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Qinba Mountain Carabidae (coleoptera: Carabidae Branch) Population Genetic Structure And Population Change History

Posted on:2012-09-16Degree:DoctorType:Dissertation
Country:ChinaCandidate:H YinFull Text:PDF
GTID:1110330371452694Subject:Ecology
Abstract/Summary:PDF Full Text Request
The Tsinling-Dabashan Mountains are one of centers for the origin and evolution of biodiversity in China. These areas contain rich animal and plant resources. The Oriental and Palaearctic species congregate here forming a specific biotic province. The past climatic events, such as the Quaternary glaciation. could leave vestiges in geographical distribution of genetic diversity of population. Like other regions in the northern hemisphere, the Tsinling-Dabashan Mountains also experienced several glacial-interglacial cycles. Understanding the pattern of genetic structure and diversity condition of fauna are distributing on Tsin-ba and the effects of palaeoglaciation on geographical distribution pattern have great value. The species belonging to Carabidea family are ancient, and the most of them are beneficial insect with significial genetic differentiation. They play an important role in pest management. Complement understanding about the conditions of genetic diversity and distribution pattern of beetles on the Tsin-ba Mountains is important for species protection and also provides the foundation for pest control.In this study, mtDNA coxl-cox2 were emplyed to reveal the populations structure and historical demography of Pheropsophus jessoensis, Dolichus halensis (Schaller.1783) and Chlaenius pallies. All of them are widespread species. The results of investigations are offered as follows:1. A total of 184 adults of the ground beetle P. jessoensis were collected from 25 locations on the Tsinling-Dabashan Mountains. In length of 1601bp fragment, a total of 879 bp were sequenced for the mtCoI gene, and 653 bp for the mtCoII gene. The intervening tRNA Leu gene was 69 bp in length, which contained a 1-bp deletion.81 positions were polymorphic sites, composed of 43 parsimony informative sites and 38 singleton variable sites. These polymorphic sites identified 92 haplotypes. The total genetic diversity HT (0.960) among all sampled populations, the average within-population diversity Hs (0.880) and the haplotype diversity Hd (0.963) of total population were considerable high, but the nucleotide diversity Pi (0.0037) of total population was fairly low. And 79.34% of total haplotypes are private haplotypes with lower frequency. Phylogenetic analysis (Bayesian inference) and parsimonious network of the 92 haplotypes revealed eight major clades (A-H). AMOVA analysis suggested that most of the variation was attributed to within populations and among clades and the genetic differentiation among populations and among clades were significiant (among population:FST=0.078, p<0.01; among phylogroups:FST=0.558, p<0.01). But the SAMOVA tests and PERMUTE analyses failed to reveal any meaningful phylogeographic structure (NST=0.107> GST=0.083, p=0.075>0.05). The results of statistical phylogeography analysis rejected the model of population fragmentation. The gene flow calculated through the Nm was high between many pairs of populations, and Mantel test results showed significant correlation between the pairwise calculated genetic distance and pairwise calculated geographical distance of the populations (R= 0.360, p=0.002< 0.01), indicating the presence of isolation-by-distance model (IBDM). The results of neutral test and mismatch distribution analyses of total population and the eight mtDNA clades suggest several demographic expansions between 0.2Myr to 0.01 Myr, and a sudden expansion was identified between 0.05 Myr to 0.01 Myr by BSP analysis. The estimated age of the origin of the P. jessoensis was 0.30 Myr, with a 95% interval of confidence between 0.20 and 0.50 Myr by BEAST.2. A total of 191 adults of the ground beetle D.halensis were collected from 24 locations on the Tsinling-Dabashan Mountains. In length of 1601bp fragment, a total of 882 bp were sequenced for the mtCol gene, and 656 bp for the mtCoâ…¡gene. The intervening tRNA Leu gene was 63 bp in length.45 positions were polymorphic sites, composed of 15 parsimony informative sites and 30 singleton variable sites. These polymorphic sites identified 53 haplotypes. The total genetic diversity HT (0.705) among all sampled populations, the average within-population diversity HS (0.612) and the haplotype diversity