An archaeological scenario for Out of Arabia

Jeffrey Rose and Anthony Marks have a preprint in which he details an archaeological scenario for the emergence of the Emiran (arguably the best candidate for the ur-Upper Paleolithic at the moment) from Arabian progenitors who themselves had Northeast African Nubian Levallois progenitors. I proposed Out of Arabia a few years ago and followed research suggestive of such a trajectory of modern humans in various posts under the Out of Arabia label.

In a nutshell, it seems to me that the 50kya OoAfrica model is wrong, falsified by (i) the dating of Neandertal adixture (which precedes it and could only have happened outside of Africa), (ii) the dating of human mtDNA and NRY trees in numerous papers that show a split that precedes 50kya. This in itself proves that the Upper Paleolithic (which is attested in the post-50kya period and rapidly spreads across Eurasia in a genetic Big Bang of expansion leading to the full disappearance of Neandertals by ~40kya) must have local Eurasian origins rather than being an import from Africa.

If UP is not linked to the Out-of-Africa event, then two questions arise: (i) how did the UP arise in Eurasia, and (ii) when did the Out-of-Africa event take place? The increasing adoption of a "slow mutation rate", the discovery of a potential ~100kya layer of ancestry separating Europeans from East Asians, and, on the archaeology side, the proliferation of evidence against the "coastal migration route" all hint in OoAfrica taking place much earlier than the UP revolution in answer to question (ii).  Indeed, one of the few stumbling blocks of a much earlier Out-of-Africa (the date of L3~70kya) may actually be falling, if it turns out that African L3 is nested within Eurasian M+N and not vice versa. The new preprint by Rose snf Marks helps answer question (i) by proposing an archaeological scenario that derives the UP of the Levant from the MP of Arabia.

From the paper:

In sum, the tool assemblages of the early Emiran include a combination of both classic UP tool types and MP Levallois points; it cannot be accurately characterized as fully UP, rather, an amalgamation of MP and UP forms. Viewed solely within a Levantine context, the technological and typological patterning of the early Emiran might suggest it derived from local innovation without significant external demographic input. 

... 

So, with no clear cut antecedents in the Levant, do the three Emiran technological traits that have no deep Levantine ancestry (i.e., bidirectional core preparation, the use of cresting, and the presence of lateral modification on Levallois points), have  demonstrable origins elsewhere? Conversely, do those deeply rooted Levantine characteristics of the Emiran (i.e., elongated Levallois point production and UP tool  manufacture) have comparable analogues in adjacent areas? 

...  

Given these technological and typological considerations, we find no direct relationship between any northeast African MIS 5 industry and the early Emiran. The African data do suggest that the Emiran preferential bidirectional Levallois point production strategy ultimately arose in northeast Africa during late MIS 6. This reduction strategy became increasingly widespread during MIS 5, where it spread as far south as the Ethiopian Rift and east into the Arabian Peninsula. This wide distribution suggests extensive cultural contact, either direct or indirect, along the Nile Valley and across the Red Sea during the Last Interglacial, when climatic conditions were optimal. 

...  

By MIS 5.3 (~ 100 ka), perhaps, even as early as the Last Interglacial, the African Nubian Complex was widespread in Arabia, from the Yemeni Hadramawt to the eastern edge of the Nejd Plateau in southern Oman. Additional manifestations of this technocomplex have been found in the Rub' al Khali, central Saudi Arabia, and the Al Jawf basin of northern Saudi Arabia, less than 300 km southeast of ‘Ain Difla. Given the Nilotic origin of the Nubian Complex, its presence in Arabia may be firmly understood as a huntergatherer range expansion out of northeast Africa.  

...  

The techno-typological patterns we have observed point to an origin of the Emiran that was neither wholly rooted in the Levant nor the result of a complete demographic replacement from groups expanding out of Africa; rather, the Emiran combines elements of the Nubian Levallois system with typological elements from the southern Levantine Mousterian. This scenario envisions a zone stretching across the interface of northwestern Arabia and the southern Levant, where the territories of Levantine and Arabian huntergatherer populations overlapped during MIS 5. Bilateral exchange over time resulted in the incorporation of an Afro-Arabian core reduction strategy with a Levantine toolmaking tradition that extends back to the Early Mousterian. 

...  

African Nubian Complex toolmakers, at least, were modern humans. AMH specimens have been documented in North Africa from 150 ka onward (Smith et al., 2007; Hublin and McPherron, 2012), while no other species has yet been found there. An AMH child burial was excavated from an extraction pit associated with Activity Phase III at Taramsa Hill 1 (Vermeersch et al., 1998; Van Peer et al., 2010), with a terminus post quem of ca. 70 ka. Given the technological similarity of the Classic Dhofar Nubian and the Late Nubian Complex of the Middle Nile Valley in Egypt, as well as the fact that there is no evidence for prior MP human occupation in southern Oman, it is reasonable to associate the distribution of Nubian Complex sites with a population of AMHs spread across northeast Africa and the Arabian Peninsula. The presence of Nubian Levallois technology in southern Arabia and the Horn of Africa (Clark, 1954; Kurashina, 1978; Clark, 1988; Beyin, 2013), as well as northern Arabia and in the Red Sea hills of Egypt, suggests that early human groups traveled to and from Africa via both the Arabian and Levantine Corridors.

