UNCOVERING GENETIC PATTERNS OF THE BARRED MUDSKIPPER ALONG THE WEST COAST OF BENGKULU USING THE COI GENE

Silver carp’s (Hypophthalmichthys molitrix) traits and genetic structure are being impacted by artificial proliferation and restocking enhancement. A clear genetic background of cultured silver carp is helpful for exploitation and utilization. Limited research reported the germplasm resources of cultured silver carp. This study was conducted to investigate the genetic diversity of cultured silver carp. Two hundred thirty‐three silver carps were sampled from eight cultured populations in Hubei province, and their population structures were analyzed by mitochondrial COI gene. Average contents of bases T, C, A, and G in the 659 bp COI gene sequence were 30.03%, 26.62%, 26.08% and 17.32%, respectively. And 18 haplotypes were defined from 77 variable nucleotides in COI gene. The haplotypes and nucleotide diversities were 0.604 and 0.00325, respectively. Meanwhile, the highest genetic diversity and lowest genetic diversity were detected in cultured populations from Jianli population (Hd: 0.883 and π: 0.00699) and Yaowan population (Hd: 0.186 and π: 0.00085), respectively. Pairwise fixation index (Fst) analysis revealed that the level of genetic diversity was moderate (Fst: 0.06). The genetic distance between and within populations were 0.00353 and 0.00329, respectively. And the genetic variation occurred mainly within populations (93.42%), but genetic variation between the population was only 6.58%. Therefore, moderate‐level genetic diversity was observed with high haplotype diversity and low nucleotide diversity, suggesting that inbreeding should be avoided among the eight cultured populations in Hubei.

Intense and prolonged marine heatwaves (MHWs) have been observed in the Indonesian seas over the past 40 years (1982–2021). The frequency and duration of MHWs have increased, while their maximum intensity has declined, reflecting the impacts of global warming. This study analyzed intense MHWs in six key regions: Western Sumatra, Southern Java, Java Sea, Makassar Strait, Maluku Sea, and Northern Papua. A heat budget analysis revealed that heat advection is the primary driver of sea surface temperature warming and MHW events in Southern Java and Western Sumatra, whereas entrainment played a more significant role in other regions. Cross-correlation and scatter plot analyses further indicated that the El Niño-Southern Oscillation (ENSO) and the Indian Ocean Dipole (IOD) also played a crucial role in MHW formation. Notably, MHW occurrences were more frequent during ENSO phases than IOD phases, suggesting ENSO’s stronger influence. Among all study regions, Southern Java exhibited the highest correlation between MHW intensity and both the Oceanic Niño Index and the Dipole Mode Index, underscoring the significant influence of ENSO and IOD in this area. From June to August 1998 to 2021, upwelling intensity in Southern Java weakened due to acute MHW events, with the strongest suppression occurring in the eastern part of the region compared to its central and western areas. These extreme and persistent oceans warming events pose a growing threat to marine ecosystems and fisheries, underscoring the urgent need for further research and mitigation strategies.

The hound needlefish Tylosurus crocodilus (Belonidae) is a highly demanded fish in the local markets of Tanzania, but the growing coastal population threatens its sustainability. As belonids are highly migratory fishes utilising various parts of the seascape, increased fishing pressure may disrupt connectivity patterns on different spatiotemporal scales and disaggregate populations. Using the COI gene, this study assessed the genetic population structure, connectivity patterns, and historical demography of T. crocodilus collected in seven sites spread along Tanzanian coastal waters. Results showed fourteen haplotypes with low overall nucleotide and haplotype diversity. Pairwise FST comparisons revealed no significant differences among the sampled sites, except for the northernmost site (Tanga) and an island in the south (Songosongo). Analysis of molecular variance (AMOVA) revealed a non-significant genetic structure among populations (FST = 0.01782), suggesting the fishery across Tanzanian waters exploits the same population. Moreover, there was no correlative relationship between genetic and pairwise geographic distances, rejecting the isolation by distance hypothesis. However, neutrality tests and mismatch distribution analysis revealed that recent demographic expansion might exist. Empirical evidence of panmixia suggests high genetic connectivity. In combination with low genetic diversity, management should be directed to actions that prevent genetic diversity loss and the effect of genetic drift on populations.

