Phylogenomics using low-depth whole genome sequencing: A case study with the olive tribe

Area of Science:

• Genomics
• Phylogenetics
• Evolutionary Biology

Background:

• Traditional species tree inference relies on limited markers, restricting genome-wide studies to model organisms or species with available fresh samples.
• Low-depth sequencing of genomes, including museum specimens, is increasing but the nuclear DNA fraction is often underutilized for phylogenetic analysis.
• Existing methods for inferring large-scale phylogenies from low-depth data are limited, hindering the study of broader species diversity.

Purpose of the Study:

• To evaluate reference-based methods for inferring phylogenies from low-depth genome data across large taxonomic groups.
• To develop and test a method for utilizing nuclear DNA from low-depth sequencing, including historical specimens, for robust phylogenetic reconstruction.
• To explore the potential of phylogenomics for studying complex genomes and reticulate evolutionary histories in diverse species.

Main Methods:

• Applied reference-based methods to infer phylogenies from low-depth genome data using single nucleotide polymorphisms (SNPs).
• Utilized two reference genomes (olive and ash trees) for SNP calling in the Oleeae tribe.
• Reduced genome complexity by using orthologous coding sequences as references and combined SNPs from multiple references to mitigate missing data issues.

Main Results:

• Inferred phylogenies using different reference genomes showed congruence but also differences, potentially due to reference distance and missing data.
• Combining SNPs from multiple references using orthologous coding sequences improved phylogenetic inference.
• Phylogenetic trees revealed evidence of incomplete lineage sorting and/or hybridization during the diversification of the Oleeae tribe.

Conclusions:

• Genome-wide phylogenetic trees can be reliably inferred from low-depth sequence data for eukaryotes with complex genomes.
• The developed methods enable phylogenomic and biogeographical analyses of both extant and historical species diversity, including those from natural history collections.
• This approach opens new possibilities for large-scale phylogenomics, significantly expanding the scope of evolutionary studies.