Language：English   Publishing type：Research paper (scientific journal)   Publisher：Frontiers Media SA  

Species retaining ancestral features, such as species called living fossils, are often regarded as less derived than their sister groups, but such discussions are usually based on qualitative enumeration of conserved traits. This approach creates a major barrier, especially when quantifying the degree of phenotypic evolution or degree of derivedness, since it focuses only on commonly shared traits, and newly acquired or lost traits are often overlooked. To provide a potential solution to this problem, especially for inter-species comparison of gene expression profiles, we propose a new method named “derivedness index” to quantify the degree of derivedness. In contrast to the conservation-based approach, which deals with expressions of commonly shared genes among species being compared, the derivedness index also considers those that were potentially lost or duplicated during evolution. By applying our method, we found that the gene expression profiles of penta-radial phases in echinoderm tended to be more highly derived than those of the bilateral phase. However, our results suggest that echinoderms may not have experienced much larger modifications to their developmental systems than chordates, at least at the transcriptomic level. In vertebrates, we found that the mid-embryonic and organogenesis stages were generally less derived than the earlier or later stages, indicating that the conserved phylotypic period is also less derived. We also found genes that potentially explain less derivedness, such as Hox genes. Finally, we highlight technical concerns that may influence the measured transcriptomic derivedness, such as read depth and library preparation protocols, for further improvement of our method through future studies. We anticipate that this index will serve as a quantitative guide in the search for constrained developmental phases or processes.

DOI： 10.3389/fcell.2021.749963

PubMed

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Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

DOI： 10.1038/s42003-020-1091-1

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Other Link： http://www.nature.com/articles/s42003-020-1091-1

Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media {LLC}  

DOI： 10.1007/s00427-020-00665-6

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Language：Japanese   Publishing type：Research paper (scientific journal)  

CiNii Article

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DOI： 10.1007/978-4-431-56609-0_34

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：BIOMED CENTRAL LTD  

Background: Xenoturbella is a group of marine benthic animals lacking an anus and a centralized nervous system. Molecular phylogenetic analyses group the animal together with the Acoelomorpha, forming the Xenacoelomorpha. This group has been suggested to be either a sister group to the Nephrozoa or a deuterostome, and therefore it may provide important insights into origins of bilaterian traits such as an anus, the nephron, feeding larvae and centralized nervous systems. However, only five Xenoturbella species have been reported and the evolutionary history of xenoturbellids and Xenacoelomorpha remains obscure.
Results: Here we describe a new Xenoturbella species from the western Pacific Ocean, and report a new xenoturbellid structure - the frontal pore. Non-destructive microCT was used to investigate the internal morphology of this soft-bodied animal. This revealed the presence of a frontal pore that is continuous with the ventral glandular network and which exhibits similarities with the frontal organ in acoelomorphs.
Conclusions: Our results suggest that large size, oval mouth, frontal pore and ventral glandular network may be ancestral features for Xenoturbella. Further studies will clarify the evolutionary relationship of the frontal pore and ventral glandular network of xenoturbellids and the acoelomorph frontal organ. One of the habitats of the newly identified species is easily accessible from a marine station and so this species promises to be valuable for research on bilaterian and deuterostome evolution.

DOI： 10.1186/s12862-017-1080-2

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Language：English   Publishing type：Research paper (scientific journal)  

CiNii Article

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-BLACKWELL  

The early stalked stages of an isocrinid sea lily, Metacrinus rotundus, were examined up to the early pentacrinoid stage. Larvae induced to settle on bivalve shells and cultured in the laboratory developed into late cystideans. Three-dimensional (3D) images reconstructed from very early to middle cystideans indicated that 15 radial podia composed of five triplets form synchronously from the crescent-shaped hydrocoel. The orientation of the hydrocoel indicated that the settled postlarvae lean posteriorly. In very early cystideans, the orals, radials, basals and infrabasals, with five plates each in the crown, about five columnals in the stalk, and five terminal stem plates in the attachment disc, had already formed. In mid-cystideans, an anal plate appeared in the crown. Late cystideans cultured in the field developed into pentacrinoids about 5 months after settlement. These pentacrinoids shared many crown structures with adult sea lilies. On the other hand, many features of the stalk differed from those in adult isocrinids, while sharing many characteristics with the stalk of feather star pentacrinoids, including disc-like proximal columnals, high and slender median columnals, synarthrial articulations developmentally derived from the symplexial articulations, limited formation of cirri only in the proximal columnal(s), and an attachment disc. On the basis of these findings, phylogenetic relationships among extant crinoid orders are discussed.

DOI： 10.1111/azo.12109

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

JAMBIO, Japanese Association for Marine Biology, has been organizing JAMBIO Coastal Organism Joint Surveys at Shimoda Marine Research Center, University of Tsukuba, and Misaki Marine Biological Station, the University of Tokyo. The aims of the Surveys are to uncover the benthic marine fauna of the coastal areas in and around Sagami Bay, and to form a collaborative network between marine biologists across Japan. We have so far performed six surveys, with over 100 participants in total, using common equipment such as dredges, bottom mud samplers, and epibenthic sleds. Even in Sagami Bay, one of the most intensively studied marine environments in the world, we have succeeded in collecting about 50 probable undescribed species. Other species were collected for the first time from Sagami Bay or found from previously unreported depth. The Surveys could be useful for ecological and environmental studies as well. We plan to continue the JAMBIO Coastal Organism Joint Surveys to further reveal the rich biodiversity within and around Sagami Bay and to accelerate nationwide research collaborations. We also hope to expand the Surveys to include plants and protists, and to perform them at other areas in Japan. Through the Surveys, we aim to develop new cross-disciplinary research areas and to record the long-term transition of biota along the Japanese coast. (C) 2015 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.rsma.2015.05.003

