Boreskov

Under methodical mistakes I mean first of all a set of mistakes at the very first step ofanalysis of sequencing data which inevitably will lead to a wrong result. The key momenthere is the analysis of alignment. The backbone of multiple alignment is the hypothesis onhomology of nucleotides/amino acids and the hypothesis on homology is the keystone inany kind of phylogenetic analysis. Noteworthy that very often while comparing molecularand conventional approaches as a main distinctive feature propose the objectivity of resultsin molecular studies independent of the researcher prior ideas, while conventional approachis highly subjective and require an expert knowledge. It is interesting that this argumentoften use both proponents and opponents of molecular data in phylogeny and systematic inorder to strength their point of view. However, it is important to underline that there is notless subjectivity in establishing homology in molecular data (alignment) than in morphology.Alignment is a mathematical process totally independent from biological reality and thequestion always rises to what extent mathematically optimal alignment is optimalbiologically? Alignment of sequences is no doubt one of the most hard and disputable tasksin molecular analysis due to insertions, deletions, sometimes it is even better to refute fromaligning ambiguous sequences what is often the case when the taxa are too distant. Thereare a great number of papers on alignment and here I want only to underline in the contextof all said above that this first procedure of molecular analysis does not lack subjectivity andrequire an expert knowledge not less than in any other kind of research.The other issues producing ambiguity of solutions in molecular phylogenetic studies arerelated to multiple substitutions in one site leading to high phylogenic noise. This issue quitecorresponds to the homeoplasy in morphological characters. Specific issues to moleculardata are bias in nucleotide frequencies and codon usage. These issues are well known andwell described in literature; there are certain ways to deal with but one need to keep it inmind while using molecular data.Beside methodical mistakes quite often one may come across the case when the analysisitself was carried out properly, the alignment, model of nucleotide substitution andalgorithms of analysis are appropriate and the obtained tree is robust but interpretation isincorrect. Generally this is related to the simple fact that gene trees and organism trees arenot the same. Wrong conclusions on phylogenetic relationships despite the correct dataanalysis more often happen when only one gene is analyzed. Results obtained from theanalysis of mitochondrial genes should be treated particularly careful. As an example of such125