Supplementary Material

Figure S1. Predicted protein sequence alignment of the 33 new MHC class II-β sequences found in Chilean and Falkland brown trout. A dot indicates amino acid identity with the consensus sequences.

Figure S2. STUCTURE analysis: Values of Ln (P) for each number of putative genetic groups (K) in (A) Chilean rainbow trout populations (K=1-6) and (B) Chilean brown trout samples (K=1-8), indicating lack of population structuring in both cases.


Figure S3. STURCTURE analysis: (A) Values of Ln (P) and Delta (K) (Evanno et al. 2005) for each number of putative genetic groups (K) in Chilean and Falkland brown trout samples. (B) Estimation of the membership fraction to each of the three inferred clusters for brown trout populations, based on the MHC class II-β locus. Each vertical bar represents one individual while colours represent different clusters.

Figure S4. Mean and 95% CI (confidence interval) of Observed MHC class II-β dissimilarity (Ka) of (A) nine brown trout populations in Chile and Falklands (B) ten rainbow trout populations in Chile.

Figure S5. Results of cluster analysis paired linkage (A) Pearson’s correlation, (B) Cosine distance measure and (C) Euclidean of 40 MHC class II-β alleles defining brown trout supertypes, derived from physicochemical properties of amino acids at 6 positively selected codon sites. Bootstrapping values (n = 1000) are indicated.


Figure S6. Results of cluster analysis paired linkage (A) Pearson’s correlation, (B) Cosine distance measure and (C) Euclidean of 29 MHC class II-β alleles defining rainbow trout supertypes, derived from physicochemical properties of amino acids at 13 positively selected codon sites. Bootstrapping values (n = 1000) are indicated.

Model / L / Estimates of Parameters / Positively selected sites
(A) Brown Trout Chile
M1 (Nearly neutral) / -1179.32 / po = 0.619 (ωo = 0.029) p1 = 0.381 (ω1 = 1) / Not allowed
M2 (Positive selection) / -1140.70 / po = 0.462 p1 = 0.325 p2 = 0.213 (ω2 = 7.724) / 4Y**, 6R*, 8A**, 22L*, 31A**, 33Y**, 52K*, 63I**, 66Q**, 74Y**, 77P**, 80D**, 81I**, 82D**
M3 (Discrete) / -1139.93 / po = 0.517 (ωo = 0.021) p1 = 0.283 (ω1 = 1.731) p2 = 0.199 (ω2 = 10.026) / 4Y**, 6R**, 8A**, 9E**, 11R**, 12F**, 22L*, 24D**, 30Q**, 31A**, 33Y**, 34I**, 43Y**, 49H**, 52K**, 57W**, 62G**, 63I**, 66Q**, 67E**, 68R**, 70E**, 74Y**, 77P**, 78T**, 80D**, 81I**, 82D**
M7 / -1180.59 / p = 0.014 ω = 0.245 q = 0.028 / Not allowed
M8 / -1140.71 / po = 0.786 p1 = 0.214 (ω = 7.649) p = 0.005 q = 0.007 / 4Y**, 6R*, 8A**, 12F*, 22L*, 31A**, 33Y**, 52K*, 63I**, 66Q**, 74Y**, 77P**, 80D**, 81I**, 82D**
(B) Brown Trout Falklands
M1 (Nearly neutral) / -1626.33 / po = 0.575 (ωo = 0.008) p1 = 0.425 (ω1 = 1) / Not allowed
M2 (Positive selection) / -1551.66 / po = 0.504 p1 = 0.279 p2 = 0.216 (ω2 = 8.053) / 4E**, 6V**, 8R**, 11R**, 12F**, 20I**, 22F**, 43Y**, 52K** 63E**, 74V**, 77G**, 80A**, 81I**, 82D**
M3 (Discrete) / -1542.37 / po = 0.554 (ωo = 0.021) p1 = 0.257 (ω1 = 3.909) p2 = 0.189 (ω2 = 19.715) / 4E**, 5Q**, 6V**, 7V**, 8R**, 9Q**, 11R** ,12F**, 19G**, 20I**, 22F**, 24D**, 27V**, 30K**, 31A**, 33Y**, 34V**, 43Y**, 49H**, 52K**, 57W**, 61G**, 62P**, 63E**, 66Q**, 67E**, 68L**, 70E**, 74V**, 77G**, 78N**, 80A**, 81I**, 82D**
M7 / -1623.68 / p = 0.017 ω = 0.287 q = 0.034 / Not allowed
M8 / -1551.82 / po = 0.785 p1 = 0.214 (ω = 8.216) p = 0.005 q = 0.007 / 4E**, 6V**, 8R**, 11R**, 12F**, 20I**, 22F**, 43Y**, 52K**, 63E**, 66Q*, 74V**, 77G**, 80A**, 81I**, 82D**
(C) Rainbow Trout
M1 (Nearly neutral) / -1021.23 / po = 0.638 (ωo = 0.006) p1 = 0.362 (ω1 = 1) / Not allowed
M2 (Positive selection) / -976.02 / po = 0.528 p1 = 0.231 p2 = 0.241 (ω2 = 10.765) / 4I**, 6F**, 11V*, 15V*, 17H**, 27Y**, 35V**, 41W*, 47L**, 53G**, 58Y**, 61H**, 64D*, 65I**, 66Y**
M3 (Discrete) / -970.16 / po = 0.642 (ωo = 0.059) p1 = 0.194 (ω1 = 5.867) p2 = 0.164 (ω2 = 22.562) / 4I**, 6F**, 7I*, 8D**, 11V**, 14K**, 15V**, 17H**, 18I**, 27Y**, 35V*, 41W**, 47L**, 53G**, 54E**, 57S**, 58Y**, 61H**, 63A**, 64D**, 65I**, 66Y**
M7 / -1021.75 / p = 0.0097 ω = 0.074 q = 0.019 / Not allowed
M8 / -976.02 / po = 0.759 p1 = 0.241 (ω = 10.725) p = 0.005 q = 0.012 / 4I**, 6F**, 11V**, 15V*, 17H**, 27Y**, 35V**, 41W*, 47L**, 53G**, 58Y**, 61H**, 64D**, 65I**, 66Y**

Table S1. Log-likelihood values (L) and parameter estimates (ω = non-synonymous/synonymous rates ratio estimates; pi = fraction of the codons having a discrete ω or following a ω distribution, p and q = statistical parameters of the beta distribution under random-sites models for the Chilean (A) and Falkland (B) brown trout and rainbow trout (C). Positively selected sites (* represents 95%, ** represents 99%) were identified by a Bayesian method implemented in CODEML.