Data Analyses
Aligned nucleotide sequences were edited using with Geneious Prime® v.
2021.0.0 (Biomatters, www.geneious.com).
To find the phylogenetic position of our study, we obtained 82
additional sequences from Genbank which were added to our dataset (see
Table S1). To alignments of the gene dataset, MAFFT v. 7
(https://mafft.cbrc.jp/alignment/server/) was used in a final 617
bp alignment and Hemiculter
beleekeri was chosen as outgroup.
We used the PartitionFinder v.2 (Lanfear et al., 2016) to best-fit
partitioning scheme.
The phylogenetic tree from maximum likelihood (ML) and Bayesian
Inference (BI) was inferred by MrBayes v.3.2 (Huelsenbeck & Ronquist,
2001). Analysis was performed with Markov Chain Monte Carlo (MCMC)
sampling for six million generations and parameters were saved every 100
iterations, which produced 6001 trees during the analysis. Finally, 10%
of trees were discarded as burn-in, and the remaining trees were used to
reconstruct the 50% majority-rule consensus tree.
The performance of each run and evaluate convergence explored using
Tracer v.1.7 (Rambaut et al., 2009).
DnaSP v.5 was used to determine molecular diversity indices that
contains the number of haplotypes (H), haplotype diversity (Hd), number
of polymorphic sites (s) and nucleotide diversity (π). These diversity
indices were estimated for the regional clades based on cytb.
A median-joining (MJ) network was constructed using NETWORK v.10.2
(Bandelt et al., 1999) to find the possible origins of introductions for
each detected specimens in Iran.