Phylogenomic analyses are recovering previously hidden histories of hybridization, revealing the genomic consequences of these events on the architecture of extant genomes. We applied phylogenomic techniques and several complementary statistical tests to show that introgressive hybridization appears to have occurred between close relatives of Arabidopsis, resulting in cytonuclear discordance and impacting our understanding of species relationships in the group. The composition of introgressed and retained genes indicates that selection against incompatible cytonuclear and nuclear-nuclear interactions likely acted during introgression, while linkage also contributed to genome composition through the retention of ancient haplotype blocks. We also applied divergence-based tests to determine the species branching order and distinguish donor from recipient lineages. Surprisingly, these analyses suggest that cytonuclear discordance arose via extensive nuclear, rather than cytoplasmic, introgression. If true, this would mean that most of the nuclear genome was displaced during introgression, while only a small proportion of native alleles were retained.

中文翻译：

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面对渗入的偏向基因保留会掩盖物种关系

系统生物学分析正在恢复以前隐藏的杂交历史，揭示了这些事件对现存基因组架构的基因组后果。我们应用了植物遗传学技术并进行了一些补充统计检验，结果表明拟南芥的近亲之间似乎发生了渗入性杂交，从而导致细胞核不一致，并影响了我们对该物种间物种关系的理解。渗入和保留基因的组成表明，在渗入过程中可能针对不相容的细胞核和核-核相互作用进行选择，而连锁也通过保留古代单倍型块而有助于基因组组成。我们还应用了基于散度的测试来确定物种的分支顺序，并区分供体与受体谱系。令人惊讶的是，这些分析表明，细胞核不一致是通过广泛的核渗入而不是胞质渗入引起的。如果为真，则意味着大部分核基因组在渗入过程中被置换，而仅保留一小部分天然等位基因。