Supplementary Text

Contents

Part 1, Filters for variants and selection of calculation points

Part 2, Discussion about history of modern populations

Part 1, Filters for variants and selection of calculation points

To obtain a confident dataset for age estimation, we applied a seriesof strict filters on the original variants file, including: 1, restrict to confident region (~8.439M bp) that are widely used by Poznik et al.¹, Karmin et al.² and Adamov et al.³; 2, restrict to variants that are single nucleotide polymorphisms (Y-SNP); 3, remove all position with call rate <90% on all samples; 4, remove position with heterozygosis call rate >5% on all samples; 5, base coverage ≥3, base quality >20, and distance between SNPs >10 bp; 6, remove all recurrent or triadic mutations even though they are confident on the currently known phylogenetic tree. Back imputation was also done on Y-SNP markers on the known phylogenetic tree, so as to infer missing genotype on some samples.

After applying these filters, we found that the accumulated mutations of samples varied significantly among different haplogroup (see the Maximum Parsimony tree in Figure S1). This means that the mutation rates on each haplogroup are different from each other after they split from the common ancestor. The haplogroup D-M174, C-M130 and NO-M214 had been separated from each other for more than 73k years. Therefore, we concluded that a unified mutation rate is unsuitable for the age calculation of a dataset that contain samples of all three haplogroups. We used the age for haplogroup CT-M168 (71,760 years, 95% confidence interval [CI] = 69,777–73,799)² as the calibration point for estimating the coalescent times of all studied samples. All of four major paternal haplogroups in East Eurasian (D-M174, C-M130, NO-M214, and Q-M242) are sub-branches of CT-M168. Using the age of CT-M168 as the calibration point will resolve the issue caused by different mutation rate on its sub-branches.

On the other hand, as indicated by the study of Icelandic males, the genealogical mutation rate of Y-chromosome (0.871x10-10 mutations per position per year)⁴ is slightly higher than the evolutionary mutation rate (0.74 x10-10 mutations per position per year) calculated by ancient DNA of Ust’Ishim male.² This means that more mutations will be accumulated in the recent historical age. Thus, we also use the splitting time (470±20 years ago) of samples from Aisin Gioro family as a recent calibration point.⁵

Part 2, Discussion about history of modern populations

 In this section, we discussed about the founding history of Manghit, Keneges tribes in moder Nogay, Uzbeks and Karakalpak populations, Dulat, Uysun, and Kerey in modern Kazakhs, and Hazara population is Afghanistan. Also, we discussed their connection with ancient Mongol Niru’un clan or ordinary ancient Mongols.

   According to Rashid Al-din,⁶ all the Mongol people were divided into two sub-tribes. One was the Darlakin Mongol tribe and the other was the Niru’un Mongol tribe. The Darlakin Mongol referred to the commonality of the Mongol people, while the Niru’un Mongol (means “The pure Mongol”) was believed to be the descendants of Alan Quo’a. Genghis Khan belonged to Kiyan clan, one clan of Niru’un tribe. Combining the data from published researches, C3*-ST were found in several modern populations who can traced back to Mongol Niru’un clan.

Manghit

   Manghit was also called Manghuds and Mangqut. According to history records, Manghit was derived from the Niru’un Mongols.^6,7,8 They moved westward together with Jochi’s armies and lived in the Golden Horde ( the Mongol empire in Central Asia and Northeast of Europe, 1219 A.D. - 1502 A.D.). They extensively involved in the political activities of the Khanates.^6,8 At the beginning, they followed Nogai Khan (d.1299) to establish their own semi-independent horde from the Golden Horde in Sarai. Then, they supported their own commander Edigu (1352-1419) to found Nogai Horde or Manghit Horde in the 14th-15th century.⁸ Their descendants called themselves Nogay and lived in the plains of northern Caucasus and the Crimea since 17th century. Another group of them moved southward as a part of Uzbeks and finally established the Manghit Dynasty to rule the Emirate of Bukhara in Transoxania in 1785.⁹ Descendants of them became parts of modern Uzbeks and Karakalpakpopulation.¹⁰

Most of the C3 samples in Nogay belong to C3*-ST.^11,12 In addition, the only one sample of Manghit tribe in Uzbekstan reported by Sabitov et.al¹³ also belongs to the above lineage. Among Qarasyraq clan of Manghit tribe reported by Chaix et.al 2007,¹⁴ 11 out of 14 haplotypes process the same Y-STR profile as C3*-ST. These data indicated that they shared a common ancestor. Nogay population was list as Nogaits, population No. 26 in Supplementary Table S1. Manghit tribe was included in Karakalpaks, population No. 28 in Supplementary Table S1.

