fixation indices
Recently Published Documents


TOTAL DOCUMENTS

53
(FIVE YEARS 9)

H-INDEX

16
(FIVE YEARS 1)

2021 ◽  
Vol 20 (2) ◽  
pp. 87-98
Author(s):  
Mistura Temitope Adeleke ◽  
Oladunni Nimota Adekunle ◽  
Roseline Tolulope Feyisola ◽  
Folarin Ojo Owagboriaye ◽  
Olayemi Tope Arowosegbe ◽  
...  

The spiralling whitefly, Aleurodicus dispersus Russell (Hemiptera: Aleyrodidae), has a wide range of anatomy, physiology, behaviour, and ecology depending on the host plant. This research looked at the genetic variations between A. dispersus populations on two separate host plants (Citrus aurantifolia and Ocimum gratissimum). The existence of host-related genetic variation in A. dispersus populations was determined using Rapid Amplification of Polymorphic DNA (RAPD) markers. Our findings revealed that the A. dispersus populations on the two host plants had a considerable amount of genetic divergence. The spiralling whiteflies on the adaxial part of Citrus aurantifolia were genetically distinct from those on the abaxial part of the same plants. Various population genetic parameters such as heterozygosity, Nei's genetic gap, and fixation indices (FST) revealed that spiralling whitefly populations vary genetically, which may be attributable to spiralling whitefly populations originating from multiple sources. These findings also have consequences for the invasive pest's quarantine safety strategy.


Author(s):  
Morten Mattingsdal ◽  
S. Sunna Ebenesersdóttir ◽  
Kristjan H. S. Moore ◽  
Ole A. Andreassen ◽  
Thomas F. Hansen ◽  
...  

AbstractThe aim of the present study was to describe the genetic structure of the Norwegian population using genotypes from 6369 unrelated individuals with detailed information about places of residence. Using standard single marker- and haplotype-based approaches, we report evidence of two regions with distinctive patterns of genetic variation, one in the far northeast, and another in the south of Norway, as indicated by fixation indices, haplotype sharing, homozygosity, and effective population size. We detect and quantify a component of Uralic Sami ancestry that is enriched in the North. On a finer scale, we find that rates of migration have been affected by topography like mountain ridges. In the broader Scandinavian context, we detect elevated relatedness between the mid- and northern border areas towards Sweden. The main finding of this study is that despite Norway’s long maritime history and as a former Danish territory, the region closest to mainland Europe in the south appears to have been an isolated region in Norway, highlighting the open sea as a barrier to gene flow into Norway.


Animals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 2154
Author(s):  
Doolyawat Kladkempetch ◽  
Sahatchai Tangtrongsup ◽  
Saruda Tiwananthagorn

Ancylostoma ceylanicum is a zoonotic helminth that is commonly found in domestic dogs and cats throughout Asia but is largely neglected in many countries. This study aimed to confirm the species of hookworm in dogs and soil environments and investigate the evolutionary analyses of A. ceylanicum among Thai and Asian populations. In a total of 299 dog fecal samples and 212 soil samples from 53 temples, the prevalence rates of hookworm infection by microscopic examination were 26.4% (79/299) and 10.4% (22/212) in dog and soil samples, respectively. A PCR-RFLP targeting the ITS region was then utilized to identify the hookworm species. In dogs, A. ceylanicum was the main hookworm species, and the rates of A. ceylanicum and A. caninum infections were 96.6% and 3.5%, respectively. The genetic characterization and diversity indices of the A. ceylanicumcox1 gene among Thai and Asian populations were evaluated. Nine haplotypes were identified from Thai A. ceylanicum, in which the haplotype diversity and the nucleotide diversity were 0.4436 and 0.0036, respectively. The highest nucleotide diversity of Chinese A. ceylanicum populations suggested that it could be the ancestor of the populations. Pairwise fixation indices indicated that Thai A. ceylanicum was closely related to the Malaysian population, suggesting a gene flow between these populations. The temples with hookworm-positive dogs were associated with the presence of hookworm-contaminated soil, as these levels showed an approximately four-fold increase compared with those in temples with hookworm-negative dogs (OR = 4.38, 95% CI: 1.55–12.37). Interestingly, the genotypes of A. ceylanicum in the contaminating soil and infecting dogs were identical. Therefore, increased awareness and concern from the wider public communities with regard to the responsibility of temples and municipal offices to provide proper deworming programs to community dogs should be strongly endorsed to reduce the risk of the transmission of this zoonotic disease. In addition, parasitic examination and treatment should be strongly implemented before dogs are imported and exported worldwide.


2020 ◽  
Author(s):  
Ann C. Gregory ◽  
Kenji Gerhardt ◽  
Zhi-Ping Zhong ◽  
Benjamin Bolduc ◽  
Ben Temperton ◽  
...  

