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.

异源多倍性（allopolyploidy）在被子植物的演化进程中扮演了关键角色。基因组融合往往伴随染色体重排、串联与分散重复DNA家族的动态改变，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，使得全面解析植物基因组的重复组分成为可能。解析异源多倍化后的演化动力学，需同时明确异源多倍体的亲本起源与起源时间。通常，亲本起源可通过细胞遗传学与系统发育数据推断，但起源时间的推断却受限于系统发育关系的网状本质。若将异源多倍体的亚基因组视作隶属于不同物种（即假设亚基因组间无重组），并采用交叉定年约束（即对同一事件相关节点的年龄差异施加约束），则可在BEAST2软件的多物种溯和模型框架下推断异源多倍体的起源时间。本研究结合使用RepeatExplorer分析流程对重复DNA组分进行全面表征，并将该定年方法应用于菊科（Asteraceae）黑足菊属（Melampodium）中一组紧密相关的异源多倍体及其亲本物种。我们对异源四倍体狭叶黑足菊（M. strigosum）及其两个共享亲本起源与杂交方向的异源六倍体衍生物——M. pringlei与M. sericeum的起源时间进行了定年，结果显示其起源于更新世（Pleistocene，距今不足1.4 Ma）。据此推测，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，这也为推断M. sericeum与M. pringlei的异源多倍体物种分化精确时序带来了挑战。这些异源多倍体的较晚起源，或许是其基因组重复组分几乎未发生显著改变的重要原因。受多倍化后变化影响最显著的重复元件为Ty1-copia类反转录转座子Maximus谱系，以及占比相对较低的Ty3-gypsy家族Athila元件。