scholarly journals Neither Coral- nor Symbiont- Genetic Diversity may Explain the Resistance of the Coral Echinopora lamellosa to Bleaching

2021 ◽  
Vol 6 (2) ◽  
pp. 66161
Author(s):  
Imam Bachtiar ◽  
Muhammad Irsyad Abiyusfi Ghafari ◽  
Ibadur Rahman ◽  
Baiq Hilda Astriana
Keyword(s):  
Genetic Diversity ◽  
Haplotype Diversity ◽  
Its Region ◽  
Haplotype Network ◽  
Restricted Gene Flow ◽  
Long Distance ◽  
Reproduction Mode ◽  
Algal Symbiont ◽  
Different Populations ◽  
The Stability

Genetic diversity has an important role in the stability of coral populations in coping with disturbances. In the last three bleaching events, the coral Echinopora lamellosa survived better in the eastern- than the western- Lombok waters that are not related to algal symbiont diversity. The present study aimed to assess the genetic diversity of E. lamellosa from the two locations in the Lombok waters. The ITS1-5.8S-ITS2 (whole ITS region) marker was used to identify and to determine the genetic structure, genetic variation, and demographic pattern of E. lamellosa. The results showed that E. lamellosa of the two locations are two different populations. The haplotype diversity was very high indicating a predominance of sexual reproduction mode for both eastern and western populations. The phylogenetic topology suggests there is possible connectivity between populations, whereas the haplotype network exhibits a restricted gene flow between the two populations.  The results suggest that the present E. lamellosa populations were from both surviving colonies and new recruitment of long-distance larvae. Both population likely shares the same larvae supply brought from source-reefs in the Flores Sea or Makassar Strait by the Indonesian Throughflow. The present and previous studies revealed that genetic diversity alone yet to explain the resistance of E. lamellosa in eastern and western Lombok waters.   

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.

Population genetic structure of the endangered yellow spotted mountain newt (Neurergus derjugini: Amphibia, Caudata) inferred from mitochondrial DNA sequences

2019 ◽  
pp. 37-47 ◽  
Author(s):  
Tayebe Salehi
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Transition Period ◽  
Isolation By Distance ◽  
Haplotype Diversity ◽  
Haplotype Network ◽  
Molecular Dating ◽  
Middle Pleistocene ◽  
Restricted Gene Flow ◽  
Historical Factors

The yellow spotted mountain newt (Neurergus derjugini) is a critically endangered species restricted to fragmented habitats in highland streams of the middle Zagros Mountain in Iran and Iraq. We examined the species phylogeography by investigating sequences of a mitochondrial fragment of the ND2 gene for 77 individuals from 15 locations throughout the species known distribution. We found relatively high haplotype diversity (0.82 ± 0.025) but low nucleotide diversity (0.0038 ± 0.00022) across all populations. Phylogenetic trees supported monophyly, and the segregation of haplotypes was concordant with the haplotype network. We found a significant correlation between geographical and genetic distances among populations (r = 0.54, P ˂ 0.01), suggesting restricted gene flow. Molecular dating suggested that haplogroups diverged during the early or middle Pleistocene. Bayesian skyline plot provided evidence for an expansion of populations during the Pleistocene-Holocene transition period. Taken together, isolation by distance due to low dispersal capability, habitat fragmentation, and historical factors have shaped the current population structure of N. derjugini.

scholarly journals Genetic Diversity and Distribution ofBlastocystisSubtype 3 in Human Populations, with Special Reference to a Rural Population in Central Mexico

2018 ◽  
Vol 2018 ◽  
pp. 1-7 ◽  
Author(s):  
Liliana Rojas-Velázquez ◽  
Patricia Morán ◽  
Angélica Serrano-Vázquez ◽  
Leonardo D. Fernández ◽  
Horacio Pérez-Juárez ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Human Population ◽  
Haplotype Diversity ◽  
Haplotype Network ◽  
Human Populations ◽  
High Haplotype Diversity ◽  
Genetic Diversity And Structure ◽  
High Prevalence ◽  
The World ◽  
Parasitic Protist

Blastocystissubtype 3 (ST3) is a parasitic protist found in the digestive tract of symptomatic and asymptomatic humans around the world. While this parasite exhibits a high prevalence in the human population, its true geographic distribution and global genetic diversity are still unknown. This gap in knowledge limits the understanding of the spread mechanisms, epidemiology, and impact that this parasite has on human populations. Herein, we provided new data on the geographical distribution and genetic diversity ofBlastocystisST3 from a rural human population in Mexico. To do so, we collected and targeted the SSU-rDNA region in fecal samples from this population and further compared its genetic diversity and structure with that previously observed in populations ofBlastocystisST3 from other regions of the planet. Our analyses reveled that diversity ofBlastocystisST3 showed a high haplotype diversity and genetic structure to the world level; however, they were low in the Morelos population. The haplotype network revealed a common widespread haplotype from which the others were generated recently. Finally, our results suggested a recent expansion of the diversity ofBlastocystisST3 worldwide.

