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Lau, Jen-Shi; Ransangan, Julian; Rodrigues, Kenneth Francis

doi:10.4194/1303-2712-v18_1_12

Cited by 6 publications

(6 citation statements)

References 31 publications

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“…Geological evidence suggests that the river systems of Sarawak were historically interconnected with most major river systems of Peninsular Malaysia via the Sunda River during Pleistocene glaciation (about 10000 years ago), thus allowing gene flow among these drainages (Kamarudin and Esa 2009). Gene flow from populations in the Straits of Malacca to those in Sarawak has been reported in several studies including Ryan and Esa (2006), Azhar and Hassan (2015), Samani et al (2016) and Lau et al (2018). Meanwhile, populations of SN-KN, which are separated by the South China Sea, showed high genetic connectivity (pairwise F ST = 0.0702).…”

Section: Genetic Structurementioning

confidence: 89%

Genetic diversity and population structure of Terapon jarbua (Forskål, 1775) (Teleostei, Terapontidae) in Malaysian waters

Chanthran

Lim

et al. 2020

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A background study is important for the conservation and stock management of a species. Terapon jarbua is a coastal Indo-Pacific species, sourced for human consumption. This study examined 134 samples from the central west and east coasts of Peninsular (West) Malaysia and East Malaysia. A 1446-bp concatenated dataset of mtDNA COI and Cyt b sequences was used in this study and 83 haplotypes were identified, of which 79 are unique haplotypes and four are shared haplotypes. Populations of T. jarbua in Malaysia are genetically heterogenous as shown by the high level of haplotype diversity ranging from 0.9167–0.9952, low nucleotide diversity ranging from 0.0288–0.3434, and high FST values (within population genetic variation). Population genetic structuring is not distinct as shown by the shared haplotypes between geographic populations and mixtures of haplotypes from different populations within the same genetic cluster. The gene flow patterns and population structuring observed among these regions are likely attributed to geographical distance, past historical events, allopatric speciation, dispersal ability and water currents. For instance, the mixture of haplotypes revealed an extraordinary migration ability of T. jarbua (>1200 km) via ancient river connectivity. The negative overall value of the neutrality test and a non-significant mismatch distribution are consistent with demographic expansion(s) in the past. The median-joining network concurred with the maximum likelihood haplotype tree with three major clades resolved. The scarcity of information on this species is an obstacle for future management and conservation purposes. Hence, this study aims to contribute information on the population structure, genetic diversity, and historical demography of T. jarbua in Malaysia.

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Section: Genetic Structurementioning

confidence: 89%

Genetic diversity and population structure of Terapon jarbua (Forskål, 1775) (Teleostei, Terapontidae) in Malaysian waters

Chanthran

Lim

et al. 2020

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“…However, in the ATPase 6/8 analysis, H17 was clustered with an outgroup species, and one probable explanation is that H17 underwent a distinct mutational history. Nevertheless, the mitochondrial D-loop region generated more mutations and genetic variation than the ATPase region as reported in earlier studies (Mandal et al, 2012;Lau et al, 2018). Mutation rates in the D-loop and ATPase regions are different in different river populations; therefore, it is logical to analyze genetic diversity using multiple mitochondrial sequences.…”

Section: Discussionmentioning

confidence: 91%

“…This also indicates that other river populations might have experienced a population bottleneck followed by a rapid population growth (Bowen et al, 2001;Meng et al, 2015). The mismatch distribution and neutral test analysis helps us to investigate demographic history (Guo et al, 2014;Lau et al, 2018). Tajima's D value of low significance indicates that a population is deviating from the neutral expectations, and negative F s values signify deviation from neutrality, which may be due to the effect of population expansion and/or selection.…”

Section: Discussionmentioning

confidence: 99%

Genetic characterization of minor carp (Labeo gonius) from Indian rivers revealed through mitochondrial ATPase 6/8 and D-loop region analysis: implications for conservation and management

Roy,

Behera,

V. L.

et al. 2024

Front. Mar. Sci.

