scholarly journals Genomic Insights into the Demographic History of Southern Chinese

2020 ◽  
Author(s):  
Xiufeng Huang ◽  
Zi-Yang Xia ◽  
Xiaoyun Bin ◽  
Guanglin He ◽  
Jianxin Guo ◽  
...  
Keyword(s):  
Southeast Asia ◽  
Southern China ◽  
Demographic History ◽  
Phylogenetic Analyses ◽  
East Asian ◽  
Genetic Profile ◽  
East Asians ◽  
Southeast Asians ◽  
Southern Chinese ◽  
East And Southeast Asia

ABSTRACTSouthern China is the birthplace of rice-cultivating agriculture, different language families, and human migrations that facilitated these cultural diffusions. The fine-scale demographic history in situ, however, remains unclear. To comprehensively cover the genetic diversity in East and Southeast Asia, we generated genome-wide SNP data from 211 present-day Southern Chinese and co-analyzed them with more than 1,200 ancient and modern genomes. We discover that the previously described ‘Southern East Asian’ or ‘Yangtze River Farmer’ lineage is monophyletic but not homogeneous, comprising four regionally differentiated sub-ancestries. These ancestries are respectively responsible for the transmission of Austronesian, Kra-Dai, Hmong-Mien, and Austroasiatic languages and their original homelands successively distributed from East to West in Southern China. Multiple phylogenetic analyses support that the earliest living branching among East Asian-related populations is First Americans (∼27,700 BP), followed by the pre-LGM differentiation between Northern and Southern East Asians (∼23,400 BP) and the pre-Neolithic split between Coastal and Inland Southern East Asians (∼16,400 BP). In North China, distinct coastal and inland routes of south-to-north gene flow had established by the Holocene, and further migration and admixture formed the genetic profile of Sinitic speakers by ∼4,000 BP. Four subsequent massive migrations finalized the complete genetic structure of present-day Southern Chinese. First, a southward Sinitic migration and the admixture with Kra-Dai speakers formed the ‘Sinitic Cline’. Second, a bi-directional admixture between Hmong-Mien and Kra-Dai speakers gave rise to the ‘Hmong-Mien Cline’ in the interior of South China between ∼2,000 and ∼1,000 BP. Third, a southwestward migration of Kra-Dai speakers in recent ∼2,000 years impacted the genetic profile for the majority of Mainland Southeast Asians. Finally, an admixture between Tibeto-Burman incomers and indigenous Austroasiatic speakers formed the Tibeto-Burman speakers in Southeast Asia by ∼2,000 BP.

Picturing Commerce in and from the East Asian Maritime Circuits, 1550-1800

2019 ◽  
Keyword(s):  
Southeast Asia ◽  
Early Modern ◽  
East Asia ◽  
East Asian ◽  
Musical Instruments ◽  
American Colonies ◽  
East And Southeast Asia ◽  
Ceramic Vessels ◽  
The Look ◽  
Visual Cultures

Combining strikingly new scholarship by art historians, historians, and ethnomusicologists, this interdisciplinary volume illuminates trade ties within East Asia, and from East Asia outwards, in the years 1550 to 1800. While not encyclopedic, the selected topics greatly advance our sense of this trade picture. Throughout the book, multi-part trade structures are excavated; the presence of European powers within the Asian trade nexus features as part of this narrative. Visual goods are highlighted, including lacquerwares, paintings, prints, musical instruments, textiles, ivory sculptures, unfired ceramic portrait figurines, and Chinese, Japanese, Korean, and Southeast Asian ceramic vessels. These essays underscore the significance of Asian industries producing multiples, and the rhetorical charge of these goods, shifting in meaning as they move. Everyday commodities are treated as well; for example, the trans-Pacific trade in contraband mercury, used in silver refinement, is spelled out in detail. Building reverberations between merchant networks, trade goods, and the look of the objects themselves, this richly-illustrated book brings to light the Asian trade engine powering the early modern visual cultures of East and Southeast Asia, the American colonies, and Europe.

