For SNPs, a total of 3,399,707 (90.85%) were found in both databases; 155,810 (4.16%) and 43,562 (1.16%) were identified in dbSNP set and 1000 genomes set, respectively; and 143,155 (3.83%) were novel (fig. Clade D in Y haplogroup is widely found in Tibeto-Burman populations in Asia, and it has been proposed as the most ancient lineage in East Asia (Shi et al. Data deposition: All genomic data have been deposited at NCBI SRA database under the accession SRA105951. Chromosomes were typed with a minimum of 16 binary markers (Qamar et al. In the analysis, the same number of individuals was selected for each group. L* represents all L lineages but L3, including L0, L0, L2, L4, L5, and L6; L3* represents all L3 lineages but M, including L3a to L3f, L3h, L3i, L3k, L3x, and N; M* represents all lineages prefixed M, D, and Q, but G; G* represents G1, G3, and G4. Przewalski's horse - Wikipedia The part of North/East Asians might have been resulted from the recent common ancestor before moving into East Asia and gene flows after divergence from groups in other continents. In this work, we used the assembly-based SOAP detection pipeline (Li et al. Y chromosome haplotype diversity in Mongolic-speaking - Nature 2002; our unpublished observations), including RPS4Y and M48, to define the lineage C*(xC3c) (Y-Chromosome-Consortium 2002), also known as haplogroup 10, derived for RPS4Y and ancestral for M48. In this study, we used a resource-efficient computing program ADMIXTURE (Alexander et al. Y-chromosome evidence confirmed the Kerei-Abakh origin of - Nature 2002). 2006). 2012). phenomena and found that the two heterochromatic chromosomes of the Mongolian gerbil have distinct underpinnings: Chromosome 5 has a large block of intra-arm heterochromatin as the result of a massive expansion of centromeric repeats, while chromosome 13 is comprised of extremely large (>150kb) repeated sequences. 1994), , suggested 860 (5901,300) years. We also predicted Mendelian diseases risk for the individual by analyzing potential functional SNPs. This indicates that the studied individual is representative of the normal, healthy population. Historians have documented a series of polities based in inner Asia between 200 bc and the eighteenth century, such as the Qing Dynasty. The team identified 11 Y-chromosome sequences that were each shared by more than 20 of the 5,321 genomes. Our findings nevertheless demonstrate a novel form of selection in human populations on the basis of social prestige. The analysis indicates that Mongolians mainly possess four ancestral proportions, including East Asians, South/Central Asians, Europeans, and from the Americas. Although this possibility cannot be entirely ruled out, the small number of genes on the Y chromosome and their specialized functions provide few opportunities for selection (Jobling and Tyler-Smith 2000). Median-joining network (Bandelt et al. the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in The geographically representative estimation of K = 9 (fig. Down syndrome, also called Down's syndrome, trisomy 21, or (formerly) mongolism, congenital disorder caused by the presence in the human genome of extra genetic material from chromosome 21. Przewalski's horse (/ v l s k i z / sh-VAHL-skeez or / p r v l s k i z / pur-sh-VAHL-skeez ( Russian: [prvalskj]), Polish: [pvalski]) (Equus ferus przewalskii or Equus przewalskii), also called the takhi, Mongolian wild horse or Dzungarian horse, is a rare and endangered horse originally native to the steppes . Am J Hum Genet 70:11071124, Slatkin M, Bertorelle G (2001) The use of intraallelic variability for testing neutrality and estimating population growth rate. 1Department of Biochemistry, University of Oxford, Oxford; 2Department of Medical Biology, Harbin Medical University, Harbin, China; 3Dipartimento di Biologia, Universit di Ferrara, Ferrara, Italy; 4Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, United Kingdom; 5Institute of Genetics, Chinese Academy of Sciences, Beijing; 6Biomedical and Genetic Engineering Labs, Islamabad; 7Institute of Immunology, Academy of Sciences, Tashkent, Uzbekistan; 8McDonald Institute, University of Cambridge, Cambridge, United Kingdom; and 9Institute of Biotechnology, Mongolian Academy of Sciences, Ulaanbaatar, Mongolia. Furthermore, we were able to align 96% of the scaffolds onto chromosomes by mapping the representative seed sequences (20 kb) to the human reference genome. Science pours in from Rosetta comet mission, GM microbes created that cant escape the lab, Crunch time for pet theory on dark matter. 