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1. Variation of Genomic Sites Associated with Severe Covid-19 Across Populations: Global and National Patterns

Author

Balanovsky O, Petrushenko V, Mirzaev K, Abdullaev S, Gorin I, Chernevskiy D, Agdzhoyan A, Balanovska E, Kryukov A, Temirbulatov I, and Sychev D

Subjects
severe covid-19, genetic markers, ab0, rs11385942, rs657152, gene geography, Therapeutics. Pharmacology, RM1-950
Abstract

Oleg Balanovsky,1– 3 Valeria Petrushenko,1,4 Karin Mirzaev,2,5 Sherzod Abdullaev,5 Igor Gorin,1,4 Denis Chernevskiy,2 Anastasiya Agdzhoyan,1,2 Elena Balanovska,2,3 Alexander Kryukov,5 Ilyas Temirbulatov,2,5 Dmitriy Sychev5 1Laboratory of Genome Geography, Vavilov Institute of General Genetics, Moscow, Russia; 2Laboratory of Human Population Genetics, Research Centre for Medical Genetics, Moscow, Russia; 3Biobank of North Eurasia, Moscow, Russia; 4Department of Bioinformatics Moscow Institute of Physics and Technology, Moscow, Russia; 5Department of Clinical Pharmacology and Therapeutics, Russian Medical Academy of Continuous Professional Education, Moscow, RussiaCorrespondence: Elena BalanovskaLaboratory of Human Population Genetics, Research Centre for Medical Genetics, Moscow, RussiaTel +7 499 612-81-79Email balanovska@mail.ruDmitriy SychevDepartment of Clinical Pharmacology and Therapeutics, Russian Medical Academy of Continuous Professional Education, Moscow, RussiaTel +7 495 680-05-99Email dmitry.alex.sychev@gmail.comBackground: Information about the distribution of clinically significant genetic markers in different populations may be helpful in elaborating personalized approaches to the clinical management of COVID-19 in the absence of consensus guidelines.Aim: Analyze frequencies and distribution patterns of two markers associated with severe COVID-19 (rs11385942 and rs657152) and look for potential correlations between these markers and deaths from COVID-19 among populations in Russia and across the world.Methods: We genotyped 1883 samples from 91 ethnic groups pooled into 28 populations representing Russia and its neighbor states. We also compiled a dataset on 32 populations from other regions using genotypes extracted or imputed from the available databases. Geographic maps showing the frequency distribution of the analyzed markers were constructed using the obtained data.Results: The cartographic analysis revealed that rs11385942 distribution follows the West Eurasian pattern: the marker is frequent among the populations of Europe, West Asia and South Asia but rare or absent in all other parts of the globe. Notably, the transition from high to low rs11385942 frequencies across Eurasia is not abrupt but follows the clinal variation pattern instead. The distribution of rs657152 is more homogeneous. The analysis of correlations between the frequencies of the studied markers and the epidemiological characteristics of COVID-19 in a population revealed that higher frequencies of both risk alleles correlated positively with mortality from this disease. For rs657152, the correlation was especially strong (r = 0.59, p = 0.02). These reasonable correlations were observed for the “Russian” dataset only: no such correlations were established for the “world” dataset. This could be attributed to the differences in methodology used to collect COVID-19 statistics in different countries.Conclusion: Our findings suggest that genetic differences between populations make a small yet tangible contribution to the heterogeneity of the pandemic worldwide.Keywords: severe COVID-19, genetic markers, AB0, rs11385942, rs657152, gene geography

Published
2021

8. Demographic and Genetic Portraits of the Ulchi Population

Author

Balanovska, E. V., Bogunov, Y. V., Kamenshikova, E. N., Balaganskaya, O. A., Agdzhoyan, A. T., Bogunova, A. A., Skhalyakho, R. A., Alborova, I. E., Zhabagin, M. K., Koshel, S. M., Daragan, D. M., Borisova, E. B., Galakhova, A. A., Maltceva, O. V., Mustafin, Kh. Kh., Yankovsky, N. K., and Balanovsky, O. P.

Published
2018
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12. Population biobanks: Organizational models and prospects of application in gene geography and personalized medicine

Author

Balanovska, E. V., Zhabagin, M. K., Agdzhoyan, A. T., Chukhryaeva, M. I., Markina, N. V., Balaganskaya, O. A., Skhalyakho, R. A., Yusupov, Yu. M., Utevska, O. M., Bogunov, Yu. V., Asilguzhin, R. R., Dolinina, D. O., Kagazezheva, Zh. A., Damba, L. D., Zaporozhchenko, V. V., Romanov, A. G., Dibirova, Kh. D., Kuznetsova, M. A., Lavryashina, M. B., Pocheshkhova, E. A., and Balanovsky, O. P.

Published
2016
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27. Characterizing the genetic history of admixture across inner Eurasia

Author

Jeong, C., Balanovsky, O., Lukianova, E., Kahbatkyzy, N., Flegontov, P., Zaporozhchenko, V., Immel, A., Wang, C., Ixan, O., Khussainova, E., Bekmanov, B., Zaibert, V., Lavryashina, M., Pocheshkhova, E., Yusupov, Y., Agdzhoyan, A., Sergey, K., Bukin, A., Nymadawa, P., Churnosov, M., Skhalyakho, R., Daragan, D., Bogunov, Y., Bogunova, A., Shtrunov, A., Dubova, N., Zhabagin, M., Yepiskoposyan, L., Churakov, V., Pislegin, N., Damba, L., Saroyants, L., Dibirova, K., Artamentova, L., Utevska, O., Idrisov, E., Kamenshchikova, E., Evseeva, I., Metspalu, M., Robbeets, M., Djansugurova, L., Balanovska, E., Schiffels, S., Haak, W., Reich, D., and Krause, J.

Abstract

The indigenous populations of inner Eurasia, a huge geographic region covering the central Eurasian steppe and the northern Eurasian taiga and tundra, harbor tremendous diversity in their genes, cultures and languages. In this study, we report novel genome-wide data for 763 individuals from Armenia, Georgia, Kazakhstan, Moldova, Mongolia, Russia, Tajikistan, Ukraine, and Uzbekistan. We furthermore report genome-wide data of two Eneolithic individuals (~5,400 years before present) associated with the Botai culture in northern Kazakhstan. We find that inner Eurasian populations are structured into three distinct admixture clines stretching between various western and eastern Eurasian ancestries. This genetic separation is well mirrored by geography. The ancient Botai genomes suggest yet another layer of admixture in inner Eurasia that involves Mesolithic hunter-gatherers in Europe, the Upper Paleolithic southern Siberians and East Asians. Admixture modeling of ancient and modern populations suggests an overwriting of this ancient structure in the Altai-Sayan region by migrations of western steppe herders, but partial retaining of this ancient North Eurasian-related cline further to the North. Finally, the genetic structure of Caucasus populations highlights a role of the Caucasus Mountains as a barrier to gene flow and suggests a post-Neolithic gene flow into North Caucasus populations from the steppe.

Published
2018

28. The genetic prehistory of the Greater Caucasus

Author

Wang, C., Reinhold, S., Kalmykov, A., Wissgott, A., Brandt, G., Jeong, C., Cheronet, O., Ferry, M., Harney, E., Keating, D., Mallick, S., Rohland, N., Stewardson, K., Kantorovich, A., Maslov, V., Petrenko, V., Erlikh, V., Atabiev, B., Magomedov, R., Kohl, P., Alt, K., Pichler, S., Gerling, C., Meller, H., Vardanyan, B., Yeganyan, L., Rezepkin, A., Mariaschk, D., Berezina, N., Gresky, J., Fuchs, K., Knipper, C., Schiffels, S., Balanovska, E., Balanovsky, O., Mathieson, I., Higham, T., Berezin, Y., Buzhilova, A., Trifonov, V., Pinhasi, R., Belinskiy, A., Reich, D., Hansen, S., Krause, J., and Haak, W.

