51
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Gómez‐Rodríguez C, Timmermans MJTN, Crampton‐Platt A, Vogler AP. Intraspecific genetic variation in complex assemblages from mitochondrial metagenomics: comparison with DNA barcodes. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12667] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Carola Gómez‐Rodríguez
- Department of Life Sciences Natural History Museum London SW7 5BD UK
- Departamento de Zoología Facultad de Biología Universidad de Santiago de Compostela c/Lope Gómez de Marzoa s/n Santiago de Compostela 15782 Spain
| | - Martijn J. T. N. Timmermans
- Department of Life Sciences Natural History Museum London SW7 5BD UK
- Department of Natural Sciences Middlesex University Hendon Campus London NW4 4BT UK
| | - Alex Crampton‐Platt
- Department of Life Sciences Natural History Museum London SW7 5BD UK
- Department of Genetics, Evolution and Environment University College London Gower Street London WC1E 6BT UK
| | - Alfried P. Vogler
- Department of Life Sciences Natural History Museum London SW7 5BD UK
- Department of Life Sciences Imperial College London Silwood Park Campus Ascot SL5 7PY UK
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52
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Krehenwinkel H, Kennedy S, Pekár S, Gillespie RG. A cost‐efficient and simple protocol to enrich prey
DNA
from extractions of predatory arthropods for large‐scale gut content analysis by Illumina sequencing. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12647] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Henrik Krehenwinkel
- Department of Environmental Science, Policy and Management University of California Berkeley 130 Mulford Hall #3114 Berkeley CA 94720 USA
| | - Susan Kennedy
- Department of Environmental Science, Policy and Management University of California Berkeley 130 Mulford Hall #3114 Berkeley CA 94720 USA
| | - Stano Pekár
- Department of Botany and Zoology Faculty of Science Masaryk University Kotlářská 2 Brno 61137 Czech Republic
| | - Rosemary G. Gillespie
- Department of Environmental Science, Policy and Management University of California Berkeley 130 Mulford Hall #3114 Berkeley CA 94720 USA
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53
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Breeschoten T, Doorenweerd C, Tarasov S, Vogler AP. Phylogenetics and biogeography of the dung beetle genus Onthophagus inferred from mitochondrial genomes. Mol Phylogenet Evol 2016; 105:86-95. [PMID: 27568212 DOI: 10.1016/j.ympev.2016.08.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 08/19/2016] [Accepted: 08/23/2016] [Indexed: 11/26/2022]
Abstract
Phylogenetic relationships of dung beetles in the tribe Onthophagini, including the species-rich, cosmopolitan genus Onthophagus, were inferred using whole mitochondrial genomes. Data were generated by shotgun sequencing of mixed genomic DNA from >100 individuals on 50% of an Illumina MiSeq flow cell. Genome assembly of the mixed reads produced contigs of 74 (nearly) complete mitogenomes. The final dataset included representatives of Onthophagus from all biogeographic regions, closely related genera of Onthophagini, and the related tribes Onitini and Oniticellini. The analysis defined four major clades of Onthophagini, which was paraphyletic for Oniticellini, with Onitini as sister group to all others. Several (sub)genera considered as members of Onthophagus in the older literature formed separate deep lineages. All New World species of Onthophagus formed a monophyletic group, and the Australian taxa are confined to a single or two closely related clades, one of which forms the sister group of the New World species. Dating the tree by constraining the basal splits with existing calibrations of Scarabaeoidea suggests an origin of Onthophagini sensu lato in the Eocene and a rapid spread from an African ancestral stock into the Oriental region, and secondarily to Australia and the Americas at about 20-24 Mya. The successful assembly of mitogenomes and the well-supported tree obtained from these sequences demonstrates the power of shotgun sequencing from total genomic DNA of species pools as an efficient tool in genus-level phylogenetics.
