Molecular study is important to detect variations and similarities among species from the same genus, in case if they do not encompass any morphological or physiological differences. The study was conducted to differentiate among species of Meretrix spp. (Meretrix lyrata, M. meretrix, and M. lusoria) obtained from two locations in Malaysia through the phylogenetic tree. The adductor muscle tissues were used to extract DNA and to perform other procedures; the samples were subjected to analyses using PCR and gel electrophoresis. The multiple sequence comparison was conducted by MUSCLE and the phylogenetic relationships were established using Maximum Likelihood (ML) statistical methods with MEGA 6.0 statistical software. M. lyrata samples showed 99% similarity to the three accessions sequence, where M. lyrata indicated 87% similarities, and M. meretrix showed not more than 89% similarities from the deposited sequence. The nucleotide base composition sequences consisted of the mean of Thiamine (T) 37.9%, Cytosine (C) 15.4%, Adenine (A) 27.4%, and Guanine (G) 19.4%. Maximum Likelihood (ML) analysis was conducted using the Tamura 3-parameter model to establish five major clades on Meretrix spp. and two out-groups clades significantly different from the Meretrix spp. These major clades were closely related to each other at the 50% evidence of bootstrap, which grouped as genus Meretrix. The present study on Meretrix spp. from the Sarawak locality was able to differentiate COI sequences between M. lyrata, M. meretrix, and M. lusoria. M. lusoria was close related to M. meretrix with strong bootstrap supporting evidence at 96% scoring. Moreover, M. lyrata was inferred as the ancestor to M. meretrix, and M. lusoria from Sarawak, Malaysia.
Genetic profile of local buffalo (Bubalus bubalis) populations in Pacitan and...AbdulBasith222525
DOI: 10.26740/jrba. v5n1.p.37-42
ABSTRACT. The genetic profile of buffaloes is important information to support their breeding efforts, therefore the assessment of genetic profile needs to be carried out continuously. This study aimed to analyze the application of microsatellite marker at the INRA032 locus for genetic profile assessment in buffalo (Bubalus bubalis) populations in Pacitan and Tuban Regencies, East Java, Indonesia. The total number of samples used was 16, with each population represented by 8 samples. Genetic profile assessment parameters include allele frequency, the Polymorphism Information Content (PIC), and heterozygosity. The results showed that based on the INRA032 locus, the Tuban buffalo population had a higher allele frequency range (0.08 to 0.33) than the Pacitan population (0.18 to 0.31). The average PIC value in both populations was 0.39, so it can be concluded that the INRA032 locus is informative enough to detect polymorphisms in both populations. The percentage heterozygosity of the Pacitan buffalo population is 88%, which is higher than the Tuban population at 50%, suggesting that the genetic diversity of the two populations is still quite high despite the decreasing trend in population numbers. The INRA032 locus was shown to be moderately effective for assessing genetic profile in local buffaloes, but its application in future studies will require an increase in the number of samples representing the population and the addition of other microsatellite markers to obtain a more accurate conclusion.
Genetic profile of local buffalo (Bubalus bubalis) populations in Pacitan and...AbdulBasith222525
DOI: 10.26740/jrba. v5n1.p.37-42
ABSTRACT. The genetic profile of buffaloes is important information to support their breeding efforts, therefore the assessment of genetic profile needs to be carried out continuously. This study aimed to analyze the application of microsatellite marker at the INRA032 locus for genetic profile assessment in buffalo (Bubalus bubalis) populations in Pacitan and Tuban Regencies, East Java, Indonesia. The total number of samples used was 16, with each population represented by 8 samples. Genetic profile assessment parameters include allele frequency, the Polymorphism Information Content (PIC), and heterozygosity. The results showed that based on the INRA032 locus, the Tuban buffalo population had a higher allele frequency range (0.08 to 0.33) than the Pacitan population (0.18 to 0.31). The average PIC value in both populations was 0.39, so it can be concluded that the INRA032 locus is informative enough to detect polymorphisms in both populations. The percentage heterozygosity of the Pacitan buffalo population is 88%, which is higher than the Tuban population at 50%, suggesting that the genetic diversity of the two populations is still quite high despite the decreasing trend in population numbers. The INRA032 locus was shown to be moderately effective for assessing genetic profile in local buffaloes, but its application in future studies will require an increase in the number of samples representing the population and the addition of other microsatellite markers to obtain a more accurate conclusion.
Characterization of Arsenic contaminated Rice (Oryza Sativa L.) through RAPD ...IOSR Journals
Rice being cultivated under anaerobic condition is vulnerable to arsenite, a mobile arsenic speciation Both arsenate and arsenite are highly toxic to human body. Experiments were conducted in Nonaghata (Nadia) and De-ganga (North 24 parganas) with 40 genotypes of rice in Boro season. A few varieties have been identified with low arsenic. Simultaneously some of them were characterized at molecular level by RAPD technique. It is worth to be seen how the low grain and high grain arsenic varieties behave in RAPD fingerprinting. Fourteen out of the 18 decamer random primers showed amplification of genomic DNA in all individuals. A total of 59 fragments were scored, of these fragments, 10 (16.94%) were common to all accessions, 49 (83.06%) were polymorphic and shared by at least eight accessions. It is interesting to mention that the genotypes Azucena and Lemont have already been identified as low grain arsenic genotypes and occupied a distinct different cluster for all primers at the molecular level also. More research is needed in arsenic research in crop plants in different agro climatic situation to have a meaningful and stable conclusion so that the farmers and also the people of West Bengal do not suffer from arsenic hazards at least from the consumption of rice.
Genetic diversity in pea germplasm using RAPD MarkersShujaul Mulk Khan
Selection of the genotypes using plasmid assisted technology provides an efficient and useful tool for elaborating genetic relationships among genotypes. In present study, 48 Pea (Pisum sativum var sativum L.) genotypes obtained from different sources were analyzed through 20 RAPD, DNA markers for assessment of intraspecific DNA variations. Results revealed that significant variations were present in minor bands. Major bands also showed significant diversity. Considerable variations were also recorded in density of some common bands. Maximum and minimum genetic diversity i.e., 80% and 20% was found among 08 and 23 comparisons, respectively from banding profile. These variations can be
used further for enhancing variability, a prerequisite for crop breeding. Phylogenetic clustering (through dendrogram analysis) of genotypes revealed that genetic diversity is independent of origin of genotypes. Forty eight genotypes of pea clustered in three main groups A, B and C comprising 23, 5 and 20 genotypes, respectively. Group A1 and C1 included the most distantly related genotypes and hence can be recommended for breeding to obtain genetically diverse segregating populations.
APPLICATION OF DNA ANALYSIS APPROACH CONTRIBUTES TO THE IDENTIFICATION OF SEV...nguyenxuanhung16
DNA barcoding has been widely used to assess species diversity in a variety of ecosystems, including
temperate, subtropical, and tropical rain forests. However, due to the difficulties associated with field
exploration, most of the species in Truong Sa archipelago have never been barcoded. The purpose of this study
is to barcode five species of plants from the Truong Sa archipelago and to provide valuable evolutionary
information that will aid in future understanding of the plant community assembly on those particular islands.
Using DNA markers (ITS-rDNA), this study created a DNA barcode database for five plant species found on
the Truong Sa archipelago. We used the sequence similarity and a phylogenetic based method to the identify 15
samples from five plant species collected in Truong Sa archipelago, Vietnam. Results showed that the PCR
success rate for ITS-rDNA region was 100%. The success rate of bidirectional sequencing of PCR product was
100% for 650 bp long the ITS-rDNA region fragment. Phylogenetic analyses using maximum likelihood (ML)
indicated that five plant species (PB, BT, BV, NH and TR) had a close relationship with T. argentea, S.
taccada, B. asiatica, M. citrifolia, M. citrifolia and C. uvifera, respectively. The current study provided further
evidence for ITS-rDNA region as a useful molecular marker for species identification found on other tropical
coral islands
Inter Simple Sequence Repeats (ISSR) markers were utilized to identify the levels of heritable varieties and patterns of the populace structure among the five populaces of Pteris biaurita, a natural fern in India. A comprehensive examination was directed in three replicates at 2013-14 seasons in the Western Ghats, South India. Five wild P. biaurita, accessions (maiden hair) were assessed for genotyping studies. Results demonstrated a pivotal discrepancy among genotypes for they were characterized in view of this uniqueness in four groups by the genetic cluster examination. In this trial, ISSR primers amplified 63 polymorphic groups. In view of the genetic identity data, genotypes were figured and differed from 0.5714 to 0.6984. The percentage of polymorphism indicated predominant genotype that may be utilized for the conservation of species. ISSR appeared to be an obliging marker for prediction of genotype inside a closed group of inter specific populace in the investigation territory.
Inter Simple Sequence Repeats (ISSR) markers were utilized to identify the levels of heritable varieties and patterns of the populace structure among the five populaces of Pteris biaurita, a natural fern in India. A comprehensive examination was directed in three replicates at 2013-14 seasons in the Western Ghats, South India. Five wild P. biaurita, accessions (maiden hair) were assessed for genotyping studies. Results demonstrated a pivotal discrepancy among genotypes for they were characterized in view of this uniqueness in four groups by the genetic cluster examination. In this trial, ISSR primers amplified 63 polymorphic groups. In view of the genetic identity data, genotypes were figured and differed from 0.5714 to 0.6984. The percentage of polymorphism indicated predominant genotype that may be utilized for the conservation of species. ISSR appeared to be an obliging marker for prediction of genotype inside a closed group of inter specific populace in the investigation territory
Genetic variability and phylogenetic relationships studies of Aegilops L. usi...Innspub Net
Studying of genetic relationships among Aegilops L. species is very important for broadening the cultivated wheat genepool, and monitoring genetic erosion, because the genus Aegilops includes the wild relatives of cultivated wheat which contain numerous unique alleles that are absent in modern wheat cultivars and it can contribute to broaden the genetic base of wheat and improve yield, quality and resistance to biotic and abiotic stresses of wheat. The use of molecular markers, revealing polymorphism at the DNA level, has been playing an increasing part in plant biotechnology and their genetics studies. There are different types of markers, morphological, biochemical and DNA based molecular markers. These DNA-based markers based on PCR (RAPD, AFLP, SSR, ISSR, IRAP), amongst others, the microsatellite DNA marker has been the most widely used, due to its easy use by simple PCR, followed by a denaturing gel electrophoresis for allele size determination, and to the high degree of information provided by its large number of alleles per locus. Day by day development of such new and specific types of markers makes their importance in understanding the genomic variability and the diversity between the same as well as different species of the plants. In this review, we will discuss about genetic variability and phylogenetic relationships studies of Aegilops L. using some molecular markers, with theirs Advantages, and disadvantages.
