, and two Paleo-European ones.

This graphic shows pretty well how the ancient populations of West Eurasia are expressed as a mixture of those four founder populations:


That is if you can get through the nomenclature, which is inherited in many cases from a long array of recent studies. I'm not even sure myself in many cases what samples exactly and where from are thrown in each category. But the most important part is that Iran_N and Levant_N are the two Neolithic-specific founder populations of the Fertile Crescent (yeah, N stands for "Neolithic", not "North") and that the other two founder populations from pre-Neolithic Europe are WHG (Epi-Magdalenian peoples from Western and Central Europe) and EHG (Eastern European hunter-gatherers, of Epigravettian culture and maybe even proto-Uralic in one case).

Then we see in the case of Europe how:

1. Anatolia_N (precursors of mainline European Neolithic) are a mix of both West Asian farmer groups, plus a sizable fraction of Western Paleo-european ancestry already.

2. This fraction of Western Paleoeuropeanness increases as the farmers expanded into Europe (EN) and then as there was probably some backflow of Western origins in relation to Megalithism and Bell Beaker (MNChL). But in general remains the same basic genetic composition and in no known case incorporates any Eastern Paleoeuropean component at all, not yet.

3. It is only with the Indoeuropean ("Kurgan") invasions reflected in the category LNBA, when the EHG component begins feeling very important in Europe. If I'm correct, all those samples are from Germany other areas of Central and North Europe, with the Iberian and Italian ones of similar chronology placed in the MNChL tag instead. The LNBA/MNChL contrast is not a strictly chronological analysis but an analysis by categories of ancestry that do overlap in time.

4. In Armenia instead, we see a decrease of the minor EHG component but then an increase in the MLBA ("middle and late Bronze Age") when Armenians arrive from the Balcans and Phrygia, conquering the pre-existing Hurro-Urartean peoples (whose language was probably related to Chechen and other NE Caucasian languages), which should correspond to the formation of Urartu and more specifically to the Hayasa-Azzi and Shupria stages, both considered Urartean (Hurrian). The WHG and Levant-N components we see since the Chalcolithic is similar to what we see in West Anatolia and probably reflect interactions corresponding to Central-Eastern Anatolia, Kurdistan and Syria, for which we have no direct ancient data yet.

Ancient samples (colored and labeled) projected on a PCA of modern West Eurasian populations (in gray):


For a reference on which are the modern populations in gray, a good reference is this older but fully labeled PCA by Olalde.

Briefly: Natufians fall on top of modern Palestinians, their slightly admixed Neolithic descendants fall between Palestinians and Jews, Middle Neolithic European Farmers fall on top of Sardinians, the so-called Europe-Steppe continuum (early Western Indoeuropeans) fall between Central Europe, France and the Balcans, most Western Europeans do not overlap with ancient samples but appear to have even greater Paleoeuropean admixture instead, etc.

Y-DNA Haplogroups

Iranian Mesolithic and Neolithic samples carried the following patrilineages:
  • Mesolithic: J(xJ2a1b3,J2b2a1a1)
  • Ganj Dareh Neolithic: P1(xQ,R1b1a2,R1a1a1b1a1b,R1a1a1b1a3a,R1a1a1b2a2a) and an undefined CT
  • Late Neolithic: G2a1(xG2a1a)

Meanwhile Palestinian Mesolithic and Neolithic samples carried: 

  • Natufian (Mesolithic): E1b1b1b2(xE1b1b1b2a,E1b1b1b2b), E1b1(xE1b1a1,E1b1b1b1), E1b1b1b2(xE1b1b1b2a,E1b1b1b2b), plus two undefined CT.
  • Pre-Pottery Neolithic B/C: H2, E(xE2,E1a,E1b1a1a1c2c3b1,E1b1b1b1a1,E1b1b1b2b), E1b1b1, T(xT1a1,T1a2a), E1b1b1(xE1b1b1b1a1,E1b1b1a1b1,E1b1b1a1b2,E1b1b1b2a1c), plus three ill-defined CT.

CT is the main pan-Eurasian macro-haplogroup and is not informative, except in Palestine because it implies exclusion of E.

