The forest for the trees: evaluating molecular phylogenies with an emphasis on higher-level Decapoda

Abstract

Since the late 1800s, several infraordinal relationships have been proposed for Decapoda; however, reaching a consensus among higher-level relationships is proving difficult. Molecular methods were first applied to higher-level decapod phylogenetics in the 1990s and have significantly contributed to our understanding of the group: sampling is becoming more thorough, a greater number of phylogenetically informative characters are being sequenced, and analysis procedures are becoming more consistent between studies. However, relationships among the deep lineages of Decapoda remain unclear. Several phylogenetic hypotheses have been suggested, and while there is some agreement among studies, an ultimate consensus among higher-level relationships has yet to be reached. This is largely the result of differences in sampling effort, marker selection, data-recycling, and analysis. Because most studies have generated conflicting phylogenetic hypotheses, the foundation on which the trees were built (data and analysis procedures) must be considered and evaluated. In this review, we summarize the early morphological decapod studies, address common problems that are causing a lack of consensus in molecular studies, present a means of evaluating molecular trees, offer suggestions for good phylogenetic practice, review the previous molecular studies of infraordinal decapod phylogeny, and discuss the future directions of the field, with special attention paid to next-generation sequencing (NGS) techniques.