Irish and British cattle may have greater wild auroch admixture

Quickies

Stephen D.E. Park et al., Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle. Genome Biology 2015. Open access → LINK [doi:10.1186/s13059-015-0790-2]

Abstract

Background

Domestication of the now-extinct wild aurochs, Bos primigenius, gave rise to the two major domestic extant cattle taxa, B. taurus and B. indicus. While previous genetic studies have shed some light on the evolutionary relationships between European aurochs and modern cattle, important questions remain unanswered, including the phylogenetic status of aurochs, whether gene flow from aurochs into early domestic populations occurred, and which genomic regions were subject to selection processes during and after domestication. Here, we address these questions using whole-genome sequencing data generated from an approximately 6,750-year-old British aurochs bone and genome sequence data from 81 additional cattle plus genome-wide single nucleotide polymorphism data from a diverse panel of 1,225 modern animals.

Results

Phylogenomic analyses place the aurochs as a distinct outgroup to the domestic B. taurus lineage, supporting the predominant Near Eastern origin of European cattle. Conversely, traditional British and Irish breeds share more genetic variants with this aurochs specimen than other European populations, supporting localized gene flow from aurochs into the ancestors of modern British and Irish cattle, perhaps through purposeful restocking by early herders in Britain. Finally, the functions of genes showing evidence for positive selection in B. taurus are enriched for neurobiology, growth, metabolism and immunobiology, suggesting that these biological processes have been important in the domestication of cattle.

Conclusions

This work provides important new information regarding the origins and functional evolution of modern cattle, revealing that the interface between early European domestic populations and wild aurochs was significantly more complex than previously thought.

Fig. 5. Geographic contour map of aurochs genomic admixture with individual European breed D statistics (ABBA/BABA test results) plotted according to population origin and visualized using the ArcMap component of the ArcGIS software suite. The ABBA/BABA test tree topology is also shown and the contour point value for each European breed (P1) was generated from the mean D statistic where P2 is set to each of seven West African taurine populations in turn

Ainu genetics in their geographical context

Quickies

Timothy A. Jinam et al., Unique characteristics of the Ainu population in Northern Japan. Journal of Human Genetics 2015. Open access → LINK [doi:10.1038/jhg.2015.79]

Abstract

Various genetic data (classic markers, mitochondrial DNAs, Y chromosomes and genome-wide single-nucleotide polymorphisms (SNPs)) have confirmed the coexistence of three major human populations on the Japanese Archipelago: Ainu in Hokkaido, Ryukyuans in the Southern Islands and Mainland Japanese. We compared genome-wide SNP data of the Ainu, Ryukyuans and Mainland Japanese, and found the following results: (1) the Ainu are genetically different from Mainland Japanese living in Tohoku, the northern part of Honshu Island; (2) using Ainu as descendants of the Jomon people and continental Asians (Han Chinese, Koreans) as descendants of Yayoi people, the proportion of Jomon genetic component in Mainland Japanese was ~18% and ~28% in Ryukyuans; (3) the time since admixture for Mainland Japanese ranged from 55 to 58 generations ago, and 43 to 44 generations ago for the Ryukyuans, depending on the number of Ainu individuals with varying rates of recent admixture with Mainland Japanese; (4) estimated haplotypes of some Ainu individuals suggested relatively long-term admixture with Mainland Japanese; and (5) highly differentiated genomic regions between Ainu and Mainland Japanese included EDAR and COL7A1 gene regions, which were shown to influence macroscopic phenotypes. These results clearly demonstrate the unique status of the Ainu and Ryukyuan people within East Asia.

Figure 1. Principal component analysis (PCA) plot after omitting closely related Ainu individuals.

The study detected some differences between Ainu and other East Asians in genes that produce differences in appearance, these are:

Two out of five genes for facial morphology (PAX3 and COL17A1) contain highly differentiated SNPs, as with the hair/tooth morphology gene (EDAR).

Ancient mitochondrial DNA from Alaska babies

Quickies

Two new ancient Native American mtDNA sequences from what is now Alaska and back in the day, some 11,500 years ago, was linked to Asia forming the Beringia isthmus.

