scholarly journals A genetic history of migration, diversification, and admixture in Asia

2022 ◽  
pp. 1-32
Author(s):  
Melinda A. Yang
Keyword(s):  
Large Scale ◽  
Sequence Data ◽  
Evolutionary Genetics ◽  
Genetic Distances ◽  
Chromosome 21 ◽  
Late 20Th Century ◽  
Genetic History ◽  
Asian Populations ◽  
Human Dispersal ◽  
History Of

L.L. Cavalli-Sforza spearheaded early efforts to study the genetic history of humans, recognizing the importance of sampling diverse populations worldwide. He supported research on human evolutionary genetics in Asia, with research on human dispersal into Asia and genetic distances between present-day East Asians in the late 20th century. Since then, great strides have been made in understanding the genetic history of humans in Asia, through large-scale genomic sequencing of present-day humans and targeted sequencing of DNA from ancient humans. In this review, I survey the genetic prehistory of humans in Asia, based on research using sequence data from humans who lived in Asia as early as 45,000 years ago. Genetic studies comparing present-day Australasians and Asians show that they likely derived from a single dispersal out of Africa, rapidly differentiating into three main lineages: one that persists partially in South Asia, one that is primarily found today in Australasia, and one that is widely represented across Siberia, East Asia, and Southeast Asia. Studies of ancient DNA from human remains in Asia dating from as far back as 45,000 years has greatly increased our understanding of the population dynamics leading to the current Asian populations. Based on "Jin L, Underhill PA, Doctor V, Davis RW, Shen P, Cavalli-Sforza LL, Oefner PJ. Distribution of haplotypes from a chromosome 21 region distinguishes multiple prehistoric human migrations. Proc Natl Acad Sci U S A. 1999;96(7):3796-3800”.

scholarly journals The speciation and hybridization history of the genusSalmonella

2019 ◽  
Author(s):  
Alexis Criscuolo ◽  
Sylvie Issenhuth-Jeanjean ◽  
Xavier Didelot ◽  
Kaisa Thorell ◽  
James Hale ◽  
...  
Keyword(s):  
Large Scale ◽  
Sequence Data ◽  
Binary Fission ◽  
Bacterial Lineage ◽  
Food Borne ◽  
European Nucleotide Archive ◽  
Reference Collection ◽  
Illumina Sequence ◽  
History Of ◽  
Food Borne Infections

AbstractBacteria and archaea make up most of natural diversity but the mechanisms that underlie the origin and maintenance of prokaryotic species are poorly understood. We investigated the speciation history of the genusSalmonella, an ecologically diverse bacterial lineage, within whichS. entericasubsp.entericais responsible for important human food-borne infections. We performed a survey of diversity across a large reference collection using multilocus sequence typing, followed by genome sequencing of distinct lineages. We identified eleven distinct phylogroups, three of which were previously undescribed. Strains assigned toS. entericasubsp.salamaeare polyphyletic, with two distinct lineages that we designate Salamae A and Salamae B. Strains of subspecieshoutenaeare subdivided into two groups, Houtenae A and B and are both related to Selander’s group VII. A phylogroup we designate VIII was previously unknown. A simple binary fission model of speciation cannot explain observed patterns of sequence diversity. In the recent past, there have been large scale hybridization events involving an unsampled ancestral lineage and three distantly related lineages of the genus that have given rise to Houtenae A, Houtenae B and VII. We found no evidence for ongoing hybridization in the other eight lineages but detected more subtle signals of ancient recombination events. We are unable to fully resolve the speciation history of the genus, which might have involved additional speciation-by-hybridization or multi-way speciation events. Our results imply that traditional models of speciation by binary fission and divergence may not apply inSalmonella.Data summaryIllumina sequence data were submitted to the European Nucleotide Archive under project number PRJEB2099 and are available from INSDC (NCBI/ENA/DDBJ) under accession numbers ERS011101 to ERS011146. The MLST sequence and profile data generated in this study have been publicly available on theSalmonellaMLST web site between 2010 and the migration of theSalmonellaMLST website to EnteroBase (https://enterobase.warwick.ac.uk/), and subsequently from there.

scholarly journals Ancient Xinjiang mitogenomes reveal intense admixture with high genetic diversity

