Molecular Phylogenetic and Phylogenomic Approaches in Studies of Lichen Systematics and Evolution

Abstract

Molecular phylogenies and phylogenomics are important for addressing several biological questions such as evolutionary relationships among organisms or genes or genomes, trait evolution, the demographic changes, distribution patterns, and diversification of species, DNA barcoding, prediction of gene function, prediction, and retracing gene transfer. The advancement of DNA sequencing technologies such as next generation sequencing has taken phylogenetic analysis to a new summit. Molecular phylogenies have encompassed almost every branch of biology including lichens , and various phylogenetic methods and software packages are now available. Here, we review the main methods for phylogenetic and phylogenomic analyses, including distance, maximum parsimony, maximum likelihood, and Bayesian approaches; and assembly of phylogenomic dataset and approaches based on whole genome features. We provide a practical guide for their uses and discuss their strengths and weaknesses.