Computational protocol: Genetic architecture of trout from Albania as revealed by mtDNA control region variation

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Protocol publication

[…] Sequences of the 5'-end of the mtDNA CR (ca. 561 bp) were aligned using the computer program ClustalX []. To assign individual haplotypes to trout species and lineages previously identified within the brown trout species complex, data were aligned against at least three haplotypes from each lineage (Me: Mediterranean; Ma: marmoratus; Da: Danubian; At: Atlantic), and compared to all known haplotypes found in trout samples across the Adriatic river system (Ad; Table ).Aligned haplotypes were imported into the program PAUP Version 4.0b10 [] for phylogenetic analysis. Neighbour-Joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and Bayesian analysis were used for phylogenetic reconstruction. For NJ, a Kimura 2-parameter model was chosen. For MP, insertions or deletions (indels) were included as a fifth character. A heuristic search (10 replicates) with Tree Bisection Reconnection (TBR) branch-swapping was employed to find the most parsimonious trees. For ML, a sequence evolution model was first chosen using the program Modeltest Version 3.7 [] incorporated into PAUP. After choosing a model, a heuristic search (10 replicates) was used to estimate the most likely topology. Support values for the nodes were obtained with 1000 bootstrap replicates for MP, NJ, or ML analysis, whereby the fast stepwise addition method was used for ML. Bayesian analysis was performed with MrBayes version 3.1.2 [] where posterior probabilities were obtained using the Markov chain Monte Carlo (MCMC) technique (Nst = 6, Rates = gamma, Ngen = 5,000,000, chains = 4).Because of weak support for the Adriatic clade as a whole (see Results,) the genealogical relation of these haplotypes was also depicted using a 95% statistical parsimony network constructed from the 5'-end of mtDNA CR sequences using program TCS 1.3 []. Resolution of ambiguous loops in the TCS network was performed by comparing ML pair-wise distances of the haplotypes within a loop and identifying the most likely connections within it, reflected by the smallest pair-wise distances. ML pair-wise distances were computed under the model (HKY 85) using the program PAUP Version 4.0b10 []. […]

Pipeline specifications

Software tools Clustal W, PAUP*, ModelTest-NG, MrBayes
Application Phylogenetics
Organisms Salmo trutta