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Affiliation(s)
- Thijmen Breeschoten
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom; Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands; Institute Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.
| | - Camiel Doorenweerd
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands; Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Sergei Tarasov
- National Institute for Mathematical and Biological Synthesis, University of Tennessee, 1122 Volunteer Blvd, Ste. 106, Knoxville, TN 37996, USA
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom; Department of Life Sciences, Silwood Park Campus, Imperial College London, Buckhurst Road, Ascot SL5 7PY, United Kingdom
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54
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Linard B, Arribas P, Andújar C, Crampton-Platt A, Vogler AP. Lessons from genome skimming of arthropod-preserving ethanol. Mol Ecol Resour 2016; 16:1365-1377. [DOI: 10.1111/1755-0998.12539] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/06/2016] [Accepted: 05/06/2016] [Indexed: 01/16/2023]
Affiliation(s)
- B. Linard
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
| | - P. Arribas
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
- Department of Life Sciences; Imperial College London; Silwood Park Campus Ascot SL5 7PY UK
| | - C. Andújar
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
- Department of Life Sciences; Imperial College London; Silwood Park Campus Ascot SL5 7PY UK
| | - A. Crampton-Platt
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
- Department of Genetics, Evolution and Environment; University College London; Gower Street London WC1E 6BT UK
| | - A. P. Vogler
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
- Department of Life Sciences; Imperial College London; Silwood Park Campus Ascot SL5 7PY UK
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55
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Elbrecht V, Taberlet P, Dejean T, Valentini A, Usseglio-Polatera P, Beisel JN, Coissac E, Boyer F, Leese F. Testing the potential of a ribosomal 16S marker for DNA metabarcoding of insects. PeerJ 2016; 4:e1966. [PMID: 27114891 PMCID: PMC4841222 DOI: 10.7717/peerj.1966] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 04/03/2016] [Indexed: 11/29/2022] Open
Abstract
Cytochrome c oxidase I (COI) is a powerful marker for DNA barcoding of animals, with good taxonomic resolution and a large reference database. However, when used for DNA metabarcoding, estimation of taxa abundances and species detection are limited due to primer bias caused by highly variable primer binding sites across the COI gene. Therefore, we explored the ability of the 16S ribosomal DNA gene as an alternative metabarcoding marker for species level assessments. Ten bulk samples, each containing equal amounts of tissue from 52 freshwater invertebrate taxa, were sequenced with the Illumina NextSeq 500 system. The 16S primers amplified three more insect species than the Folmer COI primers and amplified more equally, probably due to decreased primer bias. Estimation of biomass might be less biased with 16S than with COI, although variation in read abundances of two orders of magnitudes is still observed. According to these results, the marker choice depends on the scientific question. If the goal is to obtain a taxonomic identification at the species level, then COI is more appropriate due to established reference databases and known taxonomic resolution of this marker, knowing that a greater proportion of insects will be missed using COI Folmer primers. If the goal is to obtain a more comprehensive survey the 16S marker, which requires building a local reference database, or optimised degenerated COI primers could be more appropriate.
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Affiliation(s)
- Vasco Elbrecht
- Department of Animal Ecology, Evolution and Biodiversity, Ruhr University Bochum, Bochum, Germany; Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine (LECA), CNRS, Grenoble, France; Laboratoire d'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Grenoble, France
| | | | | | | | - Jean-Nicolas Beisel
- Ecole Nationale du Génie de l'Eau et de l'Environnement de Strasbourg, Strasbourg, France; UMR CNRS 7362-LIVE, Université de Strasbourg, Strasbourg, France
| | - Eric Coissac
- Laboratoire d'Ecologie Alpine (LECA), CNRS, Grenoble, France; Laboratoire d'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Grenoble, France
| | - Frederic Boyer
- Laboratoire d'Ecologie Alpine (LECA), CNRS, Grenoble, France; Laboratoire d'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Grenoble, France
| | - Florian Leese
- Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany; Centre for Water and Environmental Research (ZWU) Essen, University of Duisburg-Essen, Essen, Germany
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56
