Supplementary material from "Substantially adaptive potential in polyploid cyprinid fishes: evidence from biogeographic, phylogenetic and genomic studies"

Whole genome duplication (WGD) is commonly believed to play key roles in vertebrate evolution. However, nowadays polyploidy exists in a few fish, amphibian and reptile groups only, and seems to be an evolutionary dead-end in vertebrates. We investigate the evolutionary significance of polyploidization in Cyprinidae—a fish family that contains more polyploid species than any other vertebrate groups with integrating biogeographic, phylogenetic and genomic analyses. First, polyploid species are found to be significantly frequent in higher altitude and lower mean annual temperature areas compared to diploid species in Cyprinidae. Second, a polyploidy-related diversification rate shift is observed in Cyprinidae. It is that increased net diversification rate is only seen in three polyploid lineages, and other polyploid lineages have similar net diversification rate as well as diploid lineages in Cyprinidae. Interestingly, significant ‘lag-times’ existed between polyploidization and radiation in Cyprinidae. Multiple polyploid lineages were established approximately 15 Ma through recurrent allopolyploidization events but the net diversification rate did not start to increase until approximately 5 Ma—long after polyploidization events. Environmental changes associated with the continuous uplift of Tibetan Plateau and climate change have likely promoted the initial establishment and subsequent radiation of polyploidy in Cyprinidae. Finally, the unique retention of duplicated genes in polyploid cyprinids adapted to harsh environments is found. Taken together, our results suggest that polyploidy in Cyprinidae is far more than an evolutionary dead-end, but rather shows substantially adaptive potential. Polyploid cyprinids thus constitute an ideal model system for unveiling largely unexplored consequences of WGD in vertebrates, from genomic evolution to species diversification.