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Comparative phylogeography has historically been defined as the study of how genetic variation of co-distributed species has been shaped by biogeographical history. This is a mature field of study out of which several techniques have been developed directed at identifying the role ecology and geography in diversification patterns across time. I employ the tools developed in classical comparative phylogeography across multiple taxonomic scales and across regions that historically have been understudied. My first two chapters study the complex history of host-switching, codiversification, and reassortment of hantaviruses in their mammal hosts across North America. By taking a host-centric comparative phylogeographic approach to pathogen divergence, I highlighted complex evolutionary processes in host-pathogen systems and the role of host history in shaping the distribution and diversity of pathogens. My final chapter uses a comparative approach to examine the interplay between ecology and climate in shaping divergence and contact within four East Asian pika species during the Quaternary. I show that small mammals in this vast, poorly studied region responded to Pleistocene climatic cycling on finer geographic scales when compared to the North American fauna that is distributed at similar latitudes.

The mammalian gut microbiome has shown to be essential to host fitness and health assisting in both nutrient acquisition from diet as well as protection from pathogens and can include beneficial bacteria as well as parasites such as helminths and protozoans. In this study, I analyzed the cestode and bacterial communities found in the intestines of two North American species of shrew, Sorex monticola and Sorex cinereus. Specimens were collected approximately every three weeks from May to October during 2016 and 2017 as well as during April and May of 2018 and September of 2009 from the Sangre de Cristo Mountains in Cowles, New Mexico. A total of 186 shrews were dissected and surveyed for cestode and bacterial taxa. I extracted DNA from the whole GI tract of each specimen and amplified 2 loci (28S rRNA for cestodes and 16S rRNA for bacteria) using one-step PCR amplification and sequencing on an Illumina MiSeq. Collection month, shrew species, sex, and weight class all significantly influenced the gut microbiome communities in S. cinereus and S. monticola, however some of the effect of collection month and shrew species on community composition is likely due to variances in within-group distributions. Mathevolepis and Monocercus both significantly altered the bacterial community composition of their hosts, but further analysis could be conducted controlling for the presence of one or the other to parse out any confounding due to coinfection. This study provides novel descriptions of cestode taxa infecting S. monticola and provides a first survey of cestodes infecting shrews in New Mexico.

The intestinal microbiome of mammals plays a significant role in host health and response to environmental stimuli and can include both beneficial native bacteria as well as parasitic worms. In this study, I examined the intestinal cestode and bacterial communities of two closely related species of shrew, Sorex monticola and Sorex cinereus, over a six month period in 2016. Specimens were collected approximately every three weeks from May to October from the Sangre de Cristo Mountains in Cowles, New Mexico. A total of 79 shrews were prepared with the gastrointestinal tracts removed and flash-frozen in liquid nitrogen. An additional 9 whole frozen samples were obtained from the Museum of Southwestern Biology, which were collected from the same area in September 2009. I extracted DNA from the whole GI tract, and amplified 3 loci (28S rRNA, 16S mtDNA, 16S rRNA) using one-step PCR amplification and sequencing on the Illumina MiSeq system 28S rRNA gene. On average, shrews were infected by 6 cestode genera and colonized by an average of 11 bacterial phyla, with Lineolepis and Epsilonbacteraeota being the most abundant, respectively. I tested both environmental and host-related metrics and found that the cestode infections of S. monticola and S. cinereus are most significantly affected by host species, host weight, and time of year, and bacterial community compositions were most significantly affected by time of year and host weight with some effect from host species and collection locality. Variation across weight and time likely reflects variations in the shrews’ arthropod diet. Cestode variation across host species reflects their high host specificity. Bacterial variation in locality reflects the high degree of individual variation of intestinal microbiomes. Variation with respect to host species may be due to a difference in inflammatory response or an artefact of uneven sample sizes.

Understanding the distributions of organisms is key to deciphering their biogeography. Shrews of the genus Blarina are some of the most common and abundant mammals in this region. Two species are found in southeast Tennessee: Blarina brevicauda and Blarina carolinensis. To clarify their geographic ranges, Blarina vouchers were collected throughout the study area and mitochondrial DNA cytochrome b genes were isolated and sequenced. I collected and compared 53 DNA sequences from shrews throughout southeast Tennessee and southwest North Carolina to 101 samples obtained from Genbank. Results indicate Blarina brevicauda is found in areas north and west of the Tennessee River and Blarina carolinensis is found in most areas south and east of the Tennessee River. B. brevicauda specimens fell into a monophyletic B. brevicauda clade, resolving with Genbank sequence data into haplotypes classified as either 'Appalachian’ or ‘East-Central’. B. carolinensis specimens were monophyletic, resolving into an ‘Eastern’ haplotype.

