5 612 ACXM ATG GAC CAC CCC GTG CAG ACC GAG CTG TGC AAA GCG CAC ACG CTG GAG GAA CTG ATC CGC ATC CTG CAC CAG CTG TTC GCC GGA GAC AAA GTC AAT GTG GAC GAA GTG CAG ACC CTG ATG GAG TCC TAC GAG AGC AAC CCC GAG GAG TGG AGC CAG TAT GCC CAG TTC GAC CAG TTC AGA TAC ACA AGA AAT CTT GTG GAT AAA GGA AAT GGA AAG TTC AAT CTC ATG ATC CTA TGC TGG GGG GAA GGC CAT GGC AGC AGC ATC CAC GAT CAC ACA GAC TCA CAC TGC TTC ATG AAG ATT CTT CAA GGA AAT CTC AAA GAA ACA TTA TTT GAG TGG CCA GAC AAA AAG GCG GTT GGA GAG ATG CAG AAG AAG TCA GAA AGG GTT TTG AAG GAA AAT CGG TGT GCC TAT ATT AAC GAC ACC ATT GGC TTG CAT CGA GTG GAG AAC CCA AGC CAT ACT GAA ACA GCT GTT AGT CTC CAT TTG TAC AGC CCA CCT TTC GCA TCC TGC AAT ACT TTT GAC CAA AGA ACT GGA CAC AAA CAG AAA GTG AAA ATG ACC TTC TTT AGC CAA TTT GGA GAA AGA ACA CCA TAT ACA ACA TCA ATT TCA CAA GAG AAC AAC SM8_m AGG ATG GCT CTC CTT CAG ACG GAG GTG GGC CAG CTC CAG GCG CTG GAG GAG CTG GTC CAG GAG CTC CAT CAC TTG TTC TCC GGA GAG AAG GTC AAC GCG GCC CAG GTC CAG ACC GCC ATG GAG TCC TAC GAG AGC AAC CCC GGG GAC TGG GCC AGA TAC GCC CAG TTC GAC CAG TTC AGA TAC ACA AGA AAT CTT GTG GAT AAA GGA AAT GAG AAG TTC AAT CTC ATG ATC TTA TGC TGG GGA GAA GGC CAT GGC AGC AGC ATC CAT GAT CAC ACA GAT TCA CAT TGC TTC ATG AAG ATA CTT CAG GGA AAT CTA AAA GAA ACA TTA TTT GAG TGG CCT GAC AAA AAA GGG GTT GGA GAA ATG CAG AAG AAA TCA GAA AGA GTT TTG AAG GAA AAT CAG TGC GCC TAC ATT AAT GAC ACC ATT GGC TTG CAT CGA GTG GAG AAC CCA AGC CAT ACT GAA ACA GCT GTT AGC CTG CAT TTG TAC AGC CCA CCT TTT GAA TCC TGC TAT ACC TTT GAC CAA AGA ACT GGA CAC AAG CAA AGA GTG AAA ATG ACA TTC TAT AGC CAG TTT GGA GAA AGG ACT CCA TAT ACA ACA TCA GTT TCA CAA GAG AAC AAC NHlacerata ATG GCT CTC CTT TTG GGG ATG GAG TGC CCA GAG GCT CCA GCG CTG GAG GAC TTG GTC CAG GCG CTC CAT CAC TTG TTC TCC GGA GAG AAG GTC AAT GTG GCC CAG GTC CAG AGC GCC ATG GAG GCC TAT GAG AGC AAG CCC CAG GAC TGG GCC AGG TAT GCC CAG TTC GAC CAG TTC AGA TAC ACG AGA AAT CTT GTG GAT AAA GGA AAT GAG AAG TTC AAT CTC ATG ATC TTA TGC TGG GGA GAA GGC CAT GGC AGC AGC ATC CAT GAT CAC ACA GAT TCA CAC TGC TTC ATG AAG ATA CTT CAG GGA AAT CTA AAA GAA ACA TTA TTT GAG TGG CCT GAC AAA AAG GGG GTT GGA GAG ATG CAG AAG AAA TCA GAA AGG GTT TTG AAG GAA AAT CAG TGT GCC TAC ATT AAT GAC ACC ATT GGC TTG CAT CGA GTG GAG AAC CCA AGC CAT ACT GAA ACA GCT GTT AGT CTG CAT TTG TAC AGC CCA CCT TTT GAA TCC TGC TAT ACC TTT GAT CAA AGA ACT GGA CAC AAG CAA AAA GTG AAA ATG ACA TTC TAT AGC CAG TTT GGA GAA AGG ACT CCA TAT ACA ACG TCA GTT TCA CAA GAG AAC AAC Hmaculata ATG GCT CTC CTT TTG GGG ACA GAG TGC CCA GAG GCT CCA GCG CTG GAG GAC CTG GTC CAG GCG CTC CAT CAC TTG TTC TCC GGA GAG AAG GTC AAT GTG GCC CAG GTC CAG AGC GCC ATG GAG GCC TAC CAG AGC AAG CCC CAG GAC TGG GCC AGG TAT GCC CAG TTC GAC CAG TTC AGA TAC ACG AGA AAT CTT