Otherwise we see an important presence of E (mostly E1b1b) a lineage we know was carried by early farmers into Europe and that has ultimately African origins. It probably indicates migration of NE Africans into Palestine in the Mesolithic, something also supported by Archaeology. However these NE Africans were surely already mixed with Eurasian ancestry, which probably arrived to the Nile Basin in the early LSA, some 50-40 Ka ago. So it's a complex story of multiple admixture events in the continental crossroads that is Egypt and also Palestine and other nearby areas.

We also see G2a1 in Late Neolithic Iran, and this one is the main lineage brought to Europe by the early farmers if we are to judge on known ancient sequences (today it is not more important that E1b but it is maybe more evenly distributed). However we only see it in the Late Neolithic, so it may have originated further west.

We see too little J, only J(xJ1a,J2a1,J2b) in Chalcolithic Iran and in Bronze Age Jordan: J(xJ1,J2a,J2b2a) again and J1(xJ1a). I guess that a lot remains to be researched on this issue because J is by far nowadays the most common haplogroup of West Asia, and also impacted Europe and South Asia (J2) and North and NE Africa (J1).


On the issue of "Basal Eurasian": African or West Asian?

The question remains unanswered, as I said before but there are two clues: on one side the presence of E1b in Mesolithic and Neolithic Palestine clearly supports a direct NE African influence, also backed by archaeological evidence. But there is some nuance in the issue of FST distances that I want to highlight.

The distances are available in a very extensive supplementary table, so I took just a few to get a better understanding, not only of this issue but in general of the genetic distances of the four founder populations:



Quite ironically it is not the Natufians who are the closest to the African reference population (Yoruba) but the CHG, Iran-N and Levant-N groups. In fact the Natufians are the most distant ones after the WHG population. However this is tricky because the affinity to Yoruba may also be caused by the "ghost" Basal Eurasian population, claimed first of all by Lazaridis 2014, which would be a remnant of the Out of Africa Migration (not strictly African but close enough and impossible to discern from true African admixture in most analyses).

So we may imagine that the "Highlander" (CHG and Iran-N) populations were somehow influenced by that Basal Eurasian ghostly population, which might have survived in the Persian Gulf oasis, for example. Or whatever else.

The presence of the same or similar element in Levant-N reflects possibly admixture with Iran-N or a similar population, something that is implicit in the table above but I'll address below more explicitly.

If there is (and there must be, because of Y-DNA E1b) some African admixture in the Natufian population, it was very diluted already in the autosomal (general DNA) aspect before farming began.

A visual of smallest genetic distances between (each "-" represents 0.01 in the table above):

a) Ancient West Asians:

CHG-----IrN-------LeN----Nat
Neolithic peoples of West Asia, even if different, are closer among them than their pre-Neolithic precursors.

b) Pre-Neolithic West Eurasians:

WHG--------EHG----------CHG--------------Nat
The distances between Natufians and everyone else are comparable to those with Han Chinese, however only in the case of the populations that appear to have extra affinity to East Asia (Iran, Caucasus and Eastern Europe), otherwise it is smaller.
All four populations were distant enough from each other to be considered clearly distinctive. Even EHG and WHG were quite dissimilar.

c) The four West Eurasian founders considered above:

WHG--------EHG----------IrN-------LeN
There is much greater similitude between Iran and Levant Neolithic peoples than between their Mesolithic precursors. This implies some sort of intense admixture as agriculture and herding developed. Not enough to erase the differences but enough to blur them significantly.

Genetic influence from East Asia or a related population is also apparent in all Northeastern populations but even more so in Iran Neolithic. Why?

There is much more in the study and supp. materials but I can only review so much.

June 9, 2016

Neolithic DNA from Greece and NW Anatolia and their influence on Europe

This is a most interesting study that brings to us potentially key information on the expansion of European Neolithic and the formation of modern European peoples.

