Fish, reconsidered: An updated ‘Tree of Life’ draws surprising connections

In a major new work, Yale ichthyologist Thomas Near revises branches of the Tree of Life concerning most fish species based on the latest scientific knowledge.
Many species of small fish underwater


At first glance, tube-eyes and cods seem nothing alike. The former, a ribbon-shaped, deep-sea fish, has bizarre tubular eyes that resemble goggles. The latter, one of the world’s most commercially important fishes, has unremarkable looks but pairs well with French fries.

It turns out, however, that these seemingly dissimilar fishes are cousins, both members of the order Gadiformes, according to an updated and revised version of the fish Tree of Life co-authored by Yale evolutionary ichthyologist Thomas J. Near.

The updated version is described in an 800-page monograph forthcoming in the journal Bulletin of the Peabody Museum of Natural History. A pre-print of the monograph released in September has been downloaded more than 9,000 times and has made a big splash within the ichthyology community.

Near and co-author Christine E. Thacker, curator emerita of ichthyology at the Natural History Museum of Los Angeles County, drew many surprising connections while completely revising the Tree of Life branches concerning ray-finned fishes, which represent more than 35,000 species — tunas, clown fish, catfish, piranhas, etc. – accounting for nearly all vertebrate fish species and about half of living vertebrate species. (Sharks, hagfish, and lampreys are not ray-finned fish.) They based their revisions on an analysis of centuries of scientific literature, starting with writings from the 1500s, moving through the pioneering work of Carl Linnaeus and Charles Darwin, and ending with recent discoveries made using genetic data.

Prior to the new revisions, ray-finned fishes were sorted into taxonomic groups largely based on morphology — their physical forms and structures — and other observable traits, which doesn’t capture all relationships among lineages, Near explained. Molecular genetic analysis, including Near’s own research, has clarified relationships among lineages but, until now, those discoveries have never been synthesized and incorporated into an updated Tree of Life.

Our knowledge of the fish Tree of Life is dramatically different than it was 20 years ago,” said Near, professor of ecology and evolutionary biology in Yale’s Faculty of Arts and Sciences and the Bingham Oceanographic Curator of Ichthyology at the Yale Peabody Museum. “Genetics has upended our understanding of how major fish lineages relate to each other.

We’ve incorporated all the latest science into an updated fish Tree of Life, did some careful pruning, and hopefully made better sense of its branches. In the process, we provide new and provocative insights about how fish are related.”

Near and Thacker chart the entire phylogeny, or evolutionary history, of all ray-finned fishes from the taxonomic rank of family and higher. (Genus and species rank below family in the modern classification scheme. From lowest to highest, order, class, phylum, kingdom, domain, and life rank above family.) In all, the researchers defined 97 inclusive groups based on common ancestry, accounting for 830 lineages. Only one of the 97 groups is new. They focused on consolidation, extracting more than 20 group names that they deemed redundant.

For example, tube-eyes, Stylephorus chordates, previously were the only members of the order Stylephoriformes. Genetic analyses had demonstrated that tube-eyes were, in the parlance of phylogenetics, the living sister lineage of Gadiformes, an order that also includes cod, haddock, pollock, and hakes. Instead of creating a new name that captures both groups, Near and Thacker simply reclassified tube-eyes as Gadiformes.

We wanted consolidate names as much as possible,” Near said. “There’s no way that the folks interested in Gadiformes would think tube-eyes are related because they’re just so different in their observable traits, which means we’re expanding our perception of what a gadiform can be.”

Some of the most significant rearrangements occur in Eupercaria, a group of more than 7,000 species that comprises five orders and includes colorful reef fishes like angelfishes, butterflyfishes, and wrasses; North American freshwater fishes such as basses, sunfishes, and darters; and most of the fishes found in the Arctic and Antarctic.

Understanding the relationships among groups in Eupercaria has been traditionally difficult because there are so many species and not enough good morphological characters to sort them out,” Thacker said. “Several groups of researchers have been working on fish molecular phylogenies using different types of genetic data and the amazing thing is, we’ve all been getting basically the same answer.

Our work unites and summarizes all these works and provides a unified classification, much like a roadmap to fish diversity.” 

In another example of consolidation, trout and salmon belong to the family Salmonidae, which is the sole member of the order Salmoniformes. Likewise, pikes and mud minnows, important fish for angling, comprise the family Esocidae, which is the only group in the order Esociformes. All genetic analysis shows that the two families are related, which led Near and Thacker to combine them into the order Salmoniformes, removing Esociformes in the process, which clarifies that salmon and trout, and pikes and mud minnows share a common ancestor.

This remarkable study is already being viewed as a landmark in the understanding of one of the most ecologically diverse and widespread of all evolutionary lineages,” said David Skelly, the Frank R. Oastler Professor of Ecology at Yale School of the Environment and director of the Peabody Museum. “Even as it has clarified so many aspects of fish evolution, it is going to keep a generation of ichthyologists busy unraveling the implications of some of its most critical conclusions.”

A YouTube video that light-heartedly highlights some of the unexpected connections that Near and Thacker make among fishes has, at this writing, attracted more than 725,000 views.

There are a handful of ‘big fish’ papers that all students of ichthyology need to know, and this monograph will join them as a classic,” said Prosanta Chakrabarty, the George H. Lowery Professor in the Department of Biological Sciences and Curator of Fishes at the Museum of Natural Science at Louisiana State University. “It may even change how taxonomists working on other groups of organisms reorganize their classification schemes as it lays out a solid and reasonable groundwork for streamlining higher group names.

Their methods are hard to argue with, but I’m still looking forward to seeing how the inevitable arguments will come about,” Chakrabarty added. “It’s all part of the fun of this 300-year-old discipline of taxonomy!” 

Near and Thacker plan to publish their work in an illustrated volume that will provide modern phylogenetically based classifications for all ray-finned fish.

It’ll be a comprehensive encyclopedia of fish,” Near said. 

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