Research Article |
Corresponding author: ChunGuang Wang ( wangchunguang@tio.org.cn ) Academic editor: Nathalie Yonow
© 2022 Qiong Wu, BingPeng Xing, Mao Lin, GuangCheng Chen, ChunGuang Wang.
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.
Citation:
Wu Q, Xing BP, Lin M, Chen GC, Wang CG (2022) Molecular phylogeny suggests synonymy of Sandalia bridgesi Lorenz, 2009 with S. triticea (Lamarck, 1810) (Gastropoda, Ovulidae). ZooKeys 1096: 189-206. https://doi.org/10.3897/zookeys.1096.79402
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The Ovulidae (Gastropoda, Cypraeoidea) is a family of small to medium Mollusca in the order Littorinimorpha, and Sandalia is a very small genus containing only three extant species. In the present study, 132 specimens of Ovulidae were collected, belonging to seven genera and nine species, including 54 Sandalia bridgesi and three Sandalia triticea individuals. The cytochrome c oxidase I gene, 16S rRNA, and ITS1-5.8S-ITS2 sequences were obtained from all specimens and compared with sequences downloaded from GenBank to calculate genetic distances and construct phylogenetic trees. The sequences of S. bridgesi and S. triticea exhibited a high degree of similarity, and S. bridgesi does not form a separate clade, supporting the proposal that S. bridgesi should be synonymised with S. triticea.
16S, COI, DNA sequencing, ITS, molecular phylogeny, taxonomy
The family Ovulidae is a group of small and medium sized molluscs distributed in widely tropical and subtropical seas. Sandalia Cate, 1973 is a genus belonging to this family, and its known distribution is Korea, Japan (type locality), New Caledonia, and eastern Australia. Shells are mainly characterised by having a pointed adapical terminal beak, peculiarly curving outer lips, and a shoe-like ventral appearance (
Recent collections of 132 specimens of ovulid from Chinese coasts prompted an investigation into the identities of the species of Sandalia based on 57 fresh specimens.
Sandalia bridgesi differs from its congeners by the obvious and striking transparency of the dorsum in contrast to the calloused labrum and terminals. As described by
DNA barcoding, which involves using a short DNA sequence for species classification, was used as a tool for species identification and received widespread attention 15 years ago (
We collected 132 specimens of Ovulidae from depths of 0–6 m during low spring tides in Hainan, Guangxi, Guangdong, Fujian, and Zhejiang provinces between July 2020 and September 2021. Detailed information of the collected specimens is shown in Fig.
All specimens were morphologically identified by WQ, Fan Shihao, and Han Yida in accordance with the identification keys published by
Dorsal, ventral, and lateral views of shells of Sandalia A S. bridgesi Lorenz, 2009 (20200722H1) B S. bridgesi (20200722H5) C S. bridgesi (20200722H6) D S. bridgesi (20200722H9) E S. bridgesi (20200722H10) F S. triticea (Lamarck, 1810) (20210626H14) G S. triticea (20200722T1) H S. triticea (20200722T2). Scale bar: 2 mm.
Amplification was performed on three gene regions for each specimen, namely the mitochondrial markers 16S rRNA and COI, and the nuclear ribosomal internal transcribed spacer (ITS) region.
