Editorial: Gene Regulation as a Driver of Adaptation and Speciation

One fundamental goal in evolutionary biology is to understand the interaction between adaptation and speciation and how it can generate and maintain biodiversity (Wolf et al., 2010). Speciation leads to the diversification of lineages, whereas adaptation maximizes the survival and reproductive success of organisms in an ever-changing environment, thereby further increasing diversification. Genetic approaches have been critical for examining the molecular basis of adaptation and speciation. The availability of an increasing number of genome assemblies allows for the identification of genomic components that underlie these processes, providing new insights into the proximate mechanisms of diversification and deeper understanding of biodiversity evolution. Recent discoveries suggest that gene regulation plays an important role in speciation and adaptive diversification (Jones et al., 2012; Mack et al., 2018). We present this collection of papers, eight of original research, one opinion and one review, that explore genomic features that foster divergence in gene regulation and how evolutionary changes of regulation systems impact adaptation and speciation. The incorporation of gene regulation in evolutionary processes is multifaceted, and so are the approaches to its understanding. This multiplicity is reflected by the scope of the articles in our collection, ranging from the interplay between regulation and evolutionary patterns on a molecular level (e.g., Aviña-Padilla et al., Mohanty) to the investigation of adaptations of organisms to certain conditions (Wang et al.). Changes caused by epigenetics, structural variants, transcription factors (TFs) and regulatory sequences that elicit modifications in gene expression and drive adaptation and diversification are also explored. Here, we briefly summarize the authors’ findings. We start with contributions that investigated genome architecture. In interspecific hybridization in Saccharomyces yeast described by Hovhannisyan et al., the coexistence of two distinct genomes after hybridization is supported by the limited regulatory interference on broad transcriptional changes. This may explain the unusually strong ability of these organisms to successfully hybridize. In instances of genome duplications, the genomic history can play a crucial role in adaptation. As shown by Zhao et al., genes can be regulated differently depending on whether or not they have been duplicated. The authors evaluated transcriptional changes in cultivated and wild Glycine soybeans with highly duplicated genomes after whole genome duplications. They found more trans-only regulation in duplicated genes than in singletons, especially in tandem duplications. Their results suggest that genes with different duplication modes accumulate different types of regulatory divergence. Two papers show how changes on a chromosomal level can be instrumental in adaptation and speciation. Pabuayon et al. presented plant architectural modifications created through transgressive segregation in Pokkali rice. The authors examined morpho-developmental and physiological profiles and used transcriptomic data of recombinant inbred lines varying in salt tolerance to build genetic networks. The network analysis indicated novel adaptive architectures correlating with levels of Edited and reviewed by: Denis Baurain, University of Liège, Belgium