2021 ◽  
Vol 7 (14) ◽  
pp. eabd6690
Author(s):  
Wenjun Wang ◽  
Manyu Ding ◽  
Jacob D. Gardner ◽  
Yongqiang Wang ◽  
Bo Miao ◽  
...  
Keyword(s):  
Bronze Age ◽  
Iron Age ◽  
Genetic Admixture ◽  
Archaeological Sites ◽  
High Genetic Diversity ◽  
Genetic History ◽  
Asian Populations ◽  
History Of ◽  
Genetic Continuity ◽  
The Bronze Age

Xinjiang is a key region in northwestern China, connecting East and West Eurasian populations and cultures for thousands of years. To understand the genetic history of Xinjiang, we sequenced 237 complete ancient human mitochondrial genomes from the Bronze Age through Historical Era (41 archaeological sites). Overall, the Bronze Age Xinjiang populations show high diversity and regional genetic affinities with Steppe and northeastern Asian populations along with a deep ancient Siberian connection for the Tarim Basin Xiaohe individuals. In the Iron Age, in general, Steppe-related and northeastern Asian admixture intensified, with North and East Xinjiang populations showing more affinity with northeastern Asians and South Xinjiang populations showing more affinity with Central Asians. The genetic structure observed in the Historical Era of Xinjiang is similar to that in the Iron Age, demonstrating genetic continuity since the Iron Age with some additional genetic admixture with populations surrounding the Xinjiang region.

scholarly journals A history of biogeographical regionalisation in Australia

Zootaxa ◽  
2012 ◽  
Vol 3392 (1) ◽  
pp. 1 ◽  
Author(s):  
MALTE C. EBACH
Keyword(s):  
20Th Century ◽  
Large Scale ◽  
Biological Diversity ◽  
Short Term ◽  
Late 20Th Century ◽  
Biodiversity Crisis ◽  
History Of

The development of Australian biogeographical regionalisation since 1858 has been driven by colonial 19th-centuryexploration and by the late 20th-century biodiversity crisis. The intervening years reduced existing large scaleregionalisation into smaller taxon specific areas of vegetation or endemism. However, large scale biotic biogeographicalregionalisation was rediscovered during multi-disciplinary meetings and conferences, sparking short-term revivals whichhave ended in constant revisions at smaller and smaller taxonomic scales. In 1995 and 1998, the Interim BiogeographicRegionalisation for Australia and the Integrated Marine and Coastal Regionalisation of Australia, AustralianCommonwealth funded initiatives in order to “identify appropriate regionalisations to assess and plan for the protectionof biological diversity”, have respectively replaced 140 years of Australian biogeographical regionalisation schemes. Thispaper looks at the rise and slow demise of biogeographical regionalisation in Australia in light of a fractured taxonomic biogeographical community.

scholarly journals Temporal lags and overlap in the diversification of weevils and flowering plants

2009 ◽  
Vol 106 (17) ◽  
pp. 7083-7088 ◽  
Author(s):  
Duane D. McKenna ◽  
Andrea S. Sequeira ◽  
Adriana E. Marvaldi ◽  
Brian D. Farrell
Keyword(s):  
Large Scale ◽  
Sequence Data ◽  
Divergence Times ◽  
Resource Tracking ◽  
Crown Group ◽  
Dna Sequence Data ◽  
Angiosperm Diversification ◽  
History Of ◽  
Fossil Data ◽  
Diversification Event

The extraordinary diversity of herbivorous beetles is usually attributed to coevolution with angiosperms. However, the degree and nature of contemporaneity in beetle and angiosperm diversification remain unclear. Here we present a large-scale molecular phylogeny for weevils (herbivorous beetles in the superfamily Curculionoidea), one of the most diverse lineages of insects, based on ≈8 kilobases of DNA sequence data from a worldwide sample including all families and subfamilies. Estimated divergence times derived from the combined molecular and fossil data indicate diversification into most families occurred on gymnosperms in the Jurassic, beginning ≈166 Ma. Subsequent colonization of early crown-group angiosperms occurred during the Early Cretaceous, but this alone evidently did not lead to an immediate and major diversification event in weevils. Comparative trends in weevil diversification and angiosperm dominance reveal that massive diversification began in the mid-Cretaceous (ca.112.0 to 93.5 Ma), when angiosperms first rose to widespread floristic dominance. These and other evidence suggest a deep and complex history of coevolution between weevils and angiosperms, including codiversification, resource tracking, and sequential evolution.

