Breaking the taxonomic barrier
Museum scientists are using new genomic technologies to rapidly assess biodiversity in complex and changing ecosystems.
Traditional taxonomy, involving the collection, sorting and characterisation of thousands of individual species, is a slow method for assessing the biodiversity of a site.
‘It’s sometimes referred to as the taxonomic impediment to studying biodiversity, because if we don’t know the taxonomy, we cannot compare where we find what’ says Professor Alfried Vogler.
Prof Vogler and his team at the Museum have been testing a new technique to overcome the taxonomic impediment - sequencing the genomes of whole collections of creatures at once, without separating them.
Getting a quick view of how many species exist at a site, and what their phylogenetic relationships are, is a shortcut to assessing biodiversity, which can then be compared over time and between sites. This is fundamental to answering big biodiversity questions, such as what factors determine the makeup of ecological communities and how disturbance affects them.
Entomologists out in the field first collect a huge range of insects across an ecosystem, from the canopy to the soil. Each of these collections consists of a soup of hundreds of different species of insects and other arthropods, such as spiders and millipedes.
Back in the lab, using organic chemicals, DNA is extracted from the soup, sheared into sections and sequenced to give small, equal-sized fragments called reads. A computer algorithm then matches up the reads where their code overlaps to create longer fragments, building towards a whole genome.
Whole genomes can be tricky to assemble, so the technique focuses on genomes in the mitochondria, the power centres of each cell, which differs from the main cell DNA, held in the nucleus. Since many mitochondria exist in each cell, their DNA is more abundant in the soup and easier to extract.
Once all the mitochondrial reads have been assembled into various genomes, the composition of the soup is revealed. The number of different species and how they relate to each other can be mapped out onto a phylogenetic tree; a branching diagram of evolutionary connections.
‘We can go from a soup to a tree without doing much in between, and that’s a new way of looking at biodiversity,’ says Prof Vogler.
‘The names of species in the soup are actually not that important - it’s the measure of the magnitude and diversity of species that’s relevant for biodiversity research, along with the ability to quickly compare this across sites. It’s a different approach, getting over the need to sort all these specimens and instead go straight to biodiversity analysis.’
However, the specimens are not destroyed in the sequencing process, so traditional taxonomy and species identification can still be pursued.
This is an extra asset to the Museum - having the specimen and its DNA in the same place is a great reference set for any future studies of the creature.
Proof of concept
The technique has already been tested in the rainforests of Borneo, one of the most complex ecosystems on Earth. As a proof of principle, a team of molecular biologists, taxonomists, ecologists and collection managers collected arthropod soups across the habitats of the forest site.
Rainforests were chosen as they represent a biotic frontier - a habitat holding lots of small organisms that are poorly understood and have incomplete taxonomy, for example the soil and the canopy. Some interesting insights have emerged, such as the relationships between creatures living in the deeper soil layers and the adaptations they share to live in their particular environment.
The long-term goal for Prof Vogler, however, is to create a network of genomic observatories - sites with well-characterised biodiversity that can be monitored over time. Once a baseline biodiversity has been established at each site, it will be even quicker to monitor changes by sequencing soups and looking for changes in the community.
In this spirit, the multidisciplinary team recently took a series of sampling trips across Latin America to establish a subset of genomic observatory sites. The sites traverse tropical America in a west-east transect through Honduras, Panama, Guyana and French Guiana.
The Museum team was supported in Panama by the local conservation organisation Wildlife Panama, and by a student volunteer scheme in in Honduras and Guyana organised by Operation Wallacea.
While the new technique is faster than traditional methods, it still takes time to extract and process such large quantities of DNA. Building phylogenetic trees for each site should allow researchers to start asking deeper questions about biodiversity, and understand the driving forces behind global species distribution.
- Prof Alfried Vogler
- Dr Martijn Timmermans
- Dr Paul Eggleton
- Mr Max Barclay
- Ms Beulah Garner
- Ms Jacqueline Mackenzie-Dodds
- Dr Andy Polaszek
- Dr Benjamin Linard
- Dr Neil Brummitt
- Ms Alex Crampton-Platt
- Mr Thomas Creedy
Gillett C P T D, Crampton-Platt A L, Timmermans M J T N, Jordal B, Emerson B C, and Vogler A P (2014) Bulk de novo mitogenome assembly from pooled total DNA elucidates the phylogeny of weevils (Coleoptera: Curculionoidea). Molecular Biology and Evolution 31(8): 2223-2237.
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