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

Shallow CO2 seeps, where CO2 gas is venting underwater, offer great potential for studies into the effects of ocean acidification at the ecosystem level. To our knowledge, only two tropical system and two temperate systems of such seeps have been described worldwide. Here we describe two new temperate systems: the Mikama Bay and Ashitsuke sites, located on Shikine Island, Japan. The Mikama Bay site is located in a shallow bay. Investigation of the gas and water chemistry showed that the gas contained 98% CO2 and up to 90 ppm H2S. Total alkalinity was constant in time and space with an average of 2265 +/- 10 mu mol kg(-1). Mapping of Eh and pH showed that the low pH zones were the largest when currents were moderate. Under moderate currents, Eh values were globally higher and total sulfides concentration lower, supporting that a longer residence time of the bay water allow the oxidation of the sulfides to sulfates. Zones suitable for acidification studies: with a pH lower than 8.0, low saturation state of calcite and aragonite, and non-detectable sulfide concentration, can be defined a few meters from the main venting zone. The second site, Ashitsuke, is located in the inter-tidal zone on a shore composed of boulders. Several areas showed reduced pH sometimes restricted to a few meters and up to 20 m long along the shoreline. Temperature was higher in some of the reduced pH zones suggesting the presence of hot springs in addition to vents. This paper also highlights the need for discovering additional CO2 seeps, which by their nature often lack comparable replicates and can be confounded by factors other than CO2. In this regard, Japan offers great potential as it is home to numerous active volcanoes, representing potential venting sites in climates ranging from tropical to sub-polar. (C) 2015 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.rsma.2015.07.004

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER  

The presence of an anteroposterior body axis is a fundamental feature of bilateria. Within this group, echinoderms have secondarily evolved pentameral symmetric body plans. Although all echinoderms present bilaterally symmetric larval stages, they dramatically rearrange their body axis and develop a pentaradial body plan during metamorphosis. Therefore, the location of their anteroposterior body axis in adult forms remains a contentious issue. Unlike other echinoderms, sea cucumbers present an obvious anteroposterior axis not rearranged during metamorphosis, thus representing an interesting group to study their anteroposterior axis patterning. Hox genes are known to play a broadly conserved role in anteroposterior axis patterning in deuterostomes. Here, we report the expression patterns of Hox genes from early development to pentactula stage in sea cucumber. In early larval stages, five Hox genes (AjHox1, AjHox7, AjHox8, AjHox11/13a, and AjHox11/13b) were expressed sequentially along the archenteron, suggesting that the role of anteroposterior patterning of the Hox genes is conserved in bilateral larvae of echinoderms. In doliolaria and pentactula stages, eight Hox genes (AjHox1, AjHox5, AjHox7, AjHox8, AjHox9/10, AjHox11/13a, AjHox11/13b, and AjHox11/13c) were expressed sequentially along the digestive tract, following a similar expression pattern to that found in the visceral mesoderm of other bilateria. Unlike other echinoderms, pentameral expression patterns of AjHox genes were not observed in sea cucumber. Altogether, we concluded that AjHox genes are involved in the patterning of the digestive tract in both larvae and metamorphosis of sea cucumbers. In addition, the anteroposterior axis in sea cucumbers might be patterned like that of other bilateria.

DOI： 10.1007/s00427-015-0510-7

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：MAGNOLIA PRESS  

A new genus and new species of antedonid comatulid is described from southern Japan. Belonometra n. gen. has a unique appearance with ten long arms, numerous cirri, and remarkably long and crowded pinnules. The new genus shares some characters with subfamily Heliometrinae. However, the comparative length of pinnules, which is a diagnostic character to determine subfamily Antedonidae, is different. The subfamily into which the new genus should be placed is unclear.

DOI： 10.11646/zootaxa.3972.3.9

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Language：Japanese   Publishing type：Research paper (scientific journal)  

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Language：English   Publishing type：Doctoral thesis  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

The stalked crinoid, Metacrinus rotundus, is one of the most basal extant echinoderms. Here, we show the expression patterns of Six3, Pax6, and Otx in the early development of M. rotundus. All three genes are highly expressed in stages from the gastrula to the auricularia larval stage. Ectodermal expression of MrOtx appears to be correlated with development of the ciliary band. These three genes are expressed sequentially along the embryonic body axis in the anterior and middle walls of the archenteron in the order of MrPax6, MrSix3, and MrOtx. The anterior, middle, and posterior parts of the archenteron in the late gastrula differentiate into the axo-hydrocoel, the enteric sac, and somatocoels at later stages, respectively. The three genes are expressed sequentially from the tip of the axo-hydrocoel to the bottom of enteric sac in the order of MrSix3, MrPax6, and MrOtx at the later stages. This suggests that these genes are involved in patterning of the larval endo-mesoderm in stalked crinoids. The present results suggest that radical alterations have occurred in the expression and function of homeobox genes in basal echinoderms. (c) 2010 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.gep.2010.09.002

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Presentation type：Symposium, workshop panel (nominated)  

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Language：Japanese   Presentation type：Public lecture, seminar, tutorial, course, or other speech  

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Language：Japanese   Presentation type：Symposium, workshop panel (public)  

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Language：English   Presentation type：Oral presentation (general)  

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Language：Japanese   Presentation type：Oral presentation (general)  

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Language：English   Presentation type：Poster presentation  

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Language：English   Presentation type：Oral presentation (general)  

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Language：English   Presentation type：Oral presentation (general)  

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