The IUCN Bangladesh has documented a total of 31 species belonging to the Pieridae family in Bangladesh. There is currently limited knowledge regarding the genetic diversity and molecular relationships among these butterflies. The present investigation involved the generation of mitochondrial COI (mtCOI) gene sequences for ten species of butterflies belonging to the Pierid family. After that, BLAST analysis showed 96% to 100% similarity, and then the sequences were submitted to NCBI’s GenBank. MEGA10 and BioEdit were used to identify a 584 bp COI gene fragment with 179 variable sites and 128 parsimony-informative sites. The COI sequences' average base compositions were 38.56% T, 17.12% C, 30.18% A, and 14.12% G. While a significant AT bias (68.74%) existed among the Pierid species. The genetic distance between ten Pierid species was assessed using the Kimura 2-Parameter (K2P) algorithm, and the nucleotide differences ranged from 0.00172% to 0.24261%. Afterwards, the Maximum Likelihood (ML) method was used to construct a phylogenetic tree using ten sequences of Pierid species. These species belongs to two subfamilies, Pierinae and Coliadinae in Bangladesh. On the tree, the Pierinae subfamily of Pieridae formed a paraphyletic arrangement whereas the Coliadinae subfamily was shown to be monophyletic. The data analyses support the following relationships between the two subfamilies as follows: [(Appias + Leptosia) + (Pieris + Appias) + (Delias) + (Eurema + Catopsilia) + (Pareronia)]. This supported the theory that Pierinae and Coliadinae are sister taxa. Nonetheless, Pareronia hippia remains outside the main Pierinae group, requiring further study to resolve this issue. Finally, these studies generated ten mtCOI gene sequences that have the potential to serve as valuable references for the accurate identification of Pierid species. In addition, this result could be used in the future to reveal the subfamily relationships within the Pieridae taxonomic classification. Bangladesh J. Zool. 51(3): 289-299, 2023

BackgroundA total of six Neocalanus species inhabit the oceans of the world. Of these, three species plus form variants (N. cristatus, N. plumchrus, N. flemingeri large form, and N. flemingeri small form), which constitute a monophyletic group among Neocalanus copepods, occur in the Northwestern Pacific off Japan. In the present study, we have tried to discriminate the three species plus form variants of Neocalanus copepods based on sequences of four DNA marker regions.Methodology/Principal FindingsDiscrimination was performed based on the DNA sequence information from four genetic markers, including the mitochondrial COI, 12S, nuclear ITS, and 28S gene regions. Sequence dissimilarity was compared using both distance- and character-based approaches. As a result, all three species were confirmed to be distinct based on the four genetic marker regions. On the contrary, distinction of the form variants was only confirmed based on DNA sequence of the mitochondrial COI gene region.Conclusions/SignificanceAlthough discrimination was not successful for the form variants based on the mitochondrial 12S, nuclear ITS, and 28S genes, diagnostic nucleotide sequence characters were observed in their mitochondrial COI gene sequences. Therefore, these form variants are considered to be an important unit of evolution below the species level, and constitute a part of the Neocalanus biodiversity.

Marine protected areas (MPAs) are globally recognised for their role in safeguarding marine fisheries from the detrimental impacts of human activities and climate change. Tanzania, in alignment with global conservation efforts, has designated 18 MPAs and plans to establish four more in the Southwestern Indian Ocean. However, a critical challenge arises from the lack of a thorough understanding of genetic connectivity between populations in MPAs and non‐protected areas (NPAs). To address this, 151 mitochondrial D‐loop sequences (357 base pairs) of Barred mudskipper (Periophthalmus argentilineatus) were analysed to assess genetic connectivity between MPAs and NPAs in Tanzania. The findings revealed a low and insignificant index of genetic differentiation (FST = −0.0046, p > 0.05) between populations in MPAs and NPAs. Furthermore, haplotypes from both MPAs and NPAs did not cluster based on their geographical origins, with over 9 haplotypes shared between these areas. Additionally, the measured haplotype and nucleotide diversities did not differ significantly between MPAs and NPAs (p > 0.05). However, MPAs showed a significantly higher number of private haplotypes compared to NPAs (p < 0.05). These findings suggest high genetic interconnectedness between populations in MPAs and NPAs, underlining the importance of existing MPAs in preserving local genetic diversity and their potential to replenish depleted NPAs. However, realising the full potential of this interconnectedness necessitates stringent enforcement of sustainable fishing practices to alleviate pressure on fish stocks. It also requires the protection of critical habitats that serve as corridors for fish dispersal, facilitating interconnectedness between MPAs and NPAs.

