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Fulltext Complete mitochondrial genome of Zeugodacus tau (Insecta: Tephritidae) and differentiation of Z. tau species complex by mitochondrial cytochrome c oxidase subunit I gene

Yong HS, Song SL, Lim PE, Eamsobhana P

PLoS One, 2017;12(12):e0189325.
PMID: 29216281 DOI: 10.1371/journal.pone.0189325

The tephritid fruit fly Zeugodacus tau (Walker) is a polyphagous fruit pest of economic importance in Asia. Studies based on genetic markers indicate that it forms a species complex. We report here (1) the complete mitogenome of Z. tau from Malaysia and comparison with that of China as well as the mitogenome of other congeners, and (2) the relationship of Z. tau taxa from different geographical regions based on sequences of cytochrome c oxidase subunit I gene. The complete mitogenome of Z. tau had a total length of 15631 bp for the Malaysian specimen (ZT3) and 15835 bp for the China specimen (ZT1), with similar gene order comprising 37 genes (13 protein-coding genes-PCGs, 2 rRNA genes, and 22 tRNA genes) and a non-coding A + T-rich control region (D-loop). Based on 13 PCGs and 15 mt-genes, Z. tau NC_027290 (China) and Z. tau ZT1 (China) formed a sister group in the lineage containing also Z. tau ZT3 (Malaysia). Phylogenetic analysis based on partial sequences of cox1 gene indicates that the taxa from China, Japan, Laos, Malaysia, Bangladesh, India, Sri Lanka, and Z. tau sp. A from Thailand belong to Z. tau sensu stricto. A complete cox1 gene (or 13 PCGs or 15 mt-genes) instead of partial sequence is more appropriate for determining phylogenetic relationship.

Matched MeSH terms: Electron Transport Complex IV/genetics*
Cytochrome c oxidase subunit I haplotype reveals high genetic diversity of Angiostrongylus malaysiensis (Nematoda: Angiostrongylidae)

Eamsobhana P, Yong HS, Song SL, Prasartvit A, Boonyong S, Tungtrongchitr A

J Helminthol, 2018 Mar;92(2):254-259.
PMID: 28330511 DOI: 10.1017/S0022149X17000244

The rat lungworm Angiostrongylus malaysiensis is a metastrongyloid nematode parasite. It has been reported in Malaysia, Thailand, Laos, Myanmar, Indonesia and Japan. In this study, A. malaysiensis adult worms recovered from the lungs of wild rats in different geographical regions/provinces in Thailand were used to determine their haplotype by means of the mitochondrial partial cytochrome c oxidase subunit I (COI) gene sequence. The results revealed high COI haplotype diversity of A. malaysiensis from Thailand. The geographical isolates of A. malaysiensis from Thailand and other countries formed a monophyletic clade distinct from the closely related A. cantonensis. In the present study, five new haplotypes were identified in addition to the four haplotypes reported in the literature. Phylogenetic analysis revealed that four of these five new haplotypes - one from Mae Hong Song (northern region), two from Tak (western region) and one from Phang Nga (southern region) - formed a distinct clade with those from Phatthalung (southern region) and Malaysia. The haplotype from Malaysia was identical to that of Phatthalung (haplotype AM1). In general, the COI sequences did not differentiate unambiguously the various geographical isolates of A. malaysiensis. This study has confirmed the presence of high COI genetic diversity in various geographical isolates of A. malaysiensis. The COI gene sequence will be suitable for studying genetic diversity, population structure and phylogeography.

