Complete mitochondrial genome of Bugula neritina (Bryozoa, Gymnolaemata, Cheilostomata): phylogenetic position of Bryozoa and phylogeny of lophophorates within the Lophotrochozoa

<p>Abstract</p> <p>Background</p> <p>The phylogenetic position of Bryozoa is one of the most controversial issues in metazoan phylogeny. In an attempt to address this issue, the first bryozoan mitochondrial genome from <it>Flustrellidra hispida </it>(Gymnolaemata, Ctenostomata) was recently sequenced and characterized. Unfortunately, it has extensive gene translocation and extremely reduced size. In addition, the phylogenies obtained from the result were conflicting, so they failed to assign a reliable phylogenetic position to Bryozoa or to clarify lophophorate phylogeny. Thus, it is necessary to characterize further mitochondrial genomes from slowly-evolving bryozoans to obtain a more credible lophophorate phylogeny.</p> <p>Results</p> <p>The complete mitochondrial genome (15,433 bp) of <it>Bugula neritina </it>(Bryozoa, Gymnolaemata, Cheilostomata), one of the most widely distributed cheliostome bryozoans, is sequenced. This second bryozoan mitochondrial genome contains the set of 37 components generally observed in other metazoans, differing from that of <it>F. hispida </it>(Bryozoa, Gymnolaemata, Ctenostomata), which has only 36 components with loss of tRNA^ser(ucn)genes. The <it>B. neritina </it>mitochondrial genome possesses 27 multiple noncoding regions. The gene order is more similar to those of the two remaining lophophorate phyla (Brachiopoda and Phoronida) and a chiton <it>Katharina tunicate </it>than to that of <it>F. hispida</it>. Phylogenetic analyses based on the nucleotide sequences or amino acid residues of 12 protein-coding genes showed consistently that, within the Lophotrochozoa, the monophyly of the bryozoan class Gymnolaemata (<it>B. neritina </it>and <it>F. hispida</it>) was strongly supported and the bryozoan clade was grouped with brachiopods. Echiura appeared as a subtaxon of Annelida, and Entoprocta as a sister taxon of Phoronida. The clade of Bryozoa + Brachiopoda was clustered with either the clade of Annelida-Echiura or that of Phoronida + Entoprocta.</p> <p>Conclusion</p> <p>This study presents the complete mitochondrial genome of a cheliostome bryozoan, <it>B. neritina</it>. The phylogenetic analyses suggest a close relationship between Bryozoa and Brachiopoda within the Lophotrochozoa. However, the sister group of Bryozoa + Brachiopoda is still ambiguous, although it has some attractions with Annelida-Echiura or Phoronida + Entoprocta. If the latter is a true phylogeny, lophophorate monophyly including Entoprocta is supported. Consequently, the present results imply that Brachiozoa (= Brachiopoda + Phoronida) and the recently-resurrected Bryozoa concept comprising Ectoprocta and Entoprocta may be refuted.</p

Deceiving Google's Cloud Video Intelligence API Built for Summarizing Videos

Despite the rapid progress of the techniques for image classification, video annotation has remained a challenging task. Automated video annotation would be a breakthrough technology, enabling users to search within the videos. Recently, Google introduced the Cloud Video Intelligence API for video analysis. As per the website, the system can be used to "separate signal from noise, by retrieving relevant information at the video, shot or per frame" level. A demonstration website has been also launched, which allows anyone to select a video for annotation. The API then detects the video labels (objects within the video) as well as shot labels (description of the video events over time). In this paper, we examine the usability of the Google's Cloud Video Intelligence API in adversarial environments. In particular, we investigate whether an adversary can subtly manipulate a video in such a way that the API will return only the adversary-desired labels. For this, we select an image, which is different from the video content, and insert it, periodically and at a very low rate, into the video. We found that if we insert one image every two seconds, the API is deceived into annotating the video as if it only contained the inserted image. Note that the modification to the video is hardly noticeable as, for instance, for a typical frame rate of 25, we insert only one image per 50 video frames. We also found that, by inserting one image per second, all the shot labels returned by the API are related to the inserted image. We perform the experiments on the sample videos provided by the API demonstration website and show that our attack is successful with different videos and images

Molecular population genetics and phylogeographic studies of Ligia exotica and Ligia cinerascens in East Asia

