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Some Case Histories
Published in Jacques Derek Charlwood, The Ecology of Malaria Vectors, 2019
Major demographic events leave genetic signatures that could be used to gain important information about the impact of vector control interventions. Using microsatellite data, there was significant differentiation in the genetic structure of the two islands, but there was no evidence of any genetic bottleneck occurring as a result of the eradication campaign undertaken in the early 1980s. In a subsequent study, significant population differentiation revealed by the Fixation index (FST) and the analogous estimator for microsatellite data RST was found between the southernmost collection site, Porto Alegre, and northern localities. The Porto Alegre population was an ‘island within an island’. The observed patterns of population substructure are probably the result of restrictions to gene flow in the less inhabited, more densely forested and mountainous south. In all localities, the A. coluzzii appeared to be experiencing a demographic expansion consistent with a relatively recent (ca. 500 years) founder effect.
Evaluation of the genetic structure of Bromus inermis populations from chemically and radioactively polluted areas using microsatellite markers from closely related species
Published in International Journal of Radiation Biology, 2022
Elena V. Antonova, Marion S. Röder
The genetic differentiation of the smooth brome local populations was FST = 0.068 (p=.001) according to the analysis of molecular variance (AMOVA). This means that only 6.8% of the variability was apportioned among populations, and 93.2% was undistracted within populations (72% was among individuals and 21% was within individuals). The Bt-33 locus made the greatest contribution to the interpopulation variability (FST = 18.5%), and the Bt-23 locus made the smallest (FST = 3.5%). Accordingly, the gene flow (Nm) level for these loci was 1.103 (Bt-33) and 6.866 (Bt-23). The proportion of inbred individuals in local populations, estimated by the Wright fixation index (F), ranged from 0.273 to 0.570 (Table 4). The high value of the index has shown in two background samples. A low level of inbreeding was noted in chemically polluted areas. In the Kyshtym accident zone, the values of the indicator occupied an average position between the unexposed and affected populations.
An evaluation of inter and intra population structure of Uttar Pradesh, inferred from 24 autosomal STRs
Published in Annals of Human Biology, 2022
Ikramul Haque, Shivani Dixit, Akash Kumar, Akshay Kumar, Sunita Verma, Devinder Kumar, Ankit Srivastava, R. K. Kumawat, Divya Shrivastava, Gyaneshwer Chaubey, Pankaj Shrivastava
Allele frequency, number of detected alleles and the fixation index of 24 STR loci were calculated using GenAlEx 6.5 (Peakall and Smouse 2006). Arlequin software (Excoffier and Lischer 2010) was used to determine the observed heterozygosity (Hobs), expected heterozygosity (Hexp) and Hardy–Weinberg p values. The parameters of forensic and population genetic importance such as the power of discrimination (PD), power of exclusion (PE), typical paternity index (TPI), matching probability (PM) and polymorphism information content (PIC) were calculated via PowerStats spreadsheet (Tereba 1999). Allele frequency of 15 STRs were pre-set and used to generate the neighbor-joining tree based on the Nei’s DA genetic distances via MEGA software (Tamura et al. 2013). Obtained Nei’s DA genetic distances between groups of populations were used to execute principal component analyses (PCA) using PAST software (Hammer et al. 2001). Locus wise exact test of population differentiation was executed using Arlequin (Excoffier and Lischer 2010) to analyse the genetic diversity among the Uttar Pradesh population, neighbouring Indian populations and populations from other countries. The Bayesian method-based Structure software (Evanno et al. 2005) was used to uncover the genetic structure of the selected populations.
Investigation of control region sequences of mtDNA in Naqu Tibetan population from Northwestern China
Published in Annals of Human Biology, 2021
Wen-qing Yue, Mao-ling Sun, Feng Han, Jiu-jun Li, Tsewang Rigzin, Tashi Dhondup, Hai-bo Liu, Dong-yue Li, Xuan Li, Yan-ming Xu, Xiao-na Li
The sequences were screened independently by two researchers and confirmed by a third to re-examine the electropherograms, especially for point heteroplasmies and indels. The collected sequences of mtDNA HVI and HVII region were aligned and compared with the revised Cambridge reference sequence (rCRS) (Anderson et al. 1981; Andrews et al. 1999). Haplogroups were classified using mtDNA Build 16 (van Oven and Kayser 2009). Comparisons of the allele frequency distributions and principal component analysis (PCA) were calculated using SPSS PASW Statistics v. 18.0 (IBM, Chicago, IL). Genetic distances were measured between the Naqu Tibetan population and the other populations (Chen et al. 2008; Liu et al. 2011; Gomes et al. 2015; Xu and Hu 2015; Rakha et al. 2016; Li et al. 2017; Park et al. 2017; Xu et al. 2017; Xie et al. 2019) using Fst (fixation index) via Arlequin Software v3.5 (Excoffier and Lischer 2010). The rootless phylogenetic tree was visualised using Treeview software (Excoffier and Lischer 2010).