Research On The Phylogeny And Taxonomic Status Of Two Kinds Of Grayling And Scapharca Brouhtonii

1.Mitochondrial genome and phylogenetic analysis of two kinds of graylingThe complete mtDNA sequence of Thymallus arcticus grubei(Dybowski)and Thymallus brevirostris(Kessler)were determined to study genome organization,nucleotide composition,codon usage and so on.Combined with the complete mtDNA of11 grayling,we analyzed the Ka/Ks ratio and genetic distances,and constructed phylogenetic tree by Neighbour-Joining(NJ)and Maximum Likelihood(ML)methods.The results showed that the genome of T.a.grubei and T.brevirostris were 16,658 bp and16,652 bp in length,and contained 13 protein-coding genes,2 rRNAs,22 t RNAs,and a control region.The content of AT was higher than CG.Among the protein-coding genes,the ND1 and ATP6 genes had a lower Ka/Ks ratio while the ATP8 and COX2 had a higher one.The mtDNA composition and characteristics of T.a.grubei are basically same as those of T.brevirostris.The genetic distance between T.a.grubei and T.brevirostris was the nearest(0.008),which were far from below the degree of differentiation among other species within the genus.However the T.arcticus was 0.039,which had reached the degree of differentiation between species(0.038~0.058).The T.a.grubei and T.brevirostris were clustered into a small group,while T.arcticus and T.mertensii were clustered into another one.The above results prove that the T.a.grubei is not a true T.arcticus,but is the same species as the T.brevirostris.2.Phylogenetic analysis of Salmonidae fishesThe mtDNA sequences of the measured two grayling species and 40 species of Salmonidae fishes were analyzed by bioinformatics methods.We studied the structural composition and variation characteristics,evaluated the application of mtDNA in phylogenetic analysis,and explored the phylogenetic relationships.The results showed that: mtDNA composition and gene order of family Salmonidae fishes was consistent with other teleost fishes.The lengths of mtDNAs range from 16,526 bp to 16,997 bp,andcontent of AT is higher than GC.Among all coding genes,the 16 S r RNA and 12 S rRNA had the smallest degree of variation and genetic distance respectively,while the ND2 gene had the greatest.The earliest differentiation was Coregonidaeinae,which was in the ancestor position.Salmoninae and Thymallinae were sister groups.The cluster analysis showed that the fish of the same genus was monophyletic as they can cluster alone.3.The taxonomic status of Chinese population of Scapharca broughtoniiThe COX1 and 12 S rRNA sequences of the Chinese population of S.broughtonii were determined.We studied the gene sequence characteristics and genetic distances combining the homologous sequences of 27 species of shellfish,and constructed ML and NJ trees using Mytilus edulis as outgroup taxa.The results showed that the COX1 and 12 S r RNA gene were 1584 bp and 673 bp,the base composition,codon usage and variation sites were similar to those of Japanese population of S.broughtonii and A.sativa.The genetic distance between them were the smallest(0.000),and they clustered into one team then clustered with S.kagoshimensis.The classification status of Chinese population of S.broughtonii was consistent with that of S.broughtonii.4.Phylogenetic analysis of bivalve shellfishThe ND1,COX1 and Cytb sequences of the Chinese population of S.broughtonii were determined and the homologous sequences of 56 species were selected from Genbank.We studied gene variation and evolutionary relationship by constructing ML tree.The results showed that there were many indels in these sequences,they had obvious length polymorphism.The content of AT was significantly higher than GC,indicating an obvious AT usage preference.Genetic distances among families and orders were0.169~0.468 and 0.323~2.557,respectively.NJ and ML trees showed that all bivalve species formed a monophyletic branch.The phylogenetic relationship of Pteriomorphia was different constructed with different genes.The Heterodonta was clustered as a monophyletic glade,and species of Veneroida and Myoida were not completely gathered to their branches,but nested with each other.Species of the family Hiatellidae were separated from the order Myoida,the Solemyoida(Cryptodonta)located at the base of thephylogenetic tree.The Palaeotaxodonta and Palaeoheterodonta were clustered together,implying that they might have a close genetic relationship.