Marina Brasó-Vives, Diego Andrés Hartasánchez, Julien F. Ayroles, Christabel Floi Bucao, Mayra Furlan-Magaril, Paco Majic, Luisa F Pallares, James Phipps-Tan, Thea F Rogers, Aurora Ruiz-Herrera, Gabriela Santos-Rodriguez, Nikolas Vellnow, Justin JS Wilcox, Juan Antonio Rodríguez 

The missing heritability problem, defined as the failure of genetic variants to explain variance in phenotypes, has been an unsolved issue in genetics for the past two decades. A potential solution to this problem stems from the idea that single nucleotide polymorphisms and copy-number variants, the most commonly studied forms of genomic diversity, do not represent the totality of the information that is transferred from one generation to the next. In this perspective, we offer a glimpse into hidden dimensions of genomic diversity: frequently neglected as sources of variation, and only recently starting to be perceived as targets for natural selection. We begin by acknowledging the existence of disregarded genomic matter and sequence composition affecting the mutational process. We explore how selection can act on gene expression variability and offer insight into the mechanisms behind transcriptional regulation. Finally, we recognize the importance of modifications in the 3D genome architecture and other large-scale genomic changes in generating phenotypic diversity. Zooming out through these dimensions of the genome, we discuss recent findings and future avenues of research within each one of them. Judging by the pervasiveness and diverse nature of sources of genomic diversity, we foresee that the study of genomic variation within species is yet to see another burst. Showcasing these hidden dimensions, we offer a broad perspective on the complexity behind the genotype-to-phenotype map, which is crucial for understanding the action of natural selection in populations.