Xenarthra form the least diversified major clade of placental mammals, being comprised of 31 described species of sloth, armadillo, and anteater. The past decade has seen a growth in the amount of xenarthran genetic data available, including the recent publication of a phylogenetic framework based on mitochondrial genomes, but more is required to aid in conservation assessments and to elucidate the evolutionary history of this unique order. We aimed to expand upon this by generating a framework based on nuclear genes. Using molecular baits, we enriched nuclear DNA from all extant and a selection of extinct ancient Xenarthrans for 74 phenotypically relevant genes. We aim to build phylogenetic trees based on each successfully enriched loci. Comparing trees against the previous mitochondrial framework will provide a measure of robustness. By seeing how estimated divergence times and rates vary across nuclear genes, we were able to examine how particular xenarthran phenotypes were selected upon in different points of their evolutionary history. While the sequencing of certain genes and species encountered mixed success rates, we have a solid framework for further study and can confirm that nuclear and mitochondrial information yields very similar evolutionary histories. / Thesis / Master of Science (MSc) / Xenarthrans - sloths, armadillos, and anteaters - have a long and complicated evolutionary history. In recent years a growth of new genetic information has made it easier to answer questions about their relation to each other and to other species. By examining many new gene sequences across all living Xenarthra, plus some extinct species, we aim to bolster our understanding of these relationships and the importance of particular traits.

The marsh rice rat (Oryzomys palustris) is a semi-aquatic rodent endemic to the southeastern United States. Unlike most terrestrial small mammals, the marsh rice rat can easily disperse over water and has a close association with wetlands. These specialized traits have likely greatly shaped the genetic structure and diversity within this species. I studied genetic patterns within the marsh rice rat to understand how this species' specialized ecology, as well as the geologic and climatic history of the southeastern United States, affected the genetic structuring within this species. The phylogeography of many species in the southeastern United States has been studied and concordant geographic patterns of genetic variation exist among many of these species. Researchers have hypothesized that the biogeography of the southeastern United States has been influenced by the Pleistocene glacial cycles, producing similar genetic patterns within unrelated species. I first examined genetic patterns within the marsh rice rat at the macro scale of phylogenetics. This nominal species actually represents two cryptic species; populations in the eastern and western regions of its range are genetically divergent. I also identified three subspecies, in contrast to the six morphological subspecies historically recognized. The silver rice rat in the Lower Florida Keys and the Sanibel Island rice rat from Sanibel Island Florida are both subspecific taxa. Only one mainland marsh rice rat subspecies exists. I then studied the phylogeographic patterns within the marsh rice rat and determined that geographic patterns of genetic variation in this species are not concordant with the phylogeographic patterns uncovered in most other species of the southeastern United States. The genetic structuring within the marsh rice rat has been influenced not only by the geologic and climatic history of this region, but also by the species' semi-aquatic adaptation. I also studied genetic patterns at a micro scale by estimating present levels of gene flow and genetic diversity within populations. Gene flow is a contemporary factor in maintaining levels of genetic diversity within populations of the marsh rice rat. From the macro scale of phylogenetics to the micro scale of population genetics, the genetic structure of the marsh rice rat has been shaped by past climatic history and by this species' specialized ecology.

Climatic and geographic events such as glaciations, island formation, river formation, and urbanization strongly affect habitat specialist species. By contrast, it is traditionally assumed that these events have little effect on habitat generalists but few studies have tested this assumption. In this study I sought to identify the effects of historic and contemporary biogeographic events on the genetic structure of a habitat generalist, the cotton mouse (Peromyscus gossypinus). This species is distributed throughout the southeastern United States, a region that has experienced dramatic geographic changes associated with both historic Pleistocene glacial cycles, as well as contemporary anthropogenic forces. In analyzing the genetic structuring in this species I took a telescopic approach, beginning with the patterns of variation throughout the species range from a phylogenetic standpoint. Using mitochondrial sequence data I identified three reciprocally monophyletic clades of the cotton mouse, a southeastern, northeaster, and western clade. Among these clades I identified eight distinct subspecies, four of which had previously not been identified using morphological characters. Of the four previously identified subspecies, this study resulted in a restructuring of the range of all except the Key Largo cotton mouse, which is restricted to northern Key Largo Florida. Secondly, I employed phylogeographic methods to examine the genetic patterns of the cotton mouse in a geographic context. Phylogeographic breaks in the cotton mouse are largely consistent with those observed in other taxa distributed throughout the southeastern United States. Geographic structuring in this species shows deep patterns associated with glacial maxima and minima of the Pleistocene period. Many of these patterns are maintained by contemporary geographic barriers to gene flow. Thirdly, I identified geographic structuring of genetic variation at a regional and local level. This structuring is partially due to the cotton mouse’s limited dispersal ability but is strengthened and reinforced by naturally occurring contemporary barriers to gene flow and contemporary anthropogenic forces which serve to limit dispersal in this species. Finally, I determined that urbanization has a dramatic negative effect on gene flow and genetic variation in this species on a local scale. Over a twenty year period populations in urban areas experienced a marked decrease in genetic variation while populations in non-urban areas experienced an increase in variation. During this time period, gene flow was effectively cut off among populations that had previously been panmictic. This study demonstrates that small mammal habitat generalists can be affected by both historic and contemporary climatic and geographic events at multiple geographic scales. These effects range from large scale geographic structuring throughout the species’ range to fine scale structuring associated with contemporary anthropogenic forces.

The cooperative construction of shared dwellings is a phylogenetically-widespread evolutionary puzzle. Shared shelters are common goods – all individuals in the shelter benefit, at the expense of those individuals that contribute to the construction. The evolution of cooperation requires existing variation for selection to act upon and genetic benefits to cooperators, through inclusive fitness or direct rewards. This study focuses on two genera of mice, Mus and Peromyscus, to examine shared construction and social monogamy as potential transitions to more sophisticated forms of sociality, such as cooperative breeding. The mound-building mouse (Mus spicilegus) is named for the large mounds that groups of mice build and beneath which they overwinter. Variation in mtDNA and 14 microsatellites show limited genetic structure across the geographic range of M. spicilegus. Mice from the same mound are more genetically related than mice from different mounds, and males and females associated with a mound are equally likely to be relatives. However in spring, when breeding begins, male kin are more likely to share a territory than are female kin. One possible interpretation is that males associate with kin to minimize the costs of being cuckolded, as this study finds evidence of multiple paternity in every litter genotyped. By increasing the chances of the cuckold being a brother, a male still gains inclusive fitness benefits from paternal care to extra-pair offspring in this socially monogamous species. Behavioral experiments show that another socially monogamous mouse species, the oldfield mouse (Peromyscus polionotus), can coordinate construction with unfamiliar, unrelated conspecifics. In contrast, two other closely related Peromyscus species do not dig longer burrows in pairs than they would have as individuals. Male-female P. polionotus pairs tend to dig longer burrows than pairs of the same sex, but males within opposite sex pairs do most of the digging, particularly when paired with an unfamiliar female. Male burrowing could be the product of female choice in this monogamous species. In M. spicilegus and P. polionotus, shared parental care and construction shed light on the evolution of cooperation and conflict.