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Qu, J., E. Hodges, A. Molaro, P. Gagneux, M. D. Dean, G. J. Hannon, A. D. Smith. In Press. Evolutionary expansion of DNA hypomethylation in the mammalian germline genome. Genome Research. PDF
(This paper develops a much-needed model to understand evolutionary patterns of methylation divergence, taking into the account the dependence among sites and lineages. We show that over time, mammalian sperm has evolved more hypomethylation. In primates, this occurs by expansion of existing hypomethylated regions, while birth of novel hypomethylated regions is much more common in rodents.)

Lough-Stevens, M., N. G. Schultz, M. D. Dean. In Press. The baubellum is more developmentally and evolutionarily labile than the baculum. Ecology and Evolution. PDF
(Note: Michael Lough-Stevens and Nick Schultz were graduate students during this project. Our main objective was to test if and how the baubellum (a bone in the clitoris of many mammal species) correlates with the baculum (a bone in the penis). Although most species with a baculum also have a baubellum, our study uncovered multiple lines of evidence that suggest the baubellum is relatively non-functional and free to accumulate evolutionary and developmental "noise" compared to the baculum.

Chang, P. L., E. Kopania, S. Keeble, B. Sarver, E. Larson, A. Orth, K. Belkhir, P. Boursot, F. Bonhomme, J. M. Good, M. D. Dean. 2017. Whole exome sequencing of wild-derived inbred strains of mice improves power to link phenotype and genotype. Mammalian Genome 28: 416–425. PDF
(Note: Emily Kopania and Sara Keeble were graduate student in the Dean Lab during this project. We present exomes of a set of mouse strains that harbors significantly more variation than existing strains, and demonstrate they could significantly improve power of genetic studies.)
(Featured on the cover of Mammalian Genome)

Decato, B., J. Tello, A. Sferruzzi-Perri, A. D. Smith, and M. D. Dean. 2017. DNA methylation divergence and tissue specialization in the developing mouse placenta. Molecular Biology and Evolution 34: 1702-1712. PDF
(Placental biology is an important aspect of evolutionary conflict between males and females – in short, males gain by imprinting their offspring to take more resources from the mother, while females gain by moderating such effects. We discovered that methylation in the placenta varies by age, sex, and tissue layer in the placenta, all of which may influence that outcomes of this conflict, and likely contribute to overall reproductive health. Interestingly, the placenta methylome shares some similarity with cancer cell methylomes, which may lead to a deeper understanding of invasive growth phenotypes in general.)

Sarver, B., S. Keeble, T. Cosart, P. Tucker, M. D. Dean, and J. M. Good. 2017. Phylogenomic insights into genome evolution and speciation in mice. Genome Biology and Evolution 9: 726-739. PDF
(Note: Sara Keeble is a graduate student in the Dean Lab. In this study, we developed a novel method to map genetic data to different species, by iteratively building "pseudoreference" genomes, which effectively control mapping biases. In the process, we resolved some deeper evolutionary relationships among mouse species.)

Schultz, N. G., E. Otárola-Castillo, and M. D. Dean. 2017. Dissection, microCT scanning, and morphometric analyses of the baculum. Journal of Visualized Experiments 55342. PDF Video
(Nick Schultz was a graduate student during this project. This is a "methods" paper that describes in detail a novel morphometrics pipeline we developed to define semi-landmarks to enable morphometrics analyses.)

Larson, E. L., S. Keeble, D. Vanderpool, M. D. Dean, J. M. Good. 2016. The composite regulatory basis of the large X-effect in mouse speciation. Molecular Biology and Evolution 34: 282-295. PDF
(Sara Keeble was a graduate student during this project. The X chromosome has a huge impact on the evolution of reproductive isolation - i.e., speciation. In this paper, we isolate cells at different stages of spermatogenesis, and show that genes on the X chromosome are significantly mis-regulated in mice that are hybrids between two different species).

Schneider, M., R. Mangels, and M. D. Dean. 2016. The molecular basis and reproductive function(s) of copulatory plugs. Molecular Reproduction and Development 83: 755-767. PDF
(Rachel Mangels was a graduate student during this project. We review what is known about the molecular basis of copulatory plug formation, and assess various hypotheses about its function. Although copulatory plugs are ubiquitous in the animal kingdom [even some primates make them], they probably function in different [and multiple] contexts across different species.)

