Decapod Phylogeny: What Can Protein-Coding Genes Tell Us?

Abstract

The high diversity of decapods has attracted the interest of many carcinologists, but there is no consensus on their phylogeny as yet. This is in spite of numerous endeavors using both morphological and molecular approaches. New sources of information are necessary to help elucidate the phylogenetic relationships among decapods. Here we demonstrate the applicability of nuclear proteincoding genes in the phylogenetic analysis of this group. Using only two protein-coding genes, we have successfully resolved most of the infraordinal relationships with good statistical support, indicating the superior efficiency of these markers compared to nuclear ribosomal RNA and mitochondrial genes now commonly used in phylogenetic reconstruction of decapods. Available evidence suggests that these two markers suffer from the problems of alignment ambiguities and rapid saturation, respectively. We have also applied nuclear protein-coding genes in revealing inter- and intrafamilial evolutionary history. Trees with robust support can be obtained using sequences of two to three genes for the infraorders and families tested, including the most species-rich group, the Brachyura. The new genes are also shown to be informative in elucidating interspecific phylogeny. Thus, these nuclear protein-coding genes are applicable at various taxonomic levels and will provide a valuable new source of information for reconstructing the tree of life of Decapoda