Matched MeSH terms: Electron Transport Complex IV/genetics*
First genetic characterization of the brown dog tick Rhipicephalus sanguineus sensu lato in Peninsular Malaysia

Low VL, Prakash BK

Exp Appl Acarol, 2018 Jul;75(3):299-307.
PMID: 30066112 DOI: 10.1007/s10493-018-0279-2

The brown dog tick Rhipicephalus sanguineus sensu lato (s.l.) is a species complex comprising three main mitochondrial lineages, namely tropical, temperate and southeast European lineages. Despite its medical and veterinary importance, little attention has been paid to the genetic lineage of this species in Southeast Asia. Rhipicephalus sanguineus s.l. from Malaysia was investigated genetically, for the first time, using the mitochondria-encoded cytochrome c oxidase subunit I (COI) and 16S ribosomal RNA (16S) genes. Specifically, a pair of primers was developed to amplify the COI sequences in the present study. Both genes unambiguously assigned Malaysian material into the tropical lineage of R. sanguineus s.l. The 16S sequences were highly conserved; no variation site was observed. The COI sequences revealed slightly higher variation by recovering four haplotypes, one of which is restricted to the northernmost of Peninsular Malaysia. This finding will be a stepping stone in promoting more biological studies of this species complex in this region.

Matched MeSH terms: Electron Transport Complex IV/genetics
Morphological and Molecular Evidence for Multiple Taxa in Simulium parahiyangum (Diptera: Simuliidae), a Geographic Generalist Black Fly in Southeast Asia

Takaoka H, Low VL, Srisuka W, Ya'cob Z, Saeung A

J Med Entomol, 2018 Oct 25;55(6):1453-1463.
PMID: 30060220 DOI: 10.1093/jme/tjy109

Seven populations of Simulium parahiyangum Takaoka & Sigit (Diptera: Simuliidae), a geographically widespread nominal species of black fly in Southeast Asia, were morphologically and molecularly studied. Three morphoforms based on male and pupal morphological features, and two primary lineages based on the COI gene sequence analysis were recognized. Morphoform 1 (lineage 1) from Sarawak, Malaysia, is identified as S. parahiyangum sensu stricto and morphoform 2 (lineage 2) from Thailand and Vietnam, and morphoform 3 (lineage 1) from Peninsular Malaysia are each regarded as distinct species, although morphoform 3 is partially homosequential for the COI gene with morphoform 1. Morphoforms 2 and 3 are described as Simulium ngaoense sp. nov. and Simulium sazalyi sp. nov., respectively. Overall, S. parahiyangum is not a single geographic generalist but a composite of multiple species.

Matched MeSH terms: Electron Transport Complex IV/genetics
Fulltext Mitochondrial variation in subpopulations of Anopheles balabacensis Baisas in Sabah, Malaysia (Diptera: Culicidae)

Manin BO, Drakeley CJ, Chua TH

PLoS One, 2018;13(8):e0202905.
PMID: 30138386 DOI: 10.1371/journal.pone.0202905

Anopheles balabacensis, the primary vector of Plasmodium knowlesi in Sabah, Malaysia, is both zoophilic and anthropophilic, feeding on macaques as well as humans. It is the dominant Anopheles species found in Kudat Division where it is responsible for all the cases of P. knowlesi. However there is a paucity of basic biological and ecological information on this vector. We investigated the genetic variation of this species using the sequences of cox1 (1,383 bp) and cox2 (685 bp) to gain an insight into the population genetics and inter-population gene flow in Sabah. A total of 71 An. balabacensis were collected from seven districts constituting 14 subpopulations. A total of 17, 10 and 25 haplotypes were detected in the subpopulations respectively using the cox1, cox2 and the combined sequence. Some of the haplotypes were common among the subpopulations due to gene flow occurring between them. AMOVA showed that the genetic variation was high within subpopulations as compared to between subpopulations. Mantel test results showed that the variation between subpopulations was not due to the geographical distance between them. Furthermore, Tajima's D and Fu's Fs tests showed that An. balabacensis in Sabah is experiencing population expansion and growth. High gene flow between the subpopulations was indicated by the low genetic distance and high gene diversity in the cox1, cox2 and the combined sequence. However the population at Lipasu Lama appeared to be isolated possibly due to its higher altitude at 873 m above sea level.

Matched MeSH terms: Electron Transport Complex IV/genetics
High-throughput terrestrial biodiversity assessments: mitochondrial metabarcoding, metagenomics or metatranscriptomics?

