Phylogenetics and dating

PAML may be used to compare and test phylogenetic trees, but their main strengths lie in…

A cross-platform program for Bayesian phylogenetic analysis of molecular…

Molecular dating of phylogenetic trees is a growing discipline using sequence data to co-estimate the timing of evolutionary events and rates of molecular evolution.

All molecular-dating methods require converting genetic divergence between…

All molecular-dating methods require converting genetic divergence between sequences into absolute time A package of programs for phylogenetic analyses of DNA and protein sequences…

A package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML).

Mean estimates of the time of most recent common ancestor also suggest that the H2N2 and H3N2 pandemic strains may have been generated through reassortment events in unknown mammalian hosts and involved multiple avian viruses preceding pandemic recognition.

The possible generation of pandemic strains through a series of reassortment events in mammals over a period of years before pandemic recognition suggests that appropriate surveillance strategies for detection of precursor viruses may abort future pandemics.

(In my experience this can lead to some clades having unrealistically early origins.) A better solution was provided by Ruta (2006).

Pandemic influenza viruses cause significant mortality in humans.

In the 20th century, 3 influenza viruses caused major pandemics: the 1918 H1N1 virus, the 1957 H2N2 virus, and the 1968 H3N2 virus.

Here we estimated the evolutionary history and inferred date of introduction to humans of each of the genes for all 20th century pandemic influenza strains.

Our results indicate that genetic components of the 1918 H1N1 pandemic virus circulated in mammalian hosts, i.e., swine and humans, as early as 1911 and was not likely to be a recently introduced avian virus.

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