Deeply conserved synteny resolves early events in vertebrate evolution

TLDR

Early vertebrate evolution is thought to have been shaped by ancient whole‑genome duplications, yet their number, timing, and mechanisms remain unclear, and this genomic history parallels vertebrate diversification in the fossil record. The study infers vertebrate evolutionary history by comparing genomes with a new chromosome‑scale sequence of the invertebrate chordate amphioxus. Using chromosomal conserved synteny in the amphioxus genome, the authors resolve two distinct ancient duplications. They find that amphioxus and vertebrate karyotypes derive from 17 ancestral chordate linkage groups through fusion, rearrangement, and duplication; all vertebrates share an autotetraploidization duplication in the mid/late Cambrian, while jawed vertebrates additionally experienced an allotetraploidization duplication in the mid–late Ordovician from extinct progenitors.

Abstract

Abstract 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.