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

•SNPs derived from ultraconserved element loci were used to reconstruct the radiation of Holarctic ground squirrels (genus Urocitellus).•Performance of two popular SNP-based methods was compared.•Accounting for gametic phase significantly increased information content in UCEs.•Phasing SNPs improved inference at shallow, but not deeper, levels, highlighting the value of phasing for comparative analyses.•Strong support for big-eared and small-eared species groups within Urocitellus, despite conflicting mitochondrial signals.