For the salicoid duplicates that have also been associated with more recent local duplications, all possible pairwise comparisons between the lone salicoid member and the local duplicates (e.g., CHATL6 vs. CHATL1-3, and HMTL7 vs. HMTL1-6) were included.
Moreover, this approach allowed us to identify 404 WGD-derived duplicated genes (10% of all 4492) that showed higher sequence similarity to more recent local duplications.
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In contrast, the sister Clade Va exhibited extensive taxon-specific clustering (boxed region, Figure 4); Populus genes in the major subclade were associated with more than three times as many local duplications as retained salicoid duplicates.
Involvement of 1R or 2R appears possible (but we could not find any evidence for that) or of a more local event of segmental duplication.
In contrast, local duplications create only one more duplicated gene each time, and dosage imbalance is likely to occur.
Local duplications might be more likely than polyploidization events to account for the observed taxon-specific expansions of BAHD acyltransferases.
Genes related to transcription factors, protein kinases, and ribosomal proteins are preferentially retained following WGDs [ 4, 21], while those genes related to abiotic and biotic stress are more likely to be retained following local duplications [ 22, 23].
Hence, although the de novo and the duplication-divergence model are both compatible with this pattern, one could have expected for a duplication model that more local clusters could have become apparent.
Overall, we found sixty BAHD genes were associated with recent (salicoid or local) duplications (Additional File 6: Supplementaccountingls), accounting for more than half of the BAHD acyltransferases in Populus (Table 1).
