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Mol Biol Evol. 2015 Sep;32(9):2302-16. doi: 10.1093/molbev/msv111. Epub 2015 May 8.

Soup to Tree: The Phylogeny of Beetles Inferred by Mitochondrial Metagenomics of a Bornean Rainforest Sample.

Author information

1
Department of Life Sciences, Natural History Museum, London, United Kingdom Department of Genetics, Evolution and Environment, Faculty of Life Sciences, University College London, London, United Kingdom a.crampton-platt@nhm.ac.uk a.vogler@imperial.ac.uk.
2
Department of Life Sciences, Natural History Museum, London, United Kingdom Division of Biology, Imperial College London, Silwood Park Campus, Ascot, United Kingdom.
3
Department of Biology, Faculty of Education, Palacký University, Olomouc, Czech Republic.
4
Department of Life Sciences, Natural History Museum, London, United Kingdom.
5
Department of Life Sciences, Natural History Museum, London, United Kingdom Department of Zoology, University of Cambridge, Cambridge, United Kingdom.
6
Entomology Section, Forest Research Centre, Forestry Department, Sandakan, Sabah, Malaysia.
7
Department of Life Sciences, Natural History Museum, London, United Kingdom Division of Biology, Imperial College London, Silwood Park Campus, Ascot, United Kingdom a.crampton-platt@nhm.ac.uk a.vogler@imperial.ac.uk.

Abstract

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.

KEYWORDS:

Coleoptera; Illumina MiSeq; biodiversity; bulk samples; community ecology; metagenome skimming; mitochondrial genomes; mitochondrial metagenomics; phylogeny; tree-of-life

PMID:
25957318
PMCID:
PMC4540967
DOI:
10.1093/molbev/msv111
[Indexed for MEDLINE]
Free PMC Article

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