**5. Conclusions**

This study integrates reproduction information, morphological characteristics, and molecular phylogenetic analysis to increase our understanding of the genetic diversity of Merulinidae. Ten major subclades (A, B, C, D/E, F, G, H, I, J, and K) were reconstructed. Our study identified *Paragoniastrea deformis* and *Paragoniastrea australensis* in Taiwan for the first time. Together, the two species form the new subclade J. *Astrea curta* were separated from another congeneric species, *Astrea annuligera* (XVII-B), clustered with *Favites russelli* into the new subclade K. Finally, we contributed information on the species diversity of coral communities in Taiwan and fill gaps involving merulinid corals between Japan and the Philippines in the Western Pacific.

**Supplementary Materials:** The following supporting information can be downloaded at: https: //www.mdpi.com/article/10.3390/d14020144/s1, Table S1: Species and DNA sequences examined in this study. The species name in Huang et al. 2011 was updated according to World Register of Marine Species (WoRMs). GenBank accession numbers are displayed for each molecular marker (28S rDNA, histone H3, ITS rDNA and mt COI). N.D.: sequences were failed from PCR. Accession dates

of 28S rDNA sequences: 21-FEB-2011 [16], 26-OCT-2021 (this study); histone H3: 25-JUL-2016 [16], 23-NOV-2021 (this study); ITS rDNA: 21-FEB-2011 [16], 04-DEC-2021 (this study). Figure S1. Phylogeny of Merulinidae reconstructed from Huang et al. [10] and this study.

**Author Contributions:** C.-J.C. and C.-F.C. conceived and designed the experiments. C.-J.C. and Y.-Y.H. the collected samples, conducted the experiments, and analyzed the data. C.-J.C. and C.-F.C. wrote the manuscript. All authors have read and agreed to the published version of the manuscript.

**Funding:** This study was supported by MOST 104-2923-B-019-MY4, Taiwan.

**Institutional Review Board Statement:** All procedures and investigations were approved by the College of Life Science of the National Taiwan Ocean University Institutional Animal Care and Use Committee (Affidavit of Approval of Animal Use Protocol: No. 104009) and performed in accordance with standard guiding principles.

**Informed Consent Statement:** Not applicable.

**Data Availability Statement:** Data are contained within this article. Raw data are available on request from the corresponding authors.

**Acknowledgments:** We are grateful to the diving instructors, Chen-Ta Wu and Yi-Hung Li for assisting with night dives during the spawning periods. We thank Pei-Chung Lo from the Marine Biodiversity and Phylogenomics Laboratory at National Taiwan University for the stimulating discussions and insightful comments. The sampling permit was issued by the Fishes and Fishing Port Affairs Management Office, New Taipei City Government. This work was supported by research grants from the Ministry of Science and Technology, Taiwan (MOST) to C.F. Chang. Thanks also to Noah Last for editing the manuscript's English.

**Conflicts of Interest:** The authors declare no conflict of interest.
