scholarly journals Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Fan Jiang ◽  
Ruiyi Lin ◽  
Changyi Xiao ◽  
Tanghui Xie ◽  
Yaoxin Jiang ◽  
...  
Keyword(s):  
Gene Flow ◽  
South Asia ◽  
South Asian ◽  
Demographic History ◽  
Nervous System Development ◽  
Chromosome 1 ◽  
Whole Genome ◽  
Chinese Populations ◽  
Asian Populations ◽  
History Of

Abstract Background The most prolific duck genetic resource in the world is located in Southeast/South Asia but little is known about the domestication and complex histories of these duck populations. Results Based on whole-genome resequencing data of 78 ducks (Anas platyrhynchos) and 31 published whole-genome duck sequences, we detected three geographic distinct genetic groups, including local Chinese, wild, and local Southeast/South Asian populations. We inferred the demographic history of these duck populations with different geographical distributions and found that the Chinese and Southeast/South Asian ducks shared similar demographic features. The Chinese domestic ducks experienced the strongest population bottleneck caused by domestication and the last glacial maximum (LGM) period, whereas the Chinese wild ducks experienced a relatively weak bottleneck caused by domestication only. Furthermore, the bottleneck was more severe in the local Southeast/South Asian populations than in the local Chinese populations, which resulted in a smaller effective population size for the former (7100–11,900). We show that extensive gene flow has occurred between the Southeast/South Asian and Chinese populations, and between the Southeast Asian and South Asian populations. Prolonged gene flow was detected between the Guangxi population from China and its neighboring Southeast/South Asian populations. In addition, based on multiple statistical approaches, we identified a genomic region that included three genes (PNPLA8, THAP5, and DNAJB9) on duck chromosome 1 with a high probability of gene flow between the Guangxi and Southeast/South Asian populations. Finally, we detected strong signatures of selection in genes that are involved in signaling pathways of the nervous system development (e.g., ADCYAP1R1 and PDC) and in genes that are associated with morphological traits such as cell growth (e.g., IGF1R). Conclusions Our findings provide valuable information for a better understanding of the domestication and demographic history of the duck, and of the gene flow between local duck populations from Southeast/South Asia and China.

scholarly journals Whole genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection

2015 ◽  
Author(s):  
PingHsun Hsieh ◽  
Krishna R Veeramah ◽  
Joseph Lachance ◽  
Sarah A Tishkoff ◽  
Jeffrey D Wall ◽  
...  
Keyword(s):  
Gene Flow ◽  
Natural Selection ◽  
Muscle Development ◽  
Demographic History ◽  
Single Pulse ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Anatomically Modern Humans ◽  
History Of ◽  
African Pygmies

African Pygmies practicing a mobile hunter-gatherer lifestyle are phenotypically and genetically diverged from other anatomically modern humans, and they likely experienced strong selective pressures due to their unique lifestyle in the Central African rainforest. To identify genomic targets of adaptation, we sequenced the genomes of four Biaka Pygmies from the Central African Republic and jointly analyzed these data with the genome sequences of three Baka Pygmies from Cameroon and nine Yoruba famers. To account for the complex demographic history of these populations that includes both isolation and gene flow, we fit models using the joint allele frequency spectrum and validated them using independent approaches. Our two best-fit models both suggest ancient divergence between the ancestors of the farmers and Pygmies, 90,000 or 150,000 years ago. We also find that bi-directional asymmetric gene-flow is statistically better supported than a single pulse of unidirectional gene flow from farmers to Pygmies, as previously suggested. We then applied complementary statistics to scan the genome for evidence of selective sweeps and polygenic selection. We found that conventional statistical outlier approaches were biased toward identifying candidates in regions of high mutation or low recombination rate. To avoid this bias, we assigned P-values for candidates using whole-genome simulations incorporating demography and variation in both recombination and mutation rates. We found that genes and gene sets involved in muscle development, bone synthesis, immunity, reproduction, cell signaling and development, and energy metabolism are likely to be targets of positive natural selection in Western African Pygmies or their recent ancestors.

scholarly journals “Like Sugar in Milk”: Reconstructing the genetic history of the Parsi population

2017 ◽  
Author(s):  
Gyaneshwer Chaubey ◽  
Qasim Ayub ◽  
Niraj Rai ◽  
Satya Prakash ◽  
Veena Mushrif-Tripathy ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
South Asia ◽  
South Asian ◽  
Dna Markers ◽  
South Asians ◽  
Demographic History ◽  
Middle Eastern ◽  
Religious Community ◽  
Genetic Studies ◽  
History Of

