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232
APPENDICES
Appendix 1: The genetic code and degenerate primer design
Table A1.1. Standard genetic triplet codes with their accompanying amino acids (Alberts
et al., 1994). Methionine (in red) is the start codon, which is encoded by only one triplet
(ATG). The stop codons are in blue.
T C A G
T
TTT
TTC
TTA
TTG
Phe (F)
“
Leu (L)
“
TCT
TCC
TCA
TCG
Ser (S)
“
“
“
TAT
TAC
TAA
TAG
Tyr (Y)
“
Stop
Stop
TGT
TGC
TGA
TGG
Cys (C)
“
Stop
Trp (W)
C
CTT
CTC
CTA
CTG
Leu (L)
“
“
“
CCT
CCC
CCA
CCG
Pro (P)
“
“
“
CAT
CAC
CAA
CAG
His (H)
“
Gln (Q)
“
CGT
CGC
CGA
CGG
Arg (R)
“
“
“
A
ATT
ATC
ATA
ATG
Ile (I)
“
“
Met (M)
ACT
ACC
ACA
ACG
Thr (T)
“
“
“
AAT
AAC
AAA
AAG
Asn (N)
“
Lys (K)
“
AGT
AGC
AGA
AGG
Ser (S)
“
Arg (R)
“
G
GTT
GTC
GTA
GTG
Val (V)
“
“
“
GCT
GCC
GCA
GCG
Ala (A)
“
“
“
GAT
GAC
GAA
GAG
Asp (D)
“
Glu (E)
“
GGT
GGC
GGA
GGG
Gly (G)
“
“
“
233
Table A1.2. The degenerate genetic code used to design primers.
Abbreviation letter Nucleotide represented
A A
C C
G G
T T
R AG
Y CT
M AC
K GT
W AT
S CG
B CGT
D AGT
H ACT
V ACG
N ACGT
234
Appendix 2: Phylogenetic Analysis by Maximum Likelihood (PAML)
seqfile = cterminal.txt * sequence data filename treefile = wholetree.txt * tree structure file name outfile = surfactantout * main result file name
noisy = 3 * 0,1,2,3,9: how much rubbish on the screen verbose = 1 * 0: concise; 1: detailed, 2: too much runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise
seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs CodonFreq = 3 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table aaDist = 0 * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a aaRatefile = wag.dat * only used for aa seqs with model=empirical(_F) * dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own
model = 2 * models for codons: * 0:one, 1:b, 2:2 or more dN/dS ratios for branches * models for AAs or codon-translated AAs: * 0:poisson, 1:proportional, 2:Empirical, 3:Empirical+F * 6:FromCodon, 7:AAClasses, 8:REVaa_0, 9:REVaa(nr=189)
NSsites = 3 * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs; * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ * 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1; * 13:3normal>0
icode = 0 * 0:universal code; 1:mammalian mt; 2-10:see below Mgene = 0 * codon: 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff * AA: 0:rates, 1:separate
fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated kappa = 2 * initial or fixed kappa fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate omega = 1 * initial or fixed omega, for codons or codon-based AAs
fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha alpha = 0. * initial or fixed alpha, 0:infinity (constant rate) Malpha = 0 * different alphas for genes ncatG = 4 * # of categories in dG of NSsites models
clock = 0 * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis getSE = 1 * 0: don't want them, 1: want S.E.s of estimates RateAncestor = 0 * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)
Small_Diff = .5e-6* cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)?* ndata = 10* fix_blength = -1 * 0: ignore, -1: random, 1: initial, 2: fixed method = 0 * 0: simultaneous; 1: one branch at a time
* Genetic codes: 0:universal, 1:mammalian mt., 2:yeast mt., 3:mold mt.,* 4: invertebrate mt., 5: ciliate nuclear, 6: echinoderm mt., * 7: euplotid mt., 8: alternative yeast nu. 9: ascidian mt., * 10: blepharisma nu.* These codes correspond to transl_table 1 to 11 of GENEBANK.
Fig. A2.1. CODEML menu options given in the PAML program.
