Phylogeny Of Schizothoracinae Fishes And Genetic Structure Of Pampus Argenteus Population Based On Mitochondrial DNA Sequences

With the development of economy, fishing pressure was increased, andenvironmental degradation was more and more obvious, abundance of wildendangeredSchizothoracinae and the valuable seafoodPampus argenteus populationhad been recessed in recent years.Here, we used molercular biology andbioinformatics methods to analyze the phylogeny and genetic diversity ofSchizothoracinae fishes and Pampus argenteusby mitochondrial DNA sequences.These studies about genetic diversity,which would offer helpful theoreticalbasis foreffective management and development of the fishery resources of the two subjects,were helpful for understanding the species’ capacity of adaptation and potential ofevolution. The main contents of our study are as follows:1. Comparative analysis the structural features of mitochondrial genomesequences of fourSchizothoracinae fishesWe obtained the complete mitochondrial genome sequencesofSchizopygopsisthermalis,Schizopygopsis younghusbandi, Gymnocyprisdobula,Gymnocypris namensis by conventional PCR direct sequencing method. Comparisonmitochondrial genome characteristicsof four fishes, we found that the completegenome contained37coding genes and two non-coding genes. The gene order of fourmitochondrial genome sequences were sameand consistent with other bony fishes. Inaddition to one gene COXI used GTG as start codon, the rest genes of13proteincoding genes were started with ATG; Stop codon in COXII, ND4, Cytbwere notcomplete whilethe other10genes used TAA or TAG as start codon; There were someoverlapping fragments in the genome sequences; Except RNA genes, each region ofmitochondrial genome were A+T bases preference; The codonsidentified amino acidand generic codons were not exactly the same. The codon usage of AUU (I) was thehighest of all codons; Protein-coding genes of four fish were similar to each other over98%; tRNA geneswere basically the same in addition to few differences in thelength; When analyzing non-coding regions,we found that OL regions were slightlydifferent in stems. The number of TA repeat was the major difference existed in thecontrol regions. All above, four Schizothoracinae fisheshad very high similarity on themitochondrial genome sequences which indicated that their genetic relationship wereclose.2. Phylogenic analysis of Schizothoracinae fishes based on completemitochondrial genomeWe obtain mitochondrial genome sequences of13Schizothoracinae fishes fromour study and NCBI. The genome characteristics, selection pattern and phylageneticinformation were analyzed. The consensus sequences without D-loop after alignmentwere15,800base pairs in length. In which, variable rate was24.8%. The maximummutation rate (38.3%) and genetic distance values (0.188)of13protein coding genesequenceswere detected in the ND2gene. The ratios of transitions and transversionsof all genes were greater than2.0which indicated that all genes were suitable forphylogenetic analysis. Results of natural selection test,Ka/Ks1, values of Z test andTajima’s test were lower than zero,demonstrated the protein-coding genes weresubject to strong negative selection. From the resultsof phylogenetic analysiswith thecomplete genome sequences (no D-loop region) and total protein-coding genes, wefound that MP and ML treestopology were almost identical. In addition toGymnocyprisgenus, all species were located on their own genus. Our phylogeneticanalysisrevealed that the results of phylogenetic trees supported specialization theory,but highly specialized and specialized schizothoracine fishes didn’t separate twogroups in the base of all the trees.Different regions of mitochondrial genome hadvarious applicabilityfor phylogenetic analysis. In our study, ND5, Cytb, ND2,COXIwere suitable genes for phylogenetic analysisof schizothoracinae fishes.3. Genetic structure of P. argenteus populationalong the coast of China based oncomplete CytbsequencesWe collected P. argenteuspopulation from six localities in China Sea. In order toelucidate the population structure and population expansion of P.argenteuspopulations, sequence analyses on the complete mitochondrial DNACytbsequences (1137bp in length) were conducted.From all180individuals, wedetected47distinct haplotypes. Six population exhibited high haplotype diversity(0.752~0.880) and low nucleotide diversity (0.00132~0.00173). Highest pairwise Fst value was0.00640, observed between SDYC and LYGYC, while lowest was-0.01038,observed between DTYC and XPYC. The valuesof the genetic distanceswithinpopulations (0.0013-0.0017) and between populations (0.0013-0.0016) weresimilar.Hierarchical analysis of molecular variance (AMOVA), phylogenic anlysis andmedian-joining (MJ) network analysiswere conducted andwe found that six P.argenteus population had no significant phylogeographic structures. Tests of neutralevolution and mismatch distribution based on all populations suggested that P.argenteuspopulationmay have experienced a population expansion. It’s obvious inDTYC population and ZSYC population.