Detection of Genetic variation in tissue culture clones of date palm using IS...IJSRD
Date palm is a plant having high nutritional value and long life (yielding up to 100 years). Phoenix dactylifera requires 2-5 males for pollination of 100 females’ plant depending up on genetic and environment factors. Therefore paternity variation expected to very low according to PCR based techniques, Even though we have tried to find out genetic variation among tissue culture cloned plant. Tissue culture technique can be used for genetic improvement of date palm. The main purpose of this study was to evaluate the genetic variation in the tissue culture clones of date palm by using ISSR primers among mother and it’s two clones. The plant DNA was extracted and subjected to detection of genetic variation in two groups of date palm using ISSR primers. In this study ISSR primers produced monomorphic bands within group-1 and group-2. Genetic variation in tissue culture clones of date palm was not detecte by UBC primer series.
Among the large mammals of Africa, elephants are probably the worst affected by human activities. Although they have been listed as endangered and protected since 1989, illegal poaching and habitat destruction continue to diminish and isolate remaining populations that are dispersed widely over 37 sub-Saharan African countries. Their populations currently exist in small isolated habitat, and this threatens elephant genetic diversity. Although literature is available on the taxonomy and phylogeny of African elephant, few studies have focused on codon usage on mitochondrial genomes. To analyze nucleotide diversity, selective pressure and demographic history of African elephants, we used the portion of mitochondrial sequences of 102 individuals available in the genome database. Our data indicated a low codon bias index (CBI) and a relatively high effective number of codons (ENC) value in the mitochondrial genome, suggesting that African elephants are less biased in their codon usage preference. The data also support a strong purifying selection in the mitochondrial genome of African elephants. However, few sites are under positive selection in the mitochondrial genome of African elephants, with Loxodonta africana presenting more sites under positive selection compared to L. cyclotis. The present work supports the idea that different evolutionary rate among nucleotide sites in L. africana and L. cyclotis, attributable to differences in the frequency of positive selection and probably different environmental conditions, are the driving forces for the codon usage bias in African elephants. Further studies are needed to investigate the contribution of different subpopulation in the genetic structure and diversity of African elephants.
Flow Cytometric Analysis for Ploidy and DNA Content of Banana Variants Induce...paperpublications3
Abstract: Nuclear DNA content of mutated banana plants was determined by using flow cytometric techniques. It is a powerful tool for large scale screening of ploidy levels. Nuclei were isolated from young leaves from (banana mutants & Glycine plants) supplemented with Propidium- iodide (PI) and RNAse. "Glycine max" used as internal reference standard for identifying the nuclear DNA content by FCM. For ploidy estimation DAPI was used. The results showed differences in DNA content between variants indicating the effect of gamma-irradiation on the genotype of these plants. Variants of short plant stature or stunted growth showed great differences in DNA content compared to control (non-irradiated). The phenotypic variations observed at high doses were likely due to changes in the DNA sequences at the chromosomal level. Nuclear DNA contents decreased with an increase of gamma-dose from 20 Gy to 60 Gy. However, there were no significant differences between DNA content at 20 Gy and 30 Gy and also between 40 Gy and 60 Gy, while they were differed significantly from the control. The results showed no significant differences in ploidy level between all samples used (3n); while all selected mutants (variants) showed differences in DNA content.
Fish to finance: unraveling the economic threads of Bangladesh’s Blue EconomyAbdullaAlAsif1
Bangladesh, with its extensive river network, vast coastlines, and rich maritime heritage, stands at the crossroads of a transformative Blue Economy. This comprehensive review explores the rich tapestry of Bangladesh's maritime journey. Commencing with a historical lens, it traces the nation's roots in fisheries, showcasing its transformation into a diversified and dynamic Blue Economy. The significance of this transition unfolds across the review, underscoring the sector's contributions to GDP, employment, and food security, while candidly addressing challenges such as overfishing and environmental impact. This work not only chronicles historical milestones but distills valuable lessons from both successes and setbacks, offering a nuanced understanding of the economic resilience embedded in Bangladesh's fisheries sector. Beyond a historical retrospective, the review navigates through the contemporary landscape, emphasizing diversification beyond fisheries. It illuminates economic opportunities in maritime trade, explores non-fish marine resources, and delves into the transformative role of aquaculture. The policy framework governing Bangladesh's Blue Economy comes into focus, dissecting government strategies, legal landscapes, and international collaborations. The review also champions environmental sustainability, highlighting the impact of Blue Economy activities on marine ecosystems and advocating for conservation measures, thus positioning Bangladesh as a steward of its rich maritime heritage. Financial mechanisms and investments emerge as pivotal elements, shaping the trajectory of Blue Economy projects, as evidenced by case studies that weave success stories and lessons learned into the narrative. Concluding with a forward-looking perspective, the study identifies emerging trends, growth opportunities, and strategies to tackle challenges, offering a comprehensive roadmap for sustainable development. In weaving together economic vibrancy, environmental stewardship, and future aspirations, this review illuminates Bangladesh's maritime odyssey as a beacon for the global Blue Economy community.
Successful hybridization between Clarias microstomus♂ and Clarias gariepinus♀AbdullaAlAsif1
Hybridization is a significant approach to breeding that enables the creation of new varieties that enhance genetic diversity. Through fish inter-species hybridization, it is possible to produce hybrids that can be utilized in aquaculture and stocking programs to enhance growth rate, transfer desirable traits between species, and combine the favourable attributes of two parents into a single progeny. The present study revealed the successful hybridization between Clarias microstomus (Ng, 2001) ♂ and Clarias gariepinus (Burchell, 1822) ♀ for the first time in the aquaculture industry. C. microstomus is a species of Clariid catfish endemic to the island of Borneo and C. gariepinus is an introduced species widely aquacultured throughout the southeast Asian region. The embryonic development of the hybrid offspring is described with the hatching percentage of 58.63% and the early survival rate for the first 72 hours for the larvae of 85.76%. The hybrids showed no signs of deformities and developed normally. The findings of the study provide a new high yield variety of catfish for farmers and aquaculture industry for increasing production and profit margin.
More Related Content
Similar to The molecular approach reveals the relationship among Venus clams (Meretrix spp.) Community in Malaysia
Characterization of Arsenic contaminated Rice (Oryza Sativa L.) through RAPD ...IOSR Journals
Rice being cultivated under anaerobic condition is vulnerable to arsenite, a mobile arsenic speciation Both arsenate and arsenite are highly toxic to human body. Experiments were conducted in Nonaghata (Nadia) and De-ganga (North 24 parganas) with 40 genotypes of rice in Boro season. A few varieties have been identified with low arsenic. Simultaneously some of them were characterized at molecular level by RAPD technique. It is worth to be seen how the low grain and high grain arsenic varieties behave in RAPD fingerprinting. Fourteen out of the 18 decamer random primers showed amplification of genomic DNA in all individuals. A total of 59 fragments were scored, of these fragments, 10 (16.94%) were common to all accessions, 49 (83.06%) were polymorphic and shared by at least eight accessions. It is interesting to mention that the genotypes Azucena and Lemont have already been identified as low grain arsenic genotypes and occupied a distinct different cluster for all primers at the molecular level also. More research is needed in arsenic research in crop plants in different agro climatic situation to have a meaningful and stable conclusion so that the farmers and also the people of West Bengal do not suffer from arsenic hazards at least from the consumption of rice.
Genetic diversity in pea germplasm using RAPD MarkersShujaul Mulk Khan
Selection of the genotypes using plasmid assisted technology provides an efficient and useful tool for elaborating genetic relationships among genotypes. In present study, 48 Pea (Pisum sativum var sativum L.) genotypes obtained from different sources were analyzed through 20 RAPD, DNA markers for assessment of intraspecific DNA variations. Results revealed that significant variations were present in minor bands. Major bands also showed significant diversity. Considerable variations were also recorded in density of some common bands. Maximum and minimum genetic diversity i.e., 80% and 20% was found among 08 and 23 comparisons, respectively from banding profile. These variations can be
used further for enhancing variability, a prerequisite for crop breeding. Phylogenetic clustering (through dendrogram analysis) of genotypes revealed that genetic diversity is independent of origin of genotypes. Forty eight genotypes of pea clustered in three main groups A, B and C comprising 23, 5 and 20 genotypes, respectively. Group A1 and C1 included the most distantly related genotypes and hence can be recommended for breeding to obtain genetically diverse segregating populations.
APPLICATION OF DNA ANALYSIS APPROACH CONTRIBUTES TO THE IDENTIFICATION OF SEV...nguyenxuanhung16
DNA barcoding has been widely used to assess species diversity in a variety of ecosystems, including
temperate, subtropical, and tropical rain forests. However, due to the difficulties associated with field
exploration, most of the species in Truong Sa archipelago have never been barcoded. The purpose of this study
is to barcode five species of plants from the Truong Sa archipelago and to provide valuable evolutionary
information that will aid in future understanding of the plant community assembly on those particular islands.
Using DNA markers (ITS-rDNA), this study created a DNA barcode database for five plant species found on
the Truong Sa archipelago. We used the sequence similarity and a phylogenetic based method to the identify 15
samples from five plant species collected in Truong Sa archipelago, Vietnam. Results showed that the PCR
success rate for ITS-rDNA region was 100%. The success rate of bidirectional sequencing of PCR product was
100% for 650 bp long the ITS-rDNA region fragment. Phylogenetic analyses using maximum likelihood (ML)
indicated that five plant species (PB, BT, BV, NH and TR) had a close relationship with T. argentea, S.
taccada, B. asiatica, M. citrifolia, M. citrifolia and C. uvifera, respectively. The current study provided further
evidence for ITS-rDNA region as a useful molecular marker for species identification found on other tropical
coral islands
Inter Simple Sequence Repeats (ISSR) markers were utilized to identify the levels of heritable varieties and patterns of the populace structure among the five populaces of Pteris biaurita, a natural fern in India. A comprehensive examination was directed in three replicates at 2013-14 seasons in the Western Ghats, South India. Five wild P. biaurita, accessions (maiden hair) were assessed for genotyping studies. Results demonstrated a pivotal discrepancy among genotypes for they were characterized in view of this uniqueness in four groups by the genetic cluster examination. In this trial, ISSR primers amplified 63 polymorphic groups. In view of the genetic identity data, genotypes were figured and differed from 0.5714 to 0.6984. The percentage of polymorphism indicated predominant genotype that may be utilized for the conservation of species. ISSR appeared to be an obliging marker for prediction of genotype inside a closed group of inter specific populace in the investigation territory.
