Supplementary alignment, phylogenetic, and biogeographic analysis data for: Phylogenomics of Gars

Reconstructing deep-time biogeographic histories is limited by the comparatively recent diversification of most extant lineages. Ray-finned fishes (Actinopterygii), which include more than half of living vertebrates, are no exception. Although many of the most species-rich clades of ray-finned fishes diversified after the Cretaceous-Paleogene mass extinction, a handful of ancient and species-depauperate lineages persist today. One of the most iconic ancient lineages of ray-finned fishes are gars, a clade of seven freshwater species restricted to continental North America and Cuba. Here, we use DNA sequences of more than 1,000 exons collected for all living species of gars and a morphological dataset that includes 16 fossil species to infer their phylogenetic relationships and estimate divergence times using fossil-tip dated relaxed molecular clock analyses. Our analyses show that the two major lineages of living gars, Atractosteus and Lepisosteus, diverged approximately 105 million years ago. Using the time-calibrated phylogeny of the living and fossil gar species and model-based biogeographic reconstructions, we find that many of the inferred vicariant events in the evolutionary history of gars closely track the Mesozoic fragmentation of Laurasia in the Northern Hemisphere and the Cretaceous reorganization of North American river drainage systems. In particular, we tie the initial diversification of living gars to the expansion of the early Atlantic and subsequent loss of shallow marine habitat between the Americas and Africa in the Cretaceous. All living gar species originated after the Cretaceous in eastern North America, implying that this region has both served as the ancestral area of extant gar diversity and a refugium of this iconic ancient vertebrate lineage.