Maximum likelihood and Bayesian phylogenetic trees

Tree files named as “RAxML_PB2.tre” et al. are maximum likelihood (ML) trees of six internal segments (PB2, PB1, PA, NP, M and NS) composed of the same 2343 North America AIV strains, which were reconstructed using RAxML v7.04. In each ML tree, the Mexico H7N3 strains are colored in red, and the lineage in which H7N3 Mexico fell is colored in blue; Tree files named as “HA.mcc.tre” et al. are temporally structured maximum clade credibility (mcc) time-scaled phylogenetic trees of all eight segments, which were generated using Beast V 1.7.3 and annotated with ancestral state changes (A: host order; B: host species; C: flyway; D: state/province; E: subtype) recovered from the discrete trait analyses. In each mcc tree, the branches are colored according to the trait state in the tree nodes. All tree files can be visualized in FigTree V 1.4.0.

以"RAxML_PB2.tre"等命名的树文件为基于同一组2343株北美禽流感病毒（Avian Influenza Virus, AIV）株构建的6个内部片段（PB2、PB1、PA、NP、M和NS）的最大似然（maximum likelihood, ML）树，使用RAxML v7.04软件完成构建。在每棵ML树中，墨西哥H7N3毒株以红色标注，其所属的进化分支则以蓝色标注；以"HA.mcc.tre"等命名的树文件为全部8个片段的具有时间结构的最大类群置信度（maximum clade credibility, MCC）时间标度进化树，此类进化树通过Beast V 1.7.3软件生成，并以离散特征分析得到的祖先状态变化（A：宿主类群；B：宿主物种；C：迁徙路线；D：州/省；E：亚型）进行注释。在每棵MCC时间标度进化树中，分支颜色根据树节点的特征状态进行标注。所有树文件均可通过FigTree V 1.4.0软件进行可视化。