Significant genetic differentiation between the Yellow Sea and East China Sea populations of cocktail shrimp Trachypenaeus curvirostris revealed by the mitochondrial DNA COI gene

The hard clam (Meretrix petechialis) is a commercially important shellfish in China. To provide valuable insights into management and conservation of M. petechialis, we investigated the genetic variation and population structure of M. petechialis by analysing samples from nine geographical populations. In this study, the genetic diversity and differentiation of nine populations of M. petechialis were assessed using the mitochondrial cytochrome oxidase subunit I (mtCOI) gene. A total of 90 COI sequences were obtained and each COI sequence was 699 bp in length. Fifty-one haplotypes were identified with 10 haplotypes shared among populations. The haplotype diversity was highest in Fujian, Panjin and Jiangsu (0.9778 ± 0.0540) and lowest in Dalian (0.7778 ± 0.1374). The nucleotide diversity was highest in Panjin (0.453401 ± 0.240463) and lowest in Jiangsu (0.006213 ± 0.004141). Neutral test (Fu's Fs) and mismatch distribution analysis revealed that the hard clam experienced a population expansion event. Analysis of molecular variance (AMOVA) indicated that 91.7% of the genetic variance was within populations and 0.52% of the variance was among populations, demonstrating significant genetic differentiation among populations (P < 0.05). The neighbour-joining tree showed that the haplotypes were not clustered according to the geographical location, but some haplotypes from the same or neighbouring locations grouped together. The results obtained in this study provide useful information on the genetic diversity and population structure of M. petechialis and shed light on the management and protection of resources of M. petechialis in the northwestern Pacific.

The Guizhou odorous frog Odorrana kweichowensis is endemic to Guizhou Province, China. In this study, a comparative analysis of the mitochondrial COI and ND2 gene sequences was performed to examine genetic diversity in 109 individuals from ten localities across the geographic range of the species. Haplotype diversity and nucleotide diversity were 0.576 and 0.00055, respectively. Phylogenetic analyses almost nested all haplotypes into one lineage. AMOVA indicated that total variation was mainly derived from variation within individual populations. Neutral tests indicated that a recent expansion occurred in the total population. Fst estimations indicated that genetic divergence was not correlated with geographic distance. Accordingly, the species probably experienced a recent population expansion, and there no obvious population genetic structure is apparent. The findings provide useful information for the conservation of this species.

BackgroundThe Anopheles hyrcanus group is distributed throughout the Oriental and Palaearctic regions and can transmit diseases such as malaria, Japanese encephalitis virus, and filariasis. This investigation marks the inaugural comprehensive study to undertake a phylogenetic analysis of the constituents of this malaria vector group in the northeastern region of Iran, juxtaposed with documented occurrences from different areas within Iran and worldwide.MethodsMosquitoes were collected using various methods from nine different locations in Golestan province from April to December 2023. The collected mosquitoes were identified morphologically using valid taxonomic keys. DNA was isolated using the Sambio™ Kit. COI and ITS2 primers were designed using Oligo7 and GeneRunner. PCR and purification were performed with the Qiagen kit. Subsequently, sequencing was carried out at the Mehr Mam GENE Center using an Applied Biosystems 3730XL sequencer. The nucleotide sequences were then analyzed and aligned with GenBank data using BioEdit. Kimura 2-parameter was Utilized for base substitutions. DNA models were selected based on AIC and BIC criteria. Bayesian and Maximum Likelihood trees were constructed, along with a haplotype network. Molecular diversity statistics computed using DnaSP software.ResultsIn this study, a total of 819 adult mosquitoes were collected. An. hyrcanus was the second most abundant species, predominantly found in Kalaleh and Turkman counties. The sequenced and edited COI and ITS2 sequences were deposited in GenBank under specific accession numbers. Phylogenetic analyses using ML, BI, and NJ methods confirmed a monophyletic lineage for An. hyrcanus with strong support. Molecular analysis of Iranian An. hyrcanus found 11 diverse haplotypes, with the COI gene displaying low diversity. The ITS2 gene revealed two clades - one associating with Iran, Europe, and Asia; the other originating from southwestern Iran. The haplotype network showed two main groups - one from southwest Iran and the other from north Iran. Iran exhibited six distinct haplotypes, while Turkey showcased the highest diversity.ConclusionsAn. hyrcanus in southwestern Iran exhibits a distinct haplogroup, suggesting possible subspecies differentiation. Additional studies are required to validate this phenomenon.

Androctonus crassicauda is the most medically relevant scorpion and understanding its genetic forms is essential for improvement of anti-venom sera, and risk management of scorpionism. Present study was designed to identify the variations of mitochondrial genes in different populations of A. crassicauda. Adults of A. crassicauda were collected from Zanjan Province during 2016-2017. Genomic DNA of samples was extracted and fragments of mitochondrial 16S, COI and ND1 genes were amplified and some of the amplicons were sequenced. Haplotype of samples were identified by multiple alignment of sequences, then phylogenetic trees of haplotypes were constructed. Fragments of 352bp, 618bp and 680bp were amplified from 16S, COI and ND1 genes respectively. Nucleotide sequence in COI fragments was conserved, however, five haplotypes with some specific polymorphic sites were detected in 16S and ND1 fragments. Haplotype I was dominant and found in all areas. Other haplotypes were rare and limited to specific regions. Analysis of the phylogenetic trees inferred from 16S and COI genes, confirmed a strong positive correlation between geographic and genetic distance. Mitochondrial COI, 16S and ND1 genes were detected suitable for identifying the population structure. Five genotypes were found using 16S and ND1 genes. To prepare and improve the anti-venoms quality, additional studies are necessary to identify the toxin electrophoretic profile and geographical/ecological niche models of these genotypes in future.