IntroductionSea slater, in the genus Ligia, is widespread in rocky shore habitats, and the taxon is easily isolated due to its limited dispersal capacity. Therefore, most Ligia species exhibit an allopatric distribution, but Ligia exotica and L. cinerascens exhibit an overlapping distribution distribution in East Asia. Previous studies on both species have confirmed the existence of highly divergent lineages based on 16S rRNA.MethodsIn the present study, 282 Ligia individuals were collected at ten, three, and three sites in South Korea, Japan, and Vietnam, respectively, and 41 haplotypes were observed based on 16S rRNA.Results and discussionThe results of phylogeny, phylogenetic network, and TCS network, Principal Coordinates Analysis, and four Molecular Species Delimitation Analyses revealed that six genetic lineages including L. cinerascens, Lineages N and S of L. exotica, Ligia sp. 1, sp.2 and sp.3 were present. The three genetic lineages, including L. cinerascens, Lineage N of L. exotica, and Lineage S of L. exotica, were also identified in the phylogeny based on a nuclear gene of the sodium–potassium ATPase α-subunit (Nak). Phylogeographic analysis revealed that L. cinerascens and Lineage N of L. exotica were distributed overlappingly in South Korea, Japan, and the northern region of China. Generally, the two lineages of L. exotica were distributed allopatrically, which was more evident along the coastline of mainland China than that of Japan. The results of time-calibrated phylogeny suggested that the speciation events of Ligia species might be associated with Japanese mainland formation from Oligocene to Miocene (approximately 30-5 million years ago, Mya). The results of the present study provide insights that could facilitate the understanding of the evolutionary history of Ligia, tracking of geological processes, and evolutionary effects of palaeogeographical events at the population level

The complete mitochondrial genome of the sea spider Achelia bituberculata (Pycnogonida, Ammotheidae): arthropod ground pattern of gene arrangement

<p>Abstract</p> <p>Background</p> <p>The phylogenetic position of pycnogonids is a long-standing and controversial issue in arthropod phylogeny. This controversy has recently been rekindled by differences in the conclusions based on neuroanatomical data concerning the chelifore and the patterns of <it>Hox </it>expression. The mitochondrial genome of a sea spider, <it>Nymphon gracile </it>(Pycnogonida, Nymphonidae), was recently reported in an attempt to address this issue. However, <it>N. gracile </it>appears to be a long-branch taxon on the phylogenetic tree and exhibits a number of peculiar features, such as 10 tRNA translocations and even an inversion of several protein-coding genes. Sequences of other pycnogonid mitochondrial genomes are needed if the position of pycnogonids is to be elucidated on this basis.</p> <p>Results</p> <p>The complete mitochondrial genome (15,474 bp) of a sea spider (<it>Achelia bituberculata</it>) belonging to the family Ammotheidae, which combines a number of anatomical features considered plesiomorphic with respect to other pycnogonids, was sequenced and characterized. The genome organization shows the features typical of most metazoan animal genomes (37 tightly-packed genes). The overall gene arrangement is completely identical to the arthropod ground pattern, with one exception: the position of the <it>trnQ </it>gene between the <it>rrnS </it>gene and the control region. Maximum likelihood and Bayesian inference trees inferred from the amino acid sequences of mitochondrial protein-coding genes consistently indicate that the pycnogonids (<it>A. bituberculata </it>and <it>N. gracile</it>) may be closely related to the clade of Acari and Araneae.</p> <p>Conclusion</p> <p>The complete mitochondrial genome sequence of <it>A. bituberculata </it>(Family Ammotheidae) and the previously-reported partial sequence of <it>Endeis spinosa </it>show the gene arrangement patterns typical of arthropods (<it>Limulus</it>-like), but they differ markedly from that of <it>N. gracile</it>. Phylogenetic analyses based on mitochondrial protein-coding genes showed that Pycnogonida may be authentic arachnids (= aquatic arachnids) within Chelicerata <it>sensu lato</it>, as indicated by the name 'sea spider,' and suggest that the Cormogonida theory – that the pycnogonids are a sister group of all other arthropods – should be rejected. However, in view of the relatively weak node confidence, strand-biased nucleotide composition and long-branch attraction artifact, further more intensive studies seem necessary to resolve the exact position of the pycnogonids.</p

Complete mitochondrial genome of a golden orb-web spider Trichonephila clavata (Chelicerata, Arachnida) from South Korea

