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Table S1 Distance matrix of population genetic measures for all possible pairwise comparisons between the 11 individuals used for expression analysis

Table S2 Expression similarity matrix between all pairs of 11 individuals

Table S3 Gene expression differences between six carrion crow (CC) and four hooded crow (HC) individuals

Fig. S1 Average normalized coverage of transcripts with fully annotated UTRs in zebra finch shown for (A) 131 short transcripts (250–746 bp) (B) 180 medium sized transcripts (747–956 bp) and (B) for 225 long transcripts (1318–6890 bp). Error bars depict 95% confidence intervals.

Fig. S2 Volcano plot indicating differentially expressed genes for groups identified by multivariate analyses (6 CC + 1 HC, 4 HC). Grey scale indicated different false discovery rates (FDR).

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