Exploring the phylogeography of a hexaploid freshwater fish by RAD sequencing

Area of Science:

• Genetics
• Ichthyology
• Conservation Biology

Background:

• The KwaZulu-Natal yellowfish (Labeobarbus natalensis) is an abundant, endemic cyprinid species in South Africa's KwaZulu-Natal Province.
• Understanding its population genetic structure is vital for effective conservation strategies.

Purpose of the Study:

• To develop a high-quality single-nucleotide polymorphism (SNP) dataset for Labeobarbus natalensis using double-digest restriction site-associated DNA (ddRAD) sequencing.
• To investigate the population genetic structure and evolutionary history of L. natalensis across its distribution.
• To identify key areas for conservation based on genetic diversity patterns.

Main Methods:

• Double-digest restriction site-associated DNA (ddRAD) sequencing was employed to generate a SNP dataset.
• Rigorous filtering of RAD data and parameter selection for polyploid lineages were addressed.
• Population genetic structure was analyzed using the high-quality SNP dataset, with Approximate Bayesian Computation (ABC) used for scenario testing.

Main Results:

• A well-supported genetic division into northern and southern lineages was identified, with further subdivision into five distinct populations.
• One population exhibited evidence of north-south admixture.
• Nucleotide diversity was highest in the Mbokodweni river system, the smallest river system studied.

Conclusions:

• The study identified significant population structure in L. natalensis, supporting a divergence model of northern and southern lineages.
• The Mbokodweni river system and adjacent coastal systems represent critical catchments for the conservation of L. natalensis due to high genetic diversity.
• Proper data filtering and parameter selection are crucial for analyzing population genetics in polyploid species like L. natalensis.