﻿ <i>Pinctadaphuketensis</i> sp. nov. (Bivalvia, Ostreida, Margaritidae), a new pearl oyster species from Phuket, western coast of Thailand

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Abstract

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 .

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MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

Fredrik Ronquist, Maxim Teslenko, Paul van der Mark … (2012)

Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d N /d S rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.

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ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates

Subha Kalyaanamoorthy, Bui Minh, Thomas Wong … (2017)

Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates. The improvement is achieved by incorporating a model of rate-heterogeneity across sites not previously considered in this context, and by allowing concurrent searches of model-space and tree-space.

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IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

Bui Minh, Heiko Schmidt, Olga Chernomor … (2020)

Abstract IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.

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Author and article information

Contributors

Supannee Somrup:

ORCID: https://orcid.org/0000-0003-3217-098X

Role: Formal analysisRole: InvestigationRole: MethodologyRole: ValidationRole: Writing - original draft

Akkarasiri Sangsawang: Role: Formal analysisRole: InvestigationRole: MethodologyRole: SupervisionRole: ValidationRole: Writing - original draft

Nichanun McMillan: Role: MethodologyRole: Visualization

Supanida Winitchai: Role: Funding acquisitionRole: ResourcesRole: Visualization

Jitti Inthoncharoen: Role: Funding acquisitionRole: ResourcesRole: Visualization

Shikai Liu:

ORCID: https://orcid.org/0000-0001-5777-489X

Role: Funding acquisitionRole: SupervisionRole: ValidationRole: Writing - original draft

Narongrit Muangmai:

ORCID: https://orcid.org/0000-0001-7954-7348

Role: ConceptualizationRole: Data curationRole: Formal analysisRole: MethodologyRole: Project administrationRole: SupervisionRole: Writing - original draft

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: 2022

Publication date (Electronic): 02 September 2022

Volume: 1119

Pages: 181-195

Affiliations

[1 ] Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China

[2 ] Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand

[3 ] Kasetsart Agricultural and Agro-Industrial Product Improvement Institute (KAPI), Kasetsart University, Bangkok 10900, Thailand

[4 ] Phuket Pearl Industry, Co. Ltd., Phuket 83000, Thailand

[5 ] Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand

[6 ] Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand

[7 ] Biodiversity Center Kasetsart University (BDCKU), Bangkok 10900, Thailand

Author notes

Corresponding authors: Narongrit Muangmai (ffisnrm@ku.ac.th), Akkarasiri Sangsawang (ffisais@ku.ac.th), Shikai Liu (liushk@ouc.edu.cn)

Academic editor: Graham Oliver

Author information

Supannee Somrup https://orcid.org/0000-0003-3217-098X

Shikai Liu https://orcid.org/0000-0001-5777-489X

Narongrit Muangmai https://orcid.org/0000-0001-7954-7348

Article

Publisher ID: 87724

DOI: 10.3897/zookeys.1119.87724

PMC ID: 9848700

SO-VID: 12ee8a61-5d41-4093-9057-72d0e087e0e6

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 June 2022

Date accepted : 11 August 2022

Funding

China Scholarship Council through Ocean University of China Faculty of Fisheries, Kasetsart University Phuket Pearl Co., Ltd National Research Council of Thailand (NRCT) and Biodiversity-Based Economy Development Office (Public Organization)

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