Computational protocol: Ecological and Genetic Differences between Cacopsylla melanoneura (Hemiptera, Psyllidae) Populations Reveal Species Host Plant Preference

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Protocol publication

[…] Descriptive statistics such as range of allele sizes (SR) in a base pair (bp), number of alleles (Na) and allelic richness (AR) were calculated using FSTAT ver. . Observed (HO) and expected (HE) heterozygosity were calculated using GENETIX ver. 4.05.2 . Tests for conformity with Hardy-Weinberg equilibrium (HWE) and linkage disequilibrium between pairs of loci in each population were performed using the online version of GENEPOP .Significance levels for multiple comparisons were adjusted the standard Bonferroni technique , . [...] In a first evaluation only samples collected from apple and hawthorn of Trentino region were considered; in a second evaluation all samples were included in the analysis. FSTAT ver. was used to compute the overall and population pair-wise FST values. The 95% confidence intervals were estimated using 1,000 bootstrap replicates over the loci and probability values were determined using 1,000 permutations. The nominal significance level was set at α = 0.05. Statistical significance level for multiple comparisons was adjusted using a standard Bonferroni as described above. To provide a better visualization of population samples relationship, a matrix of Slatkin’s linearized FST values for all population sample pairs was obtained with ARLEQUIN ver. 3.5 software and used to produce a Neighbour-Joining unrooted population tree with MEGA ver. 5.0. . The molecular variance analysis (AMOVA) was performed using the ARLEQUIN ver. 3.5 software to test genetic differentiation among and within groups. In a first evaluation, the analysis was carried out according to a model structure in which the eight samples of Trentino region were divided into two groups: one collected from apple (ApBO, ApOL, ApSM, ApVE and ApVI) and the other collected from hawthorn (HaCL, HaMP, HaRU). In a second analysis, we included also samples from Aosta Valley (ApAO and HaCH), Germany (ApME and HaNE) and France (ApST).Analysis of the population structure was performed with STRUCTURE ver. 2.3.3 software to infer the most likely number of populations (K), representative of the whole data set, without the use of any a priori information. Ten independent runs of structure were performed for each K value from 1 to 9. Each run consisted of a burn-in period of 100,000 steps, followed by 1,000,000 Monte Carlo Markov Chain replicates, assuming an admixture model and correlated allele frequencies. The most likely K was chosen comparing the average estimates of the likelihood of the data, ln[Pr(X/K)], for each value of K , as well as calculating ad hoc statistics ΔK values (Evanno’s method) . The value of ln[Pr(X/K)] and ΔK were obtained by Structure Harvester ver. 0.6.1 . The proportions of membership of each individual in each cluster were also calculated. Also in this case, a first analysis was performed using the Trentino data set including only collected-from-apple and hawthorn samples. Ten independent runs of structure were performed for each K value from 1 to 9. A second analysis was carried out using the whole data set. In this case, 10 independent runs were performed for each K value from 1 to 17. […]

Pipeline specifications

Software tools Genepop, Arlequin, MEGA, Structure Harvester
Application Population genetic analysis
Organisms Malus domestica