Although it is widely believed that early vertebrate evolution was shaped by ancient whole-genome duplications, the number, timing and mechanism of these events remain elusive. Here, we infer the history of vertebrates through genomic comparisons with a new chromosome-scale sequence of the invertebrate chordate amphioxus. We show how the karyotypes of amphioxus and diverse vertebrates are derived from 17 ancestral chordate linkage groups (and 19 ancestral bilaterian groups) by fusion, rearrangement and duplication. We resolve two distinct ancient duplications based on patterns of chromosomal conserved synteny. All extant vertebrates share the first duplication, which occurred in the mid/late Cambrian by autotetraploidization (that is, direct genome doubling). In contrast, the second duplication is found only in jawed vertebrates and occurred in the mid-late Ordovician by allotetraploidization (that is, genome duplication following interspecific hybridization) from two now-extinct progenitors. This complex genomic history parallels the diversification of vertebrate lineages in the fossil record.

中文翻译：

---

深度保守的同线性解决了脊椎动物进化中的早期事件。


尽管人们普遍认为早期脊椎动物的进化是由古代全基因组复制形成的，但这些事件的数量、时间和机制仍然难以捉摸。在这里，我们通过与无脊椎动物脊索动物文昌鱼的新染色体规模序列进行基因组比较来推断脊椎动物的历史。我们展示了文昌鱼和多种脊椎动物的核型是如何通过融合、重排和复制从 17 个祖先脊索动物连锁群（和 19 个祖先两侧对称动物群）衍生而来。我们根据染色体保守同线性模式解决了两个不同的古代重复。所有现存脊椎动物都有第一次重复，发生在寒武纪中/晚期，通过同源四倍化（即直接基因组加倍）。相比之下，第二次重复仅在有颌脊椎动物中发现，并通过来自两个现已灭绝的祖先的异源四倍体化（即种间杂交后的基因组重复）发生在奥陶纪中晚期。这种复杂的基因组历史与化石记录中脊椎动物谱系的多样化相似。