Justin C. Tackney et al., Two contemporaneous mitogenomes from terminal Pleistocene burials in eastern Beringia. PNAS 2015. Pay per view (free in 6 months) → LINK [doi: 10.1073/pnas.1511903112]

Abstract

Pleistocene residential sites with multiple contemporaneous human burials are extremely rare in the Americas. We report mitochondrial genomic variation in the first multiple mitochondrial genomes from a single prehistoric population: two infant burials (USR1 and USR2) from a common interment at the Upward Sun River Site in central Alaska dating to ∼11,500 cal B.P. Using a targeted capture method and next-generation sequencing, we determined that the USR1 infant possessed variants that define mitochondrial lineage C1b, whereas the USR2 genome falls at the root of lineage B2, allowing us to refine younger coalescence age estimates for these two clades. C1b and B2 are rare to absent in modern populations of northern North America. Documentation of these lineages at this location in the Late Pleistocene provides evidence for the extent of mitochondrial diversity in early Beringian populations, which supports the expectations of the Beringian Standstill Model.

A very good article in Spanish is available at Paleoantropología Hoy, which mentions that the only modern population to have both matrilineages are the Hualapai, who live in the state of Arizona (USA). 

Other populations carrying the C1b lineage are the Pima (Arizona), Delta Yuman (California), Ignacianos (Bolivia), extinct Tainos from Puerto Rico and the Norris Farm remains from pre-contact Illinois, as well as a few unspecificied "other tribes". 

B2 is more common, being found in some 37 populations, including Yakama, Wishram, Northern Paiute-Shoshone, Navajo, Zuni, Jemez (all these from North America), Quechua and Aymara (Peru, Bolivia). It was also common among the old Fremont and Anasazi populations of SW USA. 

He also mentions that the archaeological data for the remains was described by Potter et al. 2014. The two babies are post-natal and pre-natal deaths respectively and were carefully buried with ochre paint on their bodies, arrow points (bow and arrows originally, I presume) and organic remains (food). Then a hearth was built over the tomb, which had absolutely normal use, including disposing of food remains (although it can be speculated that they were additional food offerings), except for another baby that was apparently cremated at it in later times. The deaths of the two babies took place in summer, judging from the animal remains of the burial context.

The oldest known plague

New ancient DNA research has identified the bacterium Yersinia pestis, which causes the deadly and epidemic illness known as plague, in Chalcolithic and Bronze Age Central Eurasia, from Altai to Poland and the Caucasus.

S. Rasmussen, M.E. Alentoft et al., Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago. Cell 2015. Open access → LINK [doi:http://dx.doi.org/10.1016/j.cell.2015.10.009]

Summary

The bacteria Yersinia pestis is the etiological agent of plague and has caused human pandemics with millions of deaths in historic times. How and when it originated remains contentious. Here, we report the oldest direct evidence of Yersinia pestis identified by ancient DNA in human teeth from Asia and Europe dating from 2,800 to 5,000 years ago. By sequencing the genomes, we find that these ancient plague strains are basal to all known Yersinia pestis. We find the origins of the Yersinia pestis lineage to be at least two times older than previous estimates. We also identify a temporal sequence of genetic changes that lead to increased virulence and the emergence of the bubonic plague. Our results show that plague infection was endemic in the human populations of Eurasia at least 3,000 years before any historical recordings of pandemics.

The bacterium was yet unable to cause the bubonic form of the plague and could not spread by means of fleas either. Instead it probably caused pneumonic and spticemic plague and was propagated by coughing and sneezing, much like the flu. 

Figure 1

Archaeological Sites of Bronze Age Yersinia pestis
(A) Map of Eurasia indicating the position, radiocarbon dated ages and associated cultures of the samples in which Y. pestis were identified. Dates are given as 95% confidence interval calendar BC years. IA: Iron Age.
(B) Burial four from Bulanovo site. Picture by Mikhail V. Khalyapin. See also Table S1.

In spite of the hype, the prevalence of the plague was low: only 7 out of 101 samples tested positive for the bacterium, ranging from c. 2800 BCE (Altai) to c. 1000 BCE (Southern Azerbaijan, Iran). A 7% prevalence is still significant but it's also obvious that 93% of the people in the period studied did not die from the plague, so let's not exaggerate, alright?

The exaggeration is already seeded in the study with passages as this one:

These early plagues may have been responsible for the suggested population declines in the late 4^th millennium BC and the early 3^rd millennium BC (Hinz et al., 2012, Shennan et al., 2013).

