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In the broadest sense, the Dean Lab studies evolutionary biology.  More specifically, we are interested in sexual selection, and how males and females adapt to increase their own reproductive fitness.  We integrate three methodological approaches - molecular, computational, and experimental. We study a huge diversity of topics; a small subset is discussed below.

Functional genetics of male reproduction using wild mice as a model system

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Using wild, wild-derived, and knockout strains of mice, we are testing hypotheses about how male reproductive phenotypes vary within and between species.  One example of a question we are asking is whether reproductive genes evolves rapidly along lineages leading to species with high levels of promiscuity, which is predicted by sexual selection theory.  (Supported by grant #1R01GM098536-01A1 from the National Institutes of Health. People involved: Matt Dean, Jeff Good (U. Montana), Jessica Crisci, Rachel Mangels, Lorraine Provencio, Nick Schultz). 

Understanding the function of the copulatory plug

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In many species, a huge proportion of the male’s seminal fluid coagulates in the female’s reproductive tract to form what has been termed a copulatory plug (marked by the asterisk in the left panel).  We have recently established a knockout mouse that cannot form a copulatory plug, offering unprecedented power to characterize its function(s).  (Supported by a Career Award #1150259 from the National Science Foundation. People involved: Matt Dean, Kelly Kwan, Rachel Mangels, Kathleen Tsung). 

The interplay of effective population size and sexual selection

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We have recently shown that sexual selection theory cannot be rigorously tested without incoporating knowledge of a species’ effective population size.  For example, we might predict that positive selection on reproductive genes is strongest in species experiencing relatively intense sexual selection, but a species’ effective population size will place limits on the strength of selection to which it can respond.  We are incorporating effective population size in our tests of sexual selection theory across different species of mice.  (Supported by grant #1146525 from the National Science Foundation. People involved: Matt Dean, Jessica Crisci, Michael Kessler, Ryan McGee).

Do whale pelvic bones evolve in response to sexual selection?

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Cetacean pelvic bones (one shown to the right of the red asterisk) represent one of the most remarkable examples of morphological reduction in evolutionary biology.  But far from being useless vestigial structures, the pelvic bones serve as attachment sites for the muscles that control the penis.  Using some fairly intense morphometric analytical tools (thanks to Erik Otarola-Castillo), we are discovering that pelvic bones evolve in response to the strength of sexual selection in a species’ mating ecology.  (People involved: Matt Dean, Jim Dines).

Quantitative genetics of genital shapes

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Many mammals possess a bone in their penis, called a baculum. For hundreds of years, these bones have been studied as taxonomic characters. We have developed novel morphometric techniques and coupled them with powerful quantitative genetic methodology to find the genes involved in baculum shape variation. Ultimately, we want to understand the evolutionary processes that drive divergence in genital shape (People involved: Matt Dean, Jim Dines, Nick Schultz).

Alternative mating strategies in salmon

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Pacific salmon offer an interesting comparative model because they are external fertilizers.  In spite of the fact that male seminal fluid does not interact with the female reproductive tract (as it does in mammals), we are discovering that females can still “choose” which sperm fertilize their eggs, and they have a tendency to choose sperm from sneaker males (the bottom fish in the above image is a sneaker male, while the top fish is a hooknosed male).  We are currently exploring the molecular mechanisms that underlie this female choice.  (People involved: Matt Dean, Brent Young).

Other projects

The wealth of publicly available data, coupled with bioinformatic skills, allows us to investigate lots of “side projects” revolving around evolutionary biology.  Here we highlight three:

1) The relationship between codon usage bias and effective population size. It has long been suggested that the degree of codon usage bias varies with a species’ effective population size. By analyzing 41 mammalian genomes, we have discovered that this explanation fails to account for variation in codon usage bias, begging for a new hypothesis. (People involved: Matt Dean, Michael Kessler).

2) Adaptive evolution is concentrated on facultative exons. We hypothesized that adaptive evolution should be concentrated on facultative exons, which are not included in every transcript and therefore subject to fewer evolutionary constraints (at least in theory).  We have shown that this pattern is strong, although care must be taken to avoid mis-alignment and false positives when dealing with facultative exons.  (People involved: Matt Dean, Ryan McGee).    

3) Adaptation to urban environments. Mouse populations live side-by-side with humans, often in polluted environments.  We are comparing the genomes of “city mice” and “country mice” to try and understand regions of the genome that may allow mice to adapt to urban settings. We are also studying populations that have seemingly diverged in their circadian rhythms. (People involved: Matt Dean, Eric Abreu, Anna Burger, Max Cabaj). 

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(this page last updated April 3 2014)