F1000Research F1000Research 2046-1402 F1000 Research Limited London, UK 10.12688/f1000research.17319.3 Research Article Articles Biometric and genetic differences in kelabau ( Osteochilus spp.) as revealed using cytochrome c oxidase subunit 1

[version 3; peer review: 3 approved]

 Asiah Nur Data Curation Formal Analysis Investigation Project Administration Software Writing – Original Draft Preparation Writing – Review & Editing https://orcid.org/0000-0002-6440-5416 1 2 Junianto Junianto Conceptualization Supervision Validation Writing – Review & Editing 1 Yustiati Ayi Conceptualization Methodology Supervision Validation Writing – Review & Editing 1 Sukendi Sukendi Conceptualization Methodology Supervision Validation Writing – Review & Editing 2 Fahmi Melta Rini Conceptualization Formal Analysis Investigation Methodology Validation Writing – Review & Editing a 3 Muchlisin Zainal A. Validation Writing – Review & Editing https://orcid.org/0000-0002-0858-1853 4 Kadapi Muhamad Methodology Supervision Validation https://orcid.org/0000-0002-0514-3751 5 Windarti Windarti Writing – Review & Editing b 6 Department of Fisheries and Marine Science, Padjadjaran University, Indonesia, Sumedang, West Java, 45363 Sumedang, Indonesia Aquaculture Department, Riau University, Pekanbaru, Riau, 28293, Indonesia Aquaculture Department, Research Center for Ornamental Fish Culture, Depok, West Java, 16436, Indonesia Aquaculture Department, Syiah Kuala University, Banda Aceh, Aceh Darussalam, 23111, Indonesia Agronomy Department, Padjadjaran University, Sumedang, West Java, 45363, Indonesia Aquatic Resource Management Department, Riau University, Pekanbaru, Riau, 28293, Indonesia m_rinif@yahoo.com windarti.unri@gmail.com

No competing interests were disclosed.

 10 3 2020 2019 8 177 12 2 2020 Copyright: © 2020 Asiah N et al. 2020 This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Background: Kelabau ( Osteochilus spp.) is a freshwater fish commonly found in the rivers of Riau, Indonesia. Researchers believe that these are Osteochilus kelabau; however, accurate taxonomic determination of these fish in Riau waters has not been made. The purpose of this study was to facilitate the identification of the kelabau based on its morphology and genetics using biometric and cytochrome c oxidase subunit 1 ( CO1) analyses, respectively.

Methods: Fish samples were collected from the Siak, Kampar and Rokan rivers in Riau Province, Indonesia. The DNA of 90 fish was extracted from the caudal fins using a DNA extraction kit, after which it was amplified using primers Fish-F1 and Fish-R1. Sequencing was conducted by Applied Biosystems Macrogen Korea, and the DNA sequences were then edited and aligned using MEGA v. 7. All samples were BLAST-searched for identification using the National Center for Biotechnology Information and BOLD System. Phylogenetic trees were constructed, and the similarity index was calculated using accession numbers AP011385.1 and KC631202.1 in GenBank.

Results: Analysis of the consensus barcode sequence for 86 species revealed a high percentage of barcode matches (96%–97% in GenBank and 96.6%–96.76% in the BOLD System). The nucleotide distance between groups of kelabau from the different rivers based on the Kimura 2-parameter model gave the following results: 0.05% between groups from the Siak and Kampar rivers, 0.09% between those from the Siak and Rokan rivers and 0.05% between those from the Kampar and Rokan rivers. The nucleotide distance between the groups in the Siak (0.09%), Kampar (0.00%) and Rokan (0.10%) Rivers indicated that the kelabau in those rivers were related to each other.

Conclusions: Based on the results of the research data using CO1 and biometric analyses, the kelabau were confirmed to be O. melanopleurus.

DNA barcoding Kelabau Fish Common Rivers of Riau Population Structure Kementerian Riset Teknologi Dan Pendidikan Tinggi Republik Indonesia SPDIPA-042.061.401516/2018 The study was supported by Doctor’s Dissertation Research SP DIPA-042.061.401516/2018, Ministry of Research, Technology and Higher Education (MRTHE), the Republic of Indonesia; therefore, the authors thank MRTHE for the financial collaboration support with the Research Institution and Community Service of Riau University. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Amendments from Version 2

In this new version of the manuscript we have revised as follows: 1. We have added three citations in the discussion - "35,36" become "35 to 39". 2. In paragraph three in the discussion we have added reasons for limited variation and a discussion of data table 3. 3. Dr Windarti was added as a co-author for her work in improving the manuscript

 Introduction

Kelabau are ancient fish belonging to genus Osteochilus of family Cyprinidaes. Kelabau fish are distributed throughout Thailand, Vietnam, Peninsular Malaysia, Borneo and Sumatra 1, 2 . In Sumatra Island in Indonesia, these fish is commonly found in the Siak, Kampar and Rokan rivers in Riau Province 3, 4 .