Wilson JJ, Brandon-Mong GJ, Gan HM, Sing KW

Mitochondrial DNA A DNA Mapp Seq Anal, 2019 01;30(1):60-67.
PMID: 29591722 DOI: 10.1080/24701394.2018.1455189

Consensus on the optimal high-throughput sequencing (HTS) approach to examine biodiversity in mixed terrestrial arthropod samples has not been reached. Metatranscriptomics could increase the proportion of taxonomically informative mitochondrial reads in HTS outputs but has not been investigated for terrestrial arthropod samples. We compared the efficiency of 16S rRNA metabarcoding, metagenomics and metatranscriptomics for detecting species in a mixed terrestrial arthropod sample (pooled DNA/RNA from 38 taxa). 16S rRNA metabarcoding and nuclear rRNA-depleted metatranscriptomics had the highest detection rate with 97% of input species detected. Based on cytochrome c oxidase I, metagenomics had the highest detection rate with 82% of input species detected, but metatranscriptomics produced a larger proportion of reads matching (Sanger) reference sequences. Metatranscriptomics with nuclear rRNA depletion may offer advantages over metabarcoding through reducing the number of spurious operational taxonomic units while retaining high detection rates, and offers natural enrichment of mitochondrial sequences which may enable increased species detection rates compared with metagenomics.

Matched MeSH terms: Electron Transport Complex IV/genetics
Extensive sharing of mitochondrial COI and CYB haplotypes among reef-building staghorn corals (Acropora spp.) in Sabah, North Borneo

Robert R, Rodrigues KF, Waheed Z, Kumar SV

Mitochondrial DNA A DNA Mapp Seq Anal, 2019 01;30(1):16-23.
PMID: 29521145 DOI: 10.1080/24701394.2018.1448080

This study is aimed at establishing a baseline on the genetic diversity of the Acropora corals of Sabah, North Borneo based on variations in the partial COI and CYB nucleotide sequences. Comparison across 50 shallow-water Acropora morphospecies indicated that the low substitution rates in the two genes were due to negative selection and that rate heterogeneity between them was asymmetric. CYB appeared to have evolved faster than COI in the Acropora as indicated by differences in the rate of pairwise genetic distance, degrees of transition bias (Ts/Tv), synonymous-to-nonsynonymous rate ratio (dN/dS), and substitution patterns at the three codon positions. Despite the relatively high haplotype diversity (Hd), nucleotide diversity (π) of the haplotype datasets was low due to stringent purifying selection operating on the genes. Subsequently, we identified individual COI and CYB haplotypes that were each extensively shared across sympatrically and allopatrically distributed Indo-Pacific Acropora. These reciprocally common mtDNA types were suspected to be ancestral forms of the genes whereas other haplotypes have mostly evolved from autoapomorphic mutations which have not been fixed within the species even though they are selectively neutral. To our knowledge, this is the first report on DNA barcodes of Acropora species in North Borneo and this understanding will play an important role in the management and conservation of these important reef-building corals.

Matched MeSH terms: Electron Transport Complex IV/genetics*
A New Species of the Simulium (Simulium) multistriatum Species-Group (Diptera: Simuliidae) From Thailand and Its Phylogenetic Relationships With Related Species

Takaoka H, Srisuka W, Low VL, Saeung A

J Med Entomol, 2019 01 08;56(1):86-94.
PMID: 30398648 DOI: 10.1093/jme/tjy178

Simulium undecimum sp. nov. is described from Thailand. This new species is assigned to the Simulium multistriatum species-group, one of the 20 species-groups of the subgenus Simulium in the Oriental Region. It is characterized by the female cibarium with minute processes, male ventral plate with a narrow body having two vertical rows of distinct teeth on the posterior surface and without setae on the anterior and lateral surfaces, pupal gill with eight short filaments decreasing in length from dorsal to ventral, and divergent at an angle of around 90 degrees when viewed laterally, spine-combs only on abdominal segments 7 and 8, and cocoon wall-pocket shaped with anterolateral windows. Taxonomic notes to separate this new species from related species in Thailand and other countries are given. This new species is the 11th nominal member of this species-group recorded in Thailand. An analysis of the COI gene sequences shows that it is most closely related with S. malayense Takaoka & Davies (cytoform A) from Thailand but they are distantly separated by 3.01-8.87%.

