Phylogenomics of the airbreathing catfishes (Siluriformes: Clariidae)

The airbreathing, or walking, catfishes of the family Clariidae are characterized by a suprabranchial organ facilitating atmospheric respiration, and their ability to traverse significant distances over land. With 118 species in 16 genera, clariids are most diverse in Africa but also inhabit southeast Asia and the Middle East, with invasive populations worldwide. Previous phylogenetic studies, largely based on mitochondrial markers, have produced poorly resolved and often conflicting hypotheses of relationships. As a result, a well-supported framework for intrarelationships within this large, economically important group remains lacking, representing a major gap in our understanding of catfish biodiversity and evolution. Here, we present a new phylogeny based on ultraconserved elements (UCEs), incorporating 52 species across all genera. We define Clariidae to include both Horaglanis and Heteropneustes, confirm monophyly of the African clariids, and identify three major lineages among them. These comprise a clade of predominately large-bodied, widespread species, and groups mostly restricted to the Congolese, and Lower Guinean ecoregions respectively. We additionally assess the potential of historical museum specimens (hDNA) for phylogenomic studies by incorporating seven formalin-fixed, clariid specimens rare in collections, including the possibly extinct Lake Victoria deepwater Xenoclarias eupogon, the stygobitic Somalian Uegitglanis zammaranoi, and the enigmatic Asian Horaglanis krishnai. We demonstrate successful sequencing from specimens preserved 20 to 98 years ago, expanding the available genetic data for rare and historically collected taxa. Our study reveals extensive non-monophyly across the tree, including across the nominal genera Clarias, Clariallabes, Channallabes, and Gymnallabes, and underscores a need for substantial taxonomic review.