Fantastic Beasts and How To Sequence Them: Ecological Genomics for Obscure Model Organisms

The application of genomic approaches to ‘obscure model organisms’ (OMOs), meaning species with no prior genomic resources, enables increasingly sophisticated studies of the genomic basis of evolution, acclimatization, and adaptation in real ecological contexts. I consider here ecological questions that can be addressed using OMOs, and indicate optimal sequencing and data-handling solutions for each case. With this I hope to promote the diversity of OMO-based projects that would capitalize on the peculiarities of the natural history of OMOs and could feasibly be completed within the scope of a single PhD thesis. Genotyping applications are undergoing a shift from high-coverage, reduced representation sequencing to low-coverage, whole-genome sequencing. Approaches based on full allele frequency spectrum (AFS) to study population structure, migration rates, and historical population sizes are gaining popularity. There has been a rise in functional genomics studies of acclimatization and adaptation, powered by cost-efficient methods for genome-wide gene expression and DNA methylation analysis. ‘Third-generation’ sequencing technologies (PacBio and Oxford Nanopore Technologies) have been proven to produce high-quality genome and transcriptome references, and to directly detect epigenetically modified DNA bases.