Abstract
Lancelets, extant representatives of basal chordates, are prototypic examples of evolutionary stasis; they preserved a morphology and body-plan most similar to the fossil chordates from the early Cambrian. Such a low level of morphological evolution is in harmony with a low rate of amino acid substitution; cephalochordate proteins were shown to evolve slower than those of the slowest evolving vertebrate, the elephant shark. Surprisingly, a study comparing the predicted proteomes of Chinese amphioxus, Branchiostoma belcheri and the Florida amphioxus, Branchiostoma floridae has led to the conclusion that the rate of creation of novel domain combinations is orders of magnitude greater in lancelets than in any other Metazoa, a finding that contradicts the notion that high rates of protein innovation are usually associated with major evolutionary innovations. Our earlier studies on a representative sample of proteins have provided evidence suggesting that the differences in the domain architectures of predicted proteins of these two lancelet species reflect annotation errors, rather than true innovations. In the present work, we have extended these studies to include a larger sample of genes and two additional lancelet species, Asymmetron lucayanum and Branchiostoma lanceolatum. These analyses have confirmed that the domain architecture differences of orthologous proteins of the four lancelet species are because of errors of gene prediction, the error rate in the given species being inversely related to the quality of the transcriptome dataset that was used to aid gene prediction.
Highlights
Cephalochordates, the basal group of extant chordates, diverged from other chordates about 550 Mya [1,2]
The results of our analyses indicate that the domain architecture differences of orthologous proteins of the four lancelet species are due to errors of gene prediction, and that the rate of gene prediction error is inversely related to the quality of the transcriptome dataset used to aid gene prediction
If a B. belcheri protein had no ortholog in another lancelet species
Summary
Cephalochordates (lancelets), the basal group of extant chordates, diverged from other chordates (urochordates and vertebrates) about 550 Mya [1,2]. Phylogenetic analyses based on amino acid sequences of protein-coding genes of amphioxus species have revealed that the Asymmetron clade diverged first from the common ancestor of extant lancelets, followed by the Epigonichthys and Branchiostoma clades [7]. The divergence time estimates of the various amphioxus species were shown to fit well with the time estimates for the closure of seaways by continental drift, providing a plausible explanation for the differences in the geographical distribution of the diverging species. These explanations implicitly assume that the common ancestor of the extant lancelets existed in an epibenthic state, inhabiting sandy seafloors of inshore waters [7]
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