Neither of the referenced studies (see here and here) deals with Eastern Europe, West Asia or Central Asia, and the analyzed dates only slightly overlap with the period in which Y. pestis is found, so I fail to see the logic. It is true that there could be a coincidence in the case of Little Poland, where both Y. pestis and a demographic decline are apparent c. 2000 BCE but in all other cases it really needs a good deal of imagination to make any association.

In any case, it is clear that even the most virulent plague ever known, the Black Death, only managed to make a dent in the European demography and its consequences were not those of demographic re-expansion of the less affected populations (Polish, Basques) but a double socio-economic transition in two phases:

1. The lack of manpower in the decades after the Black Death allowed the lower classes to renegotiate their situation in various ways. It was the period in which the feudal system was most dramatically eroded, with peasants gaining control on their farmed lands and lords losing large shares of their exploitative profits, while being forced to compete against each other for whom offered best working conditions to the now scarce farmers, who, legally or not, migrated from the worst places to the ones offering better conditions. 
2. A reaction by profit-jealous landlords that largely replaced farming by husbandry, which requires less manpower. A well known case were the English enclosures, which would, slowly but steadily, set the foundations of Capitalism.

This is explained by historian, actor and director Terry Jones in the following video:

So the consequences and context of these epidemics must be considered adequately and not distorted nor simplified unduly in the line of the infamous Guns, Germs and Steel book, which greatly exaggerates the consequences of natural epidemics and is one of the favorite books of Eurocentric reactionaries with a distorted and overly simplistic view of things. One of the "virtues" of the epidemic hype is that it somehow absolves the winners from their historical crimes, blaming them on nature almost alone: instead of genocide, they use these deformations of reality to blame the mass destruction of whole nations and populations, be them Neanderthals or Native Americans, on "natural causes". 

Hypocrisy!

Instead I wonder about the real demographic impact, not yet well assessed, of the epidemics, and also about the real socio-economic consequences of such demographic declines. Of course, they could have allowed for localized migrations in the aftermath of the epidemics (or whatever other causes of demographic declines) but they should also have favored at least short-term renegotiations of the social order in favor of the suddenly scarce working classes (farmers). This "upward mobility" and partial "leveling" of what was already in many cases a feudal-like caste society should have dramatic effects in the constitution of the nations of the Bronze Age, regardless of later re-adjustments and expansions, which one can imagine as an imperfectly cyclical process.

More evidence supporting very old colonization of Asia by H. sapiens

Quickies

Quite worth mentioning:

Wu Liu et al., The earliest unequivocally modern humans in southern China. Nature 2015. Pay per view → LINK [doi:10.1038/nature15696]

Abstract

The hominin record from southern Asia for the early Late Pleistocene epoch is scarce. Well-dated and well-preserved fossils older than ~45,000 years that can be unequivocally attributed to Homo sapiens are lacking1, 2, 3, 4. Here we present evidence from the newly excavated Fuyan Cave in Daoxian (southern China). This site has provided 47 human teeth dated to more than 80,000 years old, and with an inferred maximum age of 120,000 years. The morphological and metric assessment of this sample supports its unequivocal assignment to H. sapiens. The Daoxian sample is more derived than any other anatomically modern humans, resembling middle-to-late Late Pleistocene specimens and even contemporary humans. Our study shows that fully modern morphologies were present in southern China 30,000–70,000 years earlier than in the Levant and Europe. Our data fill a chronological and geographical gap that is relevant for understanding when H. sapiens first appeared in southern Asia. The Daoxian teeth also support the hypothesis that during the same period, southern China was inhabited by more derived populations than central and northern China. This evidence is important for the study of dispersal routes of modern humans. Finally, our results are relevant to exploring the reasons for the relatively late entry of H. sapiens into Europe. Some studies have investigated how the competition with H. sapiens may have caused Neanderthals’ extinction (see ref. 8 and references therein). Notably, although fully modern humans were already present in southern China at least as early as ~80,000 years ago, there is no evidence that they entered Europe before ~45,000 years ago. This could indicate that H. neanderthalensis was indeed an additional ecological barrier for modern humans, who could only enter Europe when the demise of Neanderthals had already started.

When asked in private correspondence earlier today what did I think of this, I replied that María Martinón (second listed author) is a top expert in tooth morphology and that, if she says they are unmistakably H. sapiens, I have to believe it. 