Matched MeSH terms: Electron Transport Complex IV/genetics
A New Black Fly Species of the Simulium (Gomphostilbia) duolongum Subgroup (Diptera: Simuliidae) From Vietnam, and Molecular Comparisons With Related Species Using the COI Barcoding Gene

Takaoka H, Low VL, Tan TK, Ya'cob Z, Sofian-Azirun M, Dhang Chen C, et al.

J Med Entomol, 2019 02 25;56(2):432-440.
PMID: 30597034 DOI: 10.1093/jme/tjy222

Simulium (Gomphostilbia) yvonneae sp. nov. is described based on adults, pupae, and mature larvae from Vietnam. This new species belongs to the Simulium duolongum subgroup in the S. batoense species-group of the subgenus Gomphostilbia Enderlein. It is distinguished by having a relatively larger number of male upper-eye facets in 16 vertical columns and 16 horizontal rows and a pupal gill with eight filaments arranged as 3+(1+2)+2 from dorsal to ventral, of which two filaments of the ventral pair are 1.8 times as long as the longest filament of the middle and dorsal triplets. Morphological comparisons are made to distinguish this new species from all 22 related species. The genetic distinctiveness of this new species in the S. duolongum subgroup is also presented based on the DNA barcoding COI gene.

Matched MeSH terms: Electron Transport Complex IV/genetics
Molecular characterization of Phytophthora palmivora responsible for bud rot disease of oil palm in Colombia

Maizatul-Suriza M, Dickinson M, Idris AS

World J Microbiol Biotechnol, 2019 Feb 27;35(3):44.
PMID: 30810828 DOI: 10.1007/s11274-019-2618-9

Bud rot disease is a damaging disease of oil palm in Colombia. The pathogen responsible for this disease is a species of oomyctes, Phytophthora palmivora which is also the causal pathogen of several tropical crop diseases such as fruit rot and stem canker of cocoa, rubber, durian and jackfruit. No outbreaks of bud rot have been reported in oil palm in Malaysia or other Southeast Asian countries, despite this particular species being present in the region. Analysis of the genomic sequences of several genetic markers; the internal transcribe spacer regions (ITS) of the ribosomal RNA gene cluster, beta-tubulin gene, translation elongation factor 1 alpha gene (EF-1α), cytochrome c oxidase subunit I & II (COXI and COXII) gene cluster along with amplified fragment length polymorphism (AFLP) analyses have been carried out to investigate the genetic diversity and variation of P. palmivora isolates from around the world and from different hosts in comparison to Colombian oil palm isolates, as one of the steps in understanding why this species of oomycetes causes devastating damage to oil palm in Latin America but not in other regions. Phylogenetic analyses of these regions showed that the Colombian oil palm isolates were not separated from Malaysian isolates. AFLP analysis and a new marker PPHPAV, targeting an unclassified hypothetical protein, was found to be able to differentiate Malaysian and Colombian isolates and showed a clear clade separations. Despite this, pathogenicity studies did not show any significant differences in the level of aggressiveness of different isolates against oil palm in glasshouse tests.