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Arribas P, Andújar C, Hopkins K, Shepherd M, Vogler AP. Metabarcoding and mitochondrial metagenomics of endogean arthropods to unveil the mesofauna of the soil. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12557] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Paula Arribas
- Department of Life Sciences Natural History Museum Cromwell Road London SW7 5BD UK
- Department of Life Sciences Imperial College London Silwood Park Campus Ascot SL5 7PY UK
| | - Carmelo Andújar
- Department of Life Sciences Natural History Museum Cromwell Road London SW7 5BD UK
- Department of Life Sciences Imperial College London Silwood Park Campus Ascot SL5 7PY UK
| | - Kevin Hopkins
- Department of Life Sciences Natural History Museum Cromwell Road London SW7 5BD UK
| | | | - Alfried P. Vogler
- Department of Life Sciences Natural History Museum Cromwell Road London SW7 5BD UK
- Department of Life Sciences Imperial College London Silwood Park Campus Ascot SL5 7PY UK
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57
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Timmermans M, Lees D, Thompson M, Sáfián S, Brattström O. Mitogenomics of ‘Old World Acraea’ butterflies reveals a highly divergent ‘Bematistes’. Mol Phylogenet Evol 2016; 97:233-241. [DOI: 10.1016/j.ympev.2015.12.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 11/17/2015] [Accepted: 12/14/2015] [Indexed: 11/29/2022]
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58
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Crampton-Platt A, Yu DW, Zhou X, Vogler AP. Mitochondrial metagenomics: letting the genes out of the bottle. Gigascience 2016; 5:15. [PMID: 27006764 PMCID: PMC4802855 DOI: 10.1186/s13742-016-0120-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 03/06/2016] [Indexed: 01/14/2023] Open
Abstract
‘Mitochondrial metagenomics’ (MMG) is a methodology for shotgun sequencing of total DNA from specimen mixtures and subsequent bioinformatic extraction of mitochondrial sequences. The approach can be applied to phylogenetic analysis of taxonomically selected taxa, as an economical alternative to mitogenome sequencing from individual species, or to environmental samples of mixed specimens, such as from mass trapping of invertebrates. The routine generation of mitochondrial genome sequences has great potential both for systematics and community phylogenetics. Mapping of reads from low-coverage shotgun sequencing of environmental samples also makes it possible to obtain data on spatial and temporal turnover in whole-community phylogenetic and species composition, even in complex ecosystems where species-level taxonomy and biodiversity patterns are poorly known. In addition, read mapping can produce information on species biomass, and potentially allows quantification of within-species genetic variation. The success of MMG relies on the formation of numerous mitochondrial genome contigs, achievable with standard genome assemblers, but various challenges for the efficiency of assembly remain, particularly in the face of variable relative species abundance and intra-specific genetic variation. Nevertheless, several studies have demonstrated the power of mitogenomes from MMG for accurate phylogenetic placement, evolutionary analysis of species traits, biodiversity discovery and the establishment of species distribution patterns; it offers a promising avenue for unifying the ecological and evolutionary understanding of species diversity.
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Affiliation(s)
- Alex Crampton-Platt
- Department of Life Sciences, Natural History Museum, London, SW7 5BD UK ; Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT UK
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming, Yunnan Province 650223 China ; School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ UK
| | - Xin Zhou
- China National GeneBank, BGI-Shenzhen, Shenzhen, Guangdong Province 518083 China
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, SW7 5BD UK ; Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, SL5 7PY UK
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59
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60
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Liu S, Wang X, Xie L, Tan M, Li Z, Su X, Zhang H, Misof B, Kjer KM, Tang M, Niehuis O, Jiang H, Zhou X. Mitochondrial capture enriches mito‐DNA 100 fold, enabling PCR‐free mitogenomics biodiversity analysis. Mol Ecol Resour 2015; 16:470-9. [DOI: 10.1111/1755-0998.12472] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Revised: 09/19/2015] [Accepted: 09/24/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Shanlin Liu
- China National GeneBank‐Shenzhen BGI‐Shenzhen Shenzhen Guangdong Province 518083 China
- BGI‐Shenzhen Shenzhen Guangdong Province 518083 China
- Centre for GeoGenetics Natural History Museum of Denmark University of Copenhagen Øster Voldgade 5–7 1350 Copenhagen Denmark
| | - Xin Wang
- China National GeneBank‐Shenzhen BGI‐Shenzhen Shenzhen Guangdong Province 518083 China
- BGI‐Shenzhen Shenzhen Guangdong Province 518083 China
| | - Lin Xie