scholarly journals Analysis of Five Deep-sequenced Trio-genomes of the Peninsular Malaysia Orang Asli and North Borneo Populations

2019 ◽  
Author(s):  
Lian Deng ◽  
Haiyi Lou ◽  
Xiaoxi Zhang ◽  
Thiruvahindrapuram Bhooma ◽  
Dongsheng Lu ◽  
...  
Keyword(s):  
Southeast Asia ◽  
Demographic History ◽  
Peninsular Malaysia ◽  
Population Diversity ◽  
Population History ◽  
Indigenous Populations ◽  
Pedigree Information ◽  
Orang Asli ◽  
Southeast Asians ◽  
North Borneo

Abstract Background Recent advances in genomic technologies have facilitated genome-wide investigation of human genetic variations. However, most efforts have focused on the major populations, yet trio genomes of indigenous populations from Southeast Asia have been under-investigated. Results We analyzed the whole-genome deep sequencing data (~30×) of five native trios from Malaysia, and discovered approximately 6.9 million single nucleotide variants (SNVs), 1.2 million small insertions and deletions (indels), and 9,000 copy number variants (CNVs) in the 15 samples. We found 2.7% SNVs, 2.3% indels and 22% CNVs were novel, implying the insufficient coverage of population diversity in existing databases. We identified a higher proportion of novel variants in the Orang Asli (OA) samples, i.e., the indigenous people from Peninsular Malaysia, than that of the North Bornean (NB) samples, likely due to more complex demographic history and long-time isolation of the OA groups. We used the pedigree information to identify autosomal de novo variants and estimated the mutation rates to be 0.81×10-8–1.33×10-8 , 1.0×10-9–2.9×10-9, and ~0.001 per site per generation for SNVs, indels, and CNVs, respectively. The trio-genomes also allowed for accurate haplotype phasing with high accuracy, which serves as references to the future genomic studies of OA and NB populations. In addition, high-frequency inherited CNVs specific to OA or NB were identified. One example was a 50-kb duplication in DEFA1B detected only in the Negrito trios, implying plausible effects on host defense against the exposure of diverse microbial in tropical rainforest environment of these hunter-gatherers. The CNVs shared between OA and NB groups were much fewer than those specific to each group. Nevertheless, we identified a 142-kb duplication in AMY1A in all the 15 samples, and this gene is associated with the high-starch diet. Moreover, novel insertions shared with archaic hominids were identified in our samples. Conclusion Our study presents a full catalogue of the genome variants of the native Malaysian populations, which is a complement of the genome diversity in Southeast Asians. It implies specific population history of the native inhabitants, and demonstrated the necessity of more genome sequencing efforts on the multi-ethnic native groups of Malaysia and Southeast Asia.

scholarly journals Genomic Insight Into the Population Structure and Admixture History of Tai-Kadai-Speaking Sui People in Southwest China

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiaoyun Bin ◽  
Rui Wang ◽  
Youyi Huang ◽  
Rongyao Wei ◽  
Kongyang Zhu ◽  
...  
Keyword(s):  
Population Genetic ◽  
Southwest China ◽  
Yellow River ◽  
Southern China ◽  
Demographic History ◽  
Indigenous Populations ◽  
Guizhou Province ◽  
East Asians ◽  
Genome Wide ◽  
History Of

