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Figure S1. Phylogenetic relationships among insect paralogous genes Clock, Cycle and Arnt/Tango. A neighbor-joining topology resulting from the analysis of Poisson-corrected distances is shown with bootstrap values indicated when higher than 50%. For each gene, the Daphnia sequence was also included. The tree obtained shows the true orthology for each of sequences found in the Acyrthosiphon pisum genome. The anomalous positions of the pea aphid sequences, basal to Daphnia and the rest of insects, specially in the Cycle clade, further reflects the accelerated rates for these genes in A. pisum shown in Table 1.

Figure S2. Phylogenetic relationships among animal cryptochromes and the 6-4 Photolyase, including homolog sequences found in Acyrthosiphon pisum. Both Insect CRY1 (Drosophila-type) and Insect CRY2 (mammal-type) are present in the A. pisum genome, with two copies found for the latter (named AcpCRY2-1 and AcpCRY2-2). The phylogenetic inference was done using the neighbour-joining algorithm on Poisson-corrected distances. Bootstrap values are shown for nodes when higher than 50%. The 6-4 Photolyase of Arabidopsis thaliana was used to root the tree.

Table S1. Primers used for PCR amplification, sequencing and Real-time quantitative PCR of the genes characterized in the present study.

Table S2. Accession numbers for sequences included in the phylogenetic analysis.

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