scholarly journals Genetic diversity, haplotype analysis, and risk factor assessment of hepatitis a virus (HAV) isolates from the West Bank, Palestine during the period between 2014 and 2016

2020 ◽  
Author(s):  
Kamal Dumaidi ◽  
Hayah Qaraqe ◽  
Amer Al-Jawabreh ◽  
Rasmi Abu-Helu ◽  
Fekri Samarah ◽  
...  
Keyword(s):  
Risk Factors ◽  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Network Analysis ◽  
Nucleotide Diversity ◽  
Hepatitis A Virus ◽  
West Bank ◽  
Haplotype Diversity ◽  
Haplotype Network ◽  
The West

AbstractBackgroundHAV genotypes and its genetic diversity is rarely investigated in our region as well as worldwide.Aimsthe aims of the present study were to determine the HAV genotypes and its risk factors and to investigate the genetic diversity of the HAV isolates in the West bank, Palestine.Study designa cohort of 161 clinically and laboratory confirmed HAV (IgM-positive) cases and 170 IgM negative individuals from all the districts of the West Bank, Palestine during the period of 2014-2016 were tested for VP3/VP1 junction of the HAV genome using RT-PCR and sequence analysis. Phylogenetic analysis, genetic diversity and haplotypes analysis were used to characterize the VP3/VP1 sequences.ResultsOverall, all the 34 sequences of the HAV was found to be HAV-IB sub-genotype. The phylogenetic analysis showed four main clusters with cluster III exclusively consisting of 18 Palestinian isolates (18/23-78%) with weak bootstrap values. A high haplotype diversity (Hd) and low nucleotide diversity (π) were observed. Cluster III showed high number of haplotypes (h=8), but low haplotype (gene) diversity (Hd=0.69). A total of 28 active haplotypes with some consisting of more than one sequence were observed using haplotype network analysis. The Palestinian haplotypes are characterized by closely related viral haplotypes with one SNV away from each other which ran parallel to cluster III in the phylogenetic tree. A smaller Palestinian haplotype (4 isolates) was three SNVs away from the major haplotype cluster (n=10) and closer to haplotypes from Iran, Spain, and South Africa. Young age, low level of parent’s education, poor hand washing and drinking of un-treated water was considered the major HAV risk factors in the present study.ConclusionHAV-IB subgentype is endemic in Palestine. HAV showed low genetic variation and nucleotide diversity. Furthermore, haplotype network analysis revealed haplotype variation among the Palestinian sequences.

scholarly journals Genetic Diversity and Population Structure in the Ryukyu Flying Fox Inferred from Remote Sampling in the Yaeyama Archipelago

2020 ◽  
Author(s):  
Yuto Taki ◽  
Christian E. Vincenot ◽  
Yu Sato ◽  
Miho Inoue-Murayama
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Haplotype Network ◽  
Iucn Red List ◽  
The Philippines ◽  
Conservation Units ◽  
Long Distance ◽  
Flying Fox

AbstractThe Ryukyu flying fox (Pteropus dasymallus) is distributed throughout the island chain spanning across southern Japan, Taiwan, and possibly the Philippines. Although P. dasymallus is listed as VU (vulnerable) in the IUCN Red List, only few genetic works have been conducted to support its conservation. In this study we analyzed 19 markers (mtDNA haplotypes and 18 microsatellite markers) to evaluate genetic diversity and investigate the genetic structure of this species.mtDNA analysis was conducted with 142 DNA remote samples, mostly from feces, and wing tissues collected on eight islands (Miyako, Ishigaki, Kohama, Kuroshima, Hateruma, Taketomi, Iriomote, Yonaguni). 39 haplotypes were identified in 526bp of the control region, and haplotype network showed no clear genetic structure.Microsatellite analysis was also conducted with 155 samples collected on six islands (Miyako, Ishigaki, Kohama, Taketomi, Iriomote, Yonaguni). It showed that the Yonaguni population exhibits low genetic diversity, high inbreeding, and clear genetic differentiation from other populations. Gene flow between Ishigaki and Miyako through small stepstone islands might be preventing inbreeding of the Miyako population.We provide for the first time indirect proof of long-distance inter-island dispersal in the Ryukyu flying fox and revealed genetic diversity, gene flow and genetic differentiation among populations of the archipelago. These results will be useful for delineating conservation units and designing specific conservation policies for each island based on metapopulation genetic structure.

scholarly journals Genetic diversity and variation of seven Chinese grass shrimp (Palaemonetes sinensis) populations based on the mitochondrial COI gene