98.69% of the draft was covered by more than 20-folds (supplementary fig. S3, Supplementary Material online) indicating the high quality of the genome draft. However, Indians possess fewer shared ancestral alleles than non-Indians, indicating that the diluted Mongolian lineage in Indian populations might have happened after the expansion of the Mongolian empire in the 13th century, possibly a result of Mughal Empire expansion in the 16th century. Although sociocultural impacts of Mongolians have been well documented, the evidences of molecular genetics are limited and attract great attention. Mongolians dwell at the Eastern Eurasian Steppe, where is the agriculture and pasture interlaced area, practice pastoral subsistence strategies for generations, and have their own complex genetic formation history. We additionally used reconstructed haplotype blocks of representative human populations (Yoruba, French, Russian, Caucasian [Adygei], Brahui, Mongolian, Han, and Maya) to confirm the genetic imprints of Mongolians. S5, Supplementary Material online). 2011), including a peak at the size of about 300 bp, potentially caused by abundance of Alu elements (supplementary fig. (C) The ancestry proportion plot of 1,042 individuals using the ADMIXTURE with K = 9. Mongoloid ( / m..ld / [1]) is an obsolete racial grouping of various peoples indigenous to large parts of Asia, the Americas, and some regions in Europe and Oceania. S7, Supplementary Material online), compared with the YH and the reference human genome. The authors sincerely thank our sample donor for generously contributing his blood. The team's study1 points to sociopolitical factors that foster such lineages, but the identities of the men who left their genetic stamp remains unknown. We checked alleles of all markers released in the Y haplogroup phylogenetic tree (Karafet et al. 2012) and rCRS (Anderson et al. Nature (2015). 2002). Of the 14 c.235delC homozygotes selected from our cohort, 21 of the 22 Taiwanese chromosomes and five of the six Chinese chromosomes with GJB2 c.235delC shared the same A-G-T-T-A haplotype with the 8 Mongolian chromosomes with c.235delC. 2009). (B) The strategy of SNP and short indel identification. S12, Supplementary Material online). As a library, NLM provides access to scientific literature. 2006) and GENSCAN (Burge and Karlin 1997). We defined novel sequence of the Mongolian genome using unmapped reads with respect to the reference human genome. Dual origins of the Northwest Chinese Kyrgyz: the admixture of Bronze age Siberian and Medieval Niru'un Mongolian Y chromosomes J Hum Genet. The assembled genome, annotation results, SNPs, short indels, and SVs produced in the study have been deposited in our Mongolian genome database, http://dx.doi.org/10.5524/100104. 1996; Starikovskaya et al. Chromosome-level genome assembly and population genomics of Mongolian racerunner (Eremias argus) provide insights into high-altitude adaptation in lizards - PMC Back to Top Skip to main content An official website of the United States government Here's how you know The .gov means it's official. Curzon Press, Richmond, Qamar R, Ayub Q, Mohyuddin A, Helgason A, Mazhar K, Mansoor A, Zerjal T, Tyler-Smith C, Mehdi SQ (2002) Y-chromosomal DNA variation in Pakistan. 2005), and SMART (Letunic et al. According to the related items of informed consent form (supplementary fig. Nat Genet 7:169175 [, Mousavi SA (1998) The Hazaras of Afghanistan. We can deduce the most likely time to the most recent common ancestor (TMRCA) and place of origin of this unusual lineage from the observed genetic variation. Second, star-cluster chromosomes were found in 16 populations throughout a large geographical area extending from Central Asia to the Pacific (fig. It is not possible to examine his remains directly, but history provides an alternative. The case for Genghis Khans genetic legacy is strong, if circumstantial. Subsequently, three SNP sets were integrated into a final SNP set by selecting the sites that were supported by at least two of three approaches. S7, Supplementary Material online). We ultimately obtained the chromosome sequences for the Mongolian genome. 