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Applied aspects of methods to infer phylogenetic relationships amongst fungi

Authors:
Asha Janadaree Dissanayake at University of Electronic Science and Technology of China
Asha Janadaree Dissanayake
Chitrabhanu S. Bhunjun at Mae Fah Luang University
Chitrabhanu S. Bhunjun
Sajeewa Maharachchikumbura at University of Electronic Science and Technology of China
Sajeewa Maharachchikumbura
Jian-Kui Jack Liu at University of Electronic Science and Technology of China
Jian-Kui Jack Liu
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Dissanayake AJ, Bhunjun CS, Maharachchikumbura SSN, Liu JK 2020-Applied aspects of methods to infer phylogenetic relationships amongst fungi. Abstract There is a need to document the methodologies used for molecular phylogenetic analyses since the current fungal identification, classification and phylogeny are necessarily applied with DNA molecular sequence data. Hence this manuscript is mainly aimed to provide a basic reference or guideline for the mycologists venturing into the field of phylogenetic studies and to avoid unnecessary repetitions in related publications. This is not at all to elaborate the theoretical background but is intended as a compact guide of some useful software references and coding for the most commonly used phylogenetic methods applied in mycological research. This reference manuscript is originally conceived for usage with a set of programs necessary for inference of phylogenetic analyses in fungal research (taxonomy and phylogeny). For this purpose, principles, introductory texts and formulas have been omitted. Meanwhile, necessary steps from DNA extraction to DNA sequencing, sequences quality check, data alignment and general steps of phylogenetic tree reconstructions have been included.
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... Phylogenetic analyses of both individual and combined gene data were performed using maximum likelihood (ML) and Bayesian inference (BI) using RAxML-HPC2 on XSEDE (Stamatakis 2006(Stamatakis , 2014Stamatakis et al. 2008) and MrBayes v. 3.2.6 on XSEDE (Ronquist & Huelsenbeck 2003) at the CIPRES web portal (http://www.phylo.org/portal2/; Miller et al. 2010) following Dissanayake et al. (2020). The resulting trees were visualized with FigTree v. 1.4.4 and the layout was created in Adobe Illustrator 2019. ...
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