I also replied a bit more extensively that this should be no surprise, that evidence in favor of a c. 100 Ka BP migration of H. sapiens into South and Southeast Asia has been piling up for some time already. Some of the most important pieces of evidence are the Zhirendong jaw (also from Southern China, dated to c. 100 Ka BP) and the African-like Katoati toolkits (NW India, dated to c. 96 Ka BP). These dates are roughly coincident with the end of the Abbassia Pluvial (c. 125-90 Ka BP), which is in turn coincident with the period of evidence for earliest H. sapiens presence in Arabia and Palestine. 

In other words, our ancestors crossed into Arabia and Palestine (and maybe other less well documented nearby regions of West Asia) around 125 millennia ago (with a second wave c. 90 Ka ago). The Neanderthal admixture episode probably happened soon after. Then they moved to South and SE Asia, quite possibly pressed by growingly arid conditions in Arabia, and this second migration took place around 100 millennia ago (earlier is not yet supported but can't be fully discarded). 

All this has major implications for molecular clock calibration, of course: mtDNA L3 should be c. 125 Ka old and M some 100 Ka old, similarly Y-DNA CF should be around 100 Ka old as well. This is the kind of stuff that makes genetics-oriented people skeptic but the molecular clock is a mere educated hunch, while the archaeological data is serious evidence that cannot be ignored.

Neolithic genomes from Northwestern Turkey

Or yet another ancient European DNA study, with some quirks and, critically, the first ancient farmer sample from the Eastern Mediterranean, specifically Northwestern Anatolia, near Yenişehir (Bursa province).

Iain Mathieson et al. Eight thousand years of natural selection in Europe. BioRxiv (pre-pub), 2015. Freely accessible → LINK [doi: http://dx.doi.org/10.1101/016477]

Abstract

The arrival of farming in Europe around 8,500 years ago necessitated adaptation to new environments, pathogens, diets, and social organizations. While indirect evidence of adaptation can be detected in patterns of genetic variation in present-day people, ancient DNA makes it possible to witness selection directly by analyzing samples from populations before, during and after adaptation events. Here we report the first genome-wide scan for selection using ancient DNA, capitalizing on the largest genome-wide dataset yet assembled: 230 West Eurasians dating to between 6500 and 1000 BCE, including 163 with newly reported data. The new samples include the first genome-wide data from the Anatolian Neolithic culture, who we show were members of the population that was the source of Europe's first farmers, and whose genetic material we extracted by focusing on the DNA-rich petrous bone. We identify genome-wide significant signatures of selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height.

As you can see from the title and the abstract, much of the study is focused on more or less debatable selection signatures. Interesting, of course, but not what my greatest interest, less so as I perceive that there is missing data that may be crucial for the understanding of some of such selection, notably the mainstream European LCT 13910-T allele.

How can you do an analysis of selection on this allele while ignoring the first known carriers of it: Chalcolithic (proto-)Basques and Swedes (Gökhem particularly)?

Luckily there are other highlights...

Northwestern Anatolian ancient genetics

The new ancient Neolithic samples come from two sites: Menteşe Höyük (n=5) and Barcın Höyük (n=21), both located in the Yenişehir plain, southeast of Istanbul across the Marmara Sea. The archaeological context of the samples, as well as that of many other European ones, resequenced for this study with new technology, is discussed in the Supplementary Information section.

These ancient Northwest Anatolian farmers have shown to be very similar to early European farmers. The authors estimate that these were only some 10% admixed with Paleoeuropeans, relative to the Anatolian samples, although later individuals from the West did of course had further Paleoeuropean admixture.

I must emphasize the adjective "Northwestern" because Anatolia Peninsula is a large territory where the Neolithic had differential implementation in time and cultures. Critically we cannot be certain that there is any identity between these Western Anatolian first farmers and those from South-Central Anatolia, for example those of the world-famous Çatal Höyük village. This is because the Neolithic of South-Central Anatolia is much older and there are archaeological indications that suggest that the settlement of Western Anatolia and Greece took place via coastal migration. The origin of this coastal migration probably involved Cyprus, which in turn was more directly related to the Neolithic of the Levant (PPNB) than to that of South-Central Anatolia. Some genetic data also seem to suggest that the precursors of early European farmers were from the Levant, rather than from further North. But of course the full resolution of this mystery will have to await for ancient DNA from the relevant regions, something that may be aided by the recent technological breakthroughs but that will also require peace, so geneticists and archaeologists can do their field work (there are of course many other much more excruciating reasons to hope for peace and normalization in West Asia, naturally, don't get me wrong).