According to local fishers in Riau, kelabau are divided into two types on the basis of morphology; although, there is no detailed information about these fish types. The local fishers said that the first type of kelabau fish is the fish found in this study. The morphological characteristic of this fish is brownish body, with brighter bottom, dark hazy blotches present above the pectoral fins, and the size ranges from 15 to 2,778.93 gr. The second type of fish is larger sized and yellowish color. However, during the study time, from 2017 to 2018, this type was not found. Thus, a study was needed to identify the species using morphological and molecular methods to determine these types in the Siak, Rokan and Kampar rivers. Identification of any species using morphological traits can be difficult and can lead to errors 5 ; therefore, owing to morphological similarities among Osteochilus spp., molecular markers, such as DNA barcodes, are important to identify the fish species uses a specific sequence region (i.e. cytochrome c oxidase subunit 1 ( CO1)) to identify a species and is a technique that can identify taxonomic units as well as biodiversity for determining species of several organisms 5– 9 . Unlike molecular phylogeny used to determine relationships among species, the purpose of DNA barcoding is to identify unknown or undetermined species into phylogeny 10 . The common mitochondrial (mt) DNA region used as a barcode in protists and animals comprises 600 bp. In addition, CO1 is one of the genetic markers used to identify insects, birds, primates and fish to species 11– 13 . MtDNA CO1 is selected as a target in DNA barcoding because it is a highly conserved site. This method has advantages over the morphological identification approach in that it is fast, reliable and it can be used for all types of samples because it uses a single gene along with mutations in the nucleotides to acknowledge the taxonomic features of each species 13 .

The study on DNA barcoding for freshwater fish has been widely practiced in various countries, including Nigeria 14 , India 15 , Philippines 16 , Canada 9 and Indonesia 5, 17– 19 . The method has been successfully validated for the taxonomic status within Rasbora in Lake Laut Tawar 20 ; Anguillidae in Aceh waters 21 ; Ornamental fish from Peat lands 5 ; Channidae in Peninsular Malaysia, Sarawak, Sumatera, Borneo, Myanmar, Vietnam, India, Germany, Singapore and the United Kingdom 22 and Cichlidae in northeastern Nigeria 23 ; therefore, it can be used to equally successfully validate the taxonomic unit of the kelabau using its morphology supported by molecular data. This information is crucial for designing a remedial course of action about the conservation strategy for this species in the Siak, Kampar and Rokan rivers in Riau Province, Indonesia.

 Methods Ethics

The study population was collected and sampled according to the guidelines on the use of living organisms for research from the Laboratory of the Faculty of Fisheries and Marine, Riau University, Indonesia 24

Sampling sites and collection

A total of 90 kelabau (30 fish from each river) were collected from the Siak, Kampar and Rokan rivers ( Figure 1). Fish were caught using a gill net 3 m deep and 20 m long with a 12.7-cm mesh. The gill nets were installed in the river water close to the riverbank and remained for 24 h from 08:00 to 08:00 the following day. The fish collected were counted using hand-counter and cleaned using freshwater. A number of 50-mm caudal fin tissue samples were taken using a sterile scissors and preserved in ethanol, after which a photo of each fish sample was taken for documentation using a digital camera.

Sample sites for <italic toggle="yes">Osteochilus melanopleurus</italic> from the Siak (N: 00°39'22.28'' and E: 101°17'28.67''), Kampar (N: 00°22'13.64'' and E: 101°54'11.97'') and Rokan rivers (N: 01°22'33.65'' and E: 100°58'26.76''), Riau Province, Indonesia.

All samples were preserved in 3-kg sample bags which were labeled according to site location, date and serial number. Before preservation, the fish samples were injected with 10% formalin. The fish samples were then transported to the laboratory for further evaluation. The morphologies of the collected fish were identified up to species level using the identification book produced by the Indonesian Institute of Sciences ichthyology museum 1, 25 . The fish morphologies observed were length, color, shape of scales, mouth shape, barbels, number of fins and special marks on the body.

 Biometrics

Biometric analyses were used to measure morphological characteristics in this study 1 . This tool is considered conventional for identifying organisms. Molecular identification using CO1 gene sequences has been supported for providing additional organism classification.

 DNA isolation and amplification

DNA was extracted using the spin-column method from the gSYNC DNA Extrusion Kit (Geneaid Catalogue No. GS 300, Taiwan). The extracted DNA was then transferred to a 1X Tris–borate ethylenediaminetetraacetic acid (TBE) solution with a 1.5% agarose gel and Pegreen gel dye (PEQLAB Biotechnologies GmbH, Erlangen, Germany) 19 . The quantity of DNA was visualized with the help of a GeneQuant Spectrophotometer by adding 78 μL nuclease-free water in a cuvette along with 2 μL DNA. The DNA was then amplified using the universal primer Fish-F1(5’-TCA-ACC-AAC-CAC-AAA-GAC-ATT-GGC-AC-3’) and Fish-R1 (5’-TAG-ACT-TCT-GGG-TGG-CCA-AAG-AAT-CA-3’) with a target of 707 bp and 655 bp 26 , respectively. The amplification thermocycling conditions as follow: the PCR condition using pra PCR (94°C for 5 min), 35 cycles of denaturation (94°C for 30 s), annealing (56.6°C for 30 s) and extension (72°C for 30 s), followed by post-PCR extension (72°C for 5 min) and hold (4°C for 5 min). PCR results were analyzed using 1.5% agarose gel at 100 V to assess the bands, and only the clear products were sent to Applied Biosystems Macrogen Korea for sequencing.