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yingying Zhao ◽  
Xiaochen Zhu ◽  
Ye Jiang ◽  
Zhi Li ◽  
Xin Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Demographic History ◽  
Haplotype Diversity ◽  
Grass Shrimp ◽  
Haplotype Network ◽  
Coi Gene ◽  
Wild Populations ◽  
Important Species ◽  
Network Analyses ◽  
Maximum Variation

Abstract Background Chinese grass shrimp (Palaemonetes sinensis) is an important species widely distributed throughout China, which is ecologically relevant and possesses ornamental and economic value. These organisms have experienced a sharp decline in population due to overfishing. Therefore interest in P. sinensis aquaculture has risen in an effort to alleviate fishing pressure on wild populations. Therefore, we investigated the genetic diversity and variation of P. sinensis to verify the accuracy of previous research results, as well as to assess the risk of diversity decline in wild populations and provide data for artificial breeding. Methods Palaemonetes sinensis specimens from seven locations were collected and their genetic variability was assessed based on mitochondrial COI gene segments. DNA sequence polymorphisms for each population were estimated using DNASP 6.12. The demographic history and genetic variation were evaluated using Arlequin 3.11. At last, the pairwise genetic distance (Ds) values and dendrograms were constructed with the MEGA 11 software package. Results Our study obtained sequences from 325 individuals, and 41 haplotypes were identified among the populations. The haplotype diversity (Hd) and nucleotide diversity (π) indices ranged from 0.244 ± 0.083 to 0.790 ± 0.048 and from 0.0004 ± 0.0001 to 0.0028 ± 0.0006, respectively. Haplotype network analyses identified haplotype Hap_1 as a potential maternal ancestral haplotype for the studied populations. AMOVA results indicated that genetic variations mainly occurred within populations (73.07%). Moreover, according to the maximum variation among groups (FCT), analysis of molecular variance using the optimal two-group scheme indicated that the maximum variation occurred among groups (53.36%). Neutrality and mismatch distribution tests suggested that P. sinensis underwent a recent population expansion. Consistent with the SAMOVA analysis and haplotype network analyses, the Ds and FST between the population pairs indicated that the JN population was distinctive from the others. Conclusions Our study conducted a comprehensive characterization of seven wild P. sinensis populations, and our findings elucidated highly significant differences within populations. The JN population was differentiated from the other six populations, as a result of long-term geographical separation. Overall, the present study provided a valuable basis for the management of genetic resources and a better understanding of the ecology and evolution of this species.

Broad-ranging low genetic diversity among populations of the yellow finger marsh crab Sesarma rectum Randall, 1840 (Sesarmidae) revealed by DNA barcode

Crustaceana ◽  
2017 ◽  
Vol 90 (7-10) ◽  
pp. 845-864
Author(s):  
Raquel C. Buranelli ◽  
Fernando L. Mantelatto
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Isolation By Distance ◽  
Dna Barcode ◽  
Population Expansion ◽  
Haplotype Network ◽  
Sudden Expansion ◽  
Restricted Gene Flow ◽  
Western Atlantic

Population genetic studies on marine taxa, specifically in the field of phylogeography, have revealed distinct levels of genetic differentiation in widely distributed species, even though they present long planktonic larval development. A set of factors have been identified as acting on gene flow between marine populations, including physical or physiological barriers, isolation by distance, larval behaviour, and geological and demographic events. In this way, the aim of this study was to analyse the genetic variability among populations of the crab speciesSesarma rectumRandall, 1840 along the western Atlantic in order to check the levels of genetic diversity and differentiation among populations. To achieve this purpose, mtDNA cytochrome-coxidase subunit I (COI) (DNA-barcode marker) data were used to compute a haplotype network and a Bayesian analysis for genetic differentiation, to calculate an Analysis of Molecular Variance (AMOVA), and haplotype and nucleotide diversities. Neutrality tests (Tajima’sDand Fu’s ) were accessed, as well as pairwise mismatch distribution under the sudden expansion model. We found sharing of haplotypes among populations ofS. rectumalong its range of distribution and no significant indication for restricted gene flow between populations separately over 6000 km, supporting the hypothesis of a high dispersive capacity, and/or the absence of strong selective gradients along the distribution. Nevertheless, some results indicated population structure suggesting the presence of two genetic sources (i.e., groups or lineages), probably interpreted as a result of a very recent bottleneck effect due to habitat losses, followed by the beginning of a population expansion.

scholarly journals Effects of Landscape Fragmentation on Genetic Diversity of Male-Biased Dioecious Plant Pistacia chinensis Bunge Populations

Forests ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 792
Author(s):  
Lu ◽  
Qiu ◽  
Lu
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Landscape Fragmentation ◽  
Small Population ◽  
Restricted Gene Flow ◽  
Fragmented Landscape ◽  
Dioecious Plant ◽  
Male Population ◽  
Fragmented Population ◽  
Different Populations

