A Brief History of the New World Flying Squirrels: Phylogeny, Biogeography, and Conservation Genetics

Phylogeography within the Peromyscus maniculatus species group: Understanding past distribution of genetic diversity and areas of refugia in western North America

The effects of anthropogenic climate change on biodiversity have been recognized on every continent, ocean, and across different taxonomic groups. Here, we study the range dynamics and demography of a cosmopolitan species: the deer mouse, Peromyscus maniculatus. We generated a multilocus SNP dataset using the ddRADseq protocol for 218 individuals across the geographic range within three western North American lineages of this species group. We evaluated population structure using several methods and explored the correlation between geographic and genetic distances. We modeled the demographic history using a site frequency spectrum approach and used a machine learning algorithm to infer current and past (Last Glacial Maximum; LGM) environmental suitability. Lastly, we explored the origin of population expansion for the identified lineages. The genome-wide SNP dataset was able to identify-three regionally distinct groups- 1) P. m. gambelii (southern California); 2) P. keeni (Pacific Northwest); 3) P. m. sonoriensis (a broad population spanning the Pacific Northwest through central California and across the Rocky Mountains into the Great Plains). Demographic analysis indicated the splits between the three populations occurred within the last 500 thousand years, with one very recent (late Holocene) split. Ecological niche models for each of these lineages predicted suitable environment present throughout their known ranges for current conditions, and a severe reduction of northern habitat in the past. The deer mouse has responded to past climate changes by expanding its range during interglacial periods and contracting its range during glacial periods leading to strong population differentiation. But lower magnitude climate change or other processes within the Holocene interglacial period led to population differentiation as well, which is likely still ongoing today given the substantial anthropogenic climate change and other landscape transformations caused by humans during the Anthropocene. By understanding the historical processes that led to the contemporary geographic distribution of biodiversity, we can determine the relative importance of different factors that shape biodiversity, now and into the future.

Testing the parasite-mediated competition hypothesis between sympatric northern and southern flying squirrels

Competition is a driving factor in shaping ecological communities and may act directly or indirectly through apparent competition. We examined a classic example of parasite-mediated competition between northern (Glaucomys sabrinus) and southern flying squirrels (G. volans) via the intestinal nematode, Strongyloides robustus, and tested whether it could act as a species barrier in a flying squirrel hybrid zone. We live-trapped flying squirrels (G. sabrinus and G. volans), grey squirrels (Sciurus carolinensis), red squirrels (Tamiasciurus hudsonicus), and chipmunks (Tamias striatus) from June–September 2019 at 30 woodlots in Ontario, Canada. Fecal samples from squirrels were collected and analyzed for the presence of endoparasite eggs. For each individual, we calculated Scaled Mass Index (SMI) as a measure of body condition to assess the effect of S. robustus on squirrels. We found eggs of S. robustus in all species except chipmunks. Infection with S. robustus did not appear to affect body condition of southern flying squirrels and grey squirrels, but we did find a weak negative effect on northern flying squirrels and red squirrels. Despite a weak asymmetric effect of S. robustus on flying squirrels, we did not find any evidence that parasite-mediated competition could lead to competitive exclusion from woodlots. Furthermore, S. robustus eggs were common in feces of the red squirrel, a species largely sympatric with northern flying squirrel.

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Strongyloides robustus was detected in 4 squirrel species.

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The highest prevalence of S. robustus was found in red squirrels and northern flying squirrels.

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Body condition was lowest in red squirrels and northern flying squirrels infected with S. robustus.

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No evidence of parasite-mediated competition between sympatric flying squirrels leading to competitive exclusion.

A de novo genome assembly and annotation of the southern flying squirrel (Glaucomys volans)

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.

Winter nest trees of sympatric northern (Glaucomys sabrinus) and southern (Glaucomys volans) flying squirrels: a test of reinforcement in a hybrid zone

Shifting range boundaries can lead to secondary contact of closely related species, which might in turn lead to hybridization when the evolution of reproductive isolation is incomplete. We examined winter nest use of northern (Glaucomys sabrinus (Shaw, 1801)) and southern (Glaucomys volans (Linnaeus, 1758)) flying squirrels in an area of recent secondary contact and known hybridization in Ontario, Canada, to test for evidence of reinforcement due to different and diverging nesting behaviours. We radio-collared 26 flying squirrels (12 G. sabrinus and 14 G. volans) between two survey periods (winters of 2008–2009 and 2019–2020) and identified all nest trees used by individuals throughout each winter. For each nest tree, we identified the nest type and collected tree classification information to compare differences in nest use between species. We also present a novel application of habitat suitability modelling to test for evidence of divergence in nest use through time, which would suggest reinforcement. We found southern flying squirrels used a higher proportion of cavities in large, hardwood trees, whereas northern flying squirrels used more external nests and softwood trees. Conditional probabilities provided some evidence for increased differentiation in nest use by flying squirrels through time. Overall, we found relatively little overlap in winter nest use between flying squirrel species, despite evidence for hybridization at this site, and some weak evidence for increased divergence between species in nest use over 11 years.

