December 27, 2013

Reconstructing Native American migrations

Of wider interest might be the authors' estimation of the autosomal mutation rate as 1.44x10-8 mutations/bp/generation. Of course, this might depend on the archaeological calibration used (where/when did the bottleneck in the ancestry of Native Americans occur?). It might also depend on recent evidence that Native Americans are of mixed origin and thus did not really split from CHB/JPT; only part of their ancestry did. Nonetheless, this is another fairly "low" autosomal mutation rate.

(This was previously released as a preprint to the arXiv).

PLoS Genet 9(12): e1004023. doi:10.1371/journal.pgen.1004023

Reconstructing Native American Migrations from Whole-Genome and Whole-Exome Data

Simon Gravel et al.


Site frequency spectrum from reads is unbiased (from genotype calls, biased at low coverage)

Mol Biol Evol (2013) doi: 10.1093/molbev/mst229

Characterizing Bias in Population Genetic Inferences from Low-Coverage Sequencing Data

Eunjung Han et al.

The site frequency spectrum (SFS) is of primary interest in population genetic studies, because the SFS compresses variation data into a simple summary from which many population genetic inferences can proceed. However, inferring the SFS from sequencing data is challenging because genotype calls from sequencing data are often inaccurate due to high error rates and if not accounted for, this genotype uncertainty can lead to serious bias in downstream analysis based on the inferred SFS. Here, we compare two approaches to estimate the SFS from sequencing data: one approach infers individual genotypes from aligned sequencing reads and then estimates the SFS based on the inferred genotypes (call-based approach) and the other approach directly estimates the SFS from aligned sequencing reads by maximum likelihood (direct estimation approach). We find that the SFS estimated by the direct estimation approach is unbiased even at low coverage, whereas the SFS by the call-based approach becomes biased as coverage decreases. The direction of the bias in the call-based approach depends on the pipeline to infer genotypes. Estimating genotypes by pooling individuals in a sample (multisample calling) results in underestimation of the number of rare variants, whereas estimating genotypes in each individual and merging them later (single-sample calling) leads to overestimation of rare variants. We characterize the impact of these biases on downstream analyses, such as demographic parameter estimation and genome-wide selection scans. Our work highlights that depending on the pipeline used to infer the SFS, one can reach different conclusions in population genetic inference with the same data set. Thus, careful attention to the analysis pipeline and SFS estimation procedures is vital for population genetic inferences.


December 26, 2013

Ancient DNA: what 2013 has brought

I was looking at my ancient DNA tag for the last year and it seems we've learned quite a lot in 2013. Here's my short summary of some major studies, news articles and reports:
  • 400,000 year old Homo heidelbergensis in Iberia had mtDNA similar to Middle Paleolithic Denisovans from the Altai. This is important because of the age of the sample which opens up new vistas for ancient DNA research and because it is the first  link to the mysterious Denisovans.
  • A Neandertal inhabited the same cave where the Denisovan fingerbone was found. Denisovans had Neandertal admixture as well as admixture with an unknown "ultra-archaic" group; Eurasians have admixture from a Neandertal most similar to the Mezmaiskaya sample from the Caucasus; East Eurasians have a little bit of Denisovan admixture, while Australasians have a lot more; and all Sub-Saharan Africans seem to have a little bit of Neandertal admixture too, via West Eurasians during the Holocene.
  • A ~24,000 year old Upper Paleolithic Siberian from Mal'ta is related to Native Americans who are a mix of it and East Asians. Mal'ta was related to West Eurasians and not to East Eurasians. It belonged to Y-haplogroup R* and mt-haplogroup U*.
  • On the other hand, a ~40,000 year old from China was definitely East Eurasian.
  • Europeans are a 3-way mix of Neolithic farmers, Mesolithic hunter-gatherers and aforementioned UP Siberian-like "Ancient North Eurasians"; Early LBK farmers from Central Europe resemble later Oetzi, Swedish farmers, and probably Iberian farmers too. They also had mysterious "Basal Eurasian" ancestry from the deepest split of the Eurasian tree. Mesolithic Europeans had lots of Y-haplogroup I.
  • Ancient mtDNA reveals that something happened during the late Neolithic and early Bronze Age in Germany; the populations from that time are the first ones who appear quasi-modern in their haplogroup frequencies. It also turns out that hunter-gatherers didn't disappear in Germany after the LBK came along. And mtDNA haplogroup H, most frequent in modern Europeans, established itself around the Mid-to-Late Neolithic.
  • West Siberia had a West/East Eurasian admixed population during the Bronze Age, like earlier ages.
  • Lots of hints of interesting events in the European steppe too.
  • Modern Tuscans probably not descended from ancient Etruscans; discontinuity seems to be the rule.
  • Minoans were fairly regular Europeans, not North African (they had little mtDNA U, though, maybe like Mesolithic Greeks).
  • A lot more mtDNA haplogroup U from really old Europeans, and mtDNA haplogroups M+N date to ~77 thousand years ago.
  • Mesolithic west Europeans had blue eyes, but Neolithic Europeans had brown ones and European steppe populations "darker" than modern Europeans). ~8,000 year old Europeans had dark brown or black hair (at least two of them).
I bet 2014 will be equally exciting!

