The effective number of codons (N(c)) is a widely used index for characterizing codon usage bias because it does not require a set of reference genes as does codon adaptation index (CAI) and because of the freely available computational tools such as CodonW. However, N(c), as originally formulated has many problems. For example, it can have values far greater than the number of sense codons; it treats a 6-fold compound codon family as a single-codon family although it is made of a 2-fold and a 4-fold codon family that can be under dramatically different selection for codon usage bias; the existing implementations do not handle all different genetic codes; it is often biased by codon families with a small number of codons. We developed a new N(c) that has a number of advantages over the original N(c). Its maximum value equals the number of sense codons when all synonymous codons are used equally, and its minimum value equals the number of codon families when exactly one codon is used in each synonymous codon family. It handles all known genetic codes. It breaks the compound codon families (e.g., those involving amino acids coded by six synonymous codons) into 2-fold and 4-fold codon families. It reduces the effect of codon families with few codons by introducing pseudocount and weighted averages. The new N(c) has significantly improved correlation with CAI than the original N(c) from CodonW based on protein-coding genes from Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Escherichia coli, Bacillus subtilis, Micrococcus luteus, and Mycoplasma genitalium. It also correlates better with protein abundance data from the yeast than the original N(c).

No abstract

We here report the first complete mitochondrial (mt) genome of a skipper, Ctenoptilum vasava Moore, 1865 (Lepidoptera: Hesperiidae: Pyrginae). The mt genome of the skipper is a circular molecule of 15,468 bp, containing 2 ribosomal RNA genes, 24 putative transfer RNA (tRNA), genes including an extra copy of trnS (AGN) and a tRNA-like insertion trnL (UUR), 13 protein-coding genes and an AT-rich region. All protein-coding genes (PCGs) are initiated by ATN codons and terminated by the typical stop codon TAA or TAG, except for COII which ends with a single T. The intergenic spacer sequence between trnS (AGN) and ND1 genes also contains the ATACTAA motif. The AT-rich region of 429 bp is comprised of nonrepetitive sequences, including the motif ATAGA followed by an 19 bp poly-T stretch, a microsatellite-like (AT)3 (TA)9 element next to the ATTTA motif, an 11 bp poly-A adjacent to tRNAs. Phylogenetic analyses (ML and BI methods) showed that Papilionoidea is not a natural group, and Hesperioidea is placed within the Papilionoidea as a sister to ((Pieridae + Lycaenidae) + Nymphalidae) while Papilionoidae is paraphyletic to Hesperioidea. This result is remarkably different from the traditional view where Papilionoidea and Hesperioidea are considered as two distinct superfamilies.

In the last few decades, the Late Paleozoic-Early Mesozoic tectonic evolution of South China has been quite controversial. The focus of debate is on both the age of ophiolites and the Late Paleozoic-Early Mesozoic geological and geodynamic environment. The Huaiyu Domain is located in the NE part of South China and exposes numerous significant geological features that are keys to understand the tectonics of South China. In this paper, we present some new evidence on stratigraphy, petrology and SHRIMP zircon U-Pb geochronology, and together with other geological and geochemical data available in the literature, and the following conclusions are suggested: 1) The eastern Jiangnan ophiolites belt, dated at 858±11 Ma by SHRIMP zircon U-Pb method, was generated during the Neoproterozoic, but not the Late Paleozoic; 2) The sedimentary rocks associated with these oceanic rocks do not contain radiolarians but Neoproterozoic acritarchs; 3) During Permian-Early Triassic times, the Huaiyu Domain was dominantly characterized by a shallow sea depositional environment since deep sea sediments are absent; and 4) The pre-Devonian tectonics of South China has been reworked by late polyphase tectonism through the Triassic and the Cretaceous periods. A Late Paleozoic-Early Mesozoic deep marine domain floored by oceanic crust never existed in the study area. The geochronological and structural data do not comply with a Late Paleozoic