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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面对基因渗入时有偏见的基因保留模糊了物种关系


系统基因组分析正在恢复以前隐藏的杂交历史，揭示这些事件对现存基因组结构的基因组影响。我们应用系统发育学技术和一些补充统计测试来表明，渐渗杂交似乎发生在拟南芥的近亲之间，导致细胞核不一致并影响我们对该群体中物种关系的理解。渗入和保留基因的组成表明，针对不相容的细胞核和核-核相互作用的选择可能在渗入过程中起作用，而连锁也通过保留古老的单倍型块而有助于基因组组成。我们还应用基于分歧的测试来确定物种分支顺序并区分供体和受体谱系。令人惊讶的是，这些分析表明细胞核不一致是通过广泛的细胞核而不是细胞质渗入引起的。如果属实，这将意味着大部分核基因组在渗入过程中被置换，而只有一小部分天然等位基因被保留。