Evolutionary Genomics of Fast Evolving Tunicates

Abstract

Tunicates have been extensively studied because of their crucial phylogenetic location (the closest living relatives of vertebrates) and particular developmental plan. Recent genome efforts have disclosed that tunicates are also remarkable in their genome organization and molecular evolutionary patterns. Here, we review these latter aspects, comparing the similarities and specificities of two model species of the group: Oikopleura dioica and Ciona intestinalis. These species exhibit great genome plasticity and Oikopleura in particular has undergone a process of extreme genome reduction and compaction that can be explained in part by gene loss, but is mostly due to other mechanisms such as shortening of intergenic distances and introns, and scarcity of mobile elements. In Ciona, genome reorganization was less severe being more similar to the other chordates in several aspects. Rates and patterns of molecular evolution are also peculiar in tunicates, being Ciona about 50% faster than vertebrates and Oikopleura three times faster. In fact, the latter species is considered as the fastest evolving metazoan recorded so far. Two processes of increase in evolutionary rates have taken place in tunicates. One of them is more extreme, and basically restricted to genes encoding regulatory proteins (transcription regulators, chromatin remodeling proteins, and metabolic regulators), and the other one is less pronounced but affects the whole genome. Very likely adaptive evolution has played a very significant role in the first, whereas the functional and/or evolutionary causes of the second are less clear and the evidence is not conclusive. The evidences supporting the incidence of increased mutation and less efficient negative selection are presented and discussed.

A phylogenomic framework and timescale for comparative studies of tunicates

“…and Styela plicata. This confirmed earlier observations based on a reduced number of taxa and substitution rate estimations on 35 housekeeping genes [16], once again underlining the peculiar genomic evolution of tunicates that might find its root in elevated mutation rates and pervasive molecular adaptation [21,22]. Even though the difference in fit between the two relaxed clock models was not significant for our dataset, in general LN provided more consistent dating estimates than UGAM with respect to the mean divergence dates of numerous vertebrate groups reported in the latest phylogenomic study of jawed vertebrates [35].…”

Identification and population genetic comparison of three ascidian species based on mtDNA sequences

“…Of note, a previous genome‐wide study also revealed that C. savignyi exhibited the highest level of genetic diversity (Small, Brudno, Hill, & Sidow, 2007). Other comparative studies on ascidians also confirmed that they have different evolutionary rates (Berna & Alvarez‐Valin, 2014). This could be another reason causing the different levels of genetic diversity among these three species.…”

Temporal correlation of population composition and environmental variables in the marine invader Ciona robusta

“…In a different scheme, the observed temporal change in genetic composition of C. robusta might reflect a process of sweepstakes reproductive success, in which a subset of the population contributes the majority of offspring to subsequent generations (Hedgecock & Pudovkin, ), as already suggested by the existence of site‐specific haplotypes (Zhan et al, ). In broadcast‐spawning marine invertebrates with large effective population size (Berná & Alvarez‐Valin, ; Tsagkogeorga, Cahais, & Galtier, ) and low level of dispersal potential, this hypothesis deserves further investigation.…”