Matched MeSH terms: Electron Transport Complex IV/genetics
DNA barcoding of shrimps from a mangrove biodiversity hotspot

Jamaluddin JAF, Mohammed Akib NA, Ahmad SZ, Abdul Halim SAA, Abdul Hamid NK, Mohd Nor SA

Mitochondrial DNA A DNA Mapp Seq Anal, 2019 05;30(4):618-625.
PMID: 31012766 DOI: 10.1080/24701394.2019.1597073

A total of 74 shrimp specimens were sequenced at a 584 bp segment of the cytochrome oxidase subunit I (COI) gene to examine patterns of DNA barcode variation in a mangrove biodiversity hotspot. The Maximum Likelihood tree, barcode gap analysis, Automatic Barcode Gap Discovery analysis and sequence comparisons with data available from Barcode of Life Data System and GenBank recovered 18 taxa of which 15 were identified to species level, 2 at genus level and a single taxon at order level. Two deep mitochondrial DNA lineage divergences were found in the giant tiger prawn, Penaeus monodon. It is suggested that one of the lineages is a consequence of an introduction from aquaculture activity. These results have provided a reliable barcode library for cataloguing shrimps in this area.

Matched MeSH terms: Electron Transport Complex IV/genetics
A new Cosmocercoides species (Ascaridida: Cosmocercidae), C. wuyiensis n. sp., from the Asiatic frog Amolops wuyiensis (Amphibia: Anura)

Liu Y, Yu Q, Shu YL, Zhao JH, Fang JY, Wu HL

J Helminthol, 2019 Jul 12;94:e59.
PMID: 31296272 DOI: 10.1017/S0022149X19000518

We identified and characterized a new cosmocercid nematode species, Cosmocercoides wuyiensis n. sp., through microscopic examination and sequencing of the partial small ribosomal RNA gene (18S rDNA), internal transcribed spacer (ITS) and mitochondrial cytochrome c oxidase subunit 1 (COI) genes. The new species was isolated from the intestine of the Asiatic frog Amolops wuyiensis Liu and Hu, 1975 captured from four localities of the Anhui province in south-east China. Among the 25 recorded species of the Cosmocercoides genus, the morphology of C. wuyiensis n. sp. is closest to that of C. kiliwai and C. malayensis, which were isolated from various Mexican frog and Malaysian lizard species, respectively. However, C. wuyiensis n. sp. displayed several distinguishing features, such as small size of the male body, two spicules of unequal lengths in the male, small gubernaculum, pre-, ad- and post-cloacal caudal rosette papillae in the ratio of 18-24:2:6 and simple papillae in the ratio of 14:multiple:4, circle and number of punctation in each rosette at 1:11-16, sharply conical tail-end and the presence of lateral alae and somatic papillae in both sexes. BLAST and the phylogenetic analyses of the 18S rDNA and ITS sequences indicated that C. wuyiensis n. sp. belonged to the genus Cosmocercoides, while that of the COI gene sequence of C. wuyiensis n. sp. showed 16.36% nucleotide divergence with C. pulcher and 47.99% nucleotide divergence with C. qingtianensis. The morphological and molecular characterization of C. wuyiensis n. sp. provides new taxonomic data for this genus.

Matched MeSH terms: Electron Transport Complex IV/genetics
Eristalinus arvorum (Fabricius, 1787) (Diptera: Syrphidae) in Human Skull: A New Fly Species of Forensic Importance

Heo CC, Rahimi R, Mengual X, M Isa MS, Zainal S, Khofar PN, et al.

J Forensic Sci, 2020 Jan;65(1):276-282.
PMID: 31305956 DOI: 10.1111/1556-4029.14128

A body of an unknown adult female was found within a shallow burial ground in Malaysia whereas the skull was exposed and visible on the ground. During autopsy examination, nine insect larvae were recovered from the interior of the human skull and subsequently preserved in 70% ethanol. The larvae were greyish in appearance, each with a posterior elongated breathing tube. A week after the autopsy, more larvae were collected at the burial site, and some of them were reared into adults. Adult specimens and larvae from the skull and from the burial site were sequenced to obtain DNA barcodes. Results showed all adult flies reared from the burial site, as well as the larvae collected from the skull were identified as Eristalinus arvorum (Fabricius, 1787) (Diptera: Syrphidae). Here, we report the colonization of E. arvorum larvae on a human corpse for the first time.