It is unfortunate that Arabia is so poor (to wholly deficient?) in ancient human remains from this critical period. Nonetheless, it makes sense that if modern humans were present in Northeast Africa in association with Nubian Complex tools, they would be the ones who carried them to Arabia. The presence of AMH in the Levant (associated with Mousterian tools) was often dismissed until recently as the Out-of-Africa that failed, partly because the Shkul/Qafzeh hominins were the only pre-UP modern humans in Eurasia (making their extinction plausible) and partly because of the widespread view that Out-of-Africa happened ~70-50kya (which by definition would imply that the Mount Carmel hominins weren't the Out-of-Africa.

However, if AMH were also present in Arabia during the MP it is much more difficult to argue for extinction of Eurasian modern humans and later replacement by a "late" Out-of-Africa event: this would imply that both the Levantine and Arabian humans would disappear. Moreover, the genetics no longer requires a late Out-of-Africa event and the UP is no longer plausibly concurrent with the OoAfrica event. In short, a quite simple explanation is that one group of AMH (from Arabia) mixed with another group of AMH (from the Levant) and the UP arose in this population. The latter group (from the Levant) lived in proximity to Neandertals and thus the evidence for Neandertal admixture in non-Africans is easily explained (no need to invoke unattested Neandertals admixing with "coastal route" migrating humans).

"Out of Arabia" and the Middle-Upper Palaeolithic transition in the southern Levant 

Jeffrey I. Rose, Anthony E. Marks

Beginning some 50 thousand years ago, a technological transition spread across the Near East and into Eurasia, in the most general terms characterized by a shift from preferential, prepared core reduction systems to the serial production of elongated points via opposed platform cores. The earliest known occurrence of such a technological shift is the Emiran Industry, whose earliest manifestations are found in the southern Levant. The cultural and demographic source(s) of this industry, however, remain unresolved. Looking to archaeogenetic research, the emerging picture indicates a major dispersal of our species out of Africa between 100 and 50 thousand years ago. Ancient DNA evidence points to low levels of admixture between Neanderthal and these pioneering modern human populations, which some suggest occurred in the Near East between 60 and 40 thousand years ago. These propositions underscore the significance of the Emiran and beg a reassessment of its origins. In this paper, we ask whether the Emiran was a local development, a cultural/demographic replacement, or the fusion of indigenous and exogenous lithic traditions. Our analysis considers the techno-typological features of the early Emiran in relation to late Middle Palaeolithic and contemporaneous assemblages from adjacent territories in Northeast Africa and the Arabian Peninsula, in order to identify overlapping cultural features and potential antecedents. Parsimonious with the archaeogenetic scenario of admixture, the Emiran seems to represent a fusion of local southern Levantine Mousterian typological elements with the Afro-Arabian Nubian Levallois reduction strategy. We conclude that the Emiran is primarily rooted in the Early Nubian Complex of the Nile Valley, which spread into the Arabian Peninsula during the Last Interglacial and developed at the interface of these two contextual areas between 100 and 50 thousand years ago.

Link

Amphipolis caryatid

The constant stream of discoveries from the Amphipolis tomb are fascinating. It is not often that one sees archaeology reported almost in "real time".

It is clear that a tomb with a 500m perimeter from the last quarter of the 4th c. BC (i) was built for someone very important, and (ii) someone that is in the history books. 

Unfortunately, such a huge monument would be sure to have attracted attention even in antiquity and it's possible that it was robbed; the intact tomb of Philip II in Vergina (where more tombs in the royal necropolis have recently been discovered) is, by comparison, much more modest, which may have contributed to its lucky fate. Even if the tomb was robbed, the non-movable art from the site by itself would make it an amazing discovery from the ancient world.

Perhaps one day non-cremated remains from a Macedonian Argead royal will be tested for ancient DNA. In the Peloponnese, the institution of kingship waned in power and so the tombs of the descendants of the kings of Argos or Sparta might be indistinguishable from those of their Dorian compatriots. Finding the lineage of Hercules may seem like science fiction at the moment, but ancient DNA keeps revealing amazing new things about the past, so one can always hope!

Jack the Ripper = Aaron Kosminski (?)

WORLD EXCLUSIVE: Jack the Ripper unmasked: How amateur sleuth used DNA breakthrough to identify Britain's most notorious criminal 126 years after string of terrible murders

The landmark discovery was made after businessman Russell Edwards, 48, bought the shawl at auction and enlisted the help of Dr Jari Louhelainen, a world-renowned expert in analysing genetic evidence from historical crime scenes. Using cutting-edge techniques, Dr Louhelainen was able to extract 126-year-old DNA from the material and compare it to DNA from descendants of Eddowes and the suspect, with both proving a perfect match. 

... 

