Research Article |
Corresponding author: Akkarasiri Sangsawang ( ffisais@ku.ac.th ) Corresponding author: Shikai Liu ( liushk@ouc.edu.cn ) Corresponding author: Narongrit Muangmai ( ffisnrm@ku.ac.th ) Academic editor: Graham Oliver
© 2022 Supannee Somrup, Akkarasiri Sangsawang, Nichanun McMillan, Supanida Winitchai, Jitti Inthoncharoen, Shikai Liu, Narongrit Muangmai.
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:
Somrup S, Sangsawang A, McMillan N, Winitchai S, Inthoncharoen J, Liu S, Muangmai N (2022) Pinctada phuketensis sp. nov. (Bivalvia, Ostreida, Margaritidae), a new pearl oyster species from Phuket, western coast of Thailand. ZooKeys 1119: 181-195. https://doi.org/10.3897/zookeys.1119.87724
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A new species of the genus Pinctada is described from samples collected from the east coast of Phuket Island, Thailand in the Andaman Sea. Pinctada phuketensis sp. nov. is distinguished from other species on both molecular and morphological data. Morphologically, the valves of P. phuketensis are characterized by a slightly developed to undeveloped posterior auricle, a small, narrow slit-like byssal notch, the absence of hinge teeth, and a pale to transparent non-nacreous border, with a few dark brown or red blotches. This new species resembles P. fucata but differs by its smaller size and the absence of hinge teeth. Phylogenetic analyses based on both mitochondrial (COI) and nuclear (18S rDNA, ITS1 and ITS2) genes and species delimitation using COI data strongly support that P. phuketensis is a distinct species, which is closely related to Pinctada albina and Pinctada nigra.
Indian Ocean, mollusk, new species, phylogeny, taxonomy
Pearl oysters in the genus Pinctada (Röding, 1798) (family Pteriidae) are widely distributed from shallow to deep waters of the tropical and subtropical regions between the Indo-Pacific and western Atlantic (
While the pearl farming industry has expanded rapidly during recent decades, our understanding of biodiversity, evolution, and conservation of Pinctada species is still limited. Traditionally, systematics and taxonomy of Pinctada species have primarily focused on morphological parameters (
In the Southeast Asian region, nine species of Pinctada are currently recognized: P. albina (Lamarck, 1819), P. chemnitzii (Phillipi, 1849), P. fucata, P. imbricata Röding, 1798, P. maculata (Gould, 1850), P. margaritifera, P. maxima, P. nigra (Gould, 1850) and P. radiata (Leach, 1814) (
Among Thai species, P. fucata and P. maxima are the main species used for pearl culture in Phuket, the island province off the western coast of Thailand (
A total of 15 pearl oyster specimens were collected around Dok Mai Island (7°47.84'N, 98°31.84'E), Phuket Province, western coast of Thailand by SCUBA diving. All specimens were allocated a registration code (NMR) to facilitate sample tracking. A small piece of adductor muscle from each oyster was preserved in 90% ethanol for DNA analyses. For morphological observation, we carefully examined both shell and soft body features (
Genomic DNA extraction from mantle tissue was performed using NucleoSpin Tissue Kit (Macherey-Nagel, Germany). Mitochondrial cytochrome oxidase subunit 1 (COI) gene, nuclear 18S rDNA gene and nuclear ribosomal DNA internal transcribed spacer 1 and 2 (ITS1 and ITS2) regions were selected for molecular phylogenetic analysis according to previous studies (e.g.,
Newly generated sequences, including seven COI sequences, six 18S rDNA sequences and five ITS1 and ITS2 sequences, were deposited in NCBI. All sequences were edited, assembled, and aligned for individual and concatenated data sets using the Geneious Prime software package (Biomatters, available from http://www.geneious.com/) with the MAFFT sequence alignment algorithm, and were further manually refined. Additional sequences of Pinctada species were retrieved from NCBI and included in the alignment (Suppl. material
Phylogenetic trees were reconstructed for both individual (COI and 18S rDNA) and concatenated data sets (ITS1 + ITS2) using maximum likelihood (ML) implemented in IQ-TREE (
Additionally, due to low variation of nuclear DNA sequences among species, we utilized only COI sequences for the three different species delimitation methods: the general mixed Yule-coalescent (GMYC) model (
Family Pteriidae Gray, 1847
Dok Mai Island, Phuket Province, Thailand, 7°47.84'N, 98°31.84'E, at 5–10 m depth.