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India is the habitat of many freshwater fish species that make a significant contribution to endemism. However, the native species population is declining at a very fast rate due to pollution, habitat loss or degradation, new species introduction, hydrologic alterations, and overfishing. The minor carp, Labeo gonius, is one of the important fish species in the Indian river systems and holds enormous potential in culture fisheries. Therefore, the precise status of population structure is a prerequisite for the management of the species. In the present study, we assessed the potential of mtDNA ATPase 6/8 and D-loop regions as markers to determine the genetic diversity and phylogeography of L. gonius from Indian rivers. We have selected five major Indian rivers for investigation which could represent geographically distant populations of the studied fish. A total of 210 ATPase 6/8 sequences (842 bp) and 203 D-loop region sequences (683 bp) of L. gonius from the five major Indian rivers were submitted to NCBI. Results revealed that ATPase 6/8 has 17 haplotypes and 70 polymorphic sites with an overall haplotype diversity of 0.560 ± 0.036 and nucleotide diversity of 0.00347 ± 0.00. Furthermore, D-loop analysis revealed 58 haplotypes, 67 polymorphic sites, 0.954 ± 0.006 overall haplotype diversity, and 0.01914 ± 0.00 nucleotide diversity. The hierarchical AMOVA analysis indicated that a high proportion of the genetic variation (76.46% and 70.22% for the D-loop and ATPase 6/8 regions, respectively) was attributed to among-population variation under gene pool-1 (considering all the stocks from Ganga, Brahmaputra, Teesta, Narmada, and Mahanadi as a single pool). Furthermore, in gene pool-2, samples were divided into two groups: group 1 (Himalayan rivers)—Ganga, Brahmaputra, and Teesta; and group 2 (peninsular rivers)—Narmada and Mahanadi. Genetic variations in the D-loop and ATPase 6/8 regions were found among populations within groups at 70.65% and 53.48%, respectively. Haplotype network analysis revealed that there were significant differences in distributions and frequencies. The observed unique haplotypes might be useful for differentiating the stocks. In brief, the present study suggested that the D-loop and ATPase 6/8 regions are potential markers and represent a significant contribution to the genetic characterization of the minor carp L. gonius from major Indian rivers. Moreover, the L. gonius population along the east coast especially in the Himalayan rivers (Ganga, Brahmaputra, and Teesta river basin) is found to be genetically more diverse. The results would provide a scientific basis for the assessment of fisheries resources and management of this important species.

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“…This study showed that the genetic diversity of the five populations was high which indicated that the germplasm resources were in a good level. Such is the case in other shellfish populations, such as Donax vittatus (Fernandez-Perez, et al, 2017), Mytilus coruscus (Liu et al, 2019), and Perna viridis (Lau et al, 2018). The genetic diversity level is correlated with the effective population size; that is, the larger the effective population size, the greater the genetic contribution of the parents and the greater the selective response will be.…”

Section: Population Haplotype Distribution and Genetic Diversitymentioning

confidence: 94%

Population Genetic Analysis of Rainbow Clam Moerella iridescens by Using rDNA

Li¹,

Zhang²,

Lu³

et al. 2020

Israeli Journal of Aquaculture - Bamidgeh

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To assess the genetic background of the germplasm resource of rainbow clam Moerella iridescens along China coasts, population genetic structure and genetic diversity of rainbow clam from five geographical populations in the Yellow Sea and the East China Sea (Lianyungang, Chongming, Cixi, Zhoushan, and Ningde) were analyzed based on rDNA (ITS1-5.8S-ITS2) sequences. Forty-Seven rDNA haplotypes were identified among 109 rainbow clam individuals of the five populations. Gen4 and Gen21 were the dominant haplotypes, accounting for 49.5% of rDNA whole gene sequences, and shared by the five populations. Six to eight exclusive haplotypes were found in each population. The average haplotype diversity index (HD) of the five populations was 0.8733. The genetic distance among populations ranged from 0.002 to 0.004, and haplotypes from the same population were not clustered in a single clade. Molecular variance analysis (AMOVA) demonstrated that the main genetic differentiation mainly occurred within population, and the genetic differentiation coefficient (FST) among five populations was between-0.02836 and 0.01896, which meant that no genetic differentiation among populations occurred. Overall, the five geographical populations showed a high genetic diversity, but no evident genetic structure or genetic differentiation. Qinhuangdao (Hebei), Yellow River Delta (Shandong), Lianyungang (Jiangsu), Chongming Island (Shanghai), and Haimen (Guangdong), and etc. The different climate of each sea area and the diversity of ecological environment may lead to genetic differentiation among the geographical populations of M. iridescens, which is closely related to its adaptability, reproductive capacity and evolutionary potential (Sokal et al., 1989). For the recent more than a decade, over-exploitation and shrimp farming in the inning beach have led to a fragmented natural ecological environment of M. iridescens in habitat, degradation of germplasm resources, and severely declining resources quantity of M. iridescens (Li et al., 2009; You and Wang, 1990a, 1991b). So it is necessary to effectively assess genetic resources so as to take rational conservation strategies. The richer the genetic diversity of a species, the stronger its adaptability to environmental changes, and it is easy to expand its distribution range (Su et al., 2007). Therefore, assessing population genetic diversity is of great scientific and practical significance in protecting and managing the germplasm resources of M. iridescens. A few of reports are available regarding the germplasm resources and molecular biology of M. iridescens. In the analysis of geographical population morphological variation and micro chemical composition in the population, the heavy metal pollution characteristics of M. iridescens in Hangzhou Bay and Haizhou Bay were quite different, which also indicated that the habitat of M. iridescens was greatly affected by human beings (Li et al., 2010a; Dong et al., 2012). ISSR primers for germplasm evaluation of M. iridescens was established, the geneti...

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Untitled

Cited by 6 publications

References 31 publications

Genetic diversity and population structure of Terapon jarbua (Forskål, 1775) (Teleostei, Terapontidae) in Malaysian waters

Genetic diversity and population structure of Terapon jarbua (Forskål, 1775) (Teleostei, Terapontidae) in Malaysian waters

Genetic characterization of minor carp (Labeo gonius) from Indian rivers revealed through mitochondrial ATPase 6/8 and D-loop region analysis: implications for conservation and management

Population Genetic Analysis of Rainbow Clam Moerella iridescens by Using rDNA

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