Because of the genome amplification technique, I was also able to ascertain the ethnic and geographical background of the DNA I extracted. It was of a type known as the haplogroup T1a1, common in people of Russian Jewish ethnicity. I was even able to establish that he had dark hair. 

Now that it’s over, I’m excited and proud of what we’ve achieved, and satisfied that we have established, as far as we possibly can, that Aaron Kosminski is the culprit.

 DNA never ceases to amaze... Hopefully a more detailed report on this discovery will appear in time.

Chernykh on Eurasian metallurgy

Bell Beaker blogger points me to this excellent new review of the Eurasian Metallurgical Provinces scheme of Yevgeny Chernykh. I also include an abstract from an earlier study by the author.

Of interest:

The metallurgical contacts and character of interrelations between eastern and western parts we can observe in the Xinjiang among the materials of eastern focuses of the Circumpontic metallurgical province and later in the rich metal collections of the West-Asian and East-Asian steppe provinces. In this sphere extreme interest presents so called Seima-Turbino transcultural phenomenon: their impressive metal forms of eastern sources spreaded from the Western China up to Baltic Sea at the turn of the III and II millennium and in the early centuries of the II mill. BCE.

I have argued before that the Seima-Turbino phenomenon is associated with the spread of Finno-Ugrians into Europe. It would certainly be in accord with a recent thesis about Finno-Ugrians arriving to the Baltic after Indo-European speakers.

Metallurgical Provinces of Eurasia in the Early Metal Age: Problems of Interrelation

General chronological frame of the Early Metal Age (EMA) in Eurasia limited from IX/VIII up to turn II/I mill. BCE. The chronological scale of this investigation founded on the systematized date base of more than 3.5 thousand calibrated 14C analyses. EMA can be subdivided into five unequal in chronological sense periods. The Early Metal Age was the epoch clear domination of the western metallurgical centers – particularly up to III mill. BCE. In all probabilities the apogee of the western predominance was incarnated in the immense of the famous Scythian world, in the limits of the first millennium BCE – i.e. beyond the EMA. The eastern centers take up the initiative of westward pressing after collapse of the Scythian world.

Link

The “Steppe Belt” of stockbreeding cultures in Eurasia during the Early Metal Age

The stock-breeding cultures of the Eurasian “steppe belt” covered approximately 7-8 million square km2 from the Lower Danube in the West to Manchuria in the East (a distance of more than 8000 km). The initial formation of the “steppe belt’cultures coincided with the flourishing of the Carpatho-Balkan metallurgical province (V millennium BC). These cultures developed during the span of the Circumpontic metallurgical province (IV-III millennium BC). Their maturation coincided with the activity of the various centers of the giant Eurasian and East-Asian metallurgical provinces (II millennium BC). The influence of these stock-breeding nomadic cultures on the historical processes of Eurasian peoples was extremely strong. The collapse of the “steppe belt” occurred as late as the XVIIIth and XIXth centuries AD.

Link

Everything you ever wanted to know about mutation rate in humans

Annual Review of Genomics and Human Genetics Vol. 15: 47-70 (Volume publication date August 2014)

Determinants of Mutation Rate Variation in the Human Germline

Laure Ségurel, Minyoung J. Wyman, and Molly Przeworski

Because germline mutations are the source of all evolutionary adaptations and heritable diseases, characterizing their properties and the rate at which they arise across individuals is of fundamental importance for human genetics. After decades during which estimates were based on indirect approaches, notably on inferences from evolutionary patterns, it is now feasible to count de novo mutations in transmissions from parents to offspring. Surprisingly, this direct approach yields a mutation rate that is twofold lower than previous estimates, calling into question our understanding of the chronology of human evolution and raising the possibility that mutation rates have evolved relatively rapidly. Here, we bring together insights from studies of human genetics and molecular evolution, focusing on where they conflict and what the discrepancies tell us about important open questions. We begin by outlining various methods for studying the properties of mutations in humans. We review what we have learned from their applications about genomic factors that influence mutation rates and the effects of sex, age, and other sources of interindividual variation. We then consider the mutation rate as a product of evolution and discuss how and why it may have changed over time in primates.

Link

Y chromosomes and mtDNA of early farmers from Hungary

A new preprint has just appeared on the bioRxiv. It's free to read so I'll just summarize some results. First:

The haplotype of the Mesolithic skeleton from the Croatian Island Korčula belongs to the mtDNA haplogroup U5b2a5 (Dataset S3). The sub-haplogroup U5b has been shown to be frequent in pre-Neolithic hunter-gatherer communities across Europe [28–30,32,33,45,46]. 