Inter Simple Sequence Repeats (ISSR) markers were utilized to identify the levels of heritable varieties and patterns of the populace structure among the five populaces of Pteris biaurita, a natural fern in India. A comprehensive examination was directed in three replicates at 2013-14 seasons in the Western Ghats, South India. Five wild P. biaurita, accessions (maiden hair) were assessed for genotyping studies. Results demonstrated a pivotal discrepancy among genotypes for they were characterized in view of this uniqueness in four groups by the genetic cluster examination. In this trial, ISSR primers amplified 63 polymorphic groups. In view of the genetic identity data, genotypes were figured and differed from 0.5714 to 0.6984. The percentage of polymorphism indicated predominant genotype that may be utilized for the conservation of species. ISSR appeared to be an obliging marker for prediction of genotype inside a closed group of inter specific populace in the investigation territory
Genetic variability and phylogenetic relationships studies of Aegilops L. usi...Innspub Net
Studying of genetic relationships among Aegilops L. species is very important for broadening the cultivated wheat genepool, and monitoring genetic erosion, because the genus Aegilops includes the wild relatives of cultivated wheat which contain numerous unique alleles that are absent in modern wheat cultivars and it can contribute to broaden the genetic base of wheat and improve yield, quality and resistance to biotic and abiotic stresses of wheat. The use of molecular markers, revealing polymorphism at the DNA level, has been playing an increasing part in plant biotechnology and their genetics studies. There are different types of markers, morphological, biochemical and DNA based molecular markers. These DNA-based markers based on PCR (RAPD, AFLP, SSR, ISSR, IRAP), amongst others, the microsatellite DNA marker has been the most widely used, due to its easy use by simple PCR, followed by a denaturing gel electrophoresis for allele size determination, and to the high degree of information provided by its large number of alleles per locus. Day by day development of such new and specific types of markers makes their importance in understanding the genomic variability and the diversity between the same as well as different species of the plants. In this review, we will discuss about genetic variability and phylogenetic relationships studies of Aegilops L. using some molecular markers, with theirs Advantages, and disadvantages.
Detection of Genetic variation in tissue culture clones of date palm using IS...IJSRD
Date palm is a plant having high nutritional value and long life (yielding up to 100 years). Phoenix dactylifera requires 2-5 males for pollination of 100 females’ plant depending up on genetic and environment factors. Therefore paternity variation expected to very low according to PCR based techniques, Even though we have tried to find out genetic variation among tissue culture cloned plant. Tissue culture technique can be used for genetic improvement of date palm. The main purpose of this study was to evaluate the genetic variation in the tissue culture clones of date palm by using ISSR primers among mother and it’s two clones. The plant DNA was extracted and subjected to detection of genetic variation in two groups of date palm using ISSR primers. In this study ISSR primers produced monomorphic bands within group-1 and group-2. Genetic variation in tissue culture clones of date palm was not detecte by UBC primer series.
Among the large mammals of Africa, elephants are probably the worst affected by human activities. Although they have been listed as endangered and protected since 1989, illegal poaching and habitat destruction continue to diminish and isolate remaining populations that are dispersed widely over 37 sub-Saharan African countries. Their populations currently exist in small isolated habitat, and this threatens elephant genetic diversity. Although literature is available on the taxonomy and phylogeny of African elephant, few studies have focused on codon usage on mitochondrial genomes. To analyze nucleotide diversity, selective pressure and demographic history of African elephants, we used the portion of mitochondrial sequences of 102 individuals available in the genome database. Our data indicated a low codon bias index (CBI) and a relatively high effective number of codons (ENC) value in the mitochondrial genome, suggesting that African elephants are less biased in their codon usage preference. The data also support a strong purifying selection in the mitochondrial genome of African elephants. However, few sites are under positive selection in the mitochondrial genome of African elephants, with Loxodonta africana presenting more sites under positive selection compared to L. cyclotis. The present work supports the idea that different evolutionary rate among nucleotide sites in L. africana and L. cyclotis, attributable to differences in the frequency of positive selection and probably different environmental conditions, are the driving forces for the codon usage bias in African elephants. Further studies are needed to investigate the contribution of different subpopulation in the genetic structure and diversity of African elephants.
Flow Cytometric Analysis for Ploidy and DNA Content of Banana Variants Induce...paperpublications3
Abstract: Nuclear DNA content of mutated banana plants was determined by using flow cytometric techniques. It is a powerful tool for large scale screening of ploidy levels. Nuclei were isolated from young leaves from (banana mutants & Glycine plants) supplemented with Propidium- iodide (PI) and RNAse. "Glycine max" used as internal reference standard for identifying the nuclear DNA content by FCM. For ploidy estimation DAPI was used. The results showed differences in DNA content between variants indicating the effect of gamma-irradiation on the genotype of these plants. Variants of short plant stature or stunted growth showed great differences in DNA content compared to control (non-irradiated). The phenotypic variations observed at high doses were likely due to changes in the DNA sequences at the chromosomal level. Nuclear DNA contents decreased with an increase of gamma-dose from 20 Gy to 60 Gy. However, there were no significant differences between DNA content at 20 Gy and 30 Gy and also between 40 Gy and 60 Gy, while they were differed significantly from the control. The results showed no significant differences in ploidy level between all samples used (3n); while all selected mutants (variants) showed differences in DNA content.
Fish to finance: unraveling the economic threads of Bangladesh’s Blue EconomyAbdullaAlAsif1
Bangladesh, with its extensive river network, vast coastlines, and rich maritime heritage, stands at the crossroads of a transformative Blue Economy. This comprehensive review explores the rich tapestry of Bangladesh's maritime journey. Commencing with a historical lens, it traces the nation's roots in fisheries, showcasing its transformation into a diversified and dynamic Blue Economy. The significance of this transition unfolds across the review, underscoring the sector's contributions to GDP, employment, and food security, while candidly addressing challenges such as overfishing and environmental impact. This work not only chronicles historical milestones but distills valuable lessons from both successes and setbacks, offering a nuanced understanding of the economic resilience embedded in Bangladesh's fisheries sector. Beyond a historical retrospective, the review navigates through the contemporary landscape, emphasizing diversification beyond fisheries. It illuminates economic opportunities in maritime trade, explores non-fish marine resources, and delves into the transformative role of aquaculture. The policy framework governing Bangladesh's Blue Economy comes into focus, dissecting government strategies, legal landscapes, and international collaborations. The review also champions environmental sustainability, highlighting the impact of Blue Economy activities on marine ecosystems and advocating for conservation measures, thus positioning Bangladesh as a steward of its rich maritime heritage. Financial mechanisms and investments emerge as pivotal elements, shaping the trajectory of Blue Economy projects, as evidenced by case studies that weave success stories and lessons learned into the narrative. Concluding with a forward-looking perspective, the study identifies emerging trends, growth opportunities, and strategies to tackle challenges, offering a comprehensive roadmap for sustainable development. In weaving together economic vibrancy, environmental stewardship, and future aspirations, this review illuminates Bangladesh's maritime odyssey as a beacon for the global Blue Economy community.
Successful hybridization between Clarias microstomus♂ and Clarias gariepinus♀AbdullaAlAsif1
Hybridization is a significant approach to breeding that enables the creation of new varieties that enhance genetic diversity. Through fish inter-species hybridization, it is possible to produce hybrids that can be utilized in aquaculture and stocking programs to enhance growth rate, transfer desirable traits between species, and combine the favourable attributes of two parents into a single progeny. The present study revealed the successful hybridization between Clarias microstomus (Ng, 2001) ♂ and Clarias gariepinus (Burchell, 1822) ♀ for the first time in the aquaculture industry. C. microstomus is a species of Clariid catfish endemic to the island of Borneo and C. gariepinus is an introduced species widely aquacultured throughout the southeast Asian region. The embryonic development of the hybrid offspring is described with the hatching percentage of 58.63% and the early survival rate for the first 72 hours for the larvae of 85.76%. The hybrids showed no signs of deformities and developed normally. The findings of the study provide a new high yield variety of catfish for farmers and aquaculture industry for increasing production and profit margin.
Freshwater gastropod diversity in the selected lotic environment, Betong, Sar...AbdullaAlAsif1
Freshwater Gastropoda can be considered as the biological indicator in ecosystems such as rivers, streams, lakes, and ponds. The objectives of this study are to identify freshwater gastropod species, diversity, and distribution along Sungai Penebak, Sungai Nanga Tiga, and Sungai Kabo in the Betong division. The study was conducted on 10 November 2020. A 50 m transect was laid on the riverbank of all three stations. The existing specimens were counted and collected from each sampling point and stored were taken to the laboratory for species identification. The diversity index and morphological study of freshwater gastropods were performed. Five species of freshwater gastropods belonging to four families were discovered. The five species of freshwater gastropods consisted of Sulcospira pageli, which shows great abundance, followed by Clea nigricans, Brotia costula, Pila ampullacea, and Vittina pennata. The diversity indices of collected Gastropoda species from the different stations, for instance, Shannon Weiner diversity index (H’), Pielou’s evenness index (J’), and Margalef’s richness index were assessed; where station 3 showed higher diversity of Gastropoda compared to other two stations. The information presented in this paper might be helpful for ecological wealth studies and considered as the baseline data for the stream ecosystem in Sarawak, Malaysia.
Macrofaunal diversity on the surface sediment of mangrove habitat adjacent to...AbdullaAlAsif1
Macrofaunal diversity and composition are essential to understanding the ecosystem structures and functions of mangroves in any dynamic estuarine coast. To understand the temporal distribution of macrofaunal community structures and diversity on the surface sediment in the intertidal mangrove forest next to the seagrass beds, this study was conducted at Punang-Sari-River estuary, Lawas, Sarawak (Malaysian Borneo), South China Sea. Sampling was done during post-monsoon, intermediate-September, premonsoon, and monsoon from July 2019 to February 2020. The mean macrofauna abundance was higher pre-monsoon, while Gastropoda Optediceros breviculum (L. Pfeiffer, 1855) was the most abundant (RA = 0.704). Important species index (ISI = 70.36) and percentage of contribution (64.97%) were also higher of this species than any other records from the site. The ANOSIM (Analysis of Similarity), Jaccard index and SIMPER (Similarity Percentage Analysis) analysis suggested that the highest species abundance similarity was observed between pre-monsoon and monsoon, while the highest dissimilarity was observed between intermediate-September and pre-monsoon (74.67%). Seasonal PCA, nMDS, and cluster analysis revealed that pre-monsoon and monsoon were comparable in species and individual abundance. The dominance (0.85) was found significantly higher (P < 0.0001) in intermediate-September, while Simpson (0.734), Shannon (1.56) and Evenness indices (0.528) were found higher in monsoon, followed by the higher Margalef richness indices (3.21) in post-monsoon. It was observed that the seasonal ecological parameters were found to be significantly (P<0.05) different, including the temperature, salinity, rainfall, pore water nitrogenous compounds (NO2, NO3 and NH3-N), phosphorus compound (PO4) and micro minerals. The Canonical Correspondence Analysis (CCA) results suggested that ecological factors influenced several species. Considering the few studies on mangrove macrofauna in Malaysian Borneo, further research on their trophic structures and food web interactions is very important to disclose their overall characteristics and ecosystem functions.