Hd (0.769) of total population were considerable high, but the nucleotide diversity Pi (0.0033) of total population was fairly low. And 65.71% of total haplotypes are private haplotypes with lower frequency. Phylogenetic analysis (Bayesian inference) and parsimonious network of the 53 haplotypes revealed 2 major clades (A-B). AMOVA analysis suggested that most of the variation was attributed to within populations and among clades and the genetic differentiation among populations and among clades were significiant (among population:FST=0.134, p<0.01; among clades:FST=0.433,p<0.01). But the SAMOVA tests and PERMUTE analyses failed to reveal any meaningful phylogeographic structure (NST=0.154> GST=0.132,p= 0.085>0.05). The results of statistical phylogeography analysis accepted the model of population fragmentation. The gene flow calculated through the Nm was high between many pairs of populations, but Mantel test results showed no significant correlation between the pairwise calculated genetic distance and pairwise calculated geographical distance of the populations (R=0.055, p=0.679> 0.05). rejecting the supposed of isolation-by-distance model (IBDM). The results of neutral test and mismatch distribution analyses of total population and the two mtDNA haplogroups suggest several demographic expansion between 0.05 Myr to 0.01 Myr, and a sudden expansion was identified between 0.05 Myr to 0.01 Myr by BSP analysis. The tMRCA of all D.halensis was date to 0.2609 Myr before present (95% of the highest posterior density [HPD]:0.4300 to 0.1490 Myr).3. A total of 151 adults of the ground beetle C.pallipes were collected from 13 locations on the Tsinling-Dabashan Mountains. In length of 1602bp fragment, a total of 882 bp were sequenced for the mtCoâ… gene, and 658 bp for the mtCoâ…¡gene. The intervening tRNA Leu gene was 62 bp in length, which contained a 1-bp insertion.56 positions were polymorphic sites, composed of 45 parsimony informative sites and 11 singleton variable sites. These polymorphic sites identified 65 haplotypes. The total genetic diversity HT (0.985) among all sampled populations, the average within-population diversity HS (0.885) and the haplotype diversity Hd (0.972) of total population were considerable high, but the nucleotide diversity Pi (0.0025) of total population was fairly low. And 73.85% of total haplotypes are private haplotypes with lower frequency. Phylogenetic analysis (Bayesian inference) and parsimonious network of the 92 haplotypes revealed three major haplogroups (A-C). AMOVA analysis suggested that most of the variation was attributed to within populations and among haplogroups and the genetic differentiation among populations and among phylogroups were significiant (among population:FST=0.079,p<0.01; among phylogroups:FST= 0.338, p<0.01). But the SAMOVA tests and PERMUTE analyses failed to reveal any meaningful phylogeographic structure (NST=0.114> GST=0.101, p=0.33>0.05), The results of statistical phylogeography analysis rejected the model of population fragmentation. The gene flow calculated through the Nm was high between many pairs of populations, and Mantel test results showed no significant correlation between the pairwise calculated genetic distance and pairwise calculated geographical distance of the populations (R=0.126, p=0.855>0.05), rejecting the supposed of isolation-by-distance model (IBDM). The results of neutral test and mismatch distribution analyses of total population and the three mtDNA haplogroups suggest several demographic expansions between 0.125 Myr to 0.05 Myr. and a sudden expansion was identified between 0.075 Myr to 0.1 Myr by BSP analysis. The estimated age of the origin of the C.pallipes was 0.2544 Myr, with a 95% interval of confidence between 0.1594 and 0.3699 Myr by BEAST.In conclusion, we consider that there are significant genetic differentiations between populations of beetles distributing on the Tsinling-Dabashan Mountains, but we failed to reveal any meaningful phylogeographic structure for the gene flow calculated through the Nm was high between many pairs of populations. Climate change by glacial-interglacial cycles in the Quaternary glaciation led to several demographic expansions of beetles. Bottleneck effect, demographic expansion after glaciation and long-distance migration are important factor for the pattern of genetic.
Keywords/Search Tags:population genetic structure, historical demography, mitochondrial DNA, ground beetles, Tsinling-Dabashan
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