But:

Contrary to the low mtDNA diversity reported from hunter-gatherers of Central/North Europe [28–30], we identify substantially higher variability in early farming communities of the Carpathian Basin  including the haplogroups N1a, T1, T2, J, K, H, HV, V, W, X, U2, U3, U4, and U5a (Table 1). Previous studies have shown that haplogroups N1a, T2, J, K, HV, V, W and X are most characteristic for the Central European LBK and have described these haplogroups as the mitochondrial ʻNeolithic packageʼ that had reached Central Europe in the 6th millennium BC [36,37]. Interestingly, most of these haplogroups show comparable frequencies between the STA, LBKT and LBK,

N1a is the "signature group" of the LBK based on previous publications and now it seems that it was also found in the Starcevo culture of Hungary. The mtDNA PCA plot (right) shows clearly that the Hungarian farmers are very similar to the German ones so it seems that the LBK is a direct outgrowth of the Carpathian Neolithic; some earlier models of "demic diffusion" argued that Neolithic farmers spread slowly across Europe, picking up hunter-gatherer ancestry as they went along, but now it seems that at least in the Hungary->Germany part of this journey interaction with hunter-gatherers was minimum.

mtDNA change over time in Europe is pictured in Figure 3 (left) showing a shared haplotype analysis. The Y-chromosome data genetic distance is shown on the right and shows the Balkan-Anatolian-Caucasian-Mesopotamian relationship of the early farmer Y-chromosomes. Practically, this is due to haplogroup G2a (and especially G2a2b), which has turned up in lots of ancient European farmers (including the famous Iceman):

Three STA individuals belong to the NRY haplogroup F* (M89) and two specimens can be assigned to the G2a2b (S126) haplogroup, and one each to G2a (P15) and I2a1 (P37.2) (Dataset S3, S5). The two investigated LBKT samples carry haplogroups G2a2b (S126) and I1 (M253). Furthermore, the incomplete SNP profiles of eight specimens potentially belong to the same haplogroups; STA: three G2a2b (S126), two G2a (P15), and one I (M170); LBKT: one G2a2b (S126) and one F* (M89) (Dataset S5).

I believe this is the first ancient finding of haplogroup I1 which attains a peak in modern Swedes. This might be useful to those who have tied this to Germanic migrations because of this, as it was already in Central Europe with the earliest farmers.

Interestingly:

Surprisingly, Y chromosome haplogroups, such as E1b1b1 (M35), E1b1b1a1 (M78), E1b1b1b2a (M123), J2 (M172), J1 (M267), and R1b1a2 (M269), which were claimed to be associated with the Neolithic expansion [23–25], have not been found so far in the 6th millennium BC of the Carpathian Basin and Central Europe. Intriguingly, R1a and R1b, which represent the most frequent European Y chromosome haplogroups today, have been reported from cultures that emerged in Central Europe during the 3rd/2nd millennium BC, while a basal R type has been reported from a Palaeolithic sample in Siberia [60] in agreement with a proposed Central Asian/Siberian origin of this lineage. In contrast, G2a has not been detected yet in late Neolithic cultures [42,43]. This suggests further demographic events in later Neolithic or post-Neolithic periods.

A cautionary tale against over-reliance on modern distributions to trace ancient origins.

Also:

Considering the entire set of 32 published NRY records available for Neolithic Europe thus far, the low paternal diversity is indeed quite remarkable: G2a is the prevailing haplogroup in the Central European and Carpathian Basin Neolithic, and in French and Iberian Neolithic datasets [36,40,41]. There are only two exceptions, namely one E1b1b (V13) [41] individual from the Avellaner cave in Spain (~5,000-4,500 BC), and two I2a [40] individuals from Treilles, France (~3,000 BC).

biorxiv http://dx.doi.org/10.1101/008664

Tracing the genetic origin of Europe's first farmers reveals insights into their social organization

Anna Szécsényi-Nagy et al.

Farming was established in Central Europe by the Linearbandkeramik culture (LBK), a well-investigated archaeological horizon, which emerged in the Carpathian Basin, in today's Hungary. However, the genetic background of the LBK genesis has not been revealed yet. Here we present 9 Y chromosomal and 84 mitochondrial DNA profiles from Mesolithic, Neolithic Starčevo and LBK sites (7th/6th millennium BC) from the Carpathian Basin and south-eastern Europe. We detect genetic continuity of both maternal and paternal elements during the initial spread of agriculture, and confirm the substantial genetic impact of early farming south-eastern European and Carpathian Basin cultures on Central European populations of the 6th-4th millennium BC. Our comprehensive Y chromosomal and mitochondrial DNA population genetic analyses demonstrate a clear affinity of the early farmers to the modern Near East and Caucasus, tracing the expansion from that region through south-eastern Europe and the Carpathian Basin into Central Europe. Our results also reveal contrasting patterns for male and female genetic diversity in the European Neolithic, suggesting patrilineal descent system and patrilocal residential rules among the early farmers.

Link

The prehistory of New World Arctic (Raghavan et al. 2014)

Science 29 August 2014: Vol. 345 no. 6200 DOI: 10.1126/science.1255832

The genetic prehistory of the New World Arctic

Maanasa Raghavan et al.

The New World Arctic, the last region of the Americas to be populated by humans, has a relatively well-researched archaeology, but an understanding of its genetic history is lacking. We present genome-wide sequence data from ancient and present-day humans from Greenland, Arctic Canada, Alaska, Aleutian Islands, and Siberia. We show that Paleo-Eskimos (~3000 BCE to 1300 CE) represent a migration pulse into the Americas independent of both Native American and Inuit expansions. Furthermore, the genetic continuity characterizing the Paleo-Eskimo period was interrupted by the arrival of a new population, representing the ancestors of present-day Inuit, with evidence of past gene flow between these lineages. Despite periodic abandonment of major Arctic regions, a single Paleo-Eskimo metapopulation likely survived in near-isolation for more than 4000 years, only to vanish around 700 years ago.