Body-size Scaling is Related to Gut Microbial Diversity, Metabolism and Dietary Niche of Arboreal Folivorous Flying Squirrels

Thermal homeostasis of mammals is constrained by body-size scaling. Consequently, small mammals require considerable energy to maintain a high mass-specific metabolic rate (MSMR) and sustain target body temperature. In association with gut microbiota, mammalian hosts acquire absorbable molecules and fulfill their metabolic requirements. Our objective was to characterize gut microbes in wild mammals and relate those findings to host body-size scaling. Two large (Petaurista philippensis grandis and P. alborufus lena), one medium (Trogopterus xanthipes) and one small (Pteromys volans orii) species of flying squirrels (FS) were studied. Using 16S rRNA genes, 1,104 OTUs were detected from four FS, with 1.99% of OTUs shared among all FS. Although all FS gut microbiota were dominated by Firmicutes, they were constituted by different bacterial families. Moreover, Bacteroidetes accounted for up to 19% of gut microbiota in small FS, but was absent in large FS. Finally, based on metagenome predictions, carbohydrate and amino acid metabolism genes were enriched in small body-size FS. In conclusion, gut microbiota compositions and predictive metabolic functions were characteristic of body-size in FS, consistent with their adaptations to folivorous dietary niches.

Genetic structure of the arboreal squirrels (Glaucomys sabrinusandTamiasciurus hudsonicus) in the North American Black Hills

We selected two isolated mammalian populations, the Black Hills northern flying squirrel ( Glaucomys sabrinus (Shaw, 1801)) and red squirrel ( Tamiasciurus hudsonicus (Erxleben, 1777)), to elucidate their genetic structure. We trapped both squirrels from 2005 to 2007, in three regions of the Black Hills, differing in geology and vegetation, to collect ear samples for genetic analyses. Microsatellite loci (northern flying (9) and red squirrel (13)) were used to examine genetic structure. Data analyses estimated genetic variability, substructure, and gene flow. Northern flying and red squirrel populations have allelic diversity and observed heterozygosity similar to other isolated populations. Each species shows weak substructure from STRUCTURE and GENELAND analyses, suggesting squirrel movements may be inhibited by topography or unsuitable habitat. Recent gene flow estimates from BAYESASS indicate that both species experience some within population gene flow and red squirrels may be more structured than northern flying squirrels because of lower migration rates. Concordant patterns of genetic structure in northern flying and red squirrels indicate that other species’ movements in the Black Hills may be affected by topography and habitat. Because their habitat is isolated in the Black Hills, management practices and conservation measures are recommended to promote viability and survival of each species.

Post-Pleistocene range expansion of the recently imperiled eastern little brown bat (Myotis lucifugus lucifugus) from a single southern refugium

Myotis lucifugus, once among the most widespread and common bats in North America, has been forecast to be extirpated east of the Rockies in as few as 16 years by the spread of white-nose syndrome. Recent genetic research has demonstrated that this species is paraphyletic and part of a broader species complex; however, only one lineage (Myotis lucifugus lucifugus [M. l. lucifugus]) is present in eastern North America. I used molecular tools and niche modeling to validate this and investigate the role that historical biogeography has played in the phylogenetic and population genetic structure of this species to determine if the eastern subspecies represents an evolutionarily distinct population.

To establish the genetic structure within M. l. lucifugus, I densely sampled maternity colonies in Minnesota and sequenced 182 individuals for a portion of cytochrome b. Phylogenetic reconstruction and a haplotype network were used to infer the relationships among mitochondrial haplotypes. Population growth statistics were calculated to determine if there was evidence of significant expansion, and an environmental niche model (ENM) was constructed based on conditions during the last glacial maximum (LGM) to illustrate potential glacial refugia. All individuals derived from a single mitochondrial lineage. Genetic evidence points to population growth starting approximately 18 kya. ENM results show that there was likely a single large southern refugium extending across the southeastern United States and possibly several isolated refugia in western North America. Myotis lucifugus lucifugus likely maintained both a large range and a large population during the peaks of the glacial cycles, and its population appears to have expanded following the retreat of the Laurentide ice sheet. This imperiled lineage likely diverged in isolation from other members of the M. lucifugus/western long-eared Myotis during the Pleistocene.