Phylogeographic structure, cryptic speciation and demographic history of the sharpbelly (Hemiculter leucisculus), a freshwater habitat generalist from southern China

AbstractWe have used phylogeographic methods to investigate the genetic structure and population history of the endangered Himalayan snowcock (Tetraogallus himalayensis) in northwestern China. The mitochondrial cytochrome b gene was sequenced of 102 individuals sampled throughout the distribution range. In total, we found 26 different haplotypes defined by 28 polymorphic sites. Phylogenetic analyses indicated that the samples were divided into two major haplogroups corresponding to one western and one eastern clade. The divergence time between these major clades was estimated to be approximately one million years. An analysis of molecular variance showed that 40% of the total genetic variability was found within local populations, 12% among populations within regional groups and 48% among groups. An analysis of the demographic history of the populations suggested that major expansions have occurred in the Himalayan snowcock populations and these correlate mainly with the first and the second largest glaciations during the Pleistocene. In addition, the data indicate that there was a population expansion of the Tianshan population during the uplift of the Qinghai-Tibet Plateau, approximately 2 million years ago.

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

Frontiers in Genetics ◽

10.3389/fgene.2021.735084 ◽

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.

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Impact of Quaternary climatic changes and interspecific competition on the demographic history of a highly mobile generalist carnivore, the coyote

Biology Letters ◽

10.1098/rsbl.2012.0162 ◽

2012 ◽

Vol 8 (4) ◽

pp. 644-647 ◽

Cited By ~ 22

Author(s):

Stephan Koblmüller ◽

Robert K. Wayne ◽

Jennifer A. Leonard

Keyword(s):

Genetic Structure ◽

Interspecific Competition ◽

Environmental Changes ◽

Late Quaternary ◽

Demographic History ◽

Climatic Changes ◽

Phylogeographic Structure ◽

Quaternary Period ◽

Generalist Species ◽

History Of

Recurrent cycles of climatic change during the Quaternary period have dramatically affected the population genetic structure of many species. We reconstruct the recent demographic history of the coyote ( Canis latrans ) through the use of Bayesian techniques to examine the effects of Late Quaternary climatic perturbations on the genetic structure of a highly mobile generalist species. Our analysis reveals a lack of phylogeographic structure throughout the range but past population size changes correlated with climatic changes. We conclude that even generalist carnivorous species are very susceptible to environmental changes associated with climatic perturbations. This effect may be enhanced in coyotes by interspecific competition with larger carnivores.

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Fine-scale Population Structure and Demographic History of Han Chinese Inferred from Haplotype Network of 111,000 Genomes

10.1101/2020.07.03.166413 ◽

2020 ◽

Author(s):

Ao Lan ◽

Kang Kang ◽

Senwei Tang ◽

Xiaoli Wu ◽

Lizhong Wang ◽

...

Keyword(s):

Population Structure ◽

Southern China ◽

Demographic History ◽

Haplotype Network ◽

Han Chinese ◽

Fine Scale ◽

Genetic Barrier ◽

Scale Population ◽

History Of ◽

Linguistic Segregation

ABSTRACTHan Chinese is the most populated ethnic group across the globe with a comprehensive substructure that resembles its cultural diversification. Studies have constructed the genetic polymorphism spectrum of Han Chinese, whereas high-resolution investigations are still missing to unveil its fine-scale substructure and trace the genetic imprints for its demographic history. Here we construct a haplotype network consisted of 111,000 genome-wide genotyped Han Chinese individuals from direct-to-consumer genetic testing and over 1.3 billion identity-by-descent (IBD) links. We observed a clear separation of the northern and southern Han Chinese and captured 5 subclusters and 17 sub-subclusters in haplotype network hierarchical clustering, corresponding to geography (especially mountain ranges), immigration waves, and clans with cultural-linguistic segregation. We inferred differentiated split histories and founder effects for population clans Cantonese, Hakka, and Minnan-Chaoshanese in southern China, and also unveiled more recent demographic events within the past few centuries, such as Zou Xikou and Chuang Guandong. The composition shifts of the native and current residents of four major metropolitans (Beijing, Shanghai, Guangzhou, and Shenzhen) imply a rapidly vanished genetic barrier between subpopulations. Our study yields a fine-scale population structure of Han Chinese and provides profound insights into the nation’s genetic and cultural-linguistic multiformity.

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Low Nucleotide Diversity in Chimpanzees and Bonobos

Genetics ◽

10.1093/genetics/164.4.1511 ◽

2003 ◽

Vol 164 (4) ◽

pp. 1511-1518 ◽

Cited By ~ 1

Author(s):

Ning Yu ◽

Michael I Jensen-Seaman ◽

Leona Chemnick ◽

Judith R Kidd ◽

Amos S Deinard ◽

...

