5 480 ACXM CGC CAG GAG AAG GAG CCC GCC GGG CCC GGG CCC GCC TCG CCC CCC AGC TCC GCC ACC GCC TTG GAG AGG CTC GAG ATG AAG CTC TAC CTC CTC CGG CAA GAA ATG ATT GAT CTC CGA GCC ACA GAC GTC AAG CTC ATG CGG CAA CTG CTG ATC ATC AAT GAA AGC ATT GAA TCC ATC AAG TGG ATG ATA GAG GAG AAA GGG GCT GTG GCC AGT CGG GGA AGC AGC CTG AGC GGC AGC CTC TGC AGT TTA CTA GAG AGC CAA GAA ACT TCA CTC AGA GGA AGC TAC AAC AGT TTG CAG GAC TGT AGT GAT GGA TTG GAT GGA ATA TCC GTG GGG AGT TAC CTG GAC ACT TTG GCA GAT GAT CTC CCG GGC CAG CGT ACT CCT TCA GAC ATG GAT CAG TTC AGT GAC TCT TCC CTA ATA GAT GAC TCA CAG TCC CTA CAT AAA CAT TCA AAG ATT GAG TCG GAC GAG TAC TAC TGT TTT GGT SM8_m CGA AGC CCC CAG GAG CCA AGG AGC CCT GCC TCT GCC AGT GCC TCC TCT GCC AGG CTG GGC TTG GAG AGG CTG CAG ACC AAA GTG CAC CTC CTC CGC CAA GAA ATG ATT GAT CTC CGA GCT ACA GAT GTC AAG CTC ATG CGA CAG CTA CTG ATC ATC AAC GAA AGC ATT GAA TCA ATC AAG TGG ATG ATC GAA GAG AAA GGT GCA ATC GCA AGC CGG GGC AGC AGT TTG AGT GGC AGC CTC TGC AGT TTG CTG GAG AGT CAG GAG ACC TCT CTC AGA GGA AGC TAC AAC AGT TTA CAG GAC TGT AGT GAT GGA CTC GAT GGA ATA TCT GTA GGA AGT TAC CTG GAC ACT TTG GCA GAT GAT GTA CCA GGC CAG CGT ACT CCT TCA GAC ATG GAC CAG TTC AGT GAC TCT TCT CTA ATA GAT GAT TCC CAG TCT GTA CAT AAA CAT TCA AAG ATT GAG TCT GAT GAG TAC TAC TGT TTT GGT Hmaculata AGG GAA GAG GAG GAC GAA AAG AGC CCC CCA AGG AGG GTC CCC CAG TTC GCC AGG ATG GGC TTG GAG AGG CTG GAG ACC AAG CTT CAC CTC CTC CGG CAG GAA ATG ATT GAT CTC CGA GCC ACA GAT GTC AAG CTC ATG CGA CAG CTA CTA ATC ATC AAC GAA AGC ATT GAA TCA ATC AAG TGG ATG ATC GAA GAG AAA GGT GCG ATC GCA AGC CGG GGC AGC AGT TTG AGT GGT AGC CTC TGC AGT TTG TTG GAG AGT CAG GAG ACC TCA CTT AGA GGA AGC TAC AAC AGT TTG CAG GAC TGT AGT GAT GGA CTC GAT GGA ATA TCT GTA GGG AGT TAC CTG GAC ACT TTG GTA GAT GAT GTA CCA GGC CAG CGT ACT CCT TCA GAC ATG GAC CAG TTC AGT GAC TCT TCT CTA ATA GAT GAT TCC CAG TCC CTA CAT AAA CAT TCA AAG ATT GAG TCT GAT GAG TAC TAC TGT TTT GGT SHlacerata GAG GAG GAG GAG GAG GAG AAG AGC CCC CCA AGG AGG GTC CAG GAC TTC GCC AGG ATG GGC TTG GAG CGG CTG GAG ACC AAG CTT CAC CTC CTC CGG CAG GAA ATG ATT GAT CTC CGA GCC ACA GAT GTC AAG CTC ATG CGA CAG CTT CTG ATC ATC AAC GAA AGC ATT GAA TCA ATC AAG TGG ATG ATC GAA GAG AAA GGC GCG ATC GCA AGC CGG GGC AGT AGT TTG AGT GGT AGC CTC TGT AGT TTG TTG GAG AGT CAG GAG ACC TCA CTT AGA GGA AGC TAC AAC AGT TTG CAG GAC TGT AGC GAT GGA CTC GAT GGA ATA TCT GTA GGG AGT TAC CTG GAC ACT TTG GCA GAT GAT GTA CCA GGC CAG CGT ACT CCT TCA GAC ATG GAC CAG TTC AGT GAC TCT TCT CTA ATA GAT GAT TCC CAG