Revision of widespread red squirrels (genus: Tamiasciurus) highlights the complexity of speciation within North American forests

•Multi-locus assessment of Tamiasciurus reveals novel regional genetic diversity.•Hybridization across multiple contact zones influences interspecific evolution.•Forest obligate species provide a template for biome-wide conservation priorities.•Both peripheral isolates and contact zones warrant management consideration.•Continent-wide distribution allows assessment of regional evolutionary heterogeneity.

Integration of molecular methods, ecological modeling, and statistical hypothesis testing are increasing our understanding of differentiation within species and phylogenetic relationships among species by revealing environmental connections to evolutionary processes. Within mammals, novel diversity is being discovered and characterized as more complete geographic sampling is coupled with newer multi-disciplinary approaches. North American red squirrels exemplify a forest obligate genus whose species are monitored as indicators of forest ecosystem condition, yet phylogenetic relationships reflecting evolutionary history within this genus remain tentative. Through testing of competing systematic and niche-based divergence hypotheses, we recognize three species, Tamiasciurus douglasii, T. hudsonicus, and T. fremonti. Our data provide evidence of regional differences in evolutionary dynamics and continental gradients of complexity that are important both for future management and for investigating multiple pathways that can lead to the formation of new species.

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