Mitogenome-Informed Metabarcoding for Non-Invasive Identification of Sympatric Flamingos in Northern Chile

Area of Science:

• Conservation Biology
• Molecular Ecology
• Genomics

Background:

• The Chilean flamingo (Phoenicopterus chilensis) faces anthropogenic pressures across its wide South American range.
• Accurate species identification is crucial for effective conservation of flamingo populations in diverse wetland ecosystems.
• Non-invasive sampling methods are needed for monitoring species in sensitive environments.

Purpose of the Study:

• To generate mitogenomic resources for the Chilean flamingo.
• To develop and validate a molecular framework for species identification using non-invasive fecal samples.
• To assess the detectability of different flamingo species in mixed-species environments.

Main Methods:

• Sequencing and assembly of the Chilean flamingo mitogenome.
• In silico evaluation of metabarcoding markers.
• DNA extraction and Sanger sequencing from fecal samples.
• Probabilistic framework combining maximum likelihood and Bayesian inference for taxonomic assignment.

Main Results:

• A complete mitogenome for Phoenicopterus chilensis was assembled.
• The molecular framework successfully identified species from fecal DNA.
• Two genetically distinct groups, not P. chilensis, were detected in a high-Andean lagoon, indicating co-occurrence of other flamingo taxa.

Conclusions:

• Integrating mitogenomics, metabarcoding, and statistical inference enables robust non-invasive species identification.
• The developed framework is a scalable tool for biodiversity monitoring in mixed-species systems.
• This approach has significant implications for conservation strategies and policy in high-Andean ecosystems.