Abstract

Archaeogenetic studies have described the formation of Eurasian ’}steppe ancestry{’ as a mixture of Eastern and Caucasus hunter-gatherers. However, it remains unclear when and where this ancestry arose and whether it was related to a horizon of cultural innovations in the 4th millennium BCE that subsequently facilitated the advance of pastoral societies likely linked to the dispersal of Indo-European languages. To address this, we generated genome-wide SNP data from 45 prehistoric individuals along a 3000-year temporal transect in the North Caucasus. We observe a genetic separation between the groups of the Caucasus and those of the adjacent steppe. The Caucasus groups are genetically similar to contemporaneous populations south of it, suggesting that - unlike today - the Caucasus acted as a bridge rather than an insurmountable barrier to human movement. The steppe groups from Yamnaya and subsequent pastoralist cultures show evidence for previously undetected Anatolian farmer-related ancestry from different contact zones, while Steppe Maykop individuals harbour additional Upper Palaeolithic Siberian and Native American related ancestry.

Published
2018

29. Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe

Author

Lamnidis, T., Majander, K., Jeong, C., Salmela, E., Wessman, A., Moiseyev, V., Khartanovich, V., Balanovsky, O., Ongyerth, M., Weihmann, A., Sajantila, A., Kelso, J., Pääbo, S., Onkamo, P., Haak, W., Krause, J., and Schiffels, S.

Abstract

European history has been shaped by migrations of people, and their subsequent admixture. Recently, evidence from ancient DNA has brought new insights into migration events that could be linked to the advent of agriculture, and possibly to the spread of Indo-European languages. However, little is known so far about the ancient population history of north-eastern Europe, in particular about populations speaking Uralic languages, such as Finns and Saami. Here we analyse ancient genomic data from 11 individuals from Finland and Northwest Russia. We show that the specific genetic makeup of northern Europe traces back to migrations from Siberia that began at least 3,500 years ago. This ancestry was subsequently admixed into many modern populations in the region, in particular populations speaking Uralic languages today. In addition, we show that ancestors of modern Saami inhabited a larger territory during the Iron Age than today, which adds to historical and linguistic evidence for the population history of Finland.

Published
2018

32. Aboriginal Australian mitochondrial genome variation – an increased understanding of population antiquity and diversity

Author

Nagle, N, Van Oven, M, Wilcox, S, Van Holst Pellekaan, S, Tyler-Smith, C, Xue, Y, Ballantyne, KN, Wilcox, L, Papac, L, Cooke, K, Van Oorschot, RAH, McAllister, P, Williams, L, Kayser, M, Mitchell, RJ, Adhikarla, S, Adler, CJ, Balanovska, E, Balanovsky, O, Bertranpetit, J, Clarke, AC, Comas, D, Cooper, A, Der Sarkissian, CSI, Dulik, MC, Gaieski, JB, Kumar, A, Prasad, G, Haak, W, Haber, M, Hobbs, A, Javed, A, Jin, L, Kaplan, ME, Li, S, Martinez-Cruz, B, Matisoo-Smith, EA, Mele, M, Merchant, NC, Owings, AC, Parida, L, Pitchappan, R, Platt, DE, Quintana-Murci, L, Renfrew, C, Royyuru, AK, Santhakumari, AV, Santos, FR, Schurr, TG, Soodyall, H, Soria Hernanz, DF, Swamikrishnan, P, Vilar, MG, Wells, RS, Zalloua, PA, Ziegle, JS, Martinez Cruz, B, Genetic Identification, La Trobe University [Melbourne], Erasmus University Medical Center [Rotterdam] (Erasmus MC), Australian Genome Research Facility, University of Queensland [Brisbane], University of New South Wales [Canberra Campus] (UNSW), The University of Sydney, The Wellcome Trust Sanger Institute [Cambridge], Griffith University [Brisbane], The Genographic Project was supported by National Geographic Society, IBM and the Waitt Family Foundation. Y.L.X. and C.T.-S. were supported by The Wellcome Trust (098051). M.K., M.v.O., and K.N.B. were supported by Erasmus M.C., and We gratefully acknowledge the participation of Aboriginal Australians from Victoria, Queensland, the Northern Territory, South Australia, Western Australia and Tasmania whose collaboration made this study possible. We owe Tammy Williams and Jason Tatipata many thanks for their support throughout this study.

Subjects
0301 basic medicine, Mitochondrial DNA, Native Hawaiian or Other Pacific Islander, [SDV]Life Sciences [q-bio], Population, Evolutionary biology, Biology, Article, Haplogroup, 03 medical and health sciences, 0302 clinical medicine, Phylogenetics, Genetics, Humans, Clade, education, QH426, Phylogeny, [SDV.GEN]Life Sciences [q-bio]/Genetics, education.field_of_study, Multidisciplinary, Phylogenetic tree, Haplotype, Australia, Genetic Variation, Sequence Analysis, DNA, 030104 developmental biology, Haplotypes, Genome, Mitochondrial, 030217 neurology & neurosurgery, Human mitochondrial DNA haplogroup
Abstract

Aboriginal Australians represent one of the oldest continuous cultures outside Africa, with evidence indicating that their ancestors arrived in the ancient landmass of Sahul (present-day New Guinea and Australia) ~55 thousand years ago. Genetic studies, though limited, have demonstrated both the uniqueness and antiquity of Aboriginal Australian genomes. We have further resolved known Aboriginal Australian mitochondrial haplogroups and discovered novel indigenous lineages by sequencing the mitogenomes of 127 contemporary Aboriginal Australians. In particular, the more common haplogroups observed in our dataset included M42a, M42c, S, P5 and P12, followed by rarer haplogroups M15, M16, N13, O, P3, P6 and P8. We propose some major phylogenetic rearrangements, such as in haplogroup P where we delinked P4a and P4b and redefined them as P4 (New Guinean) and P11 (Australian), respectively. Haplogroup P2b was identified as a novel clade potentially restricted to Torres Strait Islanders. Nearly all Aboriginal Australian mitochondrial haplogroups detected appear to be ancient, with no evidence of later introgression during the Holocene. Our findings greatly increase knowledge about the geographic distribution and phylogenetic structure of mitochondrial lineages that have survived in contemporary descendants of Australia’s first settlers.

Published
2017
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33. The genetic history of Northern Europe

Author

Mittnik, A., Wang, C., Pfrengle, S., Daubaras, M., Zariņa, G., Hallgren, F., Allmäe, R., Khartanovich, V., Moiseyev, V., Furtwängler, A., Andrades Valtueña, A., Feldman, M., Economou, C., Oinonen, M., Vasks, A., Tõrv, M., Balanovsky, O., Reich, D., Jankauskas, R., Haak, W., Schiffels, S., and Krause, J.

Published
2017

34. Estimating the impact of the Mongol expansion upon the gene pool of Tuvans

Author

Damba, L. D., primary, Balanovskaya, Е. V., additional, Zhabagin, M. K., additional, Yusupov, Y. М., additional, Bogunov, Y. V., additional, Sabitov, Z. M., additional, Agdzhoyan, A. T., additional, Korotkova, N. A., additional, Lavryashina, M. B., additional, Mongush, B. B., additional, Kavai-ool, U. N., additional, and Balanovsky, O. P., additional

Published
2018
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35. Gene pool of the Novgorod population: Between the north and the south

Author

Balanovska, E. V., primary, Agdzhoyan, A. T., additional, Skhalyakho, R. A., additional, Balaganskaya, O. A., additional, Freydin, G. S., additional, Chernevskii, K. G., additional, Chernevskii, D. K., additional, Stepanov, G. D., additional, Kagazezheva, Z. A., additional, Zaporozhchenko, V. V., additional, Markina, N. V., additional, Palipana, D., additional, Koshel, S. M., additional, Kozlov, S. A., additional, and Balanovsky, O. P., additional

Published
2017
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36. Population distribution and ancestry of the cancer protective MDM2 SNP285 (rs117039649)

Author

Knappskog, S., Gansmo, L. B., Dibirova, K., Metspalu, A., Ozcelik, T., Zalloua, P., Mouzaya, F., Bliznetz, E., Balanovsky, O., and Lonning, P. E.

