Friday, January 30, 2015

Mitochondrial DNA control region analysis of three ethnic groups in the Republic of Macedonia

Renata Jankova-Ajanovska, Bettina Zimmermann, Gabriela Huber, Alexander W. Röck, Martin Bodner, Zlatko Jakovski, Biljana Janeska, Aleksej Duma, Walther Parson

(Open Accesss)


A total of 444 individuals representing three ethnic groups (Albanians, Turks and Romanies) in the Republic of Macedonia were sequenced in the mitochondrial control region. The mtDNA haplogroup composition differed between the three groups. Our results showed relatively high frequencies of haplogroup H12 in Albanians (8.8%) and less in Turks (3.3%), while haplogroups M5a1 and H7a1a were dominant in Romanies (13.7% and 10.3%, respectively) but rare in the former two. This highlights the importance of regional sampling for forensic mtDNA databasing purposes. These population data will be available on EMPOP under accession numbers EMP00644 (Albanians), EMP00645 (Romanies) and EMP00646 (Turks).

Goran Villages Of Albania

Tuesday, January 27, 2015

Publications of Wolfgang Haak


Refereed journal articles
Templeton JEL, Brotherton PM, Llamas B, Soubrier J, Haak W, Cooper A, Austin J. DNA capture and Next Generation Sequencing recover whole mitochondrial genomes from highly degraded samples for human identification. Investigative Genetics (in press).

Brandt G*, Haak W*, Adler CJ, Roth C, Szécsényi-Nagy A, Karimnia S, Möller-Rieker S, Meller H, Ganslmeier R, Friederich S, Dresely V, Nicklisch N, Pickrell J, Sirocko F, Reich D, Cooper A, Alt KW, The Genographic Consortium (2013). Ancient DNA Reveals Key Stages in the Formation of Central European Mitochondrial Genetic Diversity. Science 342: 257-261. doi:10.1126/science.1241844.

Mundorff AZ, Kiley S, Latham KE, Haak W, Gilson T (2013) Individualizing Unidentified Skeletal Remains: A Differential Diagnosis Combining Pathological Changes and Biomolecular Testing. Journal of Forensic Identification 63 (6): 617-632.

Boattini A, Martinez-Cruz B, Sarno S, Harmant C, Useli A, Sanz P, Yang-Yao D, Manry J, Ciani G, Luiselli D, Quintana-Murci L, Comas D, Pettener D, The Genographic Consortium (2013). Uniparental markers in Italy reveal a sex-biased genetic structure and different historical strata. PLoS One 8 (5): e65441. doi: 10.1371/journal.pone.0065441.

Elhaik E, Greenspan E, Staats S, Krahn T, Tyler-Smith C, Xue Y, Tofanelli S, Francalacci P, Cucca F, Pagani L, Jin L, Li H, Schurr TG, Greenspan B, Spencer Wells R, The Genographic Consortium (2013) The GenoChip: a new tool for genetic anthropology. Genome Biology and Evolution(5): 1021-31. doi: 10.1093/gbe/evt066.

Brotherton P*, Haak W*, Templeton J, Brandt G, Soubrier J, Adler CJ, Richards SM, Der Sarkissian C, Ganslmeier R, Friederich S, Dresely V, van Oven M, Kenyon R, Van der Hoek M, Korlach J, Luong K, Ho SYW, Quintana-Murci L, Behar DM, Meller H, Alt KW, Cooper A & The Genographic Project (2013) Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans. Nature Communications 4 (1764). doi:10.1038/ncomms2656.

Adler CJ, Dobney K, Weyrich L, Kaidonis J, Walker AW, Haak W, Bradshaw CJA, Townsend G, Sołtysiak, A, Alt KW, Parkhill J, Cooper, A (2013). Ancient DNA records the impacts of the Neolithic and Industrial revolutions on human oral microbiota and disease. Nature Genetics. Advance online publication. doi:10.1038/ng.2536.