235
Table A2.1. Chi square distribution table used to determine whether the models used in chapter 3 provided a significantly better fit to the data than
the comparative model.
df p=0.25 0.2 0.15 0.1 0.05 0.025 0.02 0.01 0.005 0.0025 0.001 0.0005
1 1.32 1.64 2.07 2.71 3.84 5.02 5.41 6.63 7.88 9.14 10.83 12.12
2 2.77 3.22 3.79 4.61 5.99 7.38 7.82 9.21 10.6 11.98 13.82 15.2
3 4.11 4.64 5.32 6.25 7.81 9.35 9.84 11.34 12.84 14.32 16.27 17.73
4 5.39 5.59 6.74 7.78 9.49 11.14 11.67 13.23 14.86 16.42 18.47 20
5 6.63 7.29 8.12 9.24 11.07 12.83 13.33 15.09 16.75 18.39 20.51 22.11
6 7.84 8.56 9.45 10.64 12.53 14.45 15.03 16.81 13.55 20.25 22.46 24.1
7 9.04 5.8 10.75 12.02 14.07 16.01 16.62 18.48 20.28 22.04 24.32 26.02
8 10.22 11.03 12.03 13.36 15.51 17.53 18.17 20.09 21.95 23.77 26.12 27.87
9 11.39 12.24 13.29 14.68 16.92 19.02 19.63 21.67 23.59 25.46 27.83 29.67
10 12.55 13.44 14.53 15.99 18.31 20.48 21.16 23.21 25.19 27.11 29.59 31.42
11 13.7 14.63 15.77 17.29 19.68 21.92 22.62 24.72 26.76 28.73 31.26 33.14
12 14.85 15.81 16.99 18.55 21.03 23.34 24.05 26.22 28.3 30.32 32.91 34.82
13 15.93 15.58 18.9 19.81 22.36 24.74 25.47 27.69 29.82 31.88 34.53 36.48
14 17.12 18.15 19.4 21.06 23.68 26.12 26.87 29.14 31.32 33.43 36.12 38.11
15 18.25 19.31 20.6 22.31 25 27.49 28.26 30.58 32.8 34.95 37.7 39.72
16 19.37 20.47 21.79 23.54 26.3 28.85 29.63 32 34.27 36.46 39.25 41.31
17 20.49 21.61 22.98 24.77 27.59 30.19 31 33.41 35.72 37.95 40.79 42.88
18 21.6 22.76 24.16 25.99 28.87 31.53 32.35 34.81 37.16 39.42 42.31 44.43
236
df p=0.25 0.2 0.15 0.1 0.05 0.025 0.02 0.01 0.005 0.0025 0.001 0.0005
19 22.72 23.9 25.33 27.2 30.14 32.85 33.69 36.19 38.58 40.88 43.82 45.97
20 23.83 25.04 26.5 28.41 31.41 34.17 35.02 37.57 40 42.34 45.31 47.5
21 24.93 26.17 27.66 29.62 39.67 35.48 36.34 38.93 41.4 43.78 46.8 49.01
22 26.04 27.3 28.82 30.81 33.92 36.78 37.66 40.29 42.8 45.2 48.27 50.51
23 27.14 28.43 29.98 32.01 35.17 38.08 38.97 41.64 44.18 46.62 49.73 52
24 28.24 29.55 31.13 33.2 36.42 39.36 40.27 42.98 45.56 48.03 51.18 53.48
25 29.34 30.68 32.28 34.38 37.65 40.65 41.57 44.31 46.93 49.44 52.62 54.95
26 30.43 31.79 33.43 35.56 38.89 41.92 42.86 45.64 48.29 50.83 54.05 56.41
27 31.53 32.91 34.57 36.74 40.11 43.19 44.14 46.96 49.64 52.22 55.48 57.86
28 32.62 34.03 35.71 37.92 41.34 44.46 45.42 48.28 50.99 53.59 56.89 59.3
29 33.71 35.14 36.85 39.09 42.56 45.72 46.69 49.59 52.34 54.97 58.3 60.73
