Taeho Kim

Phylogeny of Rhigonematomorpha based on the complete mitochondrial genome of Rhigonema thysanophora (Nematoda: Chromadorea)

We determined the complete mitochondrial genome sequence of Rhigonema thysanophora, the first representative of Rhigonematomorpha, and used this sequence along with 57 other nematode species for phylogenetic analyses. The R. thysanophora mtDNA is 15 015 bp and identical to all other chromadorean nematode mtDNAs published to date in that it contains 36 genes (lacking atp8) encoded in the same direction. Phylogenetic analyses of nucleotide and amino acid sequence data for the 12 protein‐coding genes recovered Rhigonematomorpha as the sister group to the heterakoid species, Ascaridia columbae (Ascaridomorpha). The organization of R. thysanophora mtDNA resembles the most common pattern for the Rhabditomorpha+Ascaridomorpha+Diplogasteromorpha clade in gene order, but with some substantial gene rearrangements. This similarity in gene order is in agreement with the sequence‐based analyses that indicate a close relationship between Rhigonematomorpha and Rhabditomorpha+Ascaridomorpha+Diplogasteromorpha. These results are consistent with certain analyses of nuclear SSU rDNA for R. thysanophora and some earlier classification systems that asserted phylogenetic affinity between Rhigonematomorpha and Ascaridomorpha, but inconsistent with morphology‐based phylogenetic hypotheses that suggested a close (taxonomic) relationship between rhigonematomorphs and oxyuridomorphs (pinworms). These observations must be tempered by noting that few rhigonematomorph species have been sequenced and included in phylogenetic analyses, and preliminary studies based on SSU rDNA suggest the group is not monophyletic. Additional mitochondrial genome sequences of rhigonematids are needed to characterize their phylogenetic relationships within Chromadorea, and to increase understanding of mitochondrial genome evolution.

Mitochondrial genomes advance phylogenetic hypotheses for Tylenchina (Nematoda: Chromadorea)

Within the nematode class Chromadorea, the suborder Tylenchina is an ecologically and morphologically diverse assemblage of nematodes that includes free‐living microbivores, fungivores and various types of plant parasites. A recent nematode classification system based largely on SSU rDNA phylogenetic trees classified suborder Tylenchina to include four infraorders: Panagrolaimomorpha, Cephalobomorpha, Tylenchomorpha and Drilonematomorpha, and phylogenetic relationships among species of these infraorders have not always been robustly supported. In this study, we determined the complete mitochondrial genome sequences of three Tylenchina species (Aphelenchus avenae [Aphelenchidae, Tylenchomorpha], Halicephalobus gingivalis, Panagrellus redivivus [Panagrolaimomorpha]) and the partial genome sequence of Acrobeles complexus (Cephalobomorpha) and used these sequences to infer phylogenetic relationships among representatives of the Tylenchina and other nematodes. Phylogenetic analysis of amino acid sequences for 12 protein‐coding genes of 100 nematode species supports monophyly of: Chromadorea, Spiruromorpha, Oxyuridomorpha, Ascarididae + Toxocaridae + Anisakidae, Meloidogynidae + Pratylenchidae + Heteroderidae and Aphelenchoidea. Bayesian and maximum‐likelihood analyses also show the nested position of Diplogasteromorpha within Rhabditomorpha, and Rhigonematomorpha within Ascaridomorpha. These analyses also show non‐monophyly of: clade III, Ancylostomatidae, Panagrolaimomorpha, Tylenchina and Tylenchomorpha. Reconstructed mitochondrial genome phylogeny also revealed that among two main Tylenchomorpha groups, the monophyletic group representing Aphelenchoidea species was sister to the large clade consisting of Ascaridomorpha, Diplogasteromorpha, Rhabditomorpha and Rhigonematomorpha and some Panagrolaimomorpha species, whereas Tylenchoidea species were sister to the most inclusive assemblage containing all infraordinal groups of Chromadorea, except for P. redivivus (Panagrolaimomorpha) and Acrobeles complexus (Cephalobomorpha). The monophyly of Aphelenchoidea (i.e. sister relationship between Aphelenchidae and Aphelenchoididae) recovered in this study indicates that similarity in certain aspects of pharyngeal structure between these two families appears best explained by common ancestry, rather than convergent evolution.

The complete mitochondrial genome of the Japanese mud shrimp Upogebia major (Crustacea, Decapoda)

We determined a full-length sequence of mitochondrial (mt) genome from Upogebia major. This is the first complete mt genome report for infraorder Thalassinidea in Decapoda, Crustacea. Our result showed that U. major generally followed a typical pancrustacean gene order but some tRNA genes showed a very unique gene arrangement such as duplication or translocation. Since none of the complete mt genome sequences in the infraorder Thalassinidea are available yet, this report will provide additional information in relation to mt genome diversity and evolution of the decapods.