Der Sarkissian C, Balanovsky O, Brandt G, Khartanovich V, Buzhilova A, Koshel S, Zaporozhchenko V, Moiseyev V, Gronenborn D, Kolpakov E, Shumkin V, Alt KW, Balanovska E, Cooper A, Haak W, The Genographic Consortium (2013). Ancient DNA Reveals Prehistoric Gene-Flow from Siberia in the Complex Human Population History of North East Europe. PLoS Genetics 9 (2): e1003296. doi:10.1371/journal.pgen.1003296.

Fehren-Schmitz L, Llamas B, Tomasto-Cagigao E, Haak W (2012) Ancient DNA and the early population history of western South America: what have we learned so far and where do we go from here? Boletin Arqueologia PUCP 15. [Spanish].

Badro DA, Douaihy B, Haber M, Youhanna SC, Salloum A, Ghassibe-Sabbagh M, Johnsrud B, Khazen G, Matisoo-Smith E, Soria-Hernanz DF, Wells RS, Tyler-Smith C, Platt DE, Zalloua PA, The Genographic Consortium (2013) Y chromosome and mtDNA Genetics Reveal Significant Contrasts in Affinities of Modern Middle Eastern Populations with European and African Populations. PLoS One 8 (1): e54616. doi: 10.1371/journal.pone.0054616.

Behar DM, Harman t C, Manry J, van Oven M, Haak W, Martinez-Cruz B, Salaberria J, Oyharçabal B, Bauduer F, Comas D, Quintana-Murci L, The Genographic Consortium (2012) The Basque paradigm: genetic evidence of a maternal continuity in the Franco-Cantabrian Region since the Late Paleolithic. American Journal of Human Genetics 90 (3): 486-493. doi:10.1016/j.ajhg.2012.01.002.

Arunkumar G, Soria-Hernanz DF, Kavitha VJ, Arun VS, Syama A, Ashokan KS, Gandhirajan KT, Vijayakumar K, Narayanan M, Jayalakshmi M, Ziegle JS, Royyuru AK, Parida L, Wells RS, Renfrew C, Schurr TG, Smith CT, Platt DE, Pitchappan R, The Genographic Consortium (2012) Population differentiation of southern Indian male lineages correlates with agricultural expansions predating the caste system. PLoS One 7 (11): e50269. doi:10.1371/journal.pone.0050269.

Martínez-Cruz B, Harmant C, Platt DE, Haak W, Manry J, Ramos-Luis E, Soria-Hernanz DF, Bauduer F, Salaberria J, Oyharçabal B, Quintana-Murci L, Comas D, The Genographic Consortium (2012) Evidence of Pre-Roman Tribal Genetic Structure in Basques from Uniparentally Inherited Markers. Molecular Biology & Evolution 29 (9): 2211-2222. doi: 10.1093/molbev/mss091.

Dulik MC, Owings AC, Gaieski JB, Vilar MG, Andre A, Lennie C, Mackenzie MA, Kritsch I, Snowshoe S, Wright R, Martin J, Gibson N, Andrews TD, Schurr TG, The Genographic Consortium (2012) Y-chromosome analysis reveals genetic divergence and new founding native lineages in Athapaskan- and Eskimoan-speaking populations. Proceedings of the National Academy of Sciences of the United States of America 109 (22): 8471-6.

Rębała K, Martínez-Cruz B, Tönjes A, Kovacs P, Stumvoll M, Lindner I, Büttner A, Wichmann HE, Siváková D, Soták M, Quintana-Murci L, Szczerkowska Z, Comas D, The Genographic Consortium (2012) Contemporary paternal genetic landscape of Polish and German populations: from early medieval Slavic expansion to post-World War II resettlements. European Journal of Human Genetics. Sep 12. doi: 10.1038/ejhg.2012.190.

Martinez-Cruz B, Ioana M, Calafell F, Arauna LR, Sanz P, Ionescu R, Boengiu S, Kalaydjieva L, Pamjav H, Makukh H, Plantinga T, van der Meer JW, Comas D, Netea MG, The Genographic Consortium (2012) Y-Chromosome Analysis in Individuals Bearing the Basarab Name of the First Dynasty of Wallachian Kings. PLoS One 7 (7): e41803.

