A Song of Sheep and Horses, revised edition, now available as printed books

cover-song-sheep-and-horses

As I said 6 months ago, 2019 is a tough year to write a blog, because this was going to be a complex regional election year and therefore a time of political promises, hence tenure offers too. Now the preliminary offers have been made, elections have passed, but the timing has slightly shifted toward 2020. So I may have the time, but not really any benefit of dedicating too much effort to the blog, and a lot of potential benefit of dedicating any time to evaluable scientific work.

On the other hand, I saw some potential benefit for publishing texts with ISBNs, hence the updates to the text and the preparation of these printed copies of the books, just in case. While Spain’s accreditation agency has some hard rules for becoming a tenured professor, especially for medical associates (whose years of professional experience are almost worthless compared to published peer-reviewed papers), it is quite flexible in assessing one’s merits.

However, regional and/or autonomous entities are not, and need an official identifier and preferably printed versions to evaluate publications, such as an ISBN for books. I took thus some time about a month ago to update the texts and supplementary materials, to publish a printed copy of the books with Amazon. The first copies have arrived, and they look good.

series-song-sheep-horses-cover

Corrections and Additions

Titles
I have changed the names and order of the books, as I intended for the first publication – as some of you may have noticed when the linguistic book was referred to as the third volume in some parts. In the first concept I just wanted to emphasize that the linguistic work had priority over the rest. Now the whole series and the linguistic volume don’t share the same name, and I hope this added clarity is for the better, despite the linguistic volume being the third one.

Uralic dialects
I have changed the nomenclature for Uralic dialects, as I said recently. I haven’t really modified anything deeper than that, because – unlike adding new information from population genomics – this would require for me to do a thorough research of the most recent publications of Uralic comparative grammar, and I just can’t begin with that right now.

Anyway, the use of terms like Finno-Ugric or Finno-Samic is as correct now for the reconstructed forms as it was before the change in nomenclature.

west-east-uralic-schema

Mediterranean
The most interesting recent genetic data has come from Iberia and the Mediterranean. Lacking direct data from the Italian Peninsula (and thus from the emergence of the Etruscan and Rhaetian ethnolinguistic community), it is becoming clearer how some quite early waves of Indo-Europeans and non-Indo-Europeans expanded and shrank – at least in West Iberia, West Mediterranean, and France.

Finno-Ugric
Some of the main updates to the text have been made to the sections on Finno-Ugric populations, because some interesting new genetic data (especially Y-DNA) have been published in the past months. This is especially true for Baltic Finns and for Ugric populations.

ananino-culture-new

Balto-Slavic
Consequently, and somehow unsurprisingly, the Balto-Slavic section has been affected by this; e.g. by the identification of Early Slavs likely with central-eastern populations dominated by (at least some subclades of) hg. I2a-L621 and E1b-V13.

Maps
I have updated some cultural borders in the prehistoric maps, and the maps with Y-DNA and mtDNA. I have also added one new version of the Early Bronze age map, to better reflect the most likely location of Indo-European languages in the Early European Bronze Age.

As those in software programming will understand, major changes in the files that are used for maps and graphics come with an increasing risk of additional errors, so I would not be surprised if some major ones would be found (I already spotted three of them). Feel free to communicate these errors in any way you see fit.

bronze-age-early-indo-european
European Early Bronze Age: tentative langage map based on linguistics, archaeology, and genetics.

SNPs
I have selected more conservative SNPs in certain controversial cases.

I have also deleted most SNP-related footnotes and replaced them with the marking of each individual tentative SNP, leaving only those footnotes that give important specific information, because:

  • My way of referencing tentative SNP authors did not make it clear which samples were tentative, if there were more than one.
  • It was probably not necessary to see four names repeated 100 times over.
  • Often I don’t really know if the person I have listed as author of the SNP call is the true author – unless I saw the full SNP data posted directly – or just someone who reposted the results.
  • Sometimes there are more than one author of SNPs for a certain sample, but I might have added just one for all.
ancient-dna-all
More than 6000 ancient DNA samples compiled to date.

For a centralized file to host the names of those responsible for the unofficial/tentative SNPs used in the text – and to correct them if necessary -, readers will be eventually able to use Phylogeographer‘s tool for ancient Y-DNA, for which they use (partly) the same data I compiled, adding Y-Full‘s nomenclature and references. You can see another map tool in ArcGIS.

