Introduction of Evolutionary Analysis
Evolutionary analysis can reveal the genetic sequence relationship of classification in the evolution process from the perspective of molecular evolution. In the process of biological information analysis, phylogenetic trees are often used to present the analysis results. The phylogenetic tree can reveal the biological evolution process and mechanism of related species or genes. The evolutionary tree is mainly constructed based on the gene sequence to compare and analyze the changes and differences of genes in different environments, specific species or functions at the level of molecular evolution.
Evolutionary Analysis Method
Building a phylogenetic tree generally includes the following steps: multiple sequence alignment, choose a method to construct a phylogenetic tree, build evolutionary tree, evaluate evolutionary tree, and lastly beautify the evolutionary tree.
Fig 1. Phylogenetic tree construction pipeline
The first step of phylogenetic tree construction is to perform multiple sequence alignment. Commonly used software includes MEGA, cluster X, Muscle, phylip, etc.
Methods of phylogenetic tree construction generally include distance-based and character-based methods.
Bootstrap is usually used for evolutionary tree evaluation and testing.
Commonly used evolutionary tree beautification software includes AI, PS, ggtree, GraPhlAn, treeview, Figtree, and online website ITOL.
Fig 2. Phylogenetic tree of 199 B. rapa and 119 B. oleracea accessions. The tree was constructed using 6,707 SNP loci selected from gene pairs that were syntenic in the B. rapa and B. oleracea genomes. (Cheng F, et al. 2016)
Application Field
Human, animal and plant evolution analysis.
The evolutionary relationship of a gene or gene family in different species.
During genetic evolution research, the biological evolution process of species or genes can often be displayed intuitively by constructing evolutionary trees. Using various biological information analysis software and tools, a phylogenetic tree can be easily constructed. However, constructing a phylogenetic tree accurately and intuitively requires certain biological information analysis skills. CD Genomics' professional biological information analysis team, with excellent analysis and mapping skills, can provide phylogenetic tree construction services at any time. If you have any questions, please feel free to contact us.
Reference
- Cheng F, et al. Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea. Nat Genet. 2016;48(10):1218-1224. doi:10.1038/ng.3634
