class7-En-20141114-系统发育分析

1、Bioinformatics22JIAO WANG (王娇王娇)National Center for Soybean Improvement（国家大豆改良中心）（国家大豆改良中心）Email: Tel: 84399530Evolutionary biology and Bioinformatics345 5What is Phylogenetics? In biology, phylogenetics is the study of evolutionary relatedness among various groups of organisms (for example, species

2、 or populations), which is discovered through molecular or morphological data. 6 6Phylogenetics tree A phylogenetic tree is a branching “tree” showing one species/sequence gives rise to two through successive events of speciation (branching). The taxa joined together in the tree are implied to have

3、descended from a common ancestor. Phylogenetic relationshipw “Phylogenetic relationship” refers to the relative times in the past that species shared common ancestors. 7w It does not refer to the similarities and differences among organisms.Read a tree 1 2 389 9 Traditional Phylogentics Physical and

4、 phenotypical characteristics are used to build a tree. Color, weight, height, eyes, wings. 1010Modern Molecular PhylogeneticsNucleotide or amino acid sequences11Two branches arising from each interior nodeComprise of nodes and branchesEach node represents a common ancestor. The connection lines rep

5、resent the evolutionary relationship The branch length represents the genetic distance (changes, or time estimates).Binary tree NodeBranches1212Making a Phylogenetic Tree（1）Sequences alignment（2）Model selection（3）Tree construction（4）Evaluate a tree 1313 Neighbor-joining apply sequence clustering ana

6、lysis using genetic distance as the parameter. Genetic distance is defined as the of mismatches at aligned sequences. NJ-tree is widely used in our gene family analysis. Model selection Neighbor-joining1414For example, dab = 5 dac = 8 dbc = 7uvabc13241515 Bootstrapping is a common method for assessi

7、ng confidence in phylogenetic analyses. Bootstrap results are commonly interpreted as a measure of the probability that a phylogenetic estimate represents the true phylogeny. Thousands times of data sampling from the original data (normally, 1000) are used to make different bootstrapping trees. Then

8、 the supporting rates based on the final tree represent the bootstrap values. Tree Evaluation: Bootstrapping16161717for calculation:ClustalW/X, Philip , MEGA, DNAstarfor view:Treeview, MEGAPopular phylogenetics softwares:1818Way 1: with ClustalX and TreeviewWay 2: with MEGATree Construction1919Way 1

9、: with ClustalX and Treeview 1)Mulitiple sequences alignment with ClustalX; 2)Make a NJ-tree with ClustalX; 3)View the tree by treeview.Tree Construction2020sequences:Glyma18g43310MASLLNMVSVPSRISPSSHTRTTSLQSRPVLPPFSVSFSRRRLSIRATETDTNEVQSQAPGTAPSKDGSSFNQLLGIKGASQETNKWKIRLQLTKPVTWPPLVWGVVCGAAASGNFHWNF

10、EDVAKSIVCMMMSGPFLTGYTQTMNDWYDREIDAINEPYRPIPSGAISENEVITQIWVLLLGGLSLAGILDIWAGHDFPIVFYLAVGGALLSYIYSAPPLKLKQNGWIGNFALGASYISLPWWAGQALFGTLTPDIIVLTLLYSIAGLGIAIVNDFKSVEGDRALGLQSLPVAFGAETAKWICVGAIDITQLSVAGYLLGADKPFYALALLGLIIPQVFFQFKYFLQDPVKYDVKYQASAQPFLVLGLLVTALATSH*GSVIVT01011187001MASLLNTVSSVRLSNARTTPRFLPP

11、ISLSLHRRRLVVRAAETDANEAVKSQAPDKAPAGSGSNFNQLLGIKGAAKETNKWKIRLQLTKPVTWPPLVWGVVCGAAASGNFHWNLEDVAKSIVCMIMSGPCLTGYTQTLNDWYDREIDAINEPYRPIPSGAISENEVITQIWLLLLGGLGLAGLLDVWAGHDFPIVFYLALGGSLLSYIYSAPPLKLKQNGWIGNFALGASYISLPWWAGQALFGTLNPDIIVLTLLYSIAGLGIAIVNDFKSVEGDRALGLQSLPVAFGAETAKWICVGAIDITQLSVAGYLLGAGKPYYALALVG

12、LIIPQVIFQFQYFLKDPVKYDVKYQASAQPFLVLGLLVTALATSH*POPTR_0006s10300MASVLNSALSLNLSNFKSKRVRTHSLVSPLSLPLTRRRVTIRAADTDTNEVKPQAPVSGGAGGSSFNQLLGIKGAAQETNKWKIRLQLTKPVTWPPLVWGVVCGAAASGNFNWTLEDVAKSIVCMLMSGPFLTGYTQTINDYYDREIDAINEPYRPIPSGAISENEVITQLWVLLLGGLGLAGLLDVWAGHDFPVVFYLALGGSLLSYIYSAPPLKLKQNGWIGNFALGASYISLPWW

