title: Metagenome skimming for phylogenetic community ecology: a new era in biodiversity research.
abstract: It is now well recognized that considering species evolutionary history is crucial for understanding the processes driving community assembly (Cavender-Bares et al.). Considerable efforts have been made to integrate phylogenetics and community ecology into a single theoretical framework. Yet, assessing phylogenetic structure at the community scale remains a great challenge, in particular for poorly known organisms. While DNA metabarcoding is increasingly used for assessing taxonomic composition of complex communities from environmental samples, biases and limitations of this technique can preclude the retrieval of information on phylogenetic community structure. In this issue of Molecular Ecology, Andújar et al. (2015) demonstrate that shotgun sequencing of bulk samples of soil beetles and subsequent reconstruction of mitochondrial genomes can provide a solid phylogenetic framework to estimate species diversity and gain insights into the mechanisms underlying the spatial turnover of soil mesofaunal assemblages. This work highlights the enormous potential of 'metagenome skimming' not only for improving the current standards of DNA-based biodiversity assessment but also for opening up the application of phylogenetic community ecology to hyperdiverse and poorly known biota, which was heretofore inconceivable.
authors.affiliation: Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI, 48109, USA.
authors.forename: Anna
authors.initials: A
authors.lastname: Papadopoulou
authors.affiliation: Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique, Grenoble, F-38000, France.|Laboratoire d'Ecologie Alpine (LECA), Université Grenoble Alpes, Grenoble, F-38000, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Taberlet
authors.affiliation: CNRS, ENFA, UMR 5174 EDB, Université Toulouse 3 Paul Sabatier, Toulouse, F-31062, France.
authors.forename: Lucie
authors.initials: L
authors.lastname: Zinger
mesh_terms: D000818:Animals; D044822:Biodiversity; D058448:Biota; D004272:DNA, Mitochondrial / Q000235:genetics*; D056186:Metagenomics; D010802:Phylogeny
chemical_list: D004272:DNA, Mitochondrial
keywords: NGS; genome skimming; metabarcoding; organellar metagenomics; phylogenomics; soil biodiversity