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      Diversity, phylogeny, and bathymetric zonation of Sirsoe (Annelida: Hesionidae) from colonization experiments in the South China Sea, with the description of three new species

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          Abstract

          The South China Sea (SCS) basin is hypothesized to host distinct and bathymetrically differentiated fauna due to its semi‐enclosed basin and three‐layer circulation system. To test this hypothesis, three cow falls are artificially deployed at separate depths (655, 1604, and 3402 m) on Zhongnan seamount in the middle SCS, and the associated worms, Sirsoe spp. are selected as targets to explore their diversity, phylogeny, and zonation pattern. Analyses of collected specimens reveal three new Sirsoe species, which were then nominally described and named as S. polita sp. nov. (655 m), S. nanhaiensis sp. nov. (1604 and 3402 m), and S. feitiana sp. nov. (3402 m), and one known species ( S. balaenophila lineage II). Metabarcoding analyses on cow‐fall sediments reveal seven additional Operated Taxonomic Units (OTUs) assigned to Sirsoe, increasing the Sirsoe diversity to 10 species/OTUs in the middle SCS. Their distribution along depth shows increasing diversity toward the deeper sites. Phylogenetic inferences recover S. polita closely related to S. alucia from the Southwest Atlantic, forming a lineage deeply divergent from others. The nine deep‐water species/OTUs are scattered in three distinct lineages showing closer phylogenetic relationships between 1604‐ and 3402‐m counterparts. The lineage formed by S. naihaiensis and S. feitiana is distinct from other non‐SCS congeners both morphologically and genetically. These results suggest multiple independent invasions of Sirsoe to the SCS, a new lineage potentially endemic to the SCS, and a strong zonation pattern related to depth, especially between the shallow (655 m) and the deep (1604 and 3402 m) sites. The semi‐enclosed feature combined with the physical structure of the SCS may contribute to such a pattern. This work is registered in ZooBank under: urn:lsid:zoobank.org:pub:317771C8‐42D717‐4765‐A168‐B3BE99B09FBF.

          Abstract

          A combination of specimen examination, metabarcoding, and phylogeny was used to explore the diversity of Sirsoe from colonization experiments in the South China Sea. A total of 10 species/OTUs were recovered, and their phylogenetic positions were resolved, with three new species described as well. A zonation pattern was observed.

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          Most cited references60

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          MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

          We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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            MUSCLE: multiple sequence alignment with high accuracy and high throughput.

            We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
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              FLASH: fast length adjustment of short reads to improve genome assemblies.

              Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome. We present FLASH, a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. We tested the correctness of the tool on one million simulated read pairs, and we then applied it as a pre-processor for genome assemblies of Illumina reads from the bacterium Staphylococcus aureus and human chromosome 14. FLASH correctly extended and merged reads >99% of the time on simulated reads with an error rate of <1%. With adequately set parameters, FLASH correctly merged reads over 90% of the time even when the reads contained up to 5% errors. When FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds. The FLASH system is implemented in C and is freely available as open-source code at http://www.cbcb.umd.edu/software/flash. t.magoc@gmail.com.

                Author and article information

                Contributors
                dszhang@sio.org.cn
                Journal
                Ecol Evol
                Ecol Evol
                10.1002/(ISSN)2045-7758
                ECE3
                Ecology and Evolution
                John Wiley and Sons Inc. (Hoboken )
                2045-7758
                17 July 2023
                July 2023
                : 13
                : 7 ( doiID: 10.1002/ece3.v13.7 )
                : e10256
                Affiliations
                [ 1 ] Key Laboratory of Marine Ecosystem Dynamics Second Institute of Oceanography, Ministry of Natural Resources Hangzhou China
                [ 2 ] Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Zhuhai China
                [ 3 ] School of Marine Sciences Sun Yat‐sen University Zhuhai China
                [ 4 ] State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences Xiamen University Xiamen China
                [ 5 ] School of Oceanography Shanghai Jiao Tong University Shanghai China
                Author notes
                [*] [* ] Correspondence

                Dongsheng Zhang, Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang, China.

                Email: dszhang@ 123456sio.org.cn

                Author information
                https://orcid.org/0000-0002-3577-1118
                Article
                ECE310256 ECE-2023-06-00907.R1
                10.1002/ece3.10256
                10352092
                1e2d4a3a-be69-42f5-99b7-fb41c7f29941
                © 2023 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 15 June 2023
                : 01 June 2023
                : 19 June 2023
                Page count
                Figures: 7, Tables: 3, Pages: 19, Words: 9311
                Funding
                Funded by: Innovation Group Project of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)
                Award ID: SML2022005
                Funded by: Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)
                Award ID: SML2021SP309
                Categories
                Biodiversity Ecology
                Biogeography
                Phylogenetics
                Taxonomy
                Research Article
                Research Articles
                Custom metadata
                2.0
                July 2023
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.3.2 mode:remove_FC converted:17.07.2023

                Evolutionary Biology
                biogeography,deep sea,metabarcoding,organic fall
                Evolutionary Biology
                biogeography, deep sea, metabarcoding, organic fall

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