scholarly journals Extremely low genetic variability within and among locations of the greenfish holothurianStichopus chloronotusBrandt, 1835 in Okinawa, Japan

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2410 ◽  
Author(s):  
Taha Soliman ◽  
Okuto Takama ◽  
Iria Fernandez-Silva ◽  
James D. Reimer
Keyword(s):  
Sea Cucumber ◽  
Nucleotide Diversity ◽  
East Coast ◽  
Histone H3 ◽  
Haplotype Diversity ◽  
Conservation Policies ◽  
16S Ribosomal Dna ◽  
Southern Japan ◽  
Stichopus Chloronotus ◽  
Management And Conservation

The greenfish sea cucumberStichopus chloronotusis an economically and ecologically important sea cucumber species throughout its range. This species is widely distributed, inhabiting coral reefs of the Indo-Pacific Ocean. Our study evaluated population genetic structure and levels of genetic diversity in southern Japan. A total of 180 individuals were collected from eight locations from Okinawa and Okinoerabu Islands and sequenced using mitochondrial 16S ribosomal DNA (16S) and nuclear histone H3 (H3) gene. Only three 16S haplotypes were detected (518 bp) with haplotype diversity ranging from 0 to 0.56 and nucleotide diversity from 0 to 0.1%. H3 showed no variation among the studied locations. It is plausible that such results could be due to a shift to asexual reproduction.Additionally, the presence of the species on the east coast of Okinawa could only be detected in one location and all individuals consisted of a single haplotype. Genetic differences between the east and west coasts of Okinawa have been noticed in other coral reef organisms, and attributed to either ecological or biogeographical historical differences between the coasts due to differing levels of isolation during Pleistocene ice ages. Results from the present study should inform management and conservation policies ofS. chloronotusin southern Japan.

scholarly journals Patterns of nucleotide diversity for different domains of centromeric histone H3 (CENH3) gene in Secale L.

2019 ◽  
Vol 23 (2) ◽  
pp. 135-139
Author(s):  
S. S. Gatzkaya ◽  
E. V. Evtushenko
Keyword(s):  
Nucleotide Diversity ◽  
Histone H3 ◽  
Haplotype Diversity ◽  
Nucleotide Polymorphisms ◽  
Mean Values ◽  
Geographic Ranges ◽  
Histone Fold ◽  
Histone Fold Domain ◽  
Commercial Breeding ◽  
The Mean

Rye (Secale) is among staple cereals along with other members of the Triticeae tribe: wheat and barley. The genus Secale includes perennial and annual, cross-pollinating and self-pollinating species, and they can be donors of valuable genes in wheat and rye breeding programs. Studies of the structure of the gene for centromeric histone H3 (CENH3), essential for centromere functions, are relevant to the breeding of agronomically important crops. We have investigated the nucleotide diversity of sequences of two variants of the rye CENH3 gene inside the N-terminal tail (NTT) and the conservative HFD (histone fold domain) domain in the genus Secale. The mean values of nucleotide diversity in the NTT and HFD of wild cross- and self-pollinating taxa are close in αCENH3: πtot = 0.0176–0.0090 and 0.0136–0. 0052, respectively. In the case of βCENH3, the mean values for NTT (πtot = 0.0168–0.0062) are lower than for HFD (πtot = 0.0259–0.084). The estimates of nucleotide and haplotype diversity per site for the CENH3 domains are considerably lower in taxa with narrow geographic ranges: S. cereale subsp. dighoricum and S. strictum subsp. kuprijanovii. Commercial breeding reduces the nucleotide sequence variability in αCENH3 and βCENH3. Cultivated rye varieties have π values within 0.0122–0.0014. The nucleotide and haplotype diversity values in αCENH3 and βCENH3 are close in S. sylvestre, which is believed to be the oldest rye species. The results of this study prove that the frequency of single nucleotide polymorphisms and nucleotide diversity of sequences in genes for CENH3 in Secale species are influenced by numerous factors, including reproduction habits, the geographic isolation of taxa, breeding, and the evolutionary age of species.

