**3. Results**

#### *3.1. Characteristics of the Gene Data*

In the 65 specimens collected from Taiwan, 58 newly obtained COI sequences, 59 newly ITS sequences, 63 for 28S, and 62 for histone H3 sequences were obtained for the first time (Table S1). Examining the individual gene dataset, the aligned COI sequence was 744 base pairs (bp) long, with 180 variable and 81 parsimony informative sites. That of 28S was 865 bp, with 316 variable and 147 parsimony informative sites. That of ITS was 1249 bp, with 662 variable and 459 parsimony informative sites. That of histone H3 was 344 bp, with 109 variable and 82 parsimony informative sites.

#### *3.2. Results of the Analysis Matrix*

The dataset comprised a total of 3202 bp and 186 OTUs (123 OTUs from references and 65 OTUs from the present study). ML and BI methods (using raxmlGUI and MrBayes, respectively) were used to reconstruct the phylogenies for the combined dataset. The results from the partitioned ML analysis and BI conducted with the combined dataset were congruen<sup>t</sup> (Figure 2). The ML analysis yielded a log-likelihood value of −28,909.928401 and the BI analysis yielded ( −3.069135 × 104, −3.083239 × 104).

#### *3.3. Phylogenetic Relationship*

The clades XV (Diploastreidae), XVI (Montasraeidae), and XVII (Merulinidae) were monophyletic, with high ML and BI support (100/1 and 100/0.99), whereas clades XVIII-XX (Lobophylliidae) and XXI (Mussidae) formed clusters but with weak support (63/0.8 and 58/0.84) (Figure 2). Within Merulinidae, eight major subclades (A, C, D/E, F, H, and I) formed with high ML (83–100) and BI (100) support. Subclades B and G, on the other hand, did not have high support (84/ − and −/0.99). Subclade A is composed of *Paragoniastrea australensis*, *Scapophyllia cylindrica*, as well as species of *Goniastrea* and *Merulina*. Subclade B is composed of *Astrea annuligera*, *Favites valenciennesi*, and *Trachyphyllia geoffroyi*, as well as species of *Coelastrea* and *Dipsastraea*. Subclade C is composed of *Orbicella annularis* and species of *Cyphastrea*. Subclade D/E is composed of species of *Caulastrea*, *Oulophyllia*, *Mycedium*, and *Pectinia*. Subclade F is composed of species of *Favites*. Subclade G is composed of *Favites stylifera* and species of *Platygyra* and *Leptoria*. Subclade H is composed of species of *Hydnophora*. Finally, subclade I is composed of species of *Echinopora* and *Paramontastraea salebrosa*.

**Figure 2.** Phylogenetic tree of merulinid corals and their allies based on the combined gene dataset inferred with the maximum likelihood method using the GTR+G model. Molecular subclades within Merulinidae (XVII) are defined as being A to I following Huang et al. [10]. The other two novel clades (J and K) are defined in this study. Branch lengths are proportional to inferred nucleotide substitutions. Numbers at the nodes represent bootstrap values (only ≥70 shown) from the maximum likelihood method and posterior probability (only ≥0.9 shown) from the Bayesian inference. Bold branches on the tree indicate statistically robust nodes. The spawning month of specimens in Chen et al. [32] are in brackets.

*Favites russilli* and *Astrea curta* formed a distinct cluster (BP:100, PP:1), defined as a new subclade K, separated from *Astrea annuligera*, *Paragoniastrea australensis*, and *P. deformis* were monophyletic (BP:96, PP:0.97), so we defined the genus as a new subclade J. *Paragoniastrea australensis*, not monophyletic, was placed in subclade A and new subclade J. *F. valenciennesi*, not monophyletic, was placed in subclades B and F.

#### *3.4. The Phylogenetic Tree*

The spawning specimens we examined were all nested within Merulinidae (taxa in bold font in Figure 2). These specimens were placed in five subclades B, C, E, F, and G but not in the subclades A, D, H, or I. The following were nested in subclade B: one specimen each of *Astrea annuligera*, *Coelastrea palauensis*, *Dipsastraea rotumana*, *Dipsastraea mathaii*, and *Favites valenciennesi* and two specimens of *Coelastrea aspera* collected from Kueishan Island; one specimen of *Dipsastraea favus* collected from Pitoujiiao and two from Kueishan Island; one specimen of *Dipsastraea lizardensis* collected from Longdong. Two *Cyphastrea chalcidicum* specimens, collected from Longdong, were nested in subclade C. One specimen each of *Mycedium mancaoi*, *Mycedium robokaki*, and *Pectinia paeonia*, collected from Longdong, and one *Mycedium elephantotus*, collected from Pitoujiiao, were nested in subclade E. Subclade F consisted of one specimen each of *Favites valenciennesi* and *Favites flexuosa*, collected from Pitoujiiao, and two *Favites magnistellata*, collected from Pitoujiiao and Kueishan Island. All the *Favites pentagona* specimens collected from Kueishan Island, Pitoujiiao, and Longdong were clustered with *F. pentagona* from Singapore and the Philippines. Subclade G consisted of two *Platygyra pini*, five *Platygyra ryukyuensis*, three *Platygyra verweyi*, and one *Platygyra sinensis*, collected from Longdong; one species each of *Platygyra lamellina* and *Platygyra daedalea*, collected from Pitoujiiao; and two *Favites stylifera* from Pitoujiiao and Longdong. Six *Paragoniastrea deformis*, collected from Pitoujiiao, four *Paragoniastrea australensis* specimens from Pitoujiiao, and one from Longdong were clustered into subclade J. Subclade K was a monophyletic clade, consisting of three specimens of *Astrea curta*, collected from Keelung Island, and two from Pitoujiiao, which were clustered with those from the Great Barrier Reef and the Philippines (BP:98, PP:1).
