Computational protocol: The Secondary Contact Zone of Phylogenetic Lineages of thePhilaenus spumarius(Hemiptera: Aphrophoridae): An Example of Incomplete Allopatric Speciation

Similar protocols

Protocol publication

[…] DNA sequences were edited using the BioEdit Sequence Alignment Editor 5.0.9. ( ) and aligned using ClustalX 1.8. ( ). Appropriate nucleotide substitution models were determined using MrModeltest v2. ( ) in conjunction with PAUP* ( ). For EF1-α, Bayesian phylogenetic analyses were conducted, with two independent runs of four Metropolis-coupled Monte Carlo Markov chains (three of them “heated”) were conducted for 3 × 106 generations and sampled every 100 generations ( , ). Convergence of Bayesian analyses was assessed using Tracer v. 1.5.0 ( ); ∼7,500–8,000 of the sampled trees were discarded as “burn-in”, while the remaining ones were used to reconstruct the majority rule consensus tree. The phylogenetic tree was visualized with TreeView 1.6.6 ( ). CytB haplotypes were identified and standard genetic indices, such as haplotype diversity (h), nucleotide diversity (π), and number of segregating sites (S), were computed for each species and each population using the DnaSP v5 software ( ). Pairwise genetic distances for both markers were calculated using MEGA v5 ( ). Relationships between the Carpathian P. spumarius populations and samples from the other parts of the species range were described by building haplotype networks for CytB sequences using the statistical parsimony method ( ) and TCS 1.21 software ( ). In addition, in order to determine whether the Carpathian populations are genetically distinct, we applied analysis of molecular variance (AMOVA) as implemented in ARLEQUIN 3.1. ( ), grouping populations in several ways. First, differentiation among transects was tested. Second, the distribution of genetic variation between inner and outer populations was examined (central populations were excluded, populations from the AM were assigned as inner). Third, populations were grouped according to their localization within the Carpathian arc (western: WC+WEC, eastern: EC+ESC, and southern-central: SC+AM). A Mantel test ( ) was performed using ARLEQUIN 3.1 (with pairwise Fixation index F ST values and straight-line geographic distances in kilometers) to check if the genetic structure of the populations fits an isolation by-distance (IBD) model ( ). […]

Pipeline specifications

Software tools BioEdit, Clustal W, MrModelTest, TreeViewX, DnaSP, MEGA-V, Arlequin
Applications Phylogenetics, Population genetic analysis, GWAS
Organisms Philaenus spumarius