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.

Scales of Effect for Urban Mammals Vary Among Species and Environmental Attributes

Context. Cities are increasingly recognized for their biodiversity conservation potential. Incomplete understanding of urban species habitat requirements and of the areal extents over which species-habitat interactions occur (“scale of effect”), however, restricts such conservation.Objectives.Better-understanding scales of effect for urban species could improve urban conservation by identifying areal extents to target in management. We sought to identify scales of effect for urban mammals and if and how these scales differ among species and environmental covariates.Methods. We constructed Eastern fox squirrel (Sciurus niger), red fox (Vulpes vulpes), and Virginia opossum (Didelphis virginianus) occupancy models using data from trail cameras in Iowa City, Iowa, USA. We compared models constructed using environmental covariates estimated over different extents and identified appropriate scales of effect for each covariate based on model fit.Results. Scales of effect varied among species and covariates. Environmental covariates based on home ranges sometimes provided the best model fit; however, best-fit model covariates were often estimated over other extents. The best-fit fox squirrel model included covariates estimated at different, but relatively local scales (<250 m). Both opossum and red fox models included local to landscape-level covariates. Thus, scales of effect differed among species, possibly with body size, and environmental attributes, offering clear evidence that urban mammals exhibit a multi-scalar response to their environments.Conclusions. Our findings suggest that habitat models should include covariates estimated over a range of biologically-informed extents to more accurately identify habitat relationships. Such modeling will inform the choice of extent in urban habitat management.

Melanism as a potential thermal benefit in eastern fox squirrels (Sciurus niger)

Melanistic fox squirrels (Sciurus niger) have expanded westward and increased in frequency in the Omaha, Nebraska, and Council Bluffs, Iowa, metropolitan areas. The selective advantage of melanism is currently unknown, but thermal advantages have been hypothesized, especially in winter. No difference in metabolic response curves were measured between melanistic (black) and rufus (orange) fox squirrels. When exposed to sunny skies, both melanistic and rufus squirrels had higher surface (skin and fur) temperature as ambient temperatures increased. Melanistic squirrel surface temperatures did not differ when squirrels were exposed to sunny or cloudy skies. However, rufus individuals showed significantly lower increases in surface temperatures when under cloudy skies. During fall months, rufus individuals were about 1.5 times more active throughout the day than melanistic individuals. However, in winter, melanistic fox squirrels were approximately 30% more active in the mornings (before 13:00) compared to rufus squirrels. Pre-winter body condition was higher in melanistic (25.5 ± 1.8 g/cm) compared to rufus (20.30 ± 3.6 g/cm) fox squirrels; however, there were no significant differences between melanistic (22.8 ± 1.4 g/cm) and rufus (23.9 ± 0.8 g/cm) fox squirrel post-winter body condition. The results of this study indicate that melanistic fox squirrels may have a slight winter thermal advantage over rufus fox squirrels by maintaining higher skin temperatures.