Early Phylogenetic Estimate Of The Effective Reproduction Number Of 2019-nCoV

ABSTRACTTo reconstruct the evolutionary dynamics of the 2019 novel coronavirus, 52 2019-nCOV genomes available on 04 February 2020 at GISAID were analysed.The two models used to estimate the reproduction number (coalescent-based exponential growth and a birth-death skyline method) indicated an estimated mean evolutionary rate of 7.8 × 10−4 subs/site/year (range 1.1×10−4–15×10−4).The estimated R value was 2.6 (range 2.1-5.1), and increased from 0.8 to 2.4 in December 2019. The estimated mean doubling time of the epidemic was between 3.6 and 4.1 days.This study proves the usefulness of phylogeny in supporting the surveillance of emerging new infections even as the epidemic is growing.

Genetic Relationships Among Salvelinus Species Inferred from Allozyme Data

We studied phylogenetic relationships in the genus Salvelinus with emphasis on S. alpinus, S. malma, and S. confluentus. Sixty allozyme loci were resolved in 422 individuals representing six species from a worldwide distribution. We used phenetic (UPGMA), phylogenetic (Fitch and Margoliash), and maximum-likelihood techniques to derive estimates of Salvelinus phylogeny. Three almost identical topologies were produced, but we chose the Fitch and Margoliash topology as the best phylogenetic estimate. The distances used to construct this tree assume that gene frequencies are affected only by genetic drift, which we argued was the dominant speciation force in Salvelinus. This topology was also the shortest. Jackknifing the Fitch and Margoliash tree resolved the branching order among the three Salvelinus subgenera: S. [Baione], S. [Cristivomer], and S. [Salvelinus]. It also revealed two sister groups within the Salvelinus subgenus: S. leucomaenis – S. confluentus and S. alpinus – S. malma.