Cryptic genetic diversity in the mottled rabbitfish Siganus fuscescens with mitochondrial introgression at a contact zone in the South China Sea

Abstract

The taxonomy of the mottled rabbitfish Siganus fuscescens species complex has long been challenging. In this study, we analyzed microsatellite genotypes, mitochondrial lineages, and morphometric data from 373 S. fuscescens individuals sampled from the northern Philippines and Hong Kong (South China Sea, Philippine Sea and Sulu Sea basins), to examine putative species boundaries in samples comprising three co-occurring mitochondrial lineages previously reported to characterize S. fuscescens (Clade A and Clade B) or S. canaliculatus (Clade C). We report the existence of two cryptic species within S. fuscescens in the northeast region of the South China Sea and northern Philippine Sea, supported by genetic and morphological differences. Individual-based assignment methods recovered concordant groupings of individuals into two nuclear genotype clusters (Cluster 1, Cluster 2) with (1) limited gene flow, if any, between them (FST = 0.241; P < 0.001); (2) low frequency of later-generation hybrids; (3) significant association with mitochondrial Clade A and Clade B, respectively; and (4) subtle yet significant body shape differences as inferred from geometric morphometric analysis. The divergence between mitochondrial Clade C and the two other clades was not matched by genetic differences at microsatellite marker loci. The occurrence of discordant mitonuclear combinations (20.5% of the total number of individuals) is thought to result from mitochondrial introgression, consistent with a scenario of demographic, and presumably spatial, post-Pleistocene expansion of populations from northern regions into a secondary contact zone in the South China Sea. Mitonuclear discordance due to introgression obscures phylogenetic relationships for recently-diverged lineages, and cautions against the use of mitochondrial markers alone for species identification within the mottled rabbitfish species complex in the South China Sea region.

Assessing species diversity of Coral Triangle artisanal fisheries: A DNA barcode reference library for the shore fishes retailed at Ambon harbor (Indonesia)

“…Those potentially result from introgressive hybridization and/or overlapping morphological characters. Several cases were expected as mitochondrial introgression was previously reported for Siganus based on a comprehensive assessment of genetic diversity at mitochondrial and nuclear markers (Kuriiwa, Hanzawa, Yoshino, Kimura, & Nishida, ; Ravago‐Gotanco, Cruz, Josefa Pante, & Borsa, ). In such cases that constitute a limit where sister‐species co‐occur and hybridize (Ravago‐Gotanco et al, ), mitochondrial markers will inflate the number of false positives (i.e .…”

Fine‐scale phylogeography of coastal fishes in the South China Sea: Possible roles of biological traits and geography

“…We revealed a steep change in haplotype frequency or an almost complete lack of shared genetic variation between the eastern and the western coasts of the SCS for six species of coastal fishes. Previous studies also reported a similar east‐west population break within the SCS for several species, including marine vertebrates and invertebrates [ Scomberomorus commerson (Fauvelot & Borsa, 2011); Hippocampus trimaculatus (Lourie et al, 2005); Ocypode ceratophthalmus (Ma, Chow, et al, 2018); Plectropomus leopardus (Ma, Van Herwerden, et al, 2018); Siganus fuscescens (Ravago‐Gotanco et al, 2018)]. Therefore, we newly recognize the east‐west population break within the SCS as the prevailing pattern for diverse marine organisms.…”

Evolutionary History and Taxonomic Reappraisal of Coral Reef Rabbitfishes (Siganidae): Patterns of Lineage Diversification and Speciation

“…Rabbitfish (Siganidae) comprise 29 nominal extant species that are confined to a single genus, Siganus [ 1 , 2 , 3 ]. These coral reef fish are widely distributed across the Indo-West Pacific region and inhabit a variety of habitat types, ranging from estuaries, mangroves, and seaweed mats to the reef front and reef flat [ 1 ].…”

“…Notably, intermediate body markings have been observed in some sister species that are distributed parapatrically in the Indo-West Pacific region. This suggests that introgressive hybridization may have occurred in the past, further affecting the taxonomic identification of siganids [ 3 , 4 , 5 , 6 , 7 , 8 ].…”