Cave-adapted evolution in the North American Amblyopsid fishes inferred using phylogenomics and geometric morphometrics

Cave adaptation has evolved repeatedly across the Tree of Life, famously
leading to pigmentation and eye degeneration and loss, yet its
macroevolutionary implications remain poorly understood. We use the North
American amblyopsid fishes, a family spanning a wide degree of cave
adaptation, to examine the impact of cave specialization on the modes and
tempo of evolution. We reconstruct evolutionary relationships using
ultraconserved element loci, estimate the ancestral histories of
eye-state, and examine the impact of cave adaptation on body shape
evolution. Our phylogenomic analyses provide a well-supported hypothesis
for amblyopsid evolutionary relationships. The obligate blind cavefishes
form a clade and the cave-facultative eyed spring cavefishes are nested
within the obligate cavefishes. Using ancestral state reconstruction, we
find support for at least two independent subterranean colonization events
within the Amblyopsidae. Eyed and blind fishes have different body shapes,
but not different rates of body shape evolution. North American
amblyopsids highlight the complex nature of cave-adaptive evolution and
the necessity to include multiple lines of evidence to uncover the
underlying processes involved in the loss of complex traits.