2.8 Phylogenetic reconstruction and principal component analysis
of M. bovis from the safari park
A core-SNP matrix of M. bovis genomes from the safari was
generated using a previously described algorithm (Zimpel, 2020) and
subjected to ascertainment bias correction (ASC) using IQ-Tree -fconst
(Nguyen, Schmidt, von Haeseler & Minh, 2015 ). The ASC-corrected matrix
was used in the ModelFinder program (Kalyaanamoorthy et al., 2017) to
select the best substitution model according to Bayesian Information
Criterion (BIC). The best model, TVM+F+R10, was fixed to reconstruct the
phylogeny using maximum likelihood (ML) algorithm with 1,000 UFBoot
pseudoreplicates (Hoang et al., 2017). Mycobacterium bovisAF2122/97 was included in the analysis and five representative genomes
of Mycobacterium caprae were used as outgroup (ERR1462591,
ERR1462625, ERR1462617, ERR1462581).
To evaluate clustering among M. bovis isolates, a PCA (principal
component analysis) was constructed based on the SNP matrix. The
function princomp was used in R software 3.5.0 to generate 2- and
3-dimensions PCA graphs.