NOTE. As I say in the text, if the final working map tool does not deliver the names, I will publish another supplementary table to the text, listing all tentative SNPs with their respective author(s).

If you are interested in ancient Y-DNA and you want to help develop comprehensive and precise maps of ancient Y-DNA and mtDNA haplogroups, you can contact Hunter Provyn at Phylogeographer.com. You can also find more about phylogeography projects at Iain McDonald’s website.

Graphics
I have also added more samples to both the “Asian” and the “European” PCAs, and to the ADMIXTURE analyses, too.

I previously used certain samples prepared by amateurs from BAM files (like Botai, Okunevo, or Hittites), and the results were obviously less than satisfactory – hence my criticism of the lack of publication of prepared files by the most famous labs, especially the Copenhagen group.

Fortunately for all of us, most published datasets are free, so we don’t have to reinvent the wheel. I criticized genetic labs for not releasing all data, so now it is time for praise, at least for one of them: thank you to all responsible at the Reich Lab for this great merged dataset, which includes samples from other labs.

NOTE. I would like to make my tiny contribution here, for beginners interested in working with these files, so I will update – whenever I have time – the “How To” sections of this blog for PCAs, PCA3d, and ADMIXTURE.

-iron-age-europe-romans
Detail of the PCA of European Iron Age populations. See full versions.

ADMIXTURE
For unsupervised ADMIXTURE in the maps, a K=5 is selected based on the CV, giving a kind of visual WHG : NWAN : CHG/IN : EHG : ENA, but with Steppe ancestry “in between”. Higher K gave worse CV, which I guess depends on the many ancient and modern samples selected (and on the fact that many samples are repeated from different sources in my files, because I did not have time to filter them all individually).

I found some interesting component shared by Central European populations in K=7 to K=9 (from CEU Bell Beakers to Denmark LN to Hungarian EBA to Iberia BA, in a sort of “CEU BBC ancestry” potentially related to North-West Indo-Europeans), but still, I prefer to go for a theoretically more correct visualization instead of cherry-picking the ‘best-looking’ results.

Since I made fun of the search for “Siberian ancestry” in coloured components in Tambets et al. 2018, I have to be consistent and preferred to avoid doing the same here…

qpAdm
In the first publication (in January) and subsequent minor revisions until March, I trusted analyses and ancestry estimates reported by amateurs in 2018, which I used for the text adding my own interpretations. Most of them have been refuted in papers from 2019, as you probably know if you have followed this blog (see very recent examples here, here, or here), compelling me to delete or change them again, and again, and again. I don’t have experience from previous years, although the current pattern must have been evidently repeated many times over, or else we would be still talking about such previous analyses as being confirmed today…

I wanted to be one step ahead of peer-reviewed publications in the books, but I prefer now to go for something safe in the book series, rather than having one potentially interesting prediction – which may or may not be right – and ten huge mistakes that I would have helped to endlessly redistribute among my readers (online and now in print) based on some cherry-picked pairwise comparisons. This is especially true when predictions of “Steppe“- and/or “Siberian“-related ancestry have been published, which, for some reason, seem to go horribly wrong most of the time.

I am sure whole books can be written about why and how this happened (and how this is going to keep happening), based on psychology and sociology, but the reasons are irrelevant, and that would be a futile effort; like writing books about glottochronology and its intermittent popularity due to misunderstood scientist trends. The most efficient way to deal with this problem is to avoid such information altogether, because – as you can see in the current revised text – they wouldn’t really add anything essential to the content of these books, anyway.

Continue reading

Official site of the book series:
A Song of Sheep and Horses: eurafrasia nostratica, eurasia indouralica

Bantu distinguished from Khoe by uniparental markers, not genome-wide autosomal admixture

bantu-expansion

The role of matrilineality in shaping patterns of Y chromosome and mtDNA sequence variation in southwestern Angola, by Oliveira et al. bioRxiv (2018).