Population characteristics of the Japanese threadfin bream Nemipterus japonic...AbdullaAlAsif1
Nemipterus japonicus (Japanese threadfin bream) is one of the most significant fish species throughout the Indo-Pacific regions. No previous studies on the population dynamics of N. japonicus have been carried out in the Eastern Malaysia (Malaysian Borneo). The present study focused on the population dynamics of N. japonicus from April 2013 to March 2014 in the coastal area of Bintulu, South China Sea. Local fishermen provided samples, which were then analysed. The FiSAT II software was used to evaluate the collected length frequency data. The asymptotic length (L ∞) and growth coefficient (K) were 26.78 cm and 0.85 yr-1, respectively. The growth performance index (ϕ'), total mortality coefficient (Z), natural mortality (M) and fishing mortality (F) were 2.785, 2.97, 1.63 and 1.34 per year, respectively. According to the estimates, the exploitation rate (E) for N. japonicus was 0.45, while the E 0.1 , E 0.5 and E max were determined as 0.72, 0.4 and 0.806, respectively. The obtained value of exploitation was less than E max, although slightly higher than E 0.5. The recruitment characteristics of N. japonicus have been stable throughout the year, with one peak pulse. The results contribute to the knowledge of the dynamics of N. japonicus populations and are important for the sustainable management of the Sarawak fishing resources.
Proximate and mineral composition of the long-spined Sea Urchin (Diadema seto...AbdullaAlAsif1
Gonad of sea urchin is considered as food delicacy in many parts of the world due to high nutrition and mineral contents. Several species of sea urchins are available in Malaysia and reported from different habitat, including seagrass beds, coastal breakwater, coral reefs and other ecologically important habitats. The current study was undertaken to evaluate the proximate and mineral composition of long spined sea urchin (Diadema setosum) roe collected from breakwater of Terengganu, Malaysia in October 2019, November 2019 and January 2020. The samples were analysed for proximate including protein, lipid, moisture, and ash content of sea urchin roe. The macro, micro minerals and heavy metals were also evaluated including Ca, Fe, Zn, Cu, Co, Se, Mg, Ni, Pb, Al, and Cd. The result suggested that, long spined sea urchin (Diadema setosum) roe can be considered as good sources of food due to high percentage of protein (ranged between 36.21±0.44 and 50.14±4.63). The presence of heavy metal such as Ni, Pb, and Cd suggesting the breakwater environments were not good enough and the possible sources of heavy metals contamination in sea water environment must be stopped and eradicated. This study provides important information with regard to the proximate and mineral values of D. setosum, as well as the need for a better management of its habitat before D. setosum can be widely promoted as delicacy in this region.
Trends in seagrass research and conservation in Malaysian watersAbdullaAlAsif1
The seagrass ecosystems found in the marine and coastal areas, with substantial economic and ecological services and span all over the globe excluding the Antarctic region. The Coral Triangle and Southeast Asia are recognized as a worldwide hotspot of seagrass species and habitats, encompassing 10-21 species of seagrass in every nation , although the study, understanding, and quantity of publications on seagrass ecosystems are rather limited in the region, including Malaysia. Malaysia contains 18 seagrass species from three families, which occupy 16.8 km 2 of coastal area, where the study and discovery of seagrass species and meadows began in 1904 with the report of Beccari. All of the published papers reviewed reported on Malaysian seagrass-related research, which was divided into nine topic groups: biology and distribution, carbon sequestration, fauna, remote sensing, impact and pollution genetic study, restoration , microbiological investigation, and others. The extensive study of the seagrass ecosystem began in 1993, and we have identified 183 published papers from Scopus, 141 publications from Web of Science, and 42 from Google Scholar. However, the average trend of the number of publications from 1993 to 1999 was 0.71 ± 0.36, while from 2000 to 2022 was 7.70 ± 1.16 followed by the average trend of the yearly number of publications was 6.78 ± 1.08. The highest number of publications was found on faunal categories (43.17%), followed by biology and distribution (21.85%). The number of articles that were published on Malaysian seagrass meadows each year has been discovered to be rising, which indicates that the trends in seagrass study and publishing were progressively garnering the attention of researchers, academics, and the government. However, to better understand the sustainable ecology and ecosystem services provided by seagrass habitats, an emphasis on certain research niches, such as the genetic study of flora and fauna in seagrass meadows, microbial ecology, and restoration as well as conservation of seagrass species might be helpful.
First record of saucer scallop Ylistrum balloti (Bernardi, 1861) from equator...AbdullaAlAsif1
Ylistrum balloti is one of the Pectinidae species distributed within the Indo-Pacific region. Recently, 15 live specimens of Y. balloti were recorded from the continental shelf of Sarawak, Malaysia. The main morphological characteristics were displayed on the outer valve, these being a brown-red colour and a clear concentric pattern of thin brown lines. The prominent internal ribbing numbers on both valves also helped species identification. The preliminary report of Y. balloti revealed that the species is present in Sarawak waters and can be further explored in the future.
Culture and production of Lucilia sericata Meigen (1826) larvae for rearing s...AbdullaAlAsif1
The fly larvae (Lucilia sericata) are being used as an alternative protein source in any kind of animal feed as it reduces the cost of preparation of feed. This current study focused on the physico-chemical and proximate properties of raw poultry waste, while this study also revealed the production process of fly larvae and the proximate composition of it. The poultry waste was collected from Suvro poultry farm, Sutiakhali, Mymensingh, then the physic-chemical properties of the raw poultry waste were determined using different procedures. Three treatments were considered for production of fly larvae, T 1 (3 kg), T 2 (6 kg) and T 3 (9 kg) in a 15 kg capacity tray with three replications. After production, the proximate composition were also measured of fly larvae. Physico-chemical properties such as, color, odor, texture, temperature, pH, total solids (TSS+TDS), chemical oxygen demand, dissolved oxygen, alkalinity, available N, available P, and fiber in raw poultry waste were determined and presented. Proximate composition such as, moisture, total N, total P, available N, total Ca, ash and crude fiber were found in significant amount in the poultry waste. It was found that T 3 (1350±68g) produced highest volume of live maggot compared to the other treatments, but T 2 (17.50±1.10%) produced highest percentage volume. The proximate compositions of fly larvae were assessed and found 56.60±0.25% protein value in it, suggesting that fly larvae could be the protein replacer in fish feed. The result of this study revealed cheap protein source in aquaculture production, such as production and rearing of stinging catfish Heteropneustes fossilis, and the findings might be helpful for cost reduction in aquaculture operation.
Replacement of fish meal by Lucilia sericata (Meigen, 1826) live larvae and p...AbdullaAlAsif1
Reduction of aquaculture operations and production cost is key to the success and profitability of this enterprise, while protein needs, especially the cost of fish meal, are cery expensive. The current study was conducted to investigate the post-larval production performance of Heteropneustes fossilis using Lucilia sericata maggot as a fish meal replacer in two ways, namely, live larvae and powder form. A 28 days growth trial was performed where five isonitrogenous diets for Heteropneustes fossilis post-larvae were experimented using live maggots and maggot meal, respectively. The proximate composition of each formulated diet, growth parameters of fish post-larvae, such as, weight gain, specific growth rate, protein efficiency ratio, apparent protein utilization, survival rate and the food conversion ratio were examined. After the experiment, the carcass composition of the experimental fishes were evaluated. The best final weight (1.61 g), weight gain (1.418 g), percentage of weight gain (739±1.18%), specific growth rate (2.63), protein efficiency ratio (2.29), apparent protein utilization (85%), survival rate (90%) and lower food conversion ratio (2.06) were observed in fish fed with 75% maggot meal as a substitute of fish meal. This study will help the aquaculture industry, especially the catfish culture in identifying an alternate source of protein and lowering the cost of aquaculture operation.
Disappearance or overlooked or untouched? - A brief history of aquatic gastro...AbdullaAlAsif1
The aquatic gastropods (marine and freshwater) in Malaysian Borneo (MYB) have an ancient history of 255 years, while the first record was observed in 1767 by the pioneer Carl Linnaeus. Over time, many European, native taxonomists and conservationists have worked on the diverse group of gastropods in the Malaysian part of Borneo (states of Sabah and Sarawak). No previous work has been conducted to assess the historical status of this particular class of Mollusca. The study objective was to reveal the types of aquatic gastropods and the number of published research and expeditions conducted in MYB. The bibliometric analysis found 145 research publications mentioning the names of the region and reporting at least one gastropod species from this geographic region. Over the history of 255 years, a total of 559 gastropod species were reported by different research groups. Between 1767 and 1900, a total of 150 gastropod species were reported, followed by 79 species from 1900 to 2000 and 330 species from 2001 to 2022. The Grubbs test (p<0.05) identified outlier years for the reporting of gastropod species from MYB with 54 new species each in 2011 and 2020 and 39 species in 2001. Over the history of aquatic gastropod research in MYB, the taxonomists making the greatest contribution were Han Raven and his colleagues from Naturalis who reported 111 new species from the region, followed by Nur Leena Wong from Universiti Putra Malaysia (54 new species). The results suggested that reporting of new species from MYB is increasing, which may reflect the many unexplored sites and suggests the existence of as yet unrecorded species in this ecoregion. In this regard further expeditions and research should improve estimates of the true number of aquatic gastropod species in this area. These results can help the regional governments in making a regional biodiversity database as well as in taking decisions regarding aquatic gastropod research and management.
A ray of hope in the darkness: What we have learned from Yangtze giant soft-s...AbdullaAlAsif1
The Swinhoe's softshell turtle, Rafetus swinhoei (Gray, 1873),) is one of the world's largest freshwater turtles, and possibly the most endangered turtle species on the planet (Stanford et al., 2018). It has an overall length of over 100 cm and a width of up to 70 cm, and it can easily weigh up to 70–100 kg, maximum weight was recorded at 169 kg (Solimine, 2013; Trong, 2018). Despite its enormous size and unusual look, this species is incredibly secretive and only comes to the surface to breathe, preferring to remain submerged deep down. For this species, there is very little ecological information, and the remaining distribution is unclear. This could explain why it's so difficult to positively identify and confirm occurrences of this species in the wild (Trong, 2018). If we look back to the history and biogeography of this species, it can be found that the existential records were documented in the historical literature of the Chinese and Vietnamese dynasties. This species was once thought to only live along the Red River in China and Vietnam, as well as the lower Yangtze River floodplain in China, but its current population size is estimated to be just one wild individual of undetermined sex and a solitary captivity male in Suzhou Zoo, China. Although recent thorough searches in Yunnan, China, and Vietnam failed to confirm the presence of more wild specimens, some sightings were reported until around a decade ago (Stanford et al., 2018), giving hope that more individuals may yet exist in Vietnam.
