Phylogenomics of the Ancient and Species-Depauperate Gars Tracks 150 Million Years of Continental Fragmentation in the Northern Hemisphere

Reconstructing deep-time biogeographic histories is limited by the comparatively recent diversification of most extant lineages. Ray-finned fishes, which include nearly half of all living vertebrates, are no exception. Although most lineages of ray-finned fishes radiated around the Cretaceous-Paleogene boundary, a handful of ancient, species-poor clades still persist. These lineages can illuminate very old biogeographic trends, but their low species richness can also limit the reconstruction of these patterns. The seven extant species of gars distributed in freshwater habitats in North America and Cuba are an old clade with a fossil record spanning over 150 million years of Earth history. Using a genomic data set of DNA sequences of 1105 exons for the seven living species and an updated morphological matrix of all extant and extinct taxa, we infer the phylogenetic relationships of gars and test how divergence times and biogeographic reconstructions are influenced by sequential and joint estimation and the effect on these inferences when using different taxon sets based on fossil completeness. Our analyses consistently show that the two extant gar genera Atractosteus and Lepisosteus diverged approximately 105 million years ago and many of the inferred divergences in the gar time-calibrated phylogeny closely track major Mesozoic tectonic events, including the separation of the Americas, the expansion of the early Atlantic, and the Cretaceous reorganization of North American river systems. The crown clades Atractosteus and Lepisosteus originated in the Cenozoic of eastern North America, implying that this region has served as both the origin of extant gar diversity and the refugium of this iconic ancient lineage. These results exemplify how combining phylogenomics with the fossil record provides congruence around the evolutionary history of ancient clades like gars and can reveal long-lost biogeographic patterns. [Lepisosteidae; fossilized birth death; biogeography; phylogenomics; paleontology.].