ABSTRACT
Not much more than fifteen years ago, the first decapod phylogenies based on mitochondrial DNA (mtDNA) sequences revolutionized decapod phylogenetics. Initially, this method was accepted only reluctantly. However, a wider understanding of the methods, and the realization that credibility of specific branching patterns can be measured by statistic confidence values, allowed the recognition of molecular systematics as just another phylogenetic approach, in which homologous characters are compared and interpreted in terms of apomorphic or plesiomorphic status, and best possible trees are calculated based on distances, parsimony, or likelihoods. Similar to morphological characters, some of the shared molecular characters can result from convergence, but the large quantity of potential characters to be compared (15,000-17,000 in mtDNA) promises to reveal phylogenetic signal. For many years, preference was given to mitochondrial genes among the molecular markers, because of the relative ease with which they can be amplified (stable and numerous copies per cell) and interpreted (because they are only maternally inherited and lack introns and recombination), and because of higher mutation rates and thus greater variability than nuclear DNA. More recently, some of these apparent advantages were interpreted as shortcomings of mtDNA, and the discovery of selective sweeps, mitochondrial introgressions, and nuclear copies of mtDNA (numts) have questioned the credibility of phylogenies based exclusively on mtDNA. Here, I revisit the history and importance of mtDNA-based phylogenies of decapods, present two examples of how numts can produce erroneous phylogenies, and emphasize the need for primer optimization for better PCR results and avoidance of numts. Mitochondrial DNA has distinct advantages and disadvantages and, if used in combination with other phylogenetic markers, is still a very effective tool for phylogenetic inference. In most cases, and when used with the necessary care, phylogenies and phylogeographies based on mtDNA will render absolutely reliable results that can be tested and confirmed with other molecular and non-molecular approaches.
