Data from: Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)

Interspecies hybridization has been recently recognized as potentially common in wild animals, but the extent to which it shapes modern genomes is still poorly understood. Distinguishing historical hybridization events from other processes leading to phylogenetic discordance among different markers requires a well-resolved species tree that considers all modes of inheritance, and overcomes systematic problems due to rapid lineage diversification by sampling large genomic character sets. Here we assessed genome-wide phylogenetic variation across a diverse mammalian family, Felidae (cats). We combined genotypes from a genome-wide SNP array with additional autosomal, X- and Y-linked variants to sample ~150 kilobases of nuclear sequence, in addition to complete mitochondrial genomes generated using light-coverage Illumina sequencing. We present the first robust felid timetree that accounts for unique maternal, paternal, and biparental evolutionary histories. Signatures of phylogenetic discordance were abundant in the genomes of modern cats, in many cases indicating hybridization as the most likely cause. Comparison of big cat whole-genome sequences revealed a substantial reduction of X-linked divergence times across several large recombination coldspots, which were highly enriched for signatures of selection-driven post-divergence hybridization between the ancestors of the snow leopard and lion lineages. These results highlight the mosaic origin of modern felid genomes and the influence of sex chromosomes and sex-biased dispersal in post-speciation gene flow. A complete resolution of the Tree of Life will require comprehensive genomic sampling of biparental and sex-limited genetic variation to identify and control for phylogenetic conflict caused by ancient admixture and sex-biased differences in genomic transmission.

近年来，学界逐渐认识到种间杂交在野生动物中可能普遍存在，但其对现代基因组的塑造程度仍未得到充分阐明。若要将历史杂交事件与其他导致不同分子标记间系统发育冲突的过程区分开来，需要构建同时考虑所有遗传模式的高分辨率物种树，并通过采样大规模基因组特征集，克服由快速谱系分化带来的系统性问题。本研究针对物种多样的哺乳动物类群猫科（Felidae）开展了全基因组水平的系统发育变异分析：我们整合了全基因组单核苷酸多态性（Single Nucleotide Polymorphism, SNP）芯片的基因型数据，结合额外的常染色体、X连锁及Y连锁变异位点，共获取了约150千碱基对的核序列数据，同时还通过低覆盖度Illumina测序获得了完整的线粒体基因组序列。本研究构建了首个稳健的猫科系统发育时间树，该树同时兼顾了母系、父系及双亲遗传的独特演化历史。现代猫科动物基因组中存在大量系统发育冲突的信号，在多数情况下，杂交被认为是最可能的成因。通过对大型猫科动物全基因组序列的比较分析，研究团队在多个大型重组冷点区域发现X连锁位点的分化时间显著缩短，这些区域高度富集了雪豹与狮类支系祖先之间由选择驱动的分化后杂交信号。上述研究结果揭示了现代猫科动物基因组的嵌合起源，以及性染色体和性别偏向扩散在物种形成后基因流中的作用。若要完全解析生命之树，需要对双亲遗传及性限制遗传的遗传变异开展全面的基因组采样，以识别并校正由古老基因交流及基因组传递过程中的性别偏向差异所导致的系统发育冲突。