An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes

Area of Science:

• Genetics
• Bioinformatics
• Evolutionary Biology

Background:

• Haplotype information is crucial for understanding genetic diversity and evolutionary relationships.
• Current methods often rely on DNA barcoding of pooled amplicons, which can be costly and complex.
• Short-read sequencing offers a cost-effective alternative but presents challenges in haplotype resolution from mixed samples.

Purpose of the Study:

• To develop a new computational method, AFPhyloMix, for inferring haplotype phylogeny from short-read sequences of pooled amplicons without the need for DNA barcoding.
• To assess the accuracy and performance of AFPhyloMix in reconstructing haplotype phylogenies and their relative abundances.

Main Methods:

• AFPhyloMix processes read alignments against a reference sequence to identify single-nucleotide-polymorphism (SNP) patterns.
• A Bayesian inference model is employed to estimate the phylogeny and relative abundances of haplotypes, assuming the number of haplotypes is known.
• The method was evaluated using simulated datasets and a real dataset of kangaroo mitochondrial DNA sequences.

Main Results:

• AFPhyloMix demonstrated high accuracy, achieving at least 80% accuracy in recovering phylogenies and relative abundances for mixtures containing up to 15 haplotypes in simulations.
• The method performed effectively on a real-world dataset, showcasing its applicability to biological samples.
• Successful reconstruction of haplotype phylogeny and abundance without individual DNA barcoding.

Conclusions:

• AFPhyloMix provides a robust and accurate computational approach for haplotype phylogeny reconstruction from pooled short-read sequencing data.
• This method eliminates the requirement for DNA barcoding, simplifying and potentially reducing the cost of haplotype analysis.
• AFPhyloMix has significant implications for population genetics, evolutionary studies, and the analysis of complex biological mixtures.