In any case we finally have a reference genome for what can be termed the Aegean Neolithic and it seems it was even closer to European derivatives. We cannot anyhow discard that there was some backflow from Greece or other parts of the Balcans to Western Anatolia because there was indeed some interaction across the Aegean. However a much more clear cut cultural divide has been argued to exist between the cultures of the Marmara Sea and those of inland Thrace, so, if there was any such backflow, it probably happened before the expansion of Thessalian Neolithic northwards.

Principal Component Analysis

This is the Principal Component Analysis provided by this study (fig. 1B). The modern samples are in gray with no labeling whatsoever but I guess most readers will approximately identify them easily, as the basic layout has been repeated in so many recent aDNA studies:

Figure 1: Population relationships of samples. (...) B: Principal component analysis of 777 modern West Eurasian samples (grey), with 221 ancient samples projected onto the first two principal component axes and labeled by culture. Abbreviations: [E/M/L]N Early/Middle/Late Neolithic, LBK Linearbandkeramik, [E/W]HG Eastern/Western hunter-gatherer, [E]BA [Early] Bronze Age, IA Iron Age.

As in Olalde 2015 or Haak 2015, or even Lazaridis 2014, WHGs appear located rather "towards the South", unlike in some other PCAs, particularly Europe-only ones. I do find this to be interesting and potentially informative, at least while we await for Atlantic European ancient nuclear DNA.

Therefore, you'll forgive me for the redundancy of reusing the above image a couple of times in order to make a couple of points.

The thesis that most of these studies are pushing for is a simplistic triangular scenario for the formation of modern Europeans with a formula that can be described as {x.EEF+y.WHG+z.Kurgan}. I don't deny that this is quite approximative but I am also quite certain that it is missing important clues. In fact, the triangular thesis seems to fail to explain most Northern European genetic makeup, while the origins of Basques also remain somewhat unexplained by it. Let's see:

Annotations on the PCA: triangular thesis fails, extra HG (EHG?) is needed.

It would seem quite apparent that the triangular thesis (described on the PCA by a slashed line) fails to explain most of Western and Northern European genetic makeup, which is clearly much more deviated towards Paleoeuropean hunter-gatherers than it allows.

Just including on the equation Eastern European hunter-gatherers (dotted line) would be enough to solve most of the problem, although it does of course arises other questions about how and when this extra Paleoeuropean blood was incorporated.

This solution would still leave Basques outside of it. It requires instead of a Western hunter-gatherer extra admixture on top of a simple Neolithic cluster basis:

Annotations on the PCA: Basques can be explained (?) as simple {Neo-European + WHG admixture}

Of course that the actual sources of Paleoeuropean admixture can be more complex, as suggested by some studies, like Günther & Valdiosera 2015, who claimed Scandinavian HG admixture not just in Gökhem farmers but also in Ötzi ("Iceman" in the above graph). These did not use EHG samples but in any case, if correct, it is a pre-Kurgan admixture from the Northeast of the subcontinent.

A key excerpt from the Supplementary Information 2 section that someone (Simon, I think) used to argue for steppe ancestry in Basques in a discussion at Eurogenes blog:

The Iberian Chalcolithic population lacks steppe ancestry, but Late Neolithic central and northern Europeans have substantial such ancestry (Extended Data Fig. 3E) suggesting that the spread of ANE/steppe ancestry did not occur simultaneously across Europe. All presentday Europeans have less steppe ancestry than the Corded Ware5, suggesting that this ancestry was diluted as the earliest descendants of the steppe migrants admixed with local populations. However, the statistic f4(Basque, Iberia_Chalcolithic; Yamnaya_Samara,Chimp)=0.00168 is significantly positive (Z=8.1), as is the statistic f4(Spanish, Iberia_Chalcolithic; Yamnaya_Samara, Chimp)=0.00092 (Z=4.6). This indicates that steppe ancestry occurs in present-day southwestern European populations, and that even the Basques cannot be considered as mixtures of early farmers and hunter-gatherers without it4.

