ABSTRACT
A major challenge in evolutionary biology is to understand the processes of
divergence and diversification in microorganisms, in which genes can often be
exchanged laterally and not just from parent to offspring. The proposed research will
test how a special class of selfish elements, termed homing endonucleases (HEs),
affects the genetic barriers that can form distinct groups of microorganisms, often
labeled as ecotypes or species, and use HEs to estimate how much lateral gene
exchange exists within a natural population. We have established the experimental
framework required to attain these goals in halophilic Archaea using several
complementary approaches: theoretic-computational (UConn), genetic (TAU),
genomic (UConn) and ecological (TAU). We will test how the presence of HEs can
affect gene exchange within and between groups, and investigate the spread of HEs
and its effects on recombination in an ecological context using a collection of
environmental isolates. We will perform genetic experiments and use the results
derived from them to refine computational models that describe HE dynamics. We
will then generalize these findings and generate models for the effects of HEs on
microorganism population genetics, testing them using computer simulations. The
proposed research will shed new light on the role that mobile parasitic elements play
in shaping microbial evolution.

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