River Valleys Shaped the Maternal Genetic Landscape of Han Chinese

Abstract

A general south-north genetic divergence has been observed among Han Chinese in previous studies. However, these studies, especially those on mitochondrial DNA (mtDNA), are based either on partial mtDNA sequences or on limited samples. Given that Han Chinese comprise the world’s largest population and reside around the whole China, whether the north-south divergence can be observed after all regional populations are considered remains unknown. Moreover, factors involved in shaping the genetic landscape of Han Chinese need further investigation. In this study, we dissected the matrilineal landscape of Han Chinese by studying 4,004 mtDNA haplogroup-defining variants in 21,668 Han samples from virtually all provinces in China. Our results confirmed the genetic divergence between southern and northern Han populations. However, we found a significant genetic divergence among populations from the three main river systems, that is, the Yangtze, the Yellow, and the Zhujiang (Pearl) rivers, which largely attributed to the prevalent distribution of haplogroups D4, B4, and M7 in these river valleys. Further analyses based on 4,986 mitogenomes, including 218 newly generated sequences, indicated that this divergence was already established during the early Holocene and may have resulted from population expansion facilitated by ancient agricultures along these rivers. These results imply that the maternal gene pools of the contemporary Han populations have retained the genetic imprint of early Neolithic farmers from different river basins, or that river valleys represented relative migration barriers that facilitated genetic differentiation, thus highlighting the importance of the three ancient agricultures in shaping the genetic landscape of the Han Chinese.

Population dynamics in the Japanese Archipelago since the Pleistocene

“…Figure 3 shows a Mutli Dimensional Scaling (MDS) plot of mitogenome of 1 Palaeolithic, 13 Jomon, 4 Yayoi, and 2,062 present-day individuals in the Japanese Archipelago. Minato1 has the potentially ancestral type of haplogroup M, which can be seen neither in 2,062 present-day Japanese samples newly obtained in this study nor in 21,668 present-day Han Chinese samples recently published [13]. Haplogroup M is found at high frequency in present-day Asians, Australasians, and indigenous Americans.…”

“…The results show that three of the Yayoi individuals belong to haplogroup D4 (Table 1). D4 is the most common haplogroup in present-day Japanese (34.3%) (Supplementary Table S2), which is also common throughout East Asia [13,18]. Like the Jomon individuals, all of the Yayoi individual fall into any of the clusters of the phylogenetic network, MDS and Bayesian phylogenetic tree that are constructed together with the present-day Japanese people, although the Jomon and Yayoi people have some mitochondrial sub-haplogroups characteristic to each of them (Figs.…”

Fine‐scale genetic structure of Tujia and central Han Chinese revealing massive genetic admixture under language borrowing

“…The Greater Himalayan Region served as a physical barrier to gene flow between East Asia and South Asia, and the Himalayas also promoted the complex genetic adaptation and demographic history of East Asian (Sanchez‐Mazas et al, 2008; Jeong et al, 2016; Gnecchi‐Ruscone et al, 2018). Other geographical/cultural/linguistic barriers within China can also shape the genetic architecture of East Asians, such as river valleys (Amur, Liao, Yellow, and Yangtze rivers) and islands (Li et al, 2019; He et al, 2020). Early Y‐chromosomal and mitochondrial genetic evidence (Zhang et al, 2007; Stoneking & Delfin, 2010; Kong et al, 2011; Oppenheimer, 2012; Lopez et al, 2015) postulated that our ancestors of anatomically modern human (AMH) out of Africa spread northeast toward East Asia via Southeast Asia and had populated here approximately 50 000 years before present (kybp; taken as ad 1950).…”

Uniparental Genetic Analyses Reveal the Major Origin of Fujian Tanka from Ancient Indigenous Daic Populations

“…In Tanka, the most frequent haplogroups are F2a (25%), M7c1 (11.67%), M8a2 (8.33%), F1a1 (6.67%), B4b (5%) and A15 (5%). The dominant haplogroup F2a (average 25%) in Tanka reached the highest frequency in PhuLa (26.8%) (Thuy et al 2018) and PaThen (19.44%) in northern Vietnam (Thuy et al 2018) but was sporadic occurrence in East Asian populations, like Guangxi Mien (2.44%) (Wen et al 2004a), Yunnan Yi (5-6.25%) (Wen et al 2004c), Qinghai Han (8%) (Li et al 2019), and southern Han (0.88%-2.04%) (Li et al 2019) ( Figure S3). The distribution pattern of the mtDNA haplogroup F2a indicates the Fujian Tanka experienced a strong bottleneck effect caused by isolation.…”