GTG GAT AAA GGA AAT GAG AAG TTC AAT CTC ATG ATC TTA TGC TGG GGA GAA GGC CAT GGC AGC AGC ATC CAT GAT CAC ACT GAT TCA CAC TGC TTC ATG AAG ATA CTT CAG GGA AAT TTA AAA GAA ACA TTA TTT GAG TGG CCT GAC AAA AAG GGG GTT GGA GAG ATG CAG AAG AAA TCA GAA AGG GTT TTG AAG GAA AAT CAG TGT GCC TAC ATT AAT GAC ACC ATT GGC TTG CAT CGA GTG GAG AAC CCA AGC CAT ACT GAA ACA GCT GTT AGT CTG CAT TTG TAC AGC CCA CCT TTT GAA TCC TGC TAT ACC TTT GAT CAA AGA ACT GGA CAC AAG CAA AAA GTG AAA ATG ACA TTC TAT AGC CAG TTT GGA GAA AGG ACT CCA TAT ACA ACA TCA GTT TCA CAA GAG AAC AAC SHlacerata ATG GCT CTC CTT TTG GGG ACA GAG TGC CCA GAG GCT CCA GCG CTG GAG GAC TTG GTC CAG GCG CTC CAT CAC TTG TTC TCC GGA GAG AAG GTC AAT GTG GCC CAG GTC CAG AGC GCC ATG GAG GCC TAT GAG AGC AAG CCC CAG GAC TGG GCC AGG TAT GCC CAG TTC GAC CAG TTC AGA TAC ACG AGA AAT CTT GTG GAT AAA GGA AAT GAG AAG TTC AAT CTC ATG ATC TTA TGC TGG GGA GAA GGC CAT GGC AGC AGC ATC CAT GAT CAC ACA GAT TCA CAC TGC TTC ATG AAG ATA CTT CAG GGA AAT CTA AAA GAA ACA TTA TTT GAG TGG CCT GAC AAA AAG GGG GTT GGA GAG ATG CAG AAG AAA TCA GAA AGG GTT TTG AAG GAA AAT CAG TGT GCC TAT ATT AAT GAC ACC ATT GGC TTG CAT CGA GTG GAG AAC CCA AGC CAT ACT GAA ACA GCT GTT AGT CTG CAT TTG TAC AGC CCA CCT TTT GAA TCC TGC TAT ACC TTT GAT CAA AGA ACT GGA CAC AAG CAA AAA GTG AAA ATG ACA TTC TAT AGC CAG TTT GGA GAA AGG ACT CCA TAT ACA ACG TCA GTT TCA CAA GAG AAC AAC Printing out site pattern counts 5 360 P ACXM AAA AAA AAA AAA AAC AAC AAC AAG AAG AAG AAT AAT AAT ACA ACA ACA ACA ACA ACC ACC ACC ACC ACG ACT ACT AGA AGA AGC AGC AGG AGT ATC ATC ATC ATG ATG ATT ATT ATT CAA CAA CAC CAC CAC CAC CAC CAG CAG CAG CAG CAG CAT CCA CCA CCC CCC CCT CGA CGC CGG CTA CTC CTC CTC CTG CTG CTG CTG CTG CTG CTT GAA GAA GAA GAC GAC GAC GAC GAC GAC GAG GAG GAG GAG GAG GAT GCA GCC GCC GCG GCG GCT GGA GGA GGC GGG GTC GTG GTG GTG GTG GTT TAC TAC TAT TAT TAT TCA TCC TCC TGC TGC TGG TGT TTA TTC TTC TTG TTT TTT SM8_m ... ..G .G. C.G ... ... ..T ..A ..A ... ..C ... T.. ... ... ... ... ..T ..A ... ... ..G G.. ..C ... ... ..G ... GC. ..A ..C ... GAG G.. .G. ... ..A ... G.. ... ..G ... ..G ..T ..T GCT AGA ..A ..C ... ... ... ... ..T ... .T. ... ... .AG .A. T.. ..A ... ..G ..C ... ... GCC G.. T.. ... C.G ... ..G ATG ... ... ..G ..T .C. ..A ..C ... ... .G. ... .A. ... T.. CTC .G. ... .AG ... ... ..A ... C.T .C. ..C ... ... ... ... ..C ..C ... ... ... ... G.. ... ... ..C ... ... ..T ... .A. ... NHlacerata ... ..G ... G.G ... ..G ..T ..A ... ... ... ... T.. ... ... ..G ..G ..T ..A ... .G. .TG G.. ..C ... ... ..G ... GC. ... ... ... GCG G.. ... ... ..A ... G.. ... ..G ... .CA ... ..T .T. AG. ..A ..C ... GG. ... ... ..T ... .TT ... ... .AG .A. T.. ..A ... ..G ..C ... T.. GCC TGC T.. ... C.G ... ..C .CT ... ..T ..G ..T .C. ... ..C ... ... C.. ... .A. ... T.. ..T .G. ... .AG ... ... ..A ... T.. ... ..C ... ... ... ..T ..C ... ... ... G.. ... CCA ... ... ... ... ... ..T ... .A. ... Hmaculata ... ..G ... G.G ... ..G ..T ..A ... ... ... ... T.. ... ..T ... ..G ..T ..A ... .G. ..A G.. ..C ... ... ..G ... GC. ... ... ... GCG G.. ... ... ..A ... G.. ... ..G ... .CA ... ..T .T. AG. ..A ..C ... GG. ... ... ..T ... .TT ... ... .AG .A. T.. T.A ... ..G ..C ... ... GCC TGC T.. ... C.G ... ..C .CT ... ..T ..G ..T .C. ... ..C C.. ... C.. ... .A. ... T.. ..T .G. ... .AG ... ... ..A ... T.. ... ..C ... ... ... ... ..C ... ... ... G.. ... CCA ... ... ... ... ... ..T ... .A. ... SHlacerata ... ..G ... G.G ... ..G ..T ..A ... ... ... ... T.. ... ... ..G ..G ..T ..A ... .G. ..A G.. ..C ... ... ..G ... GC. ... ... ... GCG G.. ... ... ..A ... G.. ... ..G ... .CA ... ..T .T. AG. ..A ..C ... GG. ... ... ..T ... .TT ... ... .AG .A. T.. ..A ... ..G ..C ... T.. GCC TGC T.. ... C.G ... ..C .CT ... ..T ..G ..T .C. ... ..C ... ... C.. ... .A. ... T.. ..T .G. ... .AG ... ... ..A ... T.. ... ..C ... ... ... ..T ... ... ... ... G.. ... CCA ... ... ... ... ... ..T ... .A. ... 4 2 1 1 3 1 1 1 1 4 1 5 1 3 1 1 1 1 1 1 1 1 1 1 2 3 1 6 1 1 1 2 1 1 1 5 1 2 1 2 2 2 1 1 2 1 1 1 1 4 1 4 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 6 1 1 3 1 1 1 1 1 1 1 6 1 2 1 2 1 1 1 1 1 6 3 1 1 1 1 1 3 3 2 1 1 1 1 4 1 1 1 3 3 1 1 6 1 3 1 3 CODONML (in paml version 4.9i, September 2018) OG0010384.phy Model: several dN/dS ratios for branches, Codon frequency model: F3x4 Site-class models: PositiveSelection ns = 5 ls = 204 Codon usage in sequences ---------------------------------------------------------------------------------------------------------------------- Phe TTT 4 4 4 4 4 | Ser TCT 0 0 0 0 0 | Tyr TAT 3 3 5 4 6 | Cys TGT 1 0 1 1 1 TTC 7 6 6 6 6 | TCC 2 3 2 2 2 | TAC 3 5 3 4 2 | TGC 4 4 4 4 4 Leu TTA 1 2 2 3 2 | TCA 4 4 4 4 4 | *** TAA 0 0 0 0 0 | *** TGA 0 0 0 0 0 TTG 3 4 6 5 6 | TCG 0 0 0 0 0 | TAG 0 0 0 0 0 | Trp TGG 3 3 3 3 3 ---------------------------------------------------------------------------------------------------------------------- Leu CTT 2 3 3 3 3 | Pro CCT 1 2 2 2 2 | His CAT 4 7 6 6 6 | Arg CGT 0 0 0 0 0 CTC 3 4 3 3 3 | CCC 2 1 1 1 1 | CAC 7 3 4 4 4 | CGC 1 0 0 0 0 CTA 1 1 1 0 1 | CCA 4 3 5 5 5 | Gln CAA 4 3 3 3 3 | CGA 1 1 1 1 1 CTG 6 3 2 3 2 | CCG 0 0 0 0 0 | CAG 8 12 10 11 10 | CGG 1 0 0 0 0 ---------------------------------------------------------------------------------------------------------------------- Ile ATT 4 2 2 2 2 | Thr ACT 3 3 3 4 3 | Asn AAT 7 6 7 7 7 | Ser AGT 1 0 1 1 1 ATC 4 2 2 2 2 | ACC 4 3 2 2 2 | AAC 5 5 3 3 3 | AGC 7 7 7 7 7 ATA 0 1 1 1 1 | ACA 7 7 5 6 6 | Lys AAA 8 6 6 6 6 | Arg AGA 4 6 3 3 3 Met ATG 6 6 7 6 6 | ACG 1 1 2 1 2 | AAG 