Genki Kobayashi

Abstract The annelid mitochondrial genomes (mitogenomes) have been well documented, and phylogenetic analyses based on the mitogenomes provide insightful implications for annelid evolution. However, the mitogenomes of some families remain unknown. Herein, we determined the complete mitogenome of the lugworm Abarenicola claparedi oceanica (15,524 bp), representing the first mitogenome from the family Arenicolidae. The gene order of this species is the same as the various lineages in Sedentaria. The maximum likelihood phylogenetic analyses were performed based on six different datasets, including 43 ingroups (oligochaetes, hirudineans, echiurans and closely related polychaetes) and two outgroups (Siboglinidae), namely, aligned and trimmed datasets consisting of the nucleotide sequences of protein-coding genes (PCGs) and rRNAs, and amino acid sequences of PCGs. Phylogenetic analyses based on the nucleotide sequences yielded trees with better support values than those based on the amino acid sequences. Arenicolidae is clustered with Maldanidae in all analyses. Analyses based on nucleotide sequences confirm the monophyly of Terebellidae, which was paraphyletic in recent mitogenomic phylogenetic studies. We also performed the phylogenetic analysis based on the RY-coding of the nucleotide sequences of PCGs only to yield phylogeny with generally low support values. Additional mitogenome sequences of related ingroup species would be needed to comprehensively understand the phylogenetic relationship, which was not present in this study.

Abstract Mitogenomes are useful for inferring phylogenetic relationships between organisms. Although the mitogenomes of Annelida, one of the most morphologically and ecologically diverse metazoan groups have been well sequenced, those of several families remain unexamined. This study determined the first mitogenome from the family Travisiidae (Travisia sanrikuensis), analyzed its mitogenomic features, and reconstructed a phylogeny of Sedentaria. The monophyly of the Terebellida + Arenicolida + Travisiidae clade is supported by molecular phylogenetic analysis. The placement of Travisiidae is unclear because of the lack of mitogenomes from closely related lineages. An unexpected intron appeared within the cox1 gene of T. sanrikuensis and in the same positions of five undescribed Travisia spp. Although the introns are shorter (790–1386 bp) than other group II introns, they can be considered degenerate group II introns due to type II intron maturase open reading frames, found in two of the examined species, and motifs characteristic of group II introns. This is likely the first known case in metazoans where mitochondrial group II introns obtained by a common ancestor are conserved in several descendants. Insufficient evolutionary time for intron loss in Travisiidae, or undetermined mechanisms may have helped maintain the degenerate introns.

<italic>Spirobranchus kraussii</italic> (Annelida: Serpulidae) was recognized as being widely distributed both in the Pacific and Atlantic Oceans. However, the sampling records far from its type locality (South Africa) have been questioned. Actually, recent molecular phylogenetic studies showed that <italic>S. kraussii</italic> contains genetically distinct species. In this study, we performed molecular phylogenetic analyses of <italic>S.</italic> cf. <italic>kraussii</italic> collected from Japan using the nucleotide sequences of a mitochondrial gene and two nuclear genes. Three lineages were recovered within <italic>Spirobranchus kraussii</italic>-complex in Japan, and one (<italic>Spirobranchus</italic> sp. 6) showed moderate genetic difference (approximately 4%) in the mitochondrial cytb gene sequence from <italic>Spirobranchus</italic> sp. 1, an undescribed sequenced species from Honshu Island, Japan. However, the nucleotide sequences of the 18S rRNA gene and ITS2 region were nearly indistinguishable. The other lineage was clearly distinct from the other previously sequenced species and is thus considered to be another distinct species of this species complex (<italic>Spirobranchus</italic> sp. 5). Although detailed morphological assessment of these lineages is necessary to define their taxonomic status, the present study provided further implications for the species diversity within the <italic>S</italic>.<italic> kraussii</italic>-complex.

<italic>Halla okudai</italic> Imajima, 1967 is an oenonid annelid species that inhabits the intertidal and shallow subtidal zones in China, Malaysia, Australia and Japan. This species is harvested and used as fishing bait in Japan and Malaysia; however, it has been regarded as Near Threatened in Japan based on the categories of the Japanese Red List. Here, we reconstructed the molecular phylogeny of Oenonidae based on 16S rRNA gene sequences. This study provides a new record of <italic>H. okudai</italic> on Fukue Island, in the Goto Islands, Japan.