Snapper shrimp is a symbiotic organism usually hidden under the rocks, sponges and pen shells in the seagrass and coral habitats. The relationship study within snapper shrimp and pen shell was conducted from Merambong shoal, one of the biggest seagrass beds in peninsular Malaysia. A total of 40 individual pen shells were collected randomly and four species of pen shells were identified. 40 Anchistus custoides were found inhabiting symbiotically in the mantle cavity of the pen shell as solitary males and females and heterosexual pairs. Pen shell, Pinna bicolour and Atrina vexillum recorded the highest average SH 217.79±53.15 mm, SV 2.62±1.36 dm3 and SH 164.10-224.78 mm with the SV 1.18±0.43 dm3, respectively compared to the other species. The size of Anchistus custoides ranged from 15.00 to 20.00 mm in length and it was determined to be female due to the presence of eggs in the pleopods. The length of the cephalothorax and its length were highly related (rs=0.563, p≤0.01, N=40) and found wider in females. A little difference in size between the left and right chela in males of identical length was noticed, although the left chela is much bigger than the right. The significant relationship (rs=0.450, p≤0.01, N=40) between the pen shell length and shrimp (male-female) length revealed that the size of the shell is important to be hosted the snapper shrimp in the shell cavity.
Diversity of fisheries in Sarawak, Northwest Borneo: Present status and conse...AbdullaAlAsif1
Information on fisheries resources in East Malaysia is scarce and poorly known. The current review aims to compile a checklist of fisheries resources in the Northwest Borneo (Sarawak, Malaysia) from available published literature, address the resources' present status, and suggest future monitoring needs for selected critical species. The study also aims to determine several Sarawak land-use issues that are in flux and responsible for habitat degradation. Five hundred sixty-four species belonging to 123 families and 32 orders were recorded from Sarawak waters. Freshwater fish species comprised 48.0% of the total, followed by a marine (36.6%), marine-euryhaline (12.9%), and brackish water (2.5%) species. Of this, Cyprinidae was the most dominant group accounting for the greatest number of species (82 species), followed by Balitoridae (34 species), Bagridae (21 species) and Penaeidae (21 species). Therefore, available fisheries resources should be managed carefully as 48 species (9.0%) are currently vulnerable to extinction. Furthermore, the presence of 20 alien species in Sarawak water bodies also requires attention from the authorities due to the potential disruption of aquatic ecological balance. Changing land use issues in Sarawak such as forest degradation, agricultural expansion, peatland deforestation and conversion, logging, destruction of mangrove forests, and construction of hydroelectric power dams and flood mitigation channels pose significant challenges to fishery management in Sarawak. Our study documents the priority of fishery monitoring and conservation in Sarawak water bodies to ensure sustainable management of fisheries resources.
Availability and potentiality of small indigenous species of fish throughout ...AbdullaAlAsif1
This study was conducted with aiming to know the present status of small indigenous fish species (SIS) in Oxbow Lakes/baors and rivers as well as the availability of SIS of fish and their potentiality in the study area. Regular data were collected from some important fish landing center cum markets, Oxbow Lakes and rivers of the study area. The availability of small indigenous species (SIS) of fish declined to a great extent over the years and many of them are rare or endangered due to death of rivers and baors were brought under aquaculture. Besides these, Many of SIS of fish were being increasingly used as trash fish for fish feed purpose. As an over populated country, demand of SIS of fish is increasing day by day. After 1990s almost all Oxbow Lakes have been gradually trying to bring under aquaculture through local community or Department of Fisheries. The most significant message of this study is that, some vulnerable and endangered SIS of fish are locally abundant both in fish landing center, baors and rivers. So they must be conserved for their bioavailability and nutrition throughout the country that would be most intelligent efforts in favor of global ichthyo-biodiversity conservation.
Socio-economic conditions of the fish farmers in Jessore, BangladeshAbdullaAlAsif1
The study was conducted the fish farmers in some selected area at sadar upazila in Jessore under the district of Jessore from September to December 2013. A total of 100 fishermen were selected by stratified random sampling method and interviewed. The average me mbers of single family were 5-6 people per household. Single families were much more (62 %) than joint families. Most of the fish far mers were Muslims 92% and few of them were Hindus 8%Most of them had the secondary educational background and some of them with different levels of higher education. It was found that the number of school going children was 2-3 per house. Full katcha (17 %) houses were few, while the semi-pucca (40%) and pucca (43%) houses were more abundant. Regarding health and sanitation, 31% fishermen reported to suffer fro m gastric and 17% suffered from fever. Most of the interviewees were found to take credit facilities from different sources for the subsistence of their family and their venture. The 98% were found to have their tube-wells, others using Governmental tube-well, or those belonging to schools or neighbors However, they need more institutional, organizational, and technical and credit support for their better socioeconomic and sustainable livelihood.
Socio-economic condition of fish fry and fingerling traders in greater Jessor...AbdullaAlAsif1
The present study was conducted to assess the livelihood status of fish fry and fingerling traders and socioeconomic condition in the greater Jessore, Bangladesh from April 2013 to September 2013. Data were collected through the use of well-structured questionnaire from the selected area. 73% of traders have single family but only 27% have joint family. 45% fish fry and fingerling traders family has four members. 20% family has five members, 14% family has six members, 12% family has three members 9%family has seven to eight members respectively. 92% traders has own bank account but only 7% traders uses their bank account when they trade fry and fingerling. 87% traders have secondary business like rickshaw business, fruit business, cloth business, fish trading etc. Among 300 fish fry and fingerling traders the sanitation facilities are present 100%. It was found that 69% and 31% of fish farmers used semi-pucca and pucca toilet respectively. Among 300 fish fry and fingerling traders 78% of traders have own house but only 22% of trader live in rental house or place. 46% of traders have institutional education that range from primary to higher education and other 54% of traders have no experience in education. In case of illness 58% of traders and trader's family goes to government hospital, 24% uses private clinic, 15% traders are uses local village doctor and another 3% does not get any treatment or not require no treatment. 93% traders have television, 5% house consist radio and another 2% house no instrument for entertainment. Only 10% trader wants their son and grandson engages with this fish fry and fingerling trading profession. The average monthly income of traders in the peak season is 18000 taka and off-peak season the income is less than 7000 taka per month.
Marketing of fish and fishery products in Dinajpur and livelihoods of the fis...AbdullaAlAsif1
Marketing of fish and fishery products in Dinajpur and livelihoods of the fish retailers were studied during the period from January to May, 2013. A total of 60 fish retailers were interviewed for obtaining pertinent data. A survey questionnaire was developed, pre-tested and finally used for collection of data. The collected data were tabulated using conventional statistical tools. The result showed that the livelihoods of a large number of people are associated with fish and fishery products distribution and marketing in six different markets. Three types of marketing channel were found to be operated in the selected markets. The shorter marketing chain which included the fish farmers, retailers and consumers was found to be more beneficial to the fish producers. Fish traders in village markets generally operate a capital of around TK. 8,000-10,000 and traders in town markets a capital of around TK. 10,000-20,000 per day. It was found that most of the fish traders used their own money. Price of fish depends on market structure, species, and freshness, supply demand of fish and size of fishes. There are seasonal variation in prices with the highest in summer (March to May), and lowest in pre-winter: (September to November) during the fish harvesting season. Different types of dried and salted fish were sold in the markets. Traders have broadly improved their food consumption facilities, standard of living, and purchasing power as an economic sector. However, the unhygienic conditions of the marketplace, lack of ice facilities, poor infrastructure, inadequate storage and poor transportation facilities were reported to be the major constraints hindering the marketing system in the surveyed areas. It is therefore necessary to provision of governmental, institutional and banking assistance for improvement of the marketing system.
Socio economic status of fry collectors at Sundarban regionAbdullaAlAsif1
The study was conducted on the livelihood approach of fry collectors at Shyamnagar upazila under Satkhira district. The objective of the study was to assess the present livelihood status, to identify the socio-economic condition and problem associated with the alternative livelihood approach of fry collectors. The survey was conducted on three unions of Shyamnagar upazila adjacent to Sundarban as study area. In the study area average family size was 5 persons per family. The maximum age level was 20-30 years old. Among the fry collectors 66% was male and 34% was female. Among them 62% was Muslim and 38% was Hindu. About 78% of total fry collectors are landless in the study area. Literacy was 31% of them where female literacy was 28% and male literacy was 72% and most of them can sign only. Most of the collectors about 63% lived in mud walled with golpata shed house. About 73% families have two earner and 68% have single family. Peak season of fry collection was March to May. For collecting fry they use push net, set bag net mainly. They collect fry in the early morning and in early evening for about 6-8 hours. Men collect 150-200 pieces of fry per day in peak season and 40-60 pieces of fry by women. Price varies from 800-3500 Tk. per thousand golda fry. Price is higher in the month on March-May. About 52% collectors engaged in fishing during off season as alternative income source. Their preferable alternative income source are sustainable agriculture, fry nursing, poultry farming, planned fish cultivation, cattle and goat rearing etc. The main problem of converting of fry collection to other profession was lack of other training of other works, lack of capital, poor infrastructure.facilities, absence of industrialization, lack of land, government and NGO level work is very limited.
Tilapia (Oreochromis mossambicus) marketing system in greater Jessore region,...AbdullaAlAsif1
The study was carried out to access on the present status of Tilapia (Oreochromis mossambicus) marketing in Jessore sadar in Jessore district. Study period was carried out during June 2013 to December 2013. For the market survey, two important fish markets in Jessore town, namely Boro Bazaar and Rail-station Bazaar Similarly, two important local fish markets in the Jessore Sadar namely Churamonkati Bazaar and Ambot-tola Bazaar were selected to carry out comparative studies of tilapia marketing between town and local markets. A total of 80 traders were interviewed in Local and Town markets, 40 in each area. In the study area 55% of harvested tilapias are sold to the local agents, while the rest (45%) are sold to the suppliers and about 60% of tilapias are transported to the boro bazaar. The rest (40%) of the tilapia, which are under-sized, are transported to nearby local markets. The average farm-gate prices of tilapia varied between Tk 55 and Tk 85 per kg. According to the survey, a wholesaler typically operates with capital of around Tk 11,968 per day, ranging from Tk 8,350 to Tk 27,125 per day. According to the survey, 70% of wholesalers used their own money for fish marketing including tilapia, while the rest (30%) received loans. In the study area tilapia comes from Jhenidah, Satkhira, Jessore then it is supplied to Boro Bazar to wholesaler then it is distributed towards local market. Around 20 to 25 individuals are associated with fish trading including tilapia, except for Boro Bazaar which is larger. The total average marketing costs from producers to consumers was calculated to be Tk 13.02 per kg of tilapia which is sub-divided into: primary market – Tk 3.25 (25%), secondary market – Tk 4.75 (36%), and retail market – Tk 5.02 (39%). In the study area, tilapia prices are generally lower between September and December, rising during the following four to five months. The highest average marketing margin and profit per kilogram of tilapia was found in secondary market, followed by retail and primary market. The proportion of respondents identifying poor road and transport facilities was 24%. Only 20% and 12% of traders identified lack of money for this business. In case of socio economic condition traders 25% has earthen house and 65% has Pucca house and 10% has Semi pucca house. In the study area about 35% traders goes to the MBBS and rest of 65% is goes to the quack or non trained doctor. Traders has earthen toilet of 27%, Pucca toilet is 50% and Semi pucca is 23%. All traders have education at some level, which implies that the reported literacy rate is 83%. Most traders were quite young, with an average age estimated at 36 with a range from 23 to 57. The average family size of tilapia traders was estimated at 5.5 in a single family.