Subjects
Mdm2, Promoter, Snp285, Polymorphism, Snp309
Abstract

Cataloged from PDF version of article. The MDM2 promoter SNP285C is located on the SNP309G allele. While SNP309G enhances Sp1 transcription factor binding and MDM2 transcription, SNP285C antagonizes Sp1 binding and reduces the risk of breast-, ovary- and endometrial cancer. Assessing SNP285 and 309 genotypes across 25 different ethnic populations (>10.000 individuals), the incidence of SNP285C was 6-8% across European populations except for Finns (1.2%) and Saami (0.3%). The incidence decreased towards the Middle-East and Eastern Russia, and SNP285C was absent among Han Chinese, Mongolians and African Americans. Interhaplotype variation analyses estimated SNP285C to have originated about 14,700 years ago (95% CI: 8,300 - 33,300). Both this estimate and the geographical distribution suggest SNP285C to have arisen after the separation between Caucasians and modern day East Asians (17,000 - 40,000 years ago). We observed a strong inverse correlation (r = -0.805; p < 0.001) between the percentage of SNP309G alleles harboring SNP285C and the MAF for SNP309G itself across different populations suggesting selection and environmental adaptation with respect to MDM2 expression in recent human evolution. In conclusion, we found SNP285C to be a pan-Caucasian variant. Ethnic variation regarding distribution of SNP285C needs to be taken into account when assessing the impact of MDM2 SNPs on cancer risk.

Published
2014

37. Geographic population structure analysis of worldwide human populations infers their biogeographical origins

Author

Elhaik, E., Tatarinova, T., Chebotarev, D., Piras, I.S., Maria Calò, C., De Montis, A., Atzori, M., Marini, M., Tofanelli, S., Francalacci, P., Pagani, L., Tyler-Smith, C., Xue, Y., Cucca, F., Schurr, T.G., Gaieski, J.B., Melendez, C., Vilar, M.G., Owings, A.C., Gómez, R., Fujita, R., Santos, F.R., Comas, D., Balanovsky, O., Balanovska, E., Zalloua, P., Soodyall, H., Pitchappan, R., GaneshPrasad, A., Hammer, M., Matisoo-Smith, L., Wells, R.S., Acosta, O., Adhikarla, S., Adler, C.J., Bertranpetit, J., Clarke, A.C., Cooper, A., Der Sarkissian, C.S.I., Haak, W., Haber, M., Jin, L., Kaplan, M.E., Li, H., Li, S., Martínez-Cruz, B., Merchant, N.C., Mitchell, J.R., Parida, L., Platt, D.E., Quintana-Murci, L., Renfrew, C., Lacerda, D.R., Royyuru, A.K., Sandoval, J.R., Santhakumari, A.V., Soria Hernanz, D.F., Swamikrishnan, P., and Ziegle, J.S.

Subjects
Structure analysis, Genetic genealogy, Biogeography, Sequencing data, Genética de población, General Physics and Astronomy, Geographic population, MED/03 Genetica medica, Variación genética, Biology, Bioinformatics, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, Article, Genètica de poblacions humanes, Genetics, Humans, Características de la población, 576 - Genética y evolución, Multidisciplinary, business.industry, Genome, Human, BIO/18 Genetica, General Chemistry, Quarter (United States coin), Corrigenda, Country of origin, Europe, Biological sciences, Genetics, Population, Global Positioning System, Biogeografía, Fitogeografía, business, Genètica humana -- Variació, Cartography, Pruebas genéticas, Algorithms
Abstract

The search for a method that utilizes biological information to predict humans’ place of origin has occupied scientists for millennia. Over the past four decades, scientists have employed genetic data in an effort to achieve this goal but with limited success. While biogeographical algorithms using next-generation sequencing data have achieved an accuracy of 700 km in Europe, they were inaccurate elsewhere. Here we describe the Geographic Population Structure (GPS) algorithm and demonstrate its accuracy with three data sets using 40,000–130,000 SNPs. GPS placed 83% of worldwide individuals in their country of origin. Applied to over 200 Sardinians villagers, GPS placed a quarter of them in their villages and most of the rest within 50 km of their villages. GPS’s accuracy and power to infer the biogeography of worldwide individuals down to their country or, in some cases, village, of origin, underscores the promise of admixture-based methods for biogeography and has ramifications for genetic ancestry testing., Current methods to identify the geographical origin of humans based on DNA data present limited accuracy. Here, the authors develop a new algorithm, the Genographic Population Structure (GPS), and demonstrate its ability to place worldwide individuals within their country or, in some cases, village of origin.

Published
2014

38. The GenoChip: A New Tool for Genetic Anthropology

Author

Elhaik, E, Greenspan, E, Staats, S, Krahn, T, Tyler-Smith, C, Xue, Y, Tofanelli, S, Francalacci, P, Cucca, F, Pagani, Luca, Jin, L, Li, H, Schurr, Tg, Greenspan, B, Spencer Wells, R, Acosta, O, Adhikarla, S, Adler, Cj, Balanovska, E, Balanovsky, O, Bertranpetit, J, Clarke, Ac, Comas, D, Cooper, A, Dulik, Mc, Gaieski, Jb, Ganesh Prasad AK, Haak, W, Haber, M, Kaplan, Me, Lacerda, Dr, Li, S, Martinez-Cruz, B, Matisoo-Smith, Ea, Merchant, Nc, Mitchell, Jr, Owings, Ac, Parida, L, Pitchappan, R, Platt, De, Quintana-Murci, L, Renfrew, C, Royyuru, Ak, Sandoval, Jr, Santhakumari, Av, Santos, Fr, Der Sarkissian CSI, Soodyall, S, Soria Hernanz DF, Swamikrishnan, P, Vieira, Pp, Vilar, Mg, Zalloua, Pa, and Ziegle, Js

Subjects
Letter, Anthropology, Human Migration, Population genetics, Genética de población, Ancestry-informative marker, Human genetic variation, MED/03 Genetica medica, Genética humana, DNA, Mitochondrial, Polymorphism, Single Nucleotide, Haplogroup, genetic anthropology, AimsFinder, 03 medical and health sciences, 0302 clinical medicine, Genes, Y-Linked, Human Genome Project, Genetics, Humans, Quantitative Biology - Genomics, Genographic Project, Quantitative Biology - Populations and Evolution, Genotyping, Denisovan, Antropologia, Ecology, Evolution, Behavior and Systematics, Anthropology, Cultural, History, Ancient, 030304 developmental biology, GenoChip, Oligonucleotide Array Sequence Analysis, Genomics (q-bio.GN), 0303 health sciences, Genètica humana, Genètica de poblacions, biology, BIO/18 Genetica, Populations and Evolution (q-bio.PE), population genetics, Especiación genética, biology.organism_classification, FOS: Biological sciences, haplogroups, Haplotipos, 030217 neurology & neurosurgery, Human mitochondrial DNA haplogroup
Abstract

The Genographic Project is an international effort using genetic data to chart human migratory history. The project is non-profit and non-medical, and through its Legacy Fund supports locally led efforts to preserve indigenous and traditional cultures. In its second phase, the project is focusing on markers from across the entire genome to obtain a more complete understanding of human genetic variation. Although many commercial arrays exist for genome-wide SNP genotyping, they were designed for medical genetic studies and contain medically related markers that are not appropriate for global population genetic studies. GenoChip, the Genographic Project's new genotyping array, was designed to resolve these issues and enable higher-resolution research into outstanding questions in genetic anthropology. We developed novel methods to identify AIMs and genomic regions that may be enriched with alleles shared with ancestral hominins. Overall, we collected and ascertained AIMs from over 450 populations. Containing an unprecedented number of Y-chromosomal and mtDNA SNPs and over 130,000 SNPs from the autosomes and X-chromosome, the chip was carefully vetted to avoid inclusion of medically relevant markers. The GenoChip results were successfully validated. To demonstrate its capabilities, we compared the FST distributions of GenoChip SNPs to those of two commercial arrays for three continental populations. While all arrays yielded similarly shaped (inverse J) FST distributions, the GenoChip autosomal and X-chromosomal distributions had the highest mean FST, attesting to its ability to discern subpopulations. The GenoChip is a dedicated genotyping platform for genetic anthropology and promises to be the most powerful tool available for assessing population structure and migration history., Comment: 11 pages, 5 Figures, 2 supplementary notes

Published
2013

41. The western and eastern roots of the Saami - The story of genetic 'outliers' told by mitochondrial DNA and Y chromosomes