Matched MeSH terms: Electron Transport Complex IV/genetics
Fulltext Anopheles sundaicus complex and the presence of Anopheles epiroticus in Indonesia

Syafruddin D, Lestari YE, Permana DH, Asih PBS, St Laurent B, Zubaidah S, et al.

PLoS Negl Trop Dis, 2020 Jul;14(7):e0008385.
PMID: 32614914 DOI: 10.1371/journal.pntd.0008385

Anopheles sundaicus s.l. is an important malaria vector primarily found in coastal landscapes of western and central Indonesia. The species complex has a wide geographical distribution in South and Southeast Asia and exhibits ecological and behavioural variability over its range. Studies on understanding the distribution of different members in the complex and their bionomics related to malaria transmission might be important guiding more effective vector intervention strategies. Female An. sundaicus s.l. were collected from seven provinces, 12 locations in Indonesia representing Sumatra: North Sumatra, Bangka-Belitung, South Lampung, and Bengkulu; in Java: West Java; and the Lesser Sunda Islands: West Nusa Tenggara and East Nusa Tenggara provinces. Sequencing of ribosomal DNA ITS2 gene fragments and two mitochondrial DNA gene markers, COI and cytb, enabled molecular identification of morphologically indistinguishable members of the complex. Findings allowed inference on the distribution of the An. sundaicus s.l. present in Indonesia and further illustrate the phylogenetic relationships of An. epiroticus within the complex. A total of 370 An. sundaicus s.l specimens were analysed for the ITS2 fragment. The ITS2 sequence alignment revealed two consistent species-specific point mutations, a T>C transition at base 479 and a G>T transversion at base 538 that differentiated five haplotypes: TG, CG, TT, CT, and TY. The TG haplotype matched published An. epiroticus-indicative sequences from Thailand, Vietnam and peninsular Malaysia. The previously described insertion event (base 603) was observed in all identified specimens. Analysis of the COI and cytb genes revealed no consistent nucleotide variations that could definitively distinguish An. epiroticus from other members in the Sundaicus Complex. The findings indicate and support the existence of An. epiroticus in North Sumatra and Bangka-Belitung archipelago. Further studies are recommended to determine the full distributional extent of the Sundaicus complex in Indonesia and investigate the role of these species in malaria transmission.

Matched MeSH terms: Electron Transport Complex IV/genetics
DNA Barcoding of Simulium asakoae (Diptera: Simuliidae) From Northern Thailand

Low VL, Srisuka W, Saeung A, Tan TK, Ya'cob Z, Yeong YS, et al.

J Med Entomol, 2020 09 07;57(5):1675-1678.
PMID: 32333022 DOI: 10.1093/jme/tjaa081

Previous studies suggested the presence of species complex in the so-called Simulium asakoae Takaoka & Davies (Diptera: Simuliidae) in Thailand due to its high morphological variability and genetic divergence. To investigate whether the true S. asakoae is present in Thailand, we performed a detailed morphological identification of S. asakoae and compared its DNA barcodes with the morphospecies S. asakoae from Myanmar and the typical S. asakoae from Malaysia. Phylogenetic analysis revealed the Thai materials analyzed in this study were indeed genetically similar with those from Myanmar and Malaysia, though genetic distances 0-2.27% were observed. We tentatively regard this divergence as intraspecific variation, and the automatic barcode gap discovery analysis further supports them as a single species.

Matched MeSH terms: Electron Transport Complex IV/genetics
Fulltext New vectors in northern Sarawak, Malaysian Borneo, for the zoonotic malaria parasite, Plasmodium knowlesi

Ang JXD, Kadir KA, Mohamad DSA, Matusop A, Divis PCS, Yaman K, et al.

