Using ancestral genome reconstructions to resurrect the duplication history of gene families

Multiple studies have been conducted in the last several years with the goal of understanding the evolution of genomes in the chordate lineage [1]. We used the two most recent ancestral genome reconstruction models by Nakatani et al. [2] and Putnam et al. [3] (therein referred to as “N” and “P” model respectively, see Figure 1 in main text) to clarify how the three rounds of whole genome duplications (1R, 2R and 3R) and subsequent genome rearrangements could have influenced the evolution of the RLN/INSL and RXFP families. In addition, we used the work by Kasahara et al. [4] to shed light on the effects of teleost-specific genome rearrangements on our genes of interest in medaka, tetraodon and zebrafish. We also referred to the reconstruction of the Eutherian ancestor genome to reconstruct the eutherian state [5]. Because we principally employ the Nakatani et al. [2] model, and it includes two alternative scenarios for the rearrangements of some ancestral chromosomes that ensued between the pre-1R to the post 2R vertebrate genomes, in this appendix we also include the alternative scenarios for the gene duplication of our focal genes, which are not shown in main text.