Using nuclear haplotypes with microsatellites to study gene flow between recently separated Cichlid species

Area of Science:

• Population Genetics
• Molecular Evolution
• Speciation Studies

Background:

• Recently diverged populations often exhibit shared genetic variation, making it challenging to differentiate between ongoing gene flow and ancestral polymorphism.
• Distinguishing the causes of shared genetic variation is crucial for understanding speciation processes and population histories.

Purpose of the Study:

• To develop a novel empirical protocol for analyzing genetic variation in recently diverged populations.
• To introduce a method that combines the high resolution of Short Tandem Repeats (STRs) with the low homoplasy of unique DNA sequence haplotypes.
• To present a new procedure for estimating genetic data likelihood under an Isolation with Migration model.

Main Methods:

• Development of a new genetic marker system termed 'HapSTRs', integrating unique nuclear DNA sequence haplotypes with linked microsatellites (STRs).
• Implementation of a new statistical procedure for analyzing HapSTR data within an Isolation with Migration framework.
• Application of the HapSTR protocol and analysis to Cichlid fishes from Lake Malawi to study their population genetics.

Main Results:

• The HapSTR system provides high resolution and low homoplasy, enhancing the study of genetic variation.
• The developed procedure effectively estimates genetic data likelihood under the Isolation with Migration model.
• Analysis of Cichlid fishes suggests ongoing gene flow between species since their divergence.

Conclusions:

• HapSTRs offer a powerful tool for resolving complex population genetic histories, particularly in cases of recent divergence.
• The findings support the hypothesis of historical gene flow contributing to the genetic similarity of Cichlid species in Lake Malawi.
• This approach advances the ability to infer demographic histories and gene flow patterns in closely related populations.