Table S1 Pgt MCC infection type (IT) scores across SM population. In all replications, the frequencies of all IT types were scored. To summarise our observations, in the table below, each entry ranks the frequency of each IT type (from highest to lowest) from left to right. For example, in SM001, rep1, IT 2 was most frequent, IT 1 next most frequent, IT 3 less frequent and IT 0 was not observed. To translate this into numerical data, IT’s at the first position were given a score of 1 with those at the intermediate second and third positions assigned arbitrary scores of 0.7 and 0.3 respectively. When only two IT’s were observed they would be given scores of 1 and 0.7. However, occasionally the second most frequent IT type was considered equivalent to the lesser of the two intermediate classes so a * was inserted in order to reflect this and assign a score of 0.3 (ie. only two IT types were recorded but they were given scores of 1 and 0.3). Type 4 was not observed in the St/Mx population and no line expressed all four IT’s. ‘-‘ missing data points. These numbers assigned to each frequency class were used to calculate the figures presented in Table S2 (e.g. for SM001, IT0= (1+0.7) / 5 = 0.34, IT1 = (0.7+0.7+0.7+0.7+1) / 5 = 0.76, IT2 = (1+1+1) / 5 = 0.6, IT3 = (0.3+0.3) / 5 = 0.12.

SM line / 1990 / 1991
rep1 / rep2 / rep3 / rep1 / Rep2
SM001 / 213 / 213 / 21 / 01 / 10
SM002 / 10 / 10 / 0 / 0 / 01
SM003 / 0 / 21 / 12 / 12 / 102
SM004 / 01 / 10 / 10 / 102 / 10
SM005 / - / 10 / 10 / 01 / 01
SM006 / 12 / - / 120 / 10 / 10
SM007 / 32 / 3*2 / 3 / 3 / 3
SM009 / 3 / 3 / 3 / 3 / 3
SM010 / 10 / 10 / 10 / 120 / 10
SM011 / 01 / 01 / 01 / 01 / 01
SM012 / 3 / - / 3 / 3 / 3
SM013 / 3 / - / 3 / 3 / 3
SM014 / 3 / 3 / 3 / 3 / 3
SM015 / 32 / 3 / 32 / 3 / 3
SM016 / 01 / 10 / 10 / 0 / 0
SM020 / 3 / 3 / 32 / 3 / 3
SM021 / 01 / 01 / 10 / 01 / 01
SM022 / 3 / 3 / 3 / 3 / 3
SM023 / 21 / 12 / 12 / 120 / 10
SM024 / 10 / 3 / 32 / 3 / 01
SM025 / 012 / 12 / 12 / 120 / 10
SM027 / 3 / 3 / 3 / 3 / 3
SM030 / 0 / 01 / 10 / 10 / 102
SM031 / 3 / 32 / 3 / 3 / 3
SM032 / 3 / 3 / 3 / 3 / 3
SM035 / 12 / 21 / 213 / 21 / 10
SM039 / 32 / 3 / 32 / 3*2 / 3
SM040 / 32 / 3 / 3 / 3 / 3
SM041 / 32 / 3*2 / 32 / 3 / 3
SM042 / 1*0 / 12 / 10 / 01 / 102
SM043 / 3 / 3 / 3 / 3 / 3
SM044 / 3 / 3 / 32 / 3 / 3
SM045 / 3 / 3*2 / 3 / 3 / 3
SM046 / 3 / 3 / 32 / 3 / 3
SM048 / 0 / 120 / 10 / 210 / 12
SM050 / 0 / 10 / 0 / 0 / 10
SM054 / 10 / 21 / 21 / 210 / 12
SM055 / - / 01 / 01 / 01 / 10
SM056 / 01 / 01 / 0 / 10 / 102
SM057 / 12 / 21 / 12 / 01 / 102
SM058 / 12 / 10 / 10 / 21 / 120
SM059 / 3 / 3 / 3 / 3 / 3
SM061 / 32 / 3 / 3*2 / 3 / 3
SM062 / 0 / 3 / 3*2 / 3 / 3
SM063 / 3 / - / 3 / 3 / 3
SM064 / 10 / 01 / 01 / 01 / 10
SM065 / 0 / 01 / 0 / 01 / 01
SM067 / 0 / 01 / 10 / 01 / 10
SM068 / 01 / 01 / 01 / 3 / 3
SM069 / 3 / 3 / 3 / 3 / 3
SM070 / 0 / 10 / 01 / 12 / 10
