Biology subjects

Sobek, C. J.

Publications and source records attributed to Sobek, C. J..

3 recordsLinked to original sources

bioRxiv2022

Once upon a time in Mexico: Holocene phylogeography of the spotted bat (Euderma maculatum)

Holocene-era range expansions are relevant to understanding how a species might respond to the warming and drying climates of today. The harsh conditions of North American deserts have phylogenetically structured desert bat communities but differences in flight capabilities are expected to affect their ability to compete, locate, and use habitat in the face of modern climate change. A highly vagile but data-deficient bat species, the spotted bat (Euderma maculatum) is thought to have expanded its range from central Mexico to western Canada during the Holocene. With specimens spanning this latitudinal extent, we coupled phylogeography (mtDNA) with ecological niche modeling (ENM) to investigate the Holocene biogeography from the rear to leading edges. The ENM and phylogeny supported a Holocene range expansion from Mexico with increased expansion throughout the intermountain west within the last 6 kya. Long-term isolation at the southern-most margin of the range suggests one or more populations were left behind as climate space contracted and are currently of unknown status. The species appears historically suited to track shifts in climate space but differences in flight behaviors between leading edge and core-range lineages suggest that range expansions could be influenced by differences in habitat quality or climate (e.g., drought). Although its vagility could facilitate the tracking of environmental change and thereby extinction avoidance, anthropogenic pressures at the core range could still threaten the ability for beneficial alleles to expand into the leading edge.

genetics↗

bioRxiv2022

Metagenomic analysis of coprolites from three Late Pleistocene megaherbivores from the Southwestern United States.

1.BackgroundDetermining the life-history traits of extinct species is often difficult from skeletal remains alone, limiting the accuracy of studies modeling past ecosystems. However, the analysis of the degraded endogenous bacterial DNA present in paleontological fecal matter (coprolites) may enable the characterization of specific traits such as the hosts digestive physiology and diet. An issue when evaluating the microbial composition of coprolites is the degree to which the microbiome is representative of the hosts original gut community versus the changes that occur in the weeks following deposition due to desiccation. Analyses of paleontological microorganisms are also relevant in the light of recent studies linking the Late Pleistocene and Early Holocene extinctions with modern-day zoonotic pathogen outbreaks. MethodsShotgun sequencing was performed on ancient DNA (aDNA) extracted from coprolites of the Columbian mammoth (Mammuthus Columbi), Shasta ground sloth (Nothrotheriops shastensis) and paleontological bison (Bison sp.) collected from caves on the Colorado Plateau, Southwestern USA. The novel metagenomic classifier MTSv, parameterized for studies of aDNA, was used to assign bacterial taxa to sequencing reads. The resulting bacterial community of coprolites was then compared to those from modern fecal specimens of the African savannah elephant (Loxodonta africana), the brown-throated sloth (Bradypus variegatus) and the modern bison (Bison bison). Both paleontological and modern bison fecal bacterial communities were also compared to those of progressively dried cattle feces to determine whether endogenous DNA from coprolites had a microbiome signal skewed towards aerobic microorganisms typical of desiccated fecal matter. ResultsThe diversity of phyla identified from coprolites was lower than modern specimens. The relative abundance of Actinobacteria was increased in coprolites compared to modern specimens, with fewer Bacteroidetes and Euryarchaeota. Firmicutes had a reduced relative abundance in the mammoth and bison coprolites, compared to the African savanna elephants and modern bison. There was a significant separation of samples in NMDS plots based on their classification as either paleontological or modern, and to a lesser extent, based on the host species. Increasingly dried cattle feces formed a continuum between the modern and paleontological bison samples. ConclusionOur results reveal that any coprolite metagenomes should always be compared to desiccated modern fecal samples from closely related hosts fed a comparable diet to determine the degree to which the coprolite metagenome is a result of desiccation versus true dissimilarities between the modern and paleontological hosts. Also, a large-scale desiccation study including a variety of modern species may shed light on life-history traits of extinct species without close extant relatives, by establishing the proximity of coprolite metagenomes with those from dried modern samples.

paleontology↗

bioRxiv2020

Relatedness and genetic structure of big brown bat (Eptesicus fuscus) maternity colonies in an urban-wildland interface provides insight into rabies transmission dynamics

Big brown bats (Eptesicus fuscus) are the bat species most frequently found to be rabid in North America and are a key source of sylvatic rabies in wildlife. Females can form summer maternity colonies in urban areas, often using access holes in the exterior of buildings to roost in relatively large numbers. In Flagstaff, Arizona, these roosts are commonly found in houses adjacent to golf courses, where habitat quality (food, water, shelter) is high for bats and for mesocarnivores such as striped skunks (Mephitis mephitis) and gray foxes (Urocyon cinereoargenteus). Periodic rabies outbreaks in Flagstaff involving all three of these mammals are primarily caused by an E. fuscus variant of the disease. However, little is known about E. fuscus social behavior during the summer months and how it may drive space use and hence disease exposure to conspecifics and mesocarnivores. To address this knowledge gap, we collected 88 unique genetic samples via buccal swabs from E. fuscus captured at four maternity roosts surrounding a golf course during summer of 2013. We used 7 microsatellite loci to estimate genetic relatedness among individuals and genetic structure within and among colonies in order to infer whether females selected roosts based on kinship, and used genetics and radio telemetry to determine the frequency of roost switching. We found roost switching through genetics (two mother and adult daughter pairs at the same and different roosts) and telemetry, and no evidence of elevated genetic relatedness within colonies or genetic structure between colonies. These results have important implications for disease transmission dynamics in that social cohesion based on relatedness does not act to constrain the virus to a particular roost area. Instead, geographic mobility may increase disease exposure to neighboring areas. We discuss mitigating actions for bat conservation and public health.

ecology↗