Mangels, R., K. Tsung, K. Kwan, and M. D. Dean. 2016. Copulatory plugs inhibit the reproductive success of rival males. Journal of Evolutionary Biology 29: 2289-2296. PDF
(Rachel Mangels and Kelly Kwan were graduate students, and Kathleen Tsung was a technician, in the Dean Lab. By comparing a genetically engineered mouse that is incapable of forming a plug to its wild type brothers, we showed if first males to mate with a female can form a plug, they prevent nearly all reproductive success of second males to mate. The strength of this effect was puzzling, since in nature we see evidence of multiple paternity - we discuss several possible hypotheses.)

Larson, E. L., D. Vanderpool, S. Keeble, M. Zhou, B. A. J. Sarver, A. D. Smith, M. D. Dean, and J. M. Good. 2016. Contrasting levels of molecular evolution on the mouse X chromosome. Genetics 203: 1841-1857. PDF
(This was a joint project between the Dean, Good, and Smith Labs. Sara Keeble is a grad student in the Dean Lab. We confirmed previous finding that protein-coding changes accumulate more rapidly on the X chromosome compared to autosomes, but the pattern reverses for genes expressed late in spermatogenesis and for methylation divergence. We could only discover this by isolating cells at different stages of spermatogenesis, and our work demonstrates a previously unappreciated heterogeneity in the rates of molecular evolution)

Crisci, J. L., M. D. Dean, and P. Ralph. 2016. Adaptation in isolated populations: when does it happen and when can we tell? Molecular Ecology 25: 3901-3911. PDF
(Jessica Crisci was a joint postdoc in the Dean and Ralph Labs. This paper shows that identifying genomic targets of selection, even when we know selection has occurred, will be difficult in small isolated populations. We place the results in the context of island colonization events; athough they provide many of the most exciting examples of adaptation, we might not be able to find genomic targets of selection).

Schultz, N. G., M. Lough-Stevens, E. Abreu, T. Orr, and M. D. Dean. 2016. The baculum was gained and lost multiple times during mammalian evolution. Integrative and Comparative Biology icw034. PDF
(Nick Schultz and Michael Lough-Stevens are graduate students in the lab. Eric Abreu came through the lab as a high schooler [now at Harvard] and helped with the project. This paper demonstrates that the baculum was gained and lost multiple times during mammalian evolution, helping resolve ongoing debate about its function.)
(Featured in The Washington Post and Forbes Science)

Schultz, N. G., J. Ingels, A. Hillhouse, K. Wardwell, P. L. Chang, J. M. Cheverud, C. Lutz, L. Lu, R. W. Williams, and M. D. Dean. 2016. The genetic basis of baculum size and shape variation in mice. Genes | Genomes | Genetics 6:1141-1151 PDF
(Nick Schultz is a graduate student in the lab. This paper characterizes the genetic basis of baculum variation, showing that independent genomic regions affect size and shape.)
(Featured on USC website)

Young, B. W. and M. D. Dean. 2015. To be, or not to be, related; how female guppies bias sperm usage. Molecular Ecology 24: 4039-4041. PDF
(Note: Brent Young is our lab manager. This paper is a perspective of Gasparini et al. and attempts to reconcile the seemingly equal number of studies that show dissortative vs. assortative MHC-based mate choice. In short, we think fluctuating selection might switch between the two forms of mate choice.)

Dines, J. P., S. L. Mesnick, K. Ralls, L. May Collado, I. Agnarsson, and M. D. Dean. 2015. A tradeoff between precopulatory and postcopulatory trait investment in male cetaceans. Evolution 69: 1560-1572. PDF (supplemental)
(Note: Jim Dines was a graduate student in the lab. In some whale species, the males develop obnoxiously large phenotypes thought to be important in fighting. We show that these same species invest disproportionately less in testis mass.)
(Featured on KPCC podcast)

Mangels, R., B. Young, S. Keeble, R. Ardekani, C. Meslin, Z. Ferreira, N. L. Clark, J. M. Good, and M. D. Dean. 2015. Genetic and phenotypic influences on copulatory plug survival in mice. Heredity 15: 496-502. PDF (supplemental)
(Note: Rachel Mangels and Sara Keeble are grad students in the lab; B. Young is our lab manager.)
(Featured on Heredity podcast)

Dines, J. P., E. Otárola-Castillo, P. Ralph, J. Alas, T. Daley, A. D. Smith, and M. D. Dean. 2014. Sexual selection targets cetacean pelvic bones. Evolution 68: 3296-3306. PDF (supplemental)
(Note: Jim Dines was a grad student working in the lab during this project; Jesse Alas was a local high school student from West Adams working in the lab [now at UC Irvine])
(Featured in the popular press: Science, National Geographic, Washington Post, Smithsonian Magazine, Discovery Magazine, Time, USC news, and many more)