Link

Ancient Y-DNA from China

From the paper:

Dividing the samples further using social status shows that the six aristocrats had haplogroups Q1a1, O3a, and N, the 14 commoners had haplogroups Q1a1, O3a, and O*, and the seven slaves had haplogroups O3a, O2a, and O* (Fig. 2).

Am. J. Hum. Biol. DOI: 10.1002/ajhb.22604

Ancient DNA evidence reveals that the Y chromosome haplogroup Q1a1 admixed into the Han Chinese 3,000 years ago

Yong-Bin Zhao et al.

Objectives

Y chromosome haplogroup Q1a1 is found almost only in Han Chinese populations. However, it has not been found in ancient Han Chinese samples until now. Thus, the origin of haplogroup Q1a1 in Han Chinese is still obscure. This study attempts to provide answer to this question, and to uncover the origin and paternal genetic structure of the ancestors of the Han Chinese.

Methods

Eighty-nine ancient human remains that were excavated from the presumed geographic source of the Han Chinese and dated to approximately 3,000 years ago were treated by the amelogenin gene polymerase chain reaction test, to determine their sex. Then, Y chromosome single nucleotide polymorphisms were subsequently analyzed from the samples detected as male.

Results 

Samples from 27 individuals were successfully amplified. Their haplotypes could be attributed to haplogroups N, O*, O2a, O3a, and Q1a1. Analyses showed that the assigned haplogroup of each sample is correlated to the suspected social status and observed burial custom associated with the sample.

Conclusions

The origins of the observed haplotypes and their distribution in present day Han Chinese and in the samples suggest that haplogroup Q1a1 was probably introduced into the Han Chinese population approximately 3,000 years ago. Am. J. Hum. Biol., 2014. © 2014 Wiley Periodicals, Inc.

Link

Neandertal demise followed contact with modern humans (but not immediately)

Important:

Southern Iberia has been held to represent an exception to a wider European pattern21, with late survival of Neanderthals previously argued at sites such as Gorham’s Cave, Gibraltar22. We could not reproduce any of the late dates from sites in this region15 (Supplementary Methods) and it is apparent that many previous determinations underestimate the real age. It is unclear how long Neanderthals persisted in southern Iberia15.

Nature 512, 306–309 (21 August 2014) doi:10.1038/nature13621

The timing and spatiotemporal patterning of Neanderthal disappearance

Tom Higham et al.

The timing of Neanderthal disappearance and the extent to which they overlapped with the earliest incoming anatomically modern humans (AMHs) in Eurasia are key questions in palaeoanthropology1, 2. Determining the spatiotemporal relationship between the two populations is crucial if we are to understand the processes, timing and reasons leading to the disappearance of Neanderthals and the likelihood of cultural and genetic exchange. Serious technical challenges, however, have hindered reliable dating of the period, as the radiocarbon method reaches its limit at ~50,000 years ago3. Here we apply improved accelerator mass spectrometry 14C techniques to construct robust chronologies from 40 key Mousterian and Neanderthal archaeological sites, ranging from Russia to Spain. Bayesian age modelling was used to generate probability distribution functions to determine the latest appearance date. We show that the Mousterian ended by 41,030–39,260 calibrated years BP (at 95.4% probability) across Europe. We also demonstrate that succeeding ‘transitional’ archaeological industries, one of which has been linked with Neanderthals (Châtelperronian)4, end at a similar time. Our data indicate that the disappearance of Neanderthals occurred at different times in different regions. Comparing the data with results obtained from the earliest dated AMH sites in Europe, associated with the Uluzzian technocomplex5, allows us to quantify the temporal overlap between the two human groups. The results reveal a significant overlap of 2,600–5,400 years (at 95.4% probability). This has important implications for models seeking to explain the cultural, technological and biological elements involved in the replacement of Neanderthals by AMHs. A mosaic of populations in Europe during the Middle to Upper Palaeolithic transition suggests that there was ample time for the transmission of cultural and symbolic behaviours, as well as possible genetic exchanges, between the two groups.

Link

Tuberculosis is 6,000 years old

... and sea mammals (not Europeans) introduced it to the New World.

Nature (2014) doi:10.1038/nature13591

Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis

Kirsten I. Bos et al.

Modern strains of Mycobacterium tuberculosis from the Americas are closely related to those from Europe, supporting the assumption that human tuberculosis was introduced post-contact1. This notion, however, is incompatible with archaeological evidence of pre-contact tuberculosis in the New World2. Comparative genomics of modern isolates suggests that M. tuberculosis attained its worldwide distribution following human dispersals out of Africa during the Pleistocene epoch3, although this has yet to be confirmed with ancient calibration points. Here we present three 1,000-year-old mycobacterial genomes from Peruvian human skeletons, revealing that a member of the M. tuberculosis complex caused human disease before contact. The ancient strains are distinct from known human-adapted forms and are most closely related to those adapted to seals and sea lions. Two independent dating approaches suggest a most recent common ancestor for the M. tuberculosis complex less than 6,000 years ago, which supports a Holocene dispersal of the disease. Our results implicate sea mammals as having played a role in transmitting the disease to humans across the ocean.

