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(Echinodermata Holothuroidea Elasipodida) of the Western Pacific with Phylogenetic Analyses

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(Echinodermata Holothuroidea Elasipodida) of the Western Pacific with Phylogenetic Analyses PREPRINT Author-formatted, not peer-reviewed document posted on 14/07/2021 DOI: https://doi.org/10.3897/arphapreprints.e70999 New psychropotid species (Echinodermata Holothuroidea Elasipodida) of the Western Pacific with phylogenetic analyses Chuan Yu, Dongsheng Zhang, Ruiyan Zhang, Chunsheng Wang Disclaimer on biological nomenclature and use of preprints The preprints are preliminary versions of works accessible electronically in advance of publication of the final version. They are not issued for purposes of botanical, mycological or zoological nomenclature andare not effectively/validly published in the meaning of the Codes. Therefore, nomenclatural novelties (new names) or other nomenclatural acts (designations of type, choices of priority between names, choices between orthographic variants, or choices of gender of names)should NOT be posted in preprints. The following provisions in the Codes of Nomenclature define their status: International Code of Nomenclature for algae, fungi, and plants (ICNafp) Article 30.2: “An electronic publication is not effectively published if there is evidence within or associated with the publication that its content is merely preliminary and was, or is to be, replaced by content that the publisher considers final, in which case only the version with that final content is effectively published.” In order to be validly published, a nomenclatural novelty must be effectively published (Art. 32.1(a)); in order to take effect, other nomenclatural acts must be effectively published (Art. 7.10, 11.5, 53.5, 61.3, and 62.3). International Code of Zoological Nomenclature (ICZN) Article: 21.8.3: "Some works are accessible online in preliminary versions before the publication date of the final version. Such advance electronic access does not advance the date of publication of a work, as preliminary versions are not published (Article 9.9)". Author-formatted, not peer-reviewed document posted on 14/07/2021. DOI: https://doi.org/10.3897/arphapreprints.e70999 1 New psychropotid species (Echinodermata: Holothuroidea: 2 Elasipodida) of the Western Pacific with phylogenetic analysis 3 Chuan Yu1, 2, Dongsheng Zhang1, 2, 3, Ruiyan Zhang1, Chunsheng Wang1, 2, 3, 4* 4 1 School of Oceanography, Shanghai Jiao Tong University, Shanghai, China 5 2 Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, 6 Ministry of Natural Resources, Hangzhou, China 7 3 Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 8 Guangdong, China 9 4 State Key Laboratory of Satellite Ocean Environment Dynamics, Ministry of Natural 10 Resources, Hangzhou, China 11 * Corresponding author. E-mail: [email protected]; [email protected] 12 Abstract 13 Holothurians of the family Psychropotidae are widely distributed, but remain least 14 studied deep-sea holothurians. On an expedition in the Western Pacific, six 15 psychropotid specimens were collected by the Jiaolong human operated vehicle (HOV). 16 Through morphological examination, four of them were identified as a new species, 17 Benthodytes jiaolongi sp. nov., which was characterized as having minute papillae, 18 narrow brims, and terminal anus; the ossicles were either rods or primary crosses. The 19 remaining two specimens were identified as Psychropotes verrucicaudatus Xiao, Gong, 20 Kou & Li, 2019, which was first recorded at the Kyushu-Palau Ridge. The phylogenetic 21 analysis confirmed the classification status of B. jiaolongi and P. verrucicaudatus, and 22 indicated a paraphyletic relationship within the genus Benthodytes. The new species 23 clustered with Benthodytes sanguinolenta and was separated from the clade containing 24 the other Benthodytes species. 25 26 Key words 27 Benthodytes, holothurians, new record, paraphyletic group, Psychropotes, Western 28 Pacific 29 30 Introduction 31 32 Holothurians of the family Psychropotidae (Elasipodida) were first identified by 33 Théel (1882) who defined four genera of the deep-sea sea cucumbers discovered on the 34 H.M.S. Challenger Expedition. Subsequently, Hérouard (1909) and Vinogradov (1969) 35 erected Triconus Hérouard and Nectothuria Belyaev and Vinogradov, which were later 36 regarded as synonyms of Psychropotes by Hansen (1975). Psychropotidae comprises 37 three genera and 37 species. Hansen (1975) distinguished the three genera by the 38 presence or absence of an unpaired dorsal appendage, the position of the anus, and the 39 presence or absence of circum-oral (or post-oral) papillae. Although, taxonomists have Author-formatted, not peer-reviewed document posted on 14/07/2021. DOI: https://doi.org/10.3897/arphapreprints.e70999 40 long worked on this family, Psychropotidae are still the least studied deep-sea 41 holothurians. Thus, the phylogenetic relationships within Psychropotidae remain 42 unclear. 