Research Interest

I am interested in how patterns of genetic variation found within populations are transformed into the diversity of traits we observe across species. As an evolutionary genomicist, I employ experimental, theoretical and bioinformatics approaches to understand the forces involved in species formation. My primary model of interest is the fruit fly. A century of amassed genetics data, an ever-expanding cache of genomics tools, and the recent availability of over a dozen sequenced genomes from congeneric species make Drosophila an exceptional system to study the processes of speciation and general population and species divergence. My current role as a postdoctoral fellow in both the McIntyre and Barbazuk labs will enable me to further develop Drosophila into a functional experimental model of speciation.

As we celebrate the sesquicentennial of Darwin's Origins, it is important to realize that much progress has only been recently made in the emerging field of speciation genomics.

Below are brief descriptions of my current research that is extending our knowledge of Darwinian processes at the level of the genome.

Drosophila Population & Comparative Genomics

Nucleotide variation provides a chronicle to past evolutionary events. Until recently, most of the variation found in natural populations was thought to be neutral, i.e., the result of stochastic processes. By sampling coding sequences from populations of either Drosophila melanogaster or D. simulans, we had shown, surprisingly, that selective forces have historically shaped much of structural differences that make each species unique (Sawyer et al.

2003). The evolution of such fixed differences can be fit to a variety of selective models including rapid directional selection, balancing selection, as well as non-additive modes of selection such as intramolecular epistasis (Kulathinal et al. 2004). With Andy Clark (Cornell University), we have recently sequenced the genomes of North American and African populations using next-generation sequencing technology in order to identify local selective signatures on a global scale. Given the unique nature of these data (e.g., partial site coverage), novel tests and methodologies have been developed to test for population differentiation and positive selection. Most importantly, this research will serve as a starting point to develop new theories and hypotheses to understand selection.

Recombination Rate, Diversity, and Natural Selection

We have recently revisited the relationship between recombination rate and nucleotide variation. In regions of low crossing over among species of the melanogaster subgroup, levels of within species nucleotide diversity correlate handedly with recombination rate. Coupled with observations that recombination rate does not correlate with levels of between species nucleotide divergence, these observations together suggest the strong effects of background selection and/or selective sweeps. However, these conclusions appear exclusive to Drosophila--this pair of relationships have not been found in other tested groups including primates, rodents, tomatoes, and maize. Recently, we tested whether fine-scale recombination rate correlates with nucleotide variation among species of the pseudoobscura subgroup, fruit flies that have diverged around 40-60 millions years from a common ancestor of D. melanogaster (Kulathinal and Hartl 2005). In collaboration with Mohamed Noor (Duke University), Illumina bead technology was used to genotype ~1200 F2 recombinants and polymorphism data was generated using 454 sequencing. Surprisingly, recombination rate correlated strongly to both diversity and divergence, in contrast to the melanogaster subgroup. We propose a two-phase recombination model of cross-over and gene conversion dependent on chromosomal location, hence, paving the way to understanding how selection acts under different genomic contexts (Kulathinal et al. 2008).

The Genomics of Speciation

The underlying genetic changes that are involved in species formation and divergence have, of course, a strong organismal component. A few years ago, we hypothesized that genomes become masculinized over time and that this "male-drive" can explain such diverse biological phenomenon as the greater sensitivity of spermatogenesis over oogenesis and the paucity of late-spermatogenic genes found on the X-chromosome as well as generalizations such as Haldane's rule and the lek paradox (Singh and Kulathinal 2005). To study the molecular basis of male-drive, we recently sequenced the final genome of the most studied speciation

system: the four-sibling species of the melanogaster complex. By generating a partial genomic sequence of Drosophila mauritiana, a complete experimental system containing a comprehensive comparative map of four introgressable species is now available. This speciation model includes D. melanogaster, hence, allowing us to wield many of the tools and resources from this important genetic model. Tools include a vast library of P-element and piggyBac transposable insertions lines, gene-specific transgenic RNAi constructs (based on GAL4/UAS and phiC31-targeted integration), dozens of microarrays (including a testis-enriched that we designed and printed), thousands of available mutants, and many methods and tools specific to Drosophila. The continuous release of fly modENCODE data and new proteomics data make this a very exciting time for using flies to understand the functional genomics of speciation.

The Evolution of Genomic Architecture

Decoding the genome has allowed us to identify functional regions of interest, particularly coding regions. Unlike the small fraction found in mammals, coding regions in Drosophila represent a significant proportion (nearly one

fifth) of the genome. By curating the dozen sequenced fly genomes, a detailed map of annotations can be connected to their phylogenetic history. Genomic patterns of gene density, exon/intron evolution, GC content, and regional rates of substitution can then be quickly visualized. While shaping the overall genome, the evolution and divergence of orthologous and paralogous gene clusters also provides a signature of past selective events in each lineage. As expected, genes involved in sex and reproduction appear to be among the most diverged, entertaining the intriguing possibility that sex-specific selection has played an important role in shaping genomic architecture (Kulathinal and Singh 2004). In addition to understanding the divergence of orthologous genes, I'm also interested in understanding how genes are formed. Using a combination of bioinformatics, genomic and molecular biology, we currently are identifying potential candidates of de novo chimeric genes (for an interesting example, see Kulathinal et al. 2004), dicistronic genes, and trans-spliced gene products. Our principle question is how these genes have originated and evolved over time.