Data from: Dating the species network: allopolyploidy and repetitive DNA evolution in American daisies (Melampodium sect. Melampodium, Asteraceae)

Allopolyploidy has played an important role in the evolution of the flowering plants. Genome mergers are often accompanied by significant and rapid alterations of genome size and structure via chromosomal rearrangements and altered dynamics of tandem and dispersed repetitive DNA families. Recent developments in sequencing technologies and bioinformatic methods allow for a comprehensive investigation of the repetitive component of plant genomes. Interpretation of evolutionary dynamics following allopolyploidization requires both the knowledge of parentage and the age of origin of an allopolyploid. Whereas parentage is typically inferred from cytogenetic and phylogenetic data, age inference is hampered by the reticulate nature of the phylogenetic relationships. Treating subgenomes of allopolyploids as if they belonged to different species (i.e., no recombination among subgenomes) and applying cross-bracing (i.e., putting a constraint on the age difference of nodes pertaining to the same event), we can infer the age of allopolyploids within the framework of the multi-species coalescent within BEAST2. Together with a comprehensive characterization of the repetitive DNA fraction using the RepeatExplorer pipeline, we apply the dating approach in a group of closely related allopolyploids and their progenitor species in the plant genus Melampodium (Asteraceae). We dated the origin of both the allotetraploid, M. strigosum, and its two allohexaploid derivatives, M. pringlei and M. sericeum, which share both parentage and the direction of the cross, to the Pleistocene (less than 1.4 Ma). Thus, Pleistocene climatic fluctuations may have triggered formation of allopolyploids possibly in short intervals, contributing to difficulties in inferring the precise temporal order of allopolyploid species divergence of M. sericeum and M. pringlei. The relatively recent origin of the allopolyploids likely played a role in the near-absence of major changes in the repetitive fraction of the polyploids’ genomes. The repetitive elements most affected by the post-polyploidization changes represented retrotransposons of the Ty1-copia lineage Maximus and, to a lesser extent, also Athila elements of Ty3-gypsy family.

异源多倍化（allopolyploidy）在显花植物的演化进程中发挥了关键作用。基因组融合往往伴随染色体重排、串联及散在重复DNA家族动态改变，进而引发基因组大小与结构的显著快速变化。近年来测序技术与生物信息学方法的进步，使得对植物基因组重复序列组分的全面解析成为可能。解析异源多倍化后的演化动态，需要同时明确异源多倍体的亲本来源与起源时间。尽管亲本关系通常可通过细胞遗传学与系统发育数据推断，但起源时间的推算却受限于系统发育关系的网状演化特性。将异源多倍体的亚基因组视为独立物种（即亚基因组间无重组），并应用交叉约束（即对同一事件相关节点的年龄差异设置约束），我们便可在BEAST2的多物种溯祖框架内推断异源多倍体的起源时间。结合使用RepeatExplorer流程对重复DNA组分的全面表征，我们将该定年方法应用于菊科（Asteraceae）黑足菊属（Melampodium）中一组亲缘关系紧密的异源多倍体及其祖先物种。我们将异源四倍体M. strigosum，以及与其共享亲本来源与杂交方向的两个异源六倍体衍生物种M. pringlei和M. sericeum的起源时间均定年至更新世（距今不足140万年）。由此推测，更新世的气候波动可能在短时间内多次触发异源多倍体的形成，这为精准推断M. sericeum与M. pringlei的异源多倍体物种分化时序带来了困难。这些异源多倍体起源时间较近，可能是其基因组重复序列组分几乎未发生显著变化的原因之一。受多倍化后变化影响最显著的重复元件为Ty1-copia家族Maximus谱系的反转录转座子，其次为Ty3-gypsy家族的Athila元件。