Eurotatorian paraphyly: Revisiting phylogenetic relationships based on the complete mitochondrial genome sequence of Rotaria rotatoria (Bdelloidea: Rotifera: Syndermata)

<p>Abstract</p> <p>Background</p> <p>The Syndermata (Rotifera+Acanthocephala) is one of the best model systems for studying the evolutionary origins and persistence of different life styles because it contains a series of lineage-specific life histories: Monogononta (cyclic parthenogenetic and free-living), Bdelloidea (entirely parthenogenetic and mostly benthic dweller), Seisonidea (exclusively bisexual and epizoic or ectoparasitic), and Acanthocephala (sexual and obligatory endoparasitic). Providing phylogenetic resolution to the question of Eurotatoria (Monogononta and Bdelloidea) monophyly versus paraphyly is a key factor for better understanding the evolution of different life styles, yet this matter is not clearly resolved. In this study, we revisited this issue based on comparative analysis of complete mitochondrial genome information for major groups of the Syndermata.</p> <p>Results</p> <p>We determined the first complete mitochondrial genome sequences (15,319 bp) of a bdelloid rotifer, <it>Rotaria rotatoria</it>. In order to examine the validity of Eurotatoria (Monogononta and Bdelloidea) monophyly/paraphyly, we performed phylogenetic analysis of amino acid sequences for eleven protein-coding genes sampled from a wide variety of bilaterian representatives. The resulting mitochondrial genome trees, inferred using different algorithms, consistently failed to recover Monogononta and Bdelloidea as monophyletic, but instead identified them as a paraphyletic assemblage. Bdelloidea (as represented by <it>R. rotatoria</it>) shares most common ancestry with Acanthocephala (as represented by <it>L. thecatus</it>) rather than with monogonont <it>B. plicatilis</it>, the other representative of Eurotatoria.</p> <p>Conclusion</p> <p>Comparisons of inferred amino acid sequence and gene arrangement patterns with those of other metazoan mtDNAs (including those of acanthocephalan <it>L. thecatus </it>and monogonont <it>B. plicatilis</it>) support the hypothesis that Bdelloidea shares most common ancestry with Acanthocephala rather than with Monogononta. From this finding, we suggest that the obligatory asexuality of bdelloideans may have secondarily derived from some other preexisting condition in earlier lineage of rotifers. Providing a more complete assessment of phylogenetic relationships and inferring patterns of evolution of different types of life styles among Syndermata awaits comparisons requiring mitochondrial genome sequencing of Seisonidea.</p

A new species of the genus Cephalodella (Rotifera, Monogononta) from Korea, with reports of four additional cephalodellid species

A new monogonont rotifer, Cephalodella binoculata sp. nov., was described from a soil sample collected in Korea. The new species is morphologically similar to C. carina but is distinguished by having two frontal eyespots, a vitellarium with eight nuclei, and the shape of its fulcrum. We also described four other cephalodellid species collected in Korea; Cephalodella auriculata, C. catellina, C. gracilis, and C. tinca. Of these four species, C. gracilis and C. tinca were newly recorded in Korea. We provided the morphological characteristics of the five Cephalodella species along with photographs of trophi observed with a scanning electron microscope. Furthermore, we provided the mitochondrial cytochrome c oxidase subunit I gene sequences of the five species

Redescription of Two Urostylid Ciliates (Ciliophora: Urostylida), Anteholosticha pulchra and Metaurostylopsis struederkypkeae from Korea

