A draft genome assembly for the eastern fox squirrel, Sciurus niger

The eastern fox squirrel, Sciurus niger, exhibits marked geographic variation in size and coat color, is a model organism for studies of behavior and ecology, and a potential model for investigating physiological solutions to human porphyrias. We assembled a genome using Illumina HiSeq, PacBio SMRT, and Oxford Nanopore MinION sequencing platforms. Together, the sequencing data resulted in a draft genome of 2.99 Gb, containing 32,830 scaffolds with an average size of 90.9 Kb and N50 of 183.8 Kb. Genome completeness was estimated to be 93.78%. A total of 24,443 protein-encoding genes were predicted from the assembly and 23,079 (94.42%) were annotated. Repeat elements comprised an estimated 38.49% of the genome, with the majority being LINEs (13.92%), SINEs (6.04%), and LTR elements. The topology of the species tree reconstructed using maximum-likelihood phylogenetic analysis was congruent with those of previous studies. This genome assembly can prove useful for comparative studies of genome structure and function in this rapidly diversifying lineage of mammals, for studies of population genomics and adaptation, and for biomedical research. Predicted amino acid sequence alignments for genes affecting heme biosynthesis, color vision, and hibernation showed point mutations and indels that may affect protein function and ecological adaptation.

Acrobatic squirrels learn to leap and land on tree branches without falling

Arboreal animals often leap through complex canopies to travel and avoid predators. Their success at making split-second, potentially life-threatening decisions of biomechanical capability depends on their skillful use of acrobatic maneuvers and learning from past efforts. Here, we found that free-ranging fox squirrels (Sciurus niger) leaping across unfamiliar, simulated branches decided where to launch by balancing a trade-off between gap distance and branch-bending compliance. Squirrels quickly learned to modify impulse generation upon repeated leaps from unfamiliar, compliant beams. A repertoire of agile landing maneuvers enabled targeted leaping without falling. Unanticipated adaptive landing and leaping “parkour” behavior revealed an innovative solution for particularly challenging leaps. Squirrels deciding and learning how to launch and land demonstrates the synergistic roles of biomechanics and cognition in robust gap-crossing strategies.

Urban fox squirrels exhibit habituation to humans but respond to stimuli from natural predators

Animals in urban areas that experience frequent exposure to humans often behave differently than those in less urban areas, such as less vigilance or anti-predator behavior. These behavioral shifts may be an adaptive response to urbanization and caused by habituation to humans. A possible negative consequence is cross-habituation to natural predators where urban animals exhibit reduced anti-predator behavior in the presence of humans but also to their natural predators. We tested the hypothesis that habituation to humans in urban populations of fox squirrels (Sciurus niger) causes cross-habituation to stimuli from two possible predators (hawks and domestic dogs). We exposed squirrels in multiple urban and less urban sites to acoustic playbacks of a control stimulus (non-predatory bird calls), a natural predator (hawk), and dogs and recorded their vigilance and three different anti-predator behaviors when a human approached them while either broadcasting one of these three playbacks or no playbacks at all. In trials with no playbacks, urban squirrels exhibited reduced vigilance and anti-predator behavior compared to those in less urban areas but there was little evidence that urbanization altered the correlations among the different behaviors we quantified. Urban squirrels exhibited increased vigilance and anti-predator behavior when exposed to a human paired with hawk playbacks compared to the control playbacks. This indicates that urban squirrels did perceive and assess risk to the natural predator appropriately despite exhibiting habituation to humans. There is currently little evidence that habituation to humans causes animals to lose their fear of natural predators.