TCC CTA CAT AAA CAT TCA AAG ATT GAG TCT GAT GAG TAC TAC TGT TTT GGT NHlacerata AGG GAG GAG GAG GAG GAG AAG AGC CCC CCA AGG AGG GTC CAG GAC TTC GCC AGG ATG GGC TTG GAG CGG CTG GAG ACC AAG CTT CAC CTC CTC CGG CAG GAA ATG ATT GAT CTC CGA GCC ACA GAT GTC AAG CTC ATG CGA CAG CTT CTG ATC ATC AAC GAA AGC ATT GAA TCA ATC AAG TGG ATG ATC GAA GAG AAA GGC GCG ATC GCA AGC CGG GGC AGT AGT TTG AGT GGT AGC CTC TGT AGT TTG TTG GAG AGT CAG GAG ACC TCA CTT AGA GGA AGC TAC AAC AGT TTG CAG GAC TGT AGC GAT GGA CTC GAT GGA ATA TCT GTA GGG AGT TAC CTG GAC ACT TTG GCA GAT GAT GTA TCA GGC CAG CGT ACT CCT TCA GAC ATG GAC CAG TTC AGT GAC TCT TCT CTA ATA GAT GAT TCC CAG TCC CTA CAT AAA CAT TCA AAG ATT GAG TCT GAT GAG TAC TAC TGT TTT GGT Printing out site pattern counts 5 321 P ACXM AAA AAC AAG AAG AAG AAT ACA ACC ACT ACT AGA AGC AGC AGC AGC AGG AGT AGT AGT ATA ATA ATC ATG ATG ATT CAA CAA CAG CAG CAT CCC CCC CCC CCC CCC CCG CCT CGA CGC CGG CGG CGG CGT CTA CTA CTA CTC CTC CTC CTC CTC CTG CTG CTG CTG GAA GAA GAC GAC GAG GAG GAG GAG GAG GAT GAT GCA GCC GCC GCC GCC GCC GCC GCT GGA GGA GGC GGC GGG GGG GGG GGG GGT GTC GTG GTG TAC TAC TCA TCA TCA TCC TCC TCC TCC TCG TCG TCT TGC TGG TGT TTA TTC TTG TTG TTG TTT SM8_m ... ... ..A ... C.. ..C ... CTG ..C ... ... ... ... ..T TCT ... ..C ... ... ... ..C ... .CC ... ... ... ..G AGC ... ... ..A ..T G.. T.. T.T ..A ... ... ..A ..A ..C ... ... ... ..G G.. ... ... ..G G.A G.G ..A ... ... T.. ... ..G ... ..T C.. CCC ..A ... ... ..C ... ... AGG AGG ..A ... ..T .G. ..A ... ..C ... ... A.C .CC ..A ..T ... ... A.C ..A C.. ... ... ..C ..T G.. ..A ..T ..T AGT ..T ... ... ... ... ..G ... C.C ..A ... ... Hmaculata ... ... ... ... G.. ..C ... .TG ..C ... ... ... ... ..T TT. ... ..C ... ... ... ..C ... .CC ... ... ..G ..G G.A ... ... GAA ... ... .AG AGG ..A ... ... A.G ..A ... ... ... ... T.G ... ... ..T ..G G.A ..T ..A ..A ... T.. ... ..G ... ..T ... ... ..A ..C ... ..C ... .T. AAG AGG ..A AGG ... .G. ..G ... ..C ... ..T A.C CCA ... ..T ... ... A.C ..A C.. ... ... ..C ... G.. ..A ... ..T GTC ..T ... ... ... ... ..G ... C.C ... ... ... SHlacerata ... ... ... ... G.. ..C ... .TG ..C ... ... ... ..T ..T TT. C.. ..C ..C ... ... ..C ... .CC ... ... ..G ..G G.. ... ... GAG ... .AG GA. AGG ..A ... ... GAG ..A ... ... ... ... T.G ... ... ..T ..G G.A ..T ..T ... ... T.. ... ..G ... ..T ... ... ..A ... ... ..C ... ... AAG AGG ..A AGG ... .G. ..G ... ..C ... ..T A.C CCA ... ..C ... ... A.C ..A C.. ... ... ..C ... G.. ..A ... ..T GTC ..T ... ..T ... ... ..G ... C.C ... ... ... NHlacerata ... ... ... ... G.. ..C ... .TG ..C ... ... ... ..T ..T TT. C.. ..C ..C ... ... ..C ... .CC ... ... ..G ..G G.. ... ... GAG ... .AG GA. AGG T.A ... ... A.G ..A ... ... ... ... T.G ... ... ..T ..G G.A ..T ..T ... ... T.. ... ..G ... ..T ... ... ..A ... ... ..C ... ... AAG AGG ..A AGG ... .G. ..G ... ..C ... ..T A.C CCA ... ..C ... ... A.C ..A C.. ... ... ..C ... G.. ..A ... ..T GTC ..T ... ..T ... ... ..G ... C.C ... ... ... 2 1 1 3 1 1 1 1 1 2 1 3 1 3 1 1 1 1 4 2 1 3 1 4 3 1 2 1 4 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 5 1 1 1 1 1 1 1 1 3 1 4 3 1 1 1 1 5 1 6 1 1 1 1 1 1 1 1 3 1 1 1 1 1 1 1 1 1 1 1 1 4 2 1 1 1 1 1 2 1 1 1 1 1 2 1 1 1 1 2 1 CODONML (in paml version 4.9i, September 2018) OG0010129.phy Model: several dN/dS ratios for branches, Codon frequency model: F3x4 Site-class models: PositiveSelection ns = 5 ls = 160 Codon usage in sequences ---------------------------------------------------------------------------------------------------------------------- Phe TTT 1 1 1 1 1 | Ser TCT 1 8 4 4 4 | Tyr TAT 0 0 0 0 0 | Cys TGT 2 2 2 3 3 TTC 1 1 2 2 2 | TCC 5 2 2 2 2 | TAC 5 4 4 4 4 | TGC 1 1 1 0 0 Leu TTA 1 1 0 0 0 | TCA 4 3 4 4 5 | *** TAA 0 0 0 0 0 | *** TGA 0 0 0 0 0 TTG 4 4 6 6 6 | TCG 2 0 0 0 0 | TAG 0 0 0 0 0 | Trp TGG 1 1 1 1 1 ---------------------------------------------------------------------------------------------------------------------- Leu CTT 0 0 2 3 3 | Pro CCT 1 2 1 1 1 | His CAT 2 2 2 2 2 | Arg CGT 1 1 1 1 1 CTC 9 7 6 6 6 | CCC 5 1 2 1 1 | CAC 0 1 1 1 1 | CGC 1 1 0 0 0 CTA 3 2 4 2 2 | CCA 0 2 2 2 1 | Gln CAA 3 1 0 0 0 | CGA 1 3 2 2 2 CTG 4 5 2 3 3 | CCG 1 0 0 0 0 | CAG 5 8 8 8 8 | CGG 3 1 2 3 3 ---------------------------------------------------------------------------------------------------------------------- Ile ATT 3 3 3 3 3 | Thr ACT 3 2 2 2 2 | Asn AAT 1 0 0 0 0 | Ser AGT 6 9 8 8 8 ATC 3 5 5 5 5 | ACC 1 2 2 2 2 | AAC 1 2 2 2 2 | AGC 8 7 6 6 6 ATA 3 2 2 2 2 | ACA 1 1 1 1 1 | Lys AAA 2 3 2 2 2 | Arg AGA 1 1 1 1 1 Met ATG 5 4 5 5 5 | ACG 0 0 0 0 0 | AAG 5 3 5 5 5 | AGG 1 3 5 3 4 ---------------------------------------------------------------------------------------------------------------------- Val GTT 0 0 0 0 0 | Ala GCT 1 1 0 0 0 | Asp GAT 7 9 9 9 9 | Gly GGT 1 2 3 2 2 GTC 1 1 2 2 2 | GCC 6 4 2 2 2 | GAC 7 5 6 6 6 | GGC 2 4 3 4 4 GTA 0 3 3 2 2 | GCA 1 3 1 2 2 | Glu GAA 4 4 6 4 4 | GGA 4 4 3 3 3 GTG 2 1 0 0 0 | GCG 0 0 1 1 1 | GAG 9 7 9 13 12 | GGG 4 0 1 1 1 ---------------------------------------------------------------------------------------------------------------------- Codon