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The contribution of mitochondrial metagenomics to largescale data mining and phylogenetic analysis of Coleoptera

Benjamin Linard, Alex Crampton-Platt, Jérome Moriniere, Martijn J.T.N. Timmermans, Carmelo Andujar, Paula Arribas, Kirsten E. Miller, Julia Lipecki, Emeline Favreau, Amie Hunter, Carola Gomez-Rodriguez, Christopher Barton, Ruie Nie, Conrad P.D.T Gillett, Thijmen Breeschoten, Ladislav Bocak, Alfried P. Vogler
doi: https://doi.org/10.1101/280792
Benjamin Linard
1Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom
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Alex Crampton-Platt
1Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom
3Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, United Kingdom
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Jérome Moriniere
7Bavarian State Collection of Zoology (SNSB – ZSM), Münchhausenstrasse 21, 81247 München, Germany
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Martijn J.T.N. Timmermans
1Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom
4Department of Natural Sciences, Hendon Campus, Middlesex University, London, NW4 4BT, United Kingdom
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Carmelo Andujar
1Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom
2Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, SL5 7PY, United Kingdom
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Paula Arribas
1Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom
2Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, SL5 7PY, United Kingdom
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Kirsten E. Miller
1Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom
2Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, SL5 7PY, United Kingdom
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Julia Lipecki
1Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom
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Emeline Favreau
1Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom
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Amie Hunter
1Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom
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Carola Gomez-Rodriguez
5Departamento de Zoología, Facultad de Biología, Universidad de Santiago de Compostela, c/ Lope Gómez de Marzoa s/n, 15782 Santiago de Compostela, Spain
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Christopher Barton
1Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom
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Ruie Nie
1Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom
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Conrad P.D.T Gillett
1Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom
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Thijmen Breeschoten
1Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom
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Ladislav Bocak
6Department of Zoology, Faculty of Science, Palacky University, 17. listopadu 50, 771 46 Olomouc, Czech Republic
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Alfried P. Vogler
1Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom
2Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, SL5 7PY, United Kingdom
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Abstract

A phylogenetic tree at the species level is still far off for highly diverse insect orders, including the Coleoptera, but the taxonomic breadth of public sequence databases is growing. In addition, new types of data may contribute to increasing taxon coverage, such as metagenomic shotgun sequencing for assembly of mitogenomes from bulk specimen samples. The current study explores the application of these techniques for large-scale efforts to build the tree of Coleoptera. We used shotgun data from 17 different ecological and taxonomic datasets (5 unpublished) to assemble a total of 1942 mitogenome contigs of >3000 bp. These sequences were combined into a single dataset together with all mitochondrial data available at GenBank, in addition to nuclear markers widely used in molecular phylogenetics. The resulting matrix of nearly 16000 species with two or more loci produced trees (RAxML) showing overall congruence with the Linnaean taxonomy at hierarchical levels from suborders to genera. We tested the role of full-length mitogenomes in stabilizing the tree from GenBank data, as mitogenomes might link terminals with non-overlapping gene representation. However, the mitogenome data were only partly useful in this respect, presumably because of the purely automated approach to assembly and gene delimitation, but improvements in future may be possible by using multiple assemblers and manual curation. In conclusion, the combination of data mining and metagenomic sequencing of bulk samples provided the largest phylogenetic tree of Coleoptera to date, which represents a summary of existing phylogenetic knowledge and a defensible tree of great utility, in particular for studies at the intra-familial level, despite some shortcomings for resolving basal nodes.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted March 12, 2018.
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The contribution of mitochondrial metagenomics to largescale data mining and phylogenetic analysis of Coleoptera
Benjamin Linard, Alex Crampton-Platt, Jérome Moriniere, Martijn J.T.N. Timmermans, Carmelo Andujar, Paula Arribas, Kirsten E. Miller, Julia Lipecki, Emeline Favreau, Amie Hunter, Carola Gomez-Rodriguez, Christopher Barton, Ruie Nie, Conrad P.D.T Gillett, Thijmen Breeschoten, Ladislav Bocak, Alfried P. Vogler
bioRxiv 280792; doi: https://doi.org/10.1101/280792
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The contribution of mitochondrial metagenomics to largescale data mining and phylogenetic analysis of Coleoptera
Benjamin Linard, Alex Crampton-Platt, Jérome Moriniere, Martijn J.T.N. Timmermans, Carmelo Andujar, Paula Arribas, Kirsten E. Miller, Julia Lipecki, Emeline Favreau, Amie Hunter, Carola Gomez-Rodriguez, Christopher Barton, Ruie Nie, Conrad P.D.T Gillett, Thijmen Breeschoten, Ladislav Bocak, Alfried P. Vogler
bioRxiv 280792; doi: https://doi.org/10.1101/280792

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