The mitogenomic contributions to molecular phylogenetics and evolution of fishes: a 15-year retrospect

This review summarizes the achievements and novel perspectives that our fish mitochondrial genome (mitogenome) project has brought to molecular phylogenetics and evolution of fishes during the last 15 years (1999-2014). To date, we have assembled a parts per thousand 1,340 whole mitogenome sequences from fishes, publishing 83 mitogenomic papers on all major fish lineages (except agnathans). Those papers have been cited 5,303 times in total as of 30 September 2014 and have been featured in many textbooks and scientific articles as well as various media. These results have not only had a significant impact on the scientific community, but also attracted considerable attention from the general public. The success of the project largely owes to our own development of a novel, PCR-based approach for sequencing whole mitogenomes (ca. 16,500 bp), which opened a new avenue toward addressing higher-level relationships of fishes based on longer DNA sequences from a number of taxa. Shortly after the development of the method, we explicitly demonstrated the phylogenetic utility of mitogenomic data and actually resolved a long-standing issue in basal teleostean relationships. On the basis of those encouraging results from the initial studies, we published a series of four mitogenomic papers in 2003, which together encompass the whole of actinopterygian diversity and provided a big picture phylogenetic framework for the group. Those four studies offered a useful phylogenetic basis for subsequent studies (i.e., with a different choice of outgroups and targeted taxa) and have facilitated massive sequencing efforts for a wide variety of fishes from chondrichthyians to higher teleosts living in diverse habitats from freshwaters to the deep sea. We highlight some of the 83 mitogenomic papers by subject and briefly refer to the phylogenetic and evolutionary significances of those studies. Finally, we argue that intensive taxonomic sampling from an interface between species and populations together with the massive character sampling from mitogenome sequences using next-generation sequencing (NGS) technologies would enable simultaneous attempts to delimit species boundaries and to reconstruct evolutionary relationships at much finer scale, eventually unraveling the fish part of the Tree of Life in a bottom-up manner with more accurate estimations of species diversity.