scholarly journals Genetic Diversity in the mtDNA control region and population structure of Chrysichthys nigrodigitatus from selected Nigerian rivers: Implications for conservation and aquaculture

2016 ◽  
Vol 24 (2) ◽  
pp. 85-97 ◽  
Author(s):  
Sylvanus A. Nwafili ◽  
Tian-Xiang Gao
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Control Region ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Mitochondrial Control Region ◽  
Recent Population Expansion ◽  
Base Pair Fragment ◽  
Population Structures ◽  
High Level

Abstract The genetic diversity and population structure of Chrysichthys nigrodigitatus were evaluated using a 443 base pair fragment of the mitochondrial control region. Among the eight populations collected comprising 129 individuals, a total of 89 polymorphic sites defined 57 distinct haplotypes. The mean haplotype diversity and nucleotide diversity of the eight populations were 0.966±0.006 and 0.0359±0.004, respectively. Analysis of molecular variance showed significant genetic differentiation among the eight populations (FST =0.34; P < 0.01). The present results revealed that C. nigrodigitatus populations had a high level of genetic diversity and distinct population structures. We report the existence of two monophyletic matrilineal lineages with mean genetic distance of 10.5% between them. Non-significant negative Tajima’s D and Fu’s Fs for more than half the populations suggests that the wild populations of C. nigrodigitatus underwent a recent population expansion, although a weak one since the late Pleistocene.

scholarly journals Mitochondrial DNA control region diversity in Common Terns Sterna hirundo from Slovenia and Croatia

Acrocephalus ◽  
2019 ◽  
Vol 40 (180-181) ◽  
pp. 69-78
Author(s):  
Ida Svetličić ◽  
Jelena Kralj ◽  
Miloš Martinović ◽  
Davorin Tome ◽  
Tilen Basle ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Control Region ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Mitochondrial Control Region ◽  
Diversity Indices ◽  
Common Tern ◽  
Sterna Hirundo ◽  
Mitochondrial Dna Control Region ◽  
High Level

Abstract63 Common Tern Sterna hirundo samples from Croatia and Slovenia were analysed with respect to their genetic diversity and differentiation. Samples originated from two freshwater populations (areas of the rivers Sava and Drava) and one coastal population (Sečovlje Salina). The molecular marker of choice was 709 bp long fragment of the mitochondrial control region, the fastest-evolving part of the mitochondrial genome. 21 haplotypes with 12 polymorphic sites were identified. Overall haplotype diversity was substantial and estimated at 0.8599, while the overall nucleotide diversity was low and estimated at 0.0025. Diversity indices were highest for the Drava population, followed by the Sava and the lowest for the Sečovlje population. Overall genetic structure was significantly low (Fst=0.0377) and attributed to the differences in haplotype frequencies between the populations. The high level of genetic diversity found in continental populations illustrates the importance of their habitats as reservoirs of genetic diversity and calls for their further protection and management.

scholarly journals Low Genetic Diversity in Turkish Populations of Wels Catfish Silurus glanis L., 1758 (Siluridae, Pisces) Revealed by Mitochondrial Control Region Sequences

2020 ◽  
Vol 20 (10) ◽  
pp. 767-776
Author(s):  
Yusuf Bektas ◽  
Ismail Aksu ◽  
Gokhan Kalayci ◽  
Davut Turan
Keyword(s):  
Genetic Diversity ◽  
Control Region ◽  
Mismatch Distribution ◽  
Phylogenetic Trees ◽  
Goodness Of Fit ◽  
Haplotype Diversity ◽  
Mitochondrial Control Region ◽  
Haplotype Network ◽  
Silurus Glanis ◽  
Low Genetic Diversity

