| In recent years, studies integrated with phylogeography, population historical demographic, and ecological niche modeling, which all based on gene genealogy, had become the main solution to slove the microevolutionary questions. Mitochondrial gene markers were widely used in those studies. Control region, the main non-coding region which related to replication and transcription in mithochondrial genome, is often selected as common molecular maker in molecular systematics, due to its high evolution rate.Paridae, which is characterized by variable plumage, wide distribution, adapted to various environments, and displayed diverse behaviors, is extensively used as models in many aspects of biology researches, especially in evolutionary biology. In this study, we focused on two species of Paridae and conducted two researches with selected mitochondrial fragments as molecular markers. First study dealed with the phylogeography of Yellow-bellied tit (Parus venustulus), second is about the origins and evolution of tandem repeat sequences in mitochondrial control region of Yellow-browed tit (Sylviarus modestus).Phylogeographic and population dynamic studies of Yellow-bellied tit. Yellow-bellied tit is endemic in China, and mainly distributed in mountain areas of Southwest, Southeast and North China. In the last few decades, it shown a tremendous northward range expansion, and in some areas it had a change of inhabitation. In this study, phlogeographic analyses and ecological niche models were used to investigate the population structure and demographic history of yellow-bellied tit. Phylogeographic analyses were carried out using four mitochondrial loci from 132 individuals from 20 sampling sites. Based on the current inhabitation, we divided the 20 sampling sites into 9 geographical groups. The results are as following:(1) Four mitochondrial loci from 132 individuals were sequenced, and combined them into three combined datasets. The combined dataset 1 was comprised by all four loci, the combined dataset 2 only contained cyt b and ND2 and the combined dataset 3 only contained atp6 and atp8. The former two datasets had a high haplotype diversity (hd) and the nucleotide diversity (π) ranging from 0.001-0025.(2) The haplotype network and phylogenetic analyses of the combined dataset 1 and 2 shown that no phylogeographic structure could be found in yellow-bellied tit, while the combined dataset 3 can be divided into two distinct haplotype groups, which contained only one mutated site. And the molecular dating result indicated that the divergence time within yellow-browed tit were rather young, and the divergence time among haplotypes were ranging from 40 to 70 ka. The AMOVA analysis suggested that most of variations were attributed to that among individuals. The nested clades analysis shown that contiguous range expansion or long distance colonization shaped the current range of yellow-bellied tit. While the predicted gene flows among geographical groups indicated that frequent gene flows among them could be expected. All these results suggested that continual individuals exchange occurred among different geographical groups, and yellow-bellied tit seemed to have an ability to conduct long distance migration among different geographical groups.(3) The Tajima’s D and Fu’s Fs of each geographical groups were significant negative values. The mismatch distribution of most geographical groups only had one peak, and the SSD test and Raggedness index of these groups were not significant. These results indicated that most of geographical groups experienced rapid expansion. Bayes skyline plot suggested two historical demographic expansion during the two cold periods, MIS3b and MIS3, in last glacial.(4) Ecological niche modeling results shown that the mountain areas of Southwest China were stable ranges for yellow-bellied tit, and the populations in North China were more likely to be established in the last few decades after recent range expansion.The following main conclusions could be drawn based on these results described above. (1) The reason why yellow-bellied tit did not have any deep split could be related its recent divergence within species and its strong capability to conduct long distance migration. (2) atp6 had two distinct haplotype groups in yellow-bellied tit, and this could be supported by Ecological Niche Modeling; but this split of atp6 appeared not to be correlate with isolation of elevation. (3) The gene flows among newly colonized population and ancient populations of yellow-bellied tit were frequent, this could maintain high genetic diversity in the newly colonized population, and the high genetic diversity could contribute to colonization success. (4) The results of Ecological Niche Modeling of yellow-bellied tit suggested that a slightly niche shift during range expansion which could be related to both its breeding environment and its expanded population size, and there should have some unreported breeding sites in mountain areas of Northeast China.The origins and evolution of tandem repeat sequence in mitochondrial genome of Yellow-browed tit. In previous study on obtaining the mitochondrial genome of yellow-browed tit, we found a tandem repeat sequence with a 117 bp-long repeat unit which repeat twice. In this study, we used 15 individuals from 5 sampling sites, obtained the sequence of control region and another four mitochondrial loci of these individuals, and mapped number of repeat units onto phylogenetic trees. Based these analyses, we discussed the origins and evolution of this tandem repeat sequence in yellow-browed tit. The results are as following:(1) The repeat unit repeated once, twice and three times in different individuals. And two types of repeat units existed in some individuals, and the two repeat unit types could form four arrangement patterns. At the downstream of repeat sequence, there was a 5’imperfect copy with the former 96 bp of repeat unit which shown 5 variable sites. And at the downstream of repeat sequence, there was a 3’imperfect copy with the last 23 bp of repeat unit which exhibited 6 variable sites. The repeat unit could not find any homologs in other parids or passerines. But the combined 3’imperfect copy and 5’ imperfect copy could find its homologs in other parids and passerines. So that combined sequence should be the original sequence before tandem duplication.(2) The haplotype network showed that yellow-browed tit could split into at least three haplotype clusters. When mapped the repeat numbers onto the phylogenetic tree we found that same repeat number could be found in different clusters. The result of ancestral state reconstruction exhibited that the four arrangement patterns were not monophyly. The only shared haplotype contain two individuals with different repeat numbers. These results suggested even the same repeat numbers could originated multiply, and the change of repeat numbers seemed not to be correlated with the affinities among different individuals.Based on these results described above, the following five conclusions could be drawn. (1) The arrangement of tandem repeat in yellow-browed tit, which had a 3’im copy at its upstream and a 5’im copy at its downstream, were rarely reported. (2) The same repeat number seemed have multiple origins, and the change of repeat numbers was not a suitable marker on discussing the lineage divergence or phylogenetic relationships among or within certain taxon. (3) The accumulation of repeat numbers and that of nucleotide mutations were two inconsistent process, and the accumulation of repeat numbers seemed to more faster than that of nucleotide mutation. (5) Recombination might be a better explanation for the origin of the tandem repeat in yellow-browed tit, for the combined 3’and 5’ imperfect copy and its adjacent sequence could form a complex secondary structure, which could prevent the slipped-strand misparing. And the recombination process should induced by the mini cycles which formed by the short sequence excised from the mtDNA molecule. |
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