Fat greenling (Hexagrammos otakii) is an important commercial fish in the Northwestern Pacific, being distributed along the coastal waters of the East/Japan Sea and the Yellow Sea. To investigate population genetic structure and demographic history of this species, one hundred and fifty five individuals were collected from five localities in the distribution range of the species and sequence variations in the mitochondrial genes COI, COIII-ND3-ND4L, and cytochrome b were examined. For all the genes in every sampling location, the nucleotide diversities were very low (0.001 ∼ 0.005) although the haplotype diversities were relatively high, 0.55 ∼ 0.81 for COI, 0.79 ∼ 0.84 for COIII-ND3-ND4L, and 0.95 ∼ 0.97 for cytochrome b. Hierarchical analysis of molecular variance (AMOVA), the conventional population statistic FST, and exact test of population differentiation revealed no significant genetic structuring among the samples, indicating that fat greening is panmictic throughout the range of its distribution. Neutrality tests such as Tajima’s D and Fu’s FS statistics and mismatch distribution analyses suggested that fat greening has undergone the demographic history of population expansion during the late Pleistocene period approximately 91,000 ∼ 327,000 years ago. The star-burst patterns of haplotype networks and low nucleotide diversities also indicated recent population expansion. These results help establish the fisheries management strategy for fat greenling in the Northwestern Pacific.

Genetic population structure in Nacella magellanica: Evidence of rapid range expansion throughout the entire species distribution on the Atlantic coast

Interpretation of occurrence records outside the known range of the species for many freshwater copepods remains difficult due to unresolved taxonomy and/or sparse occurrence data. We report for the first time the occurrence in South America of two cyclopid species with very different evolutionary histories. Mesocyclops granulatus Dussart and Fernando, 1988, a (sub)tropical Asian species with close relatives in the Old World tropics, was found in an artificial lake in the Pacific coastal plain of Ecuador. Acanthocyclops trajani Mirabdullayev and Defaye, 2002, a northern temperate species with Holarctic relatives, was encountered in a high mountain lake in the Andes, Titicaca. Morphology (female and male) is described for both species in detail, nomenclature issues are discussed, and morphological comparisons to the South American congeners and/or close relatives are provided. Morphology-based identification of A. trajani is confirmed by three molecular markers, the nuclear 18S ribosomal DNA and the mitochondrial 12S rRNA and COI genes. While the non-native status of M. granulatus in Ecuador is supported by the biogeographical, phylogenetic and ecological evidence, the origin of the Titicaca populations of A. trajani remains poorly understood. The global distribution of A. trajani and its putative close relatives, as well as the numerous historical occurrence records of some congeners that may be confused with A. trajani in South America, seem to indicate a relict native distribution of the species in the Andes. On the other hand, a phylogenetic tree based on the mitochondrial COI gene in A. trajani populations from Lake Titicaca, North America and Europe does not confirm either the native or non-native status of A. trajani in South America, which may be due to limited information available on the spatial distribution of the haplotype diversity.

Barred mudskipper (Periophthalmus argentilineatus) has a potency to be developed as protein for human consumption and ornamental fish. The fish also has an important role in mangrove ecosystems. Nevertheless, many barred mudskippers have been considered a cryptic species. Therefore, accurate identification is needed to clarify species identification of the barred mudskipper using DNA barcoding. This research aimed to identify barred mudskippers from Tekolok Estuary (East Lombok, West Nusa Tenggara, Indonesia) using COI mitochondrial gene as a DNA barcode and analyze genetic relationship with other barred mudskippers from several regions of Indonesia recorded in GenBank. This study used a PCR method with universal primers FishF2 and FishR2. The data was then analysed using DNASTAR, BLAST, Mesquite, MEGA, DnaSP, BEAST, GenAlEx, and NETWORK. The results revealed that barred mudskipper from Tekolok Estuary has been verified as Periophthalmus argentilineatus. The results also exhibited that P. argentilineatus from Tekolok Estuary has a close genetic relationship to P.argentilineatus from Tukad Bilukpoh (Jembrana, Bali). In addition, phylogenetic analysis showed that P.argentilineatus from Indonesia consisted of two clades with a genetic distance of approximately 6.64%. This analysis revealed evidence of the cryptic diversity of P.argentilineatus from Indonesia. Further detailed studies are needed to clarify whether Indonesian P.argentilineatus should be categorized into more than one species or single species with several subspecies.