Finding stories in noise: Mitochondrial portraits from RAD data

Area of Science:

• Genomics
• Evolutionary Biology
• Bioinformatics

Background:

• Mitochondrial DNA (mtDNA) has been crucial for phylogeography, but genome-wide analyses are now prevalent.
• Next-generation sequencing (NGS) data, like RAD sequencing, can be noisy and require calibration.
• Many SNPs in genome-wide data are mitochondrial, potentially biasing analyses if not properly accounted for.

Purpose of the Study:

• To develop and validate methods for extracting mitochondrial markers from RAD sequencing data.
• To reconstruct mitogenomes and analyze population genetics in South African yellowfish (Labeobarbus).
• To investigate the impact of genetic exchange and hybridization on Labeobarbus populations.

Main Methods:

• Utilized the program stacks for SNP discovery and haplotype reconstruction from RAD sequencing data.
• Mapped RAD sequence reads directly against a mitochondrial genome reference to reconstruct mitogenomes.
• Validated mitogenome reconstructions using BLAST searches and Sanger sequencing of the cytochrome b gene.

Main Results:

• Successfully identified mitochondrial markers and reconstructed up to 98% of the Labeobarbus mitogenome.
• Validated the accuracy of the reconstructed mitogenomes through independent methods.
• Revealed evidence of ancient genetic exchange, recent translocations, and interspecific hybridization within Labeobarbus species.

Conclusions:

• The presented methods enable robust extraction of mitochondrial markers from RAD-seq data, enhancing phylogeographic studies.
• Accurate mitogenome reconstruction from RAD-seq data is feasible and valuable for population genetics.
• These findings provide insights into the evolutionary history and population dynamics of South African yellowfish.