Schurr TG, Dulik MC, Owings AC, Zhadanov SI, Gaieski JB, Vilar MG, Ramos J, Moss MB, Natkong F, The Genographic Consortium (2012) Clan, language, and migration history has shaped genetic diversity in Haida and Tlingit populations from Southeast Alaska. American Journal of Physical Anthropology 148 (3): 422-35. doi: 10.1002/ajpa.22068.

Haber M, Platt DE, Ashrafian Bonab M, Youhanna SC, Soria-Hernanz DF, Martínez-Cruz B, Douaihy B, Ghassibe-Sabbagh M, Rafatpanah H, Ghanbari M, Whale J, Balanovsky O, Wells RS, Comas D, Tyler-Smith C, Zalloua PA, The Genographic Consortium (2012) Afghanistan's ethnic groups share a Y-chromosomal heritage structured by historical events. PLoS One 7 (3) :e34288.

Lu Y, Wang C, Qin Z, Wen B, Farina SE, Jin L, Li H, The Genographic Consortium (2012) Mitochondrial origin of the matrilocal Mosuo people in China. Mitochondrial DNA 23 (1): 13-9.

Kang L, Lu Y, Wang C, Hu K, Chen F, Liu K, Li S, Jin L, Li H, The Genographic Consortium (2012) Y-chromosome O3 haplogroup diversity in Sino-Tibetan populations reveals two migration routes into the eastern Himalayas. Annuals of Human Genetics 76 (1): 92-9. doi: 10.1111/j.1469-1809.2011.00690.x.

Javed A, Melé M, Pybus M, Zalloua P, Haber M, Comas D, Netea MG, Balanovsky O, Balanovska E, Jin L, Yang Y, Arunkumar G, Pitchappan R, Bertranpetit J, Calafell F, Parida L, The Genographic Consortium (2012) Recombination networks as genetic markers in a human variation study of the Old World. Human Genetics 131 (4): 601-13. doi: 10.1007/s00439-011-1104-8.

Melé M, Javed A, Pybus M, Zalloua P, Haber M, Comas D, Netea MG, Balanovsky O, Balanovska E, Jin L, Yang Y, Pitchappan RM, Arunkumar G, Parida L, Calafell F, Bertranpetit J, and The Genographic Consortium (2012) Recombination gives a new insight in the effective population size and the history of the Old World human populations. Molecular Biology and Evolution 29 (1): 25-30.

Adler CJ, Haak W, Donlon D, Cooper A, The Genographic Consortium (2011) Survival and recovery of DNA from ancient teeth and bones. Journal of Archaeological Science 38 (5): 956-964.

Balanovsky O, Dibirova K, Dybo A, Mudrak O, Frolova S, Pocheshkhova E, Haber M, Platt D, Schurr T, Haak W, Kuznetsova M, Radzhabov M, Balaganskaya O, Druzhinina E, Zakharova T, Soria Hernanz DF, Zalloua P, Koshel S, Ruhlen M, Renfrew C, Wells RS, Tyler-Smith C, Balanovska E, The Genographic Consortium (2011) Parallel Evolution of Genes and Languages in the Caucasus Region. Molecular Biology & Evolution 28 (10): 2905-2920.

Gaieski JB, Owings AC, Vilar MG, Dulik MC, Gaieski DF, Gittelman RM, Lindo J, Gau L, Schurr TG, The Genographic Consortium (2011) Genetic ancestry and indigenous heritage in a Native American Descendant Community in Bermuda. American Journal of Physical Anthropology 146 (3): 392-405. doi: 10.1002/ajpa.21588.

Cai X, Qin Z, Wen B, Xu S, Wang Y, Lu Y, Wei L, Wang C, Li S, Huang X, Jin L, Li H, The Genographic Consortium (2011) Human migration through bottlenecks from Southeast Asia into East Asia during Last Glacial Maximum revealed by Y chromosomes. PLoS One 6 (8): e24282.

Haber M, Platt DE, Badro DA, Xue Y, El-Sibai M, Bonab MA, Youhanna SC, Saade S, Soria-Hernanz DF, Royyuru A, Wells RS, Tyler-Smith C, Zalloua PA, The Genographic Consortium (2011) Influences of history, geography, and religion on genetic structure: the Maronites in Lebanon. European Journal of Human Genetics 19(3): 334-340.