Mexicans got type 2 diabetes risk allele from Neandertals

Nature (2013) doi:10.1038/nature12828

Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico

The SIGMA Type 2 Diabetes Consortium

Performing genetic studies in multiple human populations can identify disease risk alleles that are common in one population but rare in others1, with the potential to illuminate pathophysiology, health disparities, and the population genetic origins of disease alleles. Here we analysed 9.2 million single nucleotide polymorphisms (SNPs) in each of 8,214 Mexicans and other Latin Americans: 3,848 with type 2 diabetes and 4,366 non-diabetic controls. In addition to replicating previous findings2, 3, 4, we identified a novel locus associated with type 2 diabetes at genome-wide significance spanning the solute carriers SLC16A11 and SLC16A13 (P = 3.9 × 10−13; odds ratio (OR) = 1.29). The association was stronger in younger, leaner people with type 2 diabetes, and replicated in independent samples (P = 1.1 × 10−4; OR = 1.20). The risk haplotype carries four amino acid substitutions, all in SLC16A11; it is present at ~50% frequency in Native American samples and ~10% in east Asian, but is rare in European and African samples. Analysis of an archaic genome sequence indicated that the risk haplotype introgressed into modern humans via admixture with Neanderthals. The SLC16A11 messenger RNA is expressed in liver, and V5-tagged SLC16A11 protein localizes to the endoplasmic reticulum. Expression of SLC16A11 in heterologous cells alters lipid metabolism, most notably causing an increase in intracellular triacylglycerol levels. Despite type 2 diabetes having been well studied by genome-wide association studies in other populations, analysis in Mexican and Latin American individuals identified SLC16A11 as a novel candidate gene for type 2 diabetes with a possible role in triacylglycerol metabolism.


December 24, 2013

Europeans = Neolithic farmers, Mesolithic hunter-gatherers and "Ancient North Eurasians" (etc.)

A new preprint on the bioRxiv reports ancient DNA from a Mesolithic European hunter-gatherer from Luxembourg whose mtDNA was published a few years ago and a Neolithic European LBK farmer from Germany, as well as several Mesolithic hunter-gatherers from Sweden.

The Luxembourg sample is similar to the Iberian La Brana samples and the Swedish Mesolithic samples are similar to Swedish Neolithic hunter-gatherers. The LBK farmer is similar to Oetzi and a Swedish TRB farmer and to Sardinians. The authors also study the recently published Mal'ta Upper Paleolithic sample from Lake Baikal and find that it is part of an "Ancient North Eurasian" population that also admixed into West Eurasians on top of the Neolithic/Mesolithic mix.

