Rapid divergence and gene flow at high latitudes shape the history of Holarctic ground squirrels (Urocitellus)

•A taxonomically-comprehensive multilocus phylogeny of Holarctic ground squirrels (Urocitellus) is inferred.•ILS and hybridization are identified as sources of gene tree discordance.•Two high-latitude hybridization events in now-allopatric taxa are supported by topologies and posterior predictive checking.•The prevalence and role of hybridization across marmotine ground-dwelling squirrels is discussed.

Across the animal tree of life, the prevalence and evolutionary role(s) of hybridization remain incompletely understood. Rapidly radiating clades can serve as important systems for investigating these issues; however, such groups are often characterized by additional, widespread sources of gene tree discordance (e.g., incomplete lineage sorting). In this paper, we employed a multilocus dataset, Bayesian gene tree inference, and multiple species tree reconstruction methods to infer phylogeny of Holarctic ground squirrels (Urocitellus). We tested phylogenetic hypotheses based on previous morphological, cytological and single-locus datasets, and began to parse the causes of pervasive gene tree discordance that was observed. There is widespread incomplete lineage sorting in Urocitellus, consistent with rapid diversification embedded within the larger radiation of marmotine ground squirrels. We also recovered strong support for 2 instances of mitonuclear discord due to ancient hybridization among members of the high-latitude parryii-richardsonii-elegans clade. These results add to a growing number of documented hybridization events in ground squirrels, suggesting their radiation is a fertile system for understanding the interplay of diversification and hybridization in animal evolution.

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