Sui people, which belong to the Tai-Kadai-speaking family, remain poorly characterized due to a lack of genome-wide data. To infer the fine-scale population genetic structure and putative genetic sources of the Sui people, we genotyped 498,655 genome-wide single-nucleotide polymorphisms (SNPs) using SNP arrays in 68 Sui individuals from seven indigenous populations in Guizhou province and Guangxi Zhuang Autonomous Region in Southwest China and co-analyzed with available East Asians via a series of population genetic methods including principal component analysis (PCA), ADMIXTURE, pairwise Fst genetic distance, f-statistics, qpWave, and qpAdm. Our results revealed that Guangxi and Guizhou Sui people showed a strong genetic affinity with populations from southern China and Southeast Asia, especially Tai-Kadai- and Hmong-Mien-speaking populations as well as ancient Iron Age Taiwan Hanben, Gongguan individuals supporting the hypothesis that Sui people came from southern China originally. The indigenous Tai-Kadai-related ancestry (represented by Li), Northern East Asian-related ancestry, and Hmong-Mien-related lineage contributed to the formation processes of the Sui people. We identified the genetic substructure within Sui groups: Guizhou Sui people were relatively homogeneous and possessed similar genetic profiles with neighboring Tai-Kadai-related populations, such as Maonan. While Sui people in Yizhou and Huanjiang of Guangxi might receive unique, additional gene flow from Hmong-Mien-speaking populations and Northern East Asians, respectively, after the divergence within other Sui populations. Sui people could be modeled as the admixture of ancient Yellow River Basin farmer-related ancestry (36.2–54.7%) and ancient coastal Southeast Asian-related ancestry (45.3–63.8%). We also identified the potential positive selection signals related to the disease susceptibility in Sui people via integrated haplotype score (iHS) and number of segregating sites by length (nSL) scores. These genomic findings provided new insights into the demographic history of Tai-Kadai-speaking Sui people and their interaction with neighboring populations in Southern China.

scholarly journals Out of Asia: Mitochondrial evolutionary history of the globally introduced supralittoral isopod Ligia exotica

2017 ◽  
Author(s):  
Luis A Hurtado ◽  
Mariana Mateos ◽  
Chang Wang ◽  
Carlos A Santamaria ◽  
Jongwoo Jung ◽  
...  
Keyword(s):  
Southeast Asia ◽  
16S Rdna ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Marine Species ◽  
Genetic Lineages ◽  
East And Southeast Asia ◽  
History Of ◽  
Marine Vessels ◽  
Establishment Process

The native ranges and invasion histories of many marine species remain elusive due to a dynamic dispersal process via marine vessels. Molecular markers can aid in identification of native ranges and elucidation of the introduction and establishment process. The supralittoral isopod Ligia exotica has a wide tropical and subtropical distribution, frequently found in harbors and ports around the globe. This isopod is hypothesized to have an Old World origin, from where it was unintentionally introduced to other regions via wooden ships and solid ballast. Its native range, however, remains uncertain. Recent molecular studies uncovered the presence of two highly divergent lineages of L. exotica in East Asia, and suggest this region is a source of nonindigenous populations. In this study, we conducted phylogenetic analyses (Maximum Likelihood and Bayesian) of a fragment of the mitochondrial 16S ribosomal (r)DNA gene using a dataset of this isopod that greatly expanded previous representation from Asia and putative nonindigenous populations around the world. For a subset of samples, sequences of 12S rDNA and NaK were also obtained and analyzed together with 16S rDNA. Our results show that L. exotica is comprised of several highly divergent genetic lineages, which probably represent different species. Most of the 16S rDNA genetic diversity (48 haplotypes) was detected in East and Southeast Asia. Only seven haplotypes were observed outside this region (in the Americas, Hawai’i, Africa and India), which were identical or closely related to haplotypes found in East and Southeast Asia. Phylogenetic patterns indicate the L. exotica clade originated and diversified in East and Southeast Asia, and only members of one of the divergent lineages have spread out of this region, recently, suggesting the potential to become invasive is phylogenetically constrained.

scholarly journals Hmong-Mien Languages

Linguistics ◽  
2014 ◽  
Author(s):  
David Mortensen
Keyword(s):  
United States ◽  
Southeast Asia ◽  
Southern China ◽  
The United States ◽  
Language Family ◽  
Western Countries ◽  
Worldwide Distribution ◽  
East And Southeast Asia ◽  
French Guyana ◽  
Northern Highlands

