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. 2020 Mar 31;12(4):386. doi: 10.3390/v12040386

Figure 2.

Figure 2

Maximum clade credibility tree of LASV Lineages’ glycoprotein (GP) gene. A phylogenetic analysis of the GP gene of members of confirmed and proposed (*) LASV lineages. The tree is rooted in Lineage I and each node shows the Bayesian posterior probabilities support. The tree tips are labelled to shown country, strain, year of collection, and GenBank accession numbers. Precursor glycoprotein (GPC) nucleotide sequences with greater than 60% coverage for the LASV GPC coding sequence (CDS) were retrieved from the GenBank, a maximum likelihood tree was generated in RAxML v8.2.12 [39] on CIPRES [40]. Bayesian phylogenetic inference was performed using BEAST v1.10.4 [41] with Generalized Time Reversible (GTR) plus gamma substitution model, uncorrelated relaxed clock model in lognormal distribution, SkyGrid coalescent tree prior setting, and the maximum likelihood tree as starting tree. Markov chain Monte Carlo (MCMC) chains were run for 250 million iterations, sampled every 10,000 states and 2500 trees were discarded as burn-in, to obtain an effective sample size (ESS) >200 for all parameters. Maximum clade credibility tree was drawn in Tree Annotator v1.10.4 [41].