What does this say in fact? It says nothing about Western Hunter-Gatherers, only that Basques appear as more Yamna-like than the Iberian Chalcolithic sample. I see no reason why this cannot be caused by simple extra WHG admixture, although it can also imply other Paleoeuropean such as SHG or EHG inflow. What I do see from other studies (and again for all I can discern in this one) is that Basques do lack any clear Yamna signature and notably their Caucasus or Northern West Asian component (always present where Kurgan admixture is unmistakable and therefore a clear indicator of it) is effectively zero (some individuals may have tiny non-zero such component, all very normal).

Admixture analysis with two and three source populations

The authors find that, while many populations can be modeled as product of simple two-way admixture, many need a three-way model, notably from the late Chalcolithic onwards:

Extended Data Figure 2: Early isolation and later admixture between farmers and steppe populations. A [actually B]: Mainland European populations later than 3000 BCE are better modeled with steppe ancestry as a 3rd ancestral population. B [actually A]: Later (post-Poltavka) steppe populations are better modeled with Anatolian Neolithic as a 3rd ancestral population. C: Estimated mixture proportions of mainland European populations without steppe ancestry. D: Estimated mixture proportions of Eurasian steppe populations without Anatolian Neolithic ancestry. E: Estimated mixture proportions of later populations with both steppe and Anatolian Neolithic ancestry. [F is below]

However this varies, because notably the Iberian Chalcolithic sample can still be modeled as a two-way admixture, what is in conformity with the consideration that the increase in the complexity took place not in any single event but rather first in Central and Eastern Europe and only later further West. This is in full conformity with the Kurgan model of Indoeuropean expansion, although it may require some refinement here and there.

For example it is becoming quite obvious that there was not only a westward movement of Eastern European populations but also a subsequent eastward backflow of the resulting admixed Central European ones. This is discussed in the supplementary materials, from page 43 onwards.

Extended Data Figure 2: (...) F: ADMIXTURE plot at k=17 showing population differences over time and space.
(click to expand)

To this I must add my conviction that the triangular model is not enough to actually explain modern European genetics and that greater Paleoeuropean genetic input in Northern and Western Europe is required as well. The great challenge in this regard is to sample Atlantic (and Baltic) Europe properly and extract whatever consequences that ancient genomes from these areas may provide. 

Naturally there is also some other research to be done in West Asia, where a good deal of the European (and also West Asian, naturally) ancestors lived once upon a time. That is the other major challenge. In this sense this study must be commended for its breakthrough in sampling ancient Northwestern Anatolians, which is a step in the right direction.

There are other blank zones to be researched as well in Southern Europe (Italy, Balcans) that may well provide complementary information.

Alleged selection

The authors claim to have found evidence for selection in twelve different alleles. I remain mildly skeptic because it is hard to judge if this was all selection or founder effect was involved as well. 

Some of the alleged targets of selection are:

Lactase persistance: rs4988235, also known as 13910-T, already mentioned above. The authors mention that the allele’s earliest appearance in our data is in a central European Bell Beaker sample (individual I0112) that lived between approximately 2300 and 2200 BCE. Older signals from the Chalcolithic Basque Country (fixated in a subpopulation) and Sweden are totally ignored. Of course it is a draft so far but it is clear that key information, widely available, is being ignored.

A light skin allele known as rs16891982 (in the gene SLC45A2). This allele was low in the studied ancient populations (but again might have been higher in the blank under-researched areas, I can't say). Unlike it, the derived allele of gene SLC24A5, was fixated in Neolithic NW Anatolians, as well as derived European ancient populations, being a clear case of founder effect (although it may have also helped with adaption to the low vitamin D diet caused by transition to agriculture). There are other pigmentation genes that may have been selected in complex interaction, as they seem to be partly correlated with latitude and are hard to explain based on ancient populations alone.

An important datum here is that: unlike closely related western hunter-gatherers, the Motala samples have predominantly derived pigmentation alleles at SLC45A2 and SLC24A5. So... is there another source of these light skin alleles (there are others and much is unknown anyhow) that is not from Neolithic farmers?

Another selection target is in the TLR1-TLR6-TLR10 gene cluster, which seems related to resistance to mycobacteria such as those causing leprosy, tuberculosis, etc. Regarding this complex cluster, I rather quote:

The strongest signal is at rs2269424 near the genes PPT2 and EGFL8 but there are at least six other apparently independent signals in the MHC (Extended Data Fig. 3); and the entire region is significantly more associated than the genome-wide average (residual inflation of 2.07 in the region on chromosome 6 between 29-34 Mb after genome-wide genomic control correction). This could be the result of multiple sweeps, balancing selection, or background selection in this gene-rich region.

