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.