30 34.8 36.25 37.99 40.26 43.77 46.98 47.96 50.89 53.67 56.33 59.7 62.16
40 45.62 47.27 49.24 51.81 55.76 59.34 60.44 63.69 66.77 69.7 73.4 76.09
50 56.33 53.16 60.35 63.17 67.5 71.42 72.61 76.15 79.49 82.66 86.66 89.56
237
6.35.3 15.3 1 00.7 7 6 65.3 1 0 0 65.3 1 0 0 6 02.2 4.1 3.1 3.1 2.9 3.1 3.15 1.3 0.3 0.3 5.7 0.3 0.3 2.8
2.7 9 8 8 2 8 8 4.9 7.72 8.3 7.3 7.3 1.3 7.3 7.3 4.2 7 0.7
5.7 0.6 0.4 0.4 6.4 0.4 0.4 3.5 0.7 8.4 7.70.1 6.4 5.4 5.4 0.6 5.4 5.4 2.3 5.1 2.6 1.9 5.81 7.3 6.3 6.3 0.3 6.3 6.3 3.2 6 1.7 1 6.7 0.9
3.4 2.9 1.9 1.9 4.1 1.9 1.9 1.2 1.6 6.1 5.4 2.3 3.5 4.42.6 3.7 2.7 2.7 3.3 2.7 2.7 0.4 2.4 5.3 4.6 3.1 2.7 3.6 0.82.5 3.8 2.8 2.8 3.2 2.8 2.8 0.3 2.5 5.2 4.5 3.2 2.6 3.5 0.9 0.12.7 3.6 2.6 2.6 3.4 2.6 2.6 0.5 2.3 5.4 4.7 3 2.8 3.7 0.7 0.1 0.23.1 3.2 2.2 2.2 3.8 2.2 2.2 0.9 1.9 5.8 5.1 2.6 3.2 4.1 0.3 0.5 0.6 0.42.4 8.7 7.7 7.7 1.7 7.7 7.7 4.6 7.4 0.3 0.4 8.1 2.3 1.4 5.8 5 4.9 5.1 5.5
A R N D C Q E G H I L K M F P S T W Y VAla Arg Asp Asn Cys Glu Gln Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val1.8 -4.5 -3.5 -3.5 2.5 -3.5 -3.5 -0.4 -3.2 4.5 3.8 -3.9 1.9 2.8 -1.6 -0.8 -0.7 -0.9 -1.3 4.2
Fig. A2.2. Distance matrix composed for hydrophobicity using values from Haig and Hurst (1991), originally taken from Kyte and Doolittle (1982).
The distances are calculated as the absolute value of the difference between one amino acid value and another.
238
2.16 3.93 0.9 3
2.2 4.3 8.2 5.25.5 3.4 0.5 2.5 7.71.6 0.5 4.4 1.4 3.8 3.90.9 1.2 5.1 2.1 3.1 4.6 0.71.4 0.7 4.6 1.6 3.6 4.1 0.2 0.52.1 4.2 8.1 5.1 0.1 7.6 3.7 3 3.52.1 4.2 8.1 5.1 0.1 7.6 3.7 3 3.5 03.1 1 2.9 0.1 5.3 2.4 1.5 2.2 1.7 5.2 5.21.7 3.8 7.7 4.7 0.5 7.2 3.3 2.6 3.1 0.4 0.4 4.82 4.1 8 5 0.2 7.5 3.6 2.9 3.4 0.1 0.1 5.1 0.3
0.4 2.5 6.4 3.4 1.8 5.9 2 1.3 1.8 1.7 1.7 3.5 1.3 1.60.5 1.6 5.5 2.5 2.7 5 1.1 0.4 0.9 2.6 2.6 2.6 2.2 2.5 0.90.4 2.5 6.4 3.4 1.8 5.9 2 1.3 1.8 1.7 1.7 3.5 1.3 1.6 0 0.91.8 3.9 7.8 4.8 0.4 7.3 3.4 2.7 3.2 0.3 0.3 4.9 0.1 0.2 1.4 2.3 1.41.6 3.7 7.6 4.6 0.6 7.1 3.2 2.5 3 0.5 0.5 4.7 0.1 0.4 1.2 2.1 1.2 0.21.4 3.5 7.4 4.4 0.8 6.9 3 2.3 2.8 0.7 0.7 4.5 0.3 0.6 1 1.9 1 0.4 0.2
A R N D C Q E G H I L K M F P S T W Y VAla Arg Asp Asn Cys Glu Gln Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val7 9.1 13 10 4.8 12.5 8.6 7.9 8.4 4.9 4.9 10.1 5.3 5 6.6 7.5 6.6 5.2 5.4 5.6
Fig. A2.3. Distance matrix composed for polar requirement using values from Haig and Hurst (1991), originally taken from Woese et al. (1966).