This study aimed to investigate the genetic diversity and population structure of Wels catfish Silurus glanis L. 1758 in Turkey using squences of the mitochondrial DNA control region The 887-bp fragment of D-loop was aligned for 112 S. glanis individuals from ten wild populations in Turkey, defined by 29 polymorphic sites comprising 16 haplotypes. The low haplotype diversity and nucleotide diversity within each population ranged from 0.000 to 0.378 and from 0.0000 to 0.0045, respectively. Analysis of molecular variance showed significant genetic differentiation among ten populations (FST =0.940; P<0.01). AMOVA revealed that the most of genetic variation was found between Thrace and Anatolia clades (74,07 %). The phylogenetic trees and haplotype network topologies were consistent with the results of AMOVA analysis. The non-significant negative Tajima's D (-0.875 P<0.05) and Fu's Fs (-0.381, P<0.02) values and mismatch distribution for S. glanis populations indicated no evidence for changes in population size. Furthermore, goodness-of-fit of the observed versus the theoretical mismatch distribution tested the sum of squared deviation (SSD; 0.00308, P>0.05), Harpending’s raggedness index (Hri; 0,300, P>0.05) and Ramos-Onsins & Rozas (R2; 0,0771, P>0.05), supporting population neutrality.

scholarly journals Genetic diversity, population structure and historical demography of the two-spined yellowtail stargazer (Uranoscopus cognatus)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Nur Ilham Syahadah Mohd Yusoff ◽  
Tun Nurul Aimi Mat Jaafar ◽  
Veera Vilasri ◽  
Siti Azizah Mohd Nor ◽  
Ying Giat Seah ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Resource Management ◽  
Nuclear Dna ◽  
Incomplete Lineage Sorting ◽  
Dna Recombination ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Management Program ◽  
Sampling Station

AbstractBenthic species, though ecologically important, are vulnerable to genetic loss and population size reduction due to impacts from fishing trawls. An assessment of genetic diversity and population structure is therefore needed to assist in a resource management program. To address this issue, the two-spined yellowtail stargazer (Uranoscopus cognatus) was collected within selected locations in the Indo-West Pacific (IWP). The partial mitochondrial DNA cytochrome c oxidase subunit 1 and the nuclear DNA recombination activating gene 1 were sequenced. Genetic diversity analyses revealed that the populations were moderately to highly diversified (haplotype diversity, H = 0.490–0.900, nucleotide diversity, π = 0.0010–0.0034) except sampling station (ST) 1 and 14. The low diversity level, however was apparent only in the matrilineal marker (H = 0.118–0.216; π = 0.0004–0.0008), possibly due to stochastic factors or anthropogenic stressors. Population structure analyses revealed a retention of ancestral polymorphism that was likely due to incomplete lineage sorting in U. cognatus, and prolonged vicariance by the Indo-Pacific Barrier has partitioned them into separate stock units. Population segregation was also shown by the phenotypic divergence in allopatric populations, regarding the premaxillary protrusion, which is possibly associated with the mechanism for upper jaw movement in biomechanical feeding approaches. The moderate genetic diversity estimated for each region, in addition to past population expansion events, indicated that U. cognatus within the IWP was still healthy and abundant (except in ST1 and 14), and two stock units were identified to be subjected to a specific resource management program.

scholarly journals Genetic diversity and population structure of the human malaria parasite Plasmodium falciparum surface protein Pfs47 in isolates from the lowlands in Western Kenya

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0260434
Author(s):  
Shirley A. Onyango ◽  
Kevin O. Ochwedo ◽  
Maxwell G. Machani ◽  
Collince J. Omondi ◽  
Isaiah Debrah ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Falciparum ◽  
Population Structure ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Surface Protein ◽  
Dried Blood Spots ◽  
Cross Sectional ◽  
Western Kenya ◽  
Study Sites

