Introgression allows polyploid species to acquire new genomic content from diploid progenitors or from other unrelated diploid or polyploid lineages, contributing to genetic diversity and facilitating adaptive allele discovery. In some cases, high levels of introgression elicit the replacement of large numbers of alleles inherited from the polyploid’s ancestral species, profoundly reshaping the polyploid’s genomic composition. In such complex polyploids, it is often difficult to determine which taxa were the progenitor species and which taxa provided additional introgressive blocks through subsequent hybridization. Here, we use population-level genomic data to reconstruct the phylogenetic history of Betula pubescens (downy birch), a tetraploid species often assumed to be of allopolyploid origin and which is known to hybridize with at least four other birch species. This was achieved by modeling polyploidization and introgression events under the multispecies coalescent and then using an approximate Bayesian computation rejection algorithm to evaluate and compare competing polyploidization models. We provide evidence that B. pubescens is the outcome of an autoploid genome doubling event in the common ancestor of B. pendula and its extant sister species, B. platyphylla, that took place approximately 178,000–188,000 generations ago. Extensive hybridization with B. pendula, B. nana, and B. humilis followed in the aftermath of autopolyploidization, with the relative contribution of each of these species to the B. pubescens genome varying markedly across the species’ range. Functional analysis of B. pubescens loci containing alleles introgressed from B. nana identified multiple genes involved in climate adaptation, while loci containing alleles derived from B. humilis revealed several genes involved in the regulation of meiotic stability and pollen viability in plant species.

中文翻译：

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复杂多倍体：起源、基因组组成和渐渗等位基因的作用


基因渗入允许多倍体物种从二倍体祖细胞或其他不相关的二倍体或多倍体谱系获得新的基因组内容，有助于遗传多样性并促进适应性等位基因的发现。在某些情况下，高水平的基因渗入会引起从多倍体祖先物种继承的大量等位基因的替换，从而深刻地重塑多倍体的基因组组成。在这种复杂的多倍体中，通常很难确定哪些类群是祖先物种以及哪些类群通过随后的杂交提供了额外的渐渗块。在这里，我们使用种群水平的基因组数据来重建毛桦（绒毛桦）的系统发育历史，毛桦是一种四倍体物种，通常被认为是异源多倍体起源，并且已知它与至少四种其他桦树物种杂交。这是通过对多物种合并下的多倍化和基因渗入事件进行建模，然后使用近似贝叶斯计算拒绝算法来评估和比较竞争性多倍化模型来实现的。我们提供的证据表明，B. pubescens 是 B. pendula 及其现存姐妹物种 B. platyphylla 共同祖先同倍体基因组加倍事件的结果，该事件发生在大约 178,000-188,000 代之前。在同源多倍化之后，与 B. pendula、B. nana 和 B. humilis 进行了广泛的杂交，这些物种对毛 B. pubescens 基因组的相对贡献在物种范围内显着变化。对含有从 B. nana 渗入的等位基因的 B. pubescens 基因座进行功能分析，鉴定出多个与气候适应有关的基因，而含有源自 B. pubescens 等位基因的基因座。 humilis揭示了几个参与植物物种减数分裂稳定性和花粉活力调节的基因。