 Controlling molecular samples and sequence quality

The PCR amplicon was 707 bp, which implied that no sequence of DNA was derived from mtDNA nuclear mitochondrial DNA segments (NUMTs), because a NUMT barely reaches 600 bp 9 . The selected CO1 sequences were entered into GenBank and the BOLD System databases to compare the alignment of nucleotide sequences and 99%–100% values with that with no insertions/deletions. All sequences were aligned using ClaustalW with MEGA v.7 27 .

 Data analysis Blasting of <italic toggle="yes">CO1</italic> by NCBI (GenBank) and BOLD System (online)

The entire nucleotide sequence obtained from the sequence chromatogram was assembled using DNA Baser Assembler, aligned and then analyzed using MEGA 7. It was further aligned (multiple alignments) using the reference NCBI GenBank accession numbers AP011385.1 and KC631202.1. Similarly, the percentages of CO1 sequences were blasted using NCBI Blast and BOLD Systems databases.

 Nucleotide variations

Nucleotide variations among samples were analyzed using dnaSP v.5 28 . The parameters of these calculations were haplotype number, variable site, parsimony site, haplotype diversity and nucleotide diversity.

 Phylogenetic tree

Phylogenetic trees were estimated using all samples from the three populations and calculated according to the Tamura-Nei model 29 using MEGA 7 27 .

 Nucleotide distance

The distance among the nucleotide bases of the mtDNA CO1s was analyzed using the Kimura 2-parameter model 30 . The nucleotide distances between and within the populations were examined according to the model based on the similarity of frequencies and ratios of transition to transversion (Ti:Tv) using MEGA 7 27 .

 Results Morphological identification

The morphological traits of all kelabau used in this study matched those of O. melanopleurus. We used the important morphological traits to identify these fish according to Kottelat et al. 1 . The morphological characteristics measurement of O. melanopleurus showed that the fish have 16–19 branched dorsal rays, the number of scales was ranged from 10.5 to 12.5 in between dorsal origin and lateral line, the number of circum peduncu-lar rows of scale was ranged from 20 to 24 and lips covered with folds and plicae and there was no hard tubule at the tip of the mouth ( Figure 2a). This species has one pair of barbels at above and one pair at bottom, dark hazy blotches near above of the pectoral fins. The body is brownish, with the bottom brighter than the top and the type of steroid scales ( Figure 2b). Raw biometric data are available on OSF 31 . as ~707 bp.

( a) Kelabau ( O. melanopleurus) and ( b) ctenoid scale of O. melanopleurus.

 Genetic analysis

A sequence amplified by Fish-F1 primer was successfully identified in 86 of 90 samples of mtDNA fish. The base length of the CO1 nucleotide obtained from the formulation process and electrophoresis ( Figure 3)

DNA amplified using Fish-F1 and Fish-R1 primers; M= Marker 100 bp (Vivantis, Malaysia); 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209 and 210= Rokan River; 211= Kampar River.

Based on genetic analysis using the Tamura-Nei model, there was an unequal distribution of all nucleotides with the following frequencies: adenine (A), 26.73%; thymine (T), 30.44%; cytosine (C), 25.93% and guanine (G), 16.90% ( Table 1). The rates ratio between transition and transversion was 10.257 purines and 1.915 pyrimidines, and the overall transition and transversion bias were R= 2.499 based on Tamura-Nei model 32 . The pattern of nucleotide distribution of A, T, C and G was T > A > C > G, but the carps which cultivated in India have the following pattern of nucleotide distribution: T > C > A > G 33 .

Maximum composite likelihood estimates of the pattern of nucleotida substitution.
A T C G
A - 4.03 3.34 22.95
T 3.54 - 6.57 2.24
C 3.54 7.72 - 2.24
G 36.29 4.03 3.34 -

i Bold: different transitional subtitutions; italic: tranversional subtitutions.

The nucleotide distances between nucleotide bases within the groups indicated that the values of the nucleotide base sequences within the fish population were 0.0009, 0.0000 and 0.0010 in the Siak, Kampar and Rokan rivers, respectively. The evolutionary distance between the nucleotides of the groups had a comparative difference in the nucleotide sequences of 0.0005 for fish from the Siak and Kampar rivers, of 0.0009 in those from the Siak and Rokan rivers and of 0.0005 for those from the Rokan and Kampar rivers. Based on the nucleotide distance, the fish were identified as being from the same species (0.06%) ( Table 2).

Nucleotide distances among the populations.
1 2 3 4
Siak -
Kampar 0.0005 -
Rokan 0.0009 0.0005 -
GenBank (AP011385.1) 0.0367 0.0366 0.0368 -
GenBank (KC631202.1) 0.0351 0.0350 0.0351 0.0048

i Source: Kimura estimation of 1980: “Evolutionary Divergence over Sequence Pair Between Groups” 30 .