Author

Tambets, K Rootsi, S Kivisild, T Help, H Serk, P and Loogvali, EL Tolk, HV Reidla, M Metspalu, E Pliss, L and Balanovsky, O Pshenichnov, A Balanovska, E Gubina, M and Zhadanov, S Osipova, L Damba, L Voevoda, M Kutuev, I and Bermisheva, M Khusnutdinova, E Gusar, V Grechanina, E and Parik, J Pennarun, E Richard, C Chaventre, A Moisan, JP and Barac, L Pericic, M Rudan, P Terzic, R Mikerezi, I and Krumina, A Baumanis, V Koziel, S Rickards, O De Stefano, GF Anagnou, N Pappa, KI Michalodimitrakis, E and Ferak, V Furedi, S Komel, R Beckman, L Villems, R

Abstract

The Saami are regarded as extreme genetic outliers among European populations. In this study, a high-resolution phylogenetic analysis of Saami genetic heritage was undertaken in a comprehensive context, through use of maternally inherited mitochondrial DNA ( mtDNA) and paternally inherited Y-chromosomal variation. DNA variants present in the Saami were compared with those found in Europe and Siberia, through use of both new and previously published data from 445 Saami and 17,096 western Eurasian and Siberian mtDNA samples, as well as 127 Saami and 2,840 western Eurasian and Siberian Y-chromosome samples. It was shown that the “Saami motif” variant of mtDNA haplogroup U5b is present in a large area outside Scandinavia. A detailed phylogeographic analysis of one of the predominant Saami mtDNA haplogroups, U5b1b, which also includes the lineages of the “Saami motif,” was undertaken in 31 populations. The results indicate that the origin of U5b1b, as for the other predominant Saami haplogroup, V, is most likely in western, rather than eastern, Europe. Furthermore, an additional haplogroup (H1) spread among the Saami was virtually absent in 781 Samoyed and Ob-Ugric Siberians but was present in western and central European populations. The Y-chromosomal variety in the Saami is also consistent with their European ancestry. It suggests that the large genetic separation of the Saami from other Europeans is best explained by assuming that the Saami are descendants of a narrow, distinctive subset of Europeans. In particular, no evidence of a significant directional gene flow from extant aboriginal Siberian populations into the haploid gene pools of the Saami was found.

Published
2004

42. Characteristics of Populations of the Russian Federation over the Panel of Fifteen Loci Used for DNA Identification and in Forensic Medical Examination

Author

Stepanov, V A, primary, Balanovsky, O P, additional, Melnikov, A V, additional, Lash-Zavada, A Yu, additional, Khar'kov, V N, additional, Tyazhelova, T V, additional, Akhmetova, V L, additional, Zhukova, O V, additional, Shneider, Yu V, additional, Shil'nikova, I N, additional, Borinskaya, S A, additional, Marusin, A V, additional, Spiridonova, M G, additional, Simonova, K V, additional, Khitrinskaya, I Yu, additional, Radzhabov, M O, additional, Romanov, A G, additional, Shtygasheva В, O V, additional, Koshel', S M, additional, Balanovskaya, E V, additional, Rybakova, A V, additional, Khusnutdinova, E K, additional, Puzyrev, V P, additional, and Yankovsky, N K, additional

Published
2011
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43. Allele frequency distributions of - 174G/ C polymorphism in regulatory region of interleukin 6 gene ( IL6) in Russian and worldwide populations.

Author

Borinskaya, S., Gureev, A., Orlova, A., Sanina, E., Kim, A., Gasemianrodsari, F., Shirmanov, V., Balanovsky, O., Rebrikov, D., Koshechkin, A., and Yankovsky, N.

Subjects
GENE frequency, GENETIC polymorphisms, GENETIC regulation, INTERLEUKIN-6 genetics, POPULATION genetics, CYTOKINES
Abstract

Allele and genotype frequencies of the − 174G/ C polymorphism (rs1800795) in the regulatory region of the IL6 gene, which encode anti-inflammatory cytokine interleukin 6, were determined in seven populations representing five ethnic groups from the European part of Russia (440 individuals), as well as in small cohorts that represent populations from 24 countries of Africa and Eurasia (365 individuals). The maps of the geographic distribution of the − 174G/ C allele frequencies were constructed based on personal (22 populations) and the literature data (66 populations), and the data from dbSNP database obtained by the HapMap project (10 populations). The frequency of the − 174G allele varied from 45 to 100% and was characterized by nonrandom geographic distribution. These data could reflect the adaptive load of the alleles examined, which was different in different regions of the world. It is suggested that the level of pathogen prevalence is one of the environmental factors that determine different adaptive values of the IL6*-174G/ C alleles. This suggestion is supported by a positive correlation between the − 174G allele frequency and level of pathogen prevalence calculated based on historical data ( R = 0.768; p < 0.0001). [ABSTRACT FROM AUTHOR]

Published
2013
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47. Genomic evidence for the Pleistocene and recent population history of Native Americans

