Transcription of 分子系統解析 - jst.go.jp
1 (node) (branch, edge) . (graph). (branch, edge). (node) (leaf), external node . (root). Internal nodes .. (Topology) .. A. A C. B. R. C D. B. D. E. Time E.. Operational taxonomic unit (OTU) .. outgroup . internal node .. Newick format Newick format: . 1. 2. 3. 4. 5.. (((1,2),(3,4)),5). Newick format . 2 3 ((1,2),(3,4),5). ((1,2),5),3,4). 4 (1,((3,4),5),2). 1.. 5.. (distance matrix method). (UPGMA). (neighbor joining method, N-J ). (character state method). (maximum parsimony method, MP ). (maximum likelihood method ML ). (Bayesian method) .. UPGMA .. A. A B C. (AB) C. B dAB B. C d(AB)C. C dAC dBC. C. D d(AB)D dCD. D dAD dBD dCD. D. d(ABC)D. 2. A. A. B. B. C. dAB d(AB)C. 2 2. UPGMA . 1.. 2.. A B ) OTU(AB .. 3. OTU AB . AB dAB . 1.. 2. OTU . 3.. 1.. 2.. 3.. Sij . 4. Sij . 2 . 5. OTU . 6. 6. step S12 . 3. 5. 4. Li .. L1 + L2 = d12. 3 1 L1 + L3 + L5 = d13. L3 L1. L5. L1 + L3 + L4 = d14.. 4 L4 L2 2 . S12=L1+L2 L3+L4+L5.. Maximum Parsimony Method (MP ).. 1.
2 2.. 3.. (Maximum likelihood method, ML . k k a . Lak .. S1 S2 S3 S4 S0, S1, S6: (A, C, G, T). 1 2 3 4 v1, v6 . gs0: 0 s0 . Pij v : i v j . v1 v2. v3. v4 S0, S5, S6 . S5 5. (A, C, G, T) . S6 6. v5 Lak = gs0 Psos5(v5) Ps5s1(v1) Ps5s2(v2). v6 S0 S5 S6 Ps0s6(v6) Ps6s3(v3) Ps6s4(v4). S0 0. a 1 n . La = La1 La 2 L Lan .. MEGA ( ).. PHYLIP. ( ).. PAUP* ( ) .. Molphy ( ).. PAML ( ).. phyML .. MrBayes ( ). (1). DNA .. DNA .. (2). DNA .. / .. , homology . / .. (homology) . homologous . (homologous) A B . homologs/homologues . (homology) similarity .. convergent evolution .. 70 .. 2 . (orthologs .. (paralogs .. A A A' . ' A B' .. '.. CLUSTALW .. CLUSTALW .. (NJ Neighbor Joining) .. Yes .. DDBJ CLUSTALW.. DNA/Protein .. TreeView . Njprot . Njprot.)))
