Supplementary information for: From scales to armour: scale losses and trunk bony plate gains in ray-finned fishes

Actinopterygians (ray-finned fishes) are the most diversified group of
vertebrates and are characterized by a variety of protective structures
covering their integument, the evolution of which has intrigued biologists
for decades. Paleontological records showed that the first mineralized
vertebrate skeleton was composed of dermal bony plates covering the body,
including odontogenic and skeletogenic components. Later in evolution, the
exoskeleton of actinopterygian's trunk was composed of scale
structures. Although scales are nowadays a widespread integument cover,
some contemporary lineages do not have scales but bony plates covering
their trunk, whereas other lineages are devoid of any such structures. To
understand the evolution of the integument coverage and particularly the
transition between different structures, we investigated the pattern of
scale loss events along actinopterygian evolution and addressed the
functional relationship between the scaleless phenotype and the ecology of
fishes. Furthermore, we examined whether the emergence of trunk bony
plates was dependent over the presence or absence of scales. To this aim,
we used two recently published actinopterygian phylogenies, one including
> 11,600 species, and by using stochastic mapping and Bayesian
methods, we inferred scale loss events and trunk bony plate acquisitions.
Our results reveal that a scaled integument is the most frequent state in
actinopterygians, but multiple independent scale loss events occurred
along their phylogeny with essentially no scale re-acquisition. Based on
linear mixed models, we found evidence supporting that after a scale loss
event, fishes tend to change their ecology and adopt a benthic lifestyle.
Furthermore, we show that trunk bony plates appeared independently
multiple times along the phylogeny. By using fitted likelihood models for
character evolution, we show that trunk bony plate acquisitions were
dependent on a previous scale loss event. Overall, our findings support
the hypothesis that integument cover is a key evolutionary trait
underlying actinopterygian radiation.