Computational protocol: How much of the invader's genetic variability can slip between our fingers? A case study of secondary dispersal of Poa annua on King George Island (Antarctica)

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Protocol publication

[…] GenAlEx 6.5 (Peakall & Smouse, , ) was used to evaluate allele frequencies; number of bands shared among individuals with a frequency greater or equal to 5%; number of unique bands; Shannon's Information Index (I); and expected heterozygosity (H e) for each population from binary data assuming Hardy–Weinberg equilibrium (Nei , Bensch & Ĺkesson, ), percentage of polymorphic bands (P%). This software was also used to perform AMOVA (Analysis of Molecular Variance) and to estimate the ФPT value with 1,023 permutations and 20,000 bootstraps to evaluate statistical significance. The Tajima's D, Fu's F S neutrality tests, and the mismatch distribution and demographic processes affecting the populations were estimated with the Arlequin software, version 3.11 (Excoffier, ; Fu ).The bottleneck hypothesis was tested using the Bottleneck software (Cornuet & Luikart, ). The population structure was analyzed with Structure Harvester ver. 0.6.94 (Earl & Vonholdt, ) software set to the default parameters (Falush, Stephens, & Pritchard, ; Foll & Gaggiotti, ). The admixture model with correlated allele frequencies between populations was applied without using a priori information on population origin. Lambda (λ), the parameter of the distribution of allelic frequencies, was set to 1. A pilot study with the length of the burn‐in and MCMC (Markov chain Monte Carlo) of 100,000–300,000 each was performed. Finally, 500,000 burn‐ins and 500,000 iterations with 10 runs were carried out on the bioportal server (www.bioportal.uio.no) to quantify the amount of variation of the likelihood for each K. The range of possible Ks tested was 1–10. In order to determine the optimal number of clusters (K), an ad hoc statistic ΔK (Evanno, Regnaut, & Goudet, ) was used. Additionally, in order to investigate patterns of genetic subdivision of analyzed populations of P. annua, dendrogram using UPGMA (unweighted pair‐group method with arithmetical averages) was created (STATISTICA 12.0, StatSoft Polska; Figure ). […]

Pipeline specifications

Software tools GenAlEx, Arlequin, Structure Harvester, Statistica
Databases BioPortal
Applications Miscellaneous, Population genetic analysis
Organisms Homo sapiens