Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization

Area of Science:

• Evolutionary Biology
• Genomics
• Bioinformatics

Background:

• Phylogenetic inference is challenged by limited molecular variation, lack of markers, and conflicting signals from genomic regions.
• Restriction site Associated DNA sequencing (RAD-seq) offers a promising approach for generating genome-wide data without prior genomic knowledge.

Purpose of the Study:

• To evaluate the efficacy of RAD-seq for phylogenetic inference across varying divergence times.
• To assess the impact of data quality issues on RAD-seq-based phylogenies.

Main Methods:

• Simulated RAD-seq data from 12 Drosophila genomes with divergence times from 5 to 63 million years.
• Phylogenetic analyses incorporating BLASTN and SiLiX for RAD locus clustering.

Main Results:

• RAD-seq successfully recovered the known Drosophila phylogeny with robust statistical support, including ancient nodes.
• Phylogenetic accuracy remained high despite simulated sequencing errors, heterozygosity, and low coverage.
• BLASTN and SiLiX clustering enhanced orthologous RAD locus recovery, particularly for distantly related species.

Conclusions:

• RAD-seq is a powerful and reliable tool for phylogenetic inference, even for deep evolutionary timescales.
• Optimized data processing significantly improves RAD-seq utility for reconstructing evolutionary relationships.