Zuzana Hofmanová, Susanne Kreutzer et al., Early farmers from across Europe directly descended from Neolithic Aegeans. PNAS 2016. Open accessLINK [doi:10.1073/pnas.1523951113]

Abstract

Farming and sedentism first appeared in southwestern Asia during the early Holocene and later spread to neighboring regions, including Europe, along multiple dispersal routes. Conspicuous uncertainties remain about the relative roles of migration, cultural diffusion, and admixture with local foragers in the early Neolithization of Europe. Here we present paleogenomic data for five Neolithic individuals from northern Greece and northwestern Turkey spanning the time and region of the earliest spread of farming into Europe. We use a novel approach to recalibrate raw reads and call genotypes from ancient DNA and observe striking genetic similarity both among Aegean early farmers and with those from across Europe. Our study demonstrates a direct genetic link between Mediterranean and Central European early farmers and those of Greece and Anatolia, extending the European Neolithic migratory chain all the way back to southwestern Asia.



Uniparental DNA

One of the most important findings is that the two Epipaleolithic samples from Theopetra yielded mtDNA K1c, being the first time in which haplogroup K has been detected in pre-Neolithic Europe. Sadly enough these two individuals could not be sequenced for full genome. 

The other five individuals are all Neolithic (three early, two late) and did provide much more information.
  • Rev5 (c. 6300 BCE): mtDNA X2b
  • Bar31 (c. 6300 BCE): mtDNA X2m, Y-DNA G2a2b
  • Bar8 (c. 6100 BCE): mtDNA K1a2
  • Pal7 (c. 4400 BCE): mtDNA J1c1
  • Klei10 (c. 4100 BCE): mtDNA K1a2, Y-DNA G2a2a1b (same as Ötzi's)
I color coded their abbreviated names according to the usage in the study's many maps, for easier reference: green shades are for Greece (Western Macedonia), red shades for Turkey (Bursa district). It is also very convenient to get straight their real geography because many of the map-styled graphs are not precise at all about that:

Fig. 1.
North Aegean archaeological sites investigated in Turkey and Greece.



Autosomal DNA affinities

This is probably the most interesting part. There is a lot about it in the supplementary information appendix but I find that the really central issue is how they relate to each other (or not) and to other ancient and modern Europeans. I reorganized figs S21 and S22 to better visualize this:


Ancient samples compared to each other and other ancient samples ("inferred proportions of ancestry")
Ancient samples compared to modern Europeans ("inferred proportions of ancestry")


So what do we see here? First of all that the strongest contribution of known Aegean Neolithic peoples on mainline European Neolithic is from Bar31, which is from NW Anatolia, and not from Greece. Bar8 is a less important contributor but may have impacted particularly around the Alps (Stuttgart-LBK, modern North Italians).

This goes against most archaeology-based interpretations, which rather strongly suggest a Thessalian and West Macedonian origin of the Balcanic and, therefore, other European branches of the mainline Neolithic of Aegean roots, and do instead support some sort of cultural barrier near the European reaches of the Marmara Sea. Of course we lack exhaustive sampling of Greek Neolithic so far, so it might be still possible that other populations from Thessaly or Epirus could have been more important. However the lack of Anatolian-like influence on the Western Macedonian Neolithic until c. 4100 BCE, makes it quite unlikely.

So it seems that, once again, new archaeogenetic information forces us to rethink the interpretative theories based on other data.

However we do see a strong influence of Greek Neolithic and particularly the oldest sample, Rev5, in SW Europe, very especially among Basques, who seem to have only very minor Anatolian Neolithic ancestry, unlike everyone else relevant here. This impact is also apparent in Sardinia and to some extent North Italy (but overshadowed in these two cases by the one from Anatolia, particularly Bar31).

There are also similar analyses for other four ancient samples (Lochsbour, Stuttgart, Hungary Neolithic and Hungary Bronze) but they don't provide truly new information, so I'm skipping them here. As I said before, there's a hoard of analyses in the SI appendix, enjoy yourselves browsing through them and feel free to note in the comments anything you believe important.

A synthesis of the various "inferred proportions of ancestry" analyses is anyhow shown in fig. 3:

Fig. 3. (click to expand)
Inferred mixture coefficients when forming each modern (small pies) and ancient (large pies, enclosed by borders matching key at left) group as a mixture of the modern-day Yoruba from Africa and the ancient samples shown in the key at left.