The distances are calculated in the same way as for Fig. A2.2.
239
4.763.23 7.990.59 5.35 2.640.93 5.69 2.3 0.342.78 7.54 0.45 2.19 1.850.35 5.11 2.88 0.24 0.58 2.430.03 4.79 3.2 0.56 0.9 2.75 0.321.59 3.17 4.82 2.18 2.52 4.37 1.94 1.620.02 4.74 3.25 0.61 0.95 2.8 0.37 0.05 1.570.02 4.78 3.21 0.57 0.91 2.76 0.33 0.01 1.61 0.043.74 1.02 6.97 4.33 4.67 6.52 4.09 3.77 2.15 3.72 3.760.26 5.02 2.97 0.33 0.67 2.52 0.09 0.23 1.85 0.28 0.24 40.52 5.28 2.71 0.07 0.41 2.26 0.17 0.49 2.11 0.54 0.5 4.26 0.260.3 4.46 3.53 0.89 1.23 3.08 0.65 0.33 1.29 0.28 0.32 3.44 0.56 0.82
0.32 5.08 2.91 0.27 0.61 2.46 0.03 0.29 1.91 0.34 0.3 4.06 0.06 0.2 0.620.16 4.6 3.39 0.75 1.09 2.94 0.51 0.19 1.43 0.14 0.18 3.58 0.42 0.68 0.14 0.480.11 4.87 3.12 0.48 0.82 2.67 0.24 0.08 1.7 0.13 0.09 3.85 0.15 0.41 0.41 0.21 0.270.34 5.1 2.89 0.25 0.59 2.44 0.01 0.31 1.93 0.36 0.32 4.08 0.08 0.18 0.64 0.02 0.5 0.230.04 4.8 3.19 0.55 0.89 2.74 0.31 0.01 1.63 0.06 0.02 3.78 0.22 0.48 0.34 0.28 0.2 0.07 0.3
A R N D C Q E G H I L K M F P S T W Y VAla Arg Asp Asn Cys Glu Gln Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val6 10.76 2.77 5.41 5.07 3.22 5.65 5.97 7.59 6.02 5.98 9.74 5.74 5.48 6.3 5.68 6.16 5.89 5.66 5.96
Fig. A2.4. Distance matrix composed for isoelectric point using values from Haig and Hurst (1991), originally taken from Alff-Steinberger (1969).
The distances are calculated in the same way as for Fig. A2.2.