The mitochondrial genome of a golden orb-web spider Trichonephila clavata (L. Koch, 1878) from South Korea is determined and characterized in detail, which is the second mitochondrial genome reported from this species: the first was published from the Chinese sample by Pan et al. (). It was 14,436 bp in length being composed of 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and one control region (CR). It has a base composition of 35.99% for ‘A,’ 14.88% for ‘G,’ 9.09% for ‘C,’ and 40.04% for ‘T.’ Comparing the South Korean and Chinese mitochondrial genomes, we observed 8% nucleotide sequence differences between their CRs, caused by the different numbers and sorts of possessed tandem repeats, suggesting a promising molecular marker to distinguish South Korean individuals from Chinese ones. The phylogenetic trees using the maximum likelihood (ML) method were reconstructed with nucleotides (without 3rd codon position) and amino acids from 13 PCGs, respectively, which consistently confirmed that T. clavata (Subfamily Nephilinae) from South Korea and China are clustered together, distinctly separated from the other subfamily Araneinae in the monophyletic family Araneidae

The complete mitochondrial genome of an endangered triton snail Charonia lampas (Littorinimorpha: Charoniidae) from South Korea

The complete mitochondrial genome of an endangered triton snail Charonia lampas (Littorinimorpha: Charoniidae) from South Korea was determined with the size of 15,330 bp, which contained 13 protein-coding genes, 22 tRNAs, and two rRNAs. The overall features of the mitochondrial genome are similar to those of typical gastropod mitochondrial genomes, except for the absence of a control region (CR): a conserved gene order, a high A + T content (67.45% for C. lampas), preference for AT-rich codons, etc. It is the second mitochondrial genome reported from this species after Cho et al. (2017), and there is ca. 98% sequence similarity between those of the species. According to the maximum-likelihood tree, C. lampas placed within the monophyletic Tonnoidea, forming a monoclade with Cypraeoidea and Stromboidea within Littorinimorpha. Interestingly, we confirmed that Vermetoidea is placed at the basal position of the monophyletic Littorinimorpha

A revision and phylogenetic analysis of the millipede genus &lt;i&gt;Oxidus&lt;/i&gt; Cook, 1911 (Polydesmida, Paradoxosomatidae)

The genus Oxidus Cook, 1911 is revised to contain five species, O. avia (Verhoeff, 1937), O. gigas (Attems, 1953), O. gracilis (C.L. Koch, 1847), O. riukiaria (Verhoeff, 1940), and “species inquirenda” O. obtusus (Takakuwa, 1942). A cosmopolitan species, O. gracilis, is widely found in temperate and sub-tropical regions over the world, but other species have limited distribution in restricted regions, e.g., O. gigas in northern Vietnam, O. riukiaria and O. avia in the Ryukyu Islands (Japan). Four species, O. gracilis, O. riukiaria, O. avia and O. gigas, are confirmed as different from each other in gonopod characters, coloration and body size. The status of the last species, O. obtusus, is still doubtful and requires examination of further fresh material. The phylogenetic relationships among species of Oxidus is analyzed using two fragments of the mitochondrial genes COI (Cytochrome c Oxidase subunit I) and 16S rRNA. Three species of Oxidus are clearly separated from each other; O. gigas and O. gracilis form a monophyletic sister group with O. riukiaria. The genus Oxidus is also monophyletic and more closely related to the genus Tylopus Jeekel, 1968 than to the genera Sellanucheza Enghoff, Golovatch &amp; Nguyen, 2004 or Kronopolites Attems, 1914. In addition, an identification key to species of Oxidus is provided.</p

The mitochondrial genome of an Endangered freshwater snail Koreoleptoxis nodifila (Caenogastropoda: Semisulcospiridae) from South Korea

The mitochondrial genome of the Endangered freshwater snail Koreoleptoxis nodifila (Caenogastropoda: Semisulcospiridae) from South Korea is determined and characterized in detail. It is 15,737 bp in length being composed of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and one control region. It has a base composition of 31.23% for A, 16.29% for G, 17.84% for C, and 34.64% for T. The phylogenetic trees reconstructed based on the maximum-likelihood (ML) method and Bayesian inference (BI) confirmed that K. nodifila belongs to the Semisulcospiridae clade in the monophyletic caeonogastropod superfamily Cerithioidea

The first record of the millipede genus Streptogonopus Attems, 1914 from Vietnam, with description of a new species (Diplopoda, Polydesmida, Paradoxosomatidae)

This paper describes a new species of the millipede genus Streptogonopus Attems, 1914, S. montanus sp. n. from Vietnam, the first record of Streptogonopus in Vietnam. The new species is characterised by the solenophore completely sheathing the solenomere, both coiled twice, and the solenophore with a small spine at its middle. The species was found at ca. 1,800–2,100 m on Ngoc Linh Mountain. This first record for the genus in the Indochina peninsula has expanded its distributional range to the easternmost part of Southeast Asian mainland. An identification key to Streptogonopus species is also provided