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      A new chemosymbiotic bivalve species of the genus Acharax Dall, 1908 (Bivalvia, Solemyida, Solemyidae) from the Haima cold seep of the South China Sea

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          Abstract

          Solemyidae is an ancient group of protobranch bivalves that typically inhabit unusual environments, such as deep-sea chemosynthetic environments, and are symbiotic with chemoautotrophic and gill-hosted bacteria. In May 2018, a living solemyid bivalve was collected using a remotely operated vehicle at a depth of 1,390 m from the Haima cold seep in the northwestern slope of the South China Sea. Through a comprehensive taxonomic approach combining morphological observations and molecular phylogeny reconstruction of concatenated mitochondrial COI,16S rRNA and 18S rRNA gene sequences, a new species, Acharax haimaensis sp. nov. is identified and described. The discovery of this new species contributes to the diversity of known solemyids in deep-sea chemosynthetic environments.

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          IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

          Lam-Tung Nguyen, Heiko Schmidt, Arndt von Haeseler … (2014)
          Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.
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            MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.

            Koichiro Tamura, Glen Stecher, Daniel Walter Peterson … (2013)
            We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.
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              MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization

              Kazutaka Katoh, John Rozewicki, Kazunori Yamada (2017)
              Abstract This article describes several features in the MAFFT online service for multiple sequence alignment (MSA). As a result of recent advances in sequencing technologies, huge numbers of biological sequences are available and the need for MSAs with large numbers of sequences is increasing. To extract biologically relevant information from such data, sophistication of algorithms is necessary but not sufficient. Intuitive and interactive tools for experimental biologists to semiautomatically handle large data are becoming important. We are working on development of MAFFT toward these two directions. Here, we explain (i) the Web interface for recently developed options for large data and (ii) interactive usage to refine sequence data sets and MSAs.
              Article 0 comments Cited 1906 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Baoquan Li
                Xinzheng Li
                Journal
                Journal ID (nlm-ta): Zookeys
                Journal ID (iso-abbrev): Zookeys
                Journal ID (publisher-id): 2
                Journal ID (index): urn:lsid:arphahub.com:pub:45048D35-BB1D-5CE8-9668-537E44BD4C7E
                Journal ID (aggregator): urn:lsid:zoobank.org:pub:91BD42D4-90F1-4B45-9350-EEF175B1727A
                Title: ZooKeys
                Publisher: Pensoft Publishers
                ISSN (Print): 1313-2989
                ISSN (Electronic): 1313-2970
                Publication date Collection: 2024
                Publication date (Electronic): 24 April 2024
                Volume: 1198
                Pages: 185-192
                Affiliations
                [1 ] Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China Institute of Oceanology, Chinese Academy of Sciences Qingdao China
                [2 ] Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai China
                [3 ] Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China Center for Ocean Mega-Science, Chinese Academy of Sciences Qingdao China
                [4 ] University of Chinese Academy of Sciences, Beijing 100049, China University of Chinese Academy of Sciences Beijing China
                Author notes
                Corresponding authors: Baoquan Li ( bqli@ 123456yic.ac.cn) ; Xinzheng Li ( lixzh@ 123456qio.ac.cn)

                Academic editor: Fedor Konstantinov

                Article
                Publisher ID: 112618
                DOI: 10.3897/zookeys.1198.112618
                PMC ID: 11063622
                PubMed ID: 38698807
                SO-VID: 42babb40-804a-46e8-b47f-8dc155c8eb43
                Copyright © Mei Yang, Baoquan Li, Zhibin Gan, Dong Dong, Xinzheng Li
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                Date received : 13 September 2023
                Date accepted : 22 March 2024
                Funding
                Funded by: National Natural Science Foundation of China 501100001809 http://doi.org/10.13039/501100001809
                Funded by: Institute of Oceanology, Chinese Academy of Sciences 501100010554 http://doi.org/10.13039/501100010554
                Categories
                Subject: Research Article
                Subject: Bivalvia
                Subject: Solemyidae
                Subject: Solemyoida
                Subject: Systematics
                Subject: Taxonomy
                Subject: Asia
                Subject: Central Asia
                Subject: China

                ScienceOpen disciplines: Animal science & Zoology
                Keywords: acharaxhaimaensis sp. nov.,bathyal,deep-sea,taxonomy
                Data availability:
                ScienceOpen disciplines: Animal science & Zoology
                Keywords: acharaxhaimaensis sp. nov., bathyal, deep-sea, taxonomy

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