Figure 2. Molecular evolution and allotetraploidya. (top) The distribution of pseudogene ages, as described in Supplemental Note 9. (bottom) Phylogenetic tree illustrating the different epochs in Xenopus, with times based on protein-coding gene phylogeny of pipids, including Xenopus, Pipa carvalhoi, Hymenochirus boettgeri, and Rana pipiens (only Xenopus depicted). We date the speciation of X. tropicalis and the X. laevis ancestor at 48 Mya, the L and S polyploid progenitors at 34 Mya, and the divergence of the polyploid Xenopus radiation at 17 Mya. Using these times as calibration points, we estimate bursts of transposon activity at 18 Mya (mariner, blue star) and 33–34 Mya (harbinger, red star). The purple star is the time of hybridization, around 17–18 Mya.b. Phylogenetic tree based on protein-coding genes of tetrapods, rooted by elephant shark (not shown). Alignments were done by MACSE, the maximum-likelihood tree was built by PhyML. Branch length scale shown on bottom. The difference in branch length between Xenopus laevis-L and Xenopus laevis-S is similar to that seen between mouse and rat. Both subgenomes of X. laevis have longer branch lengths than X. tropicalis.
Image published in: Session AM et al. (2016)
Image downloaded from an Open Access article in PubMed Central. Image reproduced on Xenbase with permission of the publisher and the copyright holder.
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