Author

Raghavan, M., Steinrücken, M, Harris, M, Schiffels, Stephan, DeGiorgio, Michael, Albrechtsen, M, Valdiosera, M, Ávila-Arcos, M, Malaspinas, M, Eriksson, Anders, Moltke, M, Homburger, M, Wall, Jeff, Cornejo, Omar, Moreno-Mayar, M, Korneliussen, M, Pierre, M, Rasmussen, Rasmus, Campos, Paul, de Barros Damgaard, Peter, Allentoft, M., Lindo, John, Metspalu, M., Rodríguez-Varela, Carlos, Mansilla, M, Henrickson, Celeste, Seguin-Orlando, M, Malmström, M, Stafford, M, Shringarpure, M, Moreno-Estrada, M, Karmin, M., Tambets, Kristiina, Bergström, Anders, Xue, Yali, Vera, Vera, Friend, Andrew, Singarayer, M, Valdes, Paul, Balloux, François, Leboreiro, M, Vera, M, Rangel-Villalobos, M, Pettener, David, Luiselli, Donata, Davis, Loren, Heyer, M, Zollikofer, Chris, Ponce de León, M, Smith, M, Grimes, John, Pike, John, Deal, John, Fuller, M, Arriaza, Bernardo, Standen, Vivien, Luz, M., Ricaut, M, Guidon, M, Osipova, Ludmila, Voevoda, M., Posukh, Olga, Balanovsky, M, Lavryashina, M., Bogunov, M, Khusnutdinova, M, Gubina, M., Balanovska, M, Fedorova, M, Litvinov, Sergey, Malyarchuk, M, Derenko, M., Mosher, M., Archer, David, Cybulski, Jerome, Petzelt, Barbara, Mitchell, Joycelynn, Worl, Rosita, Norman, Paul, Parham, Peter, Kemp, Brian, Kivisild, Toomas, Smith, Chris, Sandhu, Manjinder, Crawford, Michael, Villems, Richard, Smith, David, Waters, Michael, Goebel, Ted, Johnson, John, Malhi, Ripan, Jakobsson, Mattias, Meltzer, David, Manica, Andrea, Durbin, Richard, Bustamante, Carlos, Song, Yun, Nielsen, Rasmus, Willerslev, Eske, Steinrucken, M., Harris, K., Rasmussen, S., Albrechtsen, A., Valdiosera, C., Avila-Arcos, M., Malaspinas, S., Moltke, I., Homburger, J., Moreno-Mayar, J., Korneliussen, S., Pierre, T., Rasmussen, M., Damgaard, P., Metspalu, E., Rodriguez-Varela, R., Mansilla, J., Seguin-Orlando, A., Malmstrom, H., Stafford, T., Shringarpure, S., Moreno-Estrada, A., Bergstrom, A., Warmuth, V., Singarayer, J., Leboreiro, I., Vera, J., Rangel-Villalobos, H., Heyer, E., Ponce De Leon, M., Grimes, V., Pike, K., Deal, M., Fuller, T., Ricaut, F., Guidon, N., Balanovsky, O., Bogunov, Y., Khusnutdinova, E., Balanovska, E., Fedorova, S., Malyarchuk, B., Norman, J., Kemp, M., Malhi, S., Meltzer, J., Song, S., Swedish Institute of Space Physics [Uppsala] (IRF), Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Human Evolution, The Wellcome Trust Sanger Institute [Cambridge], Centre National de la Recherche Scientifique (CNRS), School of Geographical Sciences [Bristol], University of Bristol [Bristol], University of Edinburgh, University of Bologna, Universidad de Tarapaca, Institute of Cytology and Genetics, Russian Academy of Sciences [Moscow] (RAS), School of Health Science, Higher Education Centre Novo mesto, Departments of Chemistry and of Structural Biology, Stanford University, Department of Anthropology, Washington State University (WSU), Leverhulme Centre for Human Evolutionary Studies University of Cambridge, University of Cambridge [UK] (CAM), Centre for Cybercrime and Computer Security [Newcastle], School of Computing Science [Newcastle], Newcastle University [Newcastle]-Newcastle University [Newcastle], Strangeways Research Laboratory, MRC, UMR 6578 : Anthropologie Bio-Culturelle (UAABC), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Harvard Medical School [Boston] (HMS), Evolutionary Biology, Uppsala University, Department of Biological Statistics and Computational Biology, Cornell University [New York], Dept Integrat Biol, Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Eco-Anthropologie et Ethnobiologie (EAE), Muséum national d'Histoire naturelle (MNHN)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Department of Nuclear Medicine, Austin Health-Centre for Positron Emission Tomography (PET)-Austin Hospital [Melbourne], Austin Health, Laboratoire d'études spatiales et d'instrumentation en astrophysique (LESIA (UMR_8109)), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Fundaçao Museu do Homem Americano (FUMDHAM), Department of Mechanical Engineering, Sogang University, parent, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA), Stanford University [Stanford], UMR 6578 : Adaptabilité Biologique et Culturelle (UAABC), Cornell University, PSL Research University (PSL)-PSL Research University (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Raghavan, Maanasa, Steinrücken, Matthia, Harris, Kelley, Schiffels, Stephan, Rasmussen, Simon, Degiorgio, Michael, Albrechtsen, Ander, Valdiosera, Cristina, Ávila-Arcos, María C., Malaspinas, Anna-Sapfo, Eriksson, Ander, Moltke, Ida, Metspalu, Mait, Homburger, Julian R., Wall, Jeff, Cornejo, Omar E., Moreno-Mayar, J. Víctor, Korneliussen, Thorfinn S., Pierre, Tracey, Rasmussen, Morten, Campos, Paula F., De Barros Damgaard, Peter, Allentoft, Morten E., Lindo, John, Metspalu, Ene, Rodríguez-Varela, Ricardo, Mansilla, Josefina, Henrickson, Celeste, Seguin-Orlando, Andaine, Malmstöm, Helena, Stafford, Thoma, Shringarpure, Suyash S., Moreno-Estrada, André, Karmin, Monika, Tambets, Kristiina, Bergström, Ander, Xue, Yali, Warmuth, Vera, Friend, Andrew D., Singarayer, Joy, Valdes, Paul, Balloux, Francoi, Leboreiro, Ilán, Vera, Jose Lui, Rangel-Villalobos, Hector, Pettener, Davide, Luiselli, Donata, Davis, Loren G., Heyer, Evelyne, Zollikofer, Christoph P. E., Ponce De León, Marcia S., Smith, Colin I., Grimes, Vaughan, Pike, Kelly-Anne, Deal, Michael, Fuller, Benjamin T., Arriaza, Bernardo, Standen, Vivien, Luz, Maria F., Ricaut, Francoi, Guidon, Niede, Osipova, Ludmila, Voevoda, Mikhail I., Posukh, Olga L., Balanovsky, Oleg, Lavryashina, Maria, Bogunov, Yuri, Khusnutdinova, Elza, Gubina, Marina, Balanovska, Elena, Fedorova, Sardana, Litvinov, Sergey, Malyarchuk, Bori, Derenko, Miroslava, Mosher, M.J., Archer, David, Cybulski, Jerome, Petzelt, Barbara, Mitchell, Joycelynn, Worl, Rosita, Norman, Paul J., Parham, Peter, Kemp, Brian M., Kivisild, Tooma, Tyler-Smith, Chri, Sandhu, Manjinder S., Crawford, Michael, Villems, Richard, Smith, David Glenn, Waters, Michael R., Goebel, Ted, Johnson, John R., Malhi, Ripan S., Jakobsson, Mattia, Meltzer, David J., Manica, Andrea, Durbin, Richard, Bustamante, Carlos D., Song, Yun S., Nielsen, Rasmu, Willerslev, Eske, Université Nice Sophia Antipolis (1965 - 2019) (UNS), University of Bologna/Università di Bologna, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, and University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)

Subjects
ARCHAEOLOGICAL SEQUENCE, Gene Flow, Pleistocene, CRANIAL MORPHOLOGY, CLOVIS, MIGRATION, Human Migration, Population, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Population genetics, NEW-WORLD, America, Biology, Beringia, Gene flow, SOUTH-AMERICA, 03 medical and health sciences, 0601 history and archaeology, education, History, Ancient, 030304 developmental biology, 0303 health sciences, education.field_of_study, CONDITIONAL SAMPLING DISTRIBUTION, Multidisciplinary, 060102 archaeology, Models, Genetic, Human migration, business.industry, Medicine (all), 06 humanities and the arts, BRAZIL, MODEL, Siberia, South american, ORIGINS, Genomic, Indians, North American, Ethnology, Athabascans, business, Human
Abstract

How and when the Americas were populated remains contentious. Using ancient and modern genome wide data we found that the ancestors of all present day Native Americans including Athabascans and Amerindians entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000 year isolation period in Beringia. After their arrival to the Americas ancestral Native Americans diversified into two basal genetic branches around 13 ka one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present day East Asians (including Siberians) and more distantly Australo Melanesians. Putative “Paleoamerican” relict populations including the historical Mexican Pericúes and South American Fuego Patagonians are not directly related to modern Australo Melanesians as suggested by the Paleoamerican Model. INTRODUCTION The consensus view on the peopling of the Americas is that ancestors of modern Native Americans entered the Americas from Siberia via the Bering Land Bridge and that this occurred at least {\textasciitilde}14.6 thousand years ago (ka). However the number and timing of migrations into the Americas remain controversial with conflicting interpretations based on anatomical and genetic evidence. RATIONALE In this study we address four major unresolved issues regarding the Pleistocene and recent population history of Native Americans: (i) the timing of their divergence from their ancestral group (ii) the number of migrations into the Americas (iii) whether there was {\textasciitilde}15000 years of isolation of ancestral Native Americans in Beringia (Beringian Incubation Model) and (iv) whether there was post Pleistocene survival of relict populations in the Americas related to Australo Melanesians as suggested by apparent differences in cranial morphologies between some early (“Paleoamerican”) remains and those of more recent Native Americans. We generated 31 high coverage modern genomes from the Americas Siberia and Oceania; 23 ancient genomic sequences from the Americas dating between {\textasciitilde}0.2 and 6 ka; and SNP chip genotype data from 79 present day individuals belonging to 28 populations from the Americas and Siberia. The above data sets were analyzed together with published modern and ancient genomic data from worldwide populations after masking some present day Native Americans for recent European admixture. RESULTS Using three different methods we determined the divergence time for all Native Americans (Athabascans and Amerindians) from their Siberian ancestors to be {\textasciitilde}20 ka and no earlier than {\textasciitilde}23 ka. Furthermore we dated the divergence between Athabascans (northern Native American branch together with northern North American Amerindians) and southern North Americans and South and Central Americans (southern Native American branch) to be {\textasciitilde}13 ka. Similar divergence times from East Asian populations and a divergence time between the two branches that is close in age to the earliest well established archaeological sites in the Americas suggest that the split between the branches occurred within the Americas. We additionally found that several sequenced Holocene individuals from the Americas are related to present day populations from the same geographical regions implying genetic continuity of ancient and modern populations in some parts of the Americas over at least the past 8500 years. Moreover our results suggest that there has been gene flow between some Native Americans from both North and South America and groups related to East Asians and Australo Melanesians the latter possibly through an East Asian route that might have included ancestors of modern Aleutian Islanders. Last using both genomic and morphometric analyses we found that historical Native American groups such as the Pericúes and Fuego Patagonians were not “relicts” of Paleoamericans and hence our results do not support an early migration of populations directly related to Australo Melanesians into the Americas. CONCLUSION Our results provide an upper bound of {\textasciitilde}23 ka on the initial divergence of ancestral Native Americans from their East Asian ancestors followed by a short isolation period of no more than {\textasciitilde}8000 years and subsequent entrance and spread across the Americas. The data presented are consistent with a single migration model for all Native Americans with later gene flow from sources related to East Asians and indirectly Australo Melanesians. The single wave diversified {\textasciitilde}13 ka likely within the Americas giving rise to the northern and southern branches of present day Native Americans. View larger version: In this page In a new window Download PowerPoint Slide for Teaching Population history of present day Native Americans.The ancestors of all Native Americans entered the Americas as a single migration wave from Siberia (purple) no earlier than {\textasciitilde}23 ka separate from the Inuit (green) and diversified into “northern” and “southern” Native American branches {\textasciitilde}13 ka. There is evidence of post divergence gene flow between some Native Americans and groups related to East Asians/Inuit and Australo Melanesians (yellow). Genetic history of Native Americans Several theories have been put forth as to the origin and timing of when Native American ancestors entered the Americas. To clarify this controversy Raghavan et al. examined the genomic variation among ancient and modern individuals from Asia and the Americas. There is no evidence for multiple waves of entry or recurrent gene flow with Asians in northern populations. The earliest migrations occurred no earlier than 23000 years ago from Siberian ancestors. Amerindians and Athabascans originated from a single population splitting approximately 13000 years ago. Science this issue 10.1126/science.aab3884

