Biodiversity seen through the perspective of insects: 10 simple rules on methodological choices and experimental design for genomic studies

Pável Matos-Maraví; Camila Duarte Ritter; Christopher J Barnes; Martin Nielsen; Urban Olsson; Niklas Wahlberg; Daniel Marquina; Ilari Sääksjärvi; Alexandre Antonelli

doi:10.7717/peerj.6727

Biodiversity seen through the perspective of insects: 10 simple rules on methodological choices and experimental design for genomic studies

PeerJ. 2019 Apr 30:7:e6727. doi: 10.7717/peerj.6727. eCollection 2019.

Authors

Pável Matos-Maraví^{1

2

3}, Camila Duarte Ritter⁴, Christopher J Barnes⁵, Martin Nielsen^{5

6}, Urban Olsson^{1

2}, Niklas Wahlberg⁷, Daniel Marquina^{8

9}, Ilari Sääksjärvi¹⁰, Alexandre Antonelli^{1

2

11}

Affiliations

¹ Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
² Gothenburg Global Biodiversity Centre, Gothenburg, Sweden.
³ Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic.
⁴ Department of Eukaryotic Microbiology, University of Duisburg-Essen, Essen, Germany.
⁵ Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
⁶ Section for Evolutionary Genomics, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
⁷ Department of Biology, Lund University, Lund, Sweden.
⁸ Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
⁹ Department of Zoology, Stockholm University, Stockholm, Sweden.
¹⁰ Biodiversity Unit, University of Turku, Turku, Finland.
¹¹ Royal Botanical Garden, Kew, Richmond, Surrey, UK.

Abstract

Massively parallel DNA sequencing opens up opportunities for bridging multiple temporal and spatial dimensions in biodiversity research, thanks to its efficiency to recover millions of nucleotide polymorphisms. Here, we identify the current status, discuss the main challenges, and look into future perspectives on biodiversity genomics focusing on insects, which arguably constitute the most diverse and ecologically important group among all animals. We suggest 10 simple rules that provide a succinct step-by-step guide and best-practices to anyone interested in biodiversity research through the study of insect genomics. To this end, we review relevant literature on biodiversity and evolutionary research in the field of entomology. Our compilation is targeted at researchers and students who may not yet be specialists in entomology or molecular biology. We foresee that the genomic revolution and its application to the study of non-model insect lineages will represent a major leap to our understanding of insect diversity.

Keywords: Evolution; High-throughput sequencing; Insect genomics; Museomics; Taxonomic impediment.

Grants and funding

Funding to Pável Matos-Maraví was provided by a Marie Skłodowska-Curie fellowship (project MARIPOSAS-704035). Camila Duarte Ritter received support from CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico–Brazil-249064/2013-8) and the Alexander von Humboldt Foundation. Christopher Barnes was funded by the Aage V. Jensen Naturfond of Denmark (1121721001). Daniel Marquina and Niklas Wahlberg received funding from European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 642241 (BIG4 project). Niklas Wahlberg received funding from the Swedish Research Council. Alexandre Antonelli is supported by a grant from the Knut and Alice Wallenberg Foundation, the Swedish Research Council (B0569601), the Swedish Foundation for Strategic Research, the Faculty of Sciences at the University of Gothenburg, and the David Rockefeller Center for Latin American Studies at Harvard University. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.