CO1 had 612 conserved sites (98%), 9 variable sites (1.45%), 4 informative parsimony (0.64%) and 5 singleton sites (0.81%). The highest nucleotide variation was in the Rokan river population (0.00100 ± 0.00032); whereas, the Kampar river population had no nucleotide variation based on DnaSP5 calculations ( Table 3). Using the NCBI database with accession numbers AP011385.1 and KC631202.1, the DNA sequence of Kelabau was identified as belonging to O. melanopleurus with 96%–97% accuracy, query coverage of 99%–100% and an E-value of 0.0. While based on the BOLD System, the identity of all samples was 96.60%–96.93% accurate.

Nucleotide variation in mtDNA <italic toggle="yes">CO1</italic> of <italic toggle="yes">Osteochilus melanopleurus</italic> by DnaSP5.
Sampling location Number of sites Number of sequences Haplotype number Variable site Parsimony site Haplotype diversity Nucleotide diversity
Siak 621 28 6 6 2 0.439 ± 0.114 0.00090 ± 0.00029
Kampar 621 30 1 0 0 0 0
Rokan 621 28 6 6 2 0.437 ± 0.113 0.00100 ± 0.00032

i Source: Nei, 1987 for haplotype and nucleotide diversity 34 .

In the phylogenetic tree consisted of two major groups ( Figure 4). The first group was Cirrhinus moltonela (Gen-Bank KC631192.1) and it was divided from O. melanopleurus. The second group was differentiated into two sub groups, O. melanopleurus from GenBank (AP011385.1 and C631202.1) and 86 fish samples from Kampar, Siak and Rokan rivers. The 86 samples have BLASTN similarity values with O. melanopleurus of 96%–97%.

Phylogenetic tree of kelabau ( <italic toggle="yes">Osteochilus melanopleurus</italic>) based on the neighbour-joining model. Discussion

Overall, the morphological traits and DNA barcoding showed that the majority of, if not all, kelabau fish in the three rivers at Riau Province were O. melanopleurus. there were 2 types of kelabau fish present in Riau. The first type is relatively small (15 gr to 2,778.93 gr) fish with dark colored dorsal and whitish ventral. This type of fish is used in this study. The second type of kelabau fish is larger, with yellowish color. This fish was not found during the study.

Environmental changes can cause fish death orbmigration to suitable habitats. Overfishing using both legal and illegal methods has also triggered the decline of certain species 35– 39 . In addition, our results suggested that there was little nucleotide diversity among O. melanopleurus in the Siak, Rokan and Kampar rivers in Riau Province, particularly the fish in the Kampar river

The lack nucleotide diversity of O. melanopleurus from the three rivers was likely to be caused by limited opportunities for kelabau migration, so that the genetic exchanges with other populations are very small 36 ; moreover, the lack nucleotide diversity is believed to be caused by inbreeding, and overfishing 5, 40 . Variation in nucleotide diversity of the fish from the sampling areas is different. In the Kampar River, the fish was sampled from the relatively narrow area and it may cause the lowness of the nucleotide diversity. The diversity was 0 and it means that the nucleotide of the fish samples was almost identic. The low nucleotide diversity may occur as the habitat of the fish is very suitable and the fish may not face environmental related problem that trigger any genetic changing 41 . However the nucleotid diversity of the fish from the Siak and Rokan River was higher than Kampar River. Siak and Rokan Rivers have relatively low water quality that was caused mainly by anthropogenic activities. Changing in water quality may trigger the fish to adapt with that environmental condition and it may cause changes in genetic variation. Freeland et al. 41 stated that fish population with high genetic variation may be able to face problems related to environmental changing

In addition, Kelabau from the Siak and Rokan rivers were designated as one sub-sub group in group two ( Figure 4) because both rivers are geographically connected, allowing for hybridisation, whereas, there is inbreeding of these fish in the Kampar River, which causes a nucleotide diversity value of 0.0. Geographically, these three rivers (Siak, Kampar and Rokan rivers) have different environmental condition, that cause variations in morphology in fish ( O. melanopleurus) based on truss morphometric 42 . Factors causing morphological variations are environmental differences, habitat pollution levels, long-term isolation and crossbreeding in populations 43, 44 . The same deductions were drawn from previous studies on Desmopuntius pentazona and D. rombochelatus, although the taxonomies of the two fish are different. Nevertheless, based on a genetic difference of only 0.4%, the two species were grouped into one cluster 5 . These are distributed throughout Asia, the Mekong and Chao Praya river basins, Peninsular Malaysia, Sumatra and Borneo 1, 2 .

The identity of a species was derived using the morphological identification method to distinguish between species or individuals 45, 46 . Basically, the genetic identification of a species can be done using mtDNA CO1, a more effective approach than using rRNA 5, 33 . The nucleotide locus and mutations were used as references to conduct DNA barcoding in all fish samples 13 . Previous studies have identified several species using DNA bar-coding, such as ornamental fish of wetlands 5 , wetland fish larvae 46 , rainbow fish 47 , Cyprinidae fish 48 , salmon and trout 7 and freshwater fish 9, 19 . Furthermore, the phylogenetics of CO1 sequences can effectively show congeneric and confamilial species 9 .

The phylogenetic trees could describe the line of biological evolution from species or organisms with a different ancestry 49 . Nonetheless, the results of all these species did not show a 100% undistinguishable identity. The branch length between species leading to a gap in the pairwise distance distribution is referred to as the barcoding gap in CO1 23 . Intra-species relationships were quite high in all samples, which confirmed that kelabau melanopleurus) were native in the three rivers and could to adapt to changes in environmental conditions 40 .

