Project description:Northern (Glaucomys sabrinus) and southern (Glaucomys volans) flying squirrels are widespread species distributed across North America. Northern flying squirrels are common inhabitants of the boreal forest, also occurring in coniferous forest remnants farther south, whereas the southern flying squirrel range is centered in eastern temperate woodlands. These two flying squirrel species exhibit a hybrid zone across a latitudinal gradient in an area of recent secondary contact. Glaucomys hybrid offspring are viable and can successfully backcross with either parental species, however, the fitness implications of such events are currently unknown. Some populations of G. sabrinus are endangered, and thus, interspecific hybridization is a key conservation concern in flying squirrels. To provide a resource for future studies to evaluate hybridization and possible introgression, we sequenced and assembled a de novo long-read genome from a G. volans individual sampled in southern Ontario, Canada, while four short-read genomes (two G. sabrinus and two G. volans, all from Ontario) were resequenced on Illumina platforms. The final genome assembly consisted of approximately 2.40 Gb with a scaffold N50 of 455.26 Kb. Benchmarking Universal Single-Copy Orthologs reconstructed 3,742 (91.2%) complete mammalian genes and genome annotation using RNA-Seq identified the locations of 19,124 protein-coding genes. The four short-read individuals were aligned to our reference genome to investigate the demographic history of the two species. A principal component analysis clearly separated resequenced individuals, while inferring population size history using the Pairwise Sequentially Markovian Coalescent model noted an approximate species split 1 million years ago, and a single, possibly recently introgressed individual.
Project description:Most mammals rely on vocal communication to increase survival and reproductive success. While the functions of audible vocalizations have been well-studied across mammal species, ultrasonic vocalizations in small mammals outside of bats are less understood. North American flying squirrel species (Glaucomys spp.), including the newly described Humboldt's flying squirrel (Glaucomys oregonensis), produce numerous call-types that extend into the ultrasonic range. To investigate the potential function of ultrasonic call-types in the Humboldt's flying squirrels, we used ultrasonic recorders to record squirrels in the wild across multiple seasons to determine if there are temporal and seasonal patterns in nightly vocal activity and rates of different call-types. We recorded Humboldt's flying squirrels in two geographic locations - Humboldt and San Bernardino counties-in California from 2018 to 2022 in the summer and winter across multiple study areas. We found that although seasonal weather conditions differ between locations, flying squirrels in Humboldt and San Bernardino had similar vocal activity patterns across nightly active periods between locations and between summer and winter. Nightly activity patterns of when the three main chirp-like call-types (arc chirps, tonal chirps, upsweeps) were given varied between seasons in both geographic locations, and these call-types were given at greater rates in the summer in San Bernardino, but rates did not vary by season in Humboldt. Trills, the most structurally complex of the four main call-types, were produced more in the summer than in winter, and also differed in their nightly activity patterns, in both geographic locations. Flying squirrels may use certain call-types earlier or later in the nightly active period due to their potentially varying functions, and may produce more trills in the summer coinciding with the breeding season. Further understanding of the function of different call-types can provide insight into social, foraging, and antipredator behavior of this nocturnal and elusive species.
Project description:We report the first functionally-annotated de novo transcriptome assembly for North American flying squirrels (genus Glaucomys). RNA was extracted from tissue samples obtained from two northern flying squirrels and two southern flying squirrels sampled from Ontario, Canada, and sequenced on an Illumina paired-end sequencing platform. We reconstructed 702,228 Glaucomys transcripts using 193,323,120 sequence read pairs and captured sequence homologies, protein domains, and gene function classifications. Introgressive hybridization between northern (Glaucomys sabrinus) and southern flying squirrels (G. volans) has been observed in some areas of North America. However, existing molecular markers lack the resolution to discriminate late-generation introgressants and describe the extent to which hybridization influences the Glaucomys gene pool. These genomic resources can increase the resolution of molecular techniques used to examine the dynamics of the Glaucomys hybrid zone.