Faculty Opinions recommendation of Inference of human population history from individual whole-genome sequences.

2011 ◽  
Author(s):  
Stephen Wright
Keyword(s):  
Human Population ◽  
Population History ◽  
Whole Genome ◽  
Genome Sequences

scholarly journals Inference of human population history from individual whole-genome sequences

Nature ◽  
2011 ◽  
Vol 475 (7357) ◽  
pp. 493-496 ◽  
Author(s):  
Heng Li ◽  
Richard Durbin
Keyword(s):  
Human Population ◽  
Population History ◽  
Whole Genome ◽  
Genome Sequences

scholarly journals Tracking human population structure through time from whole genome sequences

PLoS Genetics ◽  
2020 ◽  
Vol 16 (3) ◽  
pp. e1008552 ◽  
Author(s):  
Ke Wang ◽  
Iain Mathieson ◽  
Jared O’Connell ◽  
Stephan Schiffels
Keyword(s):  
Population Structure ◽  
Human Population ◽  
Whole Genome ◽  
Genome Sequences

scholarly journals Inferring human population size and separation history from multiple genome sequences

2014 ◽  
Author(s):  
Stephan Schiffels ◽  
Richard Durbin
Keyword(s):  
Population Genetic ◽  
Human Population ◽  
Evolutionary History ◽  
Population History ◽  
Genome Sequences ◽  
Peopling Of The Americas ◽  
The World ◽  
Population Genetic Inference ◽  
Inference Methods ◽  
Genetic Inference

The availability of complete human genome sequences from populations across the world has given rise to new population genetic inference methods that explicitly model their ancestral relationship under recombination and mutation. So far, application of these methods to evolutionary history more recent than 20-30 thousand years ago and to population separations has been limited. Here we present a new method that overcomes these shortcomings. The Multiple Sequentially Markovian Coalescent (MSMC) analyses the observed pattern of mutations in multiple individuals, focusing on the first coalescence between any two individuals. Results from applying MSMC to genome sequences from nine populations across the world suggest that the genetic separation of non-African ancestors from African Yoruban ancestors started long before 50,000 years ago, and give information about human population history as recently as 2,000 years ago, including the bottleneck in the peopling of the Americas, and separations within Africa, East Asia and Europe.

scholarly journals Molecular Epidemiology and Whole-Genome Analysis of Bovine Foamy Virus in Japan

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1017
Author(s):  
Hirohisa Mekata ◽  
Tomohiro Okagawa ◽  
Satoru Konnai ◽  
Takayuki Miyazawa
Keyword(s):  
Phylogenetic Analyses ◽  
Foamy Virus ◽  
Pcr Analysis ◽  
Whole Genome ◽  
Genome Sequences ◽  
Whole Genome Analysis ◽  
Virus Family ◽  
Bovine Foamy Virus ◽  
Novel Genotype

Bovine foamy virus (BFV) is a member of the foamy virus family in cattle. Information on the epidemiology, transmission routes, and whole-genome sequences of BFV is still limited. To understand the characteristics of BFV, this study included a molecular survey in Japan and the determination of the whole-genome sequences of 30 BFV isolates. A total of 30 (3.4%, 30/884) cattle were infected with BFV according to PCR analysis. Cattle less than 48 months old were scarcely infected with this virus, and older animals had a significantly higher rate of infection. To reveal the possibility of vertical transmission, we additionally surveyed 77 pairs of dams and 3-month-old calves in a farm already confirmed to have BFV. We confirmed that one of the calves born from a dam with BFV was infected. Phylogenetic analyses revealed that a novel genotype was spread in Japan. In conclusion, the prevalence of BFV in Japan is relatively low and three genotypes, including a novel genotype, are spread in Japan.

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