In spite of the growth of molecular ecology, systematics and next-generation sequencing, the discovery and analysis of
diversity is not currently integrated with building the tree-of-life. Tropical arthropod ecologists are well placed to
accelerate this process if all specimens obtained through mass-trapping, many of which will be new species, could be
incorporated routinely into phylogeny reconstruction. Here we test a shotgun sequencing approach, whereby mitochondrial
genomes are assembled from complex ecological mixtures through mitochondrial metagenomics, and demonstrate
how the approach overcomes many of the taxonomic impediments to the study of biodiversity. DNA from approximately
500 beetle specimens, originating from a single rainforest canopy fogging sample from Borneo, was pooled and shotgun
sequenced, followed by de novo assembly of complete and partial mitogenomes for 175 species. The phylogenetic tree
obtained from this local sample was highly similar to that from existing mitogenomes selected for global coverage of
major lineages of Coleoptera. When all sequences were combined only minor topological changes were induced against
this reference set, indicating an increasingly stable estimate of coleopteran phylogeny, while the ecological sample
expanded the tip-level representation of several lineages. Robust trees generated from ecological samples now enable
an evolutionary framework for ecology. Meanwhile, the inclusion of uncharacterized samples in the tree-of-life rapidly
expands taxon and biogeographic representation of lineages without morphological identification. Mitogenomes from
shotgun sequencing of unsorted environmental samples and their associated metadata, placed robustly into the phylogenetic
tree, constitute novel DNA “superbarcodes” for testing hypotheses regarding global patterns of diversity.