DNA was extracted from each muscle tissue using the DNeasy Blood & Tissue Kit (QIAGEN, China) following the corresponding protocol for animal tissues. The nucleic acid concentration in the DNA extracts was measured using BioDrop (BioDrop, UK). Due to the presence of inhibitors in the specimen tissues, all DNA extracts were diluted 50–500 fold before PCR amplification (
Each PCR had a reaction volume of 50 µL and contained the following: 25 µL PCR mixture [Taq plus Master Mix II (Dye Plus)], 2 µL of each primer (10 µM), 5 µL (diluted) DNA extract, and 16 µL extra pure water. The details of the PCR performed for the three gene regions are given in Table
Gene region | Fragment size (bp) | Primers | Annealing temperature | Reference |
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COI | ~680 | Lco1490/Hco2198 | 45 °C, +0.5 °C /cycle,15 cycle, 49 °C, 20 cycle |
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16S | ~550 | 16SAR/16SBR | 52 °C |
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ITS1-5.8S-ITS2 | ~1200 | GastF/GastR | 56 °C |
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The quality of the direct sequences obtained for the ITS region was insufficient because of intra-individual variation, secondary structures, and simple sequence repeats (SSRs). Thus, the PCR products were sent to Sangon Biotech Co., Ltd (Shanghai, China) for TA cloning and sequencing. DNA fragments were cloned into Escherichia coli cells using the pESI-T Vector System. For each individual, 3–5 clones were sequenced, and the most common sequence of these positive clones was used in the alignment and ITS data treatments. The sequences have been submitted to GenBank (http://www.ncbi.nlm.nih.gov) and the accession data is provided in Suppl. material
Joining and alignment of the sequences and trimming of ends with low signal strength were performed using DNAMAN v. 9 (Lynnon Biosoft, Canada) and SeqMan v. 7.1.0 (DNAStar, USA). Multiple sequences were aligned with MAFFT (
Evolutionary divergence analyses were conducted in MEGA v. 11(
Based on the photographs and descriptions provided by
In total, 122 COI sequences were successfully amplified. After editing, the consensus length of all barcode sequences was 615 bp, and no stop codons, insertions, or deletions were observed in any of the sequences. The sequences were aligned with the 16 COI sequences obtained from GenBank, with detailed information of downloaded sequences provided in Suppl. material
Gene region | The best fit models | Reference |
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COI | HKY+I+G4+F |
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16S | TPM3+G4+F |
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ITS1-5.8S-ITS2 | HKY+F+G4 |
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The greatest and smallest genetic distances between S. bridgesi and S. triticea among our specimens were 0.0215% (Sandalia bridgesi (MW410840) and Sandalia triticea (MW410844)) and 0% (Sandalia bridgesi (MW410824) and Sandalia rhodia (= triticea; MG450349); Sandalia bridgesi (OL674267) and Sandalia rhodia (= triticea; MG450349), respectively. The smallest and greatest interspecific genetic distances among specimens other than S. bridgesi and S. triticea were 0.1220% (Primovula formosa (OL674268) and Crenavolva traillii (OL471931)), and 0.2663% (Phenacovolva sp. (OL471933) and Crenavolva traillii (OL471920)), respectively (for more details see Suppl. material
Gene region | The best fit models | Reference |
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COI | HKY+I+G+F |
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16S | HKY+G+F |
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ITS1-5.8S-ITS2 | HKY+F+G4 |
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One hundred 16S rRNA sequences with lengths of approximately 520 bp were successfully amplified. After trimming, segments with lengths of 460 bp were obtained and aligned with 16 16s rRNA sequence data from GenBank to find the best model. Accession numbers of downloaded sequences are provided in Suppl. material
There are some differences between the two trees. As shown in Bayesian tree (Suppl. material
The greatest genetic distance between S. triticea and S. bridgesi was 0.0220% (MW411381 and OL589299). By contrast, the smallest interspecific genetic distance among the other specimens was 0.0860% (Primovula formosa (OL589307) and Crenavolva traillii (OL614740); Primovula formosa (MW411392) and Crenavolva traillii (KP033145). For more details, see Suppl. material
The amplified ITS sequences had lengths of 1200–1300 bp before trimming and approximately 1200 bp after trimming. Different clones (from the same individual) were highly similar, and the differences were concentrated in the SSR regions. In the high-quality part of the sequencing, the most common sequence of clones was selected. The ITS sequences used to build the tree were assembled by different clones (from the same individual). Results of BIC analysis showed that the best-fit models of ML tree and Bayesian tree are provided in Tables
Based on morphological and molecular data, Sandalia bridgesi Lorenz, 2009 is here synonymised with S. triticea (Lamarck, 1810).