0.48% of all bases in the uniquely mapped reads mismatched the human reference genome. Natural selection can act to remove deleterious variants (purifying selection), maintain polymorphism (balancing selection), or produce a trend (directional selection). Oxford University Press is a department of the University of Oxford. We found varying degrees of gene flows between Mongolians and populations living in Europe, South/Central Asia, and the Indian subcontinent. Using the integrated strategy of de novo prediction and homology-based alignment, the assembled genome was annotated for repeat elements, coding genes, and other noncoding RNAs. A chromosome-assigned Mongolian gerbil genome with sequenced - bioRxiv Genghis Khan is reputed to have sired hundreds of children. S2, Supplementary Material online), which presents high assembly accuracy at the nucleotide level. All three lineages seem to have expanded westwards, possibly along the Silk Road trade route. The Mongolian ethnic group, a population of East Asia, has approximately 10 million individuals. A total of 8,592 haplotype blocks were first obtained based on the genotype data of 11 Mongolian individuals (ten of HGDP and Mongolian genome), which cover 9.1% of human reference genome. These included China, where the Yan Dynasty emperors remained in power until 1368, after which the Mongols continued to dominate the country north of the Great Wall for several more centuries, and the region west to the Aral Sea, where the Chaghatai Khans ruled. Novel sequences possess typical individual and population specificity (Li R, Li Y, et al. aThe shared haplotype blocks had been filtered by using the haplotype blocks of Africans. Thank you for visiting nature.com. To obtain The mutations labeled with an exclamation point are reported in the mitochondria sequence of rCRS version. Clear examples of the latter are rare in humans, but probable cases, such as those associated with resistance to malaria (Hamblin and Di Rienzo 2000) or unidentified pathogens (Stephens et al. An additional eight chromosomes with the c.235delC mutation were identified from East Asians in the 1000 . HHS Vulnerability Disclosure, Help Their dates coincide with the emergence of hierarchical, authoritarian societies in Asia during the Bronze Age, such as the Babylonians. These authors contributed equally to this work. The Mughal Empire expanded the reign of Mongolian lineage to the Indian subcontinent (Richards 1993) (fig. 2011) to identify short indels (fig. Length of the majority of candidates ranges from 50 bp to 100 kb. ANNOVAR software (Wang et al. CAS Unique spectra of deafness-associated mutations in Mongolians provide For the final step of gap filling, we used the read pairs that had one read anchored on a contig and the mate read located within the gap region to perform local assembly. The original article indicated that Giocangga was a member of the Qing dynasty. Sign up for the Nature Briefing newsletter what matters in science, free to your inbox daily. The Przewalski's horse has . 2009) was used to detect SNPs of the Mongolian genome, respectively. Risks of Mendelian Diseases Based on Functional SNPs. P value is the statistical significance based on the chi-square test (2 test, P = 0.05). In total, 99.74% and 94.42% of the effective genome was covered by at least 1 read and 20 reads, respectively (supplementary table S7, Supplementary Material online). 1996; Merriwether et al. Out of 34 SNPs tested, both alleles of 31 SNPs (all 12 homozygous and 19 heterozygous) were verified completely. 2010). Annotation of gene function was finally performed based on alignment of the genes to the SwissProt and Translated EMBL Nucleotide Sequence Data Library databases (Bairoch and Apweiler 2000). In surveys of DNA variation in Asia, we typed 2,123 men with 32 markers to produce a Y haplotype for each man; these included 1,126 individuals described elsewhere (Qamar et al. They are increasingly necessary to explore characteristics of population evolution, disease, and personal healthcare. The results of D test showed that the Indian groups share different amounts of ancestral alleles with Mongolians (supplementary table S19, Supplementary Material online). This can be categorised into various types: Aneuploidy: loss or gain of a chromosome. Ligated fragments were size selected for 200, 500, and 800 bp on agarose gel and were purified by polymerase chain reaction (PCR) amplification to produce the corresponding libraries. Millions of men bear the genetic legacy of Genghis Khan,the famously fertile Mongolian ruler who died in 1227. 