Dan's research at the Australian Museum integrates biodiversity and systematics, including "biodiversity informatics". Much of his work is concerned with theory and applications of quantitative biodiversity assessment; it extends from the scale of genes to whole countries. Special emphasis has been given to the best-possible use of Museum collections in regional biodiversity assessment, and to the links from biodiversity assessment to ecosystem services, sustainability, and economics. Applied biodiversity research also includes work on methods for detecting environmental impacts.
A phylogenetic component of his biodiversity research arises through investigations of "phylogenetic diversity" and conservation. Other work in phylogenetics involves development and application of phylogenetic methods, philosophy of science, and editorial work for Systematic Biology.