Next-generation technologies applied to age-old challenges in Madagascar

Abstract

Madagascar is a biodiversity hotspot that is facing rapid rates of deforestation, habitat destruction, and poverty. Urgent action is required to document the status of biodiversity to facilitate efficacious conservation plans. With the recent advent of portable and affordable genetic technologies, it is now possible to take genomic approaches out of the lab and into the field. Mobile genetics labs can produce scientifically reproducible data under field conditions, dramatically minimizing the time between sample collection and data analysis. Here, we show “proof of concept” by deploying miniPCR bio’s miniaturized thermal cycler alongside Oxford Nanopore’s MinION DNA sequencer in Madagascar. Specifically, we deployed this technology at Anjajavy, northwestern Madagascar for rapid biodiversity assessment. We successfully extracted mouse lemur DNA, amplified and sequenced a phylogenetically informative mitochondrial gene (cytochrome-b; cytb), and thereby confirmed the presence of Danfoss’ mouse lemur (M. danfossi) within the Anjajavy Reserve. We show that a mobile genetics lab can provide expeditious results, and allow scientists to conduct genetic analyses, potentially allowing for rapid interventions under emergency conditions in situ. Additionally, mobile labs offer powerful training opportunities for in-country scientists for whom training opportunities were previously confined to ex-situ locations. By bringing genomic technologies to Madagascar and other economically challenged and biodiverse regions of the world, the next generation of scientists and conservationists can more fully implement their leadership roles. Local laboratory and training facilities are changing the polarity of research programs in Madagascar and empowering national researchers to take charge of environmental stewardship.

Global Commitments to Conserving and Monitoring Genetic Diversity Are Now Necessary and Feasible

“…This work is informed by foundational efforts that identified legislation for which genetic diversity is relevant (Laikre et al 2010 , Santamaría and Méndez 2012 ). Genetic diversity assessment capacity is also emerging in lower-income, high-biodiversity regions (Torres-Florez et al 2018 ), including through international collaborations (Blanco et al 2020 ). Efforts are also being made to identify barriers preventing practitioners from using genetic data (Taylor et al 2017 ), synthesize the evidence base to guide decision-making (Cook and Sgrò 2017 ), determine how frequently genetic research findings are used by nature management agencies (Bowman et al 2016 ), improve dissemination and accessibility of genetic findings (Hoban et al 2013 ), and increase the relevance of research to practice and policy (Taft et al 2020 ).…”

Noninvasive Technologies for Primate Conservation in the 21st Century

“…Lastly, innovations in portable labs have also enhanced our ability to remotely detect primates. Several studies have demonstrated the possibility of using portable sequencers for species identification in the field through DNA barcoding, which is limited to one gene region per sample (Blanco et al 2020;Menegon et al 2017;Pomerantz et al 2018). Further, metabarcoding offers the potential to sequence mixed DNA barcode amplicons from bulk community or pooled samples (Krehenwinkel et al, 2019b).…”

“…The process of extracting and sequencing DNA was rapid (~2 hr), mobile, and cost-effective (<US$1.00 per sample). Additionally, DNA amplification using PCR and subsequent detection by electrophoresis have been performed on site for microsatellite genotyping of two primate species (Propithecus verreauxi and P. coquereli) in Madagascar (Guevara et al 2018) (Guevara et al 2018), and a fully portable field lab including the MinION facilitated the molecular species assignment of a Malagasy lemur species within a week, from animal capture to tissue collection, to phylogenetic analysis (Blanco et al 2020). Finally, a recent study using threegene PCR and high resolution melting analysis showed encouraging accuracy for East African wildlife species identification (Ouso et al 2020).…”

“…Solar panels can offer solutions in some sun-rich areas, and power stations can provide temporary energy solutions, allowing for 1 or 2 days of genetic analyses depending on the type of research being done. The energy requirements will have to be assessed per research project and location, but complete off-grid analyses are possible (Blanco et al 2020;Gowers et al 2019;Guevara et al 2018).…”

Nanopore sequencing in non-human forensic genetics

“…While its long-read length (of up to ∼1 Mb, [6]) makes it very attractive for the generation of de novo genome assemblies (see e.g. [6,7]), its low upfront costs (∼1000 USD) and its portability offer huge advantages for DNA-or metabarcoding experiments in countries with limited infrastructure and funds for molecular biomonitoring [8][9][10][11][12], and for teaching and local capacity building [13,14]. The use of the MinION has been extensively investigated for biodiversity research and biomonitoring projects (reviewed in [15]).…”