240
0.190.03 0.220.18 0.36 0.150.07 0.26 0.05 0.100.04 0.15 0.07 0.22 0.120.14 0.33 0.11 0.04 0.06 0.180.04 0.15 0.06 0.21 0.11 0.01 0.170.43 0.24 0.46 0.61 0.50 0.39 0.57 0.390.11 0.08 0.14 0.29 0.19 0.07 0.25 0.07 0.320.10 0.09 0.13 0.28 0.18 0.06 0.24 0.07 0.33 0.010.16 0.03 0.19 0.33 0.23 0.12 0.30 0.12 0.27 0.05 0.060.07 0.12 0.10 0.24 0.14 0.03 0.21 0.03 0.36 0.04 0.03 0.090.55 0.36 0.57 0.72 0.62 0.51 0.68 0.51 0.12 0.44 0.45 0.39 0.480.09 0.10 0.12 0.27 0.17 0.05 0.23 0.06 0.34 0.02 0.01 0.07 0.03 0.450.04 0.23 0.02 0.13 0.03 0.09 0.09 0.08 0.47 0.15 0.15 0.20 0.11 0.59 0.140.10 0.29 0.07 0.08 0.02 0.14 0.04 0.14 0.53 0.21 0.20 0.26 0.17 0.65 0.19 0.060.60 0.41 0.63 0.78 0.68 0.56 0.74 0.57 0.17 0.49 0.50 0.44 0.53 0.06 0.51 0.65 0.700.49 0.30 0.52 0.67 0.57 0.45 0.63 0.45 0.06 0.38 0.39 0.33 0.42 0.06 0.40 0.53 0.59 0.110.05 0.23 0.02 0.13 0.03 0.09 0.09 0.08 0.48 0.16 0.15 0.20 0.11 0.59 0.14 0.00 0.05 0.65 0.54
A R N D C Q E G H I L K M F P S T W Y VAla Arg Asp Asn Cys Glu Gln Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val
-0.11 0.08 -0.14 -0.29 -0.18 -0.07 -0.25 -0.07 0.32 0.00 -0.01 0.05 -0.04 0.44 -0.02 -0.15 -0.21 0.49 0.38 -0.16
Fig. A2.5. Distance matrix composed for aromaticity using values from Xia (2000). The distances are calculated in the same way as for Fig. A2.2.
241
9325 6823 70 224 69 1 154 39 29 31 3052 41 27 29 28 228 121 53 51 52 82 8065 28 40 42 41 11 13 9380 13 55 57 56 26 28 108 1580 13 55 57 56 26 28 108 15 088 5 63 65 64 34 36 116 23 8 874 19 49 51 50 20 22 102 9 6 6 14
101 8 76 78 77 47 49 129 36 21 21 13 271.5 91.5 23.5 21.5 22.5 52.5 50.5 29.5 63.5 78.5 78.5 86.5 72.5 99.51 92 24 22 23 53 51 29 64 79 79 87 73 100 0.5
30 63 5 7 6 24 22 58 35 50 50 58 44 71 28.5 29139 46 114 116 115 85 87 167 74 59 59 51 65 38 138 138 109105 12 80 82 81 51 53 133 40 25 25 17 31 4 104 104 75 3453 40 28 30 29 1 1 81 12 27 27 35 21 48 51.5 52 23 86 52
A R N D C Q E G H I L K M F P S T W Y VAla Arg Asp Asn Cys Glu Gln Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val31 124 56 54 55 85 83 3 96 111 111 119 105 132 33 32 61 170 136 84
Fig. A2.6. Distance matrix composed for volume using values from Grantham (1974). The distances are calculated in the same way as for Fig.
A2.2.
242
0.651.33 0.681.38 0.73 0.052.75 2.1 1.42 1.370.89 0.24 0.44 0.49 1.860.82 0.17 0.51 0.56 1.93 0.070.74 0.09 0.59 0.64 2.01 0.15 0.080.58 0.07 0.75 0.8 2.17 0.31 0.24 0.16
0 0.65 1.33 1.38 2.75 0.89 0.82 0.74 0.580 0.65 1.33 1.38 2.75 0.89 0.82 0.74 0.58 0
0.33 0.32 1 1.05 2.42 0.56 0.49 0.41 0.25 0.33 0.330 0.65 1.33 1.38 2.75 0.89 0.82 0.74 0.58 0 0 0.330 0.65 1.33 1.38 2.75 0.89 0.82 0.74 0.58 0 0 0.33 0
0.39 0.26 0.94 0.99 2.36 0.5 0.43 0.35 0.19 0.39 0.39 0.06 0.39 0.391.42 0.77 0.09 0.04 1.33 0.53 0.6 0.68 0.84 1.42 1.42 1.09 1.42 1.42 1.030.71 0.06 0.62 0.67 2.04 0.18 0.11 0.03 0.13 0.71 0.71 0.38 0.71 0.71 0.32 0.710.13 0.52 1.2 1.25 2.62 0.76 0.69 0.61 0.45 0.13 0.13 0.2 0.13 0.13 0.26 1.29 0.580.2 0.45 1.13 1.18 2.55 0.69 0.62 0.54 0.38 0.2 0.2 0.13 0.2 0.2 0.19 1.22 0.51 0.070 0.65 1.33 1.38 2.75 0.89 0.82 0.74 0.58 0 0 0.33 0 0 0.39 1.42 0.71 0.13 0.2
A R N D C Q E G H I L K M F P S T W Y VAla Arg Asp Asn Cys Glu Gln Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val0.00 0.65 1.33 1.38 2.75 0.89 0.82 0.74 0.58 0.00 0.00 0.33 0.00 0.00 0.39 1.42 0.71 0.13 0.20 0.00
Fig. A2.7. Distance matrix composed for chemical composition of the side chain using values from Grantham (1974). The distances are calculated
in the same way as for Fig. A2.2.