Hmong-Mien is a compact language family of East and Southeast Asia. Its speakers are found primarily in southern China and the northern highlands of Vietnam, Thailand, Laos, and Myanmar (Burma). Most speakers of Hmong-Mien languages belong to the so-called Miao and Yao ethnicities (or nationalities). Due to geopolitical circumstances, many speakers of two Hmong-Mien languages from Laos—Hmong and Iu Mien—emigrated to Western countries (the United States, Canada, Australia, Argentina, France, French Guyana, and Germany) between 1970 and 1998, leading to the current worldwide distribution of this language family. Hmong-Mien has two primary branches: Hmongic and Mienic. Hmongic is larger (in terms of number of speakers) and has greater internal diversity. It has also been the focus of more efforts at documentation. As a result, more literature is available on Hmongic languages than Mienic languages. This bibliography represents an attempt to include as many resources on Mienic as possible but nevertheless reflects this fundamental imbalance in sources.

scholarly journals Analysis of Five Deep-sequenced Trio-genomes of the Peninsular Malaysia Orang Asli and North Borneo Populations

2019 ◽  
Author(s):  
Lian Deng ◽  
Haiyi Lou ◽  
Xiaoxi Zhang ◽  
Thiruvahindrapuram Bhooma ◽  
Dongsheng Lu ◽  
...  
Keyword(s):  
Southeast Asia ◽  
Demographic History ◽  
Peninsular Malaysia ◽  
Population Diversity ◽  
Population History ◽  
Indigenous Populations ◽  
Pedigree Information ◽  
Orang Asli ◽  
Southeast Asians ◽  
North Borneo

Abstract Background Recent advances in genomic technologies have facilitated genome-wide investigation of human genetic variations. However, most efforts have focused on the major populations, yet trio genomes of indigenous populations from Southeast Asia have been under-investigated. Results We analyzed the whole-genome deep sequencing data (~30×) of five native trios from Malaysia, and discovered approximately 6.9 million single nucleotide variants (SNVs), 1.2 million small insertions and deletions (indels), and 9,000 copy number variants (CNVs) in the 15 samples. We found 2.7% SNVs, 2.3% indels and 22% CNVs were novel, implying the insufficient coverage of population diversity in existing databases. We identified a higher proportion of novel variants in the Orang Asli (OA) samples, i.e., the indigenous people from Peninsular Malaysia, than that of the North Bornean (NB) samples, likely due to more complex demographic history and long-time isolation of the OA groups. We used the pedigree information to identify autosomal de novo variants and estimated the mutation rates to be 0.81×10-8–1.33×10-8 , 1.0×10-9–2.9×10-9, and ~0.001 per site per generation for SNVs, indels, and CNVs, respectively. The trio-genomes also allowed for accurate haplotype phasing with high accuracy, which serves as references to the future genomic studies of OA and NB populations. In addition, high-frequency inherited CNVs specific to OA or NB were identified. One example was a 50-kb duplication in DEFA1B detected only in the Negrito trios, implying plausible effects on host defense against the exposure of diverse microbial in tropical rainforest environment of these hunter-gatherers. The CNVs shared between OA and NB groups were much fewer than those specific to each group. Nevertheless, we identified a 142-kb duplication in AMY1A in all the 15 samples, and this gene is associated with the high-starch diet. Moreover, novel insertions shared with archaic hominids were identified in our samples. Conclusion Our study presents a full catalogue of the genome variants of the native Malaysian populations, which is a complement of the genome diversity in Southeast Asians. It implies specific population history of the native inhabitants, and demonstrated the necessity of more genome sequencing efforts on the multi-ethnic native groups of Malaysia and Southeast Asia.

