Fig. 1.

Co-linear patterns and Ks histograms illustrating differences between whole-genome duplication and putative bursts of segmental duplications observed in this study: a conceptual co-linearity pattern of (ancient) whole-genome duplication; black represents ancestral chromosome; light blue represents a duplicated chromosome containing gene duplicates with similar synonymous divergence (Ks). Genome rearrangements will fragment duplicated chromosomes into syntenic blocks. bKs frequency distribution of L. polyphemus (an arthropod that underwent WGD). Orange-red, histogram of the node-weighted whole-paranome Ks distribution; light-blue violin plot and histogram, Ks distribution of gene duplicates anchored in co-linear blocks as inferred from MCScanX; inlay, circos plot of co-linear blocks: all duplicate segments reside on separate scaffolds. c conceptual co-linearity pattern of a burst of segmental duplication; black represents an ancestral chromosome; light blue represents duplicated segments. Duplicated segments may end up on a position in another chromosome (gray bar), or on the same chromosome giving rise to tandem repeats and palindromes graphically represented as arches on a single scaffold. A burst of segmental duplication is hypothesized if the Ks values of gene pairs anchored in co-linear blocks are not clustered in a distinctive Ks peak corresponding to a peak in the whole-paranome distribution. dKs histogram and circos plot of co-linear blocks of gene duplicates from F. candida. Orange-red, Ks histogram using all gene duplicates; light-blue violin plot and histogram, Ks distribution for gene duplicates anchored in co-linear blocks. Inlay, circos plot showing co-linear block distribution among and within scaffolds. See “Results” for further interpretation. Note that the older a potential genome duplication event, the more difficult it is to discriminate between alternative explanations. Silhouettes are derived from phylopic.org