Tuesday, June 26, 2012

Worldwide Distribution of Dodecad K10a Components

Numerous ADMIXTURE runs have been completed by the Dodecad Ancestry Project since its' inception approximately two years ago. The status of certain components remained tenuous despite subsequent runs, whilst others provided fairly stable values for the bulk of the project's participants.

With the completion of the latest K10a run, I have composed a series of geographically accurate frequency maps with the intention of effectively presenting the trends that can be seen through the raw data.


Method

Data; values from over 130 groups obtained through the Dodecad K10a Spreadsheet. Only groups with at least 5 participants considered. Composites of populations were taken where appropriate and denoted with _cmp. Labels shown otherwise identical to source. The O_Italian_D group was excluded because no information on their origins were found online. 

Mapping; Dodecad participant populations allocated to national capitals. Exact location of reference populations obtained where possible (see Citations) however some allowances were made regarding those accompanied by scant information. Refer to the Data Sink for the population list, coordinates and commentary made during mapping process. No numerical data, aside from those shown for certain populations, was shown to minimise clutter and to remain faithful to the intention of this entry.

Population depiction; I deemed it necessary to separately consider the genetic structure of Jewish, Indian and expatriate/New World populations and exclude them from the rest of Europe, Asia or Africa. Including Jewish minorities with their gentile compatriots would render the maps uninformative. The complexity of India's demographics, particularly because of the caste system, makes frequency maps an improper choice for revealing inter-group genetic differences. 


Results






















Acknowledgement

The raw values used in this investigation are attributed to Dienekes Pontikos, author of the Dodecad Ancestry Project.


Addenum I [04/07/2012]: Inclusion of All Components Colourised map, shown below:




Citations
http://www.uvm.edu/~rsingle/stat295/F05/papers/Cavalli-Sforza-NRG-2005_Ceph-HGDP-CDP.pdf
http://www.1000genomes.org/about 

Sunday, June 17, 2012

Secrets of Central Asia: Chapter I - The Pokrovsk Man

The first of a series focused entirely on ancient and prehistoric Central Asian ancient DNA (aDNA), this entry covers the furthering of an investigation into frozen remains found in a remote part of Siberian Russia.


Pokrovsk, Sakha Republic, Russia
Introduction

In 2006, Amory et al. tested bone fragments of a grave found near Pokrovsk, a locale the Russian federal republic of Sakha (Yakutia) with the intention of discerning the remain's origins. [1] Amory et al. briefly elaborate on the purported archaeological history of Siberia, where an autochthonous hunter-gatherer population was either subjugated or partially displaced by expanding Tungus-Manchurian nomadic tribes, before the movement of Yakut herdsmen northwards into their present demographic range as a result of Mongolian domination in the region between the sixth and thirteenth centuries. The Abstract of the paper below:


"The Yakuts, Middle Age Turkic speakers (15th–16th centuries), are widely accepted as the first settlers of the Altai-Baikal area in eastern Siberia. They are supposed to have introduced horses and developed metallurgy in this geographic area during the 15th or 16th century a.d. The analysis of the Siberian grave of Pokrovsk, recently discovered near the Lena River (61_29_ N) and dated by accelerator mass spectrometry from 2,400 to 2,200 years b.p., may provide new elements to test this hypothesis. The exceptional combination of various artifacts and the mitochondrial DNA data extracted from the bone remains of the Pokrovsk man might prove the existence of previous contacts between autochthonous hunters of Oriental Siberia and the nomadic horse breeders from the Altai-Baikal area (Mongolia and Buryatia). Indeed, the stone arrowhead and the harpoons relate this Pokrovsk man to the traditional hunters of the Taiga. Some artifacts made of horse bone and the pieces of armor, however, are related to the tribes of Mongolia and Buryatia of the Xiongnu period (3rd century b.c.). This affinity has been confirmed by the match of the mitochondrial haplotype of this subject with a woman of the Egyin Gol necropolis (Mongolia, 2nd/3rd century a.d.) as well as with two modern Buryats. This result allows us to postulate that contacts between southern steppe populations and Siberian tribes occurred before the 15th century."
[Link]


Grave Features

The Pokrovsk grave is located at the top of a glacial terrace near the Lena-Pokrovsk river junction. Radiocarbon dating places the site at approximately 2390-2190YBP. The physical type of The Pokrovsk Man was found to be gracile skeletally with a brachycephalic skull. The physical type was found to be Mongoloid, although the authors note it was "less accentuated" than that of Middle-Age Yakuts. It was also noted that the torus mandibularis, a normal variational bony protuberance located within the interior aspect of the mandible, was absent, despite it occurring commonly in East Asian and Native American populations. [2] Several material items were observed in the grave, including bone tools, harpoon heads, reindeer bone armour and flint arrowheads connected to archaic Siberian culture. However, other goods, including an iron arrowhead, are reputedly of South Siberian built. [1]