Interesting excerpts (emphasis mine):

The origins of NRY diversity in SW Angola

In accordance with our previous mtDNA study9, the present NRY analysis reveals a major division between the Kx’a-speaking !Xun and the Bantu-speaking groups, whose paternal genetic ancestry does not display any old remnant lineages, or a clear link to pre-Bantu eastern African migrants introducing Khoe-Kwadi languages and pastoralism into southern Africa (cf. 15). This is especially evident in the distribution of the eastern African subhaplogroup E1b1b1b2b29, which reaches the highest frequency in the !Xun (25%) and not in the formerly Kwadi-speaking Kwepe (7%). This observation, together with recent genome-wide estimates of 9-22% of eastern African ancestry in other Kx’a and Tuu-speaking groups35, suggests that eastern African admixture was not restricted to present-day Khoe-Kwadi speakers. Alternatively, it is likely that the dispersal of pastoralism and Khoe-Kwadi languages involved a series of punctuated contacts that led to a wide variety of cultural, genetic and linguistic outcomes, including possible shifts to Khoe-Kwadi by originally Bantu-speaking peoples36.

Although traces of an ancestral pre-Bantu population may yet be found in autosomal genome-wide studies, the extant variation in both uniparental markers strongly supports a scenario in which all groups of the Angolan Namib share most of their genetic ancestry with other Bantu groups but became increasingly differentiated within the highly stratified social context of SW African pastoral societies11.

bantu-pastoralists
Y chromosome phylogeny, haplogroup distribution and map of the sampling locations. The phylogenetic tree was reconstructed in BEAST based on 2,379 SNPs and is in accordance with the known Y chromosome topology. Main haplogroup clades and their labels are shown with different colors. Age estimates are reported in italics near each node, with the TMRCA of main haplogroups shown with their corresponding color. A map of the sampling locations, re-used with permission from Oliveira et al. (2018) 9, is shown on the bottom left, and the haplogroup distribution per population is shown on the bottom right, with color-coding corresponding to the phylogenetic tree.

The influence of socio-cultural behaviors on the diversity of NRY and mtDNA

A comparison of the NRY variation with previous mtDNA results for the same groups 9 identifies three main sex-specific patterns. First, gene flow from the Bantu into the !Xun is much higher for male than for female lineages (31% NRY vs. 3% mtDNA), similar to the reported male-biased patterns of gene flow from Bantu to Khoisan-speaking groups33, and from non-Pygmies to Pygmies in Central Africa 37. A comparable trend, involving exclusive introgression of NRY eastern African lineages into the !Xun (25%) was also found. (…)

Secondly, the levels of intrapopulation diversity in the Bantu-speaking peoples from the Namib were found to be consistently higher for mtDNA than for the NRY, reflecting the marked association between the Bantu expansion and the relatively young NRY E1b1a1a1 haplogroup, which has no parallel in mtDNA25,39. (…)

In the context of the Bantu expansions, these patterns have been mostly interpreted as the result of polygyny and/or higher levels of assimilation of females from resident forager communities38,40. However, most groups from the Angolan Namib are only mildly polygynous11 and ethnographic data suggest that the actual rates of polygyny in many populations may be insufficient to significantly reduce Nem2,41. In addition, the finding of a large Nef/ Nem ratio in the Himba (Fig. S5), who have almost no Khoisan-related mtDNA lineages9, indicates that female biased introgression cannot fully explain the observed patterns.

An alternative explanation may be sought in the prevailing matrilineal descent rules, which might have created a sex-specific structuring effect, similar to that proposed for patrilineal groups from Central Asia (…)

bantu-xun-plot
Bayesian skyline plots (BSP) of effective population size change through time, based on mtDNA (red) and the NRY (black). Thick lines show the mean estimates and dashed lines show the 95% HPD intervals. The vertical line highlights the 2 ky before present mark. Effective sizes are plotted on a log scale. Generation times of 25 and 31 years were assumed for mtDNA and the NRY, respectively32.