scholarly journals A history of the biogeography of Amazonian fishes

2018 ◽  
Vol 16 (3) ◽  
Author(s):  
Fernando C. P. Dagosta ◽  
Mário C. C. de Pinna
Keyword(s):  
Large Scale ◽  
Distribution Patterns ◽  
Fish Distribution ◽  
South American ◽  
Late 20Th Century ◽  
Amazonian Fish ◽  
Historical Continuity ◽  
Fast Pace ◽  
History Of ◽  
Phylogenetic Hypotheses

ABSTRACT The history of knowledge about Amazonian biogeography is as rich as its fish community, and a fascinating theme of study in itself. Several current paradigms and controversies about Amazonian fish biogeography are rooted in principles dating from the second half of the 18th to the first half of the 19th centuries. The present work establishes a relationship between current biogeographical ideas and their old predecessors, on the basis of a chronologically-oriented historical continuity analysis. The advent of evolutionary theory has not contributed significantly to a transformation of the knowledge on the biogeography of Amazonian fishes. On the other hand, the two main schools of biogeographical thought (dispersalist and vicariant) had major implications on how Amazonian fish distribution is interpreted. The process was gradual and many hypotheses have combined elements from each of the two schools. Chronologically, practically the entire tradition of Amazonian biogeography takes place within the evolutionary paradigm, although its founder Louis Agassiz was himself an anti-evolutionist. The birth of Amazonian biogeography is Agassiz´s travel in Amazon. That document makes it clear that the author did not consider dispersal as a valid explanation for the biogeographical patterns he found. Later, Carl Eigenmann helps to spread the dispersalist tradition as a model for biogeographical explanations in fish distributions, a phase which lasted until the late 20th century. A major shift occurs with the contributions of Marylin Weitzman, Stanley Weitzman and Richard Vari, who associated the temporal framework of phylogenetic hypotheses with distribution patterns, underscoring the predictive power of vicariant biogeography. The present-day paradigm begins with the work of John Lundberg and attempts to incorporate geomorphological and phylogenetic information into integrative biogeographical hypotheses. Some emblematic problems have delayed proposition of general hypotheses on the phylogenetic biogeography of South American fishes, such as the poor state of knowledge of their species-level systematics; an incomplete distributional record for most species and sparse or non-existent data on the phylogenetic history of most supraspecific taxa. Such drawbacks are now being corrected at a fast pace. Recent advances on geographical distribution and an increasing number of phylogenetic hypotheses will allow unprecedented large-scale biogeographic analyses, including those based on event models and Bayesian inference. Thus, the biogeography of South American fishes, especially Amazonian ones, should soon experiment a new age of progress. The success of that new phase will depend on its ability to recognize and segregate multiple overlapping temporal layers of hydrological changes, and to develop analytical tools that can deal with temporal mixing.

scholarly journals Coalescent tree recording with selection for fast forward-in-time simulations

2021 ◽  
Author(s):  
Remi Matthey-Doret
Keyword(s):  
Evolutionary Genetics ◽  
Genetic History ◽  
Simulation Techniques ◽  
Genome Wide ◽  
Parental Haplotype ◽  
History Of ◽  
Speed Up ◽  
Coalescent Tree ◽  
Fitness Measures ◽  
Fitness Calculation

Forward simulations are increasingly important in evolutionary genetics to simulate selection with realistic demography, mating systems and ecology. To reach the performance needed for genome-wide simulations a number of new simulation techniques have been developed recently. Kelleher et al. (2018) introduced a technique consisting in recording the entire genetic history of the population and placing mutations on the coalescent tree. This method cannot model selection. I recently introduced a simulation technique that speed up fitness calculation by assuming that fitness effects among haplotypes are multiplicative (Matthey-Doret, 2021). More precisely, fitness measures are stored for subsets of the genome and, at time of reproduction, if no recombination happen within a given subset, then the fitness for this subset for the offspring haplotype is directly inferred from the parental haplotype. Here, I present a hybrid of the above two techniques. The algorithm records the genetic history of a species, directly places the mutations on the tree and infers fitness of subsets of the genome from parental haplotypes. At recombinant sites, the algorithm explores the tree to reconstruct the genetic data at the recombining segment. I benchmarked this new technique implemented in SimBit and report an important improvement of performance compared to previous techniques to simulate selection. This improvement is particularly drastic at low recombination rate. Such developments of new simulation techniques are pushing the horizon of the realism with which we can simulate species molecular evolution.

