Auditorium 2 - Symposium 18 - Americas Hub - Genome assembly, spatiotemporal variation, and genetic admixture in Asia

Auditorium 2 - Symposium 18 - Americas Hub - Genome assembly,
spatiotemporal variation, and genetic admixture in Asia
10:00am - 1:00pm Monday, 5th July, 2021
Presentation type Oral

Symposia organisers: Shuhua Xu, Qiaomei Fu
Please note, some speakers in this symposium also have a poster available to view.
Oral presentations occur in the Auditorium listed and the Posters are available in one of two Poster Halls.
Please do a search for "Presenters" via the search function of the online program for more information.

SYMP18-1 Haplotype-resolved de novo assembly of a Tujia genome suggests
the necessity for high-quality population-specific genome references

Haiyi Lou1, Yang Gao1,2, Bo Xie1, Yimin Wang1, Haikuan Zhang3, Miao Shi3, Sen Ma1, Xiaoxi Zhang1,2, Chang
Liu1, Shuhua Xu1,2,4,5,6
1Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai

Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences,
Shanghai, China. 2School of Life Science and Technology, ShanghaiTech University, Shanghai, China. 3Berry
Genomics, Beijing, China. 4Center for Excellence in Animal Evolution and Genetics, Chinese Academy of
Sciences, Kunming, China. 5Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University,
Zhengzhou, China. 6Collaborative Innovation Center of Genetics and Development, Shanghai, China

Abstract

While the human reference assembly is continually being improved, it remains debatable whether a
population-specific reference is necessary for each ethnic group. We applied multiple sequencing technologies
to de novo assemble an individual genome (TJ1) from the Tujia population, an ethnic minority group most
closely related to the Han Chinese. TJ1 provides a haplotype-resolved assembly of chromosome-scale high
quality with N50 scaffold size >78 Mb. Notably, compared with GRCh38 and other de novo assemblies, TJ1
remarkably improved short-read mapping by ~2%, comparable to inter-individual genome-length difference,
and enhanced calling precision by ~6-16% for structural variants. Furthermore, TJ1 facilitates detecting rare or
low-frequency variants and identifying the fine-scale difference between closely-related populations,
outstanding examples including population-stratified variants between Tujia and Han Chinese on genes like
LCT and UBXN8. Our results support the necessity of a population-specific assembly and exemplify its
particular value in the genetic analysis, especially for studying close-related populations.

Keywords
de novo assembly; Tujia; Population-specific reference genome; Haploid genome; Structural variation.

All authors contributed equally to this work.

SYMP18-2 Genetic admixture in the culturally unique Peranakan Chinese
population in Southeast Asia

Degang Wu1, Roger Foo2, Chaolong Wang1
1Huazhong University of Science and Technology, Wuhan, Hubei, China. 2National University of Singapore,

Singapore, Singapore

Abstract

The Peranakan Chinese are culturally unique descendants of immigrants from China who settled in the Malay
Archipelago ~300-500 years ago. Today, among large communities in Southeast Asia, the Peranakans have
preserved Chinese traditions with strong influence from the local indigenous Malays. Yet, whether or to what
extent genetic admixture co-occurred with the cultural mixture has been a topic of ongoing debate. We
performed whole-genome sequencing (WGS) on 177 Singapore (SG) Peranakans and analyzed the data jointly
with WGS data of Asian and European populations. We estimated that Peranakan Chinese inherited ~5.62%
(95% confidence interval [CI]: 4.75-6.46%) Malay ancestry, much higher than that in SG Chinese (1.08%, 0.69-
1.53%), southern Chinese (0.86%, 0.57-1.31%), and northern Chinese (0.25%, 0.18-0.33%). A sex-biased
admixture history, in which the Malay ancestry was contributed primarily by females, was supported by X
chromosomal variants, and mitochondrial (MT) and Y haplogroups. Finally, we identified an ancient admixture
event shared by Peranakan Chinese and SG Chinese ~1,612 (95% CI: 1,345-1,923) years ago, coinciding with
the settlement history of Han Chinese in southern China, apart from the recent admixture event with Malays
unique to Peranakan Chinese ~190 (159-213) years ago. These findings greatly advance our understanding of
the dispersal history of Chinese and their interaction with indigenous populations in Southeast Asia.