The third important sex-specific pattern observed in this study is the much lower amount of between-group differentiation for NRY than for mtDNA among Bantu-speaking populations (4.4% NRY vs. 20.2% mtDNA), in spite of the patrilocal residence patterns of all ethnic groups (Table S5). This difference can hardly be explained by unequal levels of introgression of “Khoisan” mtDNA lineages into the Bantu, since the percentage of mtDNA variation remains high (18.8%) when the Kuvale, who have high frequencies of “Khoisan”-related mtDNA, are excluded from the comparisons. It therefore seems more plausible that differentiation is higher in the mtDNA simply because there is more ancestral mtDNA than NRY variation that can be sorted among different populations (see 45). Moreover, due to the matriclanic organization of all Bantu-speaking communities, factors enhancing inter-group differentiation, like kin-structured migration and kin-structured founder effects46, would have been restricted to mtDNA. Finally, it is also likely that the discrepancy between among-group divergence of mtDNA and NRY might have been influenced by higher migration rates in males than females. In fact, although all Bantu-speaking populations have patrilocal residence patterns, the observance of endogamy rules severely constrains the between-group mobility of females. In this context, the children from extramarital unions involving members from different populations tend to be raised in the mother’s group, effectively increasing male versus female migration rates. Moreover, it is likely that, in the highly hierarchized setting of the Namib, most intergroup extramarital unions would involve men from dominant groups and women from peripatetic communities. This hypothesis is indirectly supported by the finding that in NRY-based clusters (but not in mtDNA) pastoralist populations are grouped together with peripatetic communities that share their cultural traits (Figs. S6 and 3b), suggesting that migration of NRY lineages follows a path that is similar to horizontally transmitted cultural features.

Related:

Y-DNA relevant in the postgenomic era, mtDNA study of Iron Age Italic population, and reconstructing the genetic history of Italians

iron_age_europe_mediterranean

Open Access Annals of Human Biology (2018), Volume 45, Issue 1, with the title Human population genetics of the Mediterranean.

Among the most interesting articles (emphasis mine):

Iron Age Italic population genetics: the Piceni from Novilara (8th–7th century BC), by Serventi, Panicucci, Bodega, et al.

Background: Archaeological data provide evidence that Italy, during the Iron Age, witnessed the appearance of the first communities with well defined cultural identities. To date, only a few studies report genetic data about these populations and, in particular, the Piceni have never been analysed.

Aims: To provide new data about mitochondrial DNA (mtDNA) variability of an Iron Age Italic population, to understand the contribution of the Piceni in shaping the modern Italian gene pool and to ascertain the kinship between some individuals buried in the same grave within the Novilara necropolis.

Subjects and methods: In a first set of 10 individuals from Novilara, we performed deep sequencing of the HVS-I region of the mtDNA, combined with the genotyping of 22 SNPs in the coding region and the analysis of several autosomal markers.

Results: The results show a low nucleotide diversity for the inhabitants of Novilara and highlight a genetic affinity of this ancient population with the current inhabitants of central Italy. No family relationship was observed between the individuals analysed here.

Conclusions: This study provides a preliminary characterisation of the mtDNA variability of the Piceni of Novilara, as well as a kinship assessment of two peculiar burials.


Reconstructing the genetic history of Italians: new insights from a male (Y-chromosome) perspective, by Grugni, Raveani, Mattioli, et al.

Background: Due to its central and strategic position in Europe and in the Mediterranean Basin, the Italian Peninsula played a pivotal role in the first peopling of the European continent and has been a crossroad of peoples and cultures since then.

Aim: This study aims to gain more information on the genetic structure of modern Italian populations and to shed light on the migration/expansion events that led to their formation.

Subjects and methods: High resolution Y-chromosome variation analysis in 817 unrelated males from 10 informative areas of Italy was performed. Haplogroup frequencies and microsatellite haplotypes were used, together with available data from the literature, to evaluate Mediterranean and European inputs and date their arrivals.

Results: Fifty-three distinct Y-chromosome lineages were identified. Their distribution is in general agreement with geography, southern populations being more differentiated than northern ones.

Conclusions: A complex genetic structure reflecting the multifaceted peopling pattern of the Peninsula emerged: southern populations show high similarity with those from the Middle East and Southern Balkans, while those from Northern Italy are close to populations of North-Western Europe and the Northern Balkans. Interestingly, the population of Volterra, an ancient town of Etruscan origin in Tuscany, displays a unique Y-chromosomal genetic structure.

italy-y-dna
Frequencies of the main Y-chromosome haplogroups E1b, J2 and R1b and their sub-clades in the 10 analysed Italian population samples. Black sectors in the primary pies are proportional to the frequency of the main haplogroup in each population. Coloured sectors in the secondary pies are proportional to the frequencies of sub-haplogroups within the relative main haplogroup.

