MTaxi

MTaxi assigns mitochondrial sequencing reads to discriminate between pairs of closely related species by analyzing mtDNA transversion-type substitutions for taxonomic identification of low-coverage and ancient samples.

Key Features:

• Mitochondrial DNA Utilization: Focuses on mtDNA transversion-type substitutions to differentiate between candidate species, avoiding reliance on high-quality nuclear reference genomes.
• Read Assignment and Statistical Testing: Assigns sequencing reads to candidate species based on identified mtDNA variations and employs a binomial test to ascertain taxonomic identity.
• Efficiency at Low Coverage: Demonstrated performance at mitochondrial coverages as low as 0.5x, enabling analysis of degraded ancient samples with limited sequencing depth.
• Accuracy and Reliability: In tests with simulated ancient genomes and archaeological samples (n=18 sheep/goat and n=10 horse/donkey), achieved 100% accuracy without false positives.

Scientific Applications:

• Zooarchaeology: Distinguishes between morphologically similar taxa such as sheep and goat or horse and donkey from small bone fragments using mtDNA markers.
• Taxonomic classification of degraded samples: Enables reliable species identification from low-coverage and ancient DNA where traditional morphological or nuclear-genome-based methods are limited.

Methodology:

Detect transversion-type mtDNA substitutions between candidate species, assign sequencing reads to species based on those substitutions, and validate taxonomic identity using a binomial test.