Abstract
A recent analysis of the genomes of Chinese and Florida lancelets has concluded that the rate of creation of novel protein domain combinations is orders of magnitude greater in lancelets than in other metazoa and it was suggested that continuous activity of transposable elements in lancelets is responsible for this increased rate of protein innovation. Since morphologically Chinese and Florida lancelets are highly conserved, this finding would contradict the observation that high rates of protein innovation are usually associated with major evolutionary innovations. Here we show that the conclusion that the rate of proteome innovation is exceptionally high in lancelets may be unjustified: the differences observed in domain architectures of orthologous proteins of different amphioxus species probably reflect high rates of gene prediction errors rather than true innovation.
Highlights
Living fossil seems to hold for the lophotrochozoan Lingula
Whereas the low rate of amino acid substitution appears to be in harmony with the low rate of morphological evolution in lancelets, the exceptionally high rate of creation of novel proteins would suggest that major changes in the complexity of the lancelet proteomes are not coupled to significant changes in phenotype
Gene models of B. belcheri and B. floridae suffer from high rates of gene prediction errors
Summary
Living fossil seems to hold for the lophotrochozoan Lingula. the abundance of Lingula fossils from the Silurian, with morphology very similar to that of extant species, inspired Darwin with the idea of ‘living fossils’. Luo et al.[12] have shown recently that Lingula genes associated with basic metabolism, such as ribonucleoprotein complex biogenesis and RNA processing, show the slowest evolutionary rate among lophotrochozoans[12]. Whereas the low rate of amino acid substitution appears to be in harmony with the low rate of morphological evolution in lancelets, the exceptionally high rate of creation of novel proteins (with novel domain combinations) would suggest that major changes in the complexity of the lancelet proteomes are not coupled to significant changes in phenotype. It must be emphasized that this seems to contradict the observation that high rates of creation of novel proteins are usually associated with major evolutionary innovations such as those that accompanied the appearance of metazoa and vertebrates[13]. We suggest that the conclusion that the rate of protein innovation is exceptionally high in lancelets may be unjustified: we demonstrate that the differences in domain architecture of orthologous proteins of the two amphioxus species reflect gene prediction errors rather than true innovation
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