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
This pdf is about the Schizophrenia.
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This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
Nutraceutical market, scope and growth: Herbal drug technology
The molecular approach reveals the relationship among Venus clams (Meretrix spp.) Community in Malaysia
1. BIOTROPIA Vol. 29 No. 3, 2022: 213 - 224 DOI: 10.11598/btb.2022.29.3.1583
213
THE MOLECULAR APPROACH REVEALS THE
RELATIONSHIP AMONG VENUS CLAMS (Meretrix spp.)
COMMUNITY IN MALAYSIA
MOHD HANAFI IDRIS1, ABU HENA MUSTAFA KAMAL1, HADI HAMLI2*,
AMY HALIMAH RAJAEE2,3 AND ABDULLA-AL-ASIF2
1
Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, 21300 Kuala Nerus, Terengganu, Malaysia
2
Department of Animal Science and Fishery, Faculty of Agricultural and Forestry Sciences, Universiti Putra Malaysia,
Bintulu Sarawak Campus, Bintulu, Sarawak, Malaysia
3
Institut Ekosains Borneo, Universiti Putra Malaysia, Bintulu Sarawak Campus, Bintulu, Sarawak, Malaysia
Received 12 April 2021/Accepted 2 June 2022
ABSTRACT
Molecular study is important to detect variations and similarities among species from the same genus, in case
if they do not encompass any morphological or physiological differences. The study was conducted to
differentiate among species of Meretrix spp. (Meretrix lyrata, M. meretrix, and M. lusoria) obtained from two
locations in Malaysia through the phylogenetic tree. The adductor muscle tissues were used to extract DNA and
to perform other procedures; the samples were subjected to analyses using PCR and gel electrophoresis. The
multiple sequence comparison was conducted by MUSCLE and the phylogenetic relationships were established
using Maximum Likelihood (ML) statistical methods with MEGA 6.0 statistical software. M. lyrata samples
showed 99% similarity to the three accessions sequence, where M. lyrata indicated 87% similarities, and M.
meretrix showed not more than 89% similarities from the deposited sequence. The nucleotide base composition
sequences consisted of the mean of Thiamine (T) 37.9%, Cytosine (C) 15.4%, Adenine (A) 27.4%, and Guanine
(G) 19.4%. Maximum Likelihood (ML) analysis was conducted using the Tamura 3-parameter model to establish
five major clades on Meretrix spp. and two out-groups clades significantly different from the Meretrix spp. These
major clades were closely related to each other at the 50% evidence of bootstrap, which grouped as genus
Meretrix. The present study on Meretrix spp. from the Sarawak locality was able to differentiate COI sequences
between M. lyrata, M. meretrix, and M. lusoria. M. lusoria was close related to M. meretrix with strong bootstrap
supporting evidence at 96% scoring. Moreover, M. lyrata was inferred as the ancestor to M. meretrix, and M. lusoria
from Sarawak, Malaysia.
Keywords: bivalve, BLAST, Borneo, mtDNA, PCR, phylogenetic analysis
INTRODUCTION
Genetic variation can be characterized into
two groups which are intraspecific and
interspecific (Arruda et al. 2009; Ehlers et al.
2016; Layton et al. 2016; Thia et al. 2016).
Intraspecific is the variation within individuals
from similar species such as subspecies (Stevens
et al. 2010). On the other hand, interspecific is
the variation within individuals above the
species level. Genetic variation of natural
populations is thought to be governed by the
mutual effects of irregular genetic drift,
restricted gene flow, and variance of selection
pressures. Intense natural selection is an
important factor influencing variation among,
and within groups (Endler 1986). The natural
selection can be stabilized the species characters
such that genetic variation within the population
might be reduced. Disruptive selection may lead
to genetic divergence, and therefore, may
eventually increase genetic variation among
population (Backeljau et al. 2001).
Mitochondrial DNA (mtDNA) is one of the
DNA markers that are popular for DNA
identification. This marker is the maternal
inheritance that supplies information absent in
nuclear markers (Okumuú & Çiftci 2003).
*Corresponding author, email: hadihamli@upm.edu.my
2. BIOTROPIA Vol. 29 No. 3, 2022
214
Therefore, selecting tissue from the female
individual is essential to ensure information
regarding the species ancestor. However, the
maternal inheritance by mtDNA can be
restricted by the geographical with no mixing of
mtDNA haplogroups from the different
geological regions (Luttikhuizen et al. 2003;
Mishmar et al. 2003; Layton et al. 2016).
Furthermore, inheritance characteristics on a
particular defect gene could be recognized using
an mtDNA marker (Wallace et al. 1999). This is
significant, particularly in aquaculture, to ensure
cultured species are free from any inherited
diseases from the parents. Moreover, mtDNA
could be applied for species identification and
phylogeny studies due to the particular inherited
gene variance.
The typical mitochondria gene used for the
phylogenetic study is cytochrome C oxidase
subunit I (COI). This mtDNA marker has been
applied for genetic relationship and phylogenetic
analysis for Meretrix spp. from Japan, Korea, and
China (Yamakawa et al. 2008, Chen et al. 2009;
Torii et al. 2010; Kim & Yoon 2014; Sato et al.
2016). Parentage assignment from a similar
population but different parents was also
successfully implemented for Meretrix meretrix
culture (Lu et al. 2011). Due to the intensive
mtDNA marker application, the universal
primer of COI had been created based on the
conserve gene sequence across the species to
facilitate COI analyzing region on different
metazoan species (Folmer et al. 1994).
The study of Mollusca started from the study
of Morris & Purchon (1981), their approach was
to enlist and taxonomic study of available
species; however, the story of mollusk study
goes on, and Malaysian scientists and
academician studied a different aspect of
Mollusca; from taxonomy to diversity, along
with the genetic aspect of this community
(Hamli et al. 2012a, b; 2013; 2015; 2017; 2019;
2020a, b, c; Foon et al. 2017; Al-Asif et al. 2020;
Al-Asif et al. 2021; Idris et al. 2017a, b). Genetic
and molecular study of class Bivalvia and
Gastropoda is not new in Malaysian territory,
including East Malaysia (Sabah and Sarawak
Provinces). Some previous study revealed the
genetic diversity of Asian green mussel (Perna
viridis) in the Waters of Sabah (Lau et al. 2018),
DNA study of Neritid (Chee & Mohd Nor
2016), genetic diversity of razor clam in Kuala
Selangor, Malaysia (Hassan & Kanakaraju 2016).
There is no genetic approach of Venus clam
(Meretrix spp.) was found in Malaysia, and the
genetic relationship among the available Venus
clam species is still unknown. Therefore, the
present study aims to differentiate among
Meretrix spp. from different through the
phylogenetic tree.
MATERIALS AND METHODS
Sample Collection
A total of 30 samples of Meretrix lyrata, M.
meretrix, and M. lusoria were collected from two
areas, Kuching and Kabong, Sarawak Province,
Malaysia (Fig. 1). Adductor muscle tissues from
the females were separated from the shell and
preserved with 95% of ethanol (Wang et al.
2010) for further analysis at the Parasitology
Laboratory, Department of Animal Science and
Fishery, Universiti Putra Malaysia, at the Bintulu
Sarawak Campus.
DNA Extraction
About 10 to 20 mg of adductor muscle tissue
from each sample was used for extraction
using a tissue DNA extraction kit (Vivantis)
following the manufacturer's instructions and
stored at -20 °C. The extracted DNA was then
quantified through agarose gel electrophoresis.
DNA Quantification and Gel Electrophoresis
Extracted DNA was quantified following
Rengarajan et al. (2002) to ensure the amount of
DNA within 1 µL. Each quantified DNA was
adjusted to 100 µL to ensure the total amount of
DNA sample used for amplification was equal.
Quantification of genomic DNA was compared
based on Lambda Hind III marker (23130 bp).
Gel agarose concentration used for DNA
quantification was 0.8% in 1X TAE (Tris-
Acetate-EDTA) buffer and the electrophoresis
procedure was conducted following Lee et al.
(2012). A total of 5 µL of extracted genomic
sample and 1 µL of dye (EZ-Vision One dye)
were added into the well. After all the samples
and markers were loaded, electrophoresis was
run for 40 minutes with 120 Volts of electricity.
The running of electrophoresis was monitored
until the red dye was moved 3/4 of the gel
length, and the electrophoresis was stopped.
3. Molecular approach establishes relationship among Venus clams (Meretrix spp.) community – Idris et al.
215
Figure 1 Study area of Meretrix spp. for genetic study
The gel was then removed from the tank and
was photographed under a UV light gel imager
(RedTM
, Alpha Innotech). Quantification process
based on appeared bands on the gel to be
viewed with Alpha View software and band
intensity from extracted samples was compared
with Lambda Hind III marker for 100 ng of
DNA.
While 1.5% of gel agarose concentration was
used for the Polymerase Chain Reaction (PCR)
through 0.3 g of agarose powder into 20 mL of
1X TBE (Tris-Borate-EDTA) buffer, the
mixture was swirled and heated in the
microwave to ensure agarose powder was
dissolved. Heated mixture was monitored to
make sure the mixture was not boiled. After
agarose powder dissolved in the buffer, the
mixture was left to cool and then was poured
slowly into the prepared gel tank while ensuring
that no bubble was trapped. Immediately, the
comb was inserted into the poured mixture,
while letting the agarose mixture to be cool and
solidify for 30 minutes. After the gel became
solid, the comb was removed and the running
buffer 1X TBA or 1X TBE was poured into the
gel tank until all the gel parts submerged.
Polymerase Chain Reaction (PCR)
Amplification
Amplification of DNA was performed in
50 µL of PCR mixture using universal marker
cytochrome C oxidase subunit I (COI) with
sequence LCO1490: 5’-GGTCAACAAATCATA
AAGATATTGG-3’ and HCO2198: 5’-
TAAACTTCAGGGTGACCAAAAAATCA-3’
(Folmer et al. 1994). Each PCR reaction
consisted of 0.1 mM of reverse and forward
primers, 0.2 mM of dNTP, 2.0 mM MgCl2, 1x
buffer, 1.25 units of Taq polymerase, 100 ng of
template DNA, and ultrapure water to complete
50 µL.
