Arabian origin of the Upper Paleolithic in the Levant

This is a very useful review of research on the origin of the Upper Paleolithic (Emiran) in the Levant, arguing against a recent (c. 50kya ) African origin and in favor of an Arabian one. The argument is mainly archaeological, although it is informed by genetic evidence. From the chapter:

After a century of research, the origins of the Levantine UP still remain an enigma. At this point, at least one thing is clear: the Emiran has no African progenitor. As such, there is a disconnect between the archaeological database and the Replacement paradigm, which necessitates that the earliest Levantine Upper Paleolithic must have come fully developed from northeast Africa. The Replacement model should have been a parsimonious prism through which to view the transition from the MP to the UP in the Levant. It was not.

The recent acceptance of: (i) a slower autosomal mutation rate, and (ii) evidence for interbreeding with Neandertals largely predating the c. 50kya mark, and (iii) coalescence of Eurasian mtDNA haplogroup N well before that time, have all but killed, in my opinion the idea of a 50kya spread of modern humans from Africa. Modern humans must have lived in Eurasia much earlier than that time, and what remains is to figure out how much earlier.

A century of research into the origins of the Upper Palaeolithic in the Levant

Anthony E. Marks and Jeffrey I. Rose

Link

Ancient mtDNA from Rössen culture in Wittmar, Germany

Archaeological and Anthropological Sciences December 2013

Ancient DNA insights from the Middle Neolithic in Germany

Esther J. Lee et al.

Genetic studies of Neolithic groups in central Europe have provided insights into the demographic processes that have occurred during the initial transition to agriculture as well as in later Neolithic contexts. While distinct genetic patterns between indigenous hunter-gatherers and Neolithic farmers in Europe have been observed, it is still under discussion how the genetic diversity changed during the 5,000-year span of the Neolithic period. In order to investigate genetic patterns after the earliest farming communities, we carried out an ancient mitochondrial DNA (mtDNA) analysis of 34 individuals from Wittmar, Germany representing three different Neolithic farming groups (ca. 5,200–4,300 cal bc) including Rössen societies. Ancient DNA analysis was successful for six individuals associated with the Middle Neolithic Rössen and observed haplotypes were assigned to mtDNA haplogroups H5, HV0, U5, and K. Our results offer perspectives on the genetic composition of individuals associated with the Rössen culture at Wittmar and permit insights into genetic landscapes in central Europe at a time when regional groups first emerged during the Middle Neolithic.

Link

No evidence for selection since admixture in sample of 29,141 African Americans

arXiv:1312.2675 [q-bio.PE]

Genome-wide scan of 29,141 African Americans finds no evidence of selection since admixture

Gaurav Bhatia et al.

We scanned through the genomes of 29,141 African Americans, searching for loci where the average proportion of African ancestry deviates significantly from the genome-wide average. We failed to find any genome-wide significant deviations, and conclude that any selection in African Americans since admixture is sufficiently weak that it falls below the threshold of our power to detect it using a large sample size. These results stand in contrast to the findings of a recent study of selection in African Americans. That study, which had 15 times fewer samples, reported six loci with significant deviations. We show that the discrepancy is likely due to insufficient correction for multiple hypothesis testing in the previous study. The same study reported 14 loci that showed greater population differentiation between African Americans and Nigerian Yoruba than would be expected in the absence of natural selection. Four such loci were previously shown to be genome-wide significant and likely to be affected by selection, but we show that most of the 10 additional loci are likely to be false positives. Additionally, the most parsimonious explanation for the loci that have significant evidence of unusual differentiation in frequency between Nigerians and Africans Americans is selection in Africa prior to their forced migration to the Americas.

Link

Ancient DNA meeting talks audio

Some of the audio from talks of this meeting that I posted about before have been posted. I don't think I can listen to all of them, but feel free to post any interesting "nuggets" of information in the comments.

Merovingian mtDNA

From the paper:

Our approach clearly identified six different mitochondrial lineages (corresponding to five distinct haplogroups: J, H, K, X2 and W) among eight human remains, indicating noticeable mitochondrial diversity. During this period, the site might have been the cemetery for a social group with significant genetic diversity. 

Journal of Archaeological Science Volume 41, January 2014, Pages 399–405

Ancient DNA and kinship analysis of human remains deposited in Merovingian necropolis sarcophagi (Jau Dignac et Loirac, France, 7th–8th century AD)

M.F. Deguilloux et al.

The analysis of ancient DNA recovered from archaeological remains can be used to reconstruct kinship among the occupants of a necropolis and provide a more detailed portrait of the community considered. Such palaeogenetic analyses have been conducted on sarcophagi excavated from the Merovingian necropolis in Jau-Dignac et Loirac (7th–8th century AD, Aquitaine, southwest France). The genetic study consisted of the analysis of mitochondrial DNA and nuclear STRs (Short Tandem Repeats) from nine skeletons deposited in three grouped sarcophagi. Only data concerning the mitochondrial genomes could be obtained, and six different mitochondrial lineages were retrieved from eight samples. Our analyses permitted a high confidence characterisation of maternal relationships between individuals deposited in the same sepulchre. These results are important and novel for the period and region and argue that individuals were grouped inside sarcophagi according to relationship criteria. The presence of perinatal remains in one sarcophagus was particularly striking because access to this type of funerary structure during this period was generally reserved for older children. Moreover, we demonstrated genetically that the perinatal remains were not related maternally to two women found in the same sarcophagus (whereas the maternal relationship between the two young women could be determined), and we proposed different possible explanations for this unexpected observation. Overall, archaeological, anthropological and genetic data suggest that the Jau-Dignac et Loirac necropolis groups together the closely and distantly related members of a High Middle Ages familia. Our ancient DNA analyses note the important contribution of palaeogenetic analyses to archaeological kinship studies.

