Genomic repeat abundances contain phylogenetic signal.

Area of Science:

• Genomics
• Bioinformatics
• Evolutionary Biology

Background:

• Repetitive DNA elements constitute a significant portion of many genomes, especially in angiosperms.
• Traditional phylogenetic analyses often exclude repetitive genomic fractions due to their complexity.

Purpose of the Study:

• To demonstrate the utility of repetitive genomic elements in phylogenetic analyses.
• To develop a method for inferring phylogenetic relationships using repetitive DNA abundance.

Main Methods:

• Comparative graph-based clustering of next-generation sequencing reads to estimate repeat abundance.
• Phylogenetic tree inference based on genome-wide abundance of different repeat types as continuous characters.

Main Results:

• The method successfully inferred well-supported interspecific and intergeneric relationships in diverse angiosperm and insect examples.
• Results from this novel approach align with established phylogenetic analyses using standard markers.
• The methodology provides substantial data for comparative genomics and genome evolution studies.

Conclusions:

• Repetitive DNA fractions can be effectively utilized for robust phylogenetic inference.
• This approach is particularly advantageous for groups with low genetic differentiation in standard phylogenetic markers.
• The method offers a powerful new tool for understanding genome evolution and evolutionary history.