Mitochondrial variability in the Mediterranean area: a complex stage for human migrations, by De Angelis, Scorrano, Martínez-Labarga, et al.

Context: The Mediterranean area has always played a significant role in human dispersal due to the large number of migratory events contributing to shape the cultural features and the genetic pool of its populations.

Objective: This paper aims to review and diachronically describe the mitogenome variability in the Mediterranean population and the main demic diffusions that occurred in this area over time.

Methods: Frequency distributions of the leading mitochondrial haplogroups have been geographically and chronologically evaluated. The variability of U5b and K lineages has been focussed to broaden the knowledge of their genetic histories.

Results: The mitochondrial genetic makeup of Palaeolithic hunter-gatherers is poorly defined within the extant Mediterranean populations, since only a few traces of their genetic contribution are still detectable. The Neolithic lineages are more represented, suggesting that the Neolithic revolution had a marked effect on the peopling of the Mediterranean area. The largest effect, however, was provided by historical migrations.

Conclusion: Although the mitogenome variability has been widely used to try and clarify the evolution of the Mediterranean genetic makeup throughout almost 50 000 years, it is necessary to collect whole genome data on both extinct and extant populations from this area to fully reconstruct and interpret the impact of multiple migratory waves and their cultural and genetic consequences on the structure of the Mediterranean populations.

mtdna-mediterranean
Major migratory routes with the associated mtDNA haplogroups for the Upper Palaeolithic (solid lines) and the Neolithic (dashed lines) chronologies. Other hypothetical migratory routes are presented with dotted lines (see text for more details).

Mediterranean Y-chromosome 2.0—why the Y in the Mediterranean is still relevant in the postgenomic era, by Larmuseau & Ottoni.

Context: Due to its unique paternal inheritance, the Y-chromosome has been a highly popular marker among population geneticists for over two decades. Recently, the advent of cost-effective genome-wide methods has unlocked information-rich autosomal genomic data, paving the way to the postgenomic era. This seems to have announced the decreasing popularity of investigating Y-chromosome variation, which provides only the paternal perspective of human ancestries and is strongly influenced by genetic drift and social behaviour.

Objective: For this special issue on population genetics of the Mediterranean, the aim was to demonstrate that the Y-chromosome still provides important insights in the postgenomic era and in a time when ancient genomes are becoming exponentially available.

Methods: A systematic literature search on Y-chromosomal studies in the Mediterranean was performed.

Results: Several applications of Y-chromosomal analysis with future opportunities are formulated and illustrated with studies on Mediterranean populations.

Conclusions: There will be no reduced interest in Y-chromosomal studies going from reconstruction of male-specific demographic events to ancient DNA applications, surname history and population-wide estimations of extra-pair paternity rates. Moreover, more initiatives are required to collect population genetic data of Y-chromosomal markers for forensic research, and to include Y-chromosomal data in GWAS investigations and studies on male infertility.

y-dna-plot
Two-dimensional plot of the PCA of Y-chromosomal haplogroup frequencies of modern populations from Europe, the Near and Middle East and North Africa. Symbols are as in the legend. The inset shows the plot of factor coordinates of the variables used.

We are clearly seeing in the latest genomic papers that Y-DNA was indeed extremely important to assess ancient population movements.

See also:

Indo-European demic diffusion model, 3rd edition

pca-yamna-corded-ware

I have just uploaded the working draft of the third version of the Indo-European demic diffusion model. Unlike the previous two versions, which were published as essays (fully developed papers), this new version adds more information on human admixture, and probably needs important corrections before a definitive edition can be published.

The third version is available right now on ResearchGate and Academia.edu. I will post the PDF at Academia Prisca, as soon as possible:

pca-map-yamna-corded-ware-bell-beaker
Map overlaid by PCA including Yamna, Corded Ware, Bell Beaker, and other samples

Feel free to comment on the paper here, or (preferably) in our forum.

A working version (needing some corrections) divided by sections, illustrated with up-to-date, high resolution maps, can be found (as always) at the official collaborative Wiki website indo-european.info.