position x base (3x4) table for each sequence. #1: ACXM position 1: T:0.17500 C:0.24375 A:0.27500 G:0.30625 position 2: T:0.25000 C:0.20000 A:0.31875 G:0.23125 position 3: T:0.18750 C:0.35000 A:0.17500 G:0.28750 Average T:0.20417 C:0.26458 A:0.25625 G:0.27500 #2: SM8_m position 1: T:0.17500 C:0.23125 A:0.29375 G:0.30000 position 2: T:0.25000 C:0.19375 A:0.30625 G:0.25000 position 3: T:0.26250 C:0.30000 A:0.20625 G:0.23125 Average T:0.22917 C:0.24167 A:0.26875 G:0.26042 #3: Hmaculata position 1: T:0.16875 C:0.21875 A:0.30625 G:0.30625 position 2: T:0.26875 C:0.15000 A:0.33750 G:0.24375 position 3: T:0.23750 C:0.28750 A:0.19375 G:0.28125 Average T:0.22500 C:0.21875 A:0.27917 G:0.27708 #4: SHlacerata position 1: T:0.16875 C:0.21875 A:0.29375 G:0.31875 position 2: T:0.26250 C:0.15000 A:0.35000 G:0.23750 position 3: T:0.24375 C:0.28125 A:0.16875 G:0.30625 Average T:0.22500 C:0.21667 A:0.27083 G:0.28750 #5: NHlacerata position 1: T:0.17500 C:0.21250 A:0.30000 G:0.31250 position 2: T:0.26250 C:0.15000 A:0.34375 G:0.24375 position 3: T:0.24375 C:0.28125 A:0.16875 G:0.30625 Average T:0.22708 C:0.21458 A:0.27083 G:0.28750 Sums of codon usage counts ------------------------------------------------------------------------------ Phe F TTT 5 | Ser S TCT 21 | Tyr Y TAT 0 | Cys C TGT 12 TTC 8 | TCC 13 | TAC 21 | TGC 3 Leu L TTA 2 | TCA 20 | *** * TAA 0 | *** * TGA 0 TTG 26 | TCG 2 | TAG 0 | Trp W TGG 5 ------------------------------------------------------------------------------ Leu L CTT 8 | Pro P CCT 6 | His H CAT 10 | Arg R CGT 5 CTC 34 | CCC 10 | CAC 4 | CGC 2 CTA 13 | CCA 7 | Gln Q CAA 4 | CGA 10 CTG 17 | CCG 1 | CAG 37 | CGG 12 ------------------------------------------------------------------------------ Ile I ATT 15 | Thr T ACT 11 | Asn N AAT 1 | Ser S AGT 39 ATC 23 | ACC 9 | AAC 9 | AGC 33 ATA 11 | ACA 5 | Lys K AAA 11 | Arg R AGA 5 Met M ATG 24 | ACG 0 | AAG 23 | AGG 16 ------------------------------------------------------------------------------ Val V GTT 0 | Ala A GCT 2 | Asp D GAT 43 | Gly G GGT 10 GTC 8 | GCC 16 | GAC 30 | GGC 17 GTA 10 | GCA 9 | Glu E GAA 22 | GGA 17 GTG 3 | GCG 3 | GAG 50 | GGG 7 ------------------------------------------------------------------------------ Codon position x base (3x4) table, overall position 1: T:0.17250 C:0.22500 A:0.29375 G:0.30875 position 2: T:0.25875 C:0.16875 A:0.33125 G:0.24125 position 3: T:0.23500 C:0.30000 A:0.18250 G:0.28250 Average T:0.22208 C:0.23125 A:0.26917 G:0.27750 Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG): 