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 studies of human diversity in East Asia

2007 ◽  
Vol 362 (1482) ◽  
pp. 987-996 ◽  
Author(s):  
Feng Zhang ◽  
Bing Su ◽  
Ya-ping Zhang ◽  
Li Jin
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
East Asia ◽  
Pacific Islands ◽  
East Asian ◽  
Human Populations ◽  
Genetic Studies ◽  
The North ◽  
Asian Populations ◽  
Genetic Diversity And Structure

East Asia is one of the most important regions for studying evolution and genetic diversity of human populations. Recognizing the relevance of characterizing the genetic diversity and structure of East Asian populations for understanding their genetic history and designing and interpreting genetic studies of human diseases, in recent years researchers in China have made substantial efforts to collect samples and generate data especially for markers on Y chromosomes and mtDNA. The hallmark of these efforts is the discovery and confirmation of consistent distinction between northern and southern East Asian populations at genetic markers across the genome. With the confirmation of an African origin for East Asian populations and the observation of a dominating impact of the gene flow entering East Asia from the south in early human settlement, interpretation of the north–south division in this context poses the challenge to the field. Other areas of interest that have been studied include the gene flow between East Asia and its neighbouring regions (i.e. Central Asia, the Sub-continent, America and the Pacific Islands), the origin of Sino-Tibetan populations and expansion of the Chinese.

scholarly journals VARIASI GENETIK TIGA POPULASI IKAN NILA ( Oreochromis niloticus ) BERDASARKAN POLIMORFISME mt-DNA

2016 ◽  
Vol 2 (1) ◽  
pp. 67
Author(s):  
Otong Zenal Arifin ◽  
Titin Kurniasih
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Oreochromis Niloticus ◽  
Selective Breeding ◽  
Haplotype Diversity ◽  
Mt Dna ◽  
High Haplotype Diversity ◽  
Freshwater Aquaculture ◽  
Preliminary Information ◽  
Nile Tilapia Oreochromis Niloticus

Penelitian untuk mengevaluasi keragaman genetik tiga populasi ikan nila telah dilakukan di Balai Riset Perikanan Budidaya Air Tawar, Bogor. Penelitian ini bertujuan untuk mendapatkan informasi variasi genetik ikan nila populasi GET, GIFT, dan nila Danau Tempe sebagai informasi dasar bagi program seleksi karakter kuantitatif. Hasil menunjukkan bahwa ikan nila GET, GIFT, dan nila Danau Tempe memiliki keragaman genetik yang tinggi dengan nilai haplotype diversity berturut-turut sebesar 0,7579; 0,5895; dan 0,5333. Jarak genetik terdekat terdapat antara ikan nila GIFT dan nila Danau Tempe, sedangkan jarak genetik terjauh terdapat pada ikan nila GET dengan populasi Danau Tempe.Research on evaluating genetic diversity between three populations of nile tilapia ( Oreochromis niloticus ) was conducted at Research Institute for Freshwater Aquaculture, Bogor. This research aimed to obtain preliminary information related with the genetic diversity of GET, GIFT, and Tempe Lake tilapia, which will be used as basic information for the future selective breeding program. Result showed that GET, GIFT, and Tempe Lake tilapia have high haplotype diversity of 0.7579, 0.5895, and 0.5333 respectively. The closest genetic distance was found between GIFT and Tempe Lake tilapia, while the farthest genetic distance was observed between GET and the Tempe Lake population.

scholarly journals Genetic Diversity and Structure in RegionalCercospora beticolaPopulations fromBeta vulgarissubsp.vulgarisSuggest Two Clusters of Separate Origin

2019 ◽  
Vol 109 (7) ◽  
pp. 1280-1292 ◽  
Author(s):  
Noel L. Knight ◽  
Niloofar Vaghefi ◽  
Julie R. Kikkert ◽  
Melvin D. Bolton ◽  
Gary A. Secor ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
New York ◽  
Genotypic Diversity ◽  
Population Divergence ◽  
Cercospora Leaf Spot ◽  
High Genetic Diversity ◽  
Genetic Diversity And Structure ◽  
The World ◽  
Population Origin ◽  
Geographic Regions

