The role of evolutionary model and model selection criterion on phylogenetic relationships of cyprinid fishes (Teleostei: Cypriniformes) based on mitochondrial gene COI

This study aims to reconstruct the phylogenetic relationships of some cyprinid fishes using different evolutionary models and information criteria to evaluate their phylogenetic effects. Eighty-one COI sequences representing 81 cyprinid species of from 29 genera were obtained from Genbank. After alignment with one nemacheilid sequence as outgroup, GTR+I+G, HKY+I+G and SYM+I+G were selected as best nucleotide substitution models using the AIC, AICc, BIC and DT model selection criteria in jModelTest 2.1.10. Bayesian phylogenetic trees were reconstructed in MrBayes 3.2.6. To evaluate the effects of the proportion of invariable sites and gamma distribution on the tree topology, we reconstructed three Bayesian trees for GTR+I, GTR+G and GTR, and compared them to the best model tree topology. Despite different number of substitution types in GTR+I+G and HKY+I+G and base frequencies in GTR+I+G and SYM+I+G, their tree topologies were highly similar, but the posterior probability values were different. All three models implied that several genera were not monophyletic and the phylogenetic position of a number of taxa, varied according to each model. On the other hand, in reconstructed phylogenetic trees based on GTR+I, GTR+G and GTR, the phylogenetic position of several taxa has been changed. The results suggest that the number of substitution types applies its effect mainly on the posterior probabilities, while base frequencies, the proportion of invariable sites and gamma distribution affect both posterior probabilities and phylogenetic position of some of the cyprinid taxa.

Keywords:

Nucleotide substitution model , Information criterion , Phylogeny , Mitochondrial genome