Giarla, Thomas Christopher2013-10-152013-10-152013-08https://hdl.handle.net/11299/158266University of Minnesota Ph.D. dissertation. August, 2013. Major: Ecology, Evolution and Behavior. Advisor: Sharon A. Jansa. 1 computer file (ix, 156 pages) + 2 supplementary files (PDF, Excel).This project broadly explores the systematics, biogeography, and phylogeography of <italic>Thylamys</italic> mouse opossums, a genus of Neotropical marsupials from central and southern South America. Chapter 1 is part of a collaborative work with Robert Voss and Sharon Jansa (Chapter 1). In it, we resolve longstanding issues surrounding <italic>Thylamys</italic> taxonomy and nomenclature using mitochondrial DNA sequences and morphology, and provide the first phylogenetic hypothesis for all recognized species in this genus. We recognize nine species but also uncover numerous morphologically cryptic mitochondrial haplogroups within four species. In Chapter 2, I assess the evolutionary independence of a subset of these morphologically cryptic lineages within the montane species <italic>Thylamys pallidior</italic>, <italic>T. sponsorius</italic>, and <italic>T. venustus</italic>. I find evidence to support the existence of two lineages within each of the three species, and also conduct tests to determine the number of nuclear loci needed to confidently test species limits. In Chapter 3, I examine the biogeographic history of <italic>Thylamys</italic> and its monotypic sister-genus <italic>Lestodelphys</italic>, considering the impact of habitat type and physical barriers on range evolution and cladogenesis. In Chapter 4, I test predictions regarding the impact of late Quaternary glacial cycles on the evolutionary history of six montane cryptic lineages. I estimate divergence times and demographic shifts for each lineage, and find limited support for the core predictions. Two supplementary files are provided online as part of this dissertation: a file containing 15 phylogenetic trees for each of the loci considered in Chapter 2 (Online Supplementary File 1) and a file containing GenBank accession numbers and tissue voucher numbers for the sequences included in the supermatrix in Chapter 3 (Online Supplementary File 2).en-USSystematic biologyZoologyBiologyAndesBiogeographyEvolutionMarsupialsPhylogeographyThylamysThesis or Dissertation