Studies On Genetic Diversity And Population Structure Of Collichthys Lucidus

Collichthys lucidus, a member of Collichthys genus, Sciaendae, is one of the mostcommercially important warm-temperature and demersal smaller fishes around coastsof China. Due to overfishing and environmental disruption, the amounts of C. lucidusdeclined obviously in recent years. To investigate the genetic diversity of this species,we collected samples from most range of its distribution and tested thephylogeographic patterns and population genetic structures using both mtDNA andSSR markers. The taxonomic and phylogenetic relationships between C. lucidus andthe other species of Collichthys genus, C. niveatu were also estimated by mtDNAsequences variations. Our results were helpful to understand how historical climaticfluctuations, contemporary geographic and hydrologic features of the NorthwesternPacific influenced phylogenetic evolution and the population connections, wereimportant for appropriate exploitation and protection of Collichthys species.1. MtDNA sequences analyses for populations of C. lucidusThe mtDNA control region, Cytb and ND5gene complete sequences weresequenced and aligned for population samples of C. lucidus. The structure of controlregion was analyzed. All the three NJ trees constructed based on the haplotypesshowed two high distinct phylogenetic clades. One clade dominated the northernsamples, and the other mostly occupied southern samples, which had a boundarybetween Zhoushan and Wenzhou. The two clades were likely derived from theisolation between the East China Sea and the South China Sea during Pleistoceneglacial periods. The two clades occurred secondary contacts in the ND population forcontrol region and ND5, but they were also observed in YRE and FZ populations for Cytb. We postulated this could be caused by the faster evolutionary rates for controlregion than Cytb. The gene flow between population in Ningde and out sea was likelyblocked by the closed bay of Ningde which could help keep genetic imprinting fromdifferent ancestries. Haplotype diversities were high and nucleartide diversities werelow for three fragments indicating recent expansion from small effective populationsize.2. Microsatellite analyses for populations of C. lucidusNine microsatellite loci polymorphisms were scanned for the9populations of C.lucidus, of which four microsatellite loci were monomorphic in LYG populationindicating a founder event during population evolution arisen by edge effect. Highsignificant genetic differentiations were found among other eight populations, whichshowed very limited gene flow between contemporary populations. The populationscould be further divided into three geographic groups (SH, YRE vs. ZS, WZ, ND, FZvs. XM, SZ) based on an adjacent pooling AMOVA analyses which was discordantwith mtDNA grouping. Such genetic breaks in microsatellite DNA might be attributedto the blocks from fresh flows of Yangtze River and Taiwan Strait. The discordancebetween mitochondrial and microsatellites might be caused by the four-fold higherrate of drift for mtDNA than nuclear genes and fairly high mutation rate formicrosatellite DNA. The results suggested contemporary oceanic geographic andenvironmental factors played more important roles in shaping population geneticstructures than historical climate fluctuations. Historical divergence imprinting couldbe eliminated in nuclear DNA by post-glacial mixture and hybridization.3. Mitochondrial phylogenetic relationships between C. lucidus and C. niveatuC. lucidus and C. niveatu are the only two species of Collichthys genus. They arevery similar in morphological characters. In present study, we used mtDNA controlregion, Cytb and ND5gene complete sequences to investigate the phylogenetic andevolutionary relationships between the two species. The phylogenetic trees showedhigh divergence in all the three fragments, corresponding to the net genetic distances of14.5%,10.5%and2.7%respectively. According to a nucleotide divergence rate of2%/million years in Cytb, the two species might diverge genetically approximate5million years ago. And we calculated the nucleotide divergence rates for controlregion and ND5were2.8%and0.5%respectively in Collichthys species.