Hybridization and polyploidization represent an important speciation mechanism in the diploid-polyploid complex of the Chenopodium album aggregate. In the present study we successfully reconstructed the evolutionary histories of the majority of Eurasian representatives of the C. album aggregate, resulting in the most comprehensive phylogenetic analysis of this taxonomically intricate group of species to date. We applied a combination of classical karyology for precise chromosome number determination, genomic in-situ hybridization for the determination of genomic composition, flow cytometry for the estimation of genome size and sequencing of plastid (cpDNA) and nuclear (ribosomal internal transcribed spacer - ITS and the introns of the FLOWERING LOCUS T LIKE genes - FTL) markers for a phylogenetic reconstruction and the identification of parental genomes in polyploid taxa. The FTL markers identified eight well supported evolutionary lineages. Five of them include at least one diploid species, and the remaining three comprise solely the subgenomes of polyploids that probably represent extinct or unknown diploid taxa. The existence of eight basic diploid lineages explains the origin of seven Eurasian polyploid groups and brings evidence of a nearly unlimited number of subgenomic combinations. The supposed promiscuity generated new species wherever different diploid lineages met each other and gave rise to tetraploid species or whenever they met other tetraploid species to produce hexaploid species throughout their evolutionary history. Finally, we unravelled a surprisingly simple scheme of polyploid species formation within the C. album aggregate. We determined seven groups of polyploid species differing in their origin in either Eurasia or Africa and convincingly demonstrated that (1) all Chenopodium polyploid species under study are of allopolyploid origin, (2) there are eight major monophyletic evolutionary lineages represented by extant or extinct/unknown diploid taxa, (3) those monophyletic lineages represent individual subgenomes, (4) hybridization among the lineages created seven subgenomic combinations of polyploid taxa, (5) taxa represented by particular subgenome combinations were further subjected to diversification, and (6) the majority of species are relatively young, not exceeding the age of the Quaternary period.

Central Siberian Botanical Garden Siberian Branch of the Russian Academy of Sciences 630090 Novosibirsk Russia

Department of Biology Faculty of Sciences University of Isfahan Isfahan Iran

Faculty of Environmental Sciences Czech University of Life Sciences Prague Kamýcká 129 Praha 6 Suchdol CZ 165 21 Czech Republic

Faculty of Environmental Sciences Czech University of Life Sciences Prague Kamýcká 129 Praha 6 Suchdol CZ 165 21 Czech Republic; The Czech Academy of Sciences Institute of Botany Zámek 1 CZ 252 43 Průhonice Czech Republic

Plant Reproduction Laboratory Institute of Experimental Botany v v i The Czech Academy of Sciences Praha 6 Lysolaje CZ 165 00 Czech Republic

State Key Laboratory of Desert and Oasis Ecology Xinjiang Institute of Ecology and Geography Chinese Academy of Sciences 830011 Urumqi China

The Czech Academy of Sciences Institute of Botany Zámek 1 CZ 252 43 Průhonice Czech Republic

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