Selecting Molecular Markers for a Specific Phylogenetic Problem

Abstract

Submit Manuscript | http://medcraveonline.com of new technologies and the subsequent accessibility of refined methods due to cost reduction contributed to an immeasurable expansion of molecular facilities worldwide [1]. The rate of sequence submission has recently intensified for three primary reasons: the numerous and successful DNA barcoding projects [2,3], the advent of Next Generation Sequencing [4] and the subsequent decrease in prices for molecular sequencing services [5].As a consequence, genetic data repositories such as GenBank have been doubling in size every 18 months [6], rising from 606 sequences in the first 1982 release to close to 200 million sequences in the 218 th release in February 2017. Molecular data from more than 260 thousand nominal species is now widely accepted as a paramount source of biological information in all life sciences [7]. This is an exciting time. Many long existing controversies are in the process of being resolved by an unparalleled amount of data [6,8,9]. Phylogenomics, a dream just a few decades ago, is now changing the face of molecular phylogenetics. It is a revolution second only to the introduction of molecules in the field of phylogenetics in the 1960's.However, the availability of large number of sequences is not necessarily associated with an accurate estimation of phylogenies, due to analytical errors associated with very large sets of sequence data [10][11][12]. Hence, the contentious matter of molecular marker sampling is inhibiting this new breakthrough. Different genes may yield strikingly contradictory topological patterns for a given diversity group [13,14]. Thus, the selection of suitable markers is critical in obtaining accurate estimates, but it is not a straightforward task. In this review, we aim to provide some guidelines for newcomers weighing the suitability of particular molecular markers for a given phylogenetic problem. Homology in Molecular MarkersIn phylogenetic reconstruction, as in comparative biology studies, the single most important concern lies in the matter of homology, a concept that occupies a central position in evolutionary biology [15]. Homology is a qualitative term, defined by equivalence of parts due to inherited common origin [16][17][18].Homology has been more recently defined as the relationship that binds all states of a single character and sets them apart from the states of other characters, supporting the logical equivalence of the notions of homology and synapomorphy (for review see [19]). The comparison of homologous sequences is critical in a phylogenetic analysis, because only homologous characters may reveal the actual phylogenetic pattern.Nevertheless, a number of authors erroneously refer to homology as a synonym for similarity. Molecular biologists are particularly prone to this error, as they assert that 'two sequences share 70% homology' (for reviews on this problem see [15,20]). Two sequences might show 70% similarity, if 7 out of 10 aligned base pairs are identical between them.In molecular sequences, the high...

Why should we compare morphological and molecular disparity?

“…Secondly, as with morphological character data (Sereno, 2008), there is ultimately a subjective decision to include some sequences and to exclude others. Early molecular analyses required the careful-but arguably subjective-targeting of sequences evolving at rates appropriate for the antiquity and speed of the cladogenetic events being inferred (Russo et al, 2017). Phylogenomic analyses still entail data selection and processing (Collins et al, 2005), but typically encompass sequences evolving at a wide variety of rates (Klopfstein et al, 2017).…”