Shimpei F. Hiruta

Molecular phylogeny of kinorhynchs.

We reconstructed kinorhynch phylogeny using maximum-likelihood and Bayesian analyses of nuclear 18S and 28S rRNA gene sequences from 30 species in 13 genera (18S) and 23 species in 12 genera (28S), representing eight families and both orders (Cyclorhagida and Homalorhagida) currently recognized in the phylum. We analyzed the two genes individually (18S and 28S datasets) and in combination (18S+28S dataset). We detected four main clades (I-IV). Clade I consisted of family Echinoderidae. Clade II contained representatives of Zelinkaderidae, Antygomonidae, Semnoderidae, Centroderes, and Condyloderes, the latter two currently classified in Centroderidae; within Clade II, Zelinkaderidae, Antygomonidae, and Semnoderidae comprised a clade with strong nodal support. Clade III contained only two species in Campyloderes, also currently classified in the Centroderidae, indicating polyphyly for this family. Clades I-III, containing all representatives of Cyclorhagida included in the analysis except for Dracoderes abei, formed a clade with high nodal support in the 28S and 18S+28S trees. Clade IV, resolved in the 18S and 18S+28S trees with high nodal support, contained only species in order Homalorhagida, with the exception of the cyclorhagid Dracoderes abei. Order Cyclorhagida as it currently stands is thus polyphyletic, and order Homalorhagida paraphyletic. Our results indicate that Dracoderidae has been misplaced in Cyclorhagida based on homoplasious characters. Our analyses did not resolve the relationships among Clades I-III within Cyclorhagida. Neither gene alone nor the combined dataset resolved all nodes in trees, indicating that additional markers will be needed to reconstruct kinorhynch phylogeny.

Molecular Systematics of Tanaidacea (Crustacea: Peracarida) Based on 18S Sequence Data, with an Amendment of Suborder/Superfamily-Level Classification

Phylogenetic relationships within Tanaidacea were analyzed based on sequence data for the 18S rRNA gene. Our results strongly supported a monophyletic group composed of Neotanaidae, Tanaoidea, and Paratanaoidea, with the first two taxa forming a clade. These results contradict three previously suggested hypotheses of relationships. Based on the molecular results, and considering morphological similarities/differences between Neotanaidomorpha and Tanaidomorpha, we demoted Suborder Neotanaidomorpha to Superfamily Neotanaoidea within Tanaidomorpha; with this change, the classification of extant tanaidaceans becomes a two-suborder, four-superfamily system. This revision required revision of the diagnoses for Tanaidomorpha and its three super-families. The results for Apseudomorpha were ambiguous: this taxon was monophyletic in the maximum likelihood and Bayesian analyses, but paraphyletic in the maximum parsimony and minimum evolution analyses.

Description of a species of Fabaeformiscandona (Ostracoda, Crustacea) from Kushiro Marsh, Hokkaido, Japan, with the nearly complete mitochondrial genomic sequence.

Abstract Background So far, 16 species of non-marine ostracods have been reported from Kushiro Marsh, Kushiro Shitsugen National Park, eastern Hokkaido, Japan (Hiruta and Smith 2001, Smith and Hiruta 2004). Nine of these species are in Candonidae, the second-most diverse family of non-marine ostracods. This family contains ca. 550 species, or around 25% of the total number of non-marine ostracod species (Martens et al. 2008). New information We sampled ostracods in Kushiro Marsh on 27 December 2012 and identified an undescribed species in the family Candonidae, herein described as Fabaeformiscandona kushiroensis sp. nov. This species belongs to the F. acuminata species group and is characterized by the shapes of the elongate, dorsally directed medial and outer lobes on the distal end of each hemipenis. We also determined for this species the sequence of the nearly complete mitochondrial genome, the first record from the order Podocopa. The genome (ca. 17 kbp) contains two ribosomal RNA, 22 transfer RNA, and 13 protein-coding genes, as also found in other arthropods for which the mitochondrial genome has been sequenced. The gene arrangement is similar to the pancrustacean ground pattern, except that in the control region there is an approximately 2 kbp tandem repeat region composed of 220-bp motif sequences. We describe the genetic features of the mitochondrial genome, including nucleotide composition and the secondary structures of tRNAs and rRNAs, and compare them with the genome of Vargula hilgendorfii (Myodocopa, Ostracoda).