scholarly journals DNA barcoding for identification of fish species from freshwater in Enugu and Anambra States of Nigeria

2020 ◽  
Vol 12 (4) ◽  
pp. 643-658
Author(s):  
George N. Ude ◽  
David O. Igwe ◽  
Chrysten Brown ◽  
Myron Jackson ◽  
Alusine Bangura ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Fish Species ◽  
Phylogenetic Diversity ◽  
Nucleotide Diversity ◽  
Fishery Management ◽  
Haplotype Diversity ◽  
Test Statistic ◽  
Diversity Assessment ◽  
Management And Conservation ◽  
Mitochondrial Cytochrome Oxidase

Abstract Within Enugu and Anambra States, Nigeria, identification of fishes has been based on morphological traits and do not account for existing biodiversity. For DNA barcoding, assessment of biodiversity, conservation and fishery management, 44 fish sampled from Enugu and Anambra States were isolated, amplified and sequenced with mitochondrial cytochrome oxidase subunit I (COI). Twenty groups clustering at 100% bootstrap value including monophyletic ones were identified. The phylogenetic diversity (PD) ranged from 0.0397 (Synodontis obesus) to 0.2147 (Parachanna obscura). The highest percentage of genetic distance based on Kimura 2-parameter was 37.00 ± 0.0400. Intergeneric distances ranged from 15.8000 to 37.0000%. Congeneric distances were 6.9000 ± 0.0140–28.1000 ± 0.0380, with Synodontis as the existing synonymous genus. Confamilial distances in percentage were 16.0000 ± 0.0140 and 25.7000 ± 0.0300. Forty-two haplotypes and haplotype diversity of 0.9990 ± 0.0003 were detected. Nucleotide diversity was 0.7372, while Fu and Li’s D* test statistic was 2.1743 (P < 0.02). Tajima’s D was 0.2424 (P > 0.10) and nucleotide frequencies were C (17.70%), T (29.40%), A (24.82%), G (18.04%) and A + T (54.22%). Transitional mutations were more than transversions. Twenty species (99–100%) were identified with the e-value, maximum coverage and bit-score of 1e−43, 99–100 and 185–1194, respectively. Seventeen genera and 12 families were found and Clariidae (n = 14) was the most dominant among other families. The fish species resolution, diversity assessment and phylogenetic relationships were successfully obtained with the COI marker. Clariidae had the highest number of genera and families. Phylogenetic diversity analysis identified Parachanna obscura as the most evolutionarily divergent one. This study will contribute to fishery management, and conservation of freshwater fishes in Enugu and Anambra States, Nigeria.

scholarly journals Objective determination of the sea age of Atlantic salmon from the sizes and dates of capture of individual fish

2010 ◽  
Vol 68 (1) ◽  
pp. 130-143 ◽  
Author(s):  
Philip J. Bacon ◽  
William S. C. Gurney ◽  
Eddie McKenzie ◽  
Bryce Whyte ◽  
Ronald Campbell ◽  
...  
Keyword(s):  
Atlantic Salmon ◽  
Fishery Management ◽  
East Coast ◽  
Probability Distributions ◽  
Age Classes ◽  
Individual Fish ◽  
Bivariate Probability ◽  
Management And Conservation ◽  
Objective Determination