6 6 8 8 8 | AGG 1 2 3 3 3 ---------------------------------------------------------------------------------------------------------------------- Val GTT 3 4 4 4 4 | Ala GCT 1 2 3 3 3 | Asp GAT 2 3 4 4 4 | Gly GGT 0 0 0 0 0 GTC 1 3 3 3 3 | GCC 3 5 6 6 6 | GAC 8 5 5 5 5 | GGC 3 4 3 3 3 GTA 0 0 0 0 0 | GCA 1 0 0 0 0 | Glu GAA 8 8 7 7 7 | GGA 7 7 7 7 7 GTG 6 4 4 4 4 | GCG 2 2 2 2 2 | GAG 10 11 11 10 11 | GGG 1 2 2 2 2 ---------------------------------------------------------------------------------------------------------------------- Codon position x base (3x4) table for each sequence. #1: ACXM position 1: T:0.17157 C:0.22059 A:0.33333 G:0.27451 position 2: T:0.25000 C:0.17157 A:0.40686 G:0.17157 position 3: T:0.17647 C:0.31373 A:0.24510 G:0.26471 Average T:0.19935 C:0.23529 A:0.32843 G:0.23693 #2: SM8_m position 1: T:0.18627 C:0.21078 A:0.30882 G:0.29412 position 2: T:0.24020 C:0.17647 A:0.40686 G:0.17647 position 3: T:0.19118 C:0.29412 A:0.24020 G:0.27451 Average T:0.20588 C:0.22712 A:0.31863 G:0.24837 #3: NHlacerata position 1: T:0.19608 C:0.20098 A:0.30392 G:0.29902 position 2: T:0.24510 C:0.18137 A:0.40196 G:0.17157 position 3: T:0.22059 C:0.26471 A:0.22059 G:0.29412 Average T:0.22059 C:0.21569 A:0.30882 G:0.25490 #4: Hmaculata position 1: T:0.19608 C:0.20588 A:0.30392 G:0.29412 position 2: T:0.24020 C:0.18627 A:0.40196 G:0.17157 position 3: T:0.22059 C:0.26961 A:0.22549 G:0.28431 Average T:0.21895 C:0.22059 A:0.31046 G:0.25000 #5: SHlacerata position 1: T:0.19608 C:0.20098 A:0.30392 G:0.29902 position 2: T:0.24020 C:0.18627 A:0.40196 G:0.17157 position 3: T:0.22549 C:0.25980 A:0.22549 G:0.28922 Average T:0.22059 C:0.21569 A:0.31046 G:0.25327 Sums of codon usage counts ------------------------------------------------------------------------------ Phe F TTT 20 | Ser S TCT 0 | Tyr Y TAT 21 | Cys C TGT 4 TTC 31 | TCC 11 | TAC 17 | TGC 20 Leu L TTA 10 | TCA 20 | *** * TAA 0 | *** * TGA 0 TTG 24 | TCG 0 | TAG 0 | Trp W TGG 15 ------------------------------------------------------------------------------ Leu L CTT 14 | Pro P CCT 9 | His H CAT 29 | Arg R CGT 0 CTC 16 | CCC 6 | CAC 22 | CGC 1 CTA 4 | CCA 22 | Gln Q CAA 16 | CGA 5 CTG 16 | CCG 0 | CAG 51 | CGG 1 ------------------------------------------------------------------------------ Ile I ATT 12 | Thr T ACT 16 | Asn N AAT 34 | Ser S AGT 4 ATC 12 | ACC 13 | AAC 19 | AGC 35 ATA 4 | ACA 31 | Lys K AAA 32 | Arg R AGA 19 Met M ATG 31 | ACG 7 | AAG 36 | AGG 12 ------------------------------------------------------------------------------ Val V GTT 19 | Ala A GCT 12 | Asp D GAT 17 | Gly G GGT 0 GTC 13 | GCC 26 | GAC 28 | GGC 16 GTA 0 | GCA 1 | Glu E GAA 37 | GGA 35 GTG 22 | GCG 10 | GAG 53 | GGG 9 ------------------------------------------------------------------------------ Codon position x base (3x4) table, overall position 1: T:0.18922 C:0.20784 A:0.31078 G:0.29216 position 2: T:0.24314 C:0.18039 A:0.40392 G:0.17255 position 3: T:0.20686 C:0.28039 A:0.23137 G:0.28137 Average T:0.21307 C:0.22288 A:0.31536 G:0.24869 Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG): 0.00998345 0.01353207 0.01116632 0.01357938 0.00740708 0.01003992 0.00828469 0.01007503 0.01658541 0.02248069 0.00000000 0.00000000 0.00708503 0.00960340 0.00000000 0.00963698 0.01096628 0.01486424 0.01226560 0.01491621 0.00813627 0.01102831 0.00910028 0.01106687 0.01821817 0.02469382 0.02037672 0.02478016 0.00778252 0.01054882 0.00870462 0.01058570 0.01639769 0.02222625 0.01834054 0.02230396 0.01216603 0.01649044 0.01360750 0.01654810 0.02724132 0.03692425 0.03046896 0.03705336 0.01163707 0.01577347 0.01301587 0.01582862 0.01541486 0.02089407 0.01724126 0.02096713 0.01143683 0.01550206 0.01279191 0.01555626 0.02560856 0.03471112 0.02864275 0.03483249 0.01093958 0.01482805 0.01223574 0.01487990 TREE # 1: ((4, (3, 5)), 2, 1); MP score: 96 lnL(ntime: 7 np: 12): -1337.215619 +0.000000 6..7 7..4 7..8 8..3 8..5 6..2 6..1 2.440215 0.015921 0.015410 0.010174 0.005240 0.139969 0.432450 1.782267 0.759627 0.208573 0.049949 998.999858 Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). tree length = 3.059380 ((4: 0.015921, (3: 0.010174, 5: 0.005240): 0.015410): 2.440215, 2: 0.139969, 1: 0.432450); ((Hmaculata: 0.015921, (NHlacerata: 0.010174, SHlacerata: 0.005240): 0.015410): 2.440215, SM8_m: 0.139969, ACXM: 0.432450); Detailed output identifying parameters kappa (ts/tv) = 1.78227 MLEs of dN/dS (w) for site classes (K=4) site class 0 1 2a 2b proportion 0.75963 0.20857 0.02495 0.00685 background w 0.04995 1.00000 0.04995 1.00000 foreground w 0.04995 1.00000 998.99986 998.99986 Naive Empirical Bayes (NEB) analysis (please use the BEB results.) Positive sites for foreground lineages Prob(w>1): 2 D 0.680 6 Q 0.945 9 L 0.996** 10 C 0.998** 13 H 0.598 Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118) Positive sites for foreground lineages Prob(w>1): 6 Q 0.925 9 L 0.816 10 C 0.676 17 E 0.555 38 T 0.698 42 S 0.705 46 N 0.645 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: 0.957 0.043 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 w2: 0.016 0.027 0.037 0.050 0.066 0.087 0.114 0.150 0.197 0.257 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 0.001 0.006 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.005 0.072 0.113 0.157 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.002 0.005 0.011 0.017 0.089 0.106 0.354 0.038 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 0.001 0.000 0.004 0.002 0.012 0.000 sum of density on p0-p1 = 1.000000 Time used: 0:12