48. Ten millennia of hepatitis B virus evolution

Author

Oleg Balanovsky, Lourdes Marquez-Morfin, Magdalena Zoledziewska, Susannah J. Salter, Cody E. Parker, Kirsten I. Bos, Kathrin Nägele, Domingo C. Salazar-García, Kerttu Majander, Vittorio Mazzarello, Cosimo Posth, Kurt W. Alt, Elmira Khussainova, Silvia Teresita Hernández Godoy, Richard Mortimer, Ayshin Ghalichi, Alexander Herbig, Lars Fehren-Schmitz, Leyla B. Djansugurova, Dmitry A. Stashenkov, Raiko Krauß, Mikhail S. Chaplygin, Tiago Ferraz, Patrick Semal, Eva Rosenstock, Michal Kostka, Yavor Boyadzhiev, Harald Meller, Petr Limburský, Mario Küßner, Tara Ingman, Maïté Rivollat, Eva Fernández-Domínguez, Rodrigo Barquera, Robin Skeates, Kamen Boyadzhiev, Denise Kühnert, Mirjana Roksandic, Adam Ben Rohrlach, Alexandra P. Buzhilova, Alissa Mittnik, Yadira Chinique de Armas, Johannes Krause, Marie-France Deguilloux, Aleksandr Khokhlov, Rezeda I. Tukhbatova, Elizabeth Popescu, Lucy C. Salazar, Andrey A. Chizhevsky, Christopher Read, Hubert Steiner, Melanie Van Twest, Eveline Altena, Diana Iraíz Hernández-Zaragoza, Lyazzat Musralina, Megan Michel, Íñigo García-Martínez de Lagrán, Anatoly R. Kantorovich, Katrien Van de Vijver, Alžbeta Danielisová, Rachel Clarke, Duncan Sayer, Bastien Llamas, Nikolaj Makarov, Alejandro Romero, Luka Papac, Alessandra Sperduti, Vladimir E. Maslov, Rafael Garrido-Pena, Gunnar U. Neumann, Arman Z. Beisenov, Zainolla Samashev, Guido Alberto Gnecchi-Ruscone, Päivi Onkamo, Eduardo Carmona Ballestero, Javier Jimenez-Echevarria, Valery Khartanovich, Manuel Rojo-Guerra, Fredrik Hallgren, Eirini Skourtanioti, Natalia Shishlina, Luca Lai, Petr Velemínský, Antti Sajantila, Peter C. Ramsl, Claudia Sagona, Susanne Friederich, Miroslav Dobeš, Marcel Keller, Francesco Cucca, Sabine Reinhold, Florian van Bömmel, Luc Amkreutz, Vittoria Schimmenti, Raphaela Stahl, Douglas Baird, Marina K. Karapetian, Kurt Rademaker, Stephan Schiffels, Sacha Kacki, Evelyn K. Guevara, Michael Francken, Christina Warinner, Kay Prüfer, Karen Giffin, Felix M. Key, Joscha Gretzinger, Alexey Kalmykov, Svetlana Shnaider, Sandra Penske, Antje Wissgott, Tiffiny A. Tung, Biaslan Ch. Atabiev, Philippe Lefranc, Elizabeth A. Nelson, Peter de Knijff, Vladimir Slavchev, Jessica Pearson, Yılmaz Selim Erdal, Louise Loe, Jan Nováček, Micaela Alvarez Calmet, José I. Royo-Guillén, Richard L. Burger, Kristiina Mannermaa, K. Aslıhan Yener, Maria Pfefferkorn, Vyacheslav Moiseyev, Svend Hansen, Didier Binder, Michal Ernée, Maria A. Spyrou, Michal Feldman, Vladimir V. Kufterin, Murat Akar, Héctor Arcusa-Magallón, Andrej B. Belinskiy, Egor Kitov, Franziska Aron, Ron Hübler, Vanessa Villalba-Mouco, Sophie Beckett, Jessica Beckett, Arthur Kocher, Michael Schultz, Elena Batieva, Pilar Utrilla, Cristina Tejedor-Rodríguez, Kristin von Heyking, Masnav Navruzbekov, Michaela Langová, Maria Paz Miguel de Ibáñez, Stéphane Rottier, Maria V. Dobrovolskaya, Sandra Lösch, Emma D. Zilivinskaya, Dmitry V. Vasilev, Gabriel García Atiénzar, Marcello A. Mannino, Wolfgang Haak, Philipp W. Stockhammer, Sylvie Saintot, Alice Lyons, Ken Massy, Elena Kaverzneva, Susanna Sabin, Carmen Alonso-Fernández, Anna F. Kochkina, Marieke Sophia van de Loosdrecht, Stefanie Eisenmann, Max Planck Society, European Commission, Slovak Academy of Sciences, Academy of Sciences of the Czech Republic, Russian Foundation for Basic Research, German Research Foundation, Agence Nationale de la Recherche (France), Wenner-Gren Foundation, Ministry of Education and Science (Kazakhstan), Universidad de Alicante. Departamento de Prehistoria, Arqueología, Historia Antigua, Filología Griega y Filología Latina, Universidad de Alicante. Departamento de Biotecnología, Universidad de Alicante. Instituto Universitario de Investigación en Arqueología y Patrimonio Histórico, Prehistoria y Protohistoria, Grupo de Inmunología, Biología Celular y del Desarrollo, Ingman, Tara, Kocher, A., Papac, L., Barquera, R., Key, FM., Spyrou, MA., Hubler, R., Rohrlach, AB., Aron, F., Stahl, R., Wissgott, A., van Bommel, F., Pfefferkorn, M., Mittnik, A., Villalba-Mouco, V., Neumann, GU., Rivollat, M., van de Loosdrecht, MS., Majander, K., Tukhbatova, RI., Musralina, L., Ghalichi, A., Penske, S., Sabin, S., Michel, M., Gretzinger, J., Nelson, EA., Ferraz, T., Nagele, K., Parker, C., Keller, M., Guevara, EK., Feldman, M., Eisenmann, S., Skourtanioti, E., Giffin, K., Gnecchi-Ruscone, GA., Friederich, S., Schimmenti, V., Khartanovich, V., Karapetian, MK., Chaplygin, MS., Kufterin, VV., Khokhlov, AA., Chizhevsky, AA., Stashenkov, DA., Kochkina, AF., Tejedor-Rodriguez, C., de Lagran, IGM., Arcusa-Magallon, H., Garrido-Pena, R., Royo-Guillen, JI., Novacek, J., Rottier, S., Kacki, S., Saintot, S., Kaverzneva, E., Belinskiy, AB., Veleminsky, P., Limbursky, P., Kostka, M., Loe, L., Popescu, E., Clarke, R., Lyons, A., Mortimer, R., Sajantila, A., de Armas, YC., Godoy, STH., Hernandez-Zaragoza, DI., Pearson, J., Binder, D., Lefranc, P., Kantorovich, AR., Maslov, VE., Lai, L., Zoledziewska, M., Beckett, JF., Langova, M., Atienzar, GG., Ibanez, MPD, Romero, A., Sperduti, A., Beckett, S., Salter, SJ., Zilivinskaya, ED., Vasil, DV., von Heyking, K., Burger, RL., Salazar, LC., Amkreutz, L., Navruzbekov, M., Rosenstock, E., Alonso-Fernandez, C., Slavchev, V., Kalmykov, AA., Atabiev, BC., Batieva, E, Calmet, MA., Llamas, B., Schultz, M., Krauss, R., Jimenez-Echevarria, J., Francken, M., Shnaider, S., de Knijff, P., Altena, E., Van de Vijver, K., Fehren-Schmitz, L., Tung, TA., Losch, S., Dobrovolskaya, M., Makarov, N., Read, C., Van Twest, M., Sagona, C., Ramsl, PC., Akar, M., Yener, KA., Ballestero, EC., Cucca, F., Mazzarello, V., Utrilla, P., Rademaker, K., Fernandez-Dominguez, E., Baird, D., Semal, P., Marquez-Morfin, L, Roksandic, M., Steiner, H., Salazar-Garcia, DC., Shishlina, N. Erdal, YS., Hallgren, F., Boyadzhiev, Y., Boyadzhiev, K., Kussner, M., Sayer, D., Onkamo, P., Skeates, R., Rojo-Guerra, M., Buzhilova, A., Khussainova, E., Djansugurova, LB., Beisenov, AZ., Samashev, Z., Massy, K., Mannino, M., Moiseyev, V., Mannermaa, K., Balanovsky, O., Deguilloux, MF., Reinhold, S., Hansen, S., Kitov, EP., Dobes, M., Ernee, M., Meller, H., Prufer, Kay., Warinner, C., Schiffels, S., Stockhammer, PW., Bos, K., Posth, C., Herbig, A., Haak, W., Krause, J., Kuhnert, D., and Koç University Research Center for Anatolian Civilizations (ANAMED) / Koç Üniversitesi Anadolu Medeniyetleri Araştırma Merkezi (ANAMED)