Abstract Bacon, P. J., Gurney, W. S. C., McKenzie, E., Whyte, B., Campbell, R., Laughton, R., Smith, G., and MacLean, J. 2011. Objective determination of the sea age of Atlantic salmon from the sizes and dates of capture of individual fish. – ICES Journal of Marine Science, 68: 130–143. The sea ages of Atlantic salmon indicate crucial differences between oceanic feeding zones that have important implications for conservation and management. Historical fishery-catch records go back more than 100 years, but the reliability with which they discriminate between sea-age classes is uncertain. Research data from some 188 000 scale-aged Scottish salmon that included size (length, weight) and seasonal date of capture on return to the coast were investigated to devise a means of assigning sea age to individual fish objectively. Two simple bivariate probability distributions are described that discriminate between 1SW and 2SW fish with 97% reliability, and between 2SW and 3SW fish with 70% confidence. The same two probability distributions achieve this accuracy across five major east coast Scottish rivers and five decades. They also achieve the same exactitude for a smaller recent dataset from the Scottish west coast, from the River Tweed a century ago (1894/1895), and for salmon caught by rod near the estuary. More surprisingly, they also achieve the same success for rod-caught salmon taken at beats remote from the estuary and including capture dates when some fish could have been in the river for a few months. The implications of these findings for fishery management and conservation are discussed.

scholarly journals Genetic diversity analysis and phylogenetic reconstruction of groupers Epinephelus spp. from Madura Island, Indonesia based on partial sequence of CO1 gene

2021 ◽  
Vol 22 (10) ◽  
Author(s):  
ABDUL BASITH ◽  
Abinawanto Abinawanto ◽  
ENI KUSRINI ◽  
YASMAN YASMAN
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Tree ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Phylogenetic Reconstruction ◽  
Partial Sequence ◽  
Diversity Analysis ◽  
Epinephelus Coioides ◽  
Substitution Model ◽  
Genetic Diversity Analysis

Abstract. Basith A, Abinawanto, Kusrini E, Yasman. 2021. Genetic diversity analysis and phylogenetic reconstruction of groupers Epinephelus spp. from Madura Island, Indonesia based on partial sequence of CO1 gene. Biodiversitas 22: 4282-4290. Groupers populations in Indonesia, particularly from Madura Island, East Java are indicated to be over-fished, thereby requiring data collection of more accurate genetic resources as an important step for grouper conservation. A total of 14 samples of the Epinepheplus groupers were obtained from the fish landing port on Madura Island. The 617 bp CO1 gene sequence was utilized for genetic diversity analysis and phylogenetic tree reconstruction. Genetic diversity is based on the value of haplotype diversity (Hd) and nucleotide diversity (?). Reconstruction of the phylogenetic tree includes neighbor-joining (NJ) implementing K2P substitution model, while maximum likelihood (ML) is conducted by implementing HKY+G+I substitution model, both of which were evaluated by employing a bootstrap of 1000 replications. Analysis of genetic distance between species indicated that the farthest distance between E. heniochus and E. fasciatus was 0.189, while the closest distance between E. erythrurus and E. ongus was 0.099. Intrapopulation genetic diversity indicated a high value with details of Hd=0.978 and ?=0.12107. Furthermore, NJ and ML phylogenetic tree demonstrated similar topology in the observed Epinephelus spp. obtained from Madura Island grouped into 7 clades, that is Epinephelus coioides, E. bleekeri, E. areolatus, E. erythrurus, E. heniochus, E. fasciatus, and E. ongus.

scholarly journals Feeding ground indications are based on species, seagrass density and existence of Dugong dugon in Hiri Island Sea, North Maluku, Indonesia

2021 ◽  
Vol 890 (1) ◽  
pp. 012058
Author(s):  
N Akbar ◽  
I Marus ◽  
R Ridwan ◽  
A Baksir ◽  
R E Paembonan ◽  
...  
Keyword(s):  
Species Conservation ◽  
Species Density ◽  
Survey Method ◽  
Conservation Policies ◽  
Potential Habitat ◽  
Foraging Area ◽  
Seagrass Ecosystem ◽  
Seagrass Ecosystems ◽  
Halodule Uninervis ◽  
Management And Conservation