Link

Indo-Europeans preceded Finno-Ugrians in Finland and Estonia

According to an abstract of a Ph.D thesis (below). This would appear to work well with the dating of the signature Y-chromosome haplogroup of Finno-Ugrians. 

Bidrag till Fennoskandiens språkliga förhistoria i tid och rum (Heikkilä, Mikko)

My academic dissertation "Bidrag till Fennoskandiens språkliga förhistoria i tid och rum" ("Spatiotemporal Contributions to the Linguistic Prehistory of Fennoscandia") is an interdisciplinary study of the linguistic prehistory of Northern Europe chiefly in the Iron Age (ca. 700 BC―AD 1200), but also to some extent in the Bronze Age (ca. 1700―700 BC) and the Early Finnish Middle Ages (ca. AD 1200―1323). The disciplines represented in this study are Germanistics, Nordistics, Finnougristics, history and archaeology. The language-forms studied are Proto-Germanic, Proto-Scandinavian, Proto-Finnic and Proto-Sami. This dissertation uses historical-comparative linguistics and especially loanword study to examine the relative and absolute chronology of the sound changes that have taken place in the proto-forms of the Germanic, Finnic and Samic languages. Phonetic history is the basis of historical linguistics studying the diachronic development of languages. To my knowledge, this study is the first in the history of the disciplines mentioned above to examine the systematic dating of the phonetic development of these proto-languages in relation to each other. In addition to the dating and relating of the phonetic development of the proto-languages, I study Fennoscandian toponyms. The oldest datable and etymologizable place-names throw new light on the ethnic history and history of settlement of Fennoscandia. For instance, I deal with the etymology of the following place-names: Ahvenanmaa/Åland, Eura(joki), Inari(järvi), Kemi(joki), Kvenland, Kymi(joki), Sarsa, Satakunta, Vanaja, Vantaa and Ähtäri. 

My dissertation shows that Proto-Germanic, Proto-Scandinavian, Proto-Finnic and Proto-Sami all date to different periods of the Iron Age. I argue that the present study along with my earlier published research also proves that a (West-)Uralic language – the pre-form of the Finnic and Samic languages – was spoken in the region of the present-day Finland in the Bronze Age, but not earlier than that. In the centuries before the Common Era, Proto-Sami was spoken in the whole region of what is now called Finland, excluding Lapland. At the beginning of the Common Era, Proto-Sami was spoken in the whole region of Finland, including Southern Finland, from where the Sami idiom first began to recede. An archaic (Northwest-)Indo-European language and a subsequently extinct Paleo-European language were likely spoken in what is now called Finland and Estonia, when the linguistic ancestors of the Finns and the Sami arrived in the eastern and northern Baltic Sea region from the Volga-Kama region probably at the beginning of the Bronze Age. For example, the names Suomi ʻFinlandʼ and Viro ʻEstoniaʼ are likely to have been borrowed from the Indo-European idiom in question. (Proto-)Germanic waves of influence have come from Scandinavia to Finland since the Bronze Age. A considerable part of the Finnic and Samic vocabulary is indeed Germanic loanwords of different ages which form strata in these languages. Besides mere etymological research, these numerous Germanic loanwords make it possible to relate to each other the temporal development of the language-forms that have been in contact with each other. That is what I have done in my extensive dissertation, which attempts to be both a detailed and a holistic treatise.

ISBA 2014 titles

Some interesting talks and posters from the upcoming International Symposium on Biomolecular Archaeology. I don't see any abstracts on the site (yet?) but the titles are intriguing. Some that caught my eye:

• Investigating the maternal lineage diversity from an early medieval site in Southern Italy
• Ancient mitochondrial and Y chromosomal DNA reveals the western Carpathian Basin as a corridor of the Neolithic expansion
• Ancient mitochondrial DNA from the Northern fringe of the Neolithic farming expansion in Europe sheds light on the dispersion process
• The effect of demography and natural selection on pigmentation heterogeneity in late Pleistocene and early Holocene Europeans
• The genomics of equine speciation and domestication
• Ancient population genetics: new insights on horse domestication
• Species identification and analysis of the Tyrolean Iceman's clothes using next generation sequencing of ancient DNA.
• Early evidence for the use of pottery: extending the ancient lipid record to the Pleistocene.
• Whey to go – first identification of lactose in prehistoric pottery
• Use of the earliest pottery on the Western and Eastern side of the Baltic
• The geographical distribution of the Polynesian cultural complex and its association with P33-C2a1 Y chromosomes: adding data from Aotearoa (New Zealand)
• Interdisciplinary investigation of an archaic hominin femur from the Swabian Jura (South-West Germany)
• Tracing the genetic history of farming populations of El Portalón Cave in the Sierra de Atapuerca, Spain.
• Ancient human genomes suggest three ancestral populations for present-day Europeans
• Ancient DNA from Early Neolithic farmers in Europe
• Genomic diversity and admixture in Stone-Age farmer and hunter-gatherer groups in Scandinavia
• Ancient DNA reveals the complex genetic history of the New World Arctic
• A prediction of the hybridisation potential between Hominin species using mitochondrial DNA
• Population Genomics of Vikings
• Tracing the genetic profile of Sus scrofa on Romanian territory from the Neolithic period until the Middle Ages
• The origins of the Aegean palatial civilizations from a population genetic perspective
• Ancient DNA evidence for a diversified origin of ancestor of Han Chinese

