Journal of Threatened
Taxa | www.threatenedtaxa.org | 26 June 2026 | 18(6): 29127–29132
ISSN 0974-7907 (Online) | ISSN 0974-7893 (Print)
https://doi.org/10.11609/jott.10397.18.6.29127-29132
#10397 | Received 14 January 2026 | Final received 09 March 2026| Finally
accepted 12 June 2026
Taxonomic reassessment of Ompok hypophthalmus
(Bleeker, 1846) (Actinopterygii: Siluriformes: Siluridae) in Indonesia with global
implications
Dinesh Nalage
1 ,
Tejswini Sontakke 2,
Ashwini Biradar 3 , Vidya Pradhan 4 &
P.S. Kudnar 5
1 Department of Biotechnology,
Maulana Azad College of Arts, Science & Commerce, Aurangabad, Maharashtra 431001, India.
2 Department of Zoology, MGV’s, MPH
Mahila College, Malegaon, Maharashtra 423105, India.
3 Department of Microbiology, Dr.
B.A.M. University, Subcampus Osmanabad, Osmanabad, Maharashtra 413501, India.
4 Department of Zoology, Dr. Rafiq
Zakaria Womens College, Aurangabad, Maharashtra 431001, India.
5 Department of Zoology,
Postgraduate Research Centre, Modern College of Arts, Science, and Commerce
(Autonomous), Pune, Maharashtra 411005, India.
1 dineshnalage@gmail.com
(corresponding author), 2 tejaswinisontakke27@gmail.com
(corresponding author),
3 ashwinibiradar13@gmail.com, 4
drvidya.pradhan@gmail.com, 5 kudnarzoology@moderncollegepune.edu.in
Editor: C. Sudhan, Dr. MGR
Fisheries College and Research Institute, Ponneri,
India. Date of publication: 26 June 2026 (online
& print)
Citation: Nalage, D., T. Sontakke, A. Biradar, V. Pradhan & P.S. Kudnar
(2026).
Taxonomic reassessment of Ompok hypophthalmus (Bleeker, 1846) (Actinopterygii: Siluriformes: Siluridae) in
Indonesia with global implications. Journal of Threatened Taxa 18(6): 29127–29132. https://doi.org/10.11609/jott.10397.18.6.29127-29132
Copyright: © Nalage et al. 2026. Creative Commons Attribution 4.0
International License. JoTT allows unrestricted use,
reproduction, and distribution of this article in any medium by providing
adequate credit to the author(s) and the source of publication.
Funding: The authors declare that no funds, grants, or other support were received during the preparation of this manuscript.
Competing interests: The authors declare no competing interests.
Author details: Dinesh Nalage is associated with the Department of Biotechnology and actively contributes to research in biotechnology, bioinformatics, microbiology, and molecular sciences. His work focuses on interdisciplinary biological research, scientific writing, and academic development. He has published research articles and reviews in reputed journals. His research interests include microbial diversity, computational biology, and applied biotechnology. Tejswini Sontakke is a researcher in the field of Zoology with interests in biological sciences and interdisciplinary research areas. She contributes to research activities involving molecular biology, bioinformatics, and biotechnology applications. Her academic work reflects a commitment toward scientific investigation and knowledge advancement. She participates in collaborative research and scholarly publications. Ashwini Biradar is engaged in microbiology research and academic activities with a focus on biological sciences. Her contributions involve research, scientific communication, and collaborative studies in life sciences. She has participated in research projects and publications related to microbiology and biotechnology and allied disciplines. Her work supports innovation and academic excellence. Vidya Pradhan is associated with life science research and academic activities. Her work involves contributions to zoology and related biological fields through research and scholarly communication. She participates in collaborative scientific studies aimed at improving understanding of biological systems. Her academic interests include zoology, molecular sciences, and applied research. P. S. Kudnar is a researcher and academic contributor in the field of biological sciences. His work involves scientific research, publication activities, and advancement of knowledge in biotechnology and allied areas. He contributes to collaborative research initiatives and promotes academic development through scientific exploration and innovation.
Author contribution: All authors contributed substantially to the conception, design, data collection, analysis, and interpretation of results. All authors participated in drafting and critically revising the manuscript, approved the final version for submission, and agreed to be accountable for all aspects of the work.