Abstract Seagrass ecosystems are located between mangrove ecosystems and coral reefs. Seagrass ecosystems are habitats and foraging area for many marine organisms. Eco-biological cycles in seagrass ecosystems are important for maintaining populations of many organisms. Seagrass at Hiri Island is distributed horizontally along the coast. This island is also a location where Dugong dugon is found North Maluku. Dugong dugon is a vurneable species that has been included in the IUCN and Appendix I Cites. This study aimed to identify species, density of seagrass and existence of Dugong dugong. The survey method used quadratic transect method to collect seagrass data. The Results found 6 species of seagrass at Hiri Island. Five species of those seagrass (Cymodocea serrulata, Cymodecea rotundata, Halodule uninervis, Halodule pinifolia, Halophila spinulosa) are known as food of Dugong dugon. The highest species density was shown by Halodule uninervis. The presence of Dugong dugon and its feeding trail was found during field survey. Information on seagrass species and Dugong dugon sightings location can be used for endangered species conservation policies. Management and conservation efforts need to be done to maintain seagrass ecosystem and Dugong dugon potential habitat at Hiri Island.

scholarly journals Genetic divergence in mitochondrial DNA of Anopheles nuneztovari (Diptera: Culicidae) from Brazil and Colombia

2000 ◽  
Vol 23 (1) ◽  
pp. 71-78 ◽  
Author(s):  
Vera Margarete Scarpassa ◽  
Silvia Geurgas ◽  
Ana Maria L. Azeredo-Espin ◽  
Wanderli Pedro Tadei
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Divergence ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Sequence Divergence ◽  
Brazilian Amazon ◽  
Restriction Endonucleases ◽  
Separate Species ◽  
Geographic Populations

In the present study, we have examined the variability in Anopheles nuneztovari mitochondrial DNA of three populations from the Brazilian Amazon and one from western Colombia (Sitronela), using four restriction endonucleases (BclI, ClaI, HindIII, SstI). The haplotype diversity (h) was slightly elevated in all populations (0.5000 to 0.6765), whereas the nucleotide diversity (pi) was lower in the Sitronela population (0.0029) and higher in populations from the Brazilian Amazon (0.0056 to 0.0098). The degree of sequence divergence (delta) estimated within the Brazilian Amazon and that in Sitronela (0.0329 to 0.0371) suggests that these geographic populations of A. nuneztovari may eventually constitute separate species. The low sequence divergence values among the three Brazilian Amazon populations (0.0012 to 0.0031) indicate that these populations are genetically similar. These results are consistent with those recently reported for allozymes of these same populations.

Population genetics and phylogenetic analysis of the vrs1 nucleotide sequence in wild and cultivated barley

Genome ◽  
2014 ◽  
Vol 57 (4) ◽  
pp. 239-244 ◽  
Author(s):  
Xifeng Ren ◽  
Yonggang Wang ◽  
Songxian Yan ◽  
Dongfa Sun ◽  
Genlou Sun
Keyword(s):  
Population Genetics ◽  
Phylogenetic Analysis ◽  
Genetic Variation ◽  
Hordeum Vulgare ◽  
Nucleotide Diversity ◽  
Wild Barley ◽  
Haplotype Diversity ◽  
Lateral Spikelet ◽  
Cultivated Barley ◽  
Barley Population

Spike morphology is a key characteristic in the study of barley genetics, breeding, and domestication. Variation at the six-rowed spike 1 (vrs1) locus is sufficient to control the development and fertility of the lateral spikelet of barley. To study the genetic variation of vrs1 in wild barley (Hordeum vulgare subsp. spontaneum) and cultivated barley (Hordeum vulgare subsp. vulgare), nucleotide sequences of vrs1 were examined in 84 wild barleys (including 10 six-rowed) and 20 cultivated barleys (including 10 six-rowed) from four populations. The length of the vrs1 sequence amplified was 1536 bp. A total of 40 haplotypes were identified in the four populations. The highest nucleotide diversity, haplotype diversity, and per-site nucleotide diversity were observed in the Southwest Asian wild barley population. The nucleotide diversity, number of haplotypes, haplotype diversity, and per-site nucleotide diversity in two-rowed barley were higher than those in six-rowed barley. The phylogenetic analysis of the vrs1 sequences partially separated the six-rowed and the two-rowed barley. The six-rowed barleys were divided into four groups.