Methods

DNA extraction from bone by technique outlined in Keyser-Tracqui & Ludes’  Methods for the study of ancient DNA. [3] Autosomal DNA (auDNA) was retrieved from Profiler+ Multiplex kit (nine Short Tandem Repeat’s, or STR’s). Y-Chromosomal DNA (Y-DNA) tested using Powerplex Y System (eleven STR’s) as well as a Single-Nucleotide Polymorphism (SNP) on the TAT locus. Finally, a 421 base pair (bp) segment on the sample’s mitochondrial DNA (mtDNA) at the first hypervariable segment (HVS1) was tested (position 1598916410) and compared with the Cambridge Reference Sequence (CRS). 
Consensus data obtained directly from paper; auDNA analysis was achieved through popSTR, an online research processing engine which displays auDNA STR allele frequencies within different populations. [8]
mtDNA and Y-DNA analysis would have ideally been conducted through ySearch, mitosearch, the SMGF, supplementary data from relevant scientific literature as well as online DNA projects.

Allelic Frequencies


auDNA Analysis

Nine auDNA STR’s were retrieved from the Pokrovsk Man's remains. Unfortunately, the utilisation of STR's is questionable given they have a large margin of error and lack of population specificity due to the presence of multiple alleles within a single population, as well as heavy inter-population overlapping. This investigative tool has largely been made redundant by SNP testing, which employ thousands of markers rather than a few. Nonetheless, processing of these results will still be attempted.

The allelic frequencies per worldwide regional groups for the retrieved STR’s are shown opposite. All markers from the Profiler+ Multiplex were utilised in the subsequent popSTR search. The sample populations are largely derived from the HGDP-CEPH Human Genome Diversity Cell Line Panel. [4]

African frequencies of the Pokrovsk alleles are generally lower relative to Eurasian, Oceanian and American regional groups. This warrants the exclusion of such values from the analysis hereon due to their uninformative nature, apart from confirming the Pokrovsk Man had no recent African ancestry, which is in accordance with anthropological, historical and linguistic data from Siberia. Allele frequencies of remaining regions are shown in the Data Sink.

To elucidate the regional affinities of the Pokrovsk Man, averages for the alleles across the given regions were taken and ranked in order of descending magnitude (found again in the Data Sink).

The results indicate his affinity was greatest to the Americas, followed by East Asia and Europe (discussed later) in joint position, ending with the Middle-East and South-Central Asia. The discrepancy between the American and East Asian scores are explained by the East Asia regional group being constituted largely of ethnic groups from East Asia proper and Southeast Asia, such as the She, Naxi and Japanese. The Yakuts, who are the only sample population located in Siberia, are a part of this group, reducing the specificity further. However, the greater score to native American and East Asian populations than others is still consistent with both geographic position and the known demic expansions into of both regions.

The decreased allelic frequency average of South-Central Asians and Middle-Easterners with the Pokrovsk Man supports the above further. However, the Middle-Eastern group did not include populations from West Asia or the Caucasus, such as Anatolian Turks, Iranians or Georgians. Additionally, the lack of North-Central Asian ethnic groups such as the Kazakh, Tatars or Altaians may affect the results further.

It would have been preferable if auDNA SNP’s were obtained instead and compared with specific sample populations - Better yet if IBD segment analysis was also undertaken. SNP analysis could have been possible in 2006, given the HGDP-CEPH samples were made available at least four years prior, [4] which would have opened the door to analysis far deeper than the extent undertaken by Amory et al. or even this investigation.

The authors greatly limited the extent of their own investigation, noting the Pokrovsk Man showed identical matches with Buryats, West Siberians, Altaian Mansis, ancient and modern Yakuts, one Evenk and an Egyin Gol necropolis female [5] in their private haplotype database.


mtDNA Analysis

Of the ten loci tested, only three yielded consistent nucleotide variations (16223T-16362C-16368C). The mitosearch 1-step matches with a known maternal ancestor location were considered only (Data Sink). These results not only confirm Amory et al.'s conclusion the Pokrovsk Man belonged to mtDNA Haplogroup D, but the bulk of the distribution within Asia is expected based on modern samples. [6]

Unfortunately, once more, the scope of the initial investigation has hindered any further analysis, as the lack of testing regions beyond HVS1 cannot elucidate the extent of mitochondrial sharing outside of the data showcased here.