Two urostylid ciliates, Anteholosticha pulchra (Kahl, 1932) Berger, 2003 and Metaurostylopsis struederkypkeae Shao et al., 2008, new to Korea, were collected from the Yellow Sea and the East Sea, Korea, respectively. They were identified based on live observation and protargol impregnation. Taxonomical characters of A. pulchra are as follows: 190-300×30-55 μm size in vivo; contractile vacuole located on the left side of the posterior 1/4 of the cell; spherical-reddish granules at cirral bases and around dorsal bristles, somewhat sparsely distributed throughout the cell surface; four frontal and two frontoterminal cirri; four dorsal kineties; caudal cirri absent. Metaurostylopsis struederkypkeae is characterized as follows: 80-110×40-50 μm size in vivo; caudal cirri absent; two types of cortical granules: type 1, yellow-green arranged along the ventral cirral rows and dorsal kineties; type 2, small and reddish, with an irregular arrangement; four frontal, four to eight frontoterminal, and two to six transverse cirri; five to seven left and three to five right marginal rows. Sequences of small subunit ribosomal DNA were determined from both species, and pairwise distances with their relatives were analyzed

Morphology and Molecular Phylogeny of Pseudouroleptus jejuensis nov. spec., a New Soil Ciliate (Ciliophora, Spirotrichea) from South Korea

A new soil ciliate, Pseudouroleptus jejuensis, was discovered from Jeju Island, South Korea and described based on live observation, protargol impregnation, and SSU rRNA gene sequence analyses. Pseudouroleptus jejuensis differs from other congeneric species mainly by number of dorsal kineties (5 vs. 4). Based on our observation of late dividers, we confirm that the dorsal kinety anlage 3 forms 3 kineties (i.e., dorsal kineties 3–5), and the dorsal kinety anlagen 1–3 form 3–5/1–2/0 caudal cirri, respectively. Our gene trees support the assignment of this new species in Pseudouroleptus to full supporting values

New molecular sequences for two genera of marine planarians facilitate determination of their position in the phylogenetic tree, with new records for two species (Platyhelminthes, Tricladida, Maricola)

For the first time, molecular sequences of the 18S ribosomal DNA were generated for representatives of the genera Obrimoposthia Sluys &amp;amp; Ball, 1989 and Paucumara Sluys, 1989 of the suborder of the marine triclads, or Maricola, by analyzing the species Obrimoposthia wandeli (Hallez, 1906) and Paucumara trigonocephala (Ijima &amp;amp; Kaburaki, 1916). On the basis of this molecular data the phylogenetic position of these two genera in the phylogenetic tree of the Maricola was determined and compared with their position in the phylogeny based on the analysis of anatomical features. New records for these two species are documented and their taxonomic status is determined on the basis of histological studies

A new species of the genus Pseudocrangonyx (Crustacea, Amphipoda, Pseudocrangonyctidae) from Korea

A new subterranean species of pseudocrangonyctid amphipod, Pseudocrangonyx daejeonensis sp. n. is described from the interstitial waters in Daejeon, Korea. Pseudocrangonyx daejeonensis sp. n. is distinguished from three morphologically similar congeners, P. coreanus Uéno, 1966, P. febras Sidorov, 2009, and P. gudariensis Tomikawa & Sato, 2016, by the characteristics of antenna 1, antenna 2, mandible, gnathopod 2, pleopods, uropods 1–2, and telson. Molecular phylogenetic analyses based on nuclear 28S rRNA and histone H3, and mitochondrial cytochrome c oxidase subunit I and 16S rRNA genes revealed that P. daejeonensis is a sister species of the unnamed Pseudocrangonyx sp. 3 inhabiting central Japan

The susceptibility of Anopheles lesteri to infection with Korean strain of Plasmodium vivax

