Data from: Repeated invasions into the twilight zone: evolutionary origins of a novel assemblage of fishes from deep Caribbean reefs

Mesophotic and deeper reefs of the tropics are poorly known and
underexplored ecosystems worldwide. Collectively referred to as the
‘twilight zone’, depths below ~30–50 m are home to many species of reef
fishes that are absent from shallower depths, including many undescribed
and endemic species. We currently lack even a basic understanding of the
diversity and evolutionary origins of fishes on tropical mesophotic reefs.
Recent submersible collections in the Caribbean have provided new
specimens that are enabling phylogenetic reconstructions that incorporate
deep-reef representatives of tropical fish genera. Here, we investigate
evolutionary depth transitions in the family Gobiidae (gobies), the most
diverse group of tropical marine fishes. Using divergence-time estimation
coupled with stochastic character mapping to infer the timing of
shallow-to-deep habitat transitions in gobies, we demonstrate at least
four transitions from shallow to mesophotic depths. Habitat transitions
occurred in two broad time periods (Miocene, Pliocene–Pleistocene), and
may have been linked to the availability of underutilized niches, as well
as the evolution of morphological/behavioural adaptations for life on deep
reefs. Further, our analysis shows that at least three evolutionary
lineages that invaded deep habitats subsequently underwent speciation,
reflecting another unique mode of radiation within the Gobiidae. Lastly,
we synthesize depth distributions for 95 species of Caribbean gobies,
which reveal major bathymetric faunal breaks at the boundary between
euphotic and mesophotic reefs. Ultimately, our study is the first rigorous
investigation into the origin of Caribbean deep-reef fishes and provides a
framework for future studies that utilize rare, deep-reef specimens.