Keyword(s):

Nucleotide Diversity ◽

Nuclear Dna ◽

Demographic History ◽

Nuclear Genome ◽

Limited Data ◽

Effective Population ◽

East Central ◽

Dna Diversity ◽

History Of ◽

Mtdna Diversity

Abstract Comparison of the levels of nucleotide diversity in humans and apes may provide much insight into the mechanisms of maintenance of DNA polymorphism and the demographic history of these organisms. In the past, abundant mitochondrial DNA (mtDNA) polymorphism data indicated that nucleotide diversity (π) is more than threefold higher in chimpanzees than in humans. Furthermore, it has recently been claimed, on the basis of limited data, that this is also true for nuclear DNA. In this study we sequenced 50 noncoding, nonrepetitive DNA segments randomly chosen from the nuclear genome in 9 bonobos and 17 chimpanzees. Surprisingly, the π value for bonobos is only 0.078%, even somewhat lower than that (0.088%) for humans for the same 50 segments. The π values are 0.092, 0.130, and 0.082% for East, Central, and West African chimpanzees, respectively, and 0.132% for all chimpanzees. These values are similar to or at most only 1.5 times higher than that for humans. The much larger difference in mtDNA diversity than in nuclear DNA diversity between humans and chimpanzees is puzzling. We speculate that it is due mainly to a reduction in effective population size (Ne) in the human lineage after the human-chimpanzee divergence, because a reduction in Ne has a stronger effect on mtDNA diversity than on nuclear DNA diversity.

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Speciation history of a species complex of Primulina eburnea (Gesneriaceae) from limestone karsts of southern China, a biodiversity hot spot

Evolutionary Applications ◽

10.1111/eva.12495 ◽

2017 ◽

Vol 10 (9) ◽

pp. 919-934 ◽

Cited By ~ 9

Author(s):

Jing Wang ◽

Bin Ai ◽

Hanghui Kong ◽

Ming Kang

Keyword(s):

Species Complex ◽

Southern China ◽

Hot Spot ◽

History Of

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Corrigendum to: Demographic history of the human commensal Drosophila melanogaster

Genome Biology and Evolution ◽

10.1093/gbe/evab046 ◽

2021 ◽

Vol 13 (3) ◽

Author(s):

J Roman Arguello ◽

Stefan Laurent ◽

Andrew G Clark

Keyword(s):

Drosophila Melanogaster ◽

Demographic History ◽

History Of

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Vernacular Capitalism and Intellectual History in a Gujarati Account of China, 1860–68

The Journal of Asian Studies ◽

10.1017/s0021911820003678 ◽

2021 ◽

pp. 1-26

Author(s):

Michael O'Sullivan

Keyword(s):

South China Sea ◽

Intellectual History ◽

Southern China ◽

Western Indian Ocean ◽

Port Cities ◽

Late Qing ◽

Modern Capitalism ◽

Late Qing China ◽

History Of ◽

The Many

This article examines one of the earliest Gujarati travelogues concerning China, written by Damodar Ishwardas—a Hindu resident of Bombay and a clerk for a Sunni Khoja commercial firm—and published in Bombay in 1868. Based on a three-year trip to the port cities of southern China, Ishwardas's text runs close to 400 pages and was patronized by a prominent stratum of Bombay's Gujarati-speaking commercial and bureaucratic elite. The primary intervention in this article is to analyze Ishwardas's account as a neglected relic of vernacular capitalism and vernacular intellectual history. Furthermore, the text presents an opportunity to reexamine the history of the Indian intellectual and mercantile engagement with late Qing China, especially before anticolonial nationalism and pan-Asianism supplied new paradigms for Indian writing on East Asia beginning around 1900. It further points to the many unstudied Indian materials that have yet to be integrated into the study of modern capitalism in the regions from the South China Sea to the western Indian Ocean.

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Reference genome and demographic history of the most endangered marine mammal, the vaquita

Molecular Ecology Resources ◽

10.1111/1755-0998.13284 ◽

2020 ◽

Author(s):

Phillip A. Morin ◽

Frederick I. Archer ◽

Catherine D. Avila ◽

Jennifer R. Balacco ◽

Yury V. Bukhman ◽

...

Keyword(s):

Marine Mammal ◽

Reference Genome ◽

Demographic History ◽

History Of

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Temporal fluctuations of Y-chromosomal variation in Bos taurus

Biology Letters ◽

10.1098/rsbl.2008.0342 ◽

2008 ◽

Vol 4 (6) ◽

pp. 752-754 ◽

Cited By ~ 29

Author(s):

Emma Svensson ◽

Anders Götherström

Keyword(s):

Single Nucleotide Polymorphism ◽

Bos Taurus ◽

Demographic History ◽

Northern Europe ◽

Chromosomal Gene ◽

Chromosomal Variation ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Domestic Species ◽

History Of

Phylogeography has recently become more abundant in studies of demographic history of both wild and domestic species. A single nucleotide polymorphism (SNP) in the intron of the Y-chromosomal gene UTY19 displays a north–south gradient in modern cattle. Support for this geographical distribution of haplogroups has previously also been seen in ancient cattle from Germany. However, when analysing 38 historic remains of domestic bulls and three aurochs from northern Europe for this SNP we found no such association. Instead, we noted extensive amounts of temporal variation that can be attributed to transportation of cattle and late breed formation.

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