Phylogenetic and genealogical relationships of species and paralogs in this study. Phylogenetic relationships are depicted among species, orthologs, and paralogs of a diploid with 20 chromosomes, S. tropicalis (ST), two tetraploids with 40 chromosomes, S. epitropicalis (EP) and S. new tetraploid (NT), and four tetraploids with 36 chromosomes, Xenopus laevis (XL), X. borealis (XB), X. gilli (XG), and X. muelleri (XM). (A) Clawed frogs speciate by allopolyploidization and by regular speciation without a change in genome size. Allotetraploidization occurred independently in Xenopus and in Silurana and produced two paralogs in the resulting tetraploid ancestor – α and β – that are indicated as brown and green lineages respectively. After allopolyploidization, some of the diploid lineages probably went extinct, and this is indicated by a dagger. As a result of these extinctions, the portion of some paralogous lineages that evolved in a diploid, indicated as dashed lines, cannot be dissected apart from the portion that evolved in an allopolyploid. Numbered nodes indicate (0) divergence of the genera Xenopus and Silurana, (1) divergence of the diploid (2n = 18) ancestors of Xenopus, (2) allotetraploidization in Xenopus, (3) the first speciation event of the tetraploid ancestor of extant Xenopus, (4 and 5) more recent speciation events of Xenopus tetraploids, (6) divergence of the diploid (2n = 20) ancestors of Silurana, (7) allotetraploidization in Silurana, (8) speciation of a tetraploid Silurana without change in genome size. Sequences from individual paralogs were used to construct genealogies in order to compare (B) an early to a later stage of evolution after WGD in XLα, (C) an early to a later stage of evolution after WGD of EPα and (D) an intermediate to a later stage after WGD in XLα. Depending on the paralog for which data were obtained, sometimes NTα was considered in (C) or XBα was considered in (D).