Wen Kang

Natural selection has sculpted tetrapod limbs and digits into a tremendous morphological diversity, but the underlying developmental mechanism remains unclear. This leads to an enduring debate concerning the identity of the three digits of bird wing. Here we use comparative digit transcriptomics across six tetrapod species to examine gene expression signatures of digit evolution. Here we show that the avian wing digits are homologous to reptilian forelimb digits 1,3,4. We find that birds uniquely increase fore-hindlimb transcriptome divergence during development, relaxing constraints and facilitating wing and foot digit specialization. We identify many limb- or digit- identity associated genes that have a biased expression between fore- or hind-limb, or toward specific digits. There are more limb and digit biased genes among the avian lineages than in other tetrapod lineages. Our work reveals ancient regulatory networks that maintain limb and digit molecular identity through persistent differential expression. We also show that this conserved network does not preclude independent digit evolution, especially when developmental constraints are reduced.

The amniote digits have undergone recurrent modifications with the diversified molecular mechanisms more studied among mammals than reptiles. Here we focus on the emu wings and ostrich feet, both of which experienced species specific digit changes driven respectively by secondary flight loss and adaptation to running. By comparing their digit transcriptomes to those of chicken and alligator, we identified different gene networks in skeleton/muscle development responsible for the degenerated digits in archosaur ancestor and emu, but those in epidermal development for the load-bearing digit of ostrich. These results provide new clues for developmental programs of different cell types between different digits, on which natural selection can convergently operate.

The slow-evolving invertebrate amphioxus has an irreplaceable role in advancing our understanding of the vertebrate origin and innovations. Here we resolve the nearly complete chromosomal genomes of three amphioxus species, one of which best recapitulates the 17 chordate ancestor linkage groups. We reconstruct the fusions, retention, or rearrangements between descendants of whole-genome duplications, which gave rise to the extant microchromosomes likely existed in the vertebrate ancestor. Similar to vertebrates, the amphioxus genome gradually establishes its three-dimensional chromatin architecture at the onset of zygotic activation and forms two topologically associated domains at the Hox gene cluster. We find that all three amphioxus species have ZW sex chromosomes with little sequence differentiation, and their putative sex-determining regions are nonhomologous to each other. Our results illuminate the unappreciated interspecific diversity and developmental dynamics of amphioxus genomes and provide high-quality references for understanding the mechanisms of chordate functional genome evolution.