Martínez-Cruz B, Ziegle J, Sanz P, Sotelo G, Anglada R, Plaza S, Comas D, and The Genographic Consortium (2011) Multiplex single-nucleotide polymorphism typing of the human Y chromosome using TaqMan probes. Investigative Genetics 2 (2): 13.

Jota MS, Lacerda DR, Sandoval J., Vieira PPR, Santos-Lopes SS, Bisso-Machado R, Paixão-Cortes VR, Revollo S, Paz-y-Miño C, Fujita R, Salzano FM, Bonatto SL, Bortolini MC, Tyler-Smith C, Santos FR, and The Genographic Consortium (2011) A new subhaplogroup of Native American Y-chromosomes from the Andes. American Journal of Physical Anthropology (DOI 10.1002/ajpa.21519).

Yan S, Wang CC, Li H, Li SL, Jin L, and The Genographic Consortium (2011) An updated tree of Y-chromosome Haplogroup O and revised phylogenetic positions of mutations P164 and PK4. European Journal of Human Genetics 19: 1013-1015.

Yang K, Zheng H, Qin Z, Lu Y, Farina SE, Li S, Jin L, Li D, Li H, and The Genographic Consortium (2011) Positive selection on mitochondrial M7 lineages among the Gelong people in Hainan. Journal of Human Genetics 56: 253-256.

Haak W, Balanovsky O, Sanchez JJ, Koshel S, Zaporozhchenko V, Adler CJ, Der Sarkissian CSI, Brandt G, Schwarz C, Nicklisch N, Dresely V, Fritsch B, Balanovska E, Villems R, Meller H, Alt KW, Cooper A, the Genographic Consortium (2010) Ancient DNA from European Early Neolithic Farmers Reveals Their Near Eastern Affinities. PLoS Biology 8 (11): e1000536.

Melé M, Javed A, Pybus M, Calafell F, Parida L, Bertranpetit J, The Genographic Consortium (2010) A New Method to Reconstruct Recombination Events at a Genomic Scale. PLoS Computational Biology 6(11): e1001010. doi:10.1371/journal.pcbi.1001010

Zhadanov SI, Dulik MC, Markley M, Jennings GW, Gaieski JB, Elias G, Schurr TG, and The Genographic Consortium (2010) Genetic heritage and native identity of the Seaconke Wampanoag tribe of Massachusetts. American Journal of Physical Anthropology 142: 579-589.

Qin Z, Yang Y, Kang L, Yan S, Cho K, Cai X, Lu Y, Zheng H, Zhu D, Fei D, Li S, Jin L, Li H, The Genographic Consortium (2010) A mitochondrial revelation of early human migrations to the Tibetan Plateau before and after the last glacial maximum. American Journal Physical Anthropology 143 (4): 555-69. doi: 10.1002/ajpa.21350.

Bramanti B, Thomas MG, Haak W, Unterlaender M, Jores P, Tambets K, Antanaitis-Jacobs I, Haidle MN, Jankauskas R, Kind C-J, Lueth F, Terberger T, Hiller J, Matsumura S, Forster P, Burger J (2009) Genetic discontinuity between local hunter-gatherers and central Europe's first farmers. Science 326 (5949): 137-140.

Meyer C, Brandt G, Haak W, Ganslmeier RA, Meller H, Alt KW (2009) The Eulau eulogy: Bioarchaeological interpretation of lethal violence in Corded Ware multiple burials from Saxony-Anhalt, Germany. Journal of Anthropological Archaeology 28 (4): 412-423.

Haak W*, Brandt G*, De Jong HN, Meyer C, Ganslmeier R, Heyd V, Hawkesworth C, Pike AWG, Meller H, Alt KW (2008) Ancient DNA, strontium isotopes, and osteological analyses shed light on social and kinship organization of the later stone age. Proceedings of the National Academy of Sciences of the United States of America 105 (47): 18226-18231.

Donlon D, Casey M, Haak W, Adler C (2008) Early colonial burial practices for perinates at the Parramatta convict hospital, NSW. Australasian Historical Archaeology 26: 71-84.

