Convergent genomic signatures associated with vertebrate viviparity

Viviparity—live birth—is a complex and innovative mode of reproduction that has evolved repeatedly across the vertebrate Tree of Life. The genetic basis of viviparity has garnered increasing interest over recent years, however such studies are often undertaken on small evolutionary timelines, and thus are not able to address changes occurring on a broader scale. Using whole genome data, we investigated the molecular basis of this innovation across the diversity of vertebrates to answer a long held question in evolutionary biology: is the evolution of convergent traits driven by convergent genomic changes? This dataset includes the scripts and files used to investigate the genomic basis of viviparity in vertebrates. Specifically, we use genome alignments to investigate changes to protein families, protein-coding regions, introns and untranslated regions (UTRs). We assess changes in the sizes of protein families, as well as analyse differences in substitution rates in coding and noncoding sequences.

Methods
We used newly sequenced and publicly available whole genome data to generate multi-genome alignments that allowed us to make phylogenetic, genomic, and proteomic comparisons between viviparous and oviparous species. Specifically, we extracted coding sequences, UTRs and introns from the multi-genome alignments, before re-aligning them to generate both species and time trees. We additionally extracted fourfold degenerate (4d) sites from the genome alignments to generate a neutral phylogenetic model, which was used to analyse differences in substitution rates. Finally, we aligned genomes to sequences of protein families to obtain data corresponding to protein family sizes.