The Molecular Phylogenetics Of Lutjanid Fishes Of The Genus Lutjanus From China

Molecular phylogenetics,also known as molecular systematics,is the use of the structure of molecules to gain information on an organism's evolutionary relationships.The most common approach is the comparison of sequences for genes using sequence alignment techniques to identify similarity.Another application of molecular phylogeny is in DNA barcoding,where the species of an individual organism is identified using small sections of mitochondrial DNA.The result of a molecular phylogenetic analysis is expressed in a phylogenetic tree,which is the base of revealing the mechanism of speciation.Lutjanid Fishes (Perciformes:genus Lutjanus) are important fishery resource and have been cultured in South China Sea.Through studying their molecular phylogenetics,we have achieved the fellowing results:1.Forty species of teleosts fish,including fifteen lutjanid fishes,in South China Sea,were sequenced(barcoded) for a 660 bp region of the mitochondrial cytochrome oxidase subunit I gene(cox1).Most species were represented by multiple specimens,and 89 sequences were generated.Average within-species,genus,family,and order Kimura two parameter(K2P) distances were 0.0084,0.1567,0.1839 and 0.2319, respectively.All species could be differentiated by their cox1 sequence, although single individuals of each of two species had haplotypes characteristic of a congener.Although DNA barcoding aims to develop species identification systems,some phylogenetic signal was apparent in the data.In the neighbour-joining tree for all 89 sequences,species within genera invariably clustered and three major clusters were apparent: snappers,groupers and the other fishes.The two former clades revealed after bootstrapping generally corresponded well with expectations.We conclude that cox1 sequencing,or 'barcoding',can be used to identify lutjanid fish species.2.The entire mitochondrial DNA sequence(mitogenome) of five species, Lutjanus bengalensis,L.Malabaricus,L.Sebae,L.Kasmira and cobia (Rachycentridae:Rachycentron canadum) were determined using long PCR and primer-walking methodology,and their GenBank Accession numbers are FJ171339,FJ416614,FJ824741,FJ824742 and NC 011219, respectively.The mitochondrial genomic sequence in snappers and cobia are similar to other vertebrate mitochondrial genomes with respect to gene order and genomic organization.Phylogenetic relationships derived from mtDNA sequences of L.russellii,L.rivulatus,L.bengalensis,L. Malabaricus,L.Sebae,L.Kasmira,cobia and Dark banded fusilier (Caesioninae:Pterocaesio tile) were incongruent with those derived from morphological taxonomic analyses.Beyond expected,high homogeneities were observed between some lutjanids and fusilier, belonging to Lutjaninae and Caesioninae.Further efforts may clarify the phylogenetic relationships among these snappers.3.Two data sets were constructed firstly.One comprised 32 complete mitochondrial DNA genomes of Perciformes downloaded from GenBank. The other was mainly based on the snappers' mitochondrial DNA we determined in this study.Then we investigated the performance of all mitochondrial protein-coding genes to recover two phylogenies of Perciformes and genus Lutjanus.According to these tests,mitochondrial protein-coding genes can be roughly classified into four groups,(1) at the level of family,of very good(ND6 and cox2),good(ND4 and ND5), medium(ND1,ND2,cox3,Cyt b,cox1 and ATPase 6),and poor(ND3, ND4,ND4L,and ATPase 8);and(2) at the level of genus,of very good (ATPase 6 and cox2),good(cox1 and ND2),medium(cox3,ND1,ND4, ND4L and ND5),and poor(ND3,ND6,and ATPase 8).Moreover,we inform that simple length differences and rate differences between these genes cannot account for their different phylogenetic performance.We advice the careful selected genes and their combinations should be helpful for high resolved phylogenetic analysis for different level taxon.4.The phylogenetic relationships of thirteen snapper species from the South China Sea(SCS) have been established based on the combined DNA sequences of three full-length mitochondrial genes(cox1,cox2 and Cyt b) and two partial nuclear genes(RAG1,RAG2).These thirteen species(genus Lutjanus) were selected after DNA barcoding of 72 individuals representing twenty species.5389 base pairs of combined DNA sequence were used to infer the phylogenetic relationship.Our data strongly suggests that the inter-specific relationships of all thirteen recognized species in SCS are consistent with Allen's morphology-based classification.There is a strong correlation between the molecular and morphological characteristics,particularly body coloration and band patterns.Our finding is also consistent with the findings in other coral reef fish.The two distinct classes of stripes,blue(L.kasmira,L. bengalensis and L.quinquelineatus,mainly distributed in outer shelf reefs) and red(L.malabaricus,L.erythropterus and L.sebae,distributed in inshore and estuaries),may be evidence for speciation through sensory drive without geographical isolation.In addition,our study suggested that although DNA barcoding aims to develop species identification systems, this approach can also aid the construction of phylogenies by aiding the selection of taxa.The combined mitochondrial and nuclear gene data has advantage over the individual dataset due to its higher resolution power.5.Comparisons of functionally important changes at the molecular level in model systems have identified key adaptations driving isolation and speciation.To test the hypothesis that the evolution of the speciation of snappers is associated with opsin gene diversity,we sequenced long wavelength-sensitive(LWS) opsin genes in ten species of the genus lutjanus.Relationships among higher taxonomic groups were well resolved in the tree reconstructed from LWS opsin sequences.There is high(＞75%) bootstrap support for monophyly of lutjnaus,the family Cyprinidae(goldfish,carp,blind cavefish and zebrafish) and terrestrial animals(horse,cat,bovine and green anole).In contrast to mtDNA and RAG gene,the ratio of phylogenetically informative characters is very low in the third codon positions of LWS.And the signifiant diversity have been observed between LWS opsins of L.vitta and L.ophuysenii.These evidences imply that selective adaption of LWS may play a important role in the sympatric diversity of snappers.