Species Delimitation, Phylogenetics And Biogeography Of The Sinipercids And Population Genetic And Evolution History Of The Genus, Coreoperca

The sinipercids(Perciformes)are freshwater fishes endemic to East Asia,mainly in China.Its distribution is limited by the water system.Scattered habitat limits its dispersal and gene flow,promoting population differentiation.It is a good material for studying freshwater fish fauna in China.Delimiting species status and resolving the phylogenetic relationship among sinipercids are prerequisites to understand the origin of the sinipercids,the influence of geography historical events on its evolutionary trajectory and the Chinese freshwater fish fauna in general.The genetic structure and genetic diversity of different water systems and different populations in time and space can reflect the history of the geographical changes of the water systems.Most species of sinipercids are found only in China,some of those are important economically,such as the Chinese mandarin fish,Siniperca chuatsi.In the early days,the wild resources of the sinipercids were abundant,but it started decreasing sharply from the 1970 s,and many sinipercid species are depleted from most of the areas north of the Yangtze River.Thus,the genetic structure and genetic diversity of the sinipercids are in urgent needs to be evaluated for better protection measures to the sinipercids.As an ideal taxon for studying the evolution and geographical distribution of fish in East Asia,researches on species delimitation and taxonomy of the sinipercids have a long history,but validity of some species,population genetics,classification of some genus,interspecific relationships and evolutionary history of the sinipercids are still controversial.At present,studies on the sinipercids were mainly based on morphological,mitochondrial DNA and/or a few nuclear gene loci.Different scholars have inconsistent conclusions based on various methods and experimental data.Coreoperca is a major group of the sinipercids,distributed in China,Korea,and Japan.The special geographical distribution characteristics make Coreoperca a good material for studying the crustal movement in the East Asian coastal areas and its biogeography of freshwater fish fauna.At present,the research on Coreoperca is mainly focused on morphological classification and surveys on its genetic resource.There are few studies on the genetic structure and phylogenetic relationship among the species and populations of Coreoperca.Furthermore,the data of these studies are insufficient and their results are not conclusive.In this thesis,I have carried out two parts of research regarding the above-mentioned issues: the first part is set to delimitate controversial species of the sinipercids and reconstruct a robust phylogeny of the sinipercids,the second part is focused on analyzing the evolutionary history of the genus,Coreoperca and biogeography of freshwater fish fauna in East Asia.Phylogenetic studies on the sinipercids have made great progress in the last decades,but interspecific relationships and evolutionary history of the sinipercids remain unresolved.Lack of distinctive morphological characters leads to problems in validating of some species,such as Siniperca loona.Moreover,genetic data are needed to delimitate species pairs with explicit hypothesis testing,such as in S.chuatsi vs.S.kneri and Coreoperca whiteheadi vs.C.liui.Here we reconstructed phylogeny of the sinipercids with an unprecedented scale of data,16,943 loci of single-copy coding sequence data from nine sinipercid species,eight putative sister taxa and two outgroups.Targeted sequences were collected using gene enrichment and Illumina sequencing,yielding thousands of protein coding sequences and single nucleotide polymorphisms(SNPs)data.Maximum likelihood and coalescent species tree analyses resulted in identical and highly supported trees.We confirmed that the centrarchids are sister to the sinipercids.A monophyletic Sinipercidae with two genera,Siniperca and Coreoperca was also supported.Different from most previous studies,S.scherzeri was found as the most basal taxon to other species of Siniperca,which consists of two clades: a clade having S.roulei sister to S.chuatsi and S.kneri,and a clade consisting S.loona sister to S.obscura and S.undulata.We found that both S.loona and C.liui are valid species using Bayes factor delimitation(BFD*)based on SNPs data.Species delimitation also provided decisive support for S.chuatsi and S.kneri being two distinct species.We calibrated a chronogram of the sinipercids based on 100 loci and three fossil calibration points using BEAST,and reconstructed ancestral ranges of the sinipercids using Lagrange Analysis(DEC model)and Statistical Dispersal-Vicariance Analysis(S-DIVA)implemented in RASP.Divergence time estimates and ancestral habitat reconstruction suggested a wide-ranging distribution of the common ancestor of the sinipercids in southern China at 53.1 million years ago(CI: 30.4-85.8 Ma).The calibrated time tree is consistent with historical climate changes and geological events that might have shaped the current distribution of the sinipercids.The second part is focused on the genus Coreoperca,including its phylogenetics,population structure and gene flow,and reconstructing the evolutionary history and the origin of the Coreoperca,providing new evidences for evaluating the history of freshwater ichthyofauna in East Asia.Targeted sequences were collected using gene enrichment and Illumina sequencing,yielding 14,246 loci of single-copy coding sequence and 3,509 single nucleotide polymorphisms(SNPs)data from 51 Coreoperca samples,seven sinipercid samples and two outgroups.Phylogenetic relationship of the Coreoperca was reconstructed based on three different sub-set data using RaxML,Maximum likelihood analyses resulted in identical and highly supported gene trees.Coreoperca kawamebari of Japan was found as he most basal taxon to other species of Coreoperca,C.herzi of Korea is sister to the Chinese C.whiteheadi and C.liui.We confirmed that Coreoperca has four genetic groups using Structure and PCA analyses based on SNPs data.Migrate-n analysis showed that the gene flow between C.whiteheadi C.liui similar in both direction,and so are their population size.The migration of C.whiteheadi from the Hainan region to the Guangdong area was significantly larger than other migrations of other directions among Hainan,Guangdong and Guangxi regions.We calibrated a chronogram of the Coreoperca based on 100 loci and three fossil calibration points using BEAST,and reconstructed ancestral ranges of the Coreoperca using Lagrange Analysis(DEC model)and Statistical Dispersal-Vicariance Analysis(S-DIVA)implemented in RASP.Divergence time estimates and ancestral habitat reconstruction suggested that the Coreoperca was widely distributed in China and Japan and differentiated in Early Miocene,further supporting the suggestion that the fish faunas in Eastern China and Japan belonged to the same one during Miocene.The results of this study not only provide a scientific basis for the species conservation,evolutionary history and biogeography of sinipercids and Coreoperca,but also provide new evidence for the historical evolution of freshwater fish fauna in East Asia.