Subjects
Phylogeographic history, Hepatitis B/history, 01 natural sciences, The Republic, Communicable Diseases, Emerging, German, Communicable Diseases, Emerging/history, Agency (sociology), Science and technology, ComputingMilieux_MISCELLANEOUS, History, Ancient, Phylogeny, media_common, 0303 health sciences, Multidisciplinary, Ancient DNA, European research, virus diseases, Genomics, Hepatitis B, 3. Good health, Europe, language, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, Christian ministry, Paleogenomic analyses, Asian Continental Ancestry Group, 010506 paleontology, Hepatitis B virus, Asia, Hepatitis B virus/classification, European Continental Ancestry Group, Library science, Biología Celular, White People, Marie curie, Evolution, Molecular, 03 medical and health sciences, American Natives, Asian People, Political science, Genomic data, media_common.cataloged_instance, Humans, Slovak, European union, American Indian or Alaska Native, 030304 developmental biology, 0105 earth and related environmental sciences, Genetic Variation, Paleontology, Prehistoria, A300, language.human_language, digestive system diseases, American natives, Americas, Asian continental ancestry group, Communicable diseases, Emerging, European continental ancestry group, Evolution, molecular, Genetic variation
Abstract

Hepatitis B virus (HBV) has been infecting humans for millennia and remains a global health problem, but its past diversity and dispersal routes are largely unknown. We generated HBV genomic data from 137 Eurasians and Native Americans dated between ~10,500 and ~400 years ago. We date the most recent common ancestor of all HBV lineages to between ~20,000 and 12,000 years ago, with the virus present in European and South American hunter-gatherers during the early Holocene. After the European Neolithic transition, Mesolithic HBV strains were replaced by a lineage likely disseminated by early farmers that prevailed throughout western Eurasia for ~4000 years, declining around the end of the 2nd millennium BCE. The only remnant of this prehistoric HBV diversity is the rare genotype G, which appears to have reemerged during the HIV pandemic., The research was funded by the Max Planck Society, the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (771234–PALEoRIDER, to W.H.; 805268–CoDisEASe to K. Bos; 834616–ARCHCAUCASUS to S.H.), the Slovak Academy of Sciences and the European Union’s Seventh Framework Programme and Marie Curie Actions under the Programme SASPRO (1340/03/03 to P.C.R.), the ERA.NET RUS Plus–S&T programm of the European Union’s Seventh Framework Programme (277–BIOARCCAUCASUS to S.Re. and S.H.), the Werner Siemens Stiftung (“Paleobiochemistry”, to CW), the Award Praemium Academiae of the Czech Academy of Sciences (to M.E.), the Institute of Archaeology of the Czech Academy of Sciences (RVO 67985912, to M.Dobe.), the Russian Foundation for Basic Research (19-09-00354a, to M.K.K. and V.V.K.; 19-78-10053 to SSh), the German Research Foundation (DFG-HA-5407/4-1–INTERACT to W.H. and RE2688/2 to S.Re.), the French National Research Agency (ANR-17-FRAL-0010–INTERACT, to M.F.D., M.Ri., S.Ro., S.Sai., D.Bi., and P.Le.), the Wenner-Gren Dissertation Fieldwork Grant (9558 to S.Sab.), and the Ministry of Education and Science of the Republic of Kazakhstan (AP08856654 to L.B.D., L.M., and E.Kh. and AP08857177 to A.Z.B.).

Published
2021

49. The Genomic Impact of European Colonization of the Americas

Author

Alessandro Raveane, Shahlo Turdikulova, Donata Luiselli, Pongsakorn Wangkumhang, Marta E. Alarcón-Riquelme, Francesco Montinaro, Guido Alberto Gnecchi-Ruscone, Damir Marjanović, Mait Metspalu, Sarabjit S. Mastana, Oleg Balanovsky, Alessandro Achilli, Antonio Torroni, Lejla Kovacevic, L. A. Atramentova, Anna Olivieri, Maria Fernanda Lima-Costa, Linda Ongaro, Cristian Capelli, Toomas Kivisild, Bernardo L. Horta, Nédio Mabunda, Marilia O. Scliar, Roy J. King, Etienne Patin, Kristiina Tambets, Garrett Hellenthal, Mauricio Lima Barreto, Celia A. May, Miguel Gonzalez-Santos, Andreja Leskovac, Andrés Moreno-Estrada, Eduardo Tarazona-Santos, Alexandre C. Pereira, Rodrigo Flores, Anastasia Kouvatsi, Luca Pagani, Stefania Sarno, Elena Balanovska, Ornella Semino, Davide Marnetto, Ongaro L., Scliar M.O., Flores R., Raveane A., Marnetto D., Sarno S., Gnecchi-Ruscone G.A., Alarcon-Riquelme M.E., Patin E., Wangkumhang P., Hellenthal G., Gonzalez-Santos M., King R.J., Kouvatsi A., Balanovsky O., Balanovska E., Atramentova L., Turdikulova S., Mastana S., Marjanovic D., Mulahasanovic L., Leskovac A., Lima-Costa M.F., Pereira A.C., Barreto M.L., Horta B.L., Mabunda N., May C.A., Moreno-Estrada A., Achilli A., Olivieri A., Semino O., Tambets K., Kivisild T., Luiselli D., Torroni A., Capelli C., Tarazona-Santos E., Metspalu M., Pagani L., Montinaro F., Institute of Genomics [Tartu, Estonia], University of Tartu, Universidade de São Paulo = University of São Paulo (USP), Dipartimento di Biologia e Biotecnologie 'Lazzaro Spallanzani' = Department of Biology and Biotechnology [Univ di Pavia] (DBB UNIPV), Università degli Studi di Pavia = University of Pavia (UNIPV), Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), Max Planck Institute for the Science of Human History (MPI-SHH), Max-Planck-Gesellschaft, Centre for Genomics and Oncological Reearch (GENYO), Génétique Evolutive Humaine - Human Evolutionary Genetics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), University College of London [London] (UCL), University of Oxford, Stanford University School of Medicine [CA, USA], Aristotle University of Thessaloniki, Vavilov Institute of General Genetics, Russian Academy of Sciences [Moscow] (RAS), V.N. Karazin Kharkiv National University (KhNU), Institute of Bioorganic Chemistry [Tashkent, Uzbekistan], Academy of Sciences of Republic of Uzbekistan, Loughborough University, International Burch University [Sarajevo], University of Belgrade [Belgrade], Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP), Universidade Federal da Bahia (UFBA), Universidade Federal de Pelotas = Federal University of Pelotas (UFPel), Instituto Nacional de Saude [Maputo, Mozambique] (INS), University of Leicester, National Laboratory of Genomics for Biodiversity (LANGEBIO), Centro de Investigacion y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Dipartimento di Biologia e Biotecnologie 'L. Spallanzani', Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), University of Bologna/Università di Bologna, Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), University of São Paulo (USP), Dipartimento di Biologia e Biotecnologie ‘Lazzaro Spallanzani’, University of Pavia, University of Pavia, BIGEA, Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum – University of Bologna, Bologna, Italy, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), University of Oxford [Oxford], Fundação Oswaldo Cruz (FIOCRUZ), Universidade de São Paulo (USP), and University of Bologna