Moreover, the existence of inter-nucleotide patterns and distances between A, T, C and G in the chromosomes showed the characteristics and genetic signs that distinguished each of the individuals, even though they belong to the same species 50 . This is reinforced by referencing the phylogenetic tree made using the neighbor-joining model.

The identification of fish species is normally conducted using morphological characteristics such as dorsal fins, pelvic fins, pectoral fins, anal fins, linea lateral fins, upper linea lateral fins, lower linea lateral fins, around body fins, and caudal peduncle fins; however, in this study, we used 12 morphological traits as described by the classification system of Kottelat et al. 1 . These results supported the classification using biometric data that all fish in the three rivers were O. melanopleurus. The morphological characteristics were consistent with the species having a relatively large body with a standard length of 119–560 mm, lips covered with folds and plicae, no tubercles on the snout, a pair of maxillary barbels, and a pair of lower jaw barbels. The body is brownish, with the bottom brighter than the top. Dark hazy blotches near above of the pectoral fins, which is a special trait of O. melanopleurus.

However, this method can be difficult, and molecular identification is necessary. In particular, using mtDNA CO1 was an effective approach 9, 17 . The results from nucleotide distance data based on the Kimura 2-parameter model indicated that the nucleotide distance among the fish was short in intraspecific species using mtDNA CO1 40 , which was supported by data showing that the percentage identity in O. melanopleurus species ranged between 96% and 97%. The Kelabau fish from the three sample sites were identified as O. melanopleurus by percentage identity, supported by an E-value of 0.0 and a 99%–100% query cover. The p-value indicated that the BLASTN results contained no errors. Besides, the low nucleotide distance values (<3%–5%) among the samples of O. melanopleurus from the Siak, Kampar and Rokan rivers, indicated that all samples were monophyletic.

 Conclusion

Based on our findings, we concluded that 86 of the 90 samples of kelabau from the Siak, Kampar and Rokan rivers in Riau were O. melanopleurus, as revealed by their morphological traits and the molecular analyses.

 Data availability Underlying data

CO1 gene sequences and raw biometric data of Osteochilus melanopleurus from Riau rivers can be found on OSF.

CO1 gene sequence DOI: https://doi.org/10.17605/OSF.IO/XGEZD 51

Raw biometric data DOI: https://doi.org/10.17605/OSF.IO/CFGM8 31 .

Data are available under the terms of the Creative Commons Zero "No rights reserved" data waiver (CC0 1.0 Public domain dedication).

The raw CO1 sequence data were also deposited in GenBank and can be found under sequential accession numbers MH430827-MH430854 and MH459085-MH459142.

 Acknowledgements

The authors thank Neli Safrina as a staff Laboratory of Fisheries and Marine Faculty, Riau University and Gema Wahyu Dewantoro, as a staff researcher at the Laboratory of Ichtiology in the Field of Zoology, Research Center for Biology of the Indonesian Institute of Sciences (LIPI) on the identification of the Kelabau fish using morphological traits. Also, thanks to Ornamental Fish Aquaculture Research and Development Center, Ministry of Marine and Fisheries Republic of Indonesia, Depok for providing laboratory facilities.

