This dissertation integrates results of macro and microevolutionary studies of phylogeny and diversification in salamanders based on mitochondrial and nuclear DNA sequence data and allozymic gene frequency data. The second chapter presents a molecular phylogenetic study of the evolution of fertilization mechanisms among extant salamanders. Bayesian phylogenetic analysis of mtDNA and nuclear gene sequences significantly reject monophyly of a group containing all internally fertilizing salamanders, while parsimony analysis of the mtDNA sequence data is equivocal. Simulations of molecular evolution indicate that loss of phylogenetic information along deep branches through multiple and parallel substitutions can preclude parsimony analysis from recovering the correct topology and, on average, an internal branch must have been at least 7 to 10 million years in duration to be recovered with robust measures of branch support if subsequent terminal evolution has occurred for 10 million years.; The third chapter is a detailed examination of geographic variation and speciation in the Plethodon jordani species complex using mtDNA and allozyme data. I show through ordination and phylogenetic analyses that allozyme variation can be partitioned into statistically differentiated groups corresponding to previously recognized species. I also show that phylogenetic and network analyses of mtDNA haplotypes produce groups that statistically correspond to previously recognized species. Historical range expansions have produced introgression of mtDNA haplotypes across species boundaries.; The fourth chapter focuses specifically on Plethodon shermani , from the P. jordani complex. Allozyme data statistically support P. shermani as a distinct phylogenetic species, despite extensive hybridization with species of the P. glutinosus complex. In contrast, mtDNA haplotypes from P. shermani form multiple divergent clades and reveal patterns of extensive introgression between P. shermani and species of the P. glutinosus complex.; The fifth chapter summarizes a phylogenetic study of the “true” salamanders from the family Salamandridae using mtDNA sequence data. I show that monophyly of the genus Mertensiella is statistically rejected, with the species Mertensiella luschani being more closely related to the genus Salamandra and the species Mertensiella caucasica being more closely related to the genus Chioglossa. Mertensiella luschani comprises at least six divergent lineages of approximately equal evolutionary age.
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