A minimalist macroparasite diversity in the round goby of the Upper Rhine reduced to an exotic acanthocephalan lineage

Parasitology ◽  
2017 ◽  
Vol 145 (8) ◽  
pp. 1020-1026 ◽  
Author(s):  
Gwendoline M. David ◽  
Cybill Staentzel ◽  
Olivier Schlumberger ◽  
Marie-Jeanne Perrot-Minnot ◽  
Jean-Nicolas Beisel ◽  
...  
Keyword(s):  
Western Europe ◽  
Nucleotide Diversity ◽  
Round Goby ◽  
Haplotype Diversity ◽  
Neogobius Melanostomus ◽  
Molecular Barcoding ◽  
Wide Range ◽  
Using Data ◽  
Upper Rhine ◽  
Invasion Corridor

AbstractThe round goby, Neogobius melanostomus, is a Ponto-Caspian fish considered as an invasive species in a wide range of aquatic ecosystems. To understand the role that parasites may play in its successful invasion across Western Europe, we investigated the parasitic diversity of the round goby along its invasion corridor, from the Danube to the Upper Rhine rivers, using data from literature and a molecular barcoding approach, respectively. Among 1666 parasites extracted from 179 gobies of the Upper Rhine, all of the 248 parasites barcoded on the c oxidase subunit I gene were identified as Pomphorhynchus laevis. This lack of macroparasite diversity was interpreted as a loss of parasites along its invasion corridor without spillback compensation. The genetic diversity of P. laevis was represented by 33 haplotypes corresponding to a haplotype diversity of 0·65 ± 0·032, but a weak nucleotide diversity of 0·0018 ± 0·00015. Eight of these haplotypes were found in 88·4% of the 248 parasites. These haplotypes belong to a single lineage so far restricted to the Danube, Vistula and Volga rivers (Eastern Europe). This result underlines the exotic status of this Ponto-Caspian lineage in the Upper Rhine, putatively disseminated by the round goby along its invasion corridor.

scholarly journals Low Discounting Behavior among Small-Scale Fishers in Fiji and Sabah, Malaysia

2011 ◽  
Vol 3 (6) ◽  
pp. 897-913 ◽  
Author(s):  
Louise S. L. Teh ◽  
Lydia C. L. Teh ◽  
U. Rashid Sumaila
Keyword(s):  
Experimental Approach ◽  
Small Scale ◽  
Economic Factors ◽  
Discount Rates ◽  
Cultural Economic ◽  
Conservation Policies ◽  
Management Interventions ◽  
Tropical Reef ◽  
Management And Conservation ◽  
Socio Economic Factors

Understanding the socio-economic factors that are associated with fishers’ willingness to delay gratification may be useful for designing appropriate fisheries management and conservation policies. We aim to identify the predictors of low discounting behaviour among fishers, which is analogous to having a longer-term outlook. We base our empirical study on two small-scale tropical reef fisheries in Sabah, Malaysia, and Fiji. We use an experimental approach to identify fishers with low discount rates, and then use a logistic regression model to identify predictors of low discount rates. We find that 42% of the respondents have low discount rates, and that site and village level variables are significant predictors of low discount rates. Within Sabah and Fiji, boat ownership and relative catch differentiate low discounting from non-low discounting fishers, but these variables have contradictory effects in Sabah and Fiji. Overall, our results imply that a substantial proportion of reef fishers may be willing to engage in conservation initiatives; however, local socio-cultural, economic, and ecological conditions have to be considered first during the process of designing management interventions.

Sign in / Sign up

Export Citation Format

Share Document