The Degenerate Tale of Ascidian Tails

Abstract

Ascidians are invertebrate chordates, with swimming chordate tadpole larvae that have distinct heads and tails. The head contains the small brain, sensory organs, including the ocellus (light) and otolith (gravity) and the presumptive endoderm, while the tail has a notochord surrounded by muscle cells and a dorsal nerve cord. One of the chordate features is a post-anal tail. Ascidian tadpoles are nonfeeding, and their tails are critical for larval locomotion. After hatching the larvae swim up toward light and are carried by the tide and ocean currents. When competent to settle, ascidian tadpole larvae swim down, away from light, to settle and metamorphose into a sessile adult. Tunicates are classified as chordates because of their chordate tadpole larvae; in contrast, the sessile adult has a U-shaped gut and very derived body plan, looking nothing like a chordate. There is one group of ascidians, the Molgulidae, where many species are known to have tailless larvae. The Swalla Lab has been studying the evolution of tailless ascidian larvae in this clade for over 30 years and has shown that tailless larvae have evolved independently several times in this clade. Comparison of the genomes of two closely related species, the tailed Molgula oculata and tailless Molgula occulta reveals much synteny, but there have been multiple insertions and deletions that have disrupted larval genes in the tailless species. Genomics and transcriptomics have previously shown that there are pseudogenes expressed in the tailless embryos, suggesting that the partial rescue of tailed features in their hybrid larvae is due to the expression of intact genes from the tailed parent. Yet surprisingly, we find that the notochord gene regulatory network is mostly intact in the tailless M. occulta, although the notochord does not converge and extend and remains as an aggregate of cells we call the "notoball." We expect that eventually many of the larval gene networks will become evolutionarily lost in tailless ascidians and the larval body plan abandoned, with eggs developing directly into an adult. Here we review the current evolutionary and developmental evidence on how the molgulids lost their tails.

Fig. 1

Molgulid phylogeny. A) Cladogram showing Molgulidae in relation to other tunicates. Molgulid representatives (M. occulta, M. oculata, M. occidentalis) are the species for which genomes are available on ANISEED (Brozovic et al. 2015). The family Molgulidae is a sister group to the rest of the order Stolidobranchia. B) Phylogeny of Molgulidae inferred from Bayesian analysis of 18S rDNA with posterior probabilities indicated on branches. The four distinct molgulid clades are labeled with roman numerals (Huber et al. 2000). I. Roscovita clade, II. Woods Hole clade, III. Circum-Northern clade, IV. The Eugryid clade. Species with tailed larvae are indicated with a tadpole shape, and species with tailless larvae are indicated with an ellipse. Within Molgulidae, the genera Eugyra and Bostrichobranchus are made up entirely of species with tailless larvae as indicated with an asterisk (*) with 47 and 5 described species, respectively (WoRMS Editorial Board 2021). (Cladogram drawn from Delsuc et al. [2018], Kocot et al. [2018], and DeBiasse et al. [2020]).

Fig. 2

Hox cluster organization in the Molgula ascidians compared with other deuterostomes. Orthologous Hox genes are indicated by the same colors. Homo sapiens has four Hox gene clusters, as a result of two genome duplications found in all vertebrates. Invertebrate deuterostomes each have a single cluster, with B. floridae containing a single perfectly aligned cluster that includes 15 Hox genes. Saccoglossus kowalevskii shows a loss of Hox12 but has three independent duplications in the posterior genes, Hox11/13a, 11/13b, and 11/13c, and the latter two show opposite orientation to the rest of the Hox cluster (Freeman et al. 2012). All five tunicates lack some middle Hox genes (6–9). Molgula species have eight Hox genes, with linkage being established only between Hox4–Hox5 and Hox10–Hox12–Hox13. Botrylloides leachii has seven identified Hox genes, three of which (Hox10, Hox12, Hox13) are linked on the same chromosome; linkage of Hox1, Hox2, Hox4, and Hox5 is unknown. Ciona robusta has nine identified Hox genes on two chromosomes, though some are not particularly close to the others (>35 kb distance), which is indicated by diagonal lines separating them. Oikopleura dioica has 10 identified Hox genes, but their linkage is unclear as the O. dioica genome assembly lacks chromosomal resolution. However, none of the Hox genes are found within <250 kb of one another (Seo et al. 2004). Saccoglossus kowalevskii, H. sapiens, and B. floridae only show embryo/larval stage Hox expression. In C. robusta, both adult and larva stages are shown with Hox expression, but only the larval expression of O. dioica is shown in the figure.