Program version 3.5

Manufactured by Arlequin

Arlequin is a software program designed for population genetics analysis. Version 3.5 includes tools for calculating population genetic statistics, testing hypotheses, and visualizing data. The core function of Arlequin is to provide a comprehensive framework for analyzing genetic data from various sources.

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Arlequin program version 3.1 (2 citations)

3 protocols using program version 3.5

Genetic Associations Analysis Protocol

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Hardy-Weinberg equilibrium (HWE) was examined by the Arlequin program (version 3.5) [20 (link)]. The differences in the genotype and allele frequencies between cases and controls were analyzed by the CLUMP22 software with 10,000 Monte Carlo simulations [21 (link)]. Power analysis was performed by Power and Sample Size Calculation software [22 (link)]. Meta-analysis was made by REVMAN 5.0 (Cochrane Collaboration, Oxford, United Kingdom) and Strata 11.0 software (Strata Corporation, College Station, TX) [23 (link), 24 (link)]. Publication bias was evaluated by Begg and Egger regression tests [25 (link)]. The combined ORs with 95% CI values were calculated by either fixed-effect or random-effect method [26 (link)]. A two-tailed P value of 0.05 or lower was defined to be statistically significant.

Ye H., Zhao Q., Huang Y., Wang L., Liu H., Wang C., Dai D., Xu L., Ye M, & Duan S. (2014). Meta-Analysis of Low Density Lipoprotein Receptor (LDLR) rs2228671 Polymorphism and Coronary Heart Disease. BioMed Research International, 2014, 564940.

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Population Genetics Analysis Protocol

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Using forward and reverse sequences, consensus sequences were produced for each individual using ClustalW (Larkin et al. 2007 (link)) and subsequently checked by hand. All individuals were aligned in ClustalX 2.1 (Larkin et al. 2007 (link)). Using DnaSP version 5.10.1 (Librado and Rozas 2009 (link)), within and between population haplotype diversity (h) (Nei 1987 ) and nucleotide diversity (π) (Tajima 1983 (link)) were estimated. Pairwise population F_ST (a measure of pairwise population differentiation) and N_em (a measure of temporal gene flow between populations) values were calculated with the Arlequin program version 3.5 using the methods of Tajima and Nei (1984) (link), Slatkin and Hudson (1991) (link), and Slatkin (1993) (link). A parsimony network connecting the haplotypes was plotted with TCS version 1.21 (Clement et al. 2000 (link)).

Lord J.P, & Williams L.M. (2017). Increase in density of genetically diverse invasive Asian shore crab (Hemigrapsus sanguineus) populations in the Gulf of Maine. Biological invasions, 19(4), 1153-1168.

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Genetic Association Analysis of CHD

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Comparison of genotype and allele frequencies between patients with CHD and controls were determined by the CLUMP22 software with 10,000 Monte Carlo simulations (Sham and Curtis, 1995) . Consistency of the genotype frequencies with Hardy-Weinberg equilibrium (HWE) was performed by the Arlequin program (version 3.5) ( Excoffier and Lischer, 2010) . A two-sided P value < 0.05 was considered to indicate a statistically significant result.

Zhong J.Y., Zheng X.W., Ye H.D., Cui H.B., Du W.P., Zhang Z.X., Fei X.H., Lin S.Y., Wang J., Su J., Chen X.M, & Duan S.W. (2015). Male-specific association of the APC rs383830 T allele with the risk of coronary heart disease. Genetics and molecular research : GMR, 14(4).

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