Holotype
: KUMF.MOLL.1206 (NMR079) (Figs
Shell of Pinctada phuketensis sp. nov. from Dok Mai Island, Phuket, Thailand. External and internal views of left and right valves A paratype, KUMF.MOLL.1204 (NMR077) (scale bar: 5 cm) B holotype, KUMF.MOLL.1206 (NMRA079) C paratype, KUMF.MOLL.1205 (NMR078) (scale bar: 4 cm). Abbreviations: LV, left valve; RV, right valve.
Shell is anteriorly oblique, inequilateral, laterally compressed, and subcircular to quadrate in outline. Byssal notch is small, narrow and slit-like. Hinge teeth are absent. Adductor muscle scar is kidney- or bean-shaped with the distal extremities of the posterior pedo-byssal retractor muscle scar inserted into the concavity on its anterior border. The non-nacreous border is relatively pale to transparent, with few dark brown or black blotches.
Holotype, KUMF.MOLL.1206 (NMR079), specimen is approximately 60.4 mm height, 53.1 mm length, 23.1 mm depth, and 22.9 mm width (Figs
Right valve of holotype, KUMF.MOLL.1206 (NMR079), of Pinctada phuketensis sp. nov., showing shell shape and structures. Abbreviations: ad.m, adductor muscle scar; ant.a, anterior auricle; by.n, byssal notch; hl, hinge line; lig, ligament; na, nacreous; nn.b, non-nacreous border; post.a, posterior auricle; um, umbo.
The shell is rather thin and small. The shell height, which does not exceed 80 mm, is slightly greater than the length (Figs
For the soft body, the foot is a tongue-shaped organ located in the dorsal-anterior region of body, between the mouth and the byssus (Fig.
External view of the soft body parts of adult Pinctada phuketensis sp. nov. A and close-up view of overall of byssus B. Scale bars: 4 cm (A); 2 cm (B). Abbreviations: au, auricle; by, byssus; mm, mantle margin; pam, posterior adductor muscle; prm, posterior pedo-byssal retractor muscle; vm, visceral mass.
The specific epithet refers to the locality of Phuket Island, where this species was found.
Partial sequences of COI, 18S rDNA, ITS1, and ITS2 of recently collected Pinctada samples were successfully generated in this study. All sequences of P. phuketensis were identical for COI and 18S rDNA, and nearly identical for ITS1 (0.1–0.9% pairwise difference) and ITS2 (0.1–0.8% pairwise difference) but differed from sequences from other Pinctada species by at least 7% for COI, 0.2% for 18S rDNA, 2% for ITS1 and 1% for ITS2.
The COI-based phylogenetic trees obtained by ML and BI analyses were topologically similar, and only the ML tree is shown (Fig.
Maximum likelihood tree (-In L 4923.702) of partial COI sequences. Sequences of Pinctada specimens generated in this study are highlighted in bold. Support values are bootstrap/posterior probabilities. Asterisks indicate bootstrap (ML) value of 100% and posterior probability (BI) value of 1.00. Values < 50% ML bootstrap and < 0.90 posterior probability are not shown. GenBank accession numbers are given in parentheses. After the registration number or species name. Results of three species delimitation methods, namely GMYC model (blue column), bPTP (red column) and ASAP (yellow column), are indicated at the right edge of the tree.
Additionally, phylogenetic analyses based on partial 18S rDNA sequences using ML and BI methods were highly congruent (Fig.
Maximum likelihood tree (-In L 3134.144) of 18S rDNA sequences. Sequences of Pinctada specimens generated in this study are highlighted in bold. Support values are bootstrap/posterior probabilities. Asterisks indicate bootstrap (ML) value of 100% and posterior probability (BI) value of 1.00. Values < 50% ML bootstrap and < 0.90 posterior probability are not shown. GenBank accession numbers are given in parentheses after the registration number or species name.
Similarly, the phylogenetic relationships constructed by ML and BI methods based on the concatenated ITS1 and ITS 2 data set showed very similar topologies (Fig.
Maximum likelihood tree (-In L 4787.958) of combined ITS 1 and ITS 2 sequences. Sequences of Pinctada specimens generated in this study are highlighted in bold. Support values are bootstrap/posterior probabilities. Asterisks indicate bootstrap (ML) value of 100% and posterior probability (BI) value of 1.00. Values < 50% ML bootstrap and < 0.90 posterior probability are not shown.
Three different methods used for species delineation yielded the same number of putative species within Pinctada (Fig.
