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.

多倍体化（polyploidy）是真核生物演化进程中的关键影响因素之一，在被子植物中尤为普遍，且常与杂交作用协同产生异源多倍体（allopolyploid）。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，但尽管异源多倍体化在推动异源多倍体与其亲本物种产生分化中发挥着核心作用，学界对异源多倍体化所引发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）与核序列标记，明确了一类美洲雏菊类群中四倍体与六倍体的起源，并借此得以表征多倍体相较于其二倍体祖先的基因组动态变化特征。所有多倍体物种均为异源多倍体。在四个二倍体基因库中，异源多倍体化的倾向在系统发育树上分布不均，少数物种似乎更易参与异源多倍体的形成，但其背后的深层机制仍未阐明。多倍体基因组的典型特征为核糖体DNA（rDNA）位点（5S与35S rDNA）的差异性丢失——这类位点是染色体演化的已知热点区域，但多倍体基因组却表现出基因组大小的加和性，这提示要么仅存在有限的、除影响rDNA位点之外的其他基因组改变，要么存在抵消基因组缩减的调控过程。rDNA序列转换模式与丢失位点的起源具有高度的个体特异性，即便亲本来源完全相同的异源多倍体之间也存在显著差异，这表明由同一较低倍性亲本物种形成的异源多倍体可遵循截然不同的演化路径。