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Taxonomic revision of the genus Poropuntius (Teleostei: Cyprinidae) in Peninsular Malaysia

Muhammad-Rasul AH, Ramli R, Low VL, Ahmad A, Grudpan C, Koolkalya S, et al.

Zootaxa, 2018 Sep 10;4472(2):327-342.
PMID: 30313371 DOI: 10.11646/zootaxa.4472.2.6

Up to three nominal species of the cyprinid fish genus Poropuntius (i.e. P. deauratus [Valenciennes in Cuvier Valenciennes 1842], P. normani [Smith 1931], and P. smedleyi [de Beaufort 1933]) have been reported to occur in Peninsular Malaysian freshwater ecosystems. However, low morphological differentiation among species of Poropuntius causes confusion and it is still unknown how many valid species of Poropuntius occur in this region. The goal of this study is to review the taxonomic status of Poropuntius in Peninsular Malaysia by using morphological and molecular characters. Principal Component Analysis (PCA) on a morphometric dataset including 281 specimens of Poropuntius from Peninsular Malaysia and P. normani from Thailand (type locality) failed to identify non-overlapping clusters within sampled specimens. A phylogenetic tree based on cytochrome oxidase subunit I (COI) showed intraspecific levels of genetic differentiation within Poropuntius of Peninsular Malaysia and the specimens of P. normani from Thailand form a monophyletic group. Our results strongly support the presence of only one species of Poropuntius in Peninsular Malaysia, P. normani. We demonstrate that P. smedleyi described from Johor, southern Peninsular Malaysia, is a junior synonym of P. normani. The previous reports of the presence of P. deauratus in Peninsular Malaysia are doubtful because this species was described from Vietnam where, in all evidence, it is endemic.
Contrasting genetic and morphological differentiation among geographical lineages of a stenotopic miniature rasborine, Boraras maculatus, in Peninsular Malaysia

Fam YQ, Jamaluddin JAF, Muhammad-Rasul AH, Ilham-Norhakim ML, Rosely NFN, Lavoué S

J Fish Biol, 2024 Jan;104(1):171-183.
PMID: 37775959 DOI: 10.1111/jfb.15572

The variability in the stenotopic miniature rasborine Boraras maculatus (Cypriniformes: Danionidae: Rasborinae) across acidic-water habitats of Peninsular Malaysia (PM) was investigated using two molecular markers (the mitochondrial cytochrome c oxidase subunit I [COI] gene and the nuclear rhodopsin gene), as well as morphological evidence. Molecular phylogenetic analyses revealed differentiation among populations of B. maculatus in PM with the distinction of four allopatric lineages. Each of them was recognized as a putative species by automatic species delimitation methods. These lineages diverged from each other between 7.4 and 1.9 million years ago. A principal component analysis (PCA) was conducted to examine the multivariate variation in 11 morphometric measurements among three of these lineages. PCA results showed a significant overlap in morphological characteristics among these lineages. Additionally, a photograph-based machine learning approach failed to fully differentiate these lineages, suggesting limited morphological differentiation. B. maculatus represents a case of morphological stasis in a stenotopic miniature species. Strong habitat preference, coupled with long-term habitat fragmentation, may explain why each lineage of B. maculatus has a restricted distribution and did not disperse to other regions within and outside of PM, despite ample possibilities when the Sunda shelf was emerged and drained by large paleodrainages for most of the past 7 million years. The conservation status of B. maculatus and its peat swamp habitats are discussed, and it is concluded that peat swamps comprise several evolutionary units. Each of these units is considered a conservation unit and deserves appropriate protection.
Co-occurrence of dual lineages within Simulium (Gomphostilbia) atratum De Meijere in the Indonesian Archipelago along Wallace's Line

Hew YX, Ya'cob Z, Chen CD, Lau KW, Sofian-Azirun M, Muhammad-Rasul AH, et al.

Acta Trop, 2024 Feb;250:107097.
PMID: 38097150 DOI: 10.1016/j.actatropica.2023.107097

Mitochondrial cytochrome c oxidase subunit I (COI) sequences were utilized to infer the population genetic structure of Simulium (Gomphostilbia) atratum De Meijere, an endemic simulid species to Indonesia. Both median-joining haplotype network and maximum-likelihood tree revealed two genetic lineages (A and B) within the species, with an overlap distribution in Lombok, which is situated along Wallace's line. Genetic differentiation and gene flow with varying frequencies (FST = 0.02-0.967; Nm = 0.01-10.58) were observed between populations of S. (G.) atratum, of which population pairs of different lineages showed high genetic differentiation. Notably, the high genetic distance of up to 5.92 % observed within S. (G.) atratum in Lombok was attributed to the existence of two genetically distinct lineages. The co-occurrence of distinct lineages in Lombok indicated that Wallace's line did not act as faunistic border for S. (G.) atratum in the present study. Moreover, both lineages also exhibited unimodal distributions and negative values of neutrality tests, suggesting a pattern of population expansion. The expansion and divergence time estimation suggested that the two lineages of S. (G.) atratum diverged and expanded during the Pleistocene era in Indonesia.
DNA barcoding of black flies (Diptera: Simuliidae) in Indonesia

Hew YX, Ya'cob Z, Adler PH, Chen CD, Lau KW, Sofian-Azirun M, et al.

Parasit Vectors, 2023 Jul 22;16(1):248.
PMID: 37480109 DOI: 10.1186/s13071-023-05875-1

BACKGROUND: DNA barcoding is a valuable taxonomic tool for rapid and accurate species identification and cryptic species discovery in black flies. Indonesia has 143 nominal species of black flies, but information on their biological aspects, including vectorial capacity and biting habits, remains underreported, in part because of identification problems. The current study represents the first comprehensive DNA barcoding of Indonesian black flies using mitochondrial cytochrome c oxidase subunit I (COI) gene sequences.
METHODS: Genomic DNA of Indonesian black fly samples were extracted and sequenced, producing 86 COI sequences in total. Two hundred four COI sequences, including 118 GenBank sequences, were analysed. Maximum likelihood (ML) and Bayesian inference (BI) trees were constructed and species delimitation analyses, including ASAP, GMYC and single PTP, were performed to determine whether the species of Indonesian black flies could be delineated. Intra- and interspecific genetic distances were also calculated and the efficacy of COI sequences for species identification was tested.
RESULTS: The DNA barcodes successfully distinguished most morphologically distinct species (> 80% of sampled taxa). Nonetheless, high maximum intraspecific distances (3.32-13.94%) in 11 species suggested cryptic diversity. Notably, populations of the common taxa Simulium (Gomphostilbia) cheongi, S. (Gomphostilbia) sheilae, S. (Nevermannia) feuerborni and S. (Simulium) tani in the islands of Indonesia were genetically distinct from those on the Southeast Asian mainland (Malaysia and Thailand). Integrated morphological, cytogenetic and nuclear DNA studies are warranted to clarify the taxonomic status of these more complex taxa.
CONCLUSIONS: The findings showed that COI barcoding is a promising taxonomic tool for Indonesian black flies. The DNA barcodes will aid in correct identification and genetic study of Indonesian black flies, which will be helpful in the control and management of potential vector species.