Cercospora leaf spot, caused by Cercospora beticola, is a highly destructive disease of Beta vulgaris subsp. vulgaris worldwide. C. beticola populations are usually characterized by high genetic diversity, but little is known of the relationships among populations from different production regions around the world. This information would be informative of population origin and potential pathways for pathogen movement. For the current study, the genetic diversity, differentiation, and relationships among 948 C. beticola isolates in 28 populations across eight geographic regions were investigated using 12 microsatellite markers. Genotypic diversity, as measured by Simpson’s complement index, ranged from 0.18 to 1.00, while pairwise index of differentiation values ranged from 0.02 to 0.42, with the greatest differentiation detected between two New York populations. In these populations, evidence for recent expansion was detected. Assessment of population structure identified two major clusters: the first associated with New York, and the second with Canada, Chile, Eurasia, Hawaii, Michigan, North Dakota, and one population from New York. Inferences of gene flow among these regions suggested that the source for one cluster likely is Eurasia, whereas the source for the other cluster is not known. These results suggest a shared origin of C. beticola populations across regions, except for part of New York, where population divergence has occurred. These findings support the hypothesis that dispersal of C. beticola occurs over long distances.

scholarly journals Indo-Pacific Phylogeography of the Lemon Sponge Leucetta chagosensis

Diversity ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 466
Author(s):  
Olivier Pasnin ◽  
Oliver Voigt ◽  
Gert Wörheide ◽  
Andrea P. Murillo Rincón ◽  
Sophie von der Heyden
Keyword(s):  
Genetic Diversity ◽  
Spatial Variation ◽  
Haplotype Diversity ◽  
Wide Distribution ◽  
Evolutionary Patterns ◽  
High Haplotype Diversity ◽  
Sponge Diversity ◽  
The Indian Ocean ◽  
Biogeographic Regions ◽  
First Time

The sponge Leucetta chagosensis Dendy (1913) has a wide distribution throughout the Indo-Pacific (IP) region, with previous studies focussing primarily on the western Pacific Ocean. To increase our knowledge of the spatial variation of genetic diversity throughout the IP, we constructed a phylogeny for L. chagosensis for the IP to assess the evolutionary patterns for this species. We generated 188 sequences of L. chagosensis and constructed maximum likelihood and Bayesian inference trees, using concatenated mitochondrial cytochrome oxidase subunit 3 gene (cox3) and nuclear ribosomal RNA gene (28S) markers for the first time. The spatial variation of genetic diversity of L. chagosensis was assessed using a phylogeographic approach. Leucetta chagosensis is composed of five cryptic lineages confined to different biogeographic regions with the specimens found in the Indian Ocean differing significantly from those found in the rest of the IP region. Genetic divergence was particularly high for the cox3 marker, with a low nucleotide diversity but high haplotype diversity for most lineages. This study highlights the need for a sustained effort in studying sponge diversity, boosted by the ongoing discovery of hidden biodiversity among this ecologically important taxon.

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, 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 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.   

Polymorphism and Genetic Diversity among Cassava Cultivars based on ITS1-5.8S-ITS2 Sequences of rDNA

2017 ◽  
Vol 6 (6) ◽  
pp. 220-227
Author(s):  
Djirabaye Nadjiam ◽  
Aliou Guisse ◽  
Mbacké Sembéne ◽  
Fatimata Mbaye
Keyword(s):  
Genetic Diversity ◽  
Bayesian Approach ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Genetic Erosion ◽  
Nucleotide Sequences ◽  
Its2 Region ◽  
Neighbor Joining ◽  
High Haplotype Diversity ◽  
The Bayesian Approach