The EDAR gene, related to tooth morphology (remember Pippi?) and hair thickness, as well denser sweat and mammary glands, in East Asians is also listed. Curiously enough, half of the Motala individuals (Epipaleolithic Sweden), carried the derived allele of rs3827760. Modern Scandinavians often have this derived allele, although the authors believe that it is because of more recent admixture:

The EDAR derived allele is largely absent in present-day Europe except in Scandinavia, plausibly due to Siberian movements into the region millennia after the date of the Motala samples.

Uh, really? How can you be so sure? I am very skeptic here again and would rather suspect a more complex pattern of partial Paleolithic (or at least Epipaleolithic) continuity, which may indeed have been brought from East Asia with the proto-Uralic migrations (or whatever). 

Another trait for which the authors claim selection is what they call "genetic height", i.e. height not measured from the actual individuals but from alleles that are believed to influence it. They argue for selection for lower height in Neolithic and Chalcolithic Iberia and for greater height in the Steppe instead, both being corrected to greater height in modern populations. Without objective measures to control for the assumed "genetic height", among other reasons, I find the whole story a bit hard to believe but who knows?

The production of this entry took a whole 8 hours working journey, including a half hour break but not preliminary reading and related discussions. If you liked it and have some coin to spare, consider donating. Thank you.

First African ancient nuclear DNA

Major update (Feb 12 2016): the authors have publicly corrected their conclusions: the alleged Eurasian admixture in Yoruba and Mbuti does not exist. See HERE for further details.

Mota cave

Whatever we may think of the conclusions (see below), this study is a most important breakthrough because it shows that ancient DNA can be obtained from remains preserved in hostile (hot) conditions, removing the technical barriers for research in these areas, which make up most of the inhabited world. The method, which relies in the vault-like conditions of the inner petrous earbone, was demonstrated earlier this year by Pinhasi et al. (open access) and is in itself a technical revolution in ancient DNA research.

M. Gallego Llorente, E.R. Jones et al., Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent. Science 2015. Pay per view → LINK [doi:10.1126/science.aad2879]

Supplementary materials are free (as usual) and most information seems to be there anyhow.

Abstract

Characterizing genetic diversity in Africa is a crucial step for most analyses reconstructing the evolutionary history of anatomically modern humans. However, historic migrations from Eurasia into Africa have affected many contemporary populations, confounding inferences. Here, we present a 12.5x coverage ancient genome of an Ethiopian male (‘Mota’) who lived approximately 4,500 years ago. We use this genome to demonstrate that the Eurasian backflow into Africa came from a population closely related to Early Neolithic farmers, who had colonized Europe 4,000 years earlier. The extent of this backflow was much greater than previously reported, reaching all the way to Central, West and Southern Africa, affecting even populations such as Yoruba and Mbuti, previously thought to be relatively unadmixed, who harbor 6-7% Eurasian ancestry.

Massive and late European Neolithic-like migration into Africa, even into the Bushmen, Pygmy and Hadza hunter-gatherers?! Well, that's the thesis and the authors seem to have some reasons to believe it. However I am a bit skeptic to say the least. 

The logic behind Llorente & Jones' conclusions is that, when replacing the "non-admixed African" baseline from the usual reference populations such as the Yoruba (a major SW Nigerian population) and Mbuti (Eastern Pygmies from the Ituri jungle of NE Congo) to this newly sequenced paleo-Ethiopian genome from Mota cave, all Africans appear more similar to West Eurasians, particularly to the reference ancient farmer "Stuttgart" (LBK) or his closest modern relatives: Sardinians. 

However this is untrue for some of the populations from the same region as Mota: most Ethiopian populations actually show a slight but significant decrease in their putative Eurasian ancestry (table S5). This is very intriguing, as is the main thesis of the study, and I have the impression that at least part of that appearance of European-like admixture may be explained by ancient internal African structure rather than true immigration. This possibility is not addressed in the study, so we will have to wait for counter-studies, be them professional or amateur. It would not be the first case where a pioneer study "finds" things that become less clear as new research is done, I am thinking of course on stuff like the problematic "ANE" component of Lazaridis 2014 or the extreme "Indoeuropean admixture" conclusions of Haak & Lazaridis 2015, which are much milder and clinal in other comparable studies.

