Y chromosomes and mtDNA from the Maldives

 

Of interest from the paper:

The haplogroup J(M304) Y chromosomes are all in subgroup J2(M172).

...

However, Eaaswarkhanth et al. (2010) report that Muslims and non-Muslims in India largely have the same Y-haplogroup frequency distribution, except that in Muslims low frequencies of Y-E1b1b1a(M78), Y-J(M304)(xJ2(M172)), and Y-G(M201) are found that are absent in non-Muslims (Eaaswarkhanth et al., 2010). In our Maldivian sample, none of those Y-haplogroups were found.

AJPA DOI: 10.1002/ajpa.22256
Indian ocean crossroads: Human genetic origin and population structure in the maldives
Jeroen Pijpe et al.
The Maldives are an 850 km-long string of atolls located centrally in the northern Indian Ocean basin. Because of this geographic situation, the present-day Maldivian population has potential for uncovering genetic signatures of historic migration events in the region. We therefore studied autosomal DNA-, mitochondrial DNA-, and Y-chromosomal DNA markers in a representative sample of 141 unrelated Maldivians, with 119 from six major settlements. We found a total of 63 different mtDNA haplotypes that could be allocated to 29 mtDNA haplogroups, mostly within the M, R, and U clades. We found 66 different Y-STR haplotypes in 10 Y-chromosome haplogroups, predominantly H1, J2, L, R1a1a, and R2. Parental admixture analysis for mtDNA- and Y-haplogroup data indicates a strong genetic link between the Maldive Islands and mainland South Asia, and excludes significant gene flow from Southeast Asia. Paternal admixture from West Asia is detected, but cannot be distinguished from admixture from South Asia. Maternal admixture from West Asia is excluded. Within the Maldives, we find a subtle genetic substructure in all marker systems that is not directly related to geographic distance or linguistic dialect. We found reduced Y-STR diversity and reduced male-mediated gene flow between atolls, suggesting independent male founder effects for each atoll. Detected reduced female-mediated gene flow between atolls confirms a Maldives-specific history of matrilocality. In conclusion, our new genetic data agree with the commonly reported Maldivian ancestry in South Asia, but furthermore suggest multiple, independent immigration events and asymmetrical migration of females and males across the archipelago. Am J Phys Anthropol 000:000–000, 2013. © 2013 Wiley Periodicals, Inc.

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Revised timescale of human mtDNA evolution (Fu et al. 2013)

 

An important new paper has just appeared in Current Biology. It is very exciting for a couple of reasons:

• The paper uses the idea of branch shortening to infer dates for the mtDNA phylogeny. Briefly, if one counts differences between a present-day sample P and an ancient sample A, one can get a sense of when their most recent common ancestor X, lived. But PX and PA are not equal: PA is shorter, because A has "missed" a few thousand years of evolution (depending on its age). If we know the age of A (and this can be reliably known by direct dating for many samples), then we can infer the time of X.

Looking at the ages of many haplogroups, I don't see any that immediately strike me as inconsistent with recent published age estimates based on modern mtDNA alone, such as those from the Copernican reassessment paper. In any case, this is an exciting new application of an idea that will yield good dates for haplogroup ages in the future. For example, it could be used to date Y-chromosome lineages as well, when high-quality sequences of ancient human Y-chromosomes become available.

• The paper also presents a number of new and exciting ancient DNA samples:

Please note that the "Cro Magnon" sample is actually revealed to be non-ancient in the study; that is another utility of the "branch shortening" idea, since it can demonstrate that purported very old samples are in fact fairly recent.
Note the important new samples from Dolni Vestonice, Oberkassel, Continenza, all of which are Paleolithic Europeans and all of which belong, without exception to subgroups of haplogroup U. It appears that Europe was indeed dominated by this haplogroup down to Mesolithic times, with a sharp discontinuity with early Neolithic Europeans.
The only outlier in the European context is Paglicci Str. 4b which is assigned to haplogroup H1. However:

Using this criterion, we excluded Paglicci Str. 4b from further analysis as the rate of C to T misincorporation at the 50 end was only 8.8%, thus making an ancient origin for the DNA in this sample uncertain [14].