Abstract: Indonesia harbors exceptional
freshwater fish diversity, yet taxonomic uncertainty persists for several
economically important species, including Ompok
hypophthalmus. This study provides a critical
assessment of the morphological and molecular identification of O. hypophthalmus in Indonesia by analyzing published
literature and publicly available mitochondrial DNA sequence data retrieved
from resources such as NCBI. Morphological revisions by Ng (2003) recognized
three distinct taxa within the O. hypophthalmus
complex (O. hypophthalmus, O. rhadinurus, and O. urbaini),
yet subsequent studies have frequently applied species names inconsistently,
particularly in Sumatra. Analysis of available cytochrome c oxidase subunit I
(COI) and cytochrome b (Cyt b) sequences reveals
substantial genetic structuring among river populations, suggesting historical
misidentification and possible cryptic diversity. Limited sequence availability
and incomplete geographic coverage preclude definitive conclusions regarding
species boundaries in some river systems. This study highlights the urgent need
for integrative taxonomy, i.e., combining morphology, standardized DNA
barcoding, and expanded sampling to resolve species identities and to support
effective fisheries management and conservation planning in Indonesian
freshwater ecosystems.
Keywords: C oxidase subunit (COI), cryptic diversity,
DNA barcoding, fish diversity conservation, mitochondrial DNA, morphological
identification, molecular taxonomy, river system, species.
Introduction
Indonesia is home to 4,970
documented fish species, accounting for approximately 15% of the world’s fish
diversity (Reid et al. 2013; Reis et al. 2016). According to FAO assessments
between the late 1990s and 2003, the number of recorded fish species in
Indonesia increased by approximately 300. Despite this growth, the global total
of fish species rose by over 11,000, reducing Indonesia’s proportional share
from approximately 25% in 2003 to about 15% by 2016. Of these, approximately
1,258 species represent about 10% of the world’s freshwater fish diversity (Gustiano et al. 2021). Dudgeon (2000) estimated that around
1,700 freshwater species are found in Indonesia (Dudgeon 2000). Regarding
endemism, 19.5% of the fish species are unique to the region (Gustiano et al. 2021). Among the main Indonesian Islands,
Sulawesi boasts the highest number of endemic species, with about 76% of the
species on the island being native (Partasasmita et
al. 2015). The limited increase in newly documented species and the decline in
Indonesia’s percentage of global species raise important conservation
questions.
Catfishes belonging to the genus Ompok (La Cepede) are
species within the Siluridae family, commonly found
in lentic and lotic systems across southeastern and southern Asia. According to
Bornbusch (1995), the genus is paraphyletic,
comprised of four distinct clades: group of O. hypophthalmus
(Bleeker, 1846), group of O. bimaculatus
(Bloch, 1794), group of O. eugeneiatus (Vaillant,
1893), and group of O. leiacanthus (Bornbusch, 1995). The group of O. hypophthalmus
is characterized by cartilaginous plates supporting the mandibular barbels. These plates possess two posterior extensions, in
contrast to other conditions where the plates are underdeveloped, exhibit a
single dorsolateral extension, or appear elongated and hourglass-shaped without
extensions. The term “selais fish” is a local
vernacular name used in Sumatra and Kalimantan to refer to several
morphologically similar silurid catfishes, primarily
within the genus Ompok. The non-specific use
of this term has contributed to taxonomic ambiguity in both ecological and
molecular studies.
The rapid advancement of
molecular technology worldwide has significantly enhanced the identification of
new species, as highlighted by Kalyankar et al.
(2012), Bachry et al. (2019), Patil
et al. (2023), and Sontakke et al. (2023). Studies
focusing on systematics and evolutionary genetics, including taxonomy and
phylogeny, have played a crucial role in documenting genetic resources. The use
of DNA barcoding for quick and precise species identification is essential for
enhancing fish diversity initiatives (Hubert et al. 2015; Tiknaik
et al. 2019). In Indonesia, this method has not been widely adopted, with
conventional, taxonomy-based species identification still being the predominant
approach.
Materials
and Methods
Molecular analysis
Mitochondrial DNA sequences of Ompok species were retrieved from BOLD Systems and
GenBank, including 18 COI and five cytochrome b (Cyt
b) sequences with verified locality information. Sequence alignment was
performed using MUSCLE implemented in MEGA X v10.x, with manual trimming to
equal lengths. Genetic distances were calculated using the Kimura 2-parameter
(K2P) model. Phylogenetic relationships were inferred using the
Neighbor-Joining (NJ) method with 1,000 bootstrap replicates. Species
delimitation was preliminarily explored using GMYC and PTP models based on the
COI dataset. Only sequences with unambiguous taxonomic annotation and
river-level metadata were included in downstream analyses.
Results
The analysis revealed that the
distribution of O. hypophthalmus in Indonesia
is restricted to specific river systems, suggesting a narrower range than
previously reported. The findings highlight the importance of accurate species
identification and continuous monitoring, as populations may be vulnerable to
environmental changes, habitat fragmentation, and anthropogenic disturbances.
Current Status of O. hypophthalmus in Indonesia
The distribution of O. hypophthalmus in Indonesia appears to be confined to
specific river systems, indicating a more restricted range than previously
understood. This emphasizes the need for accurate species identification and
continuous monitoring to support effective conservation measures. The habitats
of these fish may be vulnerable to environmental changes, habitat
fragmentation, and anthropogenic activities.