Cassava is an important crop in the southern area of the Chad and it is char- acterized by many cultivars. But these cultivars have never been evaluated at the molecular level. Therefore, the objective of this study was to analyze their genetic diversity and their phylogenetic relationships. After DNA extraction, amplification and sequencing, the nucleotide sequences of the ITS1- 5.8S-ITS2 region of the ribosomal DNA of 12 selected cultivars have been analyzed. The Neighbor-Joining method, Maximum Parsimony, Maximum Likelihood and the Bayesian approach allowed studying the ancestral links. The identified nucleotide sequences have 542 bp. The targeted genes showed 468 conserved sites and 59 polymorphic sites. The nucleotide frequency was 18.64% for Adenine, 14.01% for Thymine, 34.46% for Cytosine and 32.89% for Guanine. The (G + C) content was 67.35% compared to 32.65% for the (A+T). The substitution rate was in favor of the transversions (67.46%) against the transitions (32.54%). The analysis revealed high haplotype diversity (Hd=0.954) and low nucleotide diversity (π=0.026) with an average number of pairwise nucleo de di erences (k=14.045). On the all popula on, 9 haplotypes, including 6 individual and 3 double, were identified. Gene c di eren a on is medium (FST=0.314) with a low number of migrants (Nm=0.55) and a medium genetic distance (0.028). Phylogenetic analysis based on the Bayesian approach revealed three groups of cul vars with the existence of two strongly supported clades. The cultivars studied are characterized by demographic stability or moderate population growth.They will be incorporated in the breeding program in order to limit their genetic erosion and to select the interesting characters. 

scholarly journals The Emerging of The 2019 Novel Coronavirus 2019-nCoV

2020 ◽  
Vol 2 (1) ◽  
Author(s):  
Hassan S. Naji
Keyword(s):  
Genetic Diversity ◽  
New Species ◽  
Human Population ◽  
Surveillance Systems ◽  
Large Genome ◽  
The World ◽  
Novel Coronavirus

The world is witnessing a major pandemic caused by the 2019 novel coronavirus (2019 nCoV). Efforts are undergoing in order to identify the phylogeny of this elusive virus. It turned out that 2019 nCoV is closely related to two viruses found in bats. Similar to their distant cousins, SARS CoV and MERS CoV, 2019-CoV evolved from bats due to their large genome and greater genetic diversity. Such genetic diversity enables coronaviruses to mutate and form new species that frequently surface among the human population. Developing vaccine and predicting mutation trends in coronaviruses along with surveillance systems are proven pivotal in controlling current and future outbreaks.

scholarly journals Population structure and genetic diversity of invasive Fall Armyworm after 2 years of introduction in India

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
N. Nayyar ◽  
R. G. Gracy ◽  
T. R. Ashika ◽  
G. Mohan ◽  
R. S. Swathi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Haplotype Diversity ◽  
Fall Armyworm ◽  
Western Hemisphere ◽  
Coi Gene ◽  
Polymorphism Analysis ◽  
Distribution Analysis ◽  
Maize Production ◽  
Multiple Introductions ◽  
The World

AbstractFall Armyworm (FAW), Spodoptera frugiperda, is a polyphagous pest capable of feeding over 80 plant species and was indigenous to the Western Hemisphere. Within a span of 4 years, FAW has established itself throughout most of the regions in Africa and Asia causing significant losses in maize production. Owing to its revamped distribution range, it would be prudent to analyze the ensuing genetic changes and study the emerging phylogeographic patterns across the world. In this regard, we would like to provide a current snapshot of genetic diversity of FAW in India 2 years after the initial introduction and compare it with the worldwide diversity in order to trace the origins and evolutionary trajectories of FAW in India. We have investigated around 190 FAW samples from different regions in India for strain identity and polymorphism analysis on the basis of partial mitochondrial cytochrome oxidase I (COI) gene sequences. Apart from the ancestral rice and corn strain haplotype, our study demonstrates the presence of 14 more haplotypes unique to India at a haplotype diversity of 0.356. We were also able to record inter-strain hybrid haplotypes of rice and corn strains in India. Regional heterogeneity within Indian populations seems to be quite low representative of extensive migration of FAW within India. Distribution analysis of pairwise differences and rejection of neutrality tests suggest that the FAW population in India might be undergoing expansion. Our data is consistent with the findings suggesting a recent and common origin for invasive FAW populations in Asia and Africa, and does not indicate multiple introductions to India. This study reports the highest genetic diversity for Indian FAW populations to date and will be useful to track the subsequent evolution of FAW in India. The findings would have important ramifications for FAW behavior and composition throughout the world.

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