2010). Am. The evaluation of the assembled genome shows that the distribution of GC content is comparable to the other two genomes. After excluding missing sites and sites with low quality from the chip genotyping data, the genotype concordance rate between the SNP call set and the chip genotyping set (both position and two alleles) reached 98.48% in a total of 2,356,566 sites. Based on the released markers reported in the previous Y haplogroup study (Karafet et al. Introduction The Mongolian ethnic group, a population of East Asia, has approximately 10 million individuals. In the meantime, to ensure continued support, we are displaying the site without styles 1996; Merriwether et al. ISSN 1476-4687 (online) This project was supported by the National Basic Research Program of China (973 program no. Using this method, we estimated the chance of finding the low degree of variation observed in the star cluster, with a current frequency of 8%, under neutral conditions. Representative genomes of increasing numbers of human populations have been sequenced to dissect the structure and history, including Indian (Reich et al. 2022 Mar;67 . The group is broadly considered to be a founding population of the New World (Kolman et al. The .gov means its official. 2009), American (Reich et al. 2012). Jobling says that these civilizations could have fostered dominant male lineages after the sons of a fecund founder decamped to satellite outposts, where they, in turn, fathered powerful descendants. We performed inference of patrilineal inheritance of the individual through Y haplogroup analysis. Genetic Imprints of Mongolian Genome on Global Populations Based on Shared Haplotype Blocks. We also constructed a detailed personal genetic variation map. Total of 392.37-Gb genomic data were produced (supplementary table S1, Supplementary Material online). The genomic DNA was extracted from the peripheral blood of the individual. Accessibility The rise of the Mongolian Empire and conquests of the Eurasia continent (from the 13th to 19th centuries) (Twitchett and Fairbank 1994; Weatherford 2005) under Genghis Khan and his successors have played a major role in the last 1,000 years of human evolution. In addition, genome-wide genetic variation maps have been compiled for population-specific genetics research, such as Dutch (Genome of the Netherlands Consortium 2014) and British (http://www.uk10k.org). For commercial re-use, please contact journals.permissions@oup.com, Genome of the Lord Howe Island stick insect reveals a highly conserved Phasmid X chromosome. D Test between Mongolians and Other Modern Humans. We then presented a high-quality Mongolian genome draft produced from hierarchical de novo assembly strategy. Genetics 158:865874, Stephens JC, Reich DE, Goldstein DB, Shin HD, Smith MW, Carrington M, Winkler C, et al (1998) Dating the origin of the CCR5-32 AIDS-resistance allele by the coalescence of haplotypes. 2010) and M haplogroup (Derenko et al. For large scaffolds (40 kb), multiple seeds (20 kb) were extracted from each one. We then used two approaches to calculate a TMRCA for the star-cluster chromosomes. The prediction was based on the repeat-masked assembly using Augustus (Stanke et al. Genghis Khan's Genetic Legacy Has Competition The shared haplotypes of different population pairs were compared against each other and Pearson chi-square tests were calculated to determine the significance of differences. J. Hum. Mol Biol Evol 16:3748 [, Hamblin MT, Di Rienzo A (2000) Detection of the signature of natural selection in humans: evidence from the Duffy blood group locus. 