《生物信息学》(第二版)(樊龙江主编,2021)配套PPT5 5. Phylogenetic Tree 5.1 Genetic polymorphism and phylogenetic tree 5.2 Construction of phylogenetic tree
5. Phylogenetic Tree 5.1 Genetic polymorphism and phylogenetic tree 5.2 Construction of phylogenetic tree 《生物信息学》（第二版）（樊龙江主编，2021）配套PPT5
历史与人物 达尔文 费希尔( Fisher)、莱特( Wright)和霍尔丹( Haldane)(群体遗传学三巨头) 马莱科特( Malecot)、科克汉姆( Cockerham)等 木村资生( Kimura)、根井根正( M Nei)等 Great trinity
达尔文 费希尔（Fisher）、莱特（Wright）和霍尔丹（Haldane）（群体遗传学三巨头） 马莱科特（Malecot）、科克汉姆（Cockerham）等 木村资生（Kimura）、根井根正（M. Nei）等 Wright Fisher Haldane Great trinity 历史与人物
5.1 Genetic polymorphism and phylogenetic tree Polymorphism in the genomes Introduction about tree
5.1 Genetic polymorphism and phylogenetic tree • Polymorphism in the genomes • Introduction about tree
Polymorphism in the genomes Types of polymorphism Single nucleotide polymorphism(SNP) Insertion/deletion (indel) Copy-number variation(CNV) ● Frame- shift Presence and absence variation(PAv)
• Types of polymorphism • Single nucleotide polymorphism (SNP) •Insertion/deletion (indel) • Copy-number variation (CNV) • Frame-shift • Presence and absence variation (PAV) Polymorphism in the genomes
indica 1 ATG CGG GAT CCA TTC CTT AAT GAG TTT CCT AAA ACG GTG CAC GGT TTT ATG TGG GAT CCA TTC CTT AAT GAG TTT CCC GAA ACG GTG CAC GGT TTT indica 3 ATG TGG GAT CCA TTC CTT AAT GAG TTC CCT GAA ACG GTG CAC GGT TTT joponica 1 ATG TGG CCA TTC CTT AAT GAG TTC CCT GAA ACC GTG CAC GGT TTT joponica 2 ATG CGG--- CCA TTG CTT AAT GAG TTC CCT GAA ACC GTG CAC GGT TTT joponica 3 ATG TGG GAT CCA TTG CTT AAT GAG TTC CCT GAA ACC GTG CAC GGT TTT ufipogon_ 1 ATG TGG GAT CCA TTC CTT AAT GAG TTC CCT GAA ACG GTG CAC GGT TTT rufipogon 2 ATG TGG GAT CCA TTG CTT AAT GAG TTC CCT GAA ACC GTG CAC GGT TTT rufipogon 3 ATG TGG GAT CCA TTG CTT AAT GAG TTC CCT GAA TG CAC GGT TTT 0. Nivara ATG TGG GAT CCA TTC CTT AAC GAG TTC CCT GAA ACG GTG CAC GGT TTT Measure of polymorphism T(Tajima 1983): the average pairwise nucleotide diversity 0(Watterson 1975): Watterson's estimator. Number of separating sites per nucleotide site
• Measure of polymorphism • π (Tajima 1983): the average pairwise nucleotide diversity • θ (Watterson 1975): Watterson’s estimator. Number of separating sites per nucleotide site indica_1 ATG CGG GAT CCA TTC CTT AAT GAG TTT CCT AAA ACG GTG CAC GGT TTT indica_2 ATG TGG GAT CCA TTC CTT AAT GAG TTT CCC GAA AC G GTG CAC GGT TTT indica_3 ATG TGG GAT CCA TTC CTT AAT GAG TTC CCT GAA ACG GTG CAC GGT TTT joponica_1 ATG TGG --- CCA TTC CTT AAT GAG TTC CCT GAA ACC GTG CAC GGT TTT joponica_2 ATG CGG --- CCA TTG CTT AAT GAG TTC CCT GAA ACC GTG CAC GGT TTT joponica_3 ATG TGG GAT CCA TTG CTT AAT GAG TTC CCT GAA ACC GTG CAC GGT TTT rufipogon_1 ATG TGG GAT CCA TTC CTT AAT GAG TTC CCT GAA ACG GTG CAC GGT TTT rufipogon_2 ATG TGG GAT CCA TTG CTT AAT GAG TTC CCT GAA ACC GTG CAC GGT TTT rufipogon_3 ATG TGG GAT CCA TTG CTT AAT GAG TTC CCT GAA ACC GTG CAC GGT TTT O.Nivara ATG TGG GAT CCA TTC CTT AAC GAG TTC CCT GAA AC G GTG CAC GGT TTT m n