Comparative Genomics of Transisthmian Damselfishes (Abudefduf saxatilis and A. troschelii).

The uplift of the Central American Isthmus (CAI) represents a natural laboratory for the study of allopatric speciation in marine organisms. Several geminate species pairs of both vertebrates and invertebrates formed following the uplift of the CAI, including damselfishes of the Pomacentridae family. However, to date few studies have explored the genomic differences among trainsisthmian species in the Pacific and Atlantic Oceans. In this study we present genome assemblies for the transisthmian species pair consisting of the Sergeant Major Abudefduf saxatilis (Tropical Atlantic) and the Panamic Sergeant Major Abudefduf troschelii (Tropical Eastern Pacific) derived from PacBio long-read sequencing. The new genomes are near-chromosome level, and among the highest-quality genomes currently available for coral reef fishes. We show that large structural variants distinguish the two species, including a nine-megabase inversion in linkage group (putative chromosome) six. Additionally, we show through an analysis of demographic history that alleles within the two genomes have different coalescence time distributions, which may be due to different effective population sizes, population structures, and/or selection regimes in the two oceans. Finally, we highlight gene families that were significantly expanded or contracted between A. troschelii and A. saxatilis. Some of these are related to the environmental differences between the two oceans, including gamma crystallin M (crygm), which is linked to vision, and vitellogenin (vtg), which is associated with egg provisioning. These genomes set the stage for comparative analyses of genetic structure and selection on the marine organisms that originated with the formation of the CAI.