Microphis brachyurus

Haÿ, Vincent, Mennesson, Marion I., Carpentier, Camille, Dahruddin, Hadi, Sauri, Sopian, Limmon, Gino, Wowor, Daisy, Hubert, Nicolas, Keith, Philippe & Lord, Clara, 2025, Phylogeography of Microphis retzii (Bleeker, 1856) and Microphis brachyurus (Bleeker, 1854) in the Pacific, Journal of Fish Biology 106 (2), pp. 602-620 : 608-610

3.1 | M. brachyurus

3.1.1 | Phylogeography

A total of 91 sequences (480 bp) were successfully generated and aligned. Ten haplotypes (H1–H10) were identified, including seven unique haplotypes observed in a single individual (H2, H3, H4, H5, H7, H8, and H9) (Figure 2; Table S1).

The haplotype network for M. brachyurus has two main haplogroups separated by five nucleotide substitutions (Figure 2a). Haplogroup 1, composed of haplotypes H1–H9, includes individuals from Papua New Guinea (New Britain), Indonesia (Borneo), Solomon Islands (Kolombangara and Isabel), Japan (Okinawa), and New Caledonia. Haplogroup 1 presents a star-like topology, with a central haplotype (H1) shared by several individuals from most sampling sites and radiating into eight haplotypes separated by a single or two mutations from H1. Haplogroup 2 is composed of one unique haplotype H10 carried by individuals from French Polynesia (Tahiti) only. There are no shared haplotypes between the two haplogroups.

The different sampling sites of M. brachyurus were grouped into two large geographical areas to match the spatially nested design of the AMOVA: WPO and CPO (Figure 2b), corresponding to the two haplogroups mentioned earlier. Hd and π are higher in the WPO zone (Hd = 0.667; π = 0.927) compared to the CPO zone (Hd = 0.117; π = 0.117). The values of Fu's F and Tajima's D are significantly negative for the WPO region (Table 2).

The spatial genetic structuring of M. brachyurus observed in Figure 2 is supported by a high and statistically significant Φst value (0.914) between CPO and WPO zones (p <0.05). The average genetic distance between and within CPO and WPO was calculated from the uncorrected p-distances matrix with a value of 1.26% between regions and low genetic distances on average within regions, that is, 0.17%–0% (Table 3).

3.1.2 | MOTUs delimitation and phylogenetic analysis

DNA-based species delimitation methods resulted in congruent delimitation schemes with two MOTUs for sPTP and ASAP, and one MOTU for mPTP and sGMYC (Figure 3, Table S2). mGMYC were not

Geographical areas N Fst Hd h π

WPO 44 0.913 0.667 2 0.927 CPO 47 0.916 0.117 10 0.117

T A B L E 2 Molecular diversity indices Fu's F Tajima's D

for Microphis brachyurus .

6.083 1.557

0.521 0.791

Note: Significant values (p -value <0.05) are indicated in bold.

Abbreviations: CPO, Central Pacific Ocean; F and D, neutrality tests; Fst, intra-zone differentiation parameter; Hd, haplotype diversity; h, number of haplotypes; π, nucleotide diversity; N, number of individuals sampled; WPO, West Pacific Ocean.

WPO CPO

WPO 0.17

CPO 1.26 0

Note: Intra-zone divergences are presented in bold.

available for this dataset; the Markov chain failed to run for the multiple threshold version of GMYC with splits. The final consensus scheme consisted of two MOTUs in the Pacific area: one for the West Pacific ( Indonesia, Japan, New Caledonia, Papua New Guinea, and Solomon Islands) and one for the Central Pacific ( French Polynesia). These two MOTUs were assigned to the same nominal species, M. brachyurus (Bleeker, 1854) , according to the low genetic divergence (1.26%) (Table 3). The Bayesian gene tree, based on the MOTUs recognized here, suggests a recent diversification of the M. brachyurus mitochondrial lineages (Figure 3). Among the 10 haplotypes, 2 lineages are recognized within M. brachyurus , one is restricted to the Central Pacific (H 10 in French Polynesia) and one is shared in the West Pacific area (H1–H9 from Japan to New Caledonia) with a most recent common ancestor (MRCA) dated around 0.43 MYA (95% HPD: 0.1754 – 0.759) (Figure 3).