243
2.43.5 1.14.9 2.5 1.42.6 5 6.1 7.52.4 0 1.1 2.5 54.2 1.8 0.7 0.7 6.8 1.80.9 1.5 2.6 4 3.5 1.5 3.32.3 0.1 1.2 2.6 4.9 0.1 1.9 1.42.9 5.3 6.4 7.8 0.3 5.3 7.1 3.8 5.23.2 5.6 6.7 8.1 0.6 5.6 7.4 4.1 5.5 0.33.2 0.8 0.3 1.7 5.8 0.8 1 2.3 0.9 6.1 6.42.4 4.8 5.9 7.3 0.2 4.8 6.6 3.3 4.7 0.5 0.8 5.62.9 5.3 6.4 7.8 0.3 5.3 7.1 3.8 5.2 0 0.3 6.1 0.50.1 2.5 3.6 5 2.5 2.5 4.3 1 2.4 2.8 3.1 3.3 2.3 2.81.1 1.3 2.4 3.8 3.7 1.3 3.1 0.2 1.2 4 4.3 2.1 3.5 4 1.20.5 1.9 3 4.4 3.1 1.9 3.7 0.4 1.8 3.4 3.7 2.7 2.9 3.4 0.6 0.62.7 5.1 6.2 7.6 0.1 5.1 6.9 3.6 5 0.2 0.5 5.9 0.3 0.2 2.6 3.8 3.21.9 4.3 5.4 6.8 0.7 4.3 6.1 2.8 4.2 1 1.3 5.1 0.5 1 1.8 3 2.4 0.82.2 4.6 5.7 7.1 0.4 4.6 6.4 3.1 4.5 0.7 1 5.4 0.2 0.7 2.1 3.3 2.7 0.5 0.3
A R N D C Q E G H I L K M F P S T W Y VAla Arg Asp Asn Cys Glu Gln Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val8.1 10.5 11.6 13.0 5.5 10.5 12.3 9.0 10.4 5.2 4.9 11.3 5.7 5.2 8.0 9.2 8.6 5.4 6.2 5.9
Fig. A2.8. Distance matrix composed for polarity using values from Grantham (1974). The distances are calculated in the same way as for Fig.
A2.2.
244
Table A2.2. Log likelihood values for each species group analysed using the free
parameter branch model (BM1).
Group SP-C§ lnL Group SP-C§ lnLAll W -878.490 Mustelidae3 W -210.761
C -406.099 C -94.568N -374.959 N -118.701
Castor W -163.201 Otariidae W -179.104C -96.947 C -93.066N -45.762 N -59.883
Cavia W -181.431 Otariidae2 W -173.886C -103.772 C -89.142N -51.733 N -58.984
Cetacea W -189.991 Phocidae W -199.476C -95.154 C -89.142N -59.156 N -85.085
Cetacea2 W -171.960 Pinnipedia W -209.717C -88.117 C -93.722N -52.011 N -92.606
Condylura W -200.931 Primate W -133.496C -174.720 C -75.934N -86.903 N -39.776
Hydrochaerus W -146.248 Sirenia W -159.649C -79.241 C -69.434N -44.392 N -87.509
Hydromys W -139.184 Tapirus W -182.591C -117.551 C -83.521N -63.047 N -62.640
Mustelidae W -221.646 Ursus W -205.896C -98.727 C -94.264N -122.953 N -107.755
Mustelidae2 W -215.756C -98.587N -142.173
§Region of protein analysed: W = whole protein, C = C-terminal, N = N-terminal.
