1) Evolution of young sex chromosomes

We study the evolution of young sex chromosomes in the tropical fruit crop, papaya (Carica papaya).  We use a population genomic approach to address fundamental questions in sex chromosome evolution.  By analyzing the levels and patterns of genetic diversity within and among sex-linked loci, we hope to decipher the evolutionary forces (e.g. positive and negative selection, genetic drift) that are affecting the diversification of sex chromosomes within papaya, as well as between dioecious members of the Caricaceae family.  Interestingly, we have evidence that X-

 

2) Morphological and genetic diversity of natural papaya populations

In addition to understanding the evolution of sex chromosomes in papaya, we are also interested in understanding how morphological and genetic diversity is structured in natural populations of papaya.  In collaboration with Dr. Oscar Rocha (Kent State University), we have studied vegetative and reproductive morphological variation and genetic variation from over 200 naturally occurring papaya growing throughout the lowlands of Costa Rica.  We found significant 

3) Evolution of recent gene duplicates

Gene duplication and diversification play a crucial role in the evolution of morphological diversity.  Our lab is particularly interested in the early events following gene duplication.  We seek to understand what determines the fate of a newly duplicated gene in a population: selection or drift?  To this end, we have analyzed the functional diversification and population genetics of recent gene duplicates in Arabidopsis thaliana.  These genes show less than 5% sequence divergence and are predicted to have duplicated in the A. thaliana lineage.  Interestingly, we find that functional redundancy is the exception, not the rule, for recent unlinked gene duplicates, as most have divergent gene expression patterns and exhibit the hallmarks of relaxed functional constraint and even positive selection.  We are currently interested in expanding our study to include linked, or tandem duplicate genes.  We are also interesting in investigating the evolutionary cost of gene duplication.  

linked genes involved in male development have experienced recent selective sweeps.  In contrast, we find evidence of elevated diversity on the Y, perhaps indicative of population structure on the Y.  We are currently expanding our study to include loci that span the MSY.

This work is funded by a grant from the NSF Plant Genome program, in conjunction with collaborators Ray Ming (University of Illinois), Qingyi Yu (Texas A&M), and Paul Moore (Hawaiian Agricultural Research Center).

morphological variation among papaya growing in various regions of Costa Rica, and this variation is associated with underlying genetic structure of these populations.  We have also found evidence of recent population expansion of Costa Rican papaya, which we hypothesize is due to the agronomical transformation of the landscape and with the reversion of deserted fields to pasture.  We are currently interested in expanding this study to include regions outside of Costa Rica, in particular in Southern Mexico, which is the purported domestication center of papaya.

4) Genome Evolution

Our lab is generally interested in understanding the evolution of genes and genomes and as such we have studied various aspects of genome evolution. For example, in collaboration with Dr. Mark Ungerer (Kansas State University), we have investigated the genomic fate of Ty3/gypsy-like retroelements in homoploid hybrids of sunflower (Helianthus deserticola and H. paradoxus).  Using fluorescence in situ hybridization, we found that proliferation of retroelements were confined mainly to the pericentromeric regions, suggesting negative selection on insertions into euchromatic regions of the genomes. Other projects in genome evolution we have undertaken include understanding the distribution of local variation in Arabidopsis and the evolution of ascoviruses.