Pistacia chinensis Bunge (Anacardiaceae) is a dioecious woody plant of significant economic values that is used in traditional Chinese Medicine as well as for wood production. More importantly, it is one of the ideal tree species for bio-diesel production because of the high oil content in its seeds. In this study, we aim to reveal the effects of landscape fragmentation on the genetic diversity (GD) of the dioecious plant Pistacia chinensis populations. A total of nine microsatellites were used to genotype 180 P. chinensis individuals from six populations to estimate the differences in GD between different populations. The study revealed that genetic diversity of the P. chinensis population as a whole is relatively high in the Thousand-Island Lake (TIL) region, but its fragmented landscape still led to the loss of rare alleles, especially in a fragmented small population, a post-fragmented population, and a male population. The partitioning of a large continuous population into small isolated remnant patches led to the direct loss of genetic diversity and, subsequently, because of the mediated gene flow of seeds and pollen, genetic drift, and the spatial distribution of existing plants, the GD gradually decreased. The restricted gene flow and the increase in self-pollination and inbreeding impaired the population’s long-term development. Therefore, the wild P. chinensis populations in the TIL region needs effective protective measures, including foreign artificial pollination and seedling transplantations.

scholarly journals Genetic diversity of the cyprinid fish Capoeta trutta (Heckel, 1843) populations from Euphrates and Tigris rivers in Turkey based on mtDNA COI sequences

2017 ◽  
Vol 64 (1) ◽  
pp. 18 ◽  
Author(s):  
Arif Parmaksız ◽  
Esra Eksi
Keyword(s):  
Genetic Diversity ◽  
Haplotype Diversity ◽  
Data Set ◽  
Mtdna Coi ◽  
Gene Sequence Analysis ◽  
Different Populations ◽  
The Mean ◽  
Neutrality Tests ◽  
Coi Sequences ◽  
Amova Analysis

In this study, genetic diversity of Capoeta trutta (Heckel, 1843) populations from Euphrates and Tigris rivers in Turkey was evaluated based on gene sequence analysis of mitochondrial DNA cytochrome c oxidase subunit I (mtDNA COI) locus. Six polymorphic sites and seven haplotypes were detected in 47 samples collected from four populations viz., Adiyaman, Birecik, Bismil and Batman. The mean haplotype diversity (h) and nucleotide diversity (π) were calculated as h = 0,6420 and π = 0,00138 respectively. Pairwise FST statistics of different populations were found to be negative, low and were insignificant, indicating gene flow. AMOVA analysis showed Fst = 0.09865 and p = 0.00489, indicating that the populations were isolated. The results of Neutrality tests showed an increase in Adiyaman, Birecik and Bismil populations and a decline in Batman population, all values being statistically insignificant (p>0.05). Three haplotypes determined for mtDNA COI locus in the present study form important data set for genetic diversity of this species.

scholarly journals Haplotype network branch diversity, a new metric combining genetic and topological diversity to compare the complexity of haplotype networks

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0251878
Author(s):  
Eric Garcia ◽  
Daniel Wright ◽  
Remy Gatins ◽  
May B. Roberts ◽  
Hudson T. Pinheiro ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Haplotype Diversity ◽  
Haplotype Network ◽  
Published Data ◽  
Topological Information ◽  
Network Diversity ◽  
Haplotype Networks ◽  
Evolutionary Studies ◽  
Probabilistic Values ◽  
Network Properties

A common way of illustrating phylogeographic results is through the use of haplotype networks. While these networks help to visualize relationships between individuals, populations, and species, evolutionary studies often only quantitatively analyze genetic diversity among haplotypes and ignore other network properties. Here, we present a new metric, haplotype network branch diversity (HBd), as an easy way to quantifiably compare haplotype network complexity. Our metric builds off the logic of combining genetic and topological diversity to estimate complexity previously used by the published metric haplotype network diversity (HNd). However, unlike HNd which uses a combination of network features to produce complexity values that cannot be defined in probabilistic terms, thereby obscuring the values’ implication for a sampled population, HBd uses frequencies of haplotype classes to incorporate topological information of networks, keeping the focus on the population and providing easy-to-interpret probabilistic values for randomly sampled individuals. The goal of this study is to introduce this more intuitive metric and provide an R script that allows researchers to calculate diversity and complexity indices from haplotype networks. A group of datasets, generated manually (model dataset) and based on published data (empirical dataset), were used to illustrate the behavior of HBd and both of its terms, haplotype diversity, and a new index called branch diversity. Results followed a predicted trend in both model and empirical datasets, from low metric values in simple networks to high values in complex networks. In short, the new combined metric joins genetic and topological diversity of haplotype networks, into a single complexity value. Based on our analysis, we recommend the use of HBd, as it makes direct comparisons of network complexity straightforward and provides probabilistic values that can readily discriminate situations that are difficult to resolve with available metrics.

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