The evolutionary pathways that culminated in the present day diversity of deep sea fishes remain poorly understood. Beryciform and stephanoberyciform fishes have successfully transitioned between near shore and deep-sea habitats multiple times over their 100 million year history. Thus, they provide an exceptional opportunity for investigating the evolutionary dynamics associated with transitions between these extreme habitats. This project will provide the most detailed phylogenetic study of this radiation to date, providing the necessary infrastructure for future investigations into the mode and tempo of diversification across deep-sea fish groups. Our utilization of these fishes as a model group for further developing phylogenetic theory also sets a new standard for the screening of molecular markers for phylogenetic experimental design. A common question in phylogenetic inference concerns the selection of genes to employ in a given study. This project will empirically depict the utility of screening markers for a given question a priori, and demonstrate the potential for incorrect, yet strongly supported, inferences when loci are not carefully scrutinized. This presents an objective metric from which to screen the utility of sequence data for a phylogenetic problem that is applicable to any taxonomic group. This project also provides training in phylogenetics, bioinformatics, and museum techniques to undergraduate students and further contributes specimens and data to museum collections and public databases.
The integration of advances in computing technology with major innovations in sequence data collection and phylogenetic inference has revolutionized evolutionary biology in the 21st century. In particular, the continual development of both theory and software that allow for more flexibility in utilizing molecular clock methods has radically transformed our understanding of the mode and tempo of diversification across the Tree of Life. Beryciform + stephanoberyciform fishes comprise a radiation of approximately 225 species that have successfully transitioned between near shore and deep-sea habitats multiple times over their 100 million year history. Understanding the evolutionary dynamics of this radiation has been met with difficulty by the lack of a robust phylogenetic framework for further inferences. Our project has laid the foundation for the most detailed phylogenetic study of this radiation to date, providing the necessary infrastructure for future investigations into the mode and tempo of diversification across deep-sea fish groups. Using a next-generation sequence dataset of approximately 100,000 nucleotides, our findings challenge predominant views regarding the phylogeny of teleosts and provide a strong statement on a key issue for studies of the history of more than one quarter of all living species of vertebrates. We also have provided the first detailed phylogenetic study of a subset of beryciformes, holocentrids (squirrelfishes and soldierfishes), reconciling over 100 years of taxonomic uncertainty, and suggest substantial taxonomic revisions are necessary to reflect the evolutionary history of this clade. Contemporary holocentrid species richness is concentrated in the Indo-Australian Archipelago, yet these fishes also represent some of the most numerous fossil taxa in deposits of the Eocene West Tethyan biodiversity hotspot. Following the collapse of the West Tethys and formation of the modern Mediterranean Sea, holocentrids exhibit a signature of increased range fragmentation, becoming isolated between the Atlantic and Indo-Pacific Ocean basins. However, rather than originating within the emerging Indo-Australian Archipelago biodiversity hotspot, the Indo-Australian Archipelago appears to have acted as a reservoir for holocentrid diversity that originated in adjacent regions over deep evolutionary timescales. By integrating extinct lineages, these results provide a necessary historic perspective on the formation and maintenance of global marine biodiversity. We also used data generated by this award for developing phylogenetic informativeness theory that provide an objective metric for the screening of molecular markers for phylogenetic experimental design. A common question in phylogenetic inference concerns the number of markers to employ in a given study. This project has provided two bioinformatics pipelines that empirically depict the utility of screening markers for a given question a priori, and demonstrate the potential for incorrect, yet strongly supported, inferences when loci are not carefully scrutinized. Our analyses reconcile competing age estimates for acanthomorph (spiny-rayed) fishes, which comprise 1 out of every three vertebrates. Further, we provide a metric not only for cost-effective screening of loci for pilot datasets, but also a data filtration metric for large phylogenomic datasets. This award has provided opportunities for coral reef fish survey work on both the islands of Curaçao and Guam. Collections of both tissues for DNA analysis and specimens resulting from these surveys have been deposited in the Yale Peabody Museum of Natural History where they available to the global scientific community. Specimens collected as a result of this work have already been loaned to multiple research groups and been used in multiple published studies. Findings of our research have also been disseminated in multiple scientific publications and scientific conferences.