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J Mol Evol. 1980;16(2):111–120. 7463489 10.1007/BF01731581 Asiah N : Biometric of Kelabau Fish in Riau.2019. http://www.doi.org/10.17605/OSF.IO/CFGM8 Tamura K Nei M Kumar S : Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A. 2004;101(30):11030–5. 15258291 10.1073/pnas.0404206101 491989 Mohanty M Jayasankar P Sahoo L : A comparative study of COI and 16 S rRNA genes for DNA barcoding of cultivable carps in India. Mitochondrial DNA. 2013;26(1):1–9. 24047160 10.3109/19401736.2013.823172 Nei M : Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci U S A. 1973;70(12):3321–3. 4519626 10.1073/pnas.70.12.3321 427228 Nasution S Nuraini : Grant of Feed Containing Vitamin E in Home Fish Kelabau ( Osteochilus Kelabau) to Improve Quality Eggs and Larvae. Int J Sci Eng Res. 2014;2(4):4–9. Reference Source Kusmini II Mulyasari RGD : Karakterisasi Genetik Ikan Kalabau ( Osteochilus kelabau) dari Berbagai Lokasi di Kalimantan Barat Menggunakan Metode RAPD (Random Amplified Polymorphism DNA). Ber Biol. 2011;10(4):449–454. Reference Source Fauzi M Dahelmi D Zakaria IJ : Biological aspects of lelan fish, Diplocheilichthys pleurotaenia (Cyprinidae) from the upstream and downstream of the Kampar River, Riau Province, Indonesia. AACL Bioflux. 2016;9:305–315. Reference Source Munir W Tan UM Zakaria IJ : Developmental stages of endemic bilih fish larvae ( Mystacoleucus padangensis) from Singkarak Lake, West Sumatra, Indonesia.2016;9:965–975. Reference Source West L Indonesia S Zeswita AL : Study Population Of Freshwater Shellfish CorbiculaSumatrana In Singkarak Lake West Sumatra Indonesia. Res J Pharm Biol Chem Sci. 2016;7(6):1435–1441. Reference Source Frankham R Ballou JD Briscoe DA : Introduction to conservation genetics.2002. Reference Source Freeland JR Kirk H Petersen SD : Molecular Ecology 2nd ed. West Sussex (GB): Wiley-Blackwell.2011. 10.1002/9780470979365 Asiah N Sukendi S Junianto J : Trussmorphometric and meristic characters of kelabau fish ( Osteochilus melanopleurus Bleeker, 1852) from three populations in Kampar, Siak, and Rokan Rivers, Riau Province. J Iktiologi Indones. 2019;19(2):283–295. 10.32491/jii.v19i2.462 Rawat S Benakappa S Kumar J : Identification of fish stocks based on Truss Morphometric: A review. J Fish Life Sci. 2017;2(1):9–14. Reference Source Takács P Vitál Z Ferincz Á : Repeatability, Reproducibility, Separative Power and Subjectivity of Different Fish Morphometric Analysis Methods. PLoS One. 2016;11(6):e0157890. 27327896 10.1371/journal.pone.0157890 4915670 Zhang H Yu H Gao T : Analysis of genetic diversity and population structure of Pleuronectes yokohamae indicated by AFLP markers. Biochem Syst Ecol. 2012;44:102–108. 10.1016/j.bse.2012.04.024 Hubert N Kadarusman AW Busson F : DNA barcoding Indonesian freshwater fishes: challenges and prospects. DNA Barcodes. 2015;3(1):144–169. 10.1515/dna-2015-0018 Kadarusman Hubert N Hadiaty RK : Cryptic diversity in Indo-Australian rainbowfishes revealed by DNA barcoding: implications for conservation in a biodiversity hotspot candidate. PLoS One. 2012;7(7):e40627. 22829879 10.1371/journal.pone.0040627 3400673 Collins RA Armstrong KF Meier R : Barcoding and border biosecurity: identifying cyprinid fishes in the aquarium trade. PLoS One. 2012;7(1):e28381. 22276096 10.1371/journal.pone.0028381 3262790 Pramono TB Artiati D Widodo MS : Identifikasi Ikan Genus Mystus Dengan Pendekatan Genetik. J Sumberd Akuatik Indopasifik. 2017;1(2):123–132. 10.30862/jsai-fpik-unipa.2017.Vol.1.No.2.34 Afreixo V Bastos CA Pinho AJ : Genome analysis with inter-nucleotide distances. Bioinformatics. 2009;25(23):3064–70. 19759198 10.1093/bioinformatics/btp546 2778338 Asiah N : raw data CO1 gene in Kelabau fish.2019. http://www.doi.org/10.17605/OSF.IO/XGEZD 10.5256/f1000research.24696.r61112 Reviewer response for version 3 Ja’afar Ja’afar Nuhu 1 2 Referee https://orcid.org/0000-0003-2895-2866 Department of Biotechnology, Modibbo Adama University of Technology (MAUTECH), Yola, Nigeria Chevron Biotechnology Center, Modibbo Adama University of Technology (MAUTECH), Yola, Nigeria

Competing interests: No competing interests were disclosed.

 12 3 2020 Copyright: © 2020 Ja’afar JN 2020 This is an open access peer review report distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. recommendation approve

Please find my highlighted copy of the manuscript here . The areas highlighted in the manuscript are supposed to portray the integrity and diligence of both the journal and reviewers, thus, maintaining scientific standards. Aside from this, the manuscript is ready to be indexed.

Is the work clearly and accurately presented and does it cite the current literature?

Yes

If applicable, is the statistical analysis and its interpretation appropriate?

Partly

Are all the source data underlying the results available to ensure full reproducibility?

Yes

Is the study design appropriate and is the work technically sound?

Partly

Are the conclusions drawn adequately supported by the results?

Yes

Are sufficient details of methods and analysis provided to allow replication by others?

Yes

Reviewer Expertise:

NA

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

 10.5256/f1000research.24129.r59013 Reviewer response for version 2 Zakaria Indra Junaidi 1 Referee https://orcid.org/0000-0002-7248-5276 Departement of Biology, Faculty of Math and Science, Andalas University, Padang, Indonesia

Competing interests: No competing interests were disclosed.

 10 2 2020 Copyright: © 2020 Zakaria IJ 2020 This is an open access peer review report distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. recommendation approve

Is the work clearly and accurately presented and does it cite the current literature?

Partly

If applicable, is the statistical analysis and its interpretation appropriate?

Yes

Are all the source data underlying the results available to ensure full reproducibility?

Yes

Is the study design appropriate and is the work technically sound?

Yes

Are the conclusions drawn adequately supported by the results?

Yes

Are sufficient details of methods and analysis provided to allow replication by others?

Yes

Reviewer Expertise:

Fish Biology and Fisheries biology

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

Asiah Nur Riau University, Indonesia

Competing interests: No competing interests were disclosed.

 8 2 2020

Dear Mr. Indra Junaidi Zakaria,

Thank you for your suggestions on our manuscript. Through this letter I would like to explain the revision of my article titled “Biometric and genetic differences in kalabau (Osteochillus spp) as revealed using Cytochrome C Oxidase subunit 1”. I have revised these following points:

Grammatical and spelling mistakes throughout the paper have been revised.

