scholarly journals Konservasi Genetik Ikan Kakap Putih (Lates calcarifer, Bloch, 1790) Melalui Pendekatan DNA Barcoding dan Analisis Filogenetik di Sungai Kumbe Merauke Papua

2021 ◽  
Vol 24 (2) ◽  
pp. 141-150
Author(s):  
Dandi Saleky ◽  
Muhammad Dailami
Keyword(s):  
Fisheries Management ◽  
Dna Sequences ◽  
Economic Value ◽  
Genetic Data ◽  
Swim Bladder ◽  
Molecular Approach ◽  
Lates Calcarifer ◽  
Cytochrome Oxidase I Gene ◽  
Management And Conservation ◽  
I Gene

Genetic data is very important as the basis for fisheries management and conservation related to connectivity between regions and population structure. White snapper Fish is one of the fish that has high economic value which is utilized either by its meat or by its swim bladder. This research was aimed to identify the species of white snapper fish were collected from the Kumbe River, Merauke Regency, Papua using the Cytochrome Oxidase I gene. The results shows that this sample is a species of Lates calcarifer, Bloch, 1790 with 100% similarity. The haplotype of white snapper fish from Merauke has similarities with the haplotype from Australia, Malaysia and China, this indicating that there is gene flow and connectivity among those locations. The phylogenetic tree explains the grouping of species based on genetic distance and the level of DNA Sequences similarities. Molecular approach can be used in the management and conservation of fish with high economic value.

scholarly journals Molecular evidence for the synonymy of three species of Paragonimus, P. Ohirai Miyazaki, 1939, P. iloktsuenensis Chen, 1940 and P. sadoensis Miyazaki et al., 1968

1997 ◽  
Vol 71 (4) ◽  
pp. 305-310 ◽  
Author(s):  
D. Blair ◽  
T. Agatsuma ◽  
T. Watanobe
Keyword(s):  
Dna Sequences ◽  
Single Gene ◽  
Genetic Data ◽  
Ribosomal Gene ◽  
Molecular Evidence ◽  
Nominal Species ◽  
Host Preferences ◽  
Genetic Techniques ◽  
Second Internal Transcribed Spacer ◽  
I Gene

AbstractThe Paragonimus ohirai group, named after P. ohirai Miyazaki, 1939, consists of three nominal species. Paragonimus iloktsuenensis Chen, 1940 and P. sadoensis Miyazaki et al., 1968, the other members of the group, were proposed primarily because of perceived differences in metacercarial morphology and/or host preferences. It has long been recognized that adults of the three were virtually indistinguishable. With the application of genetic techniques, it has become clear that the three forms can exchange genes freely, and that differences in metacercarial morphology constitute a polymorphism probably due to a single gene inherited in Mendelian fashion. Here, additional genetic data (DNA sequences from the second internal transcribed spacer of the nuclear ribosomal gene cluster and from the mitochondrial cytochrome c oxidase subunit I gene) are presented in support of the synonymy.

scholarly journals PHYLOGENETIC DIVERSITY OF SOME SMALL MAMMALS FROM SCIURUDAE FAMILY IN MONGOLIA

2018 ◽  
pp. 53-58
Author(s):  
Bolortuya U ◽  
Bayarmaa G ◽  
Mandakhtsetsen Kh ◽  
Oyuntsetseg D ◽  
Bayarlkhagva D
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Phylogenetic Diversity ◽  
Coi Gene ◽  
Mitochondrial Cytochrome ◽  
Neighbor Joining ◽  
Cytochrome Oxidase I Gene ◽  
Mitochondrial Cytochrome Oxidase ◽  
Insufficient Knowledge ◽  
I Gene

The squirrel family, Sciuridae, is one of the largest and widespread, ecologically common families of mammals. Due to the conspicuousness of this small mammal group with a big population, insufficient knowledge exists about its phylogenetic relationships. In this study, we identified 14 DNA sequences of mitochondrial cytochrome oxidase I gene in 6 species of Sciuridae and these sequences were compared with corresponding published COI gene sequences of the same species in Eurasia and determined their phylogenetic relationships by Neighbor-joining method.