Personally, I doubt there was any mtDNA haplogroup H in pre-Neolithic Europe, as the first author of this paper has also argued for in a previous one.
There is also a new sample from Boshan; it is probably too early to detect a pattern, but it is nonetheless noteworthy that it also belonged to mtDNA haplogroup B like the much earlier sample from Tianyuan.
Finally, the paper also discusses the issue of the mutation rate, noting that the divergence between Eurasian (M+N) and African (L3) mtDNA is much later than that inferred for autosomal DNA using new and "slow" de novo autosomal mutation rates. In my opinion there are two possible interpretations for this: one that there's something wrong with the slow rates, while another is that the earlier divergence using autosomal DNA may be a consequence of inflation due to admixture events in Africa.
Current Biology doi:10.1016/j.cub.2013.02.044
A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes
Qiaomei Fu et al.
Summary
Background
Recent analyses of de novo DNA mutations in modern humans have suggested a nuclear substitution rate that is approximately half that of previous estimates based on fossil calibration. This result has led to suggestions that major events in human evolution occurred far earlier than previously thought.
Results
Here, we use mitochondrial genome sequences from ten securely dated ancient modern humans spanning 40,000 years as calibration points for the mitochondrial clock, thus yielding a direct estimate of the mitochondrial substitution rate. Our clock yields mitochondrial divergence times that are in agreement with earlier estimates based on calibration points derived from either fossils or archaeological material. In particular, our results imply a separation of non-Africans from the most closely related sub-Saharan African mitochondrial DNAs (haplogroup L3) that occurred less than 62–95 kya.
Conclusions
Though single loci like mitochondrial DNA (mtDNA) can only provide biased estimates of population divergence times, they can provide valid upper bounds. Our results exclude most of the older dates for African and non-African population divergences recently suggested by de novo mutation rate estimates in the nuclear genome.
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Abnormalities in Pleistocene Homo

 

An excess of congenital defects is certainly compatible with high levels of inbreeding, and the publication of the Denisova genome clearly suggested "extremely low" genetic diversity in that Pleistocene human. It'll be interesting to see if more ancient DNA data will reveal high levels of inbreeding consistent with the abundance of genetic abnormalities evident in the anthropological record.

PLoS ONE 8(3): e59587. doi:10.1371/journal.pone.0059587
An Enlarged Parietal Foramen in the Late Archaic Xujiayao 11 Neurocranium from Northern China, and Rare Anomalies among Pleistocene Homo

Xiu-Jie Wu et al.

We report here a neurocranial abnormality previously undescribed in Pleistocene human fossils, an enlarged parietal foramen (EPF) in the early Late Pleistocene Xujiayao 11 parietal bones from the Xujiayao (Houjiayao) site, northern China. Xujiayao 11 is a pair of partial posteromedial parietal bones from an adult. It exhibits thick cranial vault bones, arachnoid granulations, a deviated posterior sagittal suture, and a unilateral (right) parietal lacuna with a posteriorly-directed and enlarged endocranial vascular sulcus. Differential diagnosis indicates that the perforation is a congenital defect, an enlarged parietal foramen, commonly associated with cerebral venous and cranial vault anomalies. It was not lethal given the individual’s age-at-death, but it may have been associated with secondary neurological deficiencies. The fossil constitutes the oldest evidence in human evolution of this very rare condition (a single enlarged parietal foramen). In combination with developmental and degenerative abnormalities in other Pleistocene human remains, it suggests demographic and survival patterns among Pleistocene Homo that led to an elevated frequency of conditions unknown or rare among recent humans.

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High-quality Neandertal genome online

The Max Planck institute has posted their high-coverage Neandertal genome on their site. The data can be downloaded from here. They had done the same with the high-quality Denisova genome, and it's great that they're making data available ahead of the official scientific publication, as this allows others to start using it much earlier.
From their site:

The genome sequence was generated from a toe bone discovered in Denisova Cave in southern Siberia in 2010.  The bone is described in Mednikova (Ethnology & Anthropology of Eurasia 2011. 39: 129-138).
DNA sequences were generated on the Illumina HiSeq platform and constitute an average 50-fold coverage of the genome. 99.9% of the 1.7GB of uniquely mappable DNA sequences in the human genome are covered at least ten times.
Contamination with modern human DNA, estimated from mitochondrial and nuclear DNA sequences, is around 1%.

It then appears that Neandertals occupied the same cave as the elusive Denisovans. When? I guess we'll have to wait to find out, but the preliminary genetic analysis shown on the figure (top-left) makes it clear that the "Altai" specimen marked in red which is the source of the high-coverage Neandertal genome does indeed group with other Neandertals, while Denisova is more related to Neandertals than to modern humans.
I've highlighted this before, but it bears repeating: divergence between Neandertals and Denisovans --who were in the same place (Denisova cave), perhaps some thousands of years apart-- seems to exceed that found between any two modern human groups which span the entire Earth.

