Over the past decade, there has been an increasing appreciation of the role of population biology and population-level processes in genome evolution. The disconnection between population genetics and macroevolution of the genome was likely the product of the separate domains and methods of analysis that led to theoretical gaps between microevolution and macroevolution in general. However, recent work, encapsulated in many recent studies and books, has forged new links between population genetics and phylogeography on the one hand, and major features of the genome such as gene structure and density, GC-content, sex chromosome evolution and transposable elements. Additionally, newly investigated animal and plant models have found compelling examples of large-scale transitions in genome structure captured at the microevolutionary level, yielding crucial insight into how transitions in genome structure occur in the wild.

This Research Topic will highlight recent examples from leading experts in the field about feedbacks between population biology and genome architecture. The data for this new synthesis of seemingly disparate fields is coming largely from the expanded perspective provided by new genomic technologies, such as next-generation sequencing, transcriptome and gene expression studies and early epigenetic analyses, but also from field studies of natural populations. Additionally, many researchers are now examining genome and transcriptome structure over increasingly dense phylogenetic sampling, leading to more detailed insights into how genomes and transcriptomes change over time. Finally, better theoretical connections between population genetics, geographic variation and the consequences of drift and selection for genome architecture are allowing researchers to test empirical findings of genome architecture with model predictions. The result is a new synthesis of formerly scattered observations about genome structure and an enhanced understanding of the spectrum of genomic patterns observed in nature, across taxa, chromosomes and subgenomes.

The present Research Topic will highlight several areas of genome architecture, the understanding of which has been enhanced by accounting for patterns in population biology:
• Recent advances on mixed populations with alternative segregating sex chromosome systems.
• Emerging phenomena such as variation in GC-content and isochores coming from genomic, transcriptomic and proteomic investigations.
• Genome size, architecture and life history traits: how adaptive and non-adaptive processes drive variation in genome size via changes in organismal ecology and life history.
• Density and distribution of transposable elements and overall genetic diversity in the genome.

In summary, this series of Frontiers articles will showcase a rapidly growing sub-discipline within the broader area of comparative genomics and genome evolution. Students in the area of evolutionary genomics are increasingly in need of training and empirical examples spanning both population genetics and comparative genomics. To our knowledge, this series of articles will comprise the first such compendium of articles in this field since the widespread use of next-generation sequencing. We expect it to have a high readership and serve as a benchmark as evolutionary genomics transitions from a descriptive to a hypothesis testing phase.

Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.