Molecular Phylogeny of Cypridoid Freshwater Ostracods (Crustacea: Ostracoda), Inferred from 18S and 28S rDNA Sequences

With the aim of exploring phylogenetic relationships within Cypridoidea, the most species-rich superfamily among the podocopidan ostracods, we sequenced nearly the entire 18S rRNA gene (18S) and part of the 28S rRNA gene (28S) for 22 species in the order Podocopida, with representatives from all the major cypridoid families. We conducted phylogenetic analyses using the methods of maximum likelihood, minimum evolution, and Bayesian analysis. Our analyses showed monophyly for Cyprididae, one of the four families currently recognized in Cypridoidea. Candonidae turned out to be paraphyletic, and included three clades corresponding to the subfamilies Candoninae, Paracypridinae, and Cyclocypridinae. We propose restricting the name Candonidae s. str. to comprise what is now Candoninae, and raising Paracypridinae and Cyclocyprininae to family rank within the superfamily Cypridoidea.

Trilobodrilus itoi sp. nov., with a Re-Description of T. nipponicus (Annelida: Dinophilidae) and a Molecular Phylogeny of the Genus

The marine interstitial annelid Trilobodrilus itoi sp. nov., the sixth member of the genus, is described on the basis of specimens collected intertidally at Ishikari Beach, Hokkaido, Japan; this is the second species in the genus described from the Pacific Rim. In addition, T. nipponicus Uchida and Okuda, 1943 is re-described based on fresh topotypic material from Akkeshi, Hokkaido, Japan. From both species, we determined sequences of the nuclear 18S and 28S rRNA genes, and the mitochondrial cytochrome c oxidase subunit I (COI) gene. Molecular phylogenetic trees based on concatenated sequences of the three genes showed that T. itoi and T. nipponicus form a clade, which was the sister group to a clade containing the two European congeners T. axi Westheide, 1967 and T. heideri Remane, 1925. The Kimura two-parameter distance for COI was 22.5–22.7% between T. itoi and T. nipponicus, comparable with interspecific values in other polychaete genera. We assessed the taxonomic utility of epidermal inclusions and found that the known six species can be classified into three groups.

A new, interstitial species of Terrestricythere (Crustacea: Ostracoda) and its microdistribution at Orito Beach, northeastern Sea of Japan

We describe Terrestricythere proboscidis sp. nov. from a littoral interstitial habitat at Orito Beach, Matsumae, southern Hokkaido, Japan, a site characterized by coarse sand with many pebbles. This is the fifth known species of the ostracod superfamily Terrestricytheroidea, the first interstitial species of the superfamily, and the first record of the superfamily from Japan. The new species is clearly distinguished from its four known congeners by its small carapace with a transversely flat ventral margin, and the seventh limb consisting of four podomeres; its hemipenis has a long, S-curved process. We also report here the habitat, microdistribution, and locomotory behavior of the new species. Quantitative sampling revealed that the species lives in an interstitial environment. T. proboscidis is euryhaline. Behavioral observations showed that T. proboscidis cannot swim, but uses its appendages to push itself among sediment grains. An analysis of variance showed temperature and grain size, as well as temperature-depth and temperature-grain size interactions, to be significant influences on variation in population density. Sediment moisture content is correlated with these variables and likely is a primary factor in this species’ microdistribution.

Tubulanus tamias sp. nov. (Nemertea: Palaeonemertea) with Two Different Types of Epidermal Eyes

Based on specimens collected subtidally (∼10 m in depth) in Tomioka Bay, Japan, we describe the palaeonemertean Tubulanus tamias sp. nov., which differs from all its congeners in body coloration. In molecular phylogenetic analyses based on partial sequences of the nuclear 18S and 28S rRNA genes and histone H3, as well as the mitochondrial 16S rRNA and cytochrome c oxidase subunit I genes, among selected palaeonemerteans, T. tamias nested with part of the congeners in Tubulanus, while the genus as currently diagnosed appears to be non-monophyletic. Molecular cloning detected polymorphism in 28S rDNA sequences in a single individual of T. tamias, indicating incomplete concerted evolution of multiple copies. Tubulanus tamias is peculiar among tubulanids in having 9–10 pigment-cup eyes in the epidermis on either side of the head anterior to the cerebral sensory organs, and remarkably there are two types of eyes. The anterior 8–9 pairs of eyes, becoming larger from anterior to posterior, are completely embedded in the epidermis and proximally abutting the basement membrane; each pigment cup contains bundle of up to seven, rod-shaped structure that resemble a rhabdomeric photoreceptor cell. In contrast, the posterior-most pair of eyes, larger than most of the anterior ones, have an optical cavity filled with long cilia and opening to the exterior, thus appearing to have ciliary-type photoreceptor cells. The size and arrangement of the eyes indicate that the posterior-most pair of eyes are the remnant of the larval (or juvenile) eyes.

