Genome Evolution and Biodiversity

Evolution through Hybridization and polyploidization
Interspecies hybrids and polyploids are prominent in the plant kingdom. Most eukaryotic species are the result of ancient hybridization followed by genome doubling (paleopolyploids) tens of millions of years ago.  This is the case for budding yeast as well as for Arabidopsis or maize.  Other species are young polyploids. Bread wheat for example is an hexaploid, whose genome is an hybrid combining the genome of three diploid progenitors, the A, B and D genomes.  The A and B genomes merged ~ half million years ago forming tetraploid wheat (e.g. emmer and durum wheat, genome AABB).  Hexaploid bread wheat (genome AABBDD) was formed only ~9000 years ago as a result of hybridization of the AABB tetraploid with the diploid DD genome of wheat. 
Polyploidization can occur overnight, for example through inter-specific hybridization followed by genome doubling via unreduced gametes. It is thus one of the most efficient and rapid ways to generate a new species and is a driving force in plant genome evolution.  If hybridization and polyploidization that provide heterosis and plasticity are such handy way to rapidly evolve, why aren’t all species hybrids or polyploids?  Why do these species go through a process of diploidization (elimination of some duplicated genes and genetic behavior of diploids) soon after they are formed?
We are asking what are the pros and cons of hybridity and polyploidy in evolution, studying a complex organism such as wheat (in collaboration with Prof. Moshe Feldman) and a simpler unicellular system, budding yeast (in collaboration with Naama Barkai).  We showed that side by side with growth vigor, hybrids also show signs of incompatibility:  In wheat, we showed that major genetic and epigenetic modifications occur in the newly formed hybrid and polyploid as well as potentially deleterious reactivation of silent transposons.  In yeast we showed that an heterotic hybrid between Saccharomyces cerevisiae and Saccharomyces paradoxus undergoes a major rewiring of gene expression as a result of new cis-trans interactions and we performed a genetic screen to identify genes and underlying principles of heterosis.  The rapid growth of yeast seems to be at the expense of cell cycle checkpoints that contribute to genome integrity and at the expense of defense mechanisms with increased respiration in the hybrid at the expense of ethanol production through fermentation. 
Wheat biodiversity
We are studying wheat biodiversity.  Our interest in this topic is multi-faceted:  We are interested to understand the mechanisms that are responsible for biodiversity in the wheat group in wild population as well as among domesticated lines. We are interested in the relation between genetic and epigenetic diversity and adaptation, the type of genetic variation that was selected in the process of wheat domestication, devising strategies for wheat conservation, namely in situ and ex situ conservation in wild wheat and wheat landraces.  Finally we are interested to exploit this diversity for the improvement of wheat yield and quality.  Recently we have completed a collection, in collaboration with Tel Aviv University, of a wheat population that has been studied for the past 30 years.  Genotyping of this population will provide a unique insight into the dynamics of the genetic makeup of a wild population in situ and into possible adaptive value of this genetic variation.