The fractions may be misleading however, especially for the ancients. For example: Lochsbour (a total outlier among the ancients in this study) appears best correlated with Pal7 but in fig. S24 it is clear that does no correlate with any Neolithic sample at any significant level. But in general terms it can give a good idea of where does ancestry, particularly for modern samples, come from.

Note: elsewhere someone was being a crybaby about the Polish sample (may well be an error) or the Kalmyk sample (who are obviously most related to East Asians, not used here) but those are minor issues.

Of course there's a lot more to learn from the remains of the ancients. Let's keep up the good work.

June 6, 2016

MtDNA U6 in Aurignacian Europe

The U6 haplogroup of Pestera Muierii is officially confirmed. 

Extra-officially, it also seems confirmed mtDNA H in Magdalenian El Mirón, another of the haplogroup challenged (without any reasoning) by Fu et al. In this last case, my sources suggest that Fu surely tested a bone belonging to a different individual, because the heap of bones could well include several people and the bones tested by Hervella (a tooth) and Fu (a femur) were different.

Anyhow, to the matter at hand:

Montserrat Hervella et al. The mitogenome of a 35,000-year-old Homo sapiens from Europe supports a Palaeolithic back-migration to Africa. Nature 2016. Open accessLINK [doi:10.1038/srep25501]

Abstract

After the dispersal of modern humans (Homo sapiens) Out of Africa, hominins with a similar morphology to that of present-day humans initiated the gradual demographic expansion into Eurasia. The mitogenome (33-fold coverage) of the Peştera Muierii 1 individual (PM1) from Romania (35 ky cal BP) we present in this article corresponds fully to Homo sapiens, whilst exhibiting a mosaic of morphological features related to both modern humans and Neandertals. We have identified the PM1 mitogenome as a basal haplogroup U6*, not previously found in any ancient or present-day humans. The derived U6 haplotypes are predominantly found in present-day North-Western African populations. Concomitantly, those found in Europe have been attributed to recent gene-flow from North Africa. The presence of the basal haplogroup U6* in South East Europe (Romania) at 35 ky BP confirms a Eurasian origin of the U6 mitochondrial lineage. Consequently, we propose that the PM1 lineage is an offshoot to South East Europe that can be traced to the Early Upper Paleolithic back migration from Western Asia to North Africa, during which the U6 lineage diversified, until the emergence of the present-day U6 African lineages.


The interesting part is that today U6 is pretty much constrained to Northwest Africa and parts of Iberia and it has usually been considered until now as a North African haplogroup, even if of Eurasian derivation. 

Fig. 2 - (A) Phylogenetic analysis and temporal estimates for lineages including the Peştera Muierii-1 (PM1) from the mitochondrial tree. (B) Location of the Peştera Muierii cave and surface map based on current frequencies of U6 lineages30; the European borders map was generated in ArcMap 10.1 (ESRI, http://www.esri.com) by modifying the World Borders Dataset (http://www.thematicmapping.org/downloads/world_borders.php), which is licensed under the Attribution-ShareAlike 3.0 Unported license. The license terms can be found on the following link: http://creativecommons.org/licenses/by-sa/3.0/ (This map was created by A.A.).

Another interesting bit is that U6(xU6a'b'd,U6c), U6* for short, is not known to exist today anymore. So it is reasonable to speculate about the "ancestral" position of Muierii in the lineage, regardless of whether Muierii-2 was a true ancestor or just a more or less distant relative of the real ancestor of modern day U6 carriers. 

Complementary information is to be found Secher et al. (2014), which refined the knowledge of the U6 mitochondrial haplogroup, unveiling that the key basal (and rare) U6c sublineage is not only found in Morocco (as known earlier) but also in Europe. Specifically U6c, which hangs directly from the U6 root node, is found in: Hispanic America (5.7% of all U6 carriers), Spain (2.2%), Canada (12.5%), NW Europe (16.7%), Morocco (4.5%), Algeria (10%) and Tunisia (5.9%). It is missing in Brazil, Western, Central and East Africa, Romani ("Gypsies"), Jews, Azores, Madeira, Canary and Cape Verde Islands, Portugal, Central and Eastern Mediterranean, West Sahara, Mauritania and USA (African-Americans,  European-Americans and Hispanics).