Morphological identification of Ompok species in Indonesia
In 2003, Ng reviewed the taxonomy
and distribution of the O. hypophthalmus
complex in southeastern Asia, clarifying the identities of O. hypophthalmus, O. urbaini,
and describing a new species, O. rhadinurus.
The study synonymized O. macronema with O. hypophthalmus and validated O. urbaini
as a distinct species, previously misclassified. It also delineated the
geographical distributions of these species: O. hypophthalmus
is found primarily in Java and southern Borneo, O. urbaini
in Indo-China river systems, and O. rhadinurus
in Sumatra, Borneo, and the Malay Peninsula. Key morphological differences,
such as head width, caudal peduncle depth, and the number of anal-fin rays,
were instrumental in distinguishing these species. Ng’s findings are
illustrated in Figure 1. Despite these clarifications, several subsequent
studies appear to have misidentified O. urbaini
and O. rhadinurus as O. hypophthalmus.
2. In a biodiversity study
conducted in Buaya Lake and the Indragiri River basin
in Sumatra, 22 fish species were identified across both habitats. The lake
served as a spawning and nursery ground, supporting younger specimens likely
originating from the Indragiri River. Among the identified species, O. hypophthalmus was reported from the river channel (Nofrizal et al. 2023).
3. Further research on the
reproductive biology of O. hypophthalmus in
the Kampar Kiri River floodplain revealed five stages of gonad maturity,
confirming the species as a total spawner and
iteroparous (Sjafei et al. 2008). Simanjuntak
(2008) examined fecundity, maturity, and spawning patterns of O. hypophthalmus and Clarias
macrocephalus in the same region (Simanjuntak et al. 2008).
4. Elvyra
et al. (2010) studied the gonadal maturity, fecundity, and conservation needs
of O. hypophthalmus in the Kampar River,
emphasizing the ecological importance of this species, locally known as ‘ikan lais’ (Elvyra et al. 2010).
5. Eddy & Gema
(2019) reported O. hypophthalmus from the Arut–Kumai peat waters; notably, O. rhadinurus,
which Ng (2003) reported from parts of Borneo, was not mentioned in that study,
raising the possibility of misidentification.
6. In the Siak
River, O. rhadinurus was identified by the
original authors in fish catches, highlighting the continued taxonomic
challenges in distinguishing these species (Budy et
al. 2023).
7. A year-long study in the
Mahakam River, East Kalimantan, documented the presence of O. hypophthalmus and O. miostoma
among six catfish species sampled across four locations (Jusmaldi
et al. 2018).
Molecular identification and DNA
barcoding evidence
As of late 2024, only 18 COI gene
sequences and five cytochrome b (Cyt b) sequences of O.
hypophthalmus have been submitted to the BOLD and
NCBI databases. These sequences were contributed primarily by two research
groups led by Elvyra R. and Kasayev
T. (Refer to Table 1).
1. A study by Kasayev
& Arisuryanti (2022) analyzed nine COI sequences
of selais fish from the Arut
River in Central Kalimantan, suggesting their identity as O. hypophthalmus (Kasayev & Arisuryanti, 2022). These findings revealed up to 3.6%
nucleotide divergence among COI sequences, indicating substantial genetic
structuring and raising uncertainty regarding conspecificity.
2. The 18 COI sequences available
in the BOLD database are categorized into four Barcode Index Numbers (BINs),
each corresponding to a distinct river system: the Arut,
the Tapung, the Indragiri, and the Kampar Rivers
(Refer to Figure 1 & Table 1).
3. Elvyra
et al. (2020) assigned Cyt b sequences to O. hypophthalmus based primarily on morphological
identification, as comparative Cyt b reference
sequences for confirmed O. hypophthalmus were
not available at the time. Consequently, these assignments should be
interpreted cautiously (Elvyra et al., 2020).
4. Arisuryanti
et al. (2020) investigated genetic variation in selais
fish from the Arut River by analyzing polymorphisms
in the partial 16S mitochondrial gene. Their findings revealed intra-population
genetic variation and suggested that the selais fish
represents a single species, although its specific taxonomic name remains
unresolved.
This growing body of molecular
evidence underscores notable genetic diversity among populations currently
identified as O. hypophthalmus and highlights
the importance of integrating molecular tools with morphological analyses for
accurate species identification.
Discussion
Reassessment of the distribution
of O. hypophthalmus
This section synthesizes evidence
from both morphological taxonomy and molecular barcoding to reassess the
reported distribution of O. hypophthalmus in
Indonesia. Both morphological and molecular approaches complement each other,
and each has inherent strengths and limitations. The following synthesis
summarizes the reassessment of O. hypophthalmus
distribution in Indonesia.
