Data from: Allopolyploidy, diversification, and the Miocene grassland expansion

The role of polyploidy, particularly allopolyploidy, in plant diversification is a subject of debate. Whole-genome duplications precede the origins of many major clades (e.g., angiosperms, Brassicaceae, Poaceae), suggesting that polyploidy drives diversification. However, theoretical arguments and empirical studies suggest that polyploid lineages may actually have lower speciation rates and higher extinction rates than diploid lineages. We focus here on the grass tribe Andropogoneae, an economically and ecologically important group of C4 species with a high frequency of polyploids. A phylogeny was constructed for ca. 10% of the species of the clade, based on sequences of four concatenated low-copy nuclear loci. Genetic allopolyploidy was documented using the characteristic pattern of double-labeled gene trees. At least 32% of the species sampled are the result of genetic allopolyploidy and result from 28 distinct tetraploidy events plus an additional six hexaploidy events. This number is a minimum, and the actual frequency could be considerably higher. The parental genomes of most Andropogoneae polyploids diverged in the Late Miocene coincident with the expansion of the major C4 grasslands that dominate the earth today. The well-documented whole-genome duplication in Zea mays ssp. mays occurred after the divergence of Zea and Sorghum. We find no evidence that polyploidization is followed by an increase in net diversification rate; nonetheless, allopolyploidy itself is a major mode of speciation.多倍性（polyploidy），尤其是异源多倍性（allopolyploidy）在植物物种多样化进程中的作用，长期以来都是学界争论的焦点议题。全基因组复制（whole-genome duplications）事件往往先于多个主要支系（clades）的起源出现，例如被子植物（angiosperms）、十字花科（Brassicaceae）与禾本科（Poaceae），这似乎表明多倍性能够推动物种多样化。但与此同时，理论推演与实证研究均显示，多倍体支系的物种形成速率实则低于二倍体支系，而灭绝速率则更高。本研究聚焦于禾本科蜀黍族（Andropogoneae）：这是一类兼具经济与生态价值的C4植物（C4 species）类群，其内部多倍体的出现频率极高。研究基于4个串联的低拷贝核基因座（concatenated low-copy nuclear loci）的序列信息，构建了该支系约10%物种的系统发育树（phylogeny）。研究借助双标记基因树（double-labeled gene trees）的特征模式，鉴定出了遗传异源多倍体。在所采样的物种中，至少32%为遗传异源多倍化的产物，这些多倍体均源自28次独立的四倍化事件（tetraploidy events），外加额外6次六倍化事件（hexaploidy events）。该数值仅为最低估计，实际发生的多倍化事件频率可能显著更高。多数蜀黍族多倍体的亲本基因组在中新世晚期（Late Miocene）发生分化，这一时间节点与现今主导全球陆地生态系统的主要C4草原（C4 grasslands）的扩张时期高度吻合。普通玉米（Zea mays ssp. mays）中已被广泛证实的全基因组复制事件，发生于玉米属（Zea）与高粱属（Sorghum）分化之后。本研究未发现多倍化事件伴随净多样化速率（net diversification rate）提升的证据；尽管如此，异源多倍化本身仍是一种重要的物种形成方式。