A matter of persistence: differential Late Pleistocene survival of two rocky-shore idoteid isopod species in northern Japan

The expansion–contraction (EC) model of Pleistocene biogeography and the concept of refugia are of dubious applicability for rocky-shore marine species along the northwest Pacific coast, which was not glaciated at the last glacial maximum (LGM) and likely remained largely habitable by marine communities. We examined the population structure and historical demography of two ecologically similar rocky-intertidal idoteid isopods, Idotea ochotensis and Cleantiella isopus, in northern Japan based on mitochondrial COI and (for I. ochotensis) nuclear ITS nucleotide sequences. We concluded that I. ochotensis persisted in northern Japan across one or more glacial cycles, whereas C. isopus recolonized northern Japan after the LGM. We present an alternative general model for Pleistocene biogeography in temperate to subtropical, non-glaciated coastal regions, wherein species tend to retain large population size and high genetic diversity across glacial cycles in a zone of persistence, with flanking zones of expansion and contraction where the geographical range cyclically expands and contracts (i.e., undergoes latitudinal displacements) with climatic oscillations. We also found that local sea straits had less effect in determining phylogeographic boundaries than a long stretch of unfavorable shore habitat, and that late Holocene sea current patterns appear to have affected fine-scale phylogeographic patterns.

Two new species of Scapheremaeus from Southern Japan (Acari: Oribatida: Cymbaeremaeidae), with genetic information

Abstract The present paper deals with two new species of oribatid mites of the genus Scapheremaeus Berlese, 1910 from the subtropical islands in Southern Japan. Scapheremaeus nakanoshimensis sp. nov. and Scapheremaeus boninensis sp. nov. are proposed on the basis of adults. Furthermore, we present data on distribution, diversity and habitat ecology of all known species of Scapheremaeus in Japan, and a key is provided for identification of hitherto recorded species in this country. Majority of Scapheremaeus species found in Japan are known to be restricted to areas of Southern Japan and Eastern China. Only one of the species has a relatively broad distribution in South America and East Asia. Most species of Scapheremaeus in Japan are inhabitants of soil and litter of various forests, and mosses growing on rocks, but few of them are arboreal. The D3 fragments of the 28S rRNA (28S D3) and 18S rRNA genes of Scapheremaeus nakanoshimensis sp. nov. are sequenced and data are available in the sequence database. Comparison of the 28S D3 gene sequence of Scapheremaeus nakanoshimensis sp. nov. with other oribatid mites gene sequences identifies that the representatives of Scutoverticidae (Scutovertex, Provertex, Exochocepheus) and Eremaeozetidae (Eremaeozetes), Ameronothridae (Ameronothrus) and Phenopelopidae (Eupelops) are the closest relatives to Scapheremaeus with regard to the species included in this analysis.

A preliminary molecular phylogeny shows Japanese and Austrian populations of the red mite Balaustium murorum (Acari: Trombidiformes: Erythraeidae) to be closely related

The red mite Balaustium murorum (Hermann) inhabits the Western Palaearctic realm and is well adapted to man-made structures. In Japan, B. murorum had been reported more frequently after the 1980s. A molecular phylogeny based on the nuclear 18S rRNA and mitochondrial COI genes, and including B. murorum individuals from Japan and Austria and representatives of related species from Japan showed four Balaustium species-level lineages in Japan (B. murorum, Balaustium sp. 1, Balaustium sp. 2, Balaustium sp. 3). The B. murorum lineage shared identical 18S sequence and COI haplotype with the Austrian population. Balaustium sp. 1 was detected from the Tokyo and Misaki area (Honshu Island) and was the sister group to B. murorum; the other two lineages inhabited coastal environments of Erimo, Hokkaido Island (Balaustium sp. 2) and Ainan, Shikoku Island (Balaustium sp. 3). The high genetic distances among these four lineages indicate that each lineage is a distinct species, with three of the lineages representing undescribed species. Our results are compatible with the conclusion that B. murorum was introduced to Japan from Europe, although our study did not resolve the polarity or timing of migration events.