Computational protocol: Invasion History of the Oriental Fruit Fly, Bactrocera dorsalis, in the Pacific-Asia Region: Two Main Invasion Routes

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Protocol publication

[…] Sequences were aligned using ClustalX 2.0 and then corrected manually. ARLEQUIN 3.5 was used to identify unique haplotypes. Descriptive statistics (nucleotide diversity, number of haplotypes, number of variable sites, average number of nucleotide differences and haplotype diversity) were calculated with DNAsp 5.0 .The Kimura two-parameter model in MEGA 5.0 was used to estimate pairwise genetic distances of the 35 populations, then the population phylogenetic tree was reconstructed using the neighbor-joining (NJ) method in PHYLIP 3.69 , which is the most widely used method for building phylogenetic trees from distances . Median-joining (MJ) networks of haplotypes were constructed using NETWORK 4.6 to infer the evolutionary relationships of haplotypes , .To infer asymmetric immigration rates between different regions, seven regions were defined based on geographic location and previous studies , (). Definitions were as follows (population codes in parentheses): 1) Southeast China (XM, QZ, FZ SG, MM, ZQ and GZ); 2) Taiwan Island (TW); 3) Hainan Island (WC and BWL); 4) Central China (QP, NN, HX, NC, WH, JJ, WZ, WL, XS, JS and PZH); 5) Southeast Asia (PX, JH, HK, RL, YB, PP, THA, LOU, MK, MAN and BHA); 6) South Asia ( LAH and HP); 7) Hawaii (HON).MIGRATE 3.27 was used to estimate mutation-scaled effective immigration rate for entering and leaving each region per generation (M = m/μ, where m is immigration rate and μ is mutation rate per site per generation), and mutation-scaled effective population sizes (Θ = Neμ, where Ne is effective population size), by applying a Bayesian search strategy. Four independent MIGRATE runs of 20,000,000 generations with different random start seeds were performed to examine the consistency of the results, with the first 10,000 generations discarded as “burn-in”. Analysis of molecular variation (AMOVA) and computation of fixation indices (FST) between pairwise regions were implemented in ARLEQUIN.The demographic history of each region and of all populations pooled together was examined using mismatch distributions, population size before expansion (θ0), population size after expansion (θ1), population expansion time (τ), Tajima's D, Fu's FS, and sum of squared deviations (SSD) between observed and expected mismatches. All parameters were calculated using ARLEQUIN and tested against the expected values of a recent population expansion with 1000 bootstrap replicates. […]

Pipeline specifications

Software tools Clustal W, Arlequin, DnaSP, MEGA, PHYLIP
Applications Phylogenetics, Population genetic analysis
Organisms Bactrocera dorsalis