Phylogeny and biogeography of the Enhydris clade (Serpentes: Homalopsidae)

Zootaxa ◽  
2010 ◽  
Vol 2452 (1) ◽  
pp. 18 ◽  
Author(s):  
DARYL R. KARNS ◽  
VIMOKSALEHI LUKOSCHEK ◽  
JENNIFER OSTERHAGE ◽  
JOHN C. MURPHY ◽  
HAROLD K. VORIS
Keyword(s):  
Southeast Asia ◽  
Southern China ◽  
Phylogenetic Analyses ◽  
Nuclear Gene ◽  
Sensu Stricto ◽  
Substantial Portion ◽  
Closely Related Species ◽  
Molecular Phylogenetic ◽  
Phylogenetic Hypotheses ◽  
Water Snakes

Previous molecular phylogenetic hypotheses for the Homalopsidae, the Oriental-Australian Rear-fanged Water Snakes indicate that Enhydris, the most speciose genus in the Homalopsidae (22 of 37 species), is polyphyletic and may consist of five separate lineages. We expand on earlier phylogenetic hypotheses using three mitochondrial fragments and one nuclear gene, previously shown to be rapidly evolving in snakes, to determine relationships among six closely related species: Enhydris enhydris, E. subtaeniata, E. chinensis, E. innominata, E. jagorii, and E. longicauda. Four of these species (E. subtaeniata, E. innominata, E. jagorii, and E. longicauda) are restricted to river basins in Indochina, while E. chinensis is found in southern China and E. enhydris is widely distributed from India across Southeast Asia. Our phylogenetic analyses indicate that these species are monophyletic and we recognize this clade as the Enhydris clade sensu stricto for nomenclatural reasons. Our analysis shows that E. chinensis is sister-species to a well-supported clade comprising the remaining species of the Enhydris clade (mean p distance between E. chinensis and other in-group taxa was 13.1%, range: 12.7-13.4%). Enhydris innominata, E. longicauda and E. jagorii also formed a strongly supported clade with very low interspecific p distances (mean 0.28%, range: 0–0.46%). We were unable to resolve relationships between E. enhydris and E. subtaeniata (mean divergence of 9.4%, range: 9.2-9.7%), and between these two species and E. innominata, E. longicauda and E. jagorii. We summarize classical morphological (scalation and coloration) characteristics of these species in the context of the molecular phylogeny. The Enhydris clade comprises a substantial portion of the vertebrate biomass of Southeast Asia and we discuss aspects of its biogeography, morphology and systematics.

scholarly journals Biogeography of Drosophila (Diptera: Drosophilidae) in East and Southeast Asia

2015 ◽  
Vol 15 (1) ◽  
Author(s):  
Fu-Guo Robert Liu ◽  
Shun-Chern Tsaur ◽  
Hsiao-Ting Huang
Keyword(s):  
Population Structure ◽  
Southeast Asia ◽  
Biological Diversity ◽  
Phylogenetic Analyses ◽  
Large Population ◽  
Drosophila Species ◽  
Population Isolation ◽  
Drosophila Albomicans ◽  
Sex Comb ◽  
East And Southeast Asia

Abstract The causes of high biological diversity in biodiversity hotspots have long been a major subject of study in conservation biology. To investigate this matter, we conducted a phylogeographic study of five Drosophila (Diptera: Drosophilidae) species from East and Southeast Asia: Drosophila albomicans Duda , D. formosana Duda, D. immigrans Sturtevant, D. melanogaster Meigen, and D. simulans Sturtevant. We collected 185 samples from 28 localities in eight countries. From each collected individual, we sequenced the autosomal extra sex comb gene ( esc ) and seven mitochondrial genes, including nicotinamide adenine dinucleotide hydrate-reductase dehydrogenase subunit 4 ( ND4 ), ND4L , tRNA-His , tRNA-Pro , tRNA-Thr , partial ND5 , and partial ND6 . Phylogenetic analyses using maximum- likelihood and Bayesian methods revealed interesting population structure and identified the existence of two distinct D. formosana lineages (Southeast Asian and Taiwanese populations). Genetic differentiation among groups of D. immigrans suggests the possibility of endemic speciation in Taiwan. In contrast, D. melanogaster remained one extensively large population throughout East and Southeast Asia, including nearby islets. A molecular clock was used to estimate divergence times, which were compared with past geographical events to infer evolutionary scenarios. Our findings suggest that interglacial periods may have caused population isolation, thus enhancing population differentiation more strongly for some of the Drosophila species. The population structure of each Drosophila species in East and Southeast Asia has been influenced by past geographic events.

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