SYMP18-3 A dynamic 6,000-year genetic history of Eurasia’s eastern steppe

Choongwon Jeong1, Ke Wang2, Shevan Wilkin2, William Timothy Treal Taylor2, Bryan K. Miller2, Jan H.
Bemmann3, Raphaela Stahl2, Chelsea Chiovelli2, Florian Knolle2, Sodnom Ulziibayar4, Dorjpurev
Khatanbaatar5, Diimaajav Erdenebaatar6, Ulambayar Erdenebat7, Ayudai Ochir8, Ganbold Ankhsanaa9,
Chuluunkhuu Vanchigdash5, Battuga Ochir10, Chuluunbat Munkhbayar11, Dashzeveg Tumen7, Alexey
Kovalev12, Nikolay Kradin13, Bilikto A. Bazarov14, Denis A. Miyagashev14, Prokopiy B. Konovalov14, Elena
Zhambaltarova15, Alicia Ventresca Miller2, Wolfgang Haak2, Stephan Schiffels2, Johannes Krause2, Nicole
Boivin2, Myagmar Erdene7, Jessica Hendy2, Christina Warinner2
1Seoul National University, Seoul, Korea, Republic of. 2Max Planck Institute for the Science of Human History,

Jena, Germany. 3Rheinische Friedrich-Wilhelms-Universitat, Bonn, Germany. 4Institute of Archaeology,
Mongolian Academy of Sciences, Ulaanbaatar, Mongolia. 5Mongolian University of Science and Technology,
Ulaanbaatar, Mongolia. 6Ulaanbaatar State University, Ulaanbaatar, Mongolia. 7National University of
Mongolia, Ulaanbaatar, Mongolia. 8International Institute for the Study of Nomadic Civilizations, Ulaanbaatar,
Mongolia. 9National Centre for Cultural Heritage of Mongolia, Ulaanbaatar, Mongolia. 10Institute of History and
Ethnology, Mongolian Academy of Sciences, Ulaanbaatar, Mongolia. 11University of Khovd, Khovd, Mongolia.
12Institute of Archaeology, Russian Academy of Sciences, Moscow, Russian Federation. 13Far East Branch of

the Russian Academy of Sciences, Vladivostok, Russian Federation. 14Siberian Branch of the Russian Academy
of Sciences, Ulan-Ude, Russian Federation. 15East Siberian State Institute of Culture, Ulan-Ude, Russian
Federation

Abstract

The Eastern Eurasian Steppe was home to historic empires of nomadic pastoralists, including the Xiongnu and
the Mongols. However, little is known about the region’s population history. Here, we reveal its dynamic
genetic history by analyzing new genome-wide data for 214 ancient individuals spanning 6,000 years. We
identify a pastoralist expansion into Mongolia ca. 3000 BCE, and by the Late Bronze Age, Mongolian
populations were biogeographically structured into three distinct groups, all practicing dairy pastoralism
regardless of ancestry. The Xiongnu emerged from the mixing of these populations and those from surrounding
regions. By comparison, the Mongols exhibit much higher eastern Eurasian ancestry, resembling present-day
Mongolic-speaking populations. Our results illuminate the complex interplay between genetic, sociopolitical,
and cultural changes on the Eastern Steppe.

SYMP18-4 Genetic connections and shared evolution of dark-skinned
indigenous peoples in Asia

Lian Deng1, Yuwen Pan1, Yinan Wang1, Hao Chen1, Kai Yuan1, Sihan Chen2, Dongsheng Lu1, Siti Shuhada
Mokhtar3, Thuhairah Abdul Rahman4, Boon-Peng Hoh5, Shuhua Xu1,6
1Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese

Academy of Sciences, Shanghai, China. 2Human Phenome Institute, Fudan University, Shanghai, China.
3Institute of Medical Molecular Biotechnology, Faculty of Medicine, Universiti Teknologi MARA, Selangor,

Malaysia. 4Clinical Pathology Diagnostic Centre Research Laboratory, Faculty of Medicine, Universiti Teknologi
MARA, Selangor, Malaysia. 5Faculty of Medicine and Health Sciences, UCSI University, Kuala Lumpur, Malaysia.
6State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development,

