Population genetics principles, phylogenetic analyses, rate calculations, and allele frequency spectra of derived SNPs are employed to understand evolutionary mechanisms behind eukaryotic genome complexity.
Using the Tree of Life, Lynch investigates the significant variation across diverse invertebrates and simple eukaryotic and prokaryotic organisms using a mutation-accumulation strategy.
Study of Daphnia pulex, a microcrustacean that has the ability to reproduce sexually and asexually based upon which is advantageous at particular evolutionary time points, allows for direct quantification and comparison of recombination rates in mobile genetic elements in sexual and asexual lineages.
[13] This species of Daphnia's asexual lineage is rather young in an evolutionary time perspective and rapidly go extinct.
Using Paramecium as a model species, studies of the evolutionary basis of: evolution of cellular surveillance mechanisms, barriers as a result of random genetic drift on molecular perfection, multimeric proteins, vesicle transport and gene expression.