New Neandertal remains from Mani

The age and cave origin of these remains may conceivably make them useful for ancient DNA studies.
Journal of Human Evolution doi:10.1016/j.jhevol.2013.02.002
New Neanderthal remains from Mani peninsula, Southern Greece: The Kalamakia Middle Paleolithic cave site
Katerina Harvati et al.
The Kalamakia cave, a Middle Paleolithic site on the western coast of the Mani peninsula, Greece, was excavated in 1993–2006 by an interdisciplinary team from the Ephoreia of Paleoanthropology and Speleology (Greek Ministry of Culture) and the Muséum national d'Histoire naturelle (Paris). The site is dated to between ca. 100,000 and >39,000 years BP (Before Present) and has yielded Mousterian lithics, a rich fauna, and human remains from several layers. The latter include 10 isolated teeth, a cranial fragment and three postcranial elements. The remains represent at least eight individuals, two of them subadults, and show both carnivore and anthropogenic modifications. They can be identified as Neanderthal on the basis of diagnostic morphology on most specimens. A diet similar to that of Neanderthals from mixed habitat is suggested by our analysis of dental wear (occlusal fingerprint analysis) and microwear (occlusal texture microwear analysis), in agreement with the faunal and palynological analyses of the site. These new fossils significantly expand the Neanderthal sample known from Greece. Together with the human specimens from Lakonis and Apidima, the Kalamakia human remains add to the growing evidence of a strong Neanderthal presence in the Mani region during the Late Pleistocene.
Link

Thesis of Oleg Balonovsky

is available here as pdf. Lots of interesting information, and a few striking maps. Hopefully, the fact that it's all in Russian won't be much of a problem in this day and age.
I will highlight a few pieces of information. First, a distribution of Y-chromosome haplogroups in Russian groups:

Notice:

• N1c-Tat is a general feature of the Russians, but N1b-P43 is only really found at any significant frequency in the northern groups.
• A strong contrast of E-M78 between central (present) and northern (absent) groups, consistent with a late introduction of this haplogroup in easternmost Europe.
• South-Central-North decreasing frequency of R1a; now, it's not clear how R1a came to be in Russians: some of it may be legacy of its initial entry into Europe from the east, other could be of historical import, and may have even arrived during the Slavic expansion from Central Europe. The pattern probably is the reverse of the high frequency of N1, indicating increasing importance of Finno-Ugric substratum in the north.
• Fairly interesting that of the two likely "Balkan" haplogroups E-M78 and I-P37, the former is modal in central region, the latter in southern one. The absence of both in "deep Asia" suggests a late introduction, as mentioned before, but when?

Also of interest a haplotype analysis within R1a1a-M198:

My most immediate observation is the set of mainly Indian highly divergent haplotypes on the left. There has been (well-deserved) excitement about recent Y-SNP progress within this haplogroup, but we should not neglect the occurrence of outliers/relics in our reconstruction of a haplogroup's history. I'd love to see those few Indian haplotypes SNP-tested using the currently available SNPs, or even used to develop new SNPs for this important Eurasian haplogroup.

Millet use ~11 thousand years ago in northern China

 

PNAS March 6, 2012 vol. 109 no. 10 3726-3730
Early millet use in northern China
Xiaoyan Yang et al.
It is generally understood that foxtail millet and broomcorn millet were initially domesticated in Northern China where they eventually became the dominant plant food crops. The rarity of older archaeological sites and archaeobotanical work in the region, however, renders both the origins of these plants and their processes of domestication poorly understood. Here we present ancient starch grain assemblages recovered from cultural deposits, including carbonized residues adhering to an early pottery sherd as well as grinding stone tools excavated from the sites of Nanzhuangtou (11.5–11.0 cal kyBP) and Donghulin (11.0–9.5 cal kyBP) in the North China Plain. Our data extend the record of millet use in China by nearly 1,000 y, and the record of foxtail millet in the region by at least two millennia. The patterning of starch residues within the samples allow for the formulation of the hypothesis that foxtail millets were cultivated for an extended period of two millennia, during which this crop plant appears to have been undergoing domestication. Future research in the region will help clarify the processes in place.
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