SNP-based phylogenomic inference in Holarctic ground squirrels (Urocitellus)

Area of Science:

• Evolutionary Biology
• Genomics
• Phylogenetics

Background:

• Resolving rapid evolutionary radiations necessitates maximizing signal from phylogenomic data.
• Conserved loci in non-model clades often yield limited information, impacting gene tree precision and species tree accuracy.
• Single nucleotide polymorphism (SNP)-based methods offer a valuable alternative by leveraging variant loci for species tree reconstruction without relying on resolved gene trees.

Purpose of the Study:

• To evaluate the utility of SNP-based methods for resolving the phylogeny of Holarctic ground squirrels (Urocitellus).
• To compare SNP-based phylogenies with a mitogenome phylogeny.
• To assess the impact of phasing ultraconserved elements (UCEs) on phylogenetic inference within SNP-based frameworks.

Main Methods:

• Phylogenetic inference using SNP-based methods (SNAPP, SVDQuartets) on a dataset of >3,000 UCE loci.
• Comparison with a newly generated mitogenome phylogeny.
• Systematic evaluation of UCE phasing effects on phylogenetic parameters.

Main Results:

• SNP-based methods successfully resolved key clades within the Urocitellus radiation.
• Phasing UCEs enhanced topological resolution and branch length estimation at shallow evolutionary levels (within species complexes).
• Deeper phylogenetic levels showed less improvement from phasing, potentially due to ancestral polymorphism in rapidly diverging lineages.

Conclusions:

• SNP-based phylogenomics is a powerful tool for resolving rapid vertebrate radiations.
• Phasing UCEs can improve phylogenetic resolution, particularly for shallow divergences.
• The study provides a roadmap for applying SNP methods to evolutionary radiations and informs comparative analyses across different temporal scales.