mtDNA from Chalcolithic Iberia (El Mirador cave)

A very exciting new study from Chalcolithic Iberia. The authors compare their mtDNA data with those from the Brandt et al. (2013) paper which includes German samples from the same time.

The following plot seems quite useful. From its caption:

This study: El Mirador (MIR). Published prehistoric cultures [21]: Hunter-gatherer central (HGC), Linear Pottery culture (LBK), Rössen culture (RSC), Schöningen group (SCG), Baalberge culture (BAC), Salzmünde culture (SMC), Bernburg culture (BEC), Corded Ware culture (CWC), Bell Beaker culture (BBC), Unetice culture (UC), Funnel Beaker culture (FBC), Pitted Ware culture (PWC), Hunter-Gatherer south (HGS), (Epi) Cardial (CAR), Neolithic Portugal (NPO), Neolithic Basque Country and Navarre (NBQ), Treilles culture (TRE), Hunter-gatherer east (HGE), Bronze Age Siberia (BAS), Bronze Age Kazakhstan (BAK).

From the paper:

In none of the analyses El Mirador sample shows close genetic affinities with a contemporaneous Bell Beaker population of 29 specimens gathered from three sites in Germany. The Bell Beaker mtDNA signal is characterized by high frequencies (around 50%) of H haplogroup that in El Mirador only reaches 26%. This heterogeneity in the genetic composition of geographically close populations adds further complexity to future reconstructions of these ancient expansions and correlates with the existence of contemporaneous groups with and without the typical Bell Beaker burial kit.

mtDNA may not be the best tool for studying the spread of Bell Beakers (if this involved men), but this shows that the high frequency of H in Bell Beakers of Germany (observed by Brandt et al.) is not due to an even higher frequency of H in Iberia.

PLoS ONE 9(8): e105105. doi:10.1371/journal.pone.0105105

Mitochondrial DNA from El Mirador Cave (Atapuerca, Spain) Reveals the Heterogeneity of Chalcolithic Populations

Daniel Gómez-Sánchez,Iñigo Olalde et al.

Previous mitochondrial DNA analyses on ancient European remains have suggested that the current distribution of haplogroup H was modeled by the expansion of the Bell Beaker culture (ca 4,500–4,050 years BP) out of Iberia during the Chalcolithic period. However, little is known on the genetic composition of contemporaneous Iberian populations that do not carry the archaeological tool kit defining this culture. Here we have retrieved mitochondrial DNA (mtDNA) sequences from 19 individuals from a Chalcolithic sample from El Mirador cave in Spain, dated to 4,760–4,200 years BP and we have analyzed the haplogroup composition in the context of modern and ancient populations. Regarding extant African, Asian and European populations, El Mirador shows affinities with Near Eastern groups. In different analyses with other ancient samples, El Mirador clusters with Middle and Late Neolithic populations from Germany, belonging to the Rössen, the Salzmünde and the Baalberge archaeological cultures but not with contemporaneous Bell Beakers. Our analyses support the existence of a common genetic signal between Western and Central Europe during the Middle and Late Neolithic and points to a heterogeneous genetic landscape among Chalcolithic groups.

Link

168 South Asian Genomes

PLoS ONE 9(8): e102645. doi:10.1371/journal.pone.0102645

The South Asian Genome

John C. Chambers et al.

The genetic sequence variation of people from the Indian subcontinent who comprise one-quarter of the world's population, is not well described. We carried out whole genome sequencing of 168 South Asians, along with whole-exome sequencing of 147 South Asians to provide deeper characterisation of coding regions. We identify 12,962,155 autosomal sequence variants, including 2,946,861 new SNPs and 312,738 novel indels. This catalogue of SNPs and indels amongst South Asians provides the first comprehensive map of genetic variation in this major human population, and reveals evidence for selective pressures on genes involved in skin biology, metabolism, infection and immunity. Our results will accelerate the search for the genetic variants underlying susceptibility to disorders such as type-2 diabetes and cardiovascular disease which are highly prevalent amongst South Asians.

