Empowering conservation practice with efficient and economical genotyping from poor quality samples

Area of Science:

• Conservation genetics
• Wildlife forensics
• Population genomics

Background:

• High-density genotyping is crucial for wildlife studies but limited by DNA quality.
• Existing genomic tools often require high-quality DNA, unavailable in field or market settings.
• Current methods rely on limited markers like mitochondrial DNA or microsatellites.

Purpose of the Study:

• To develop a method for genotyping using low-quality DNA from non-invasive or degraded sources.
• To demonstrate the utility of this method for endangered species and wildlife trade monitoring.
• To provide a scalable and cost-effective framework for conservation genetics.

Main Methods:

• Utilized next-generation sequencing of multiplex PCR products from degraded DNA (faeces, hair, cooked samples).
• Applied the method to endangered tigers for individual identification, relatedness, and population structure analysis.
• Tested the method on Caribbean queen conch for relatedness and population structure studies.

Main Results:

• Successfully genotyped 100 SNPs from degraded tiger samples, enabling individual and population-level insights.
• Identified 62 SNPs for conch analysis, revealing relatedness and population structure.
• Demonstrated specificity, as co-occurring carnivore DNA did not amplify or was monomorphic.

Conclusions:

• A rapid, simple, cost-effective, and scalable genotyping method for low-quality DNA is established.
• This framework significantly advances wildlife monitoring, forensics, and conservation efforts.
• Enables field-ready genetic testing, strengthening science-based policy and wildlife trade management.