The structure of natural populations and the intraspecific relationships among these populations provides a crucial context for understanding the historical, current, and future evolution of organismal phenotypes. This fact is becoming increasingly clear to biologists of all stripes, and analysis of microsatellite markers and mtDNA and nuDNA sequences are providing the substrate to add a geneological perspective to such studies. We are using this approach with various molecular techniques to evaluate the pedigrees and phylogenies of species and populations of certain North American reptiles. One project aims to resolve broad-scale phylogeographic patterns as well as local population genetic differentiation among populations of Blanding's turtles (Emys blandingii) (Kasuga & Janzen, 2008, Illinois DNR Report; Chandler et al., 2009, Illinois DNR Report). Another uses a combination of genetic, morphological, behavioral, and geographic data to look at patterns of differentiation and isolation-by-distance in a complex of sympatric and allopatric map turtle (Graptemys) species to understand how both drift and selection have contributed to variation within and divergence between species (Myers, 2008, dissertation). Past projects have involved reconstructing the relationships among isolated populations of vulnerable western pond turtles (Emys marmorata) to assess the extent of differentiation among these populations and to determine their conservation "status" (Janzen et al., 1997, Chel. Conserv. Biol.), and examining the inter- and intra-specific relationships of softshell turtles (Apalone) (Weisrock and Janzen, 2000, Mol. Phylog. Evol.; McGaugh & Janzen, 2008, Chel. Conserv. Biol.; McGaugh et al., 2008, Zool. Scripta) and reconstructing the evolutionary causes of clinal variation in thermal sensitivity of antipredator behavior. Other such molecular ecology and evolutionary studies in progress involve imperiled box turtles (Terrapene) (Kuo and Janzen, 2004, Conserv. Genet.; Howeth et al., 2008, Mol. Ecol.), hognose snakes (Heterodon), garter snakes (Thamnophis) (Janzen et al., 2002, Mol. Phylog. Evol.), and assessments of molecular systematics of painted turtles (Starkey et al., 2003, Evolution) and molecular phylogenetics and evolution among all recognized taxonomic families of extant turtles (Krenz et al., 2005, Mol. Phylog. Evol.; Chandler and Janzen, 2009, Copeia). We are also employing microsatellite markers to evaluate the breeding structure (e.g., multiple paternity) of painted turtles (Pearse et al., 2001, Heredity and Mol. Ecol.; 2002, Behav. Ecol. Sociobiol.; McGaugh and Janzen, 2010, Behav. Ecol. Sociobiol.). We are greatly expanding our work in this and related areas of ecological genetics.