The authors' proposed model and admixture estimates:

It seems that the estimates go all the way to "almost pure" Early European farmer ancestry but "West European Hunter-Gatherer" and "Ancient North Eurasian" ancestry isn't found unmixed in any modern populations. The model seems to agree with Raghavan et al. that Karitiana are "Mal'ta"-admixed but also finds the most basal Eurasian ancestry in the European Neolithic farmer. The authors write:
The successful model (Fig. 2A) also suggests 44 ± 10% “Basal Eurasian” admixture into the ancestors of Stuttgart: gene flow into their Near Eastern ancestors from a lineage that diverged prior to the separation of the ancestors of Loschbour and Onge. Such a scenario, while never suggested previously, is plausible given the early presence of modern humans in the Levant25, African-related tools made by modern humans in Arabia26, 27, and the geographic opportunity for continuous gene flow between the Near East and Africa28
The Swedish/Luxembourg Mesolithic hunter-gatherers are all mtDNA-haplogroup U and Y-chromosome haplogroup I, so again no R1a/R1b in early European samples.

An interesting finding is that the Luxembourg hunter-gatherer probably had blue eyes (like a Mesolithic La Brana Iberian, a paper on which seems to be in the works) but darker skin than the LBK farmer who had brown eyes but lighter skin. Raghavan et al. did not find light pigmentation in Mal'ta (but that was a very old sample), so with the exception of light eyes that seem established for Western European hunter-gatherers (and may have been "darker" in European steppe populations, but "lighter" in Bronze Age South Siberians?), the origin of depigmentation of many recent Europeans remains a mystery. Ancient DNA continues to surprise at every turn.

UPDATE (4/4/2014): a new version of the preprint.

bioRxiv doi: 10.1101/001552

Ancient human genomes suggest three ancestral populations for present-day Europeans

Iosif Lazaridis et al.

Analysis of ancient DNA can reveal historical events that are difficult to discern through study of present-day individuals. To investigate European population history around the time of the agricultural transition, we sequenced complete genomes from a ~7,500 year old early farmer from the Linearbandkeramik (LBK) culture from Stuttgart in Germany and an ~8,000 year old hunter-gatherer from the Loschbour rock shelter in Luxembourg. We also generated data from seven ~8,000 year old hunter-gatherers from Motala in Sweden. We compared these genomes and published ancient DNA to new data from 2,196 samples from 185 diverse populations to show that at least three ancestral groups contributed to present-day Europeans. The first are Ancient North Eurasians (ANE), who are more closely related to Upper Paleolithic Siberians than to any present-day population. The second are West European Hunter-Gatherers (WHG), related to the Loschbour individual, who contributed to all Europeans but not to Near Easterners. The third are Early European Farmers (EEF), related to the Stuttgart individual, who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model the deep relationships of these populations and show that about ~44% of the ancestry of EEF derived from a basal Eurasian lineage that split prior to the separation of other non-Africans.


December 23, 2013

mtDNA and Y chromosomes of Tungus

PLoS ONE 8(12): e83570. doi:10.1371/journal.pone.0083570

Investigating the Prehistory of Tungusic Peoples of Siberia and the Amur-Ussuri Region with Complete mtDNA Genome Sequences and Y-chromosomal Markers

Ana T. Duggan et al.

Evenks and Evens, Tungusic-speaking reindeer herders and hunter-gatherers, are spread over a wide area of northern Asia, whereas their linguistic relatives the Udegey, sedentary fishermen and hunter-gatherers, are settled to the south of the lower Amur River. The prehistory and relationships of these Tungusic peoples are as yet poorly investigated, especially with respect to their interactions with neighbouring populations. In this study, we analyse over 500 complete mtDNA genome sequences from nine different Evenk and even subgroups as well as their geographic neighbours from Siberia and their linguistic relatives the Udegey from the Amur-Ussuri region in order to investigate the prehistory of the Tungusic populations. These data are supplemented with analyses of Y-chromosomal haplogroups and STR haplotypes in the Evenks, Evens, and neighbouring Siberian populations. We demonstrate that whereas the North Tungusic Evenks and Evens show evidence of shared ancestry both in the maternal and in the paternal line, this signal has been attenuated by genetic drift and differential gene flow with neighbouring populations, with isolation by distance further shaping the maternal genepool of the Evens. The Udegey, in contrast, appear quite divergent from their linguistic relatives in the maternal line, with a mtDNA haplogroup composition characteristic of populations of the Amur-Ussuri region. Nevertheless, they show affinities with the Evenks, indicating that they might be the result of admixture between local Amur-Ussuri populations and Tungusic populations from the north.


