Morphologically characterized by the presence of a dorsal covering of paired segmental scales
(=elytra), scale worms are well represented throughout the scientific literature, and are a result of
one of the most successful radiations of annelids. However, the phylogenetic relationships of
elytrigerous annelids remain unresolved, in spite of the numerous systematic revisions the group
has undergone. Since the first morphological cladistic analysis, molecular and combined
investigations have shaken up the systematics, yielding surprising character transformations
within Aphroditiformia, and paraphyly within various groups previously thought to be
monophyletic, highlighting the necessity for further detailed systematic revisions. Herein, we
attempt to resolve these controversies within scale worms, by inclusion of previously
underrepresented taxa (i.e., caves and interstitium) in order to improve the overall resolution of
the phylogenetic relationships within Aphroditiformia. To date, this is the largest and most diverse
phylogenetic sampling of scale worms, being the first to include anchialine as well as several
previously neglected interstitial representatives. Using combined and total evidence approaches,
our phylogenetic analyses integrated morphological and molecular datasets, with subsequent
sensitivity analyses to identify those groups with unstable positioning. Our inclusion of species
from extreme environments showed several independent radiations among the deep sea,
(anchialine) caves, and the interstitium, recovering six monophyletic clades within
Aphroditiformia: Acoetidae, Aphroditidae, Eulepethidae, Iphionidae, Polynoidae, and Sigalionidae
(inclusive of the former ‘Pisionidae’ and ‘Pholoidae’), respectively. Tracing of morphological
character evolution showed a high degree of homoplasy throughout Aphroditiformia, with several
secondary losses of scales among the groups. Ultimately, our investigations into cave and
interstitial scale worms have given rise to interesting phylogeographical questions, as these groups
have wide distributions despite their habitat specificity and seemingly low dispersal potential.
While anchialine polynoids are highly habitat specific, we found strong geographic structure
between Bahamian islands, with intra-island gene flow presumably through spelean corridors.
Alternatively, our studies of interstitial taxa showed broad distributions associated to geographical
regions, with high levels of homoplasy in group-specific morphological characters. Due to the high
levels of homoplasy found by our cladistics analyses, we performed large-scale phylogenetic
comparative analyses to unravel how ecology correlates to variation across e.g., feeding, motility,
and colonization of habitats, especially the subterranean and interstitium. Focusing on these
extreme habitat colonization events, we found evidence of shared morphological adaptations in
response to aphotic conditions, as trait similarity appeared to be linked to functionality, thereby
reflecting a high degree of adaptability and convergent evolution between relatively closely
related scale worms. While some morphological and behavioral modifications in cave polynoids
reflected troglomorphism, other modifications like eye loss were found to stem from a common
ancestor inhabiting the deep sea, further corroborating the deep sea ancestry of scale worm cave
fauna. In conclusion, while morphological characterization across Aphroditiformia appears
deceptively easy due to the presence of elytra, convergent evolution during multiple early
radiations across wide ranging habitats have confounded our ability to reconstruct the evolution
of morphological characters. The high morphological variability include from loss of elytra and
development of specialized male copulatory structures, to that of reduced body size and
incorporation of elytral brooding. Our combined investigations into adaptation and evolution of
morphological and molecular characters on species, genera, and across families has illustrated the
degree to which ecology drives morphological plasticity, making it equally important