Charadriiformes Birds Mitochondrial Genetic Characteristics Of The Pseudogene And Its Evolutionary Studies

With the concurrent developments of polymerase chain reaction (PCR) and DNA sequencing technology, the mitochondrial DNA (mtDNA) has become a very useful molecular marker for studying avian systematics and evolutionary biology. Since Du Buy and Riley firstly found that the mtDNA copies might exist in nuclear genome, many research results have demonstrated that the mitochondrial pseudogenes have been integrated into the nuclear genomes. Especially researchers, in the last ten years, have amplified many nuclear mitochondrial DNA segments (Numts) from total DNA using universal primers. Numts, however, may also embarrass the applications of mtDNA. The previously study displayed that people have obtained inaccurate or false conclusions as a result of wrongly using Numts as mtDNA for phylogenetic analyses. But these Numts may also be used as a novel and powerful tool in phylogenetic studies. As a phylogenetic marker, Numts have been applied in the phylogenetic analyses of human, Arabidopsis thaliana. However, in birds, the Numts have only just a few studies as yet. It therefore is very important to further studying the Numts for revealing the molecular evolution of birds.For further elucidating the molecular phylogeny of Charadriiformes and the utility of Numts in molecular evolution of birds, in this study, we have amplified mitochondrial ATP8/6 genes (partial ATP8/ATP6 gene) and corresponding Numts in 11 species of Charadriiformes. Our findings demonstrated that the length of mitochondrial ATP8/6 genes and corresponding Numts is 626bp, 618bp respectively. By comparing with mitochondrial ATP8/6 genes, these Numts have 8bp deleted and no insertions were found. The percentage of sequence divergence of Numts (variety from 0.2% to 1.6%) is significantly different from mitochondrial ATP8/6 genes (variety from 8.7% to 25.8%), and the variable nucleotide sites (only 14) and ts/tv ratio (1.2.) of Numts also obviously differ from mitochondrial ATP8/6 genes (243,1.6 respectively). In addition, the percentage of variable sites of the first, second and third codon positions of these Numts are 34.6%, 32.3% and 33.1% respectively, without codon position biases. In contrast, these mitochondrial ATP8/6 genes possess clear codon position biases (i.e. 20.8%, 4.6% and 74.6%, respectively). We further reconstructed the Maximum-parsimony (MP) and Neighbor-joining (NJ) trees using mitochondrial ATP8/6 gene and Numts respectively. Phylogenetic analyses indicated that using mitochondrial ATP8/6 genes can uncover clearly...