Bringing genomics to the forefront of biodiversity conservation

With species extinctions taking place at an alarming rate^1,2, there is an urgent need for fast, data-driven conservation efforts. Genomics can reveal information critical to protecting ecosystems³ yet the limitations of legacy technologies mean that in many biodiverse regions, where sequencing data is most needed, it remains out of reach. Now, researchers are shifting this paradigm. By bringing Oxford Nanopore technology into species-rich ecosystems, they are unlocking insights key to informing conservation strategies — while keeping samples, data, and decision-making within the communities most affected by environmental change.

Closing the biodiversity data gap

In the face of exceptional rates of species loss, accurate monitoring and conservation begins with an accurate picture of an area’s species richness. However, as Mrinalini Watsa (San Diego Zoo Wildlife Alliance, USA) presented, this accurate picture is not always available for biodiverse regions⁴. For example, a DNA barcoding study of frogs in eastern Guyana revealed species numbers four to five times higher than previous estimates⁵.

Mrinalini Watsa presenting at the London Calling conference.

Mrinalini emphasised that these gaps exist ‘because we haven’t been sequencing locally’. The most biodiverse areas of the globe are often in remote, low-resource settings, far from the resource-rich, urban locations where most genomics laboratories are based. Relying on legacy sequencing technologies therefore requires the transport of samples outside of their country of origin, resulting in long waiting times and high costs, along with potential sample damage or loss. As well as slowing or preventing the conservation work itself, this process precludes data sovereignty and reduces the involvement of local researchers at every stage, from sequencing to publication authorship.

To address these inequalities, Mrinalini and her colleagues launched the In Situ Laboratory Initiative, which uses Oxford Nanopore technology to bring genomics directly to biodiverse areas. The initiative spans three continents, with labs in Peru, Ecuador, Rwanda, Vietnam, and Indonesia, each led by local researchers. With easy-to-use, flexible Oxford Nanopore devices requiring minimal infrastructure, the teams now sequence samples onsite without the delays of sample export.

Focusing on the Los Amigos Wildlife Conservation Laboratory, Peru, the team is demonstrating what this model can achieve. As part of the Oxford Nanopore ORG.one project⁶, a grant programme that enables rapid, open-access whole-genome sequencing of critically endangered species, the team use a PromethION 2 device — a high-output nanopore sequencer with a small footprint — to sequence and assemble reference genomes entirely on site.

The researchers generated reference genomes for the rare, near-threatened short-eared dog (Atelocynus microtis), critically endangered Peruvian yellow-tailed woolly monkey (Lagothrix flavicauda), and vulnerable Andean bear (Tremarctos ornatus). These assemblies provide the genomic foundation for downstream conservation research, from evaluating variation across and between populations, to species monitoring through targeted approaches. The team have also adapted the Oxford Nanopore Pore-C chromatin conformation capture workflow⁷ for use onsite, delivering data which can scaffold genome assemblies to the chromosome level.

Towards a true picture of biodiversity

Beyond assembling reference genomes, the team in Peru are using Oxford Nanopore sequencing to build an accurate, regional biodiversity library and monitor local species, addressing long-standing information gaps for this understudied region. Through DNA barcoding, the researchers are characterising samples from both museum specimens and onsite traps; from the latter alone, they have identified species across 70 genera. Taking this further still, they are sequencing vertebrate faecal samples, enabling non-invasive monitoring of diet and microbiomes — all in a solar-powered laboratory in the lowland Peruvian Amazon.

Elsewhere, researchers are extending these advances to other regions where genomic technology was previously inaccessible. In Zambia, Gygax et al. demonstrated how Oxford Nanopore technology enables effective biodiversity monitoring⁸. Through eDNA metabarcoding, they compared nanopore sequencing with Illumina short-read sequencing for vertebrate species identification.

From water samples collected across five locations within the Luambe and Lukusuzi National Parks, representing a range of natural and artificial ecosystems, the team extracted eDNA and performed targeted enrichment of the vertebrate-specific 12S ribosomal RNA (rRNA) and 16S rRNA genes (Figure 1). They then sequenced the libraries using both the Oxford Nanopore MinION and an Illumina device.

Figure 1. Vertebrate eDNA was identified from water samples collected from five sites within the Luambe and Lukusuzi National Parks, Zambia (A, a map of the five sites; B–G, photographs of each site). Figure from Gygax et al.⁸ and available under Creative Commons license (creativecommons.org/licenses/by/4.0/)

The researchers identified 18 taxa from the water samples that were common to both technologies. In addition, Oxford Nanopore sequencing detected seven taxa that Illumina missed, whilst Illumina sequencing identified only one taxon that was not found by Oxford Nanopore technology.

From sample to answer, in situ

Having validated nanopore sequencing for eDNA metabarcoding, the team next utilised the portable MinION device to develop a fully mobile lab for use in the field. Over six days, the researchers performed every step of their non-invasive vertebrate monitoring workflow directly within the Luambe National Park, from water sample collection across three sites, through to extraction, library preparation, nanopore sequencing, and data analysis.

Their work identified ten primary terrestrial vertebrates from the sampled areas, demonstrating the successful in situ use of their eDNA-based monitoring workflow in a remote region within a low- to middle-income country (LMIC). The authors also highlighted the potential for further conservation applications, such as pathogen surveillance.

Despite these successes, the researchers stressed that ‘building or populating genetic databases with regional genetic diversity is crucial for the successful application of eDNA based monitoring approaches’. Even for the short genetic markers they targeted for Zambian vertebrate identification, genetic information was not available for some local species. This further underlines the need for access to comprehensive sequencing data in biodiversity hotspots.

Groundbreaking research by local scientists using nanopore technology is enabling equitable access to data that drives conservation efforts. In previously understudied regions, researchers can now generate, analyse, and apply genomic information directly to the areas they are working to conserve.

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