The introduction has been improved by adding information on the difference of the characteristics of two species of kelabau fish (Osteochillus spp). As there are 2 types of fish that are named as “kelabau fish” by local people, information on the difference of those fishes was obtained by interviewing local fishermen. The presence of this information may be useful to give more explanation about the difference and the similarity of kelabau fish present in Riau in general.

A phrase “The demand for it as …” until “… the population of these as well as many other fish” has been deleted as it is not correlate with the theme of this manuscript.

Finally, the author has also added a quote in the following paragraph: “The study population was collected and sampled …” until “… of the Faculty of Fisheries and Marine Science, Riau University, Indonesia”.

The discussion section has been improved by comparing the result of this study with more articles available.

 Thank you for your suggestions and we hope that our article will be approved.

Best Regards,

Nur Asiah and the authors

 10.5256/f1000research.24129.r59015 Reviewer response for version 2 Pallipuram Jayasankar 1 Referee Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India

Competing interests: No competing interests were disclosed.

 7 2 2020 Copyright: © 2020 Pallipuram J 2020 This is an open access peer review report distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. recommendation approve

I have gone through the revision/corrections effected by the authors in the manuscript “Biometric and genetic differences in kelabau ( Osteochilus spp.) as revealed using cytochrome c oxidase subunit 1”. The manuscript has been improved as per my suggestions. I recommend to consider its indexing.

Is the work clearly and accurately presented and does it cite the current literature?

Partly

If applicable, is the statistical analysis and its interpretation appropriate?

Yes

Are all the source data underlying the results available to ensure full reproducibility?

Partly

Is the study design appropriate and is the work technically sound?

Partly

Are the conclusions drawn adequately supported by the results?

No

Are sufficient details of methods and analysis provided to allow replication by others?

Partly

Reviewer Expertise:

NA

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

Asiah Nur Riau University, Indonesia

Competing interests: No competing interests were disclosed.

 8 2 2020

Dear Mr. Pallipuram Jayasankar,

Thank you very much for your approved on our article, and thank you for your suggestions for the good of our article.

Best regards,

Nur Asiah and the authors

 10.5256/f1000research.24129.r59014 Reviewer response for version 2 Ja’afar Ja’afar Nuhu 1 2 Referee https://orcid.org/0000-0003-2895-2866 Department of Biotechnology, Modibbo Adama University of Technology (MAUTECH), Yola, Nigeria Chevron Biotechnology Center, Modibbo Adama University of Technology (MAUTECH), Yola, Nigeria

Competing interests: No competing interests were disclosed.

 3 2 2020 Copyright: © 2020 Ja’afar JN 2020 This is an open access peer review report distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. recommendation approve-with-reservations

In version 1 of the manuscript, I have highlighted some sections that may require the authors' attention. However, none of those have been effected. Perhaps, the authors did not get the script I have corrected. It is available if needed.

Is the work clearly and accurately presented and does it cite the current literature?

Yes

If applicable, is the statistical analysis and its interpretation appropriate?

Partly

Are all the source data underlying the results available to ensure full reproducibility?

Yes

Is the study design appropriate and is the work technically sound?

Partly

Are the conclusions drawn adequately supported by the results?

Yes

Are sufficient details of methods and analysis provided to allow replication by others?

Yes

Reviewer Expertise:

Molecular diagnostics

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.

Asiah Nur Riau University, Indonesia

Competing interests: No competing interests were disclosed.

 8 2 2020

Dear Mr. Ja'afar Nuhu Ja'afar,,

Thank you for your suggestions on our manuscript and we apologize for the late to response your suggestion because we need to discuss with other authors. Here we would like to inform that we already revised paragraph three by adding reasons for limited variation such as inbreeding within the species due to limited migration and we also added discussion about data on table 3.

Variation in nucleotide diversity of the fish from the sampling areas are different. In the Kampar River, the fish was sampled from the relatively narrow area and it may cause the lowness of the nucleotide diversity. The diversity was 0 and it means that the nucleotide of the fish samples was almost identical. Freeland et al., (2011) stated that the low nucleotide diversity may occur as the habitat of the fish is very suitable and the fish may not face environmental related problem that trigger any genetic changing. However, the nucleotide diversity of the fish from the Siak and Rokan River, was higher than Kampar River. Siak and Rokan Rivers have relatively low water quality that was caused mainly by anthropogenic activities. Changing in water quality may trigger the fish to adapt with that environmental condition and it may cause changes in genetic variation. Freeland et al., (2011) stated that fish population with high genetic variation may be able to face problems related to environmental changing.

Finally, we want to thank you very much for your suggestion on our manuscript and we hope that our manuscript will be approved.

Best regards,

Nur Asiah

 10.5256/f1000research.18938.r55212 Reviewer response for version 1 Pallipuram Jayasankar 1 Referee Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India

Competing interests: No competing interests were disclosed.