245
Table A2.3. Estimates of ω under the two ratios branch model (BM2).
Group SP-C§ lnL ω1 Group SP-C§ lnL ω1
All W -920.142 ωt=0.245ωd=0.382 Mustelidae3 W -214.516 ωt=0.557
ωd=0.000
C -422.518 ωt=0.062ωd=0.553 C -95.943 ωt=0.108
ωd=1.008
N -374.959 ωt=0.104ωd=0.103 N -100.037 ωt=0.349
ωd=0.000
Castor W -163.749 ωt=0.003ωd=999.00 Otariidae W -181.319 ωt=0.767
ωd=0.000
C -96.947 ωt=0.000ωd=0.694 C -95.091 ωt=0.229
ωd=0.000
N -45.785 ωt=0.042ωd=0.000 N -59.883 ωt=999.00
ωd=0.000
Cavia W -182.023 ωt=0.005ωd=999.00 Otariidae2 W -176.099 ωt=0.777
ωd=1.000
C -103.772 ωt=0.000ωd=0.306 C -91.128 ωt=0.252
ωd=999.00
N -51.826 ωt=0.048ωd=0.000 N -58.983 ωt=825.142
ωd=0.000
Cetacea W -194.044 ωt=0.473ωd=0.000 Phocidae W -199.684 ωt=0.687
ωd=999.00
C -96.065 ωt=0.093ωd=0.000 C -91.128 ωt=0.252
ωd=999.00
N -59.676 ωt=0.003ωd=0.000 N -87.131 ωt=704.302
ωd=0.328
Cetacea2 W -174.699 ωt=0.997ωd=0.000 Pinnipedia W -214.969 ωt=0.662
ωd=1.925
C -88.682 ωt=0.104ωd=0.000 C -95.749 ωt=0.228
ωd=0.000
246
Group SP-C§ lnL ω1 Group SP-C§ lnL ω1
N -52.121 ωt=0.000ωd=0.834 N -96.233 ωt=999.00
ωd=0.030
Condylura W -200.931 ωt=0.027ωd=0.489 Primate W -133.496 ωt=0.000
ωd=998.990
C -178.138 ωt=0.003ωd=0.703 C -75.935 ωt=0.000
ωd=50.320
N -89.675 ωt=0.284ωd=0.163 N -39.776 ωt=0.000
ωd=1.000
Hydrochaerus W -146.416 ωt=0.017ωd=0.000 Sirenia W -159.649 ωt=1.707
ωd=1.210
C -79.241 ωt=0.000ωd=0.000 C -69.434 ωt=0.000
ωd=0.946
N -44.421 ωt=0.047ωd=0.000 N -75.674 ωt=0.605
ωd=998.990
Hydromys W -139.825 ωt=0.090ωd=0.000 Tapirus W -183.397 ωt=0.281
ωd=0.362
C -119.713 ωt=0.312ωd=0.000 C -83.521 ωt=0.000
ωd=0.000
N -64.692 ωt=0.000ωd=0.000 N -63.010 ωt=0.004
ωd=0.051
Mustelidae W -225.366 ωt=0.510ωd=0.000 Ursus W -207.057 ωt=0.538
ωd=1.000
C -100.823 ωt=0.088ωd=0.000 C -95.640 ωt=0.109
ωd=1.000
N -102.815 ωt=0.377ωd=0.000 N -92.549 ωt=0.224
ωd=0.000
Mustelidae2 W -216.918 ωt=0.494ωd=0.000
C -100.684 ωt=0.088ωd=0.000
247
Group SP-C§ lnL ω1 Group SP-C§ lnL ω1
N -101.715 ωt=0.168ωd=1.456
§Region of protein analysed: W = whole protein, C = C-terminal, N = N-terminal. 1ω is estimated for terrestrial (ωt) and diving (ωd) lineages
separately.
248
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