Burger J, Kirchner M, Bramanti B, Haak W, Thomas MG (2007) Absence of the lactase-persistence-associated allele in early Neolithic Europeans. Proceedings of the National Academy of Sciences of the United States of America 104 (10): 3736-3741.

Burger J, Gronenborn D, Forster P, Matsumura S, Bramanti B, Haak W (2006) Response to Comment on ‘‘Ancient DNA from the First European Farmers in 7500-Year-Old Neolithic Sites'' Science 312: 1875b.

Haak W, Forster P, Bramanti B, Matsumura S, Brandt G, Tänzer M, Villems R, Renfrew C, Gronenborn D, Alt KW, Burger J (2005) Ancient DNA from the First European farmers in 7500-year-old Neolithic sites. Science 310: 1016-1018.

Haak W, Gruber P, Rühli FJ, Böni T, Ulrich-Bochsler S, Frauendorf E, Burger J, Alt KW (2005) Molecular evidence of HLA-B27 in a historical case of ankylosing spondylitis. Arthritis & Rheumatism 52(10): 3318-3319.

Haak W, Burger J, Alt KW (2004) ABO genotyping by PCR-RFLP and cloning and sequencing. Anthropologischer Anzeiger 62 (4): 397-410.
Refereed conference papers
Haak W, Brandt G, Meyer C, De Jong HN, Ganslmeier R, Pike AWG, Meller H, Alt KW (2010) Die schnurkeramischen Familiengräber von Eulau - ein außergewöhnlicher Fund und seine interdisziplinäre Bewertung. Tagungen des Landesmuseums für Vorgeschichte Halle, Band 04, pp. 80-89.

Burger J, Haak W (2010) Mitochondrial Haplotypen aus humanen neolithischen Skeletten der LBK bzw. AVK. In: Gronenborn D, Petrasch (eds) The Spread of the Neolithic to Central Europe. RGZM-Tagungen, Band 4 1/2, pp. 141-146.

"On the Internet, nobody knows you're a dog."

     Peter Steiner, The New Yorker,  July 5, 1993

Monday, January 26, 2015

"Ancient North Eurasians": North-South Ancient Admixture in Central-South Eurasia

Back in February of 2014, I put up a post discussing an Admixture components pattern that appears across populations extending from Russia in the Chuvash, to the North Kannadi people in Southern India. I describe this pattern as the "Northeast Asian" - "East Asian" admixture components pattern.
This pattern can also be observed in the Admixture run shown in the paper The genome of a Late Pleistocene human from a Clovis burial site in western Montana, Rasmussen et al, 2014, Extended data, Figure 3:

