The genus Ciona, a widely distributed group of solitary ascidians, has long been an important model in embryology and developmental biology. Ciona has also recently attracted the attention of evolutionary biologists because of the remarkably high levels of heterozygosity found within single individuals. Surprisingly, genealogical relationships in Ciona have received little attention. Here, we expand our knowledge of relationships among the members of the Ciona genus and estimate levels of polymorphism in natural populations. Previous studies have documented the outgroup status of Ciona savignyi among the shallow-water Ciona and revealed the existence of two distinct forms (Types A and B) of the widespread Ciona intestinalis. Here, using gene genealogies of six nuclear gene loci, we show Types A and B to be well-supported monophyletic groups. In spite of their morphological similarity, Type A vs. Type B divergences range from 0.035 to 0.124. In contrast, the morphologically distinct Ciona roulei is embedded within Type B in all genealogies, and a new species, Ciona sp., appears to be associated with Type B/C. roulei to the exclusion of Type A. Levels of polymorphism in natural populations are similar to levels reported in other organisms that are considered to be highly polymorphic.
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