A total of 50 µL of PCR mixture were
amplified in XP Thermal Cycler Block (Bioer
Technology co. LTD) with pre-denaturation at
95 °C for 5 minutes, then followed by 35 cycles
of 1 minute at 95 °C for denaturation, 1 minute
for annealing at 40 °C, 1 minute 30 second at
72 °C for extension and 72 °C for 7 minutes for
final extension (Folmer et al. 1994). The last
cycle temperature was maintained at 4 °C. The
PCR product then underwent electrophoresis.
Gel Electrophoresis
Gel agarose concentration used was 1.5% in
1X TBE (Tris-Borate-EDTA) buffer. The
electrophoresis procedure was carried out
following Lee et al. (2012). A total of 100 ng of
PCR product was added into the well with 1 µL
of dye (EZ-Vision One dye) and 1 µL of 100 bp
ladder (Promega) with 1 µL of dye (EZ-Vision
One dye) at the end of the well. After all
samples and markers were loaded,
electrophoresis was run for 60 minutes with 80
Volts of electricity. The running of
4. BIOTROPIA Vol. 29 No. 3, 2022
216
electrophoresis was monitored until the red dye
was moved 3/4 of the gel length, and the
electrophoresis was stopped. The gel was then
removed from the tank and was photographed
under a UV light gel imager (RedTM
, Alpha
Innotech). The appeared band was then com-
pared to the ladder to identify the fragment size.
Purification and Sequencing
PCR products were purified before
sequencing. According to the manufacturer's
instruction, purification has been done to
remove excess dinucleotide triphosphate
(dNTP) using Themo Scientific GeneJet PCR
Purification Kit. Afterward, purified samples
were sent to the First Base Laboratory, Malaysia,
for DNA sequencing. Both strands of PCR
products and primers were sequenced using the
Applied Biosystems BigDye Terminator v3.1
cycle sequencing kit.
Statistical Analysis
The obtained sequences were inspected and
assembled using BioEdit version 7.0. The
assembled sequence of M. lyrata, M. meretrix, and
M. lusoria were then compared with all species of
Meretrix spp. in GenBank of National Center for
Biotechnology Information (NCBI) using Basic
Local Alignment System Tool (BLAST) 2.2.31
(National Center for Biotechnology Information,
Bethesda, MD, USA [http://www.ncbi.nlm.
nih.gov/BLAST/]). The highest similarity
sequence from the GenBank with Meretrix spp.
was selected for phylogenetic analysis in the
present study.
The present Meretrix spp. sequence, 16
accessions sequence mtDNA, COI sequence,
and 2 species with COI sequence as an outgroup
which Mercenaria mercenaria and Paphia gallus
(Table 1) in Genbank NCBI were aligned based
on multiple sequences comparison by log-
expectation using MUSCLE (Edgar 2004).
Phylogenetic relationships were developed using
Maximum Likelihood (ML) statistical methods
with MEGA 6.0 statistical software (Tamura
et al. 2013).
The evolutionary history was inferred using
the Maximum Likelihood method based on the
Tamura 3-parameter model (Tamura 1992). The
non-uniformity of evolutionary rates among
sites was modeled using discrete Gamma
distribution (+G) with 5 rate categories. The
bootstrap agreement tree inferred from 500
replicates (Felsenstein 1985) was taken to
represent the evolutionary history of the
analyzed taxa (Felsenstein 1985). Branches
equivalent to partitions reproduced in more than
50% bootstrap replicates were illustrated. The
percentage of replicate trees in which the
associated taxa clustered together in the
bootstrap test was shown next to the branches
(Felsenstein 1985). The heuristic search's initial
tree was obtained automatically by applying
Neighbor-Join and BioNJ algorithms to a matrix
of pairwise distances estimated using the
Maximum Composite Likelihood (MCL)
approach and then selecting the topology with a
superior log-likelihood value. Evolutionary
analyses were conducted in MEGA6 (Tamura
et al. 2013).
Table 1 List of Meretrix accession sequences from the GeneBank (NCBI)
Meretrix accessions Geographical locations GenBank Acession Number Citation
Meretrix lyrate Sarawak, Malaysia Present study Present study
M. lusoria Sarawak, Malaysia Present study Present study
M. meretrix Sarawak, Malaysia Present study Present study
M. lyrata China KC832317.1 Wu et al. (2014)
M. lyrata China J N898944.1 Cheng et al. (2013)
M. lyrata China HM124580.1 Chen et al. (2011b)
M. lusoria China GQ903339.1 Wang et al. (2010)
M. lusoria Japan AB853870.1 Yamakawa & Imai (2013)
M. lusoria Japan AB853865.1 Yamakawa & Imai (2013)
M. meretrix China GQ463598.1 He et al. (2011)
M. meretrix China HM124578.1 Chen et al. (2011b)
M. meretrix China JN043623.1 Wang et al. (2011a)
M. petechialis China EU145977.1 Ren et al. (2009)
M. petechialis China HM124582.1 Chen et al. (2011b)
5. Molecular approach establishes relationship among Venus clams (Meretrix spp.) community – Idris et al.
217
Table 1 (Continued)
M. petechialis China HQ703177.1 Chen et al. (2011a)
M. lamarckii China GU071281.1 Wang et al. (2011b)
M. lamarckii China HM124579.1 Chen et al. (2011b)
M. lamarckii Japan AB059420.1 Hamaguchi et al. (2001)
M. casta India JQ773441.1 Ranjith et al. (2012)
Mercenaria mercenaria * Canada HM884239.1 Layton et al. (2014)
Paphia gallus * China HQ703232.1 Chen et al. (2011a)
Note: * = Outgroup.
RESULTS AND DISCUSSION
The COI marker produces a fragment size at 710 bp for M. lyrata, M. meretrix, and M. lusoria (Fig. 2).
Figure 2 Fragment size produced by Meretrix spp. using COI marker
Notes: 1 = M. lyrata; 2 = M. lusoria; 3 = M. meretrix.
Basic Local Alignment System Tool (BLAST)
analysis indicated that the M. lyrata samples from
the present study had 99% similarity to the three
accessions sequence (KC832317.1, JN898944.1,
HM124580.1) of M. lyrata compared to other
accessions sequence (Table 2). Different
accession sequences were only showed lower
than 87% of similarities with M. lyrata from the
Sarawak locality. The present study on M. lusoria
showed higher similarities with M. lyrata with
accessions sequence KC832317.1 and
HM124580.1, and M. meretrix with accessions
sequence HM124578.1 and JN043623.1. Other
accessions sequence were less than 89% of
similarities with the present study on M. lusoria.
There was no similarity of more than 89%
within M. meretrix from Sarawak Province with
GeneBank NCBI accessions sequence of M.
meretrix. The higher similarity sequence was
represented by the accession sequence
HM124580.1 of M. lyrata with 89% similarity.
The nucleotide sequence for M. lyrata in the
present study showed potential similarity with
the accession nucleotide sequence of M. lyrata
from the GenBank NCBI with more than 90%
similarity compared to M. meretrix and M. lusoria.
Some previous studies conferred the
morphology feature on M. lyrata as being the
easiest to distinguish from M. meretrix and M.
lusoria (Hamli et al. 2012b, 2015, 2016, 2017).
However, the nucleotide sequence for M.
meretrix and M. lusoria showed lower than 90%
similarity with the accession nucleotide sequence
from the GenBank NCBI. Hence, the BLAST
6. BIOTROPIA Vol. 29 No. 3, 2022
218
analysis could not confirm and distinguish M.
meretrix and M. lusoria from the Sarawak locality
through the COI sequence. Current findings
were contradictory with results of the
morphology and morphometric studies, which
distinguished differences between M. meretrix
and M. lusoria. However, Wang & Dunbrack
(2004) reported that the application of BLAST
only produces short and conserve fragment
alignment. Thus, the analysis was frequently
unable to identify many relationships,
particularly below 40% sequence identity. Low
sequence identity of fragment creates
uncertainty of gaps and insertion, thus
compromising confidence in overall modeling of
protein related to genome sequence annotation
(Gan et al. 2002). M. lusoria and M. meretrix were
hard to identify by rough morphological
inspection due to similar features, particularly
the outer shell. However, a detailed examination
of the inner shell generated morphological
variation of the distinct profile of the pallial
sinus scar between M. lusoria and M. meretrix.
Yet, using the BLAST application to confirm
the differences between the two species
appeared to provide uncertain results.
Rather than depending on sequence identity
percentage, phylogenetic relationship perhaps
provides more justified evidence on the present
genome characteristic of Meretrix spp. to be
evaluated against the accession sequence in the
GenBank. The current phylogenetic tree was
constructed based on Maximum Likelihood
(ML), which applied an algorithm that calculates
the probabilistic approaches to build a
relationship tree between compared species
based upon the nucleotides or amino acid
sequences (Guindon & Gascuel 2003). Meretrix
spp. from the Sarawak locality indicates the
close relationship between M. lusoria and M.
meretrix. The variation in the COI sequence of
this Meretrix spp. can be distinguished, hence, we
are able to clarify the intricacy conferred using
the BLAST application.
Moreover, M. lusoria and M. meretrix had
similar ancestors represented by M. lyrata from a
similar locality. Therefore, COI sequence in M.
lyrata had a low level of sequence identity among
Meretrix spp. This was in agreement with Chen et
al. (2009) and Wu et al. (2014), which suggested
that M. lyrata has the level of sequence that
portrays as the ancestor to other Meretrix spp. by
referring to COI and transfer RNA (tRNA),
respectively.
Sequence Characteristics
A total of 21 nucleotide sequences were
analyzed from three Meretrix spp. of Sarawak
locality, 16 accessions sequence of Meretrix spp.
and two outgroup species represented by
Mercenaria mercenaria and Paphia gallus. Codon
positions included were 1st
+ 2nd
+ 3rd
+
Noncoding. All positions containing gaps and
missing data were eliminated. There were a total
of 435 positions in the final dataset. The
nucleotide base composition sequences were
comprised with mean of Thiamine (T) 37.9%,
Cytosine (C) 15.4%, Adenine (A) 27.4%, and
Guanine (G) 19.4% (Table 3).