Our analyses using morphological and genetic data clearly distinguished the Pinctada samples recently collected from Dok Mai Island, Phuket Province, western coast of Thailand, from other Pinctada species in the region. Accordingly, these pearl oysters should be recognized as a new species, and we have named it as Pinctada phuketensis sp. nov. This new species can be distinguished from other members of the genus by its smaller size, a subquadrate shell with moderately long ligament, slightly developed to undeveloped posterior auricle, the absence of hinge teeth, a pale to transparent non-nacreous margin with dark brown or black blotches, and brownish stripes on the external surface. A morphological comparison of P. phuketensis and some closely related species is presented in Table
Comparative morphology of Pinctada phuketensis sp. nov. with other morphologically similar Pinctada species.
Character | P. phuketensis sp. nov.1 | P. albina 2,3 | P. sugillata 2,3 | P. chemnitzi 2 | P. fucata 2,4,5 | P. nigra 6 |
---|---|---|---|---|---|---|
Size | Small | Small | Small | Small | Small | Small |
Shell shape | Slightly oblique | Slightly to moderately oblique | Very oblique | Moderately oblique and markedly inequivalve | Slightly oblique | Obliquely elongate |
Anterior auricle | Small | Small | Small | Moderately to well developed | Larger | Small |
Posterior auricle | Short and broadly rounded or absent | Small | Small | Larger | Short and broadly rounded | Large |
Byssal notch | Small, narrow, slit-like | Broad | Moderately wide slit | Slit-like | Narrow and slit-like | n/a |
Hinge teeth | Absent | Absent | Present | Present | Present | Present |
External color | Green, yellow, brown, or partially continuous white blotches | White, possibly sun-bleached | Rayed or dark and white pattern to an evenly dark monochrome | Dull brownish, indistinctly rayed with paler shades | Red, brown, green and bronze | Green and dark |
Nacre | White luster, nacreous and narrow black band on the non-nacreous border | Pale yellow throughout the nacre | Narrow black band on the non-nacreous border | Yellow throughout the nacre | White metallic luster, yellow, silver, gold, or pink tint | n/a |
Among the Pinctada species distributed in Southeast Asian waters, the new species of P. phuketensis morphologically resembles P. fucata, P. nigra and P. albina, but can be distinguished from these three species based on shell shape, hinge teeth and anterior/posterior auricles. Both P. fucata and P. nigra can be easily distinguished from P. phuketensis by having conspicuous hinge teeth. In addition, P. fucata can be separated from P. phuketensis by being larger in size and having a large and developed anterior auricle (
Among the Indo-Pacific Ocean species, our new species, P. phuketensis closely resembles P. sugillata (Reeve, 1857) from Australia in having a weakly developed to undeveloped posterior ear and a nearly 1:1 ratio of the hinge line to the antero-posterior axis of the shell (
Our phylogenetic analyses and species delimitation approach showed that P. phuketensis is genetically distinct from other described Pinctada species. While our observations indicated that our new species is morphologically similar to P. fucata, genetic analyses revealed the distant phylogenetic relationship between these two species, implying that morphological traits probably do not reflect their real evolutionary history. Additionally, our phylogenetic analyses showed that P. phuketensis is more closely related to P. albina and P. nigra than to P. fucata. We also found that phylogenetic relationships of some Pinctada species in this study had weak nodal support and were incompletely resolved. It is apparent that further work on Pinctada species based on combined data of different genetic markers and more expansive sampling from different geographic regions will uncover their diversity, phylogenetic relationships and evolutionary patterns.
This work is submitted as part of the Master’s thesis by S. Somrup to the Dual-degree Program of Kasetsart University and Ocean University of China, sponsored by the China Scholarship Council through Ocean University of China. This work is also partially supported financially by Faculty of Fisheries, Kasetsart University (N. Muangmai), Phuket Pearl Co., Ltd. and National Research Council of Thailand (NRCT) and Biodiversity-Based Economy Development Office (Public Organization) (S. Winitchai). Our special thanks also go to Graham Oliver and two anonymous reviewers, who made a number of valuable suggestions for the improvement of our manuscript, and to Dave Anderson for critically reading and correcting the manuscript.
Table S1
Data type: Docx file.
Explanation note: List of additional GenBank accession numbers for ITS1 and ITS2 sequences used in the present study. New sequences produced for this study are indicated in bold type.
Table S2
Data type: Docx file.
Explanation note: The best partitioning scheme and models of maximum likelihood (ML; IQ-TREE) and Bayesian inference (BI; MrBayes) methods for all datasets.