Mitochondrial DNA Sequence Variations and Genetic Relationships among Korean Thais Species (Muricidae: Gastropoda)

Thais Roding, 1798, commonly known as rock-shell, is among the most frequently found gastropod genera worldwide on intertidal rocky shores including those of Japan, China, Taiwan and Korea. This group contains important species in many marine environmental studies but species-level taxonomy of the group is quite complicated due to the morphological variations in shell characters. This study examined the genetic variations and relationships among three Korean Thais species based on the partial nucleotide sequences of mitochondrial cox1 gene fragments. Phylogenetic trees from different analytic methods (maximum parsimony, neighbor-joining, and maximum likelihood) showed that T. bronni and T. luteostoma are closely related, indicating the most recent common ancestry. The low sequence divergence found between T. luteostoma and T. bronni, ranging from 1.53% to 3.19%, also corroborates this idea. Further molecular survey using different molecular marker is required to fully understand a detailed picture of the origin for their low level of interspecific sequence divergence. Sequence comparisons among conspecific individuals revealed extensive sequence variations within the three species with maximum values of 2.43% in T. clavigera and 1.37% in both T. bronni and T. luteostoma. In addition, there is an unexpectedly high level of mitochondrial genotypic diversity within each of the three Korean Thais species. The high genetic diversity revealed in Korean Thais species is likely to reflect genetic diversity introduced from potential source populations with diverse geographic origins, such as Taiwan, Hong Kong, and a variety of different coastal regions in South China and Japan. Additional sequence analysis with comprehensive taxon sampling from unstudied potential source populations will be also needed to address the origin and key factors for the high level of genetic diversity discovered within the three Korean Thais species studied.

The bipartite mitochondrial genome of Ruizia karukerae (Rhigonematomorpha, Nematoda)

Mitochondrial genes and whole mitochondrial genome sequences are widely used as molecular markers in studying population genetics and resolving both deep and shallow nodes in phylogenetics. In animals the mitochondrial genome is generally composed of a single chromosome, but mystifying exceptions sometimes occur. We determined the complete mitochondrial genome of the millipede-parasitic nematode Ruizia karukerae and found its mitochondrial genome consists of two circular chromosomes, which is highly unusual in bilateral animals. Chromosome I is 7,659 bp and includes six protein-coding genes, two rRNA genes and nine tRNA genes. Chromosome II comprises 7,647 bp, with seven protein-coding genes and 16 tRNA genes. Interestingly, both chromosomes share a 1,010 bp sequence containing duplicate copies of cox2 and three tRNA genes (trnD, trnG and trnH), and the nucleotide sequences between the duplicated homologous gene copies are nearly identical, suggesting a possible recent genesis for this bipartite mitochondrial genome. Given that little is known about the formation, maintenance or evolution of abnormal mitochondrial genome structures, R. karukerae mtDNA may provide an important early glimpse into this process.

First Report of Aphelenchoides bicaudatus (Nematoda: Aphelenchoididae) from South Korea

The genus Aphelenchoides (Fischer, 1894) includes a diverse group of species, some of which are of economic importance. A. bicaudatus (Imamura, 1931) Filipjev and Schuurmans Stekhoven, 1941 is reported for the first time from South Korea, with a detailed redescription of the species. Specimens were collected from chrysanthemum (Chrysanthemum morifolium) leaves and shoot tips in South Korea. The species was identified by morphological traits and molecular sequencing. A bifurcated tail distinguishes A. bicaudatus from its congeneric species. To confirm species identification, we determined the partial 18S ribosomal DNA sequence of the specimens and compared with those obtained from other Aphelenchoides species available on GenBank.

Marine Molluscan Fauna of Jindo Island

As a part of the commemorative joint faunal survey for the 30th anniversary of the Korean Society of Systematic Zoology, the molluscan fauna of Jindo Island was investigated based on sample collection from 6 localities from the 6 to the 8 of Jul 2016. A total of 114 molluscan species from 47 families were collected and identified. Among these, 42 species from 11 families are newly reported from Jindo Island and combining the previous records with the present study totals 157 species from 57 families. Distribution of species records indicates that marine biogeography of Jindo Island represent an overlapping zone for marine organisms which dwell in the Yellow sea and the southern sea areas of Korean waters.

First Record of Acrobeloides nanus (Cephalobidae:Rhabditida: Nematoda) from Korea

Acrobeloides nanus (de Man, 1880) Anderson, 1968 belonging to the family Cephalobidae Filpijev, 1934 (Cephalobomorpha) is newly reported from South Korea. This species is distinguished from other Acrobeloides species by its low and blunt labial probolae, five lateral incisures with middle incisure extending to the tail tip, and bluntly rounded tail. In this study, details of morphological characters of A. nanus is described and illustrated based on optical and scanning electron microscopy. In addition, molecular sequence data of the D2-D3 region of 28S rDNA, 18S rDNA and mitochondria DNA cox1 region from this species are provided as DNA barcode sequences.