Figure S1. (A) Posterior probability (L(K)) for the STRUCTURE analysis using all 297 aphid clones given different numbers of genetic clusters (K).

Figure S2. Genetic structure of pea aphids in England and Germany on eight plant genera assuming (A) 12 genetic clusters or (B) four genetic clusters.

Figure S3. Analysis of the subgroups found in the initial STRUCTURE analysis.

Figure S4. Genetic structure of the subpopulations identified by the STRUCTURE analysis assuming four genetic clusters in the overall population.

Figure S5. Negative log-likelihood (--log(L)) that a clone belongs to the genetic cluster that it was assigned to in the STRUCTURE analysis with K = 9 calculated in an assignment test implemented in GeneClass.

Table S1. PCR conditions for sequenced markers.

Table S2. PCR conditions for diagnostic symbiont detection.

Table S3. Genetic differentiation (measured by FST). (A) FST calculated for aphids collected from the eight different plant genera using all aphid clones (above the diagonal) and using only aphids where the collection plant matched the performance profile (below the diagonal). (B) FST calculated between genetic clusters using all available aphid clones.

Table S4. Population differentiation in juvenile survival on (i) the home plant species of pairs of aphid genetic clusters (QST home plants, above diagonal) and (ii) the away plant species of pairs of aphid genetic clusters (QST away plants, below diagonal).

Table S5. List of aphid clones classified as vagrants (an aphid clone where the genetic cluster it is assigned to matches its performance profile on the eight plant species, but that is collected from a different species) and of aphid clones where the genetic cluster did not match its performance (`Specialized on').

Table S6. Frequencies of infections with multiple symbiont species: in all screened pea aphid clones (all), in pea aphid clones collected from different plant species (collection plant) or in pea aphid clones assigned to different genetic clusters.

Table S7. Tests to determine whether co-infections with specific symbionts were observed more or less often than expected by chance, based on the frequencies of different species within populations.

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