 4 11 2019 Copyright: © 2019 Pallipuram J 2019 This is an open access peer review report distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. recommendation approve-with-reservations

DNA barcoding is an important and useful tool to ratify species status in circumstances where morphology-based taxonomy fails or nearly-fails to perform unambiguous identification of species. The authors in the present study have taken up an important group of freshwater fish. There are many grammatical errors and some technical flaws in the manuscript. I felt one major drawback could be their total silence on the nominal species of Osteochilus kelabu. Of course using barcoding they have proved that the species is O. melanopleurus. However, they should have shown a phylogenetic comparison of these two nominal species to rule out confusion in identification. Morphological method followed does not appear to be robust. They are advised to use TRUSS MORPHOMETRICS which can be performed using user-friendly software nowadays. In the phylogenetic tree the majority of bootstrap values do not appear to be robust; hence it could reflect a spurious relationship.

Is the work clearly and accurately presented and does it cite the current literature?

Partly

If applicable, is the statistical analysis and its interpretation appropriate?

Yes

Are all the source data underlying the results available to ensure full reproducibility?

Partly

Is the study design appropriate and is the work technically sound?

Partly

Are the conclusions drawn adequately supported by the results?

No

Are sufficient details of methods and analysis provided to allow replication by others?

Partly

Reviewer Expertise:

I have been working on molecular taxonomy of fish, shellfish and marine mammals since 1996, thus 23 years of experience in this field; also gained expertise in freshwater aquaculture technology during the past 11 years.

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.

 10.5256/f1000research.18938.r53842 Reviewer response for version 1 Ja’afar Ja’afar Nuhu 1 2 Referee https://orcid.org/0000-0003-2895-2866 Department of Biotechnology, Modibbo Adama University of Technology (MAUTECH), Yola, Nigeria Chevron Biotechnology Center, Modibbo Adama University of Technology (MAUTECH), Yola, Nigeria

Competing interests: No competing interests were disclosed.

 4 10 2019 Copyright: © 2019 Ja’afar JN 2019 This is an open access peer review report distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. recommendation approve-with-reservations

Generally, the article needs to be proofread by an expert. There are a lot of areas I have highlighted to guide the authors.

In paragraph three of the discussion section, the authors should be more scientific in providing reasons for limited variation such as inbreeding within the species due to limited migration. More so, if COI is known to be conserved within a species, it is not expected to change within a small time frame of genetic event. In general, the discussion should be rewritten to explain the results and interpretations of the study.

In addition, I suggest the authors contact an expert that can explain/interpret the results obtained using DNASP. The explanation of the results from the software should be more than presenting the values.

The gel result will be more appreciable if the marker has been properly labelled.

Is the work clearly and accurately presented and does it cite the current literature?

Yes

If applicable, is the statistical analysis and its interpretation appropriate?

Partly

Are all the source data underlying the results available to ensure full reproducibility?

Yes

Is the study design appropriate and is the work technically sound?

Partly

Are the conclusions drawn adequately supported by the results?

Yes

Are sufficient details of methods and analysis provided to allow replication by others?

Yes

Reviewer Expertise:

Molecular diagnostics

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.

 10.5256/f1000research.18938.r44418 Reviewer response for version 1 Zakaria Indra Junaidi 1 Referee https://orcid.org/0000-0002-7248-5276 Departement of Biology, Faculty of Math and Science, Andalas University, Padang, Indonesia

Competing interests: No competing interests were disclosed.

 4 3 2019 Copyright: © 2019 Zakaria IJ 2019 This is an open access peer review report distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. recommendation approve-with-reservations

Generally:

There are still a lot of grammatical and spelling mistakes throughout the paper. Therefore, the authors should remove all of the grammatical and typographical errors as well as spelling mistakes. Use past tense and rephrase the sentences.

Introduction:

Inconsistency in writing in the first paragraph, the first line: it is written as “genus” but in the second row it is written as “species”. Kelabau are ancient fish belonging to the genus Osteochilus of family Cyprinidaes. The species are distributed throughout Thailand, Borneo and Sumatra (etc.).

According to local fishers in Riau, kelabau are divided into two types on the basis of morphology. Although there is no detailed information about these fish types, please, the authors should explain what the differences in the characteristics are of the two species which the fishermen know.

Sentences from: “The demand for it as…” until “…the population of these as well as many other fish.” I suggest deleting it, because it has no correlation with the theme of this manuscript which explains the verification of the species of fish kelabau using cytochrome c oxidase - it is not about increasing demand and the problem of decreasing populations of kelabau fish.

Methods:

Cite references in the following paragraph: “The study population was collected and sampled…” until “…of the Faculty of Fisheries and Marine, Riau University, Indonesia.”

Results:

Ok.

Discussion:

The Discussion is not up to the mark, especially in paragraphs one and two; please rewrite back with an explanation of how the characteristics of the two species of fish differ according to fishermen and the reason that these differences were caused by environmental changes and overfishing.  

Is the work clearly and accurately presented and does it cite the current literature?

Partly

If applicable, is the statistical analysis and its interpretation appropriate?

Yes

Are all the source data underlying the results available to ensure full reproducibility?

Yes

Is the study design appropriate and is the work technically sound?

Yes

Are the conclusions drawn adequately supported by the results?

Yes

Are sufficient details of methods and analysis provided to allow replication by others?

Yes

Reviewer Expertise:

Fish Biology and Fisheries biology

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.