分子系统树法(复旦大学研究生课件).ppt

* Tradeoff between the fitting of the model and the complexity of the model. In the KH test paper, we first introduced the Akaike Information Criterion (AIC) in comparing models into the field of molecular phylogenetics, and today it has become well known to the biologists of this field. * Bootstrap.bmp * RELL.jpg * Functional constraints on sites in a gene sequence often change through time, causing shifts in site-specific evolutionary rates, a phenomenon called heterotachy (meaning ‘different speeds’) * Importance of a rich taxon sampling * Functional constraints on sites in a gene sequence often change through time, causing shifts in site-specific evolutionary rates, a phenomenon called heterotachy (meaning ‘different speeds’) * Fur-seal at Kaikoura (1996) During the last 10 years, my main interest moved to mammalian evolution, particularly placental mammals, or eutherians, and I have been working on the deep branchings of eutherian evolution. * * Molecular phylogenetics has entered the genomic age with genome-scale sequence data to analyze, and is called phylogenomics. In this paper we tried to root the eutherian tree with phylogenomic analysis, and have demonstrated that, in spite of the presence of the abundant genome-scale data, it is not easy to solve the problem. We further showed that the methodology of the data analysis particularly modeling is most important. * * 12 flanking loci; 2792 nucleotide sites Rannala Yang (2008) Annu. Rev. Genomics Hum. Genet. 9:217–231 * Song et al. (2012) the coalescent methods, which accommodate gene tree heterogeneity * * Shields et al. (2000) MPE 15:319-326 Tibetan brown bear * GENETREE * * Since I gave a talk on molecular phylogenetics of mammals here in July of the last year, today I will talk about molecular evolution and phylogenetics using plant evolution as an example. The examples I am going to show you would be useful even if you are not botanists and are analyzing other groups of organisms such as animals or