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Abstract
Cephalochordates, the sister group of tunicates plus vertebrates, have been called "living fossils" due to their resemblance to fossil chordates from Cambrian strata. The genome of the cephalochordate Branchiostoma floridae shares remarkable synteny with vertebrates and is free from whole-genome duplication. We performed RNA sequencing from larvae and adults of Asymmetron lucayanum, a cephalochordate distantly related to B. floridae. Comparisons of about 430 orthologous gene groups among both cephalochordates and 10 vertebrates using an echinoderm, a hemichordate, and a mollusk as outgroups showed that cephalochordates are evolving more slowly than the slowest evolving vertebrate known (the elephant shark), with A. lucayanum evolving even more slowly than B. floridae. Against this background of slow evolution, some genes, notably several involved in innate immunity, stand out as evolving relatively quickly. This may be due to the lack of an adaptive immune system and the relatively high levels of bacteria in the inshore waters cephalochordates inhabit. Molecular dating analysis including several time constraints revealed a divergence time of ∼120 Ma for A. lucayanum and B. floridae. The divisions between cephalochordates and vertebrates, and that between chordates and the hemichordate plus echinoderm clade likely occurred before the Cambrian.
Fig. 1.—. Side views of living Asymmetron lucayanum (top) and Branchiostoma floridae (bottom). Asymmetron lucayanum has a single row of gonads on the right side only. Branchiostoma floridae has two rows of gonads—one on each side (anterior to the right).
Fig. 2.—. Fifteen-way maximum-likelihood phylogenetic tree inferred from a concatenated orthologous gene matrix (427 orthologous gene groups). The branch length is proportional to the expected amino acid substitution rate and the scale bar represents 0.08 expected amino acid substitutions per site. The numbers at the internal nodes show the statistical support for the topology of the tree based on the approximate logarithm-likelihood test. The result shown here is based on the analysis for the asymAD library. The Bayesian tree for the asymAD library and parallel analyses for the asym20h library are shown in supplementary figs. S1–S3, Supplementary Material online.
Fig. 3.—. The time frame of cephalochordate evolution inferred by MCMCTree based on the asymAD library. The Bayesian estimations for all internal nodes (nodes a–n) are tabulated in table 5. Each grey bar represents the 95% confidence interval for the corresponding estimate.
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