Subjects
0301 basic medicine, admixture history of the America, Human genetic variation, Colonialism, Atlantic Slave Trade, Gene flow, 0302 clinical medicine, Colonization, European colonization, African Continental Ancestry Group, 0303 health sciences, Genome, Middle East, Geography, Caribbean Region, Genetic structure, Ethnology, General Agricultural and Biological Sciences, Atlantic slave trade, Human, MESH: Caribbean Region, Gene Flow, American Native Continental Ancestry Group, Demographic history, European Continental Ancestry Group, Black People, Biology, General Biochemistry, Genetics and Molecular Biology, White People, 03 medical and health sciences, sex-biased admixture, Humans, admixture history of the Americas, MESH: Gene Flow, MESH: Genome, Human, American Indian or Alaska Native, 030304 developmental biology, MESH: Central America, MESH: Humans, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Central America, North America, South America, Genome, Human, MESH: South America, MESH: North America, 030104 developmental biology, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, 030217 neurology & neurosurgery
Abstract

The complexity of the admixture dynamics that shaped American populations is unveiled by Ongaro et al., where genetic data for more than 12,000 individuals from the continents are investigated. This study evaluates the dramatic impact of events after the colonial era, revealing a spatial and temporal heterogeneity and mirroring historical records. © 2019 Elsevier Ltd The human genetic diversity of the Americas has been affected by several events of gene flow that have continued since the colonial era and the Atlantic slave trade. Moreover, multiple waves of migration followed by local admixture occurred in the last two centuries, the impact of which has been largely unexplored. Here, we compiled a genome-wide dataset of ∼12,000 individuals from twelve American countries and ∼6,000 individuals from worldwide populations and applied haplotype-based methods to investigate how historical movements from outside the New World affected (1) the genetic structure, (2) the admixture profile, (3) the demographic history, and (4) sex-biased gene-flow dynamics of the Americas. We revealed a high degree of complexity underlying the genetic contribution of European and African populations in North and South America, from both geographic and temporal perspectives, identifying previously unreported sources related to Italy, the Middle East, and to specific regions of Africa. © 2019 Elsevier Ltd Preprint version of the article: "The genomic impact of European colonization of the Americas", posted June 28, 2019 on bioRxiv. Article is now published in Current Biology doi: [dx.doi.org/10.1016/j.cub.2019.09.076]. Published version on this repository: [http://vinar.vin.bg.ac.rs/handle/123456789/8654].

Published
2019

50. POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans

Author

Maanasa, Raghavan, Matthias, Steinrücken, Kelley, Harris, Stephan, Schiffels, Simon, Rasmussen, Michael, DeGiorgio, Anders, Albrechtsen, Cristina, Valdiosera, María C, Ávila-Arcos, Anna-Sapfo, Malaspinas, Anders, Eriksson, Ida, Moltke, Mait, Metspalu, Julian R, Homburger, Jeff, Wall, Omar E, Cornejo, J Víctor, Moreno-Mayar, Thorfinn S, Korneliussen, Tracey, Pierre, Morten, Rasmussen, Paula F, Campos, Peter, de Barros Damgaard, Morten E, Allentoft, John, Lindo, Ene, Metspalu, Ricardo, Rodríguez-Varela, Josefina, Mansilla, Celeste, Henrickson, Andaine, Seguin-Orlando, Helena, Malmström, Thomas, Stafford, Suyash S, Shringarpure, Andrés, Moreno-Estrada, Monika, Karmin, Kristiina, Tambets, Anders, Bergström, Yali, Xue, Vera, Warmuth, Andrew D, Friend, Joy, Singarayer, Paul, Valdes, Francois, Balloux, Ilán, Leboreiro, Jose Luis, Vera, Hector, Rangel-Villalobos, Davide, Pettener, Donata, Luiselli, Loren G, Davis, Evelyne, Heyer, Christoph P E, Zollikofer, Marcia S, Ponce de León, Colin I, Smith, Vaughan, Grimes, Kelly-Anne, Pike, Michael, Deal, Benjamin T, Fuller, Bernardo, Arriaza, Vivien, Standen, Maria F, Luz, Francois, Ricaut, Niede, Guidon, Ludmila, Osipova, Mikhail I, Voevoda, Olga L, Posukh, Oleg, Balanovsky, Maria, Lavryashina, Yuri, Bogunov, Elza, Khusnutdinova, Marina, Gubina, Elena, Balanovska, Sardana, Fedorova, Sergey, Litvinov, Boris, Malyarchuk, Miroslava, Derenko, M J, Mosher, David, Archer, Jerome, Cybulski, Barbara, Petzelt, Joycelynn, Mitchell, Rosita, Worl, Paul J, Norman, Peter, Parham, Brian M, Kemp, Toomas, Kivisild, Chris, Tyler-Smith, Manjinder S, Sandhu, Michael, Crawford, Richard, Villems, David Glenn, Smith, Michael R, Waters, Ted, Goebel, John R, Johnson, Ripan S, Malhi, Mattias, Jakobsson, David J, Meltzer, Andrea, Manica, Richard, Durbin, Carlos D, Bustamante, Yun S, Song, Rasmus, Nielsen, Eske, Willerslev, Raghavan M, Steinrücken M, Harris K, Schiffels S, Rasmussen S, DeGiorgio M, Albrechtsen A, Valdiosera C, Ávila-Arcos MC, Malaspinas AS, Eriksson A, Moltke I, Metspalu M, Homburger JR, Wall J, Cornejo OE, Moreno-Mayar JV, Korneliussen TS, Pierre T, Rasmussen M, Campos PF, Damgaard Pde B, Allentoft ME, Lindo J, Metspalu E, Rodríguez-Varela R, Mansilla J, Henrickson C, Seguin-Orlando A, Malmström H, Stafford T Jr, Shringarpure SS, Moreno-Estrada A, Karmin M, Tambets K, Bergström A, Xue Y, Warmuth V, Friend AD, Singarayer J, Valdes P, Balloux F, Leboreiro I, Vera JL, Rangel-Villalobos H, Pettener D, Luiselli D, Davis LG, Heyer E, Zollikofer CP, Ponce de León MS, Smith CI, Grimes V, Pike KA, Deal M, Fuller BT, Arriaza B, Standen V, Luz MF, Ricaut F, Guidon N, Osipova L, Voevoda MI, Posukh OL, Balanovsky O, Lavryashina M, Bogunov Y, Khusnutdinova E, Gubina M, Balanovska E, Fedorova S, Litvinov S, Malyarchuk B, Derenko M, Mosher MJ, Archer D, Cybulski J, Petzelt B, Mitchell J, Worl R, Norman PJ, Parham P, Kemp BM, Kivisild T, Tyler-Smith C, Sandhu MS, Crawford M, Villems R, Smith DG, Waters MR, Goebel T, Johnson JR, Malhi RS, Jakobsson M, Meltzer DJ, Manica A, Durbin R, Bustamante CD, Song YS, Nielsen R, and Willerslev E

Subjects
Gene Flow, Siberia, Models, Genetic, Athabascans and Amerindians, Human Migration, Genetic history of Native American, Indians, North American, Humans, Genomics, Americas, Population genetic, History, Ancient, Article
Abstract

How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we find that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (KYA), and after no more than 8,000-year isolation period in Beringia. Following their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 KYA, one that is now dispersed across North and South America and the other is restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative ‘Paleoamerican’ relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.

Published
2015

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