Keneges

     According to history records, Keneges was also derived from the Niru’un Mongol. As one of four thousand “original” Mongol troops that Genghis Khan bequeathed as auxiliary of Jochi, Keneges (Leaded by Кутаном Кенегесом) came in Jochi Ulus (The Golden Horde) in the early 13th century.^6,7,8 After the collapse of The Golden Horde, Manghit and Keneges moved southward as a part of Uzbeks and then became a part of modern Uzbeks and Karakalpak population.^10,15

  All the three C3 samples in Keneges reported by Sabitov et.al¹³ belong to C3*-ST. Another sample was predicted as G2a-P15 according to its special Y-STR profile. G2a is now predominant in Caucasian populations¹⁶and hence can be considered as indigenous mixture after Keneges’ settlement in the Golden Horde. Keneges tribe was included in Karakalpaks (No. 28) in Supplementary Table S1.

Dulat

  Dulat, aka Duqlat or Dughlat, were also derived from the Niru’un Mongols.^6,7,15 Dulat was one of four thousand “original” Mongol troops that Genghis Khan bequeathed as auxiliary of Chagatai and eventually settled in the area comprising the Ulus of Chagatai Khan.⁶ During the last age of Moghulistan, which also called the Eastern Chagatai Khanate, many Mongol-origin tribes joined the new-born Kazakh Khanate, like Husin, Jalair and Duqlat. Later, they became Uysun, Zhalair and Dulat tribe as a part of the Great Jüz (aka Senior Juz) in modern Kazakh populations.^15,17

Within four C3 samples in Dulat tribe, three of them belong to C3*-ST.¹⁸ High frequency of C3*-ST were also found in other three sampling places within the area of the Great Jüz in southeast part of Kazakhstan (Population No.32~33, Supplementary Table S1). This lineage was also dominant in our Kazakh samples from Alban tribe at Zhaosu County, one tribe of the Great Jüz (Population No. 223, Supplementary Table S1).

Uysun and Kerey in Kazakhs

     Highest frequencies of C3*-ST were observed in both Southeast Kazakhstan (the Great Jüz) and Kazakh-Kerey (see all Kazakh in Supplementary Table S1). Kazakh Khanate was established by a group of population that separated from Uzbek Horde (late period of the Golden Horde). We found that C3*-ST is also dominant part of C3 in Uzbeks (Population No.146, Supplementary Table S1). After the joining of several tribes from Eastern Chagatai Khanate, they were called the Great Jüz (also the Uysun Jüz).^15,17 Regarding the origin of Kerey tribe in Kazakh, several genealogical legends about conflict with each other and give no well-resolved conclusion.^19,20One legend said that that Kerey-Ashmaily is the descendant of forefather Kerey and Kerey-Abakh is the descendant of the Great Jüz. The other legend said Kerey-Ashmaily originated from one of the three sons of the mythical forefather of Kazakhs. And Kerey-Abakh was derived from Kerey-Ashmaily. In this study, the most frequent haplotype in Kerey-Abkh (C3*-ST-Kazakh clade), has only one step mutation from the central haplotype of C3*-ST. So it is possible that C3*-ST-Kazakh clade was derived from the C3*- ST in either Kerey-Ashmaily or the Great Jüz. More evidences are needed to clarify these two hypotheses about the origin of Kerey-Abakh.

Hazara

   According to history records, the Hazara are the descendants of Genghis Khan’s soldiers, not male-line descendants of Genghis Khan himself. In Zerjal et al²¹, Hazara people were considered as direct descendants of Genghis Khan and hence became a strong evidence for their conclusion. However, the original material cited by Zerjal et al²¹ described that the Hazara were derived from ten military detachments sent by Genghis Khan.²²According to the available history records, those military detachments, 20,000 soldiers totally, were only ordinary people of Mongol tribe. There is no evidence that they were direct descendants of Genghis Khan, whose descendants had been well-documented at that era.^6,7 Four sets of samples of Hazara population were list in Supplementary Table S1.

Heritage of Niru’un Mongol

    According to history records, Manghit, Keneges and Dulat can be traced back clearly to Niru’un Mongol. At the time of Genghis Khan, the population of Niru’un Mongol (the Pure Mongols) had multiplied and they divided into more than twenty tribes (Figure S1). Before and after the foundation of the Mongol Empire, people of Niru’un Mongol were the core components of the Khanate’s upper classes and provided most of soldiers and generals of army. Participating in the conquest of Genghis Khan, they scattered and settled in all regions comprising the empire from East Asia to Northeast Europe. As discussed above, Manghit, Keneges, Dulat, and Hazara are all descendants of the armies sent to different regions of the Mongol Empire by Genghis Khan.

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Supplementary Table S5, The summary of depth and coverage of sequenced samples on the confident region (8.439M bp) of Y-chromosome.