Plasmodium falciparum parasites have evolved genetic adaptations to overcome immune responses mounted by diverse Anopheles vectors hindering malaria control efforts. Plasmodium falciparum surface protein Pfs47 is critical in the parasite’s survival by manipulating the vector’s immune system hence a promising target for blocking transmission in the mosquito. This study aimed to examine the genetic diversity, haplotype distribution, and population structure of Pfs47 and its implications on malaria infections in endemic lowlands in Western Kenya. Cross-sectional mass blood screening was conducted in malaria endemic regions in the lowlands of Western Kenya: Homa Bay, Kombewa, and Chulaimbo. Dried blood spots and slide smears were simultaneously collected in 2018 and 2019. DNA was extracted using Chelex method from microscopic Plasmodium falciparum positive samples and used to genotype Pfs47 using polymerase chain reaction (PCR) and DNA sequencing. Thirteen observed haplotypes of the Pfs47 gene were circulating in Western Kenya. Population-wise, haplotype diversity ranged from 0.69 to 0.77 and the nucleotide diversity 0.10 to 0.12 across all sites. All the study sites displayed negative Tajima’s D values although not significant. However, the negative and significant Fu’s Fs statistical values were observed across all the study sites, suggesting population expansion or positive selection. Overall genetic differentiation index was not significant (FST = -0.00891, P > 0.05) among parasite populations. All Nm values revealed a considerable gene flow in these populations. These results could have important implications for the persistence of high levels of malaria transmission and should be considered when designing potential targeted control interventions.

Population genetics and molecular phylogeography of Thamnaconus modestus (Tetraodontiformes, Monachanthidae) in Northwestern Pacific inferred from variation of the mtDNA control region

2019 ◽  
Vol 32 ◽  
pp. 18
Author(s):  
Tianyan Yang ◽  
Zhiyang Wang ◽  
Yong Liu ◽  
Tianxiang Gao
Keyword(s):  
Control Region ◽  
Okinawa Trough ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Mitochondrial Control Region ◽  
Selection Strategy ◽  
Northwestern Pacific ◽  
Target Sequence ◽  
Wild Populations ◽  
Thamnaconus Modestus

In order to study the genetic diversity of Thamnaconus modestus, a species of great commercial importance in Southeast Asia, the 5′-end hypervariable regions (423 bp) of the mitochondrial control region of T. modestus in nine geographical populations (248 individuals) were sequenced and analysed in this study. The target sequence fragment contained large numbers of polymorphic sites (87) involved in high levels of haplotype diversity (h = 0.97 ± 0.01) and nucleotide diversity (π = 0.0285 ± 0.0143). The genetic variations within populations (92.71%) were significantly larger than those among populations (7.29%). No significant genetic divergences were detected among the wild populations owing to their gregarious habits, strong moving ability, r-selection strategy. Significant genetic divergences were found between the cultured and wild populations, probably resulting from kin selection and aquacultural environment. Three significant phylogenetic lineages were identified, and the variation among lineages (56.90%) was greater than that among individuals within the lineages (43.10%), with the significant ΦST value (ΦST = 0.57, P = 0.0000). The results showed great and significant genetic differentiations among these three lineages, indicating that they may have independent phylogenetic dynamics. Dominant shared haplotypes that included individuals from each population and the median-joining network of haplotypes presented a star-like structure. Historic demographic analysis of each lineage showed that population expansion occurred after the Pleistocene glacial period. At the last glacial maximum, T. modestus in China seas was scattered across variable refuges, including Central South China Sea and Okinawa Trough.

scholarly journals Genetic Diversity and Population Structure of Rhododendron rex Subsp. rex Inferred from Microsatellite Markers and Chloroplast DNA Sequences

Plants ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 338 ◽  
Author(s):  
Xue Zhang ◽  
Yuan-Huan Liu ◽  
Yue-Hua Wang ◽  
Shi-Kang Shen
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Chloroplast Dna ◽  
Dna Sequences ◽  
Demographic History ◽  
Population Decline ◽  
Population Expansion ◽  
Distribution Models ◽  
Recent Population Expansion

