The repeated evolution of the same traits in distantly related groups (convergent evolution) raises a key question in evolutionary biology: do the same genes underpin convergent phenotypes? Here, we explore one such trait, viviparity (live birth), which, qualitative studies suggest, may indeed have evolved via genetic convergence. There are 150 independent origins of live birth in vertebrates, providing a uniquely powerful system to test the mechanisms underpinning convergence in morphology, physiology, and/or gene recruitment during pregnancy. We compared transcriptomic data from eight vertebrates (lizards, mammals, sharks) that gestate embryos within the uterus. Since many previous studies detected qualitative similarities in gene use during independent origins of pregnancy, we expected to find significant overlap in gene use in viviparous taxa. However, we found no more overlap in uterine gene expression associated with viviparity than we would expect by chance alone. Each viviparous lineage exhibits the same core set of uterine physiological functions. Yet, contrary to prevailing assumptions about this trait, we find that none of the same genes are differentially expressed in all viviparous lineages, or even in all viviparous amniote lineages. Therefore, across distantly related vertebrates, different genes have been recruited to support the morphological and physiological changes required for successful pregnancy. We conclude that redundancies in gene function have enabled the repeated evolution of viviparity through recruitment of different genes from genomic “toolboxes”, which are uniquely constrained by the ancestries of each lineage.

These files are the Supplementary Materials for our manuscript submission: "Different genes are recruited during convergent evolution of pregnancy and the placenta". Briefly, transcriptomes (both de novo and pre-existing) from eight vertebrates (lizards, mammals, shark) were compared to determine gene-expression changes during pregnancy. We found that, despite broad physiological and morphological convergence, there was next to no convergence in gene recruitment during pregnancy. A more in-depth explanation of methods can be found within the Supplementary Methods.

This upload to Dryad contains all files supplementary to our submission to PNAS. There are:

• 3 supplementary figures (.pdf)
• 13 supplementary tables (.pdf; .xlsx)
• A "Supplementary Materials" document (.docx) with supplementary figure captions

This upload also contains:

• All de novo transcriptome assemblies
• The raw counts for each sample from each species
• The code necessary to replicate the DE and GO analysis results (and associated accessory metadata files)
• The code for overlap analyses, and associated metadata files