scholarly journals The identification of the species of the ‘Spilogona contractifrons species-group’ and the ‘Spilogona nitidicauda species-group’ (Diptera, Muscidae) based on morphological and molecular analysis

2018 ◽  
Author(s):  
Vera S. Sorokina ◽  
Elena V. Shaikevich
Keyword(s):  
Dna Sequences ◽  
Morphological Characters ◽  
Species Group ◽  
Genetic Distances ◽  
Valid Species ◽  
Separate Species ◽  
Cytochrome Oxidase I Gene ◽  
Male Head ◽  
Morphological Differences ◽  
I Gene

Muscid species of the ‘Spilogona contractifrons species-group’ (Spilogona alticola (Malloch, 1920), S. arctica (Zetterstedt, 1838), S. contractifrons (Zetterstedt, 1838), S. orthosurstyla Xue & Tian, 1988) and of the ‘Spilogona nitidicauda species-group’ (S. nitidicauda (Schnabl, 1911), S. hissarensis Hennig, 1959, S. imitatrix (Malloch, 1921), S. platyfrons Sorokina, 2018) are notoriously difficult to distinguish. In this paper, their morphological features are analysed, images of the male head, frons and abdomen of all the species are given, and the male terminalia are figured. The study of extensive material has shown that all the morphologically recognised species in each of these groups are valid species. An identification key is provided for both groups of species. To confirm the morphological differences, genetic differences in the cytochrome oxidase I gene of flies of the ‘Spilogona contractifrons species-group’ and of the ‘Spilogona nitidicauda species-group’ were analysed. It is shown that members of both groups of species have not only distinguishing morphological characters but also fixed substitutions in the DNA sequences. Since a low interspecific polymorphism is known in the Muscidae Latreille, 1802, the revealed genetic distances confirm the existence of separate species or subspecies in each of the groups studied.

DNA Barcoding and Phylogenetic Analysis Sugarcane (Saccharum officinarum L.) Based on matK ( maturase K) Gene

2020 ◽  
Vol 840 ◽  
pp. 162-170
Author(s):  
Ganies Riza Aristya ◽  
Fauzana Putri ◽  
Rina Sri Kasiamdari ◽  
Arni Musthofa
Keyword(s):  
Phylogenetic Tree ◽  
Molecular Level ◽  
Economic Value ◽  
Saccharum Officinarum ◽  
Saccharum Spontaneum ◽  
Dna Barcodes ◽  
Pcr Method ◽  
Hybrid Cultivar ◽  
I Gene ◽  
Sequencing Process

Sugarcane (Saccharum officinarum L.) is an agricultural commodities with a great extent of diversity and high economic value. In Indonesia, the great extent of diversity of sugarcane is evidenced by a large number of cultivars cultivated. Sugarcane diversities at the molecular level can be seen using DNA barcodes, one of which is the matK. The purpose of the study was to identify and characterize matK and reconstruct the phylogenetic tree to determine the phylogeny of 24 sugarcane cultivars Indonesia. matK was amplified using the PCR method with matK F-5’ATGATTAATTAAGAGTAAGAGGAT-3’ and matK R-5’AATGCAAAAATTCGAAGGGT-3. Results showed that the matK gene was successfully amplified as many as 1531 bp. The sequencing process was done to determine the nucleotide sequence and compared with those of the GenBank database. It showed that the samples used had a similarity of 98.87%-99.44% to that of matK in Saccharum officinarum, Saccharum hybrid cultivar and Saccharum spontaneum. Reconstruction of the phylogenetic tree showed that the samples used were located in the same clade with a zero genetic distance, while all the references from NCBI were also located in the same clade. The analysis of genetic variation indicated that it had no haplotype value.

