Crossover rate is known to vary at broad scales in all species, typically being low in pericentromeric regions. In yeast and mammals, fine-scale crossover rate heterogeneity has also been thoroughly documented, with very fine "hotspots" of high recombination interspersed amidst regions of much lower recombination rate. Based primarily on research on intragenic crossing over within the rosy gene and patterns of linkage disequilibrium (rapidly decaying), many had assumed that Drosophila do not bear such fine-scale crossover rate heterogeneity. As such, investigations of recombination rate's association with polymorphism, divergence, or codon bias frequently used "smoothed" estimates of recombination rate.
In 2006, rotation student in our laboratory investigated a 2-megabase region on the XL chromosome of Drosophila pseudoobscura to look for evidence of fine-scale crossover rate heterogeneity. She found that there was significant heterogeneity (>30-fold between hottest and coldest regions), this heterogeneity was significantly associated with (CA/GT)n repeats, and this heterogeneity was significantly associated with differences in codon bias among genes within these intervals (see abstract1). Followup work by another rotation student documented similar patterns on the XR chromosome.
More recently, we examined fine-scale crossover rate heterogeneity across all of the Drosophila pseudoobscura second chromosome using 454 genome sequences (for SNP discovery) and microbead arrays (for genotyping)(see abstract2) Very similar results were obtained for D. persimilis (see abstract3), generally also showing a very high correlation in crossover rate between these two species.
We are currently examining the extent of recombination rate variation and its evolutionary correlates across multiple strains of D. pseudoobscura, and also in outgroup species D. miranda to see if the same recombinational "hotspots" persist between species. This research involves extensive computational analysis of next-generation sequencing via the illumina platform. Additionally, we are pursuing related work examining factors that affect recombination, including one gene that is also associated with cancer in humans. This work is ongoing.
Genomic patterns of nucleotide diversity and divergence
One of the most influential findings in molecular evolutionary genetics has been the repeated association of crossover rate with 
nucleotide diversity within species. An elegant report of this association in Drosophila was published in 1992 by Begun and Aquadro, and they explained this pattern as resulting from the ubiquitous action of natural selection. Part of this interpretation came from the lack of a similar association between crossover rate with divergence between species. However, studies of humans/ chimpanzee and other taxa have observed an association between crossover rate and divergence between species, suggesting possible mutational (rather than, or in addition to, selective) explanations.
Using our estimates of fine-scale crossover rate and analyses of 454 whole-genome sequences that we have generated, we are examining this association in the Drosophila pseudoobscura species group. In our first study of this, we found that crossover rate is strongly correlated with both nucleotide diversity within species and divergence between species, but that this relationship is only detectable when using fine-scale crossover rate rather than estimates of crossover rate from more distantly spaced markers. This explains why such a relationship was not detected in this species group previously, and may also explain some of the differences between species (see abstract).
We are now using far more extensive & complete illumina resequencing of many strains of D. pseudoobscura, D. miranda, and further outgroup species D. lowei to examine the association of recombination rate and both nucleotide diversity within species & divergence between species. Importantly, with our extensive linkage maps within and between species, we can focus on regions where crossover rate is conserved vs. divergent in these analyses. This research will inform us on the evolutionary forces acting to shape patterns of genomic DNA variation. This work is in progress.
Related research using genomic approaches to understand these and other evolutionary forces are continuing in the lab in both Drosophila and other systems (e.g., Saccharomyces).
Fine-mapping the genetic architecture of hybrid male sterility
One of the most fundamental problems in evolutionary genetics is why certain genes function 
normally within species (producing fertility) but fail to function in a hybrid genetic background (resulting in hybrid sterility). Further, why should the XY sex consistently evolve hybrid sterility earlier in divergence than the XX sex, a pattern called Haldane's Rule? Drosophila pseudoobscura and D. persimilis were among the first species studied to understand the genetic basis of hybrid male sterility and its evolutionary underpinnings, with work dating back to the early 1930's.
Resolving these questions requires the isolation of genes contributing to hybrid sterility and examination of their individual effects as well as their interactions with other genes. We have mapped multiple factors contributing to hybrid male sterility between D. persimilis and D. pseudoobscura bogotana in a recent study. More recently, we built on this work in several respects. First, we examined the individual and combinatorial effects of these alleles, and we have found that the dominance of the effects of these alleles is affected by alleles at other loci (see study). Second, we evaluated whether there is variation within species for these alleles, such that certain alleles from D. persimilis at a particular locus may cause sterility in a D. pseudoobscura bogotana genetic background while other alleles from D. persimilis may not (see study2).
Presently, we are studying the role of meiotic drive within species on sterility in species hybrids. Specifically, we are leveraging the driving "sex-ratio" arrangement in D. persimilis to see whether the factors causing drive also confer hybrid sterility. This research contrasts other studies, which have observed drive in hybrids and inferred an evolutionary history of drive (see review in this reference).
Genetics of Megasela scalaris
Our lab is diversifying by developing a new "model system" for addressing interesting evolutionary genetic questions: the scuttle fly, Megasela scalaris. This species offers many interesting facets: for example, it bears homomorphic sex chromosomes, and sex is determined by a male-determining region that actually transposes among chromosomes at a low, but detectable, rate. This system offers the opportunity to examine a putatively "early" stage in sex-determination, allowing one to investigate both the mechanics of sex-determination as well as various related questions such as dosage compensation, the suppression of recombination around sex-determining regions, sexually antagonistic selection, etc.
We have already obtained a low-coverage genome sequence from this species, allowing us already to document repetitive elements, develop variable molecular markers, and even assemble the full mitochondrial genome sequence (see study). We are now in the process of obtaining complete, high-coverage genome sequences from males and females to isolate the region(s) distinguishing the sexes and begin deeper investigation into the genetic and evolutionary questions.
Significantly, Megaselia scalaris is both cosmopolitan and a "pest" species, being associated with myiasis and other infections of humans, as well as having potential forensic entomological applications. We anticipate incidental benefits to society from explorations of this interesting biological system.
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