DNA-based taxonomy of a mangrove-associated community of fishes in Southeast Asia

Abstract

The Merbok Estuary comprises one of the largest remaining mangrove forests in Peninsular Malaysia. Its value is significant as it provides important services to local and global communities. It also offers a unique opportunity to study the structure and functioning of mangrove ecosystems. However, its biodiversity is still partially inventoried, limiting its research value. A recent checklist based on morphological examination, reported 138 fish species residing, frequenting or subject to entering the Merbok Estuary. In this work, we reassessed the fish diversity of the Merbok Estuary by DNA barcoding 350 specimens assignable to 134 species initially identified based on morphology. Our results consistently revealed the presence of 139 Molecular Operational Taxonomic Units (MOTUs). 123 of them are congruent with morphology-based species delimitation (one species = one MOTU). In two cases, two morphological species share the same MOTU (two species = one MOTU), while we unveiled cryptic diversity (i.e. COI-based genetic variability > 2%) within seven other species (one species = two MOTUs), calling for further taxonomic investigations. This study provides a comprehensive core-list of fish taxa in Merbok Estuary, demonstrating the advantages of combining morphological and molecular evidence to describe diverse but still poorly studied tropical fish communities. It also delivers a large DNA reference collection for brackish fishes occurring in this region which will facilitate further biodiversity-oriented research studies and management activities.

Diversity and Potential Function of Prokaryotic and Eukaryotic Communities from Different Mangrove Sediments

“…Microbial communities, either bacteria or fungi, have been reported to function importantly in decomposition processes of organic carbon, as well as other substrates in the sediments of mangroves [14][15][16]. High-throughput sequencing of 16S rDNA and 18S rDNA genes have been applied in studying the prokaryotic and eukaryotic communities, respectively, and their metabolic potentials in sediments of mangroves [17,18]. However, even though several general patterns between the mangroves and related microbial communities were reported, a few studies were conducted to investigate the diversity and functions of microorganisms under different contaminated sediments of mangroves.…”

Resurrection and redescriptions of nominal species previously regarded as synonyms of Thrissina mystax (Bloch and Schneider, 1801) (Teleostei: Clupeiformes: Engraulidae)

“…13, figure 261 (Sarawak State, Borneo, Malaysia and Gulf of Thailand, Thailand); Zanial Abidin, Lavoué, et al (2021): 615 (Sungai Merbok, Kuala Kedah, Malaysia); Zanial Abidin, Mohd. Nor, et al (2021): 3, Table 1 (Sungai Merbok, Kuala Kedah, Malaysia).…”

Cracking the glass‐perchlet code: Integrative taxonomy uncovers high species‐level diversity within the glass‐perchlet genus Ambassis (Ambassidae) in tropical Asia

“…A total of 13 nominal species of Ambassis have been reported from Peninsular Malaysia in different publications representing 11 currently valid species: A. ambassis , A. buruensis , A. dussumieri , A. interrupta , A. kopsii , A. macracanthus , A. marianus , A. nalua , A. octava , A. urotaenia and A. vachellii (Bleeker, 1874; Cantor, 1849; Duncker, 1904; Fraser‐Brunner, 1955; Ghazali, Lavoué, Mohd Nor, et al., 2023; Ghazali, Lavoué, Sukmono, et al., 2023; Günther, 1859; Herre & Myers, 1937; Ikejima et al., 2003; Kottelat, 1989; Matsunuma et al., 2011; Ng et al., 1999; Sasekumar et al., 1992; Tongnunui et al., 2002; Zainal Abidin, Lavoué, Alshari, et al., 2021; Zainal Abidin, Lavoué, Rahim, et al., 2021).…”

“…(2021) and Zainal Abidin, Lavoué, Rahim, et al. (2021) sequenced the COI gene of specimens morphologically identified as A. interrupta , A. macracanthus and A. vachellii .…”

“…Altogether, 13 nominal species have been listed from brackish and marine coastal habitats of Peninsular Malaysia, that is, A. batjanensis , A. buruensis , A. commersonii , A. dussumieri , A. gymnocephalus , A. interrupta , A. kopsii , A. macracanthus , A. marianus , A. nalua , A. octava , A. urotaenia and A. vachellii (Azmir et al., 2017; Bleeker, 1874; Cantor, 1849; Duncker, 1904; Fraser‐Brunner, 1955; Ghazali, Lavoué, Mohd Nor, et al., 2023; Günther, 1859; Herre & Myers, 1937; Ikejima et al., 2003; Kottelat, 1989; Matsunuma et al., 2011; Ng et al., 1999; Sasekumar et al., 1992; Tongnunui et al., 2002; Zainal Abidin, Lavoué, Alshari, et al., 2021; Zainal Abidin, Lavoué, Rahim, et al., 2021). Due to the difficulty in identifying some species, insufficient knowledge on the taxonomy of Ambassis , and numerous nomenclatural changes, the actual number of species in Peninsular Malaysia and the identities of these species remain to be investigated.…”