A new molecular phylogeny of salps (Tunicata: Thalicea: Salpida) and the evolutionary history of their colonial architecture

Salps are marine pelagic urochordates with a complex life cycle including
a solitary and colonial stage composed of asexually-budded individuals.
These colonies develop into species-specific architectures with distinct
zooid orientations, including transversal, oblique, linear, helical, and
bipinnate chains; as well as whorls, and clusters. The evolutionary
history of salp colony architecture has remained obscured due to the lack
of a homology-based ontology to characterize architectures, as well as a
lack of phylogenetic taxon sampling and resolution of critical nodes. We
(1) collected and first-time sequenced eight species of salps, (2)
inferred the phylogenetic relationships among salps, and (3) reconstructed
the evolutionary history of salp colony architecture. We collected salp
specimens via offshore SCUBA diving, dissected tissue samples, extracted
their DNA, amplified their 18S gene, and sequenced them using Sanger
technology. We inferred a new molecular phylogeny using both Maximum
Likelihood and Bayesian approaches. Using this phylogeny, we reconstructed
the ancestral states of colony architecture using a Bayesian ordered
Markov model informed by the presence and absence of specific
developmental mechanisms that lead to each architecture. We find that the
ancestral salp architecture is either oblique or linear, with every other
state being derived. Moreover, linear chains have evolved independently at
least three times. While transversal chains are developmentally basal and
hypothesized to be ancestral, our phylogenetic topology and
reconstructions strongly indicate that they are evolutionarily derived
through the loss of zooid torsion. These traits are likely critical to
multijet locomotory performance and evolving under natural selection. Our
work showcases the need to study the broader diversity of salp species in
order to gain a comprehensive understanding of their organismal biology,
evolutionary history, and ecological roles in pelagic ecosystems.