Evolutionary genetic patterns in shallow coastal fishes are documented with dozens
of studies, but corresponding surveys of deepwater fishes (>200m) are scarce. Here
we investigate the evolutionary history of deepwater snappers (genus Etelis), comprised
of three recognized Indo-Pacific species and one Atlantic congener, by constructing
a phylogeny of the genus with two mtDNA loci and two nuclear introns. Further, we
apply range-wide Indo-Pacific sampling to test for the presence and distribution of
a putative cryptic species pair within E. carbunculus using morphological analyses
and mtDNA cytochrome b sequences from 14 locations across the species range (N=1696).
These analyses indicate that E. carbunculus is comprised of two distinct, non-interbreeding
lineages separated by deep divergence (d=0.081 in cytochrome b). Although these species
are morphologically similar, we identified qualitative differences in coloration of
the upper-caudal fin tip and the shape of the opercular spine, as well as significant
differences in adult body length, body depth, and head length. These two species have
overlapping Indo-Pacific distributions, but one species is more widespread across
the Indo-Pacific, whereas the other species is documented in the Indian Ocean and
Western Central Pacific. The dated Etelis phylogeny places the cryptic species divergence
in the Pliocene, indicating that the biogeographic barrier between the Indian and
Pacific Oceans played a role in speciation. Based on historic taxonomy and nomenclature,
the species more widespread in the Pacific Ocean is E. carbunculus, and the other
species is previously undescribed (referred to here as E. sp.). The Atlantic congener
E. oculatus has only recently (∼0.5Ma) diverged from E. coruscans in the Indo-Pacific,
indicating colonization via southern Africa. The pattern of divergence at the Indo-Pacific
barrier, and Pleistocene colonization from the Indian Ocean into the Atlantic, is
concordant with patterns observed in shallow coastal fishes, indicating similar drivers
of evolutionary processes.