<p>Abstract</p> <p>Background</p> <p>Following its recent re-emergence, malaria has gained renewed attention as a serious infectious disease in Korea. Three species of the Hyrcanusgroup, <it>Anopheles lesteri, Anopheles sinensis </it>and <it>Anopheles pullus</it>, have long been suspected malaria vectors. However, opinions about their vector ability are controversial. The present study was designed with the aim of determining the susceptibility of these mosquitoes to a Korean isolate of <it>Plasmodium vivax</it>. Also, <it>An. sinensis </it>is primarily suspected to be vector of malaria in Korea, but in Thailand, the same species is described to have less medical importance. Therefore, comparative susceptibility of Thai and Korean strains of <it>An. sinensis </it>with Thai strain of <it>P. vivax </it>may be helpful to understand whether these geographically different strains exhibit differences in their susceptibility or not.</p> <p>Methods</p> <p>The comparative susceptibility of <it>An. lesteri</it>, <it>An. sinensis </it>and <it>An. pullus </it>was studied by feeding laboratory-reared mosquitoes on blood from patients carrying gametocytes from Korea and Thailand.</p> <p>Results</p> <p>In experimental feeding with Korean strain of <it>P. vivax</it>, oocysts developed in <it>An. lesteri</it>, <it>An. sinensis </it>and <it>An. pullus</it>. Salivary gland sporozoites were detected only in <it>An. lesteri </it>and <it>An. sinensis </it>but not in <it>An. pullus</it>. Large differences were found in the number of sporozoites in the salivary glands, with <it>An. lesteri </it>carrying much higher densities, up to 2,105 sporozoites in a single microscope field of 750 × 560 μM, whereas a maximum of 14 sporozoites were found in any individual salivary gland of <it>An. sinensis</it>. Similar results were obtained from a susceptibility test of two different strains of <it>An. sinensis </it>to Thai isolate of <it>P. vivax</it>, and differences in vector susceptibility according to geographical variation were not detected.</p> <p>Conclusion</p> <p>The high sporozoite rate and sporozoite loads of <it>An. lesteri </it>indicate that this species is highly susceptible to infection with <it>P. vivax</it>. <it>Anopheles sinensis </it>appears to have a markedly reduced ability to develop salivary gland infection, whilst in <it>An. pullus</it>, no sporozoites were found in the salivary glands. Provided that the survival rate of <it>An. lesteri </it>is sufficiently high in the field, it would be a highly competent vector of vivax malaria.</p

A new marine ciliate, Metaurostylopsis antarctica nov. spec. (Ciliophora, Urostylida) from the Antarctic Ocean

In this study, a new marine urostylid ciliate, Metaurostylopsis antarctica nov. spec. collected from the Antarctic Ocean was investigated using morphological, morphometrical, and molecular methods. Metaurostylopsis antarctica nov. spec. is characterized as follows: slender to ellipsoid form in body shape; two types of cortical granules, ellipsoid large one (type I, yellow-green, 1.5 × 1 μm) in rows along dorsal kineties and cirri, circular small one (type II, colourless, 0.3 μm in diameter) scattered throughout whole body; 19–24 adoral membranelles, 4 frontal cirri, 2–5 frontoterminal cirri, 1 buccal and 2 transverse cirri; 3–5 midventral pairs, 10–15 cirri of midventral row; 1 right and 2 left marginal rows; 3 dorsal kineties; about 43 macronuclear nodules. This new species mainly differs from the congeners by the number of marginal rows (1 vs. 3 or more on right side; 2 vs. 3 or more on left side). In addition, proter’s oral primordium  developed on the right side of the oral cavity (vs. in center of oral cavity), and the rightmost anlage splits into two parts, nam ely, the frontoterminal cirri and a transverse cirrus (vs. only frontoterminal cirri). Inter-specific dissimilarities of the SSU rRNA gene between the congeners range from 3.3 to 4.4%

Comparative analysis of complete mitochondrial genome sequences confirms independent origins of plant-parasitic nematodes