Genetic diversity is vital to the sustainable utilization and conservation of plant species. Rhododendron rex subsp. rex Lévl. is an endangered species endemic to the southwest of China. Although the natural populations of this species are facing continuous decline due to the high frequency of anthropogenic disturbance, the genetic information of R. rex subsp. rex is not yet elucidated. In the present study, 10 pairs of microsatellite markers (nSSRs) and three pairs of chloroplast DNA (cpDNAs) were used in the elucidation of the genetic diversity, population structure, and demographic history of 11 R. rex subsp. rex populations. A total of 236 alleles and 12 haplotypes were found. A moderate genetic diversity within populations (HE = 0.540 for nSSRs, Hd = 0.788 for cpDNA markers), high historical and low contemporary gene flows, and moderate genetic differentiation (nSSR: FST = 0.165***; cpDNA: FST = 0.841***) were detected among the R. rex subsp. rex populations. Genetic and geographic distances showed significant correlation (p < 0.05) determined by the Mantel test. The species exhibited a conspicuous phylogeographical structure among the populations. Using the Bayesian skyline plot and species distribution models, we found that R. rex subsp. rex underwent a population demography contraction approximately 50,000–100,000 years ago. However, the species did not experience a recent population expansion event. Thus, habitat loss and destruction, which result in a population decline and species inbreeding depression, should be considered in the management and conservation of R. rex subsp. rex.

scholarly journals MITOCHONDRIAL DNA STUDY OF MONGOLIAN EQUUS CABALLUS

2018 ◽  
pp. 77-86
Author(s):  
Bolor-Oyut B ◽  
Ochirkhuyag B ◽  
Khulan J
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Control Region ◽  
Nucleotide Diversity ◽  
Sequence Variation ◽  
Haplotype Diversity ◽  
Sequence Analyses ◽  
Mitochondrial Dna Control Region ◽  
Evolutionary Studies ◽  
High Level

In order to assess the genetic diversity and maternal lineages of Mongolian native horse populations, we examined using mitochondrial DNA control region sequence analyses. The control region of mitochondrial DNA is widely used for population and evolutionary studies because of its high level of sequence variation, in addition to a lack of recombination and maternal heritance. To determine genetic diversity and maternal heritance, we collected 19 blood samples of Darhad horses from Khuvsgul, Tes horses from Zavkhan and Taij horses from Dundgobi, Mongolia.In this study, 16 haplotypes and 51 polymorphic sites were detected. Haplotype diversity was 0.9766 and nucleotide diversity was 0.0212 in Mongolian native horses. Finally, 5 horse haplogroups (A, C, D, F, I) were identified in 16 haplotypes in this study.

Genetic diversity of Taenia hydatigena in the northern part of the West Bank, Palestine as determined by mitochondrial DNA sequences

2018 ◽  
Vol 63 (2) ◽  
pp. 299-303 ◽  
Author(s):  
Kamel Adwan ◽  
Alaa Jayousi ◽  
Sameh Abuseir ◽  
Ibrahim Abbasi ◽  
Ghaleb Adwan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Sequences ◽  
West Bank ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Economic Losses ◽  
Meat Industry ◽  
Recent Population Expansion ◽  
Taenia Hydatigena ◽  
Cysticercus Tenuicollis

Abstract Cysticercus tenuicollis is the metacestode of canine tapeworm Taenia hydatigena, which has been reported in domestic and wild ruminants and is causing veterinary and economic losses in the meat industry. This study was conducted to determine the sequence variation in the mitochondrial cytochrome c oxidase subunit 1 (coxl) gene in 20 isolates of T. hydatigena metacestodes (cysticercus tenuicollis) collected from northern West Bank in Palestine. Nine haplotypes were detected, with one prevailing (55%). The total haplotype diversity (0.705) and the total nucleotide diversity (0.0045) displayed low genetic diversity among our isolates. Haplotype analysis showed a star-shaped network with a centrally positioned common haplotype. The Tajima’s D, and Fu and Li’s statistics in cysticercus tenuicollis population of this region showed a negative value, indicating deviations from neutrality and both suggested recent population expansion for the population. The findings of this study would greatly help to implement control and preventive measures for T. hydatigena larvae infection in Palestine.

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