Table 2 Similarity percentage of Meretrix spp. in the present study with 16 selected Meretrix spp. mtDNA accessions
sequence from GenBank (NCBI)
Accession sequence
GenBank
Species
M. lyrata
(%)
M. lusoria
(%)
M. meretrix
(%)
KC832317.1 M. lyrate 99 90 88
JN898944.1 M. lyrata 99 < 83 < 84
HM124580.1 M. lyrata 99 90 89
GQ463598.1 M. meretrix 86 86 85
HM124578.1 M. meretrix 87 90 87
JN043623.1 M. meretrix 87 90 87
GQ903339.1 M. lusoria < 85 86 86
AB853865.1 M. lusoria 85 87 85
AB853870.1 M. lusoria < 85 86 85
EU145977.1 M. petechialis 86 85 85
HM124582.1 M. petechialis < 85 85 85
HQ703177.1 M. petechialis < 85 86 85
GU071281.1 M. lamarckii < 85 < 83 86
AB059420.1 M. lamarckii < 85 < 83 87
HM124579.1 M. lamarckii < 85 < 83 86
JQ773441.1 M. casta < 85 88 87
7. Molecular approach establishes relationship among Venus clams (Meretrix spp.) community – Idris et al.
219
Table 3 Nucleotide base composition for accession sequences
Species Accession T % C % A % G % Total
Meretrix lyrata Sarawak 24.8 19.5 42.1 13.6 435.0
M. lusoria Sarawak 24.4 20.2 41.8 13.6 435.0
M. meretrix Sarawak 23.7 20.7 42.1 13.6 435.0
M. lyrata KC832317.1 41.8 14.0 23.7 20.5 435.0
M. lyrata JN898944.1 42.1 13.8 24.1 20.0 435.0
M. lyrata HM124580.1 42.1 13.8 24.1 20.0 435.0
M. lusoria GQ903339.1 42.1 13.6 23.0 21.4 435.0
M. lusoria AB853870.1 23.0 20.5 43.0 13.6 435.0
M. lusoria AB853865.1 22.3 22.1 43.0 12.6 435.0
M. meretrix GQ463598.1 42.8 13.1 23.0 21.1 435.0
M. meretrix HM124578.1 41.6 14.3 22.3 21.8 435.0
M. meretrix JN043623.1 42.1 13.8 24.1 20.0 435.0
M. petechialis EU145977.1 42.8 13.1 23.0 21.1 435.0
M. petechialis HM124582.1 41.8 13.8 23.7 20.7 435.0
M. petechialis HQ703177.1 42.3 13.3 23.7 20.7 435.0
M. lamarckii GU071281.1 43.7 13.8 19.8 22.8 435.0
M. lamarckii HM124579.1 43.7 13.6 20.7 22.1 435.0
M. lamarckii AB059420.1 42.3 13.8 22.1 21.8 435.0
M. casta JQ773441.1 42.3 14.7 23.2 19.8 435.0
Mercenaria mercenaria HM884239.1 40.8 14.7 21.1 23.4 436.0
Paphia gallus HQ703232.1 44.4 12.0 23.0 20.7 435.0
Average 37.9 15.4 27.4 19.4 435.0
Phylogenetic Analysis
A discrete Gamma distribution was used to
model evolutionary rate differences among sites
(5 categories (+G, parameter = 2.0104)).
Maximum Likelihood (ML) analysis conducted
using the Tamura 3-parameter model has
constructed five major clades on Meretrix spp. in
the present study with designed out-groups
Mercenaria mercenaria and Paphia gallus. These
major clades were closely related to each other
at the 50% evidence of bootstrap, which
grouped as Meretrix genus (Fig. 3). Two
monophyly groups were formed, represented by
Clade 3 and 4, while Clade 1, 2, and 5 were
formed, paraphyly groups. Meretrix spp. from
the Sarawak locality was clustered in Clade 1
alongside two M. lusoria of Japan locality with
accession sequence number AB853865.1 and
AB853870.1. Clade 2 comprised two M. meretrix
from the China locality with accession sequence
number HM124578.1 and JN898944.1. Clade 3
consisted of M. lyrata from the China locality
with accession sequence number KC832317.1,
HM124580.1, JN898944.1, and M. casta from the
India locality with accession sequence
JQ773441.1. Meretrix lamarckii from the Japan
locality (AB059420.1) was clustered with M.
lamarckii from the China locality (GU071281.1;
HM124579.1) in Clade 4. All M. petechialis
(HM124582.1, HQ703177.1, EU145977.1) from
the China locality were clustered with M. meretrix
(GQ463598.1) and M. lusoria (EU145977.1)
from the China locality, respectively, in Clade 5.
Phylogenetic analysis on three Meretrix from
the Sarawak locality is closely related to the
M. lusoria from the Japan locality. However, the
result contrasts with M. lyrata from BLAST
analysis which inferred a high similarity
sequence with M. lyrata accession sequence. The
application of ML analysis for the phylogenetic
tree was calculated using the substitution rate in
the sample sequence and accession sequence,
which produced different inferences than
BLAST analysis (Guindon & Gascuel 2003).
Furthermore, Meretrix spp. from the Sarawak
locality and M. lusoria from the Japan locality had
a high percentage of Cytosine and Adenine than
that of other Meretrix spp. from different
localities. Meretrix spp. from the Sarawak locality
only had a relationship with other Meretrix spp.
localities at more than 50% of bootstrap scoring,
which is inferred as under Meretrix genus.
Inconsistent cladistic group between M. meretrix
(GQ463598.1) M. lusoria (GQ903339.1), M. casta
(JQ773441.1), and M. petechialis (HM124582.1,
HQ703177.1, EU145977.1) from the present
study indicated that the three species had a close
relationship following Wu et al. (2014) and Chen
et al. (2009). Hence, Chen et al. (2009) suggested
that M. lusoria and M. petechialis as a junior
synonym to M. meretrix.
8. BIOTROPIA Vol. 29 No. 3, 2022
220
Figure 3 Phylogenetic tree of Meretrix accession sequence inferred from the Maximum Likelihood analysis using
Tamura three-parameter model
Note: Only bootstrap score greater than 50% are shown.
The present study on Meretrix spp. from the
Sarawak locality was able to differentiate COI
sequences among M. lyrata, M. meretrix, and
M. lusoria. M. lusoria was closely related to
M. meretrix with strong bootstrap supporting
evidence at 96% scoring. M. lyrata became the
ancestor to M. lusoria and M. meretrix with strong
bootstrap evidence at 100% of the scoring.
Meretrix spp. from the Sarawak locality is closely
related to the M. lusoria of the Japan locality with
100% scoring on bootstrap supporting evidence
to form Clade 1. Meretrix spp. from the Sarawak
locality was closely associated with other
accession sequences for Meretrix spp. at
bootstrap supporting evidence at 50% scoring.
Based on ML phylogenetic analysis, all
M. lyrata with accession sequence KC832317.1,
JN898944.1, and HM124580.1 formed the
cladistic group with strong bootstrap evidence at
99%. All M. lamarckii with accession sequence
GU071281.1, AB059420.1, and HM124579.1
also formed cladistic at 94% of bootstrap
evidence. M. casta (JQ773441.1) formed an
individual clade which indicated this species
distance from other species except for M. lyrata.
Other Meretrix spp. accession sequence, such as
M. meretrix (GQ463598.1) M. lusoria
(GQ903339.1), and M. petechialis (HM124582.1,
HQ703177.1, EU145977.1) formed inconsistent
cladistic groups, while M. meretrix with accession
sequence HM124578.1 and JN043623.1 formed
individual clade apart from other M. meretrix
(GQ463598.1) at 99% evidence of bootstrap
scoring.
Mitochondria DNA is known to have
higher transition mutation rates, particularly
synonymous sites in the nucleotide sequence
that affected the rates of evolution in
organisms (Brown et al. 1982; Caterino et al.
2000; Overton & Rhoads 2004). This fast rate of
evolution is one of the features suitable for
phylogenetic study, particularly in higher taxa.
Moreover, higher taxa less affected by the
recombination (Guo et al. 2006), uniparental
inheritance (Passamonti et al. 2003;
Passamonti & Plazzi 2020), heteroplasmy with
paternal leakage (Bromham et al. 2003; Wolff et
al. 2013; Mastrantonio et al. 2019), and selective
sweeps (Ballard & Rand 2005; James et al. 2016;
Hill 2019). Despite proper application on higher
taxa, this is the contrast when nucleotide
sequences at the species level take into account
those which are more defected. The evolution
rate is influenced by thermal adaptation,
mitochondrial, nuclear interaction, and infection
with Wolbachia spp. (Ballard & Rand 2005).
Hence, Meretrix spp. from the Sarawak locality
possibly has a different evolution rate in
mtDNA, which caused divergence from the
Meretrix spp. from other localities, particularly
from the China regions.
9. Molecular approach establishes relationship among Venus clams (Meretrix spp.) community – Idris et al.
221
The current phylogenetic analysis is difficult
to verify that species Meretrix spp. belong to the
Sarawak locality. Bivalves had high variability in
size and gene group of mtDNA, which vary
extensively between species from a similar genus
(Xu et al. 2012). Meretrix spp. from the Sarawak
locality are separated in terms of geographical
distance. The geographical distance affects the
mtDNA feature as described by Mishmar et al.
(2003) that maternal inheritance can be
restricted by the geographical distance with no
mixing of mtDNA haplogroups from the
different geological region. Therefore, other
environmental conditions in each region
influence the organisms' mutation rate
(Massey & Buckling 2002). Ambiguous
Meretrix spp. identification from the Sarawak
locality might be possibly related to other several
features, such as sample used.
The mtDNA marker feature is the maternal
inheritance which supplies the missing
information in nuclear markers (Okumuú &
Çiftci 2003). Therefore, the female individual's
tissue selection is crucial during the genetic
study to ensure reliable information regarding
the species ancestor. However, female selections
for the genetic research have not been
mentioned in each previous study for the
GenBank accession sequence, causing the
doubtness of the reliability of accession
sequence in the GenBank, leading to the
divergence of Meretrix spp. from the Sarawak
locality compared to the previous species
sequence. Moreover, the accession sequence is
well doubted due to the non-intensive
morphological identification for each species
which only depending on the rough observation.
The present study suggested that appliance on a
single marker is insufficient to support species
identification and species-level phylogenetic
analysis. Therefore, additional variance types of
molecular markers such as allozyme and nuclear
markers are required to create substantial
evidence on species verification to ensure the
intensive morphological study's genetic
approachability. Depending on the genetic
approach, the lack of intensive morphological
evidence would create ambiguous species
naming in taxonomy.
CONCLUSION
The molecular approach application was able
to distinguish three Meretrix spp. from Sarawak
Province, Malaysia. Moreover, M. lyrata is
inferred to as the ancestor of M. meretrix and
M. lusoria from Sarawak. Regardless of ancestor
identification and species distinctions, the COI
gene in the present study was unable to verify
which species Meretrix spp. belonged to the
Sarawak locality. Several disadvantages to the
COI sequence that influence the phylogenetic
analysis involve the consistent accession
sequence from GenBank as the main reference
for the current study. The present study
suggested that additional DNA markers for
species identification and phylogenetic analysis
are recommended in supporting the intensive
morphological identification.
ACKNOWLEDGMENTS
The research team would like to acknowledge
the Ministry of Higher Education Malaysia
F.R.G.S. research grant code, FRGS/1/2018/
WAB13/UPM/02/2, and the Department of
Animal Science and Fishery, Universiti Putra
Malaysia, Bintulu Sarawak Campus, for the
technical support.
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