Data from: The promiscuous and the chaste: frequent allopolyploid speciation and its genomic consequences in American daisies (Melampodium sect. Melampodium; Asteraceae)

Polyploidy, an important factor in eukaryotic evolution, is especially abundant in angiosperms, where it often acts in concert with hybridization to produce allopolyploids. The application of molecular phylogenetic techniques has identified the origins of numerous allopolyploids, but little is known on genomic and chromosomal consequences of allopolyploidization, despite their important role in conferring divergence of allopolyploids from their parental species. Here, using several plastid and nuclear sequence markers, we clarify the origin of tetra- and hexaploids in a group of American daisies, allowing characterization of genome dynamics in polyploids compared to their diploid ancestors. All polyploid species are allopolyploids. Among the four diploid gene pools, the propensity for allopolyploidization is unevenly distributed phylogenetically with a few species apparently more prone to participate, but the underlying causes remain unclear. Polyploid genomes are characterized by differential loss of ribosomal DNA loci (5S and 35S rDNA), known hotspots of chromosomal evolution, but show genome size additivity, suggesting limited changes beyond those affecting rDNA loci or the presence of processes counterbalancing genome reduction. Patterns of rDNA sequence conversion and provenance of the lost loci are highly idiosyncratic and differ even between allopolyploids of identical parentage, indicating that allopolyploids deriving from the same lower-ploid parental species can follow different evolutionary trajectories.

多倍化（polyploidy）是真核生物演化的关键驱动因子，在被子植物（angiosperms）中分布尤为广泛，且常与杂交作用协同催生异源多倍体（allopolyploids）。分子系统发育技术的应用已解析了诸多异源多倍体的起源，但尽管异源多倍化在推动异源多倍体与其亲本物种产生分化中发挥着关键作用，学界对异源多倍化所带来的基因组与染色体层面的效应仍知之甚少。本研究依托多个质体（plastid）与细胞核序列标记，阐明了一类美洲雏菊类群中四倍体（tetraploids）与六倍体（hexaploids）的起源，进而得以对比分析多倍体与其二倍体祖先的基因组动态特征。所有多倍体物种均为异源多倍体。在四个二倍体基因库（gene pools）中，异源多倍化的发生倾向在系统发育上分布不均，少数物种似乎更易参与异源多倍化过程，但其背后的分子机制仍未明确。多倍体基因组以核糖体DNA（rDNA）位点（5S与35S rDNA）的差异性丢失为特征——这类位点是染色体演化的已知热点区域——但同时表现出基因组大小的加和性，这提示除影响rDNA位点的变化外，要么仅存在有限的基因组改变，要么存在抵消基因组缩减的演化过程。rDNA序列转化模式与丢失位点的来源具有高度的特异性，即便亲本关系完全一致的异源多倍体之间也存在差异，这表明源自同一低倍体亲本物种的异源多倍体可遵循不同的演化路径。