How organisms evolve and/or adapt is one of the central questions in population genetics. While evolution can be driven by four major forces: mutation, recombination, natural selection and random genetic drift, when investigating experimentally evolved cultures it can be difficult to determine if shared genotypes occur due to mutational hotspots in the genome or parallel adaptive evolution. Previous long-term evolution experiments conducted by Richard Lenski and collaborators have demonstrated multiple avenues of adaptation for Escherichia coli strain B in liquid culture (Elena and Lenski, 2003). Using a similar long-term investigation, we aimed to explain how ancestral genetic background, starvation, and an environment where subpopulations can inhabit their own niche affects population dynamics and long-term evolution. As such, we characterized 96 clones isolated from 12 out of 200 populations involved in a long-term evolution experiment. Our 12 focus populations were propagated from one of three possible E. coli K-12 ancestors, and transferred every 24 - 48h for 2.5 years (~4000 generations) in liquid LB medium. Among clones, auxotrophic, behavioral, morphological, and growth variations were identified. We additionally evaluated each of the clones for improved or worsened fitness compared to the wild-type ancestor through relative growth curve assays. Lastly, we applied a bioinformatics approach for lineage and mutation analysis to identify patterns and commonalities between the varied phenotypes and their respective genotypes. Here, we are able to trace homologous changes in bacterial evolution to suggesting parallel response to pressures due to their respective conditions, background, or ecological niche. The complex structuring of ecological niches among the long-term populations is reflective of the shifts in gene polymorphisms.