Comparative transcriptomics reveals that a novel form of phenotypic plasticity evolved via lineage‐specific changes in gene expression

Novel forms of phenotypic plasticity may evolve by lineage‐specific changes or by co‐opting mechanisms from more general forms of plasticity. Here, we evaluated whether a novel resource polyphenism in New World spadefoot toads (genus Spea) evolved by co‐opting mechanisms from an ancestral form of plasticity common in anurans—accelerating larval development rate in response to pond drying. We compared overlap in differentially expressed genes between alternative trophic morphs constituting the polyphenism in Spea versus those found between tadpoles of Old World spadefoot toads (genus Pelobates) when experiencing different pond‐drying regimes. Specifically, we (1) generated a de novo transcriptome and conducted differential gene expression analysis in Spea multiplicata, (2) utilized existing gene expression data and a recently published transcriptome for Pelobates cultripes when exposed to different drying regimes, and (3) identified unique and overlapping differentially expressed transcripts. We found thousands of differentially expressed genes between S. multiplicata morphs that were involved in major developmental reorganization, but the vast majority of these were not differentially expressed in P. cultripes. Thus, S. multiplicata's novel polyphenism appears to have arisen primarily through lineage‐specific changes in gene expression and not by co‐opting existing patterns of gene expression involved in pond‐drying plasticity. Therefore, although ancestral stress responses might jump‐start evolutionary innovation, substantial lineage‐specific modification might be needed to refine these responses into more complex forms of plasticity.