construction and analysis of the avian phylogenetic tree 鸟类 .pdf

Hans Journal of Computational Biology 计算生物学, 2017, 7(1), 1-11 Published Online March 2017 in Hans. /journal/hjcb /10.12677/hjcb.2017.71001 Construction and Analysis of the Avian Phylogenetic Tree * * Yongfen Zhang, Xun Zhou, Liaofu Luo , Lirong Zhang School of Physical Science and Technology, Inner Mongolia University, Hohhot Inner Mongolia th th st Received: May 15 , 2017; accepted: May 25 , 2017; published: May 31 , 2017 Abstract Based on nucleotide sequences in 394 conserved regions of 47 avian DNA sequences obtained us- ing targeted-next generation DNA sequencing, the k-mer frequency (from 9-mer to 14-mer) was counted. We calculated the distance matrix among 47 avians by k-mer Non-aligned Algorithm (KNA) and constructed the phylogenetic tree by the Neighbor-Joining method. The results showed that the phylogenetic tree is changed with increasing k and stabilized when k equals 12. Then, we compared 12-mer phylogenetic tree with two other trees constructed by Prum and Jarvis respec- tively and analyzed the evolution and classification of these birds. We found that the three phylo- genetic trees are basically same apart from a small part of sister branches on the trees. The con- sistency revealed that the frequency of 12-mer is a better dynamic variable for measuring evolu- tion of species. Keywords Avian, DNA Sequence, K-Mer, Phylogenetic Tree 鸟类基因组进化树的构建与分析 * * 张永芬，周 勋，罗辽复 ，张利绒 内蒙古大学物理科学与技术学院，内蒙古 呼和浩特 收稿日期：2017年5月15 日；录用日期：2017年5月25 日；发布日期：2017年5月31 日 摘 要 本文选取了47种鸟类的基因组作为研究对象，根据靶定下一代DNA测序技术(targeted next-generation *通讯作者。 文章引用: 张永芬, 周勋, 罗辽复, 张