43 An expedition of the Jiaolong HOV concentrated on furthering our understanding 44 of the biodiversity, connectivity, and conservation value of the Western Pacific. During 45 sampling, six specimens of Psychropotidae were collected from seamounts on the 46 Kyushu-Palau Ridge and Weijia Guyot (Fig. 1). Based on an analysis of the external 47 morphological characters and ossicles, we identified four specimens as a new species 48 (Benthodytes jiaolongi sp.nov.) and the other two as new records Psychropotes 49 verrucicaudatus Xiao, Gong, Kou & Li, 2019. 50 51 Figure 1. Red dots show the location of Benthodytes. jiaolongi sp.nov. and green dots 52 indicated Psychropotes. verrucicaudatus. 53 54 Materials and Methods 55 Sampling and morphological observations 56 The samples described in the present study were collected by the Jiaolong HOV at 57 a depth of 2408-2602 m, from the Kyushu-Palau Ridge and Weijia Guyot. Before 58 preservation, a Canon EOS 5DII camera (Canon Inc., Tokyo, Japan) was used to take 59 photographs of the specimens on board the ship. Then, a piece of tissue was cut from Author-formatted, not peer-reviewed document posted on 14/07/2021. DOI: https://doi.org/10.3897/arphapreprints.e70999 60 all specimens and frozen at -20 ℃ for DNA extraction. Finally, the specimens were 61 fixed in 10% seawater formalin or 99% alcohol and deposited at the Repository of 62 Second Institute of Oceanography (RSIO). Sodium hypochlorite was used to dissolve 63 some body tissues (tentacles, dorsum, ventrum, brim, dorsal warts and gonads), and 64 ossicles were rinsed five times with purified water. The ossicles were observed using a 65 scanning electron microscope (TM 1000; Hitachi, Ltd., Tokyo, Japan). 66 67 PCR amplification and phylogenetic analysis 68 Total genomic DNA was extracted from 100 mg of muscle tissue using a DNeasy 69 Blood & Tissue Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s 70 instructions. Two partial mitochondrial genes, 16S rRNA and COI, were amplified 71 using primers 16S-arL/brH and COI-ef/er (Miller et al. 2017). The PCR reactions were 72 performed using a 50-µL reagent mix, containing 25 μL 2× Phanta Max Master Mix 73 (Vazyme, Biotech Co., Ltd., Nanjing, China), 20-μL DNase free ddH2O, 2-μL of each 74 primer, and 1-μL template DNA, as suggested by the manufacturer. The PCR 75 amplification procedure is shown in Table 1. PCR products were confirmed by 1.5% 76 agarose gel electrophoresis, and purified using an OMEGA PCR kit (Omega, Biotek, 77 Norcross). The purified PCR products were sequenced on an ABI 3730XL sequencer 78 (Sangon, Biotech Co., Ltd., Shanghai). Sequence data were edited with Geneious 79 R6.1.6 (Kearse et al. 2012) and deposited in GenBank (Table 2). 80 81 Table 1. The PCR amplification procedures. Primer PCR procedure Sequence 5′→ 3′ COI-ef ATAATGATAGGAGGRTTTGG Pre denaturation:95 ℃ for 3 min COI-er GCTCGTGTRTCTACRTCCAT 40 cycles: Denaturation:95 ℃ for 40 s Annealing: 45 ℃ for 40 s Extension: 72 ℃ for 50 s 16S-arL CGCCGTTTATCAAAAACAT Pre denaturation:95 ℃ for 3 min 16S-brH CCGGTCTGAACTCAGATCACG 35 cycles: Denaturation:95 ℃ for 40 s Annealing: 50 ℃ for 40 s Extension: 68 ℃ for 50 s 82 83 For a more comprehensive phylogenetic analysis, we not only used the sequences 84 of Psychropotidae but also used the mitochondrial sequences of Elpidiidae and two 85 species of Molpadiidae as the outgroup (Table 2). Twenty-five COI and 18 16S 86 sequences were aligned using MAFFT 7 (Katoh and Standley 2013) using the E-INS-I 87 strategy. The 16S and COI alignments were concatenated into the dataset (COI/16S = 88 687/578 bp), while the alignment gaps and missing data were represented as ‘-’ and ‘?’. 89 Maximum likelihood (ML) and Bayesian inference (BI) analyses were performed using 90 the concatenated dataset. JModelTest 2.1.10 (Darriba et al. 2012) was used to find the 91 best-fit model from 88 competing models using Akaike information criterion (AIC) Author-formatted, not peer-reviewed document posted on 14/07/2021. DOI: https://doi.org/10.3897/arphapreprints.e70999 92 calculations. In each case, GTR+I+G was the best-fit model for BI analyses. MrBayes 93 3.2 (Huelsenbeck and Ronquist 2001) was used to conduct BI analyses. Markov Chain 94 Monte Carlo (MCMC) iterations were run for 1, 000, 000 generations with sampling 95 every 100 generations. The first 25% of trees were discarded as burn-in, and the 96 consensus trees were summarized in 75% majority-rule trees. RAxML GUI 1.5 97 (Silvestro and Michalak 2012; Stamatakis 2014) was used to perform ML analysis with 98 the GTR+GAMMA+I substitution model for 1000 bootstraps, as recommended by 99 Miller et al. (2017). 100 101 Table 2. The gene sequences of the specimens used in this study. GenBank accession number Family species 16S COI Psychropotidae Benthodytes manusensis MH627223.1 MH627222.1 Benthodytes sanguinolenta HM196507.1 Benthodytes marianensis MH049433.1 MH049435.1 Benthodytes jiaolongi sp. nov. MW992746 MW990356 Benthodytes jiaolongi sp. nov. MW992747 MW990357 Psycheotrephes exigual KX874392.1 Psychropotes longicauda DQ777099.1 KU987469.1 Psychropotes moskalevi MN310400.1 MN313655.1 Psychropotes raripes MN310403.1 MN313656.1 Psychropotes verrucicaudatus MW992749 MW980089 Psychropotes verrucicaudatus MW992748 MW980088 Elpidiidae Peniagone diaphana KX856725.1 KX874384.1 Peniagone incerta HM196402.1 Peniagone sp.
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