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. 2017 Jan 4;118(5):466–476. doi: 10.1038/hdy.2016.120

Table 2. List of 17 nonsynonymous codons encoding 22 amino acid replacements along Macquarie perch phylogeny inferred to be under positive selection by TREESAAP, MEME (P<0.05), FUBAR (PP >0.9) and/or Codeml BEB analysis under branch-site model with HNB in foreground (PP >0.8); see the list of all replacements in Supplementary Appendix 11.

Gene Codon position in a gene Amino acid replacement label (Figure 1) From codon To codon From amino acid To amino acid TREESAAP
 Codon models
              Cat α-helical tendencies Amnt α-helical tendencies Cat Equilibrium constant (ionization of COOH) Amnt Equilibrium constant (ionization of COOH)  
ND1 159 A GCT ACT Ala Thr 6 −0.59      
ND1 184 B GCC ACC Ala Thr 6 −0.59      
ND2 299 C1 ATC ACC Ile Thr     6 0.74 Codeml
ND2 299 C2 ATC ACC Ile Thr     6 0.74 Codeml
CO1 71 D ATA ACA Met Thr 6 −0.62      
CO2 150 E1 GTC ATC Val Ile     8 −0.96  
CO2 150 E2 GTC ATC Val Ile     8 −0.96  
ATP6 21 F1 GCC ACC Ala Thr 6 −0.59     FUBAR
ATP6 21 F2 GCC ACC Ala Thr 6 −0.59     FUBAR
ATP6 21 F3 GCC ACC Ala Thr 6 −0.59     FUBAR
ATP6 113 G1 ACC GCC Thr Ala 6 0.59     Codeml
ATP6 113 G2 GCC ACC Ala Thr 6 −0.59     Codeml
ND4 163 H GTT ATC Val Ile     8 −0.96  
ND4 186 I ATC ACC Ile Thr     6 0.74  
ND4 259 J AGC ATC Ser Ile     7 −0.85  
ND4 439 K ACC ATC Thr Ile     6 −0.74  
ND5 16 L TTC ATC Phe Ile         MEME
ND5 45 M GTT ATT Val Ile     8 −0.96  
ND5 178 N CTT ATT Leu Ile     8 −1 MEME
ND5 308 O GTT ATT Val Ile     8 −0.96  
ND5 511 P GCA GGA Ala Gly 8 −0.85      
Cytb 29 Q GTT ATT Val Ile     8 −0.96  

Abbreviations: Amnt, amount; BEB, Bayes empirical Bayes; Cat, category; HNB, Hawkesbury–Nepean Basin; PP, posterior probability.

Codons are labelled by letters (A–Q), multiple replacements of the same codon are numbered (see Figure 1). Amino-acid replacements of six codons (C, E, F, G, I and P, shaded grey) affected two or more sequences; these codons are candidates for positive selection. TreeSAAP: radical (categories 6–8) changes in amino-acid properties found to be significant by sliding window approach. Category and amount of change is given (negative values indicate decrease, whereas positive values indicate increase in property). Changes in Shoalhaven Basin (SB) lineage are in italics, and those basal to HNB lineage are in bold.