AbstractBackgroundThe Parsis, one of the smallest religious community in the world, reside in South Asia. Previous genetic studies on them, although based on low resolution markers, reported both Iranian and Indian ancestries. To understand the population structure and demographic history of this group in more detail, we analyzed Indian and Pakistani Parsi populations using high-resolution autosomal and uniparental (Y-chromosomal and mitochondrial DNA) markers. Additionally, we also assayed 108 mitochondrial DNA markers among 21 ancient Parsi DNA samples excavated from Sanjan, in present day Gujarat, the place of their original settlement in India.ResultsOur extensive analyses indicated that among present-day populations, the Parsis are genetically closest to Middle Eastern (Iranian and the Caucasus) populations rather than their South Asian neighbors. They also share the highest number of haplotypes with present-day Iranians and we estimate that the admixture of the Parsis with Indian populations occurred ∼1,200 years ago. Enriched homozygosity in the Parsi reflects their recent isolation and inbreeding. We also observed 48% South-Asian-specific mitochondrial lineages among the ancient samples, which might have resulted from the assimilation of local females during the initial settlement.ConclusionsWe show that the Parsis are genetically closest to the Neolithic Iranians, followed by present-day Middle Eastern populations rather than those in South Asia and provide evidence of sex-specific admixture from South Asians to the Parsis. Our results are consistent with the historically-recorded migration of the Parsi populations to South Asia in the 7thcentury and in agreement with their assimilation into the Indian sub-continent’s population and cultural milieu “like sugar in milk”. Moreover, in a wider context our results suggest a major demographic transition in West Asia due to Islamic-conquest.

Towards a More Varied Picture of Slavery

2021 ◽  
Vol 6 (2) ◽  
pp. 249-261
Author(s):  
Jessica Hinchy ◽  
Girija Joshi
Keyword(s):  
South Asia ◽  
South Asian ◽  
Historical Memory ◽  
Multiple Forms ◽  
Subaltern Studies ◽  
Crucial Question ◽  
Revenue Collection ◽  
History Of ◽  
Forms Of Violence ◽  
Slavery Studies

Abstract Indrani Chatterjee’s ground-breaking research has shown the centrality of obligation and provision to historical forms of slavery in South Asia, deepening our understanding of slave-using societies beyond the plantation systems that have dominated historiography, as well as historical memory. In this interview, Chatterjee explains why the crucial question in the context of South Asian slavery was: who do you serve and for what purpose? Enslavers were obliged to materially provide for their slaves, in return for the enslaved person’s service, labor and loyalty, creating varied relationships of dependence. By foregrounding the complex set of relationships and obligations in which slaves were enmeshed, Chatterjee seeks to “make people out of laborers.” This has led her to rethink the ways that resistance and agency have been conceptualized in slavery studies and Subaltern Studies, emphasizing the relationships within which a person became an agent. Her research has also deepened our understanding of colonialism and slavery. British colonizers generally ignored slaves’ entitlements to certain labor or taxation exemptions from the state, and colonial revenue-collection made the already-burdened doubly burdened. But in a hetero-temporal colonial context, older ways of identifying and forms of relationships endured. Chatterjee argues that this history of the provision of survival in contexts of enslavement is not “romanticizing,” but rather historicizes multiple forms of violence and shows a fuller, more varied picture of slavery.

scholarly journals Population structure and demographic history of the chukar partridge Alectoris chukar in China

2013 ◽  
Vol 59 (4) ◽  
pp. 458-474 ◽  
Author(s):  
Sen Song ◽  
Shijie Bao ◽  
Ying Wang ◽  
Xinkang Bao ◽  
Bei An ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
North America ◽  
Demographic History ◽  
Population Expansion ◽  
Northwest China ◽  
Population History ◽  
Extant Species ◽  
History Of ◽  
Chukar Partridge

Abstract Pleistocene climate fluctuations have shaped the patterns of genetic diversity observed in extant species. Although the effects of recent glacial cycles on genetic diversity have been well studied on species in Europe and North America, genetic legacy of species in the Pleistocene in north and northwest of China where glaciations was not synchronous with the ice sheet development in the Northern Hemisphere or or had little or no ice cover during the glaciations’ period, remains poorly understood. Here we used phylogeographic methods to investigate the genetic structure and population history of the chukar partridge Alec-toris chukar in north and northwest China. A 1,152 – 1,154 bp portion of the mtDNA CR were sequenced for all 279 specimens and a total number of 91 haplotypes were defined by 113 variable sites. High levels of gene flow were found and gene flow estimates were greater than 1 for most population pairs in our study. The AMOVA analysis showed that 81% and 16% of the total genetic variability was found within populations and among populations within groups, respectively. The demographic history of chukar was examined using neutrality tests and mismatch distribution analyses and results indicated Late Pleistocene population expansion. Results revealed that most populations of chukar experienced population expansion during 0.027 ? 0.06 Ma. These results are at odds with the results found in Europe and North America, where population expansions occurred after Last Glacial Maximum (LGM, 0.023 to 0.018 Ma). Our results are not consistent with the results from avian species of Tibetan Plateau, either, where species experienced population expansion following the retreat of the extensive glaciation period (0.5 to 0.175 Ma).