Y-DNA Analysis

None of the eleven Y-DNA STR's provided a successful return. The only SNP tested for was TAT, where a T→C mutation is considered equivalent to the M46 marker, which is defined as Haplogroup N1c under the current International Society of Genetic Genealogy (ISOGG) nomenclature. [7]

As the Pokrovsk Man yielded a T allele at this locus, his Y-DNA Haplogroup could not have been N1c-M46. However, this does not rule out him belonging to a lineage upstream of N1c-M46.


European Affinities & Conclusion

Despite the great limitations, several invaluable inferences can be made from the data presented in the furthering of Amory et al.'s Early influence of the steppe tribes in the peopling of Siberia which cannot be reasonably excluded as anomalous without also discarding conclusions made from other sources.

The auDNA results, though derived from STR data, fully agree with the SNP-based analysis of the Eurogenes Project by David W. in a previous run (described in an earlier Vaêdhya entry), as modern Siberian populations show trace values of various European or Caucasian ADMIXTURE components at the least with an absence of Southwest or South Asian specific components, whilst being predominantly Siberian and East Asian.

The European affinity in this investigation coming third may form a convenient explanation for why the Pokrovsk Man's features were less Mongoloid anthropometrically than Middle-Age Yakuts. It may suggest a West Eurasian physical element existed prior to the tribal and political upheavals that resulted in the Yakut settlement deeper into this portion of Siberia. Although the origins of this element were not elaborated upon, there may also be a connection with the postulated "migration corridor" covered previously and described in Malyarchuk et al.'s On the Origin of Mongoloid Component in the Mitochondrial Gene Pool of Slavs. [10]

This result supplements the picture of a West Eurasian genetic component of ambiguous origins being brought towards Siberia, challenging one interpretation of West Eurasian physical influence in the region stopping abruptly at Lake Baikal. [9] Instead, the totality of the evidence presented raises the possibility of this influence extending itself beyond the lake and manifesting itself simply as a "reduction" of Mongoloid cranial characteristics, which the Pokrovsk Man demonstrated, whose anthropometric configuration may well have been an artefact of this.

Unfortunately, the mtDNA and Y-DNA results were far too non-specific to merit further analyses. Their generality, however, do pose several questions; what subtype of mtDNA Haplogroup D did the Pokrovsk Man belong to? If he was not Y-DNA Haplogroup N1c-M46, what was he?

The material goods found in the Pokrovsk Man's gravesite may point us in the direction of the orientation his apparent European affinities came from. As South Siberia was the source of his iron and horse-derived goods, could he also have inherited West Eurasian genes from there? Were the benefactors ancient, or prehistoric?


Acknowledgements

Pokrovsk map from WolframAlpha.


References

1. Amory S, Crubézy E, Keyser C, Alekseev AN, Ludes B. Early influence of the steppe tribes in the peopling of Siberia. Hum Biol. 2006;78:531-49.

2. Apinhasmit W, Jainkittivong A, Swasdison S. Torus Palatinus and Torus Mandibularis in a Thai population. ScienceAsia. 2002;28:105-111.

3. Keyser-Tracqui C, Ludes B. Methods for the study of ancient DNA. Meth. Mol. Biol. 2005;297:253–264.

4. Rosenberg NA. Standardized subsets of the HGDP-CEPH Human Genome Diversity Cell Line Panel, accounting for atypical and duplicated samples and pairs of close relatives. Ann Hum Genet. 2006;70:841-7.

5. Keyser-Tracqui C,Crubézy E, Ludes B. Nuclear and Mitochondrial DNA Analysis of a 2,000-Year-Old Necropolis in the Egyin Gol Valley of Mongolia. Am J Hum Genet. 2003;73:247–260.

6. Mishmar D, Ruiz-Pesini E, Golik P, Macaulay V, Clark AG. Natural selection shaped regional mtDNA variation in humans. Proc Natl Acad Sci. 2003;00:171-6.

7. Zerjal T, Dashnyam B, Pandya A, Kayser M, Roewer L. Genetic relationships of Asians and Northern Europeans, revealed by Y-chromosomal DNA analysis. Am J Hum Genet. 1997;60:1174–1183.

8. Amigo J, Phillips C, Salas T, Fernández Formoso L, Carracedo A. pop.STR - An online population frequency browser for established and new forensic STRs. Forensic Sci. Int. Gene. Suppl. 2009.

9. Mooder KP, Schurr TG, Bamforth FJ, Bazaliiski VI, Savel'ev NA. Population affinities of Neolithic Siberians: A snapshot from prehistoric Lake Baikal. Am J Phys Anthropol. 2006;129:349-61

10. Maliarchuk BA, Perkova MA, Derenko MV. Origin of the Mongoloid component in the mitochondrial gene pool of Slavs. Genetika. 2008;44:401-6.