Recent origin of North African populations

This makes sense since North Africans are so close (phenotypically) to West Eurasians that it makes sense that they cannot have been isolated from them for very long, i.e., since Out-of-Africa.

PLoS ONE 8(11): e80293. doi:10.1371/journal.pone.0080293

Genome-Wide and Paternal Diversity Reveal a Recent Origin of Human Populations in North Africa

Karima Fadhlaoui-Zid, Marc Haber et al.

The geostrategic location of North Africa as a crossroad between three continents and as a stepping-stone outside Africa has evoked anthropological and genetic interest in this region. Numerous studies have described the genetic landscape of the human population in North Africa employing paternal, maternal, and biparental molecular markers. However, information from these markers which have different inheritance patterns has been mostly assessed independently, resulting in an incomplete description of the region. In this study, we analyze uniparental and genome-wide markers examining similarities or contrasts in the results and consequently provide a comprehensive description of the evolutionary history of North Africa populations. Our results show that both males and females in North Africa underwent a similar admixture history with slight differences in the proportions of admixture components. Consequently, genome-wide diversity show similar patterns with admixture tests suggesting North Africans are a mixture of ancestral populations related to current Africans and Eurasians with more affinity towards the out-of-Africa populations than to sub-Saharan Africans. We estimate from the paternal lineages that most North Africans emerged ~15,000 years ago during the last glacial warming and that population splits started after the desiccation of the Sahara. Although most North Africans share a common admixture history, the Tunisian Berbers show long periods of genetic isolation and appear to have diverged from surrounding populations without subsequent mixture. On the other hand, continuous gene flow from the Middle East made Egyptians genetically closer to Eurasians than to other North Africans. We show that genetic diversity of today's North Africans mostly captures patterns from migrations post Last Glacial Maximum and therefore may be insufficient to inform on the initial population of the region during the Middle Paleolithic period.


December 22, 2013

Neandertals could talk

PLoS ONE 8(12): e82261. doi:10.1371/journal.pone.0082261

Micro-Biomechanics of the Kebara 2 Hyoid and Its Implications for Speech in Neanderthals

Ruggero D’Anastasio et al.

The description of a Neanderthal hyoid from Kebara Cave (Israel) in 1989 fuelled scientific debate on the evolution of speech and complex language. Gross anatomy of the Kebara 2 hyoid differs little from that of modern humans. However, whether Homo neanderthalensis could use speech or complex language remains controversial. Similarity in overall shape does not necessarily demonstrate that the Kebara 2 hyoid was used in the same way as that of Homo sapiens. The mechanical performance of whole bones is partly controlled by internal trabecular geometries, regulated by bone-remodelling in response to the forces applied. Here we show that the Neanderthal and modern human hyoids also present very similar internal architectures and micro-biomechanical behaviours. Our study incorporates detailed analysis of histology, meticulous reconstruction of musculature, and computational biomechanical analysis with models incorporating internal micro-geometry. Because internal architecture reflects the loadings to which a bone is routinely subjected, our findings are consistent with a capacity for speech in the Neanderthals.


December 18, 2013

A Neandertal from the Altai Mountains (Prüfer et al. 2013)

There seems to have been a lot of inter-"species" sex during the Paleolithic (left), and that's just from a handful of Eurasian hominins sequenced so far.

Who knows what other Middle Paleolithic genomes might be in the works? My guess is that once all is said and done, the tree of Homo will fill up with "red" admixture edges, and those who argued for a single Homo lineage evolving over hundreds of thousands of years, with gene flow between regional populations, will have the upper hand.

An interesting finding is that the introgressing Neandertal (N.I.) was related to the Mezmaiskaya sample from the Caucasus rather than to the Vindija sample from Croatia or the new Altai Neandertal. It'd be great to have the genome of a bona fide "progressive" Near Eastern Neandertal.

