Ten years ago, the journal Molecular Ecology published a “road map” paper that reviewed past achievements in the discipline of molecular ecology, identified research challenges and charted a way forward (Andrew et al., 2013). That paper was motivated by a symposium organized during the First Joint Congress on Evolutionary Biology (Ottawa, July 6–10, 2012). In addition, it occurred on the heels of a major inflection point in molecular ecology and in life sciences more broadly: the development and uptake of “next”- or “second”-generation sequencing technologies, which deliver short DNA reads (typically shorter than 400 bp) at very high throughput (e.g., several billion reads per run; Goodwin et al., 2016). As such, Andrew et al. (2013) emphasized the promise of second-generation sequencing for diverse subdisciplines of molecular ecology such as phylogeography, landscape genomics, molecular adaptation and speciation. Representing more than just a technical advancement, second-generation sequencing was predicted to stimulate rapid conceptual breakthroughs in the field, especially in nonmodel species (Stapley et al., 2010; Tautz et al., 2010). As illustrated by any recent issue in the Molecular Ecology journal, these predictions were accurate.