Genetic history of Southeast Asian populations as revealed by ancient and modern human mitochondrial DNA analysis

2008 ◽  
Vol 137 (4) ◽  
pp. 425-440 ◽  
Author(s):  
Patcharee Lertrit ◽  
Samerchai Poolsuwan ◽  
Rachanie Thosarat ◽  
Thitima Sanpachudayan ◽  
Hathaichanoke Boonyarit ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Dna Analysis ◽  
Modern Human ◽  
Southeast Asian ◽  
Human Mitochondrial Dna ◽  
Genetic History ◽  
Asian Populations ◽  
Mitochondrial Dna Analysis ◽  
History Of

scholarly journals Clustering patterns mirror the geographical distribution and genetic history of Lemnos and Lesvos sheep populations

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0247787
Author(s):  
Antonios Kominakis ◽  
Eirini Tarsani ◽  
Ariadne L. Hager-Theodorides ◽  
Ioannis Mastranestasis ◽  
Ioannis Hadjigeorgiou
Keyword(s):  
Genetic Diversity ◽  
Snp Array ◽  
Genetic Distances ◽  
Admixture Analysis ◽  
Ecosystem Integrity ◽  
Genetic History ◽  
Aegean Islands ◽  
History Of ◽  
North Aegean ◽  
Historic Data

Elucidating the genetic variation and structure of Lemnos and Lesvos sheep is critical for maintaining local genetic diversity, ecosystem integrity and resilience of local food production of the two North Aegean islands. In the present study, we explored genetic diversity and differentiation as well as population structure of the Lemnos and Lesvos sheep. Furthermore, we sought to identify a small panel of markers with the highest discriminatory power to assign animals across islands. A total number of n = 424 (n = 307, Lemnos and n = 117, Lesvos) ewes, sampled from n = 24 herds dispersed at different geographic regions on the two islands, were genotyped with the 50K SNP array. Mean observed heterozygosity was higher (but not statistically significantly different) in Lesvos than in Lemnos population (0.384 vs. 0.377) while inbreeding levels were higher in Lemnos than Lesvos herds (0.065 vs. 0.031). Results of principal components along with that of admixture analysis and estimated genetic distances revealed genetic clusters corresponding to Lesvos and Lemnos origin and the existence of infrastructure within islands that were associated with geographical isolation and genetic history of the studied populations. In particular, genetic analyses highlighted three geographically isolated herds in Lemnos that are located at mountainous areas of the island and are characterized as representatives of the local sheep by historic data and reports. Admixture analysis also showed a shared genetic background between Lemnos and Lesvos sheep attributable to past gene flow. Little overall genetic differentiation was detected between the two island sheep populations, while 150 discriminatory SNPs could accurately assign animals to their origin. Present results are comparable with those reported in the worldwide sheep breeds, suggesting geography related genetic patterns across and within islands and the existence of the local Lemnos sheep.

Materials for the history of the gospel-Baptist movement in Ukraine

1996 ◽  
pp. 4-15
Author(s):  
S. Golovaschenko ◽  
Petro Kosuha
Keyword(s):  
Large Scale ◽  
Religious Studies ◽  
Theological Seminary ◽  
National Academy Of Sciences ◽  
Evangelical Christians ◽  
Evangelical Christian ◽  
First Results ◽  
History Of ◽  
Fruitful Cooperation ◽  
Academy Of Sciences

The report is based on the first results of the study "The History of the Evangelical Christians-Baptists in Ukraine", carried out in 1994-1996 by the joint efforts of the Department of Religious Studies at the Institute of Philosophy of the National Academy of Sciences of Ukraine and the Odessa Theological Seminary of Evangelical Christian Baptists. A large-scale description and research of archival sources on the history of evangelical movements in our country gave the first experience of fruitful cooperation between secular and church researchers.

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