UPDATE I (Dec. 19):

Reading the 249 pages of supplementary information is likely to reveal a lot of gems of new information.In SI 13 we see that:
We detect likely West Eurasian gene flow into the ancestors of Yoruba West Africans within the last ten thousand years, which indirectly contributed a small amount of Neandertal ancestry to Yoruba.
These results mean that we have not identified any sub-Saharan African sample that we are confident has no evidence of back-to-Africa migration. Our best candidate at present is the Dinka but it is possible that with a phased genome or large sample sizes we would detect evidence of non-African ancestry in this population as well.
Nature (2013) doi:10.1038/nature12886

The complete genome sequence of a Neanderthal from the Altai Mountains

Kay Prüfer et al.

We present a high-quality genome sequence of a Neanderthal woman from Siberia. We show that her parents were related at the level of half-siblings and that mating among close relatives was common among her recent ancestors. We also sequenced the genome of a Neanderthal from the Caucasus to low coverage. An analysis of the relationships and population history of available archaic genomes and 25 present-day human genomes shows that several gene flow events occurred among Neanderthals, Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the high-quality Neanderthal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans.


Near Eastern origin of R1a in Ashkenazi Levites

This paper is a nice cautionary tale. R1a is very common in eastern Europe and less so in the Near East. Ashkenazi Jews lived in Eastern Europe, and one group of them (Levites) had high frequency of R1a than the rest. It seemed that an eastern European patrilineage had inserted itself into the Ashkenazi Levite gene pool.

It turns out that this is not the case. The specific clade R-M582 to which Ashkenazi Levites (and other non-Levites) belong to is absent in eastern Europeans and present in non-Jewish Near Easterners, making it more likely that Jews did not pick it up from eastern Europeans, but rather from some Near Eastern population. A look at the table of frequencies suggests to me an Iranic source, but I doubt that modern populations will ever allow a full resolution of such questions.

Nature Communications 4, Article number: 2928 doi:10.1038/ncomms3928

Phylogenetic applications of whole Y-chromosome sequences and the Near Eastern origin of Ashkenazi Levites

Siiri Rootsi et al.

Previous Y-chromosome studies have demonstrated that Ashkenazi Levites, members of a paternally inherited Jewish priestly caste, display a distinctive founder event within R1a, the most prevalent Y-chromosome haplogroup in Eastern Europe. Here we report the analysis of 16 whole R1 sequences and show that a set of 19 unique nucleotide substitutions defines the Ashkenazi R1a lineage. While our survey of one of these, M582, in 2,834 R1a samples reveals its absence in 922 Eastern Europeans, we show it is present in all sampled R1a Ashkenazi Levites, as well as in 33.8% of other R1a Ashkenazi Jewish males and 5.9% of 303 R1a Near Eastern males, where it shows considerably higher diversity. Moreover, the M582 lineage also occurs at low frequencies in non-Ashkenazi Jewish populations. In contrast to the previously suggested Eastern European origin for Ashkenazi Levites, the current data are indicative of a geographic source of the Levite founder lineage in the Near East and its likely presence among pre-Diaspora Hebrews.


December 17, 2013

Reconstruction of 5,500-year old "Stonehenge Man"

I don't see any mention of DNA in the article The face of prehistoric Britain: Forensic scientist uses Neolithic man's 5,500-year-old skull to create lifelike image as part of new £27m Stonehenge centre, so it's not clear whether the pigmentation attributed to "Stonehenge Man" is the artist's imagination or based on solid evidence.

From the article:
He is the star attraction of Stonehenge's new £27million modern visitor centre that has taken decades to produce. 
A Neolithic man has been brought to life after the most advanced forensic reconstruction of a face, based on a 5,500-year-old skeleton buried in a long barrow 1.5 miles from Stonehenge. 
The new face of the model, which has been carefully reconstructed to show people what life was like

December 15, 2013

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


December 14, 2013

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.


December 12, 2013

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.


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.

December 06, 2013

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.


December 05, 2013

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.


December 04, 2013

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.