School of Life Sciences, Fudan University, Shanghai, China

Abstract

Dark-skinned indigenous (DSI) people attract much attention for their unique and outstanding appearance,
nevertheless, their genetic history and adaptive evolution remain mysteries. Here we conducted a population
genomic study to dissect the genetic distinction and connection of broad geographical DSIs. Despite DSI
groups show diverse genetic makeup and large inter-area genetic differentiation, we identified a basal Asian
ancestry (bASN) specifically shared by the Asian DSIs. Interestingly, bASN was relatively enriched in ancient
Asian human genomes dated as early as ~50,000 years before present, and diminished in more recent history.
Notably, bASN was not likely derived from archaic hominins but rather modeled as a survived lineage of the
initial peopling of Asia. Shared adaptations associated with the bASN were identified among DSI groups (e.g.,
LIMS1 for hair morphology) and enriched in neurological functions at an identical locus (e.g., NKAIN3) or
different loci in an identical gene (e.g., TENM4). It remains debatable whether the dark skin phenotype is an
ancestral feature or a result of genetic convergence. We show that the phenotypic convergence of the dark
skin in DSIs could have resulted from parallel evolution (e.g., DDB1), convergence driven by genetic admixture
(e.g., MTHFD1 and RAD18) or novel mutations (e.g., STK11), as well as notably purifying selection (e.g., MC1R).
Our results provided new insights into the initial peopling of Asia and advanced understanding of the
phenotypic convergence of DSI peoples.

Room 5-15 The brown bear (Ursus arctos) demography on Hokkaido Island,
Japan, based on whole-genomic sequence analysis

Yu Endo1, Naoki Osada1, Tsutomu Mano2, Ryuichi Masuda1
1Hokkaido University, Sapporo, Japan. 2Institute of Environmental Sciences, Hokkaido Research Organization,

Sapporo, Japan

Abstract

Previous studies of the brown bear (Ursus arctos) on Hokkaido Island, Japan, showed three allopatrically
distributed mitochondrial lineages and gene flow between the lineages due to male-biased dispersal. In this
study, we determined whole-genomic sequences for six Hokkaido brown bears and analyzed these data along
with previously published genomic sequences from 17 brown bears from other parts of the world. We found
that the Hokkaido population is genetically distinct from other populations, with higher genetic diversity than
in the endangered populations in Western Europe. A reconstruction of historical demography using the
pairwise sequential Markovian coalescent (PSMC) model showed no increase in population size for the
Hokkaido population during the Eemian interglacial period (130,000–114,000 years ago). In a phylogenetic
analysis of the autosomal data, the Hokkaido population emerged a clade distinct from North American and
European populations, showing that it had maintained genetic diversity independently from continental
populations following geographical isolation on the island. This autosomal homogeneity contrasts with the
geographically separate mitochondrial lineages on Hokkaido, and indicates the occurrence of male-driven gene
flow between subpopulations. In addition, ƒ4 statistics and genetic structure analysis suggested that male-
driven gene flow in the Hokkaido population has been affected by Isolation by distance (IBD) and geographic
barriers.

SYMP18-6 Population admixture in the Neolithization of East Asia inferred from
ancient genomes

Chuan-Chao Wang1, Panxin Du2, Guanglin He1, Kongyang Zhu1, Shaoqing Wen3
1Department of Anthropology and Ethnology, Institute of Anthropology, State Key Laboratory of Cellular Stress

Biology, State Key Laboratory of Marine Environmental Science, National Institute for Data Science in Health
and Medicine, Xiamen University, Xiamen, Fujian, China. 2MOE Key Laboratory of Contemporary Anthropology,
Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai,
Shanghai, China. 3Institute of Archaeological Science, Fudan University, Shanghai, Shanghai, China

Abstract

The establishment of the complex societies in Neolithic China appears to have been associated with rapid
population growth and cultural innovation. However, it remains unclear whether substantial human migrations
mediated the culture changes due to a lack of ancient DNA. We here sampled and sequenced 20 individuals
dating to 6000-4000 BP from Gansu and Shandong provinces in the Upper and Lower Yellow River Basin,
respectively, and genotyped more than 1000 present-day individuals from Tibeto-Burman and Tai-Kadai
speaking groups. Through the population genomic analysis, we observed a genetic structure change in the
farming populations of the late Neolithic period compared with the earlier hunter-gatherers. The cultural
innovation in the late Neolithic period had been associated with massive population migration and genetic
admixture from the Neolithic farmers from the middle reaches of the Yellow River.