Parasit Vectors, 2020 Sep 15;13(1):472.
PMID: 32933567 DOI: 10.1186/s13071-020-04345-2

BACKGROUND: Plasmodium knowlesi is a significant cause of human malaria in Sarawak, Malaysian Borneo. Only one study has been previously undertaken in Sarawak to identify vectors of P. knowlesi, where Anopheles latens was incriminated as the vector in Kapit, central Sarawak. A study was therefore undertaken to identify malaria vectors in a different location in Sarawak.
METHODS: Mosquitoes found landing on humans and resting on leaves over a 5-day period at two sites in the Lawas District of northern Sarawak were collected and identified. DNA samples extracted from salivary glands of Anopheles mosquitoes were subjected to nested PCR malaria-detection assays. The small subunit ribosomal RNA (SSU rRNA) gene of Plasmodium was sequenced, and the internal transcribed spacer 2 (ITS2) and mitochondrial cytochrome c oxidase subunit 1 (cox1) gene of the mosquitoes were sequenced from the Plasmodium-positive samples for phylogenetic analysis.
RESULTS: Totals of 65 anophelines and 127 culicines were collected. By PCR, 6 An. balabacensis and 5 An. donaldi were found to have single P. knowlesi infections while 3 other An. balabacensis had either single, double or triple infections with P. inui, P. fieldi, P. cynomolgi and P. knowlesi. Phylogenetic analysis of the Plasmodium SSU rRNA gene confirmed 3 An. donaldi and 3 An. balabacensis with single P. knowlesi infections, while 3 other An. balabacensis had two or more Plasmodium species of P. inui, P. knowlesi, P. cynomolgi and some species of Plasmodium that could not be conclusively identified. Phylogenies inferred from the ITS2 and/or cox1 sequences of An. balabacensis and An. donaldi indicate that they are genetically indistinguishable from An. balabacensis and An. donaldi, respectively, found in Sabah, Malaysian Borneo.
CONCLUSIONS: Previously An. latens was identified as the vector for P. knowlesi in Kapit, central Sarawak, Malaysian Borneo, and now An. balabacensis and An. donaldi have been incriminated as vectors for zoonotic malaria in Lawas, northern Sarawak.

Matched MeSH terms: Electron Transport Complex IV/genetics
Fulltext Genetic diversity, population structure and historical demography of the two-spined yellowtail stargazer (Uranoscopus cognatus)

Mohd Yusoff NIS, Mat Jaafar TNA, Vilasri V, Mohd Nor SA, Seah YG, Habib A, et al.

Sci Rep, 2021 Jun 25;11(1):13357.
PMID: 34172804 DOI: 10.1038/s41598-021-92905-6

Benthic species, though ecologically important, are vulnerable to genetic loss and population size reduction due to impacts from fishing trawls. An assessment of genetic diversity and population structure is therefore needed to assist in a resource management program. To address this issue, the two-spined yellowtail stargazer (Uranoscopus cognatus) was collected within selected locations in the Indo-West Pacific (IWP). The partial mitochondrial DNA cytochrome c oxidase subunit 1 and the nuclear DNA recombination activating gene 1 were sequenced. Genetic diversity analyses revealed that the populations were moderately to highly diversified (haplotype diversity, H = 0.490-0.900, nucleotide diversity, π = 0.0010-0.0034) except sampling station (ST) 1 and 14. The low diversity level, however was apparent only in the matrilineal marker (H = 0.118-0.216; π = 0.0004-0.0008), possibly due to stochastic factors or anthropogenic stressors. Population structure analyses revealed a retention of ancestral polymorphism that was likely due to incomplete lineage sorting in U. cognatus, and prolonged vicariance by the Indo-Pacific Barrier has partitioned them into separate stock units. Population segregation was also shown by the phenotypic divergence in allopatric populations, regarding the premaxillary protrusion, which is possibly associated with the mechanism for upper jaw movement in biomechanical feeding approaches. The moderate genetic diversity estimated for each region, in addition to past population expansion events, indicated that U. cognatus within the IWP was still healthy and abundant (except in ST1 and 14), and two stock units were identified to be subjected to a specific resource management program.

Matched MeSH terms: Electron Transport Complex IV/genetics

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