AbstractBackgroundMicrobes and their viruses are hidden engines driving Earth’s ecosystems from the oceans and soils to humans and bioreactors. Though gene marker approaches can now be complemented by genome-resolved studies of inter- (macrodiversity) and intra- (microdiversity) population variation, analytical tools to do so remain scattered or under-developed.ResultsHere we introduce MetaPop, an open-source bioinformatic pipeline that provides a single interface to analyze and visualize microbial and viral community metagenomes at both the macro- and micro-diversity levels. Macrodiversity estimates include population abundances and α- and β-diversity. Microdiversity calculations include identification of single nucleotide polymorphisms, novel codon-constrained linkage of SNPs, nucleotide diversity (π and θ) and selective pressures (pN/pS and Tajima’s D) within and fixation indices (FST) between populations. MetaPop will also identify genes with distinct codon usage. Following rigorous validation, we applied MetaPop to the gut viromes of autistic children that underwent fecal microbiota transfers and their neurotypical peers. The macrodiversity results confirmed our prior findings for viral populations (microbial shotgun metagenomes were not available), that diversity did not significantly differ between autistic and neurotypical children. However, by also quantifying microdiversity, MetaPop revealed lower average viral nucleotide diversity (π) in autistic children. Analysis of the percentage of genomes detected under positive selection was also lower among autistic children, suggesting that higher viral π in neurotypical children may be beneficial because it allows populations to better ‘bet hedge’ in changing environments. Further, comparisons of microdiversity pre- and post-FMT in the autistic children revealed that the delivery FMT method (oral versus rectal) may influence viral activity and engraftment of microdiverse viral populations, with children who received their FMT rectally having higher microdiversity post-FMT. Overall, these results show that analyses at the macro-level alone can miss important biological differences.ConclusionsThese findings suggest that standardized population and genetic variation analyses will be invaluable for maximizing biological inference, and MetaPop provides a convenient tools package to explore the dual impact of macro- and micro-diversity across microbial communities.


2020 ◽  
Vol 27 (4) ◽  
pp. 330
Author(s):  
Ruth Martha Winnie ◽  
Rika Raffiudin ◽  
I Nyoman Widiarta ◽  
Aunu Rauf

The brown planthopper Nilaparvata lugens (Stal.) causes hopperburn in the rice field. The wing macropterous adults of this insect have capability for long distance flight. We aimed to analyze the genetic structure of six N. lugens populations in Java inferred from the combined COI-COII mitochondrial and ten loci of microsatellites markers. This study found low levels of nucleotides and high levels of haplotype diversity of the planthopper. The demographic test might indicate the genetic bottleneck history of N. lugens population in Java. The genetic diversity analyzed by using microsatellite markers also showed high levels of heterozygosity (Ho>He) that indicated an isolated-breaking effect in the six populations in Java. Moreover, we found a homogenous genetic structure of N. lugens based on pairwise fixation indices (Fst) analyzes that appears to be maintained by high levels of gene flow and showed no correlation between genetic and geographical distance. Importantly, these studies also support accurate information of widely distributed and genetically intermixed among N. lugens across Asia populations. Thus, our results support the theory of long-distance migration among N. lugenspopulations. The genetic structure information of N. lugens in Java could support regional management, such as the new controlling strategies based on forecasting systems.


2020 ◽  
Author(s):  
Morten Mattingsdal ◽  
S. Sunna Ebenesersdóttir ◽  
Kristjan H. S. Moore ◽  
Ole A. Andreassen ◽  
Thomas F. Hansen ◽  
...  

AbstractThe aim of the present study was to describe the genetic structure of the Norwegian population using genotypes from 6369 unrelated individuals with detailed information about places of residence. Using standard single marker- and haplotype-based approaches, we report evidence of two regions with distinctive patterns of genetic variation, one in the far northeast, and another in the south of Norway, as indicated by fixation indices, haplotype sharing, homozygosity and effective population size. We detect and quantify a component of Uralic Sami ancestry that is enriched in the North. On a finer scale, we find that rates of migration have been affected by topography like mountain ridges. In the broader Scandinavian context, we detect elevated relatedness between the mid- and northern border areas towards Sweden. The main finding of this study is that despite Norway’s long maritime history and as a former Danish territory, the region closest to mainland Europe in the south appears to have been the most isolated region in Norway, highlighting the open sea as a barrier to gene flow.


ZooKeys ◽  
2019 ◽  
Vol 872 ◽  
pp. 77-90 ◽  
Author(s):  
Xiao-Xia Huang ◽  
Kui-Ching Hsu ◽  
Bin Kang ◽  
Po-Hsun Kuo ◽  
Wan-Hsin Tsai ◽  
...  