Morphological status of O. hypophthalmus in Indonesia
Ng (2003) provided a
comprehensive morphological revision of the O. hypophthalmus
species complex, recognizing O. hypophthalmus,
O. urbaini, and describing O. rhadinurus as a new species. Clear diagnostic
characters and geographically structured distributions were established;
however, these revisions have not been consistently applied in subsequent
Indonesian studies.
Following Ng’s (2003) revision,
several studies from Indonesia did not consistently apply the revised
diagnostic criteria and continued to report O. hypophthalmus
in regions where O. rhadinurus was expected.
3. Several studies conducted in
the Kampar River have investigated reproductive biology and gonadal development
of specimens identified as O. hypophthalmus (Simanjuntak et al. 2008; Sjafei
et al. 2008; Elvyra et al. 2010). Ng (2003)
did not report O. hypophthalmus from the
Kampar River based on morphological evidence.
4. Most subsequent studies
focused on ecological or fisheries-related aspects rather than taxonomic
validation, and only a limited number explicitly referenced Ng’s (2003)
revision (Akbar et al. 2020; Nofrizal et al. 2023).
5. In 2023, Budy
and Isnaniah mentioned that the O. rhadinurus species was observed in Benayah
Village, Pusako District, Siak
Regency (Budy et al. 2023).
Molecular identification status
of O. hypophthalmus
1. Elvyra
et al. (2020) investigated the molecular characteristics and phylogenetic
relationships of silurid catfishes from the Kampar
River in Indonesia, focusing on the cytochrome b gene. They found four species,
including Kryptopterus limpok,
O. eugeneiatus, O. hypophthalmus,
and Phalacronotus apogon
(Elvyra et al. 2020).
2. A study by Kasayev
& Arisuryanti (2022) mentioned selais fish from the Arut River
in central Kalimantan, confirming their identity as O. hypophthalmus.
In the same study, COI sequences from specimens collected in the Indragiri
River were assigned to O. hypophthalmus; based
on Ng’s (2003) morphological framework and observed genetic divergence
exceeding 3%, these assignments remain uncertain. This level of divergence
suggests the possibility of taxonomic misidentification or cryptic diversity;
additional integrative analyses are required before proposing taxonomic
speciation (Kasayev & Arisuryanti
2022).
3. Arisuryanti
et al. (2020) investigated 16S genetic variation in selais
fish from the Arut River; the precise taxonomic
identity of these specimens remained unresolved.
Proposed reassessment of Ompok species distributions in Indonesian Rivers
Based on the synthesis of
available morphological and molecular evidence, the following interpretations
are proposed:
Kampar River
Available morphological and Cyt b data suggest the presence of at least two silurid taxa in the Kampar River (O. eugeneiatus
and specimens currently identified as O. hypophthalmus).
The absence of comparative COI data prevents definitive confirmation of species
identity.
Indragiri & Tapung Rivers
Based on Ng’s (2003)
morphological revision and available COI divergence values, specimens from the
Indragiri and Tapung Rivers are more consistent with O.
rhadinurus than O. hypophthalmus.
Nevertheless, additional integrative sampling is required to confirm this
reassignment.
Conclusion
This study highlights persistent
taxonomic inconsistencies in the identification of O. hypophthalmus
in Indonesia. While molecular data reveal clear genetic structuring among river
populations, current evidence is insufficient to fully resolve species
boundaries across all regions. Integrative taxonomy combining standardized
morphological assessment and expanded DNA barcoding is essential before
definitive biogeographic conclusions can be drawn. Accurate species
identification is critical for fisheries management, conservation planning, and
preventing the perpetuation of taxonomic confusion in Indonesian freshwater
fishes. Accurate taxonomic recognition of O. hypophthalmus
is critical for fisheries management and conservation assessments, as
historical misidentifications may have influenced stock evaluation,
biodiversity estimates, and regional Red List assessments across its reported
distribution. The conclusions of this study are limited to a small number of
publicly available sequences, uneven geographic sampling, and the lack of
integrated morphological examination of sequenced specimens.
Table 1. COI gene
sequence details of Ompok hypophthalmus available in
BOLD and NCBI databases.
|
Listed species |
BIN ID |
Sample ID / NCBI ID |
Location |
Name of scientist who generated
sequences |
|
O. hypophthalmus |
BOLD:AEM5469 |
MZ634369, MZ634366, MZ634368,
MZ634372, MZ634367, MZ634371, MZ634373, MZ634370, MZ634374 |
Arut River, Central Kalimantan, Indonesia |
Kasayev, T. & Arisuryanti, T. |
|
BOLD:ADO3280 |
MH732890, MH732889, MH732891,
MH732887 |
Tapung River |
Elvyra, R. |
|
|
BOLD:AEH7342 |
MK473379, MK473378, MK473377,
MH732888 |
Indragiri River |
Elvyra, R. |
|
|
BOLD:ADO4263 |
MH732886 |
Kampar River |
Elvyra, R. |
For
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