[Paper Review] Inference of chromosomal inversion dynamics from Pool-Seq data in natural and laboratory populations of Drosophila melanogaster

Martin Kapun, Hester van Schalkwyk+3 more|arXiv (Cornell University)|Jul 9, 2013

Chromosomal and Genetic Variations4 citations

TL;DR

This study develops a set of diagnostic SNP markers to infer chromosomal inversion frequencies from Pool-Seq data in Drosophila melanogaster, enabling population-level analysis of inversion dynamics. Using these markers, the authors detect positive selection on In(3R)C and In(3R)Mo in experimental evolution and reveal a novel latitudinal cline for In(3R)Mo in North America, confirming known clinal patterns in both North America and Australia.

ABSTRACT

Sequencing of pools of individuals (Pool-Seq) represents a reliable and cost- effective approach for estimating genome-wide SNP and transposable element insertion frequencies. However, Pool-Seq does not provide direct information on haplotypes so that for example obtaining inversion frequencies has not been possible until now. Here, we have developed a new set of diagnostic marker SNPs for 7 cosmopolitan inversions in Drosophila melanogaster that can be used to infer inversion frequencies from Pool-Seq data. We applied our novel marker set to Pool-Seq data from an experimental evolution study and from North American and Australian latitudinal clines. In the experimental evolution data, we find evidence that positive selection has driven the frequencies of In(3R)C and In(3R)Mo to increase over time. In the clinal data, we confirm the existence of frequency clines for In(2L)t, In(3L)P and In(3R)Payne in both North America and Australia and detect a previously unknown latitudinal cline for In(3R)Mo in North America. The inversion markers developed here provide a versatile and robust tool for characterizing inversion frequencies and their dynamics in Pool- Seq data from diverse D. melanogaster populations.

Motivation & Objective

• To develop a reliable method for estimating chromosomal inversion frequencies from Pool-Seq data, which traditionally lacks haplotype resolution.
• To address the gap in genomic analysis where Pool-Seq cannot directly infer inversion states due to lack of phasing.
• To apply the new marker set to study inversion dynamics in both experimental evolution and natural latitudinal cline populations.
• To validate the method by detecting known and novel inversion frequency clines across geographic gradients.

Proposed method

• Design a set of diagnostic SNP markers specific to seven cosmopolitan inversions in Drosophila melanogaster.
• Use these markers to infer inversion frequencies from pooled sequencing data by analyzing allele frequency patterns at diagnostic sites.
• Apply the method to Pool-Seq data from an experimental evolution study to track inversion frequency changes over time.
• Analyze Pool-Seq data from North American and Australian latitudinal clines to detect geographic frequency patterns.
• Validate the method by comparing inferred inversion frequencies with known clinal trends and selection signatures.
• Use statistical analysis to detect selection signals and clinal patterns in inversion frequencies across populations.

Experimental results

Research questions

• RQ1 Can diagnostic SNP markers enable accurate inference of chromosomal inversion frequencies from Pool-Seq data in Drosophila melanogaster?
• RQ2 What evidence of selection exists for specific inversions in experimental evolution populations based on Pool-Seq-derived inversion frequencies?
• RQ3 Do known inversion clines (e.g., In(2L)t, In(3L)P, In(3R)Payne) persist in both North American and Australian populations as shown by Pool-Seq?
• RQ4 Is there a previously undetected latitudinal cline for In(3R)Mo in North American Drosophila populations?
• RQ5 How robust and versatile is the new SNP marker set for studying inversion dynamics across diverse Drosophila populations?

Key findings

• Positive selection drove the increase in frequency of In(3R)C and In(3R)Mo over time in the experimental evolution population, as inferred from Pool-Seq data.
• A significant latitudinal cline was confirmed for In(2L)t, In(3L)P, and In(3R)Payne in both North American and Australian Drosophila populations.
• A previously undetected latitudinal cline for In(3R)Mo was identified in North American populations using the new marker set.
• The diagnostic SNP marker set enables accurate and robust inference of inversion frequencies from Pool-Seq data, overcoming the limitation of haplotype ambiguity.
• The method successfully detected known clinal patterns and novel clinal trends, demonstrating its utility across diverse population types.
• The study establishes a versatile tool for population genomic studies of inversion dynamics in Drosophila melanogaster using cost-effective Pool-Seq approaches.