This project will involve investigators from eight institutions working to resolve evolutionary relationships within the euteleost fishes, which represent over one third of vertebrate diversity. An important component will be education of the public on the importance, evolutionary history, and diversity of these animals. Phylogenetic analyses will employ DNA sequence data from 20 genes in 1,500 species representing all euteleost families, and approximately 450 morphological characters from 300 euteleost lineages. Resulting phylogenetic hypotheses will be used to facilitate understanding of the evolution of fish diversity and re-assess and revise the systematics of euteleosts. Research on the euteleost tree of life will be integrated into science education by using euteleost phylogeny as a framework for exploring the evolution of morphological, genetic, developmental, and behavioral diversity of fishes. This will be developed as an instructional guide, a "Fish ToL Activity Book," directed at upper elementary and middle school children and disseminated in non-formal and school settings working in partnership with the National Science Teachers Association Press and the National 4-H Afterschool Council. Undergraduates, graduate students, and postdocs will participate directly in the research project.
The euteleosts include some 346 families, 2,935 genera and 17,419 species. Over two thirds of all fishes and nearly a third of all vertebrates are euteleosts, which include most of the economically important fishes such as salmons, basses, cods and tunas. This study will facilitate informed predictions about the poorly known characteristics of most euteleosts and will considerably improve the evolutionary context for understanding model organisms such as zebrafish, pufferfish, cichlids, medaka, and stickleback, which are central to the burgeoning fields of functional genomics, genetics and evolutionary developmental biology.
The primary goal of this project was to understand the evolutionary relationships among major groups of bony fishes. With over 30,000 known species, there are more bony fishes than all other bony vertebrates combined. Fishes exhibit extraordinary diversity in body forms and ecological, physiological, behavioral and reproductive adaptations. Understanding how these species are related will provide the framework for understanding the origin and maintenance of this incredible diversity. The tree of life of fishes is in a state of flux because we still lack a comprehensive phylogeny that includes all major groups. The situation is most critical for a large clade of euteleost fishes, traditionally referred to as percomorphs, whose uncertain relationships have plagued ichthyologists for over a century. Most of what we know about the higher-level relationships among fish lineages has been based on morphology (physical characteristics), but rapid influx of molecular studies is changing many established systematic concepts. Fish classification schemes have been based on loosely formulated syntheses and community consensus views of largely disconnected studies. The phylogenetic structure underpinning such classifications has many areas that are unresolved and poorly known, providing weak or no justification for many groups that, although formally recognized, are implicitly known to be unnatural or unrelated assemblages. A comprehensive phylogenetic tree for all major groups of fishes has been elusive because explicit analyses including representatives across their entire diversity have never been accomplished. Detailed morphological investigations of fish relationships have typically focused on lower taxonomic scales and the few attempts to synthesize morphology at higher taxonomic levels proved to be challenging and met with limited success. We performed a comprehensive molecular phylogeny for bony fishes that includes representatives of all major lineages. DNA sequence data for 21 genes (roughly 20,000 base pairs per species) were collected for 1410 bony fish taxa, plus four tetrapod species and two chondrichthyan outgroups (total 1416 species). Bony fish diversity is represented by 1093 genera (out of 4,300), 369 families (out of 502), and all orders. Phylogenetic analysis using maximum likelihood methods provided unprecedented resolution and high bootstrap support for most backbone nodes, defining for the first time a global phylogeny of fishes. The general structure of the tree is in agreement with expectations from previous morphological and molecular studies, but significant new clades arise. Most interestingly, the high degree of uncertainty among percomorphs is now resolved into nine well-supported supraordinal groups. The order Perciformes, considered by many a polyphyletic taxonomic waste basket, is defined for the first time as a monophyletic group in the global phylogeny. A new classification that reflects our phylogenetic hypothesis is proposed to facilitate communication about the newly found structure of the tree of life of fishes. Finally, the molecular phylogeny is calibrated using 60 fossil constraints to produce a comprehensive set of divergence dates for fish lineages. The new time-calibrated phylogeny will provide the basis for and stimulate new comparative studies to better understand the evolution of the amazing diversity of fishes. Specific accomplishments include: 1) Discovery, development and dissemination of a set of molecular markers informative for fish and vertebrate phylogenetic studies. 2) Assembly and evaluation of morphological characters from the published literature as putative synapomorphies (defining characteristics) for all fish groups to the level of suborder and family as available, and developmental studies of selected traits in order to understand homology among adult characters. 3) We generated DNA samples from the diversity of fishes including over 1,100 individual taxa. 4) We acquired DNA sequences from a subset of 20 loci (objective 1) for each of the DNA samples, and assembled and aligned these sequences for phylogenetic analysis. 5) We performed comprehensive molecular phylogenetic analysis of all fish groups, focusing on problematic euteleost taxa. 6) We interpret phylogenetic results with respect to fish classification and revised the classification to reflect the new understanding of relationships. 7) Results were disseminated in over 40 peer-reviewed publications, and numerous presentations at professional conferences. We have contributed content to fish- and evolution-related web sites to provide for interaction and collaboration with the larger fish systematics community. 8) We developed educational materials that enhance student understanding of concepts of evolution, phylogenetics and fish biology. This specifically includes interactive unit lessons for grade 9-12 biology students. And 9) We enhanced development of the next generation of scientists by training undergraduate and graduate students and postdoctoral scholars in fish biology, systematics, molecular phylogenetics, and evolutionary genomics. Some of the major accomplishments are illustrated here: www.deepfin.org