Pronounced "Northeast Asian" like components can be observed in the Mari (related to the Chuvash), as well as Northeast Asian populations.
Pronounced "East Asian" like components can be observed in South Asian populations such as the North Kannadi people, as well as in populations of Southeast Asia.
These two components seem to be dispersed into each other from an ancient date, as described in the February 9th post.
I have seen various blogs and papers discussing the presence of an "Ancient North Eurasian (ANE)" component.  In them, it is proposed that this "ANE" component is the cause for the "eastward" population shift in Europeans since the Mesolithic. 
I would propose that this "ANE" component is not a single "component", and does not come from a single geographic location in the last 20,000 years or so.  It is widely dispersed.  Therefore, it is likely a very ancient population process which is derived in part from archaic admixture.
In Europeans, the source for this "ANE" component likely is not derived from a single source or entry point into Europe.  If the Motala12 ancient Mesolithic DNA sample from Sweden is any indication, "ANE" like components appear to have been diffusing into Europe since the Mesolithic.  These "ANE" diffusion processes continue to the present day.
Finally, apart from the fact that the Mal'ta MA1 sample from Lake Baikal, shown on the PCA of the Lazarides paper 2013, happens to line up on the PCA with populations such as the Chuvash, I strongly doubt that the R1* y-DNA haplogroup is widely correlated with "ANE" like components.  The Mal'ta MA1 population was probably on the leading edge of an eastward expansion that was not shared across the R1* extended family.
Marnie Dunsmore (January 26th, 2015)
The February 9th, 2014 post:
Quite early in the history of this blog, on November 3rd, 2010, I wrote a post discussing a minor "signal" I had noticed buried in the Dodecad admixture results for populations of Eastern Europe, the Middle East and South Asia.  The "signal" consisted of a combination of two Admixture components: "Northeast Asian" and "East Asian".  You can read about that early post here.  I've added a few thoughts on this topic recently, noting that the pattern is likely evidence of ancient bidirectional gene flow. (See Max Born on receiving the 1954 Nobel Prize . . ., Update, February 1, 2014.) 
In this post, I look at additional major components such as the "West Asian" component.
Reviewing observations from the previous posts, a number of deductions are possible:
1.  The "Northeast Asian"-"East Asian" admixture components are geographically correlated.
2.  The pattern extends from the Volga region of Southern Russia (Chuvash), into the Caucasus and Black Sea,  then into Pakistan, splitting westward through Syria into the Fertile Crescent, touching even into Egypt, and separately, trailing south through Pakistan extending west along the South Asian coast.
3.  The pattern is widely diffused compared to other admixture components.  In particular, it is much more widely diffused compared to the "North European" component and the "West Asian" component.  This wide diffusion is possibly indicative of great age since coalescence.
4.  As argued in the February 1st update of the post Max Born on receiving the 1954 Nobel Prize . . ., the "North European" component is likely correlated with pre-Ice Age hunter gatherers. 
5.  The "North European" component does not appear to be correlated with the "Northeast Asian"-"East Asian" pattern and is likely a superposition on it.
6.  The "Northeast Asian"-"East Asian" component does not appear to be present in the following populations considered in the Dodecad Admixture run:  Lithuanians, Cypriots, Spanish, French Basques, Tuscans, French, Northern Italians, Armenians, and Mozabite Berbers.  It is therefore uncorrelated with admixture in these populations.
In this post today, I look at three other major Admixture components with respect to the "Northeast Asian"-"East Asian" pattern.  These are the "West Asian", the "Southwest Asian" and the "Southern European" components.

Again, the data is normalized on the "Northeast Asian"-"East Asian" pattern. The remaining un-normalized components are allowed to float above this.  Figure 1 shows the zoomed in view with the normalization pattern running along the bottom.  This normalization approach corresponds with a North-South geographic pattern, as described in item "2." above.  Figure 2 shows the same data, but from a "zoomed out" perspective.  Populations are listed below Figure 2.

Figure 1:  Admixture components with normalized "Northeast Asian"-"East Asian" pattern show at bottom.  Components are arranged with highest "Northeast Asian" contribution on the left and highest "East Asian" contribution on the right.
Figure 2:  As in Figure 1, but "zoomed out" to fully show the un-normalized major components floating above the normalized "Northeast Asian"-"East Asian" pattern.
    1:  Chuvash
    2:  Lezgin
    3:  Georgian
    4:  Sindhi
    5:  Belorussian
    6:  Adygei
    7.  Pathan
    8:  Syrian
    9:  Turk
   10: Jordanian
   11: Romanian
   12: Ashkenazi
   13: North Kannadi
   14: Gujarati
   15: Uygur
   16: Burusho
   17: Egyptian

Looking at the above plots, the essential question to be asked is this:  Is there a correlation between the "Northeast Asian"-"East Asian" pattern and
1.  the "West Asian" component,
2.  the "Southwest Asian" component, or
3.  the "Southern European" component
The "West Asian" component is widely distributed.  In a few noticeable cases, such as the Chuvash, the Uygurs, the Burusho, and the North Kannadi, the "West Asian" component is only a very low level admixture component.  Based on this, it cannot be argued that the "West Asian" component is strongly correlated across the ancient "Northeast Asian"-"East Asian" pattern.  Moreover, the "West Asian" component is likely a superposition on this pre-existing population.  On the other hand, it has already been argued in another post that the point of coalescence of the "West Asian" component is somewhere in the Caucasus.   The distribution of the "West Asian" component centered about Georgians is vaguely apparent here.
The distributions of the other two major components "Southwest Asian" and "Southern European" are sparse and loosely distributed.   There does not appear to be an easily observable correlation between the ancient "Northeast Asian"-"East Asian" pattern and these components, at least from this data.