BACKGROUND: The nematode infraorder Tylenchomorpha (Class Chromadorea) includes plant parasites that are of agricultural and economic importance, as well as insect-associates and fungal feeding species. Among tylenchomorph plant parasites, members of the superfamily Tylenchoidea, such as root-knot nematodes, have great impact on agriculture. Of the five superfamilies within Tylenchomorpha, one (Aphelenchoidea) includes mainly fungal-feeding species, but also some damaging plant pathogens, including certain Bursaphelenchus spp. The evolutionary relationships of tylenchoid and aphelenchoid nematodes have been disputed based on classical morphological features and molecular data. For example, similarities in the structure of the stomatostylet suggested a common evolutionary origin. In contrast, phylogenetic hypotheses based on nuclear SSU ribosomal DNA sequences have revealed paraphyly of Aphelenchoidea, with, for example, fungal-feeding Aphelenchus spp. within Tylenchomorpha, but Bursaphelenchus and Aphelenchoides spp. more closely related to infraorder Panagrolaimomorpha. We investigated phylogenetic relationships of plant-parasitic tylenchoid and aphelenchoid species in the context of other chromadorean nematodes based on comparative analysis of complete mitochondrial genome data, including two newly sequenced genomes from Bursaphelenchus xylophilus (Aphelenchoidea) and Pratylenchus vulnus (Tylenchoidea). RESULTS: The complete mitochondrial genomes of B. xylophilus and P. vulnus are 14,778 bp and 21,656 bp, respectively, and identical to all other chromadorean nematode mtDNAs in that they contain 36 genes (lacking atp8) encoded in the same direction. Their mitochondrial protein-coding genes are biased toward use of amino acids encoded by T-rich codons, resulting in high A+T richness. Phylogenetic analyses of both nucleotide and amino acid sequence datasets using maximum likelihood and Bayesian methods did not support B. xylophilus as most closely related to Tylenchomorpha (Tylenchoidea). Instead, B. xylophilus, was nested within a strongly supported clade consisting of species from infraorders Rhabditomorpha, Panagrolaimomorpha, Diplogasteromorpha, and Ascaridomorpha. The clade containing sampled Tylenchoidea (P. vulnus, H. glycines, and R. similis) was sister to all analyzed chromadoreans. Comparison of gene arrangement data was also consistent with the phylogenetic relationships as inferred from sequence data. Alternative tree topologies depicting a monophyletic grouping of B. xylophilus (Aphelenchoidea) plus Tylenchoidea, Tylenchoidea plus Diplogasteromorpha (Pristionchus pacificus), or B. xylophilus plus Diplogasteromorpha were significantly worse interpretations of the mtDNA data. CONCLUSIONS: Phylogenetic trees inferred from nucleotide and amino acid sequences of mtDNA coding genes are in agreement that B. xylophilus (the single representative of Aphelenchoidea) is not closely related to Tylenchoidea, indicating that these two groups of plant parasites do not share an exclusive most recent common ancestor, and that certain morphological similarities between these stylet-bearing nematodes must result from convergent evolution. In addition, the exceptionally large mtDNA genome size of P. vulnus, which is the largest among chromadorean nematode mtDNAs sequenced to date, results from lengthy repeated segments in non-coding regions

Stratifying non-small cell lung cancer patients using an inverse of the treatment decision rules: validation using electronic health records with application to an administrative database

To validate a stratification method using an inverse of treatment decision rules that can classify non-small cell lung cancer (NSCLC) patients in real-world treatment records. (1) To validate the index classifier against the TNM 7th edition, we analyzed electronic health records of NSCLC patients diagnosed from 2011 to 2015 in a tertiary referral hospital in Seoul, Korea. Predictive accuracy, stage-specific sensitivity, specificity, positive predictive value, negative predictive value, F1 score, and c-statistic were measured. (2) To apply the index classifier in an administrative database, we analyzed NSCLC patients in Korean National Health Insurance Database, 2002–2013. Differential survival rates among the classes were examined with the log-rank test, and class-specific survival rates were compared with the reference survival rates. (1) In the validation study (N = 1375), the overall accuracy was 93.8% (95% CI: 92.5–95.0%). Stage-specific c-statistic was the highest for stage I (0.97, 95% CI: 0.96–0.98) and the lowest for stage III (0.82, 95% CI: 0.77–0.87). (2) In the application study (N = 71,593), the index classifier showed a tendency for differentiating survival probabilities among classes. Compared to the reference TNM survival rates, the index classification under-estimated the survival probability for stages IA, IIIB, and IV, and over-estimated it for stages IIA and IIB. The inverse of the treatment decision rules has a potential to supplement a routinely collected database with information encoded in the treatment decision rules to classify NSCLC patients. It requires further validation and replication in multiple clinical settings