SM071 / 10 / 10 / 10 / 01 / 01
SM072 / 3 / 3 / 3 / 3 / 3
SM073 / 3 / 3 / 3 / 3 / 3
SM074 / 3*2 / 3 / 3 / 3 / 3
SM075 / 3 / 3 / 3 / 3 / 3
SM076 / 10 / 01 / 12 / 12 / 12
SM077 / 3 / 3*2 / 3*2 / 3 / 3
SM078 / 10 / 01 / 10 / 01 / 10
SM079 / 01 / 01 / 10 / 102 / 10
SM080 / 32 / 32 / 3 / 3 / 3
SM081 / 01 / 10 / 10 / 01 / 10
SM082 / 12 / 12 / 10 / 10 / 10
SM083 / 32 / 3 / 3 / 3 / 3
SM084 / 10 / 01 / 120 / 10 / 10
SM085 / 10 / 01 / 12 / 10 / 10
SM087 / 01 / 01 / 120 / 10 / 102
SM088 / 10 / - / 10 / 10 / 12
SM089 / 12 / 10 / 21 / 10 / 01
SM091 / 10 / - / 10 / 10 / 10
SM092 / 12 / 321 / 120 / 102 / 10
SM093 / 011 / 01 / 01 / 01 / 01
SM094 / 01 / 10 / 10 / 10 / 01
SM097 / 3 / 3 / 3 / 3 / 3
SM098 / 3 / 3 / 3 / 3 / 3
SM099 / 32 / 3*2 / 3 / 3 / 3
SM103 / 12 / 120 / 10 / 01 / 01
SM104 / 3 / 3- / 3 / 3 / 3
SM105 / 01 / 10 / 10 / 10 / 01
SM110 / 32 / 3*2 / 3 / 3 / 3
SM112 / 3 / 3 / 3 / 3 / 3
SM116 / 01 / 10 / 10 / 10 / 01
SM120 / 10 / 10 / 12 / 01 / 01
SM124 / - / 3 / - / 0 / 12
SM125 / 12 / 12 / 102 / 10 / 3
SM126 / 3 / 3 / 3 / 3 / 3
SM127 / 3 / 3 / 3 / 3 / 3
SM129 / 3 / 3 / 3 / 3 / 3
SM130 / 01 / 10 / 0 / 10 / 10
SM131 / 01 / 0 / 10 / 10 / 01
SM132 / 3 / 3 / 3 / 3 / 3
SM133 / 3*2 / 3 / 3 / 3 / 3
SM134 / 10 / 01 / 10 / 01 / 10
SM135 / 0 / 0 / 0 / 0 / 01
SM136 / 3 / 3 / 32 / - / 3
SM137 / 0 / 01 / 10 / 0 / 01
SM139 / - / 32 / 32 / 01 / 3
SM140 / 3 / - / 3 / 3 / -
SM141 / 3 / 3 / 3 / 3 / 3
SM142 / 3 / 3 / 3 / 3 / 3
SM143 / 01 / - / 0 / 0 / 10
SM144 / 3 / 3 / 3 / 3 / 3
SM145 / 3 / 3 / 32 / 3 / 3
SM146 / 21 / 21 / - / 102 / 10
SM147 / 32 / - / 3 / 3 / 3
SM149 / 3 / 32 / 3 / 3 / 3
SM150 / 01 / 0 / 0 / 00 / 01
SM151 / 01 / 0 / 10 / 10 / 01
SM152 / 01 / 01 / 01 / 01 / 0
SM153 / 3 / 3 / 3 / 3 / 3
SM154 / 3 / 3 / 3 / 3 / 3
SM155 / 10 / 01 / 01 / 01 / 01
SM156 / 10 / 10 / 21 / 01 / 10
SM157 / 10 / 01 / 10 / 01 / 01
SM158 / 3 / 3 / 3 / 3 / 3
SM159 / 3 / 3 / 3 / 3 / 3
SM160 / 3 / 3 / 3 / 3 / 3
SM161 / 10 / 01 / 10 / 01 / 10
SM162 / 3 / 3 / 3 / 3 / 3
SM164 / 3 / 3 / 32 / 3 / 3
SM165 / 10 / 0 / 10 / 01 / 01
SM166 / 0 / 01 / 0 / 10 / 01
SM167 / 0 / 10 / - / 102 / 101
SM168 / 3 / 3 / - / 3 / 32
SM169 / 3 / 3 / 3 / 3 / 0
SM170 / 01 / 01 / 10 / 01 / 10
SM171 / 3 / 3 / 3 / 3 / 3
SM172 / 3 / 3 / 3 / 32 / 3
SM173 / 10 / 01 / 10 / 10 / 10
SM174 / 10 / 01 / 01 / 10 / 01
SM176 / 3 / 3 / 3 / 3 / 3
SM177 / 10 / 10 / 10 / 01 / 01
SM179 / 3 / 3 / 3 / 3 / 3
SM180 / 01 / 01 / 10 / 01 / 01
SM181 / 01 / 01 / 10 / 01 / 01
SM182 / 21 / 01 / 10 / 01 / 01
SM183 / 10 / 01 / 10 / 0 / 21
SM184 / 3 / 3 / 3 / 3 / 3
SM185 / 3 / 3 / 3 / 3 / 3
SM186 / 10 / 10 / 10 / 10 / 10
SM187 / 3 / 3 / 3 / 3 / 3
SM188 / 3 / 3 / 3 / 3 / 3
SM189 / 32 / 01 / 0 / 10 / 10
SM193 / 3 / 3 / 3 / 3 / 3
SM194 / 3 / 3 / 3 / 3 / 3
SM196 / 01 / 01 / 10 / 01 / 01
SM197 / 10 / 10 / 01 / 01 / 10
SM198 / 3 / 3 / 32 / 3 / 3
SM199 / 01 / 10 / 01 / 01 / 10
SM200 / 10 / 12 / 10 / 10 / 10