Kessler, M. and M. D. Dean. 2014. Effective population size does not predict codon usage bias in mammals. Ecology and Evolution 4: 3887-3900. PDF (supplemental)
(Note: Michael Kessler was a USC undergrad working in the lab during this project)

Young, B., D. V. Conti, and M. D. Dean 2013. Sneaker "jack" males outcompete dominant "hooknose" males under sperm competition in Chinook salmon (Oncorhynchus tshawytscha). Ecology and Evolution (Cover of Journal) 3: 4987-4997. PDF (supplemental) (featured on cover)

Dean, M. D. 2013. Genetic disruption of the copulatory plug in mice leads to severely reduced fertility. PLoS Genetics 9:e1003185. PDF

Fang, F., E. Hodges, A. Molaro, M. D. Dean, G. J. Hannon, and A. Smith. 2012. The genomic landscape of human allele-specific DNA methylation. Proceedings of the National Academy of Sciences 109: 7332-7337. PDF

Campbell, P. J. M. Good, M. D. Dean, P. K. Tucker, and M. W. Nachman. 2012. The contribution of the Y chromosome to hybrid male sterility in house mice. Genetics 191: 1271-1281. PDF.

Dean, M. D., G. D. Findlay, M. R. Hoopmann, C. C. Wu, M. J. MacCoss, W. J. Swanson, and M. W. Nachman. 2011. Identification of ejaculated proteins in the house mouse (Mus domesticus) via isotopic labeling. BMC Genomics 12: 306. PDF

Good, J. M., T. Giger, M. D. Dean, and M. W. Nachman. 2010. Widespread over-expression of the X chromosome in sterile F1 hybrid mice. PLoS Genetics 6: e1001148. PDF

Dean, M. D., N. L. Clark, G. D. Findlay, R. C. Karn, W. J. Swanson, X. Yi, M. MacCoss, and M. W. Nachman. 2009. Proteomics and comparative genomic investigations reveal heterogeneity in evolutionary rate of male reproductive proteins in mice (Mus domesticus). Molecular Biology and Evolution 26: 1733-1743. PDF

Dean, M. D. and M. W. Nachman. 2009. Faster fertilization rate in conspecific versus heterospecific matings in house mice. Evolution 63: 20-28. PDF

Good, J. M., M. D. Dean, and M. W. Nachman. 2008. A complex genetic basis to X-linked hybrid male sterility between two species of house mice. Genetics 179:2213-2228. PDF

Dean, M. D., J. M. Good, and M. W. Nachman. 2008. Adaptive evolution of proteins secreted during sperm maturation: an analysis of the mouse epididymal transcriptome. Molecular Biology and Evolution 25:383-392. PDF

Laurie, C.C, D.A. Nickerson, A. Anderson, B.S. Weir, R.J. Livingston, M. D. Dean, K.L. Smith, E.E. Schadt, and M.W. Nachman. 2007. Linkage disequilibrium in wild mice. PLoS Genetics 3: e144. PDF

Dean, M. D., K. G. Ardlie, and M. W. Nachman. 2006. The frequency of multiple paternity suggests that sperm competition is common in house mice (Mus domesticus). Molecular Ecology 15: 4141-4151. PDF

Dean, M. D. 2006. A Wolbachia-associated fitness benefit depends on genetic background in Drosophila simulans. Proceedings of the Royal Society of London series B-Biological Sciences 273: 1415-1420. PDF

Dean, M. D. and J. W. O. Ballard. 2005. High divergence among Drosophila simulans mitochondrial haplogroups arose in midst of long term purifying selection. Molecular Phylogenetics and Evolution 36: 328-337. PDF

Dean, M. D. and J. W. O. Ballard. 2004. Linking phylogenetics with population genetics to reconstruct the geographic origin of a species. Molecular Phylogenetics and Evolution 32: 998-1009. PDF

Dean, M. D., K. J. Ballard, A. Glass, and J. W. O. Ballard. 2003. Influence of two Wolbachia strains on population structure of east African Drosophila simulans. Genetics 165: 1959-1969. PDF

James, A. C., M. D. Dean, M. E. McMahon, and J. W. O. Ballard. 2002. Dynamics of double and single Wolbachia infections in Drosophila simulans from New Caledonia. Heredity 88: 182-189. PDF

Ballard, J. W. O. and M. D. Dean. 2001. The mitochondrial genome: mutation, selection and recombination. Current Opinion in Genetics and Development 11: 667-672. PDF

Dean, M. D. and J. W. O. Ballard. 2000. Factors affecting mitochondrial DNA quality from museum preserved Drosophila simulans. Entomologia Experimentalis et Applicata 98: 279-283. PDF

(this page last updated December 15 2017)