The colouration of ovulids is variable, and many ovulid names have been introduced on basis of a few specimens; therefore, nominal species of Ovulidae often prove to be synonyms (
Sandalia bridgesi is the most recently described species in the genus Sandalia and was established based on morphological characters by
COI barcoding has been widely applied in identifying species belonging to the class Gastropoda (
From the phylogenetic tree constructed using COI sequences (Suppl. material
The phylogenetic tree constructed from the 16S rRNA sequences showed that different specimens could be clearly distinguished at the species level using 16s rRNA (Suppl. materials
Being a non-transcribed spacer region, the ITS region is subject to smaller selective pressures and generally undergoes rapid evolution (
In conclusion, the COI, 16S rRNA, and ITS1-5.8S-ITS2 data of the ovulid specimens collected in the present study indicated the absence of genetic differences between S. bridgesi and S. triticea. Both the phylogenetic trees (Suppl. materials
This study indicated that the colour pattern might not be a reliable identification feature. We also compared the L/W ratio between the S. meyeriana holotype, S. bridgesi, and S. triticea, and there were no significant differences between them. According to
As the high level of phenotypic plasticity in ovulid species results in much ambiguity in morphology-based classification criteria (
We are very grateful to Han Yida, Fan Shihao, Liu XinMin, and Gao Zhang Bin for their expertise and assistance in specimen collection and identification, and to Li Cui who assist us with data analysis. We greatly appreciate Dr Nathalie Yonow, for without her encouragement, this manuscript may have been delayed for a long time. We also extend sincere thanks to the reviewers for suggestions that improved the manuscript.
This work was supported by The Scientific Research Foundation of Third Institute of Oceanography MNR (22020017), The Marine Biological Sample Museum Upgrade and Expansion, and The National Natural Science Foundation of China (41406216).
Table S1
Data type: occurences, Date, GenBank accession numbers
Explanation note: Specimens used in the analyses, including locality, date, and GenBank accession data.
Table S2
Data type: morphological
Explanation note: L/W ratio of the genus Sandalia specimens.
Table S3
Data type: GenBank accession numbers
Explanation note: Details of sequences obtained from GenBank.
Table S4
Data type: phylogenetic
Explanation note: Pairwise genetic distance matrix of COI sequences among specimens of Ovulidae. The data of S. triticea specimens are marked in red.
Table S5
Data type: phylogenetic
Explanation note: Pairwise genetic distance matrix of 16s sequences among specimens of Ovulidae. The data of S. triticea specimens are marked in red.
Table S6
Data type: phylogenetic
Explanation note: Pairwise genetic distance matrix of ITS sequences among specimens of Ovulidae. The data of S. triticea specimens are marked in red.
Figure S1
Data type: morphological
Explanation note: Dorsal, ventral, and lateral views of shells. A Primovula formosa (G.B. Sowerby II, 1848) (20200722H2) B Crenavolva traillii (A. Adams, 1856) (20210616BHH1) C C. traillii (20210616BHH9) D Cuspivolva bellica (Cate, 1973) (20210718H5) E Phenacovolva sp. (20210515DSH2). Scale bar: 2mm
Figure S2
Data type: phylogenetic
Explanation note: ML phylogenomic tree constructed from COI sequences including Sandalia bridgesi, S. triticea, Primovula formosa, Naviculavolva deflexa, and other related species of the family Ovulidae. Bootstrap values are shown above the branch, while the support values based on MrBayes are shown in parentheses. The sequences of S. triticea are marked in red. S. rhodia is a synonym of S. triticea (Sartori 2014).
Figure S3
Data type: phylogenetic
Explanation note: Bayesian phylogenomic tree constructed from 16S rRNA sequences including Sandalia bridgesi, Sandalia triticea, Primovula formosa, Naviculavolva deflexa, and other related species of the family Ovulidae. The sequences of S. triticea specimens are marked in red. The coloured bands designate different species.
Figure S4
Data type: phylogenetic
Explanation note: ML phylogenomic tree constructed from 16S rRNA sequences including Sandalia bridgesi, S. triticea, Primovula formosa, Naviculavolva deflexa, and other related species of the family Ovulidae. The sequences of S. triticea specimens are marked in red. The coloured bands designate different species.
Figure S5
Data type: phylogenetic
Explanation note: ML phylogenomic tree constructed from ITS-region sequences including S. bridgesi, S. triticea, Primovula formosa, and Cuspivolva bellica. Bootstrap values are shown above the branch, while the support values based on MrBayes are shown in parentheses. The sequences of S. triticea specimens are marked in red.