Link

New estimates of human mtDNA node dates and substitution rates (Rieux et al. 2014)

This is a quite useful paper as it compares different methods of obtaining mutation rate estimates, either using "archaeological calibration" based on known migration events or ancient mtDNA genomes (with known archaeological dates). The authors write:

Our estimate of 143 Kya [112-180 95% HPD] for the TMRCA of all modern human mtDNA is slightly younger but highly consistent with the 157 Kya [120-197 95% HPD] value obtained by Fu et al. (2013b). We stimate the coalescence of the L3 haplogroup (the lineage from which all non-African mtDNA haplogroups descend), often used to date the “out-of-Africa” event, to 72 Kya [54-93 95%HPD], a value also onsistent with Fu et al. (2013b) estimation of 78 Kya [62-95 95%HPD]. This estimation rather places a conservative upper bound of 93 kya for the time of the last major gene exchange between non-African nd sub-Saharan African populations. As pointed out by Fu et al. (2013b), it is important to recognize that this divergence time may merely represent the most recent gene exchanges between the ancestors f non-Africans and the most closely related sub-Saharan Africans and thus may reflect only the most recent population split in a long, drawn-out process of population separation (Scally and Durbin 2012).

The 72kya date would agree quite well with my postulated Out-of-Arabia event circa 70 thousand years ago.

It should be fairly easy to pick out the common ancestor of Eurasian mtDNA (the common ancestor of M+N). I am reasonably sure that the two African red dots to the right of event "8" in the figure are African L3's, and this would place them within the Eurasian variation, and in particular as a relative of Eurasian M.

A similar observation could be found in Supplementary Figure 14 of the Lippold et al. (2014) preprint, with African L3 lineages clearly related to Eurasian M (and nested within the Eurasian phylogeny).

In any case, I don't see any evidence at all from this phylogeny that the date of L3 corresponds to an Out-of-Africa event. Unfortunately I couldn't see an estimate for the split of L3 from the rest of the phylogeny; my eyeball estimate from the figure is that it's about 20ky earlier. Hopefully, someone sooner or later will deal with the question of L3 phylogeny, because the "conventional wisdom" that Eurasian M, N are nested within African L3 variation does not appear to be quite right.

Mol Biol Evol (2014) doi: 10.1093/molbev/msu222

Improved calibration of the human mitochondrial clock using ancient genomes

Adrien Rieux et al.

Reliable estimates of the rate at which DNA accumulates mutations (the substitution rate) are crucial for our understanding of the evolution and past demography of virtually any species. In humans, there are considerable uncertainties around these rates, with substantial variation among recent published estimates. Substitution rates have traditionally been estimated by associating dated events to the root (e.g. the divergence between humans and chimpanzees) or to internal nodes in a phylogenetic tree (e.g. first entry into the Americas). The recent availability of ancient mtDNA sequences allows for a more direct calibration by assigning the age of the sequenced samples to the tips within the human phylogenetic tree. But studies also vary greatly in the methodology employed and in the sequence panels analysed, making it difficult to tease apart the causes for the differences between previous estimates. To clarify this issue, we compiled a comprehensive dataset of 350 ancient and modern human complete mtDNA genomes, among which 146 were generated for the purpose of this study, and estimated substitution rates using calibrations based both on dated nodes and tips. Our results demonstrate that, for the same dataset, estimates based on individual dated tips are far more consistent with each other than those based on nodes and should thus be considered as more reliable.

Link

mtDNA haplogroup V7 from ~5,000-year old kurgan of the Novosvobodnaya culture

I am not sure that the finding of a single mtDNA V7 sample suggest "a role of the TRB culture in the development of the Novosvobodnaya culture", or, indeed with the labeling of the TRB as "Indo-European". In any case, it's good to see some ancient DNA from the North Caucasus.

Acta Naturae. 2014 Apr-Jun; 6(2): 31–35.

Analysis of the Mitochondrial Genome of a Novosvobodnaya Culture Representative using Next-Generation Sequencing and Its Relation to the Funnel Beaker Culture

A. V. Nedoluzhko et al.

The Novosvobodnaya culture is known as a Bronze Age archaeological culture in the North Caucasus region of Southern Russia. It dates back to the middle of the 4th millennium B.C. and seems to have occurred during the time of the Maikop culture. There are now two hypotheses about the emergence of the Novosvobodnaya culture. One hypothesis suggests that the Novosvobodnaya culture was a phase of the Maikop culture, whereas the other one classifies it as an independent event based on the material culture items found in graves. Comparison between Novosvobodnaya pottery and Funnelbeaker (TRB) pottery from Germany has allowed researchers to suggest that the Novosvobodnaya culture developed under the influence of Indo-European culture. Nevertheless, the origin of the Novosvobodnaya culture remains a matter of debate. We applied next-generation sequencing to study ~5000-year-old human remains from the Klady kurgan grave in Novosvobodnaya stanitsa (now the Republic of Adygea, Russia). A total of 58,771,105 reads were generated using Illumina GAIIx with a coverage depth of 13.4x over the mitochondrial (mt) DNA genome. The mtDNA haplogroup affiliation was determined as V7, suggesting a role of the TRB culture in the development of the Novosvobodnaya culture and supporting the model of sharing between Novosvobodnaya and early Indo-European cultures.

Link