Link

Early 7th millennium BC Initial Neolithic in Franchthi Cave

Antiquity Volume: 87 Number: 338 Page: 1001–1015

Early seventh-millennium AMS dates from domestic seeds in the Initial Neolithic at Franchthi Cave (Argolid, Greece)

Catherine Perlès1, Anita Quiles2 and Hélène Valladas2

When, and by what route, did farming first reach Europe? A terrestrial model might envisage a gradual advance around the northern fringes of the Aegean, reaching Thrace and Macedonia before continuing southwards to Thessaly and the Peloponnese. New dates from Franchthi Cave in southern Greece, reported here, cast doubt on such a model, indicating that cereal cultivation, involving newly introduced crop species, began during the first half of the seventh millennium BC. This is earlier than in northern Greece and several centuries earlier than in Bulgaria, and suggests that farming spread to south-eastern Europe by a number of different routes, including potentially a maritime, island-hopping connection across the Aegean Sea. The results also illustrate the continuing importance of key sites such as Franchthi to our understanding of the European Neolithic transition, and the additional insights that can emerge from the application of new dating projects to these sites.

Link

400 thousand year old human mtDNA from Sima de los Huesos

It will come to no surprise to people who noticed an earlier paper on cave bear mtDNA from Atapuerca that the folks at the Max Planck Institute would try to do the same for the plentiful human remains found in the Pit of Bones.

A new paper in Nature reports their success, and overnight increases by an order of magnitude the time depth for which we now have human mtDNA from what is commonly designated as Homo heidelbergensis, from right in the middle of the Middle Pleistocene. Obviously, this opens new vistas for archaeogenetic research, making it possible to directly look at early pre-sapiens forms of humans, and not only on their final forms prior to their replacement, the Neandertals and Denisovans.

The most impressive aspect of the new paper is most likely the technical challenges that the researchers must've overcome to achieve this result. The cave bear DNA showed that this was possible, but human DNA adds an additional complication in the form of contamination by a closely related species, us.

But, the new evolutionary result which will interest those of us not interested in the minutiae of biomolecules will no doubt be the fact that the Sima hominin's mtDNA formed a clade with the much more recent Denisova girl.

Until now, we knew that Neandertal mtDNA grouped together and so did modern human mtDNA. The two groups shared a Middle Pleistocene common ancestor and a much more distant common ancestor (~1 million years) with the mtDNA found in Denisova. The new Sima specimen shares descent from Denisova. This is important because it shows that whatever archaic human population the Denisovan mtDNA belonged to also extended to western Europe. And, surprisingly, the Sima specimen did not group with Neandertals, as might be expected because of the incipient Neanderthaloid morphology of the Sima hominins which has been a matter of controversy as it pushes back the evolutionary lineage of H. neandertalensis deeper into the Middle Pleistocene that some researchers accept.

Before this paper, it was believed that H. heidelbergensis evolved somewhere (perhaps Near East or Africa), a subset of it evolved to H. sapiens in Africa, and a different subset evolved in Eurasia, leading up to H. neandertalensis in the west, and unknown forms in the east, of which the Denisova girl was a matrilineal descendant. The next question is: when did Neandertals and Neandertal mtDNA appear in Europe? 

It can now be hoped that such questions will be answered directly. The Sima individual studied in this paper is not some frozen specimen from the Arctic, preserved by a freak accident in pristine form for hundreds of thousands of years, but a person who lived in Southwestern Europe. I am fairly sure that this won't be the last really old human we see a paper about in the coming years. Human mtDNA used to present a simple picture at the time of the discovery of African mitochondrial Eve: the deepest splits were in Africa and Eurasians belonged to a subset of African variation. But, as more and more archaic Eurasian mtDNA is sampled, it now appears that modern human mtDNA is a subset of world human mtDNA whose deepest splits are in Eurasia, and the next deepest splits are in Africa. Obviously, this may be a consequence of the fact that archaic human mtDNA has only been sampled from Eurasia, for factors relating to DNA preservation. But, it is nonetheless interesting to wonder where on the tree the mtDNA of archaic Africans would fall.

Nature (2013) doi:10.1038/nature12788

A mitochondrial genome sequence of a hominin from Sima de los Huesos

Matthias Meyer et al.

Excavations of a complex of caves in the Sierra de Atapuerca in northern Spain have unearthed hominin fossils that range in age from the early Pleistocene to the Holocene1. One of these sites, the ‘Sima de los Huesos’ (‘pit of bones’), has yielded the world’s largest assemblage of Middle Pleistocene hominin fossils2, 3, consisting of at least 28 individuals4 dated to over 300,000 years ago5. The skeletal remains share a number of morphological features with fossils classified as Homo heidelbergensis and also display distinct Neanderthal-derived traits6, 7, 8. Here we determine an almost complete mitochondrial genome sequence of a hominin from Sima de los Huesos and show that it is closely related to the lineage leading to mitochondrial genomes of Denisovans9, 10, an eastern Eurasian sister group to Neanderthals. Our results pave the way for DNA research on hominins from the Middle Pleistocene.

Link