scholarly journals A New Statistic for Detecting Genetic Differentiation

Genetics ◽  
2000 ◽  
Vol 155 (4) ◽  
pp. 2011-2014 ◽  
Author(s):  
Richard R Hudson
Keyword(s):  
Genetic Differentiation ◽  
Dna Sequences ◽  
Genetic Data ◽  
Island Model ◽  
Wide Range ◽  
Infinite Sites Model ◽  
Parameter Values

Abstract A new statistic for detecting genetic differentiation of subpopulations is described. The statistic can be calculated when genetic data are collected on individuals sampled from two or more localities. It is assumed that haplotypic data are obtained, either in the form of DNA sequences or data on many tightly linked markers. Using a symmetric island model, and assuming an infinite-sites model of mutation, it is found that the new statistic is as powerful or more powerful than previously proposed statistics for a wide range of parameter values.

scholarly journals Harnessing mtDNA variation to resolve ambiguity in ‘Redfish’ sold in Europe

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3746 ◽  
Author(s):  
Peter Shum ◽  
Lauren Moore ◽  
Christophe Pampoulie ◽  
Cristina Di Muri ◽  
Sara Vandamme ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Species Identification ◽  
Fisheries Management ◽  
North Atlantic ◽  
Molecular Approach ◽  
Mtdna Variation ◽  
Control Region Sequences ◽  
Market Product ◽  
Reference Sequences ◽  
Pacific Rockfish

Morphology-based identification of North AtlanticSebasteshas long been controversial and misidentification may produce misleading data, with cascading consequences that negatively affect fisheries management and seafood labelling. North AtlanticSebastescomprises of four species, commonly known as ‘redfish’, but little is known about the number, identity and labelling accuracy of redfish species sold across Europe. We used a molecular approach to identify redfish species from ‘blind’ specimens to evaluate the performance of the Barcode of Life (BOLD) and Genbank databases, as well as carrying out a market product accuracy survey from retailers across Europe. The conventional BOLD approach proved ambiguous, and phylogenetic analysis based on mtDNA control region sequences provided a higher resolution for species identification. By sampling market products from four countries, we found the presence of two species of redfish (S. norvegicusandS. mentella) and one unidentified Pacific rockfish marketed in Europe. Furthermore, public databases revealed the existence of inaccurate reference sequences, likely stemming from species misidentification from previous studies, which currently hinders the efficacy of DNA methods for the identification ofSebastesmarket samples.

scholarly journals Applying a knowledge–action framework for navigating barriers to incorporating telemetry science into fisheries management and conservation: a qualitative study

2018 ◽  
Vol 75 (10) ◽  
pp. 1733-1743 ◽  
Author(s):  
Vivian M. Nguyen ◽  
Nathan Young ◽  
Steven J. Cooke
Keyword(s):  
Fisheries Management ◽  
Organizational Support ◽  
Management Practices ◽  
Relationship Building ◽  
Perceived Barriers ◽  
Aquatic Resources ◽  
Applied Ecology ◽  
Fundamental Knowledge ◽  
Fish Telemetry ◽  
Management And Conservation

Telemetry studies have produced fundamental knowledge on animal biology and ecology that has the potential to improve management of aquatic resources such as fisheries. However, the use and integration of telemetry-derived knowledge into practice remain tenuous, so we surveyed 212 fish telemetry experts to understand existing barriers for incorporating telemetry-derived knowledge into fisheries management practices. We apply a sociological knowledge–action framework to structure the findings, which revealed four primary challenges to integrating telemetry findings into management: (1) the perceived uncertainties and unclear relevance of telemetry findings; (2) the underlying motivations and constrained rationalities of actors that can lead to inaction or suboptimal decisions; (3) the constraints of institutions, governance structures, and lack of organizational support, and (4) time and mismatches in scale, culture, and world views. On a more positive note, the relational dimension (collaboration, trust, and relationship building) appears to be important for overcoming and avoiding barriers. We further provide recommendations to navigate these perceived barriers and argue that these lessons also apply to other fields of applied ecology, conservation, and resource management.

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