Development of verb-verb complexes in Indo-Aryan

2021 ◽  
pp. 249-274
Author(s):  
Benjamin Slade
Keyword(s):  
Early Modern ◽  
South Asia ◽  
South Asian ◽  
Historical Development ◽  
History Of ◽  
Verb Compounds

This chapter discusses the historical development and properties of verb-verb compounds in Indo-Aryan, with reference to verb-verb compounds in Dravidian. The history of modern Indo-Aryan verb-verb compounds is explored, including an examination of the precursors of such constructions in early Indo-Aryan, as well as the apparent earliest examples in late Middle and early modern Indo-Aryan. A number of morphosyntactic and lexical differences between verb-verb structures in different modern Indo-Aryan languages are examined, focusing particularly on differences between Hindi and Nepali. The larger picture of South Asian verb-verb compounds is examined through comparison of lexical inventories of Indo-Aryan and Dravidian languages, with some evidence pointing to independent developments within South Asia, with some later partial convergence.

South Asian Entanglements

2020 ◽  
pp. 43-79
Author(s):  
Daniel S. Markey
Keyword(s):  
South Asia ◽  
South Asian ◽  
Nuclear Weapons ◽  
Economic Security ◽  
International Pressure ◽  
History Of ◽  
The Military

This chapter describes the intersection of Chinese, Pakistani, and Indian economic, political, and security interests in South Asia. It introduces a brief history of China’s interaction with South Asia and explains how China now perceives its economic, security, and diplomatic goals in the region. It shows how Pakistanis are divided in their perceptions of China and the China-Pakistan Economic Corridor, and explains how the military and other establishment figures are likely to gain from closer ties, while liberals and other opposition groups stand to lose. It details how Pakistan benefits from its military ties to China, especially in the areas of nuclear weapons, missiles, and drone technologies, and how China’s diplomatic support shields Pakistan from international pressure. It evaluates that on balance, China’s deepened regional presence and economic, military, and diplomatic assistance to Pakistan will tend to raise tensions with India.

scholarly journals Diabolical survival in Death Valley: recent pupfish colonization, gene flow and genetic assimilation in the smallest species range on earth

2016 ◽  
Vol 283 (1823) ◽  
pp. 20152334 ◽  
Author(s):  
Christopher H. Martin ◽  
Jacob E. Crawford ◽  
Bruce J. Turner ◽  
Lee H. Simons
Keyword(s):  
Gene Flow ◽  
Demographic History ◽  
Genetic Assimilation ◽  
Death Valley ◽  
Court Case ◽  
Devils Hole ◽  
Supreme Court Case ◽  
History Of ◽  
New Perspective ◽  
Outstanding Question

One of the most endangered vertebrates, the Devils Hole pupfish Cyprinodon diabolis , survives in a nearly impossible environment: a narrow subterranean fissure in the hottest desert on earth, Death Valley. This species became a conservation icon after a landmark 1976 US Supreme Court case affirming federal groundwater rights to its unique habitat. However, one outstanding question about this species remains unresolved: how long has diabolis persisted in this hellish environment? We used next-generation sequencing of over 13 000 loci to infer the demographic history of pupfishes in Death Valley. Instead of relicts isolated 2–3 Myr ago throughout repeated flooding of the entire region by inland seas as currently believed, we present evidence for frequent gene flow among Death Valley pupfish species and divergence after the most recent flooding 13 kyr ago. We estimate that Devils Hole was colonized by pupfish between 105 and 830 years ago, followed by genetic assimilation of pelvic fin loss and recent gene flow into neighbouring spring systems. Our results provide a new perspective on an iconic endangered species using the latest population genomic methods and support an emerging consensus that timescales for speciation are overestimated in many groups of rapidly evolving species.

Karbala in London: Battle of Expressions of Ashura Ritual Commemorations among Twelver Shia Muslims of South Asian Background

2017 ◽  
Vol 6 (2) ◽  
pp. 158-178 ◽  
Author(s):  
Sufyan Abid Dogra
Keyword(s):  
South Asia ◽  
South Asian ◽  
Transnational Networks ◽  
Power Struggle ◽  
Asian Origin ◽  
South Asian Origin ◽  
History Of

Abstract The roots of the struggle for authority among various groups of Twelver Shias of South Asian background living in London revolves around the idea of what is ‘true and authentic’ Shia Islam. The theological and political genealogy of this power struggle can be traced by examining the history of Shia Islam in South Asia. This article provides historical analyses and ethnographic accounts of Shia Islam and how it is practised in London. It investigates the influence of London-based Iranian and Iraqi Shia transnational networks on South Asian Hussainias and those who attend them. While some London-based Shias of South Asian origin conform to the Iran-backed reformist versions of globally standardised ritual commemoration of Ashura, others detest this and search for religious reinterpretations that assert South Asian ways of commemorating the Ashura ritual.

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