Powell, Alexis Frederick Leo Alvey2013-02-132013-02-132012-12https://hdl.handle.net/11299/144291University of Minnesota Ph.D. dissertation. December 2012. Major: Ecology, Evolution and Behavior. Advisors: Scott M. Lanyon. 1 computer file (PDF); iv, 108 pages, appendices 1-2.The New World blackbirds (Icteridae) are among the best known songbirds, both through exemplar species, such as the Red-winged Blackbird (Agelaius phoeniceus), and collectively, as a model clade in studies of morphological, ecological, and behavioral trait evolution. Knowledge of phylogeny is a prerequisite for comparative studies and the basis for systematic classification, yet there has been no comprehensive analysis of blackbird phylogeny. In Chapter 1, I present the phylogeny of the grackles (Quiscalus spp.) inferred from cytochrome b and ND2 gene sequences. A primary concern was determining the relationships of the extinct Slender-billed Grackle (Q. palustris) and Q. nicaraguensis, which is unusual among grackles for its restricted geographic range. I found the Slender-billed Grackle to be most closely related to one of two major haplotype clades of Q. mexicanus, the other being sister to Q. major. Q. nicaraguensis appears sister to Q. lugubris. I also found that Q. mexicanus, niger, and lugubris contain deeply-divergent lineages. In Chapter 2, I present a method for partitioning whole mitochondrial genome sequences to optimize model-fitting during phylogenetic analyses. Because standards for rigorous phylogenetic analyses of mitogenomes were lacking, developing such a method was a prerequisite for analyzing the mitogenomes of a clade of South American endemic blackbirds. I found that the most useful categories for partitioning were codon position, RNA secondary structure pairing, and the coding/noncoding distinction, and that a scheme with nine data groups outperformed all of the more complex alternatives (up to 44 data groups) that I tested. In Chapter 3, I present the first comprehensive species-level phylogeny of the Icteridae. By using mitochondrial gene sequences from all ~108 currently-recognized species, together with strategic sampling of 4 nuclear loci and whole mitochondrial genomes at the generic level, I was able to resolve most relationships with high confidence. The best-resolved phylogeny is consistent with strongly-supported results of past studies, but it also contains many novel robustly-resolved inferences of relationship, including some unexpected placements of taxa that had not been included in previous molecular phylogenies, resolution of the relationships among major subclades within Icteridae. I suggest taxonomic revisions based on those results.en-USBiological sciencesPhylogeneticsNew World blackbirdsIcteridaeSongbirdsGrackleThesis or Dissertation