0.01086012 0.01386398 0.00843392 0.01305525 0.00708268 0.00904173 0.00550038 0.00851429 0.01390305 0.01774857 0.00000000 0.00000000 0.01012562 0.01292632 0.00000000 0.01217228 0.01416537 0.01808345 0.01100077 0.01702858 0.00923828 0.01179355 0.00717441 0.01110560 0.01813441 0.02315031 0.01408311 0.02179988 0.01320733 0.01686042 0.01025675 0.01587689 0.01849368 0.02360895 0.01436211 0.02223176 0.01206109 0.01539714 0.00936659 0.01449897 0.02367548 0.03022402 0.01838628 0.02846095 0.01724290 0.02201221 0.01339076 0.02072816 0.01943803 0.02481451 0.01509550 0.02336700 0.01267698 0.01618338 0.00984489 0.01523935 0.02488444 0.03176737 0.01932515 0.02991427 0.01812339 0.02313624 0.01407454 0.02178662 TREE # 1: ((3, (5, 4)), 2, 1); MP score: 98 lnL(ntime: 7 np: 12): -1161.470425 +0.000000 6..7 7..3 7..8 8..5 8..4 6..2 6..1 1.149110 0.031283 0.070907 0.006640 0.012716 0.250806 0.656972 1.555669 0.793734 0.169236 0.009737 999.000000 Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). tree length = 2.178435 ((3: 0.031283, (5: 0.006640, 4: 0.012716): 0.070907): 1.149110, 2: 0.250806, 1: 0.656972); ((Hmaculata: 0.031283, (NHlacerata: 0.006640, SHlacerata: 0.012716): 0.070907): 1.149110, SM8_m: 0.250806, ACXM: 0.656972); Detailed output identifying parameters kappa (ts/tv) = 1.55567 MLEs of dN/dS (w) for site classes (K=4) site class 0 1 2a 2b proportion 0.79373 0.16924 0.03052 0.00651 background w 0.00974 1.00000 0.00974 1.00000 foreground w 0.00974 1.00000 999.00000 999.00000 Naive Empirical Bayes (NEB) analysis (please use the BEB results.) Positive sites for foreground lineages Prob(w>1): 6 P 0.995** 10 G 0.698 11 P 0.982* 12 A 0.999** 13 S 0.564 15 P 0.537 Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118) Positive sites for foreground lineages Prob(w>1): 6 P 0.861 12 A 0.867 The grid (see ternary graph for p0-p1) w0: 0.050 0.150 0.250 0.350 0.450 0.550 0.650 0.750 0.850 0.950 w2: 1.500 2.500 3.500 4.500 5.500 6.500 7.500 8.500 9.500 10.500 Posterior on the grid w0: 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 w2: 0.020 0.027 0.037 0.050 0.067 0.090 0.118 0.152 0.194 0.246 Posterior for p0-p1 (see the ternary graph) (YWN2015, fig. 1) 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.001 0.011 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.000 0.008 0.005 0.063 0.060 0.283 0.211 0.224 0.000 0.000 0.000 0.000 0.001 0.001 0.001 0.004 0.000 0.008 0.000 0.013 0.000 0.026 0.000 0.045 0.000 0.030 0.000 sum of density on p0-p1 = 1.000000 Time used: 0:12