Figure 1
Surface maps, based on HVI frequencies (in o/oo), for total U6 (U6), total U6a (Tot U6a), U6a without 16189 (U6a), U6a with 16189 (U6a-189), U6b'd, U6c, U6b and U6d.

While the exact pattern of U6 expansion is not clear except for Africa (with a Moroccan origin surely), Sacher et al. believe that at least this part is related to the Iberomaurusian (aka Oranian) culture, which seems primarily an offshoot of Iberian Solutrean, also with origin in North Morocco (Taforalt) and European-like human looks (Cromagnoid).

Another complementary reference is Carmela L. Hernández et al. (2015):

An inspection of the U6 phylogenetic tree (S1 Dataset) showed that it is not easy to infer whether Iberia or North Africa bear more basal lineages. (...) The U6c (9.9 ky [5.0–15.0]) and U6d (12.0 ky [6.9–17.3]) are present in Iberia, Europe and North Africa at low frequencies.

While she seems to support a North African origin, the data is in fact somewhat contradictory:

Fig 5. Founder analysis for mtDNA U6 haplogroup. The plots show probabilistic distributions of U6 founder clusters for HVS-I sequences (A) and complete genomes (B) across migration times scanned at 200-year intervals from 0 to 60 ky.

Fig 7. Bayesian Skyline Plot (BSP) analysis of entire mtDNA U6 sequences.
Temporal changes of the effective population size, Ne in sub-Saharan Africa (brown color), North Africa (green color), and Iberian Peninsula (red color) are depicted. Solid lines represent the median values for the log10 of Ne on the Y-axis within each analyzed geographic region. The 95% HPD (highest posterior density) interval is shown for the three distributions (dashed lines).
Notice that the "LGM" label is very wrong: it should be around 21.000 years ago!

Usually U6 genetic history is envisioned as a migration from southwest Asia through North Africa [50]. This hypothesis is based on the general origin of haplogroup U sub-clades in Southwest Asia, which is also the center of the geographical distribution of U sub-clades: Europe, India, Central Asia, East Africa and North Africa. Two possible scenarios for the first U6 haplotype (bearing mutations 3348 and 16172) can be advanced: i) these mutations aroused in the founder region but did not leave any genetic legacy in current human populations there; ii) they originated probably somewhere in North Africa, after the arrival of the U6 founder haplotype. Within North Africa U6 is only significantly frequent at its western edge (as well as in South-western Europe). More importantly, all the most basal branches are virtually restricted to that region (U6b, U6c and U6d), what could indicate its western origin. Nevertheless, it cannot be excluded the major sub-clade U6a, which shows a richness of sub-clades in Northwest Africa [29] although a few of derivative branches also include sequences from East African and the Middle Eastern populations (e.g. U6a2).

Her conclusions (insisting on an African origin and first arrival via Egypt) are not something I can share at this stage of the research but her data is clearly very interesting and, combined with the rest, useful in discerning the possible route of primeval U6 to the Gibraltar Strait area, where it found no doubt its niche for consolidated expansion. 

After the Muierii finding the question is open: did primeval U6 arrive to North Africa via Iberia, being pruned in Europe afterwards just because of genetic drift and the sizable impact of Paleolithic migrations in low density areas? I cannot be 100% sure but I would say it is a very likely conclusion based not just on Muierii but also on the rather high basal diversity of U6 in Iberia (and surprisingly NW Europe!) and also on the archaeological data that makes almost necessary to root the first Upper Paleolithic of NW Africa (the Iberomaurusian) in the Iberian Solutrean.


(Special thanks to Jean Lohizun again).


Update (Jun 17):

The Hernández 2015 paper also mentions that  U6a1 appears to be of European and specifically Portuguese origin:

Our U6 tree built from mitogenomes shows that U6a1 is predominantly European because it contains a significant number of sequences of Mediterranean individuals mainly from the northwestern shore with a leading Iberian contribution (21 of the 29 European samples) and has an ancestral node in Portugal (accession number HQ651694).

Thanks to Geog M. for highlighting this important detail.

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.