13、AGQALFGTLTPDIIVLTLLYSIAGLGIAIVNDFKSIEGDRALGLQSLPVAFGAETAKWICVGAIDITQLSIAGYLLADGKPYYALALVGLIIPQIVFQFQYFLKDPVKYDVKYQASAQPFLVLGLLVTALATSH*AT3G51820.1MTSILNTVSTIHSSRVTSVDRVGVLSLRNSDSVEFTRRRSGFSTLIYESPGRRFVVRAAETDTDKVKSQTPDKAPAGGSSINQLLGIKGASQETNKWKIRLQLTKPVTWPPLVWGVVCGAAASGNFHWTPEDVAKSILCMMMSGPCLTGYTQTI

14、NDWYDRDIDAINEPYRPIPSGAISEPEVITQVWVLLLGGLGIAGILDVWAGHTTPTVFYLALGGSLLSYIYSAPPLKLKQNGWVGNFALGASYISLPWWAGQALFGTLTPDVVVLTLLYSIAGLGIAIVNDFKSVEGDRALGLQSLPVAFGTETAKWICVGAIDITQLSVAGYLLASGKPYYALALVALIIPQIVFQFKYFLKDPVKYDVKYQASAQPFLVLGIFVTALASQHLOC_Os05g28200MATSHLLAAASSTAASSATFRPPLLSLRSPPPSSLRLNRRRHFQVVRAAETDK

15、ETKANAPEKAPAGGSSFNQLLGIKGAKQENDIWKIRLQLTKPVTWPPLVWGVLCGAAASGNFHWTVEDVAKSIVCMIMSGPCLTGYTQTINDWYDRDIDAINEPYRPIPSGAISENEVITQIWALLLAGLGLGALLDVWAGHDFPIIFYLAVGGSLLSYIYSAPPLKLKQNGWIGNFALGASYIGLPWWAGQALFGTLTPDIVVLTSLYSIAGLGIAIVNDFKSVEGDRALGLQSLPVAFGMETAKWICVGAIDITQLSVAGYLFSSGKPYYALALLGLTIPQVVFQFQYFLKDPVKYDV

16、KYQASAQPFFVLGLLVTALATSH*GRMZM2G162672MAAAHLLAALSSSTALRPPLRLRSPQHPPHIRFNCTGRRPFPVVRAAETDAKNAKANAKAPNKAPAADGSSFNQLLGIKGAKQESDIWKIRLQLTKPVTWPPLVWGVLCGAAASGNFHWTVEDVAKSIVCMIMSGPCLTGYTQTLNDWYDRDIDAINEPYRPIPSGAISENEVITQIWVLLLGGLGLGALLDVWAGHDFPIVFYLAVGGSLLSYIYSAPPLKLKQNGWIGNFALGASYISLPWWAGQALFGTLTPDIIVLTTL

17、YSIAGLGIAIVNDFKSIEGDRTLGLQSLPVAFGMETAKWICVGAIDITQLSVAGYLLSTGKLYYALVLLGLTIPQVFFQFQYFLKDPVKYDVKYQASAQPFFVLGLLVTALATSH*Sb09g016840MAAAHLLAASAAASSSSTAFRPPLRLRSPLHPPHLRFNRTGRRPFPVVRAAETDAKDAKANAKVPEKAPAADGSSFNQLLGIKGAKQESDIWKIRLQLTKPVTWPPLVWGVLCGAAASGNFHWTVEDVAKSIVCMIMSGPCLTGYTQTLNDWYDRDIDAINEPYRPIPSGAIS

18、ENEVITQIWVLLLGGLGLGALLDVWAGHDFPIVFYLAVGGSLLSYIYSAPPLKLKQNGWIGNFALGASYISLPWWAGQALFGTLTPDIVVLTTLYSIAGLGIAIVNDFKSIEGDRTLGLQSLPVAFGMETAKWICVGAIDITQLSVAGYLLSTGKLYYALALLGLTIPQVFFQFQYFLKDPVKYDVKYQASAQPFFVFGLLVTALATSH*212223Generates .phb file 2425Exercise 11. Mulitiple alignment Exercise.fas with ClustalX;

19、2. Make a NJ-tree with ClustalX;3. View the tree by treeview.2627Way 2: with MEGA 1)Mulitiple sequences alignment; 2)Make a tree with MEGA 3)View the tree with MEGA.Tree Construction28Way 229Generates the .MEG file30Open the .MEG file31323334show phylogeny construction information35Tree/Branch Style (树形选择树形选择)36长方形长方形 Rectangular直线形直线形 Straight辐射形辐射形 Radiation环形环形 Circle37Optimi