SYMP18-7 Human back migration from Sundaland to South Asia was driven by
sea-level rises during the Last Glacial Maximum

HIE LIM KIM, Namrata Kalsi, Tanghua Li, Timothy Adam Shaw, Stephan C Schuster, Benjamin Horton
Nanyang Technological University, Singapore, Singapore

Abstract

Rapid sea-level rise between the Last Glacial Maximum (LGM) and the mid-Holocene flooded Sundaland, which
changed dramatically Southeast Asian coastal landscapes. To understand the impact of the geographical
changes on human demography, here we addressed the question by an interdisciplinary approach. We
reconstruct sea level and paleogeography in Southeast Asia since the LGM with fine resolution of time and
inferred human population history using 742 high-coverage whole-genome sequencing datasets from 59 ethnic
groups in Southeast and South Asia. We inferred that rapid sea-level rise, in particular, meltwater pulses 1A
(MWP1A, 4cm/year ~14,500–14,000 years ago) and 1B (MWP1B, 2cm/year ~11,500–11,000 years ago) caused
flooding which broke land bridges and split landmass, and at the same time, multiple population splits
occurred in Southeast Asia. Increasing population density by population expansion in the reduced land area
was inferred, and it might trigger the migration of Southeast Asians from Sundaland toward South Asia as we
found the signal of admixture in the same period. Our novel approach revealed one of the earliest instances of
human migration driven by sea-level rise.

SYMP18-8 Genetic origins and sex-biased admixture of the Huis

Xixian Ma1, Wenjun Yang2, Yang Gao1,3, Yuwen Pan1, Yan Lu1,4, Hao Chen1, Dongsheng Lu1, Shuhua
Xu1,3,4,5,6,7
1Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese

Academy of Sciences, Chinese Academy of Sciences, Shanghai, China. 2Key Laboratory of Fertility Preservation
and Maintenance, the General Hospital, Ningxia Medical University, Yinchuan, China. 3ShanghaiTech
University, Shanghai, China. 4State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for
Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China. 5Center for Excellence
in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China. 6Henan Institute of Medical
and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China. 7Human Phenome Institute, Fudan
University, Shanghai, China

Abstract

The Hui people are unique among Chinese ethnic minorities in that they speak the same language as Han
Chinese (HAN) but practice Islam. However, as the second-largest minority group in China numbering well over
10 million, the Huis are under-represented in genomic studies. Here, we present the first whole-genome
sequencing effort of 234 Hui individuals (NXH) aged over 60 who have been living in Ningxia, where the Huis
are mostly concentrated. NXH are genetically more similar to East Asian than to any other global populations.
In particular, the genetic differentiation between NXH and HAN (FST = 0.0015) is only slightly larger than that
between northern and southern HAN (FST = 0.0010), largely attributed to the western ancestry in NXH (~10%).
Highly-differentiated functional variants between NXH and HAN were identified in genes associated with skin
pigmentation (e.g., SLC24A5), facial morphology (e.g., EDAR), and lipid metabolism (e.g., ABCG8). The Huis
are also distinct from other Muslim groups such as the Uyghurs (FST = 0.0187), especially, NXH derived much
less western ancestry compared with the Uyghurs (~50%). Modeling admixture history indicated that NXH
experienced an episode of two-wave admixture. An ancient admixture occurred ~1,025 years ago, reflecting
the west-east contacts during the Tang and Song Dynasty. A recent admixture occurred ~500 years ago.
Notably, we identified considerable sex-biased admixture, i.e., excess of western males and eastern females
contributing to the NXH gene pool. The origins and the genomic diversity of the Hui people imply the complex
history of contacts between western and eastern Eurasians.

SYMP18-9 Genetic continuity of Indo-Iranian speakers since Iron Age in
Southern Central Asia

Perle Guarino-Vignon 1, Nina Marchi1,2, Evelyne Heyer1, Céline Bon1
1UMR7206 Éco-Anthropologie, MNHN, Paris, France. 2CMPG group, Institute of Ecology and Evolution (IEE -

UNIBE), Bern, Switzerland

Abstract

Since prehistoric times, South Central Asia has been a region at the crossroads of the movement of people,
cultures, and goods. Today, Central Asia is populated by populations divided into two cultural and linguistic
groups: the Indo-Iranian group and the Turko-Mongolian group. Genetics unveiled that migrations from East
Asia contributed to the spread of Turko-Mongolian populations in Central Asia and to the partial replacement of
Indo-Iranian population. However, the origin of the latter is still little known. To shed light on this, we compare
the genetic data on two current-day populations– Yaghnobis and Tajiks – with the increasing number of
genome-wide data from published ancient individuals. Using PCA, Admixture, f3 and D-statistics we show that
the present Indo-Iranian populations from Central Asia show a strong genetic continuity with the Iron Age
samples from Turkmenistan and Tajikistan. With qpAdm, we model Yaghnobis as a mixture of 93% Iron Age
individuals from Turkmenistan and 7% from Baikal. For the Tajiks, we observe a more important Baikal ancestry
and an additional admixture event with a South Asian population. Our results therefore suggest that beside
complex history and settlement, Central Asia shows a remarkable genetic continuity since the Iron Age, with
only limited gene flow.