So let's keep calm and wait for more data or improved analyses.

Fig. S6. The proportion of West Eurasian ancestry in modern eastern African populations. λYoruba,Druze (using Yoruba as the non-admixed reference and Druze as the source), estimated for individuals belonging to a number of Ethiopian populations.

Affinities

Mota seems to be most akin to modern Ari people of SW Ethiopia, who speak an Omotic language. He is also rather similar to the Sandawe of Southern Tanzania, who speak a distinct click language. These similitudes underline the importance that "tribal" nations have, among other reasons, for deciphering the ancient African demographic landscape.  

Fig. S5. PCA showing the relationship between Mota and contemporary Ethiopian populations. Components were loaded on contemporary Ethiopian populations using ~480k SNPs, with Mota projected on these dimensions.

His mtDNA haplogroup is L3x2a (table S3), described by Behar 2008 in Ethiopia and the Arabian peninsula (but most likely original from The Horn) and his Y-DNA one is E1b1 (table S4), a major African haplogroup, most likely original from the same Upper Nile region, with some offshoots in West Eurasia.

He did not carry any known allele for lactase persistance (table S13) but he was homozygous for three alleles that seem to confer altitude adaptation (resistance to hypoxia, table S14). 

He had brown eyes and dark or black hair, skin color determination was inconclusive (the matter is still ill-understood) but he did not carry any European alleles associated with lighter pigmentation, so most likely he was black (or, with more chromatic descriptive precision, brown).

Neanderthal admixture testing

This seems to be the detail that most strongly supports the thesis of the study: Mota is even less akin to Neanderthals than modern Africans. From article S11:

The two African genomes, Yoruba and Mbuti, also have slightly positive D values, indicating that they are slightly more similar to Neanderthal than Mota is. This result is likely driven by the West Eurasian component found in modern Africans.

However when we look at the raw data (table S9), we can see that, while the Yoruba Neanderthal admixture estimate is slightly larger than the error margin, the Mbuti one is markedly smaller, so we can still consider the latter to be effectively zero or at the very least negligible. 

This is potentially contradictory with the alleged 6-7% West Eurasian admixture that the study claims for Mbuti (table S5), which would be almost the same as that of Yorubas (7-8%), so I think that there is something not properly pondered and that, while Yorubas may have some (very minor?) West Eurasian admixture, the case for the Mbuti is very much suspect of false positive caused by confounding factors, such as ill understood ancient African diversity. 

Most strange is the case of Khoisan populations. While two of them (Nama and Khomani) do seem to have clear Eurasian admixture, as they stick up well above the average, several others (Xun, Juhoansi or GuiGhanaKgal) are very low when using Yoruba as reference and the tiny bit can be attributed to the pull effect caused by the mere fact that Yoruba and Khoisan are very different populations, which diverged (at least in the essentials) even before the Out-of-Africa migration took place. I strongly suspect that this confounding factor is also at play when comparing with Mota and even more strongly so, because Mota quite obviously lacks the later intra-African partial homogenization tendency caused by migrations such as the Nilotic or Bantu ones. 

Fig. S7. Maps showing the proportion of West Eurasian ancestry in African populations. The proportion of West Eurasian ancestry calculated using either (A), Druze. λMota,Druze, or (B), LBK, λMota,LBK, as a source, and Mota as the non-admixed African reference in both cases.

Early European farmers or...?

Sure, among the tested populations, Sardinians are the best apparent matches for the source of the alleged Eurasian admixture in Africa (tables S6 and S7). But next in line are Belorussians and Lithuanians, what is a bit perplexing, because in the European analyses these are two completely opposite poles along the PC1. Basques and Russians however are surprisingly bad matches, with French, Italian, Spaniards, etc. being in between. 

Among ancient populations, Stuttgart (LBK) appears as a good match when using a Yoruba reference but not so good when using a Mbuti one. Inversely, Lochsbour (Epi-Magdalenian) looks a very bad match when using Yoruba but a bit better when using Mbuti. As Mbuti seem still to be a more clear outgroup than Yoruba, I think that table S7 holds preference over S6. 

Hence I'd rather discard that the source of the apparent Eurasian admixture is LBK-like. However Sardinians (or a similar ancient population) are a better candidate. But what about Belorussians and Lithuanians, whose scores are also very high? Perplexing.

So basically I have all kind of doubts and I look forward to further research that may clarify them.