From field to genome: fast, portable SNP and SNPSTR tools for wildlife conservation | LC 25

Biography

Dr Minalini Erkenswick Watsa is the Steifel-Behner Amazonia Research Scientist at the San Diego Zoo Wildlife Alliance. A conservation biologist, she specialises in applying genomics and genetics for wildlife monitoring and biodiversity studies, particularly in resource-limited regions.

Minalini co-directs the In Situ Labs Initiative, pioneering portable field laboratories for genomic monitoring. Her research spans rare and endangered species across three continents.

Abstract

Current conservation genomics relies heavily on short tandem repeat (STR) genotyping using ABI sequencers. While these methods provide insights into individual identity, parentage, and population structure, they are labor-intensive, expensive, and reliant on centralized facilities. These limitations make them inaccessible in biodiversity hotspots with constrained resources. To address this, we have developed single-nucleotide polymorphism (SNP) and SNPSTR pipelines leveraging portable nanopore sequencing technology, offering a fast, cost-effective, and field-deployable alternative. Validated in conservation targets such as elephants, tigers, Andean bears, and giraffes, our tools can generate actionable genomic data from degraded samples like hair or scat in as little as three days. Here, I describe a protocol for species with no prior genomic resources, exclusively using nanopore sequencing technology. Starting with the generation of a single reference genome, we design SNPSTR markers and, with additional samples, identify SNPs. Each marker set undergoes rigorous validation, including primer condition optimization, sensitivity, and specificity testing. Once validated, these markers can be deployed in a highly multiplexed format on portable, low-cost laboratory equipment, producing robust genotypes validated against Sanger, Illumina, or TaqMan-based pipelines. Our approach integrates open-access protocols and laptop-compatible bioinformatics, making genomic tools accessible to conservation practitioners, forensic labs, and local stakeholders. Although genetics can provide unique insights into population dynamics, relatedness, and individual identity, it has often been dismissed as too expensive or complex. Our work aims to make in situ genomics a cornerstone of conservation, providing real-time, actionable data to revolutionize wildlife management worldwide.