2011;6:e17548. Moore, L. T., McEvoy, B., Cape, E., Simms, K. & Bradley, D. G. Am. Among the former, mutation, recombination, and migration increase variation, whereas genetic drift decreases it. The term is derived from a now-disproven theory of biological race. Similarly, by scanning the ancestral/derived alleles of all markers in the Mt haplogroup database, we discarded one aberrant mutation (C182T) and located the matrilineal ancestor of the Mongolian genome in a novel sublineage under the lineage G2a (T152C) in the RSRS tree as well as the sublineage G2a2 (T711C and C8943T) under the lineage G2a (T152C) in rCRS tree (fig. CDSP is an autosomal recessive disorder of the carnitine cycle and patients with CDSP have defects in the ability to transform fat to energy during periods of stress and fasting (Longo et al. Show more 2004; Derenko et al. Chromosomal disorders are due to the change in the number of chromosomes present. Genghis Khan's genetic legacy has competition | Nature 1). Jobling warns that these dates come with huge margins of error, but he notes that the estimates for the lineages attributed to Khan and Giocangga are very close to those of past studies. Known as a typical nomadic people, Mongolians have evolved into a modern day ethnic group with their own culture, language, life style (Komatsu et al. 2002) through recent adaptation to characteristic environments. 4B, minor plot). Although Indians have a certain amount of shared ancestral alleles, comparative analysis shows that the shared ancestral alleles with Indians are significantly fewer than that with Europeans and Central/South Asians, such as French, Italian, Balochi, and Brahui (|Z| >> 7 or P << 1012) (table 3 part 7 and supplementary table S20, Supplementary Material online). The sizes of window and sliding step are 1 and 0.5 Mb for SNP and short indel, 2 and 1 Mb for SV. Then, through scanning the SNP sites of the individual which overlapped with predicted haplotype blocks, we ultimately obtained the haplotype blocks of the Mongolian genome. https://doi.org/10.1038/nature.2015.16767, DOI: https://doi.org/10.1038/nature.2015.16767. 2012) (supplementary fig. Sixteen Y microsatellites were also typed, but DYS19 was excluded from the network analysis because it is duplicated in haplogroup C. The central star-cluster profile is 10-16-25-10-11-13-14-12-11-11-11-12-8-10-10, for the loci DYS389I-DYS389b-DYS390-DYS391-DYS392-DYS393-DYS388-DYS425-DYS426-DYS434-DYS435-DYS436-DYS437-DYS438-DYS439. According to traditional genealogy, nine of these clans have a common ancestor and constitute the Uissun tribe. Approximately 90% of the genome draft was covered by 431 scaffolds with each having size larger than 1.4 Mb, of which the largest scaffold spans 36 Mb. Careers, Unable to load your collection due to an error. 2008; Zhong et al. Manchu cluster chromosomes were present in seven populations: Xibe, Outer Mongolians, Inner Mongolians, Ewenki, Oroqen, Manchu, and Hezhe (fig. 2005), we first combined genotypes of ten Mongolian individuals of HGDP and the studied individual to infer the haplotype blocks for the small population (R2 > 0.8). The largest proportion of the repetitive sequences is LINE, contributing 31.3% of the genome (supplementary table S4, Supplementary Material online). Based on an in-house human mutation database, we obtained 16 heterozygous SNPs (table 2) after filtering with a series of criteria (see Materials and Methods). For short indels, 212,630 (28.12%) were found in both sets; 338,038 (44.7%) and 26,383 (3.49%) were only included in dbSNP or 1000 genomes, respectively; and 179,158 (23.69%) were novel (fig. The reads unmapped onto the human reference genome were collected and regarded as the primary candidates of novel sequences. It was also supported by the intramural program of NHGRI (1ZIAHG000024), the National Institute of Health (NIH) to N.N. J. Hum. government site. To predict the Mendelian diseases risks of the individual, we scanned an in-house human mutation database for each SNP of the Mongolian genome. The https:// ensures that you are connecting to the A small notch at the peak of the distribution can be seen in the Mongolian genome (supplementary fig. We calculated standard errors and Z-scores using the bootstrap method to estimate significance of the D values. The Mongolian leader left a strong footprint in the Y chromosomes of his modern descendants, but he was not the only one By Ewen Callaway, Nature magazine on January 29, 2015 Millions of men. Xue, Y. et al. We ultimately obtained 15,088 large indels (>50 bp) and 1,210 candidate inversions (from 8 bp to 45 kb) (fig. Nature 2012). 2008) as an outgroup for every comparison. 1999). For the SNP sets from GATK and SAMtools, we refined the SNPs by using the same threshold value of genotype quality (13) and read coverage (6 and 100). The lineage is carried by likely male-line descendants of Genghis Khan, and we therefore propose that it has spread by a novel form of social selection resulting from their behavior.