- BGI‐Shenzhen Shenzhen Guangdong Province 518083 China
| | - Meihua Tan
- China National GeneBank‐Shenzhen BGI‐Shenzhen Shenzhen Guangdong Province 518083 China
- BGI‐Shenzhen Shenzhen Guangdong Province 518083 China
| | - Zhenyu Li
- BGI‐Shenzhen Shenzhen Guangdong Province 518083 China
| | - Xu Su
- China National GeneBank‐Shenzhen BGI‐Shenzhen Shenzhen Guangdong Province 518083 China
- Guizhou provincial Center For Disease Control And Prevention Guiyang Guizhou province 550004 China
| | - Hao Zhang
- BGI‐Shenzhen Shenzhen Guangdong Province 518083 China
| | - Bernhard Misof
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum für Molekulare Biodiversitätsforschung (ZMB) Bonn Germany
| | - Karl M. Kjer
- Department of Entomology and Nematology UC Davis Davis CA 95616 USA
| | - Min Tang
- China National GeneBank‐Shenzhen BGI‐Shenzhen Shenzhen Guangdong Province 518083 China
- BGI‐Shenzhen Shenzhen Guangdong Province 518083 China
| | - Oliver Niehuis
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum für Molekulare Biodiversitätsforschung (ZMB) Bonn Germany
| | - Hui Jiang
- BGI‐Shenzhen Shenzhen Guangdong Province 518083 China
| | - Xin Zhou
- China National GeneBank‐Shenzhen BGI‐Shenzhen Shenzhen Guangdong Province 518083 China
- BGI‐Shenzhen Shenzhen Guangdong Province 518083 China
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61
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Papadopoulou A, Taberlet P, Zinger L. Metagenome skimming for phylogenetic community ecology: a new era in biodiversity research. Mol Ecol 2015; 24:3515-7. [PMID: 26174127 DOI: 10.1111/mec.13263] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 05/29/2015] [Indexed: 11/30/2022]
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.
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Affiliation(s)
- Anna Papadopoulou
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Pierre Taberlet
- 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
| | - Lucie Zinger
- CNRS, ENFA, UMR 5174 EDB, Université Toulouse 3 Paul Sabatier, Toulouse, F-31062, France
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62
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Linard B, Crampton-Platt A, Gillett CPDT, Timmermans MJTN, Vogler AP. Metagenome Skimming of Insect Specimen Pools: Potential for Comparative Genomics. Genome Biol Evol 2015; 7:1474-89. [PMID: 25979752 PMCID: PMC4494052 DOI: 10.1093/gbe/evv086] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2015] [Indexed: 01/08/2023] Open
Abstract
Metagenomic analyses are challenging in metazoans, but high-copy number and repeat regions can be assembled from low-coverage sequencing by "genome skimming," which is applied here as a new way of characterizing metagenomes obtained in an ecological or taxonomic context. Illumina shotgun sequencing on two pools of Coleoptera (beetles) of approximately 200 species each were assembled into tens of thousands of scaffolds. Repeated low-coverage sequencing recovered similar scaffold sets consistently, although approximately 70% of scaffolds could not be identified against existing genome databases. Identifiable scaffolds included mitochondrial DNA, conserved sequences with hits to expressed sequence tag and protein databases, and known repeat elements of high and low complexity, including numerous copies of rRNA and histone genes. Assemblies of histones captured a diversity of gene order and primary sequence in Coleoptera. Scaffolds with similarity to multiple sites in available coleopteran genome sequences for Dendroctonus and Tribolium revealed high specificity of scaffolds to either of these genomes, in particular for high-copy number repeats. Numerous "clusters" of scaffolds mapped to the same genomic site revealed intra- and/or intergenomic variation within a metagenome pool. In addition to effect of taxonomic composition of the metagenomes, the number of mapped scaffolds also revealed structural differences between the two reference genomes, although the significance of this striking finding remains unclear. Finally, apparently exogenous sequences were recovered, including potential food plants, fungal pathogens, and bacterial symbionts. The "metagenome skimming" approach is useful for capturing the genomic diversity of poorly studied, species-rich lineages and opens new prospects in environmental genomics.
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Affiliation(s)
- Benjamin Linard
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Alex Crampton-Platt
- Department of Life Sciences, Natural History Museum, London, United Kingdom Department of Genetics, Evolution and Environment, University College London, United Kingdom
| | | | - Martijn J T N Timmermans
- Department of Life Sciences, Natural History Museum, London, United Kingdom Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, United Kingdom
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, United Kingdom Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, United Kingdom
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