Polyploidy is pervasive in angiosperm evolution and plays important roles in adaptation and speciation. However, polyploid groups are understudied due to complex sequence homology, challenging genome assembly, and taxonomic complexity. Here, we study adaptive divergence in taxonomically complex eyebrights (Euphrasia), where recent divergence, phenotypic plasticity, and hybridization blur species boundaries. We focus on three closely related tetraploid species with contrasting ecological preferences that are sympatric on Fair Isle, a small isolated island in the British Isles. Using a common garden experiment, we show a genetic component to the morphological differences present between these species. Using whole-genome sequencing and a novel k-mer approach we call “Tetmer”, we demonstrate that the species are of allopolyploid origin, with a sub-genome divergence of approximately 5%. Using ∼2 million SNPs, we show sub-genome homology across species, with a very low sequence divergence characteristic of recent speciation. This genetic variation is broadly structured by species, with clear divergence of Fair Isle heathland Euphrasia micrantha, while grassland Euphrasia arctica and coastal Euphrasia foulaensis are more closely related. Overall, we show that tetraploid Euphrasia is a system of allopolyploids of postglacial species divergence, where adaptation to novel environments may be conferred by old variants rearranged into new genetic lineages.

多倍体在被子植物进化中普遍存在，并且在适应和物种形成中起重要作用。然而，由于复杂的序列同源性、具有挑战性的基因组组装和分类学的复杂性，多倍体群未被充分研究。在这里，我们研究了分类学复杂的小米（Euphrasia)，其中最近的分歧、表型可塑性和杂交模糊了物种边界。我们专注于三个密切相关的四倍体物种，它们具有不同的生态偏好，它们在不列颠群岛的一个孤立的小岛费尔岛同域。使用常见的花园实验，我们展示了这些物种之间存在的形态差异的遗传成分。使用全基因组测序和我们称为“Tetmer”的新型 k-mer 方法，我们证明该物种是异源多倍体起源，亚基因组差异约为 5%。使用~200万个SNP，我们展示了跨物种的亚基因组同源性，具有最近物种形成的非常低的序列分歧特征。这种遗传变异大致由物种构成，与费尔岛荒地有明显差异紫花苜蓿，而草原黄杨与沿海的黄杨幼稚的亲缘关系更为密切。总体而言，我们表明四倍体Euphrasia是冰期后物种分化的异源多倍体系统，其中对新环境的适应可能是由重新排列成新遗传谱系的旧变体赋予的。