Aphyocypris normalis (Teleostei: Cyprinidae) is an endemic species in South China, but little is known about its genetic structure. This study examined the population structure of A. normalis using sequences of the mitochondrial DNA control region and cytochrome b gene (2,086 bp). In total, 107 specimens were collected from nine populations. All 105 mtDNA haplotypes were identified as belonging to two allopatric phylogroups. The results of a statistical dispersal-vicariance analysis (S-DIVA) suggested that the ancestral populations of A. normalis were distributed widely on Hainan Island and east of the Leizhou Peninsula. A comparison of the fixation indices NST (0.532) and GST (0.004) revealed that the phylogeny and geography had a significant relationship. Our study found that (1) the Wuzhishan and Yinggeling Mountain Range was an important barrier limiting gene exchange between populations on both sides; (2) cyclic climate changes may have shaped migrations and population differentiations; and (3) different colonization times caused different population diversities between codistributed species. In addition, the inter- and intraspecific diversities of the genus Aphyocypris were estimated.


2019 ◽  
Vol 22 (4) ◽  
pp. 210-219 ◽  
Author(s):  
Jeffrey J. Beck ◽  
Jouke-Jan Hottenga ◽  
Hamdi Mbarek ◽  
Casey T. Finnicum ◽  
Erik A. Ehli ◽  
...  

AbstractTwin registries often take part in large collaborative projects and are major contributors to genome-wide association (GWA) meta-analysis studies. In this article, we describe genotyping of twin-family populations from Australia, the Midwestern USA (Avera Twin Register), the Netherlands (Netherlands Twin Register), as well as a sample of mothers of twins from Nigeria to assess the extent, if any, of genetic differences between them. Genotyping in all cohorts was done using a custom-designed Illumina Global Screening Array (GSA), optimized to improve imputation quality for population-specific GWA studies. We investigated the degree of genetic similarity between the populations using several measures of population variation with genotype data generated from the GSA. Visualization of principal component analysis (PCA) revealed that the Australian, Dutch and Midwestern American populations exhibit negligible interpopulation stratification when compared to each other, to a reference European population and to globally distant populations. Estimations of fixation indices (FST values) between the Australian, Midwestern American and Netherlands populations suggest minimal genetic differentiation compared to the estimates between each population and a genetically distinct cohort (i.e., samples from Nigeria genotyped on GSA). Thus, results from this study demonstrate that genotype data from the Australian, Dutch and Midwestern American twin-family populations can be reasonably combined for joint-genetic analysis.


Animals ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 250 ◽  
Author(s):  
Virág Ács ◽  
Árpád Bokor ◽  
István Nagy

Pedigree data of the Border Collie dog breed were collected in Hungary to examine genetic diversity within the breed and its different lines. The database was based on available herd books dating from the development of the breed (in the late 1800s) to the present day. The constructed pedigree file consisted of 13,339 individuals, of which 1566 dogs (born between 2010 and 2016) composed the alive reference population which was active from breeding perspective. The breed is subdivided by phenotype, showing a thicker coat, harmonic movement, a wide skull, and heavier bones for the show type, and a thinner or sometimes short coat and smaller body for the working line, while the mixed line is quite heterogeneous (a combination of the above). Thus, the reference population was dissected according to the existing lines. The number of founders was 894, but eight individuals were responsible for contributing 50% of the genetic variability. The reference population had a pedigree completeness of 99.6% up to 15 generations and an inbreeding coefficient of 9.86%. Due to the changing breed standards and the requirements of the potential buyers, the effective population size substantially decreased between 2010 and 2016. Generation intervals varied between 4.09 and 4.71 years, where the sire paths were longer due to the later initial age of breeding in males compared to females. Genetic differences among the existing lines calculated by fixation indices are not significant; nonetheless ancestral inbreeding coefficients are able to show contrasts.


2018 ◽  
Vol 2 (2) ◽  
pp. 28
Author(s):  
Amar Pecikoza ◽  
Lejla Lasic ◽  
Gabrijela Radosavljević ◽  
Anesa Ahatović ◽  
Ajla Smajlović ◽  
...  

Apart from its physiological role in the cellular oxidation of ethanol interesting feature of the ADH1B gene locus is its characteristic geographical distribution in which certain variants of ADH1B peak in different parts of the world.  Therefore, ADH1B rs2066701 polymorphism is exploited as a genetic marker in tracing of the evolutionary processes and human migrations in the past. Taking into consideration the complexity of population genetic structure and several migrations in the history of the Balkan populations, including Bosnian and Herzegovinian, this study aimed to estimate the frequency of ADH1B rs2066701 polymorphism in the population of Bosnia and Herzegovina. The total of 101 randomly sampled individuals was genotyped for rs2066701 polymorphism in ADH1B gene using PCR-RFLP method. The obtained frequencies were used to calculate heterozygosity, fixation indices and Hardy-Weinberg equilibrium. Observed population-structure parameters were compared with other population values available in ALFRED database. Dimensional relations between the investigated populations were visualised with the NM-MDS (non metric multidimensional scaling) analysis using PAST. The minor allele frequency for rs2066701 was 0,257. Inter-population analysis including other European and non-European populations from the ALFRED database proved the above-mentioned European genetic background of the B&H population.


Sign in / Sign up

Export Citation Format

Share Document