HiMAP: Robust phylogenomics from highly multiplexed amplicon sequencing.

Area of Science:

• Evolutionary Biology
• Genomics
• Bioinformatics

Background:

• High-throughput sequencing significantly increased the scale of molecular phylogenetic datasets.
• Traditional Sanger sequencing methods are limited in generating large phylogenomic datasets.
• Existing methods require substantial time and resources for data generation and analysis.

Purpose of the Study:

• To introduce HiMAP (highly multiplexed amplicon-based phylogenomics), a novel approach for phylogenomic data set construction.
• To present bioinformatic pipelines for locus selection, consensus calling, and alignment.
• To demonstrate the efficacy of HiMAP using a case study on tephritid fruit flies.

Main Methods:

• Employed single-tube, highly multiplexed amplicon sequencing for phylogenomic data generation.
• Developed bioinformatic tools for locus selection from genomic and transcriptomic resources.
• Utilized post-sequencing consensus calling and alignment, avoiding read mapping or assembly.

Main Results:

• Sequenced 878 amplicons for 82 tephritid fruit fly species, yielding a >150,000-bp alignment.
• The dataset contained >40,000 phylogenetically informative characters with ~20% missing data.
• Achieved high resolution of phylogenetic relationships, supporting the generic status of Zeugodacus.

Conclusions:

• HiMAP is an inexpensive, low-hands-on-time method for generating large-scale phylogenomic data.
• The method provides high phylogenetic resolution and is suitable for sequencing hundreds of taxa.
• HiMAP offers significant molecular and bioinformatic advantages for evolutionary studies.