Since the 19th century the remains of Quaternary mammals were an important source of data for reconstructing past environmental conditions. I tested two basic assumptions that underlie Quaternary vertebrate paleoecology. The first assumption is that fossils mammals can be identified reliably to species. The second assumption is that correlations established between extant mammals and environmental parameters can be used to interpret reliably the paleoenvironment from the latest Pleistocene. Incorrect specimen identifications could lead to errors in paleoecologic interpretations. I explicitly tested an alternative to the traditional approach to identification by identifying fossil shrews based on apomorphies. My results indicated that some traditional characters are useful for identification, but only complete specimens with a combination of characters can be identified to species. This indicates that previous authors who identified shrews to species did not compare them to the full diversity of species. I tested the reliability of cenograms and species-richness models as approaches for the reconstruction of environmental conditions in the past. I used faunal data from Hall’s Cave, Kerr County, Texas to construct cenograms and species-richness models and compared the results to independent paleoclimate proxies. Neither species-richness models nor cenograms agree with paleoenvironmental reconstructions based on proxy data from the Late Pleistocene and Holocene. Cenograms and species-richness models are unreliable and fraught with problems, and both approaches should be abandoned as tools for paleoecological reconstruction. To test for potential geographic bias in the identification of Quaternary fossils I developed a GIS (geographic information systems) database of Quaternary paleontological sites within Texas. I was able to show that the identification of species of fossil soricids, heteromyids, Odocoileus, and Spilogale was influenced by geography. Those fossils should be treated as generic identifications until they are re-evaluated against the full diversity of species. Utilizing GIS I also developed a method of paleoecological analysis. My analysis showed that the environmental conditions found today in Texas might not be limiting the current range of shrews. Based on the known geographic range of shrew fossils, other ecological factors besides environmental conditions are shaping the current distribution of shrews.

Since the 19th century the remains of Quaternary mammals were an important source of data for reconstructing past environmental conditions. I tested two basic assumptions that underlie Quaternary vertebrate paleoecology. The first assumption is that fossils mammals can be identified reliably to species. The second assumption is that correlations established between extant mammals and environmental parameters can be used to interpret reliably the paleoenvironment from the latest Pleistocene. Incorrect specimen identifications could lead to errors in paleoecologic interpretations. I explicitly tested an alternative to the traditional approach to identification by identifying fossil shrews based on apomorphies. My results indicated that some traditional characters are useful for identification, but only complete specimens with a combination of characters can be identified to species. This indicates that previous authors who identified shrews to species did not compare them to the full diversity of species. I tested the reliability of cenograms and species-richness models as approaches for the reconstruction of environmental conditions in the past. I used faunal data from Hall’s Cave, Kerr County, Texas to construct cenograms and species-richness models and compared the results to independent paleoclimate proxies. Neither species-richness models nor cenograms agree with paleoenvironmental reconstructions based on proxy data from the Late Pleistocene and Holocene. Cenograms and species-richness models are unreliable and fraught with problems, and both approaches should be abandoned as tools for paleoecological reconstruction. To test for potential geographic bias in the identification of Quaternary fossils I developed a GIS (geographic information systems) database of Quaternary paleontological sites within Texas. I was able to show that the identification of species of fossil soricids, heteromyids, Odocoileus, and Spilogale was influenced by geography. Those fossils should be treated as generic identifications until they are re-evaluated against the full diversity of species. Utilizing GIS I also developed a method of paleoecological analysis. My analysis showed that the environmental conditions found today in Texas might not be limiting the current range of shrews. Based on the known geographic range of shrew fossils, other ecological factors besides environmental conditions are shaping the current distribution of shrews.

Recent use of prescribed fire and fire surrogates to reduce fuel hazards has spurred interest in their effects on wildlife. Some studies of fire in the southern Appalachian Mountains have documented few effects on reptiles and amphibians. However, these studies were conducted after only one fire and for only a short time period (1 to 3 years) after the fire. From mid-May to mid-August 2006 and 2007, we used drift fences with pitfall traps to trap reptiles, amphibians, and shrews in western North Carolina and to asses their response to 3 fuel reduction treatments: 1) twice-burned (2003 and 2006), 2) mechanical understory cut (2002), and 3) mechanical understory cut (2002) followed by 2 burns (2003 and 2006), and a control. We captured significantly fewer salamanders in the mechanical + twice-burned treatment than in twice-burned and control treatments, but more lizards in the mechanical + twice-burned treatment. Higher lizard captures in mechanical + twice-burned treatments was likely due to increased ground temperatures and greater thermoregulatory opportunities. Higher and more variable ground temperatures and faster drying of the remaining litter and duff in mechanical + twice-burned treatments may have led to fewer salamander captures in these treatments. We captured significantly fewer southeastern shrews (Sorex longirostris) in the mechanical + twice-burned treatment than in the mechanical treatment in 2006, but southeastern shrew captures did not differ among treatments in 2007. Total shrew captures did not differ among treatments in either year. Decreases in leaf litter and canopy cover in the mechanical + twice-burned treatment may have led to decreases in moisture and therefore decreases in southeastern shrew captures. Our long-term results, after 2 prescribed burns, differ from results after 1 prescribed burn, after which eastern fence lizard (Sceloporus undulatus) captures were greater in mechanical + burn treatments but salamander captures did not differ among treatments. Low-intensity fuel reduction treatments in the southern Appalachian Mountains do not appear to greatly affect reptile, amphibian, or shrew populations. However, multiple (>2) high intensity burns may benefit lizards but negatively affect salamanders and some shrew species, at least temporarily.

Abstract: Masters thesis. Populations of four species studied south of Great Slave Lake, May 1976-December 1977.

In many terrestrial mammals, males are generally larger than females. Since shrews are the smallest living terrestrial mammals, specimens of the shrew Sorex cinereus cinereus from north central Minnesota were studied to determine if size differences between sexes also occurred at this extreme. Comparisons were based on measurements of external body lengths and individual lengths of upper quadrant locomotive muscles. External differences showed neither males nor females were consistently larger. The results from analysis of variance on individual muscle lengths showed very few significant differences between individual muscles. Those muscles that did show a significant difference were not grouped In a way that would suggest a significance due to a function specific to either sex. This study suggests that in these shrews, unlike many other living terrestial mammals, males are not larger than females.