Supplementary Texts Text S1: Extended Introduction and Systematic Overview 2 Text S2: Extended Methods (including Tables S1 and S2) 3 Text S3: Amplification success of the nuclear markers and sequence number per species 7 Text S4: Maximum likelihood test on the placement of B. turanensis in the maternal clade of the Bayesian tree shown in Fig. 1c (including Table S3) 8 Text S5: Details on the five allopolyploidization events (Fig. S2: I-V). 9 Text S1: Extended Introduction and Systematic

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... w Palearctic green toads (Bufo viridis subgroup) present a highly suitable anuran system to compare diploid and polyploid hybridization within one radiation. They comprise diploid lineages, arisen in different geological periods, forming secondary Eurasian contact zones, for which we have shown [1,2] that introgression indeed scales with divergence. In Central Asia these toads have several times evolved bisexually reproducing species of three ploidy levels (2n, 3n, and 4n; [3]), comprising meiotic and ameiotic forms. Using nuclear microsatellites without molecular dating, we have inferred the origins of two allopolyploids (Bufo baturae and B. pewzowi; [34]). Allotetraploid B. pewzowi (Uzbekistan to W-Mongolia) exhibits close mtDNA affinities and two inferred maternal chromosome sets to diploid B. turanensis [3-5] (E-Iran to S-Kazakhstan). In allo-triploid B. baturae (Karakoram, Hindukush, High Pamirs) mtDNA and microsatellites maternally link one chromosome set to diploid B. shaartusiensis (S-Tajikistan) [4,6]. The two paternal chromosome sets in both B. baturae and B. pewzowi putatively originated from a non-sampled (perhaps extinct) species, remotely related to B. latastii [4], representing the only known living diploid in the paternal ancestry. However, ancestry inference in B. baturae and B. pewzowi still requires nuclear DNA sequence evidence and dating. For three other, presumably allopolyploid species (B. oblongus, B. pseudoraddei and B. zugmayeri), maternal origins were suggested through mtDNA analyses [5] but nuclear DNA evidence is missing. Without this, however, mitochondrial capture (e.g. [7]), cannot be excluded. Allotetraploid B. oblongus (NE-Iran, W-Turkmenistan) and triploid B. zugmayeri (N-Baluchistan) closely relate mtDNA to B. turanensis [5], while B. pseudoraddei (all-triploid, W-Himalaya) forms a mitochondrial sister to B. baturae [5]. Importantly, the paternal ancestors of all three species have remained unknown. Analyses of hybrid origins should include the entire radiation of Palearctic green toads, which further includes the diploid lineages B. boulengeri (North-Africa), B. siculus (Sicily), B. balearicus (Italy, West-Mediterranean islands), B. luristanicus (SW-Iran), B. surdus (S-and SE-Iran), B. variabilis (Asia Minor, E-Europe and N-Central Asia) and B. viridis (Central and E-Europe). All diploid and tetraploid green toads reproduce meiotically ([8] incl. refs.), while triploid B. baturae reproduces by 'pre-equalizing hybrid meiosis' [9], where males produce haploid sperm, while females simultaneously transmit a clonal, and a recombined chromosome set [9]; a mechanism that is presumbaly also occurring in alltriploid B. pseudoraddei and B. zugmayeri.