Names followed by superscript PD, GS, UG, HS, or TC indicate co-authors that were members of the Dean Lab as postdocs, graduate students, undergraduates, high schoolers, or technicians, respectively
Yang, Y.UG, M. BragaUG, and M. D. Dean. 2024. Insertion-deletions are depleted in protein regions with predicted secondary structure. Genome Biology and Evolution 16: evae093. PDF (While much theory has been developed to understand the selective effects of single nucleotide mutations, much less is known about insertion-deletion events (indels), which occur when stretches of one or more bases are inserted or deleted from protein coding regions. Here we take an empirical approach, combining the recent advances of the AlphaFold Revolution with evolutionary inferences. We show that indels are depleted over areas of proteins that are predicted to form secondary structure. The inference if indels arise over secondary structure, they are more likely to disrupt protein function, and are therefore selected against.)
Lough-Stevens, M.GS, C. GhioneGS and M. D. Dean. In Press. The lifespan of corpora lutea in non-pregnant females is positively correlated with gestation length. Journal of Mammalogy. PDF
(Female mammals invest heavily in their offspring. One of the key triggers that initiates and sustains a pregnancy is hormonal signaling by the corpus luteum, an endocrine organ that forms on ovaries. Why do females retain an active corpus luteum even when they are not pregnant? Using a comparative approach, we show that the lifespan of corpora lutea in non-pregnant females is simply correlated with the gestation length of those species. In other words, in species with long gestation times, non-pregnant females retain corpora lutea for longer (and vice versa). This paper suggest that this strange phenomenon (non-pregnant females with active corpora lutea) is simply a constraint of mammalian pregnancy.
Mullis, M. N., C. GhioneGS, M. Lough-StevensGS, I. Goldstein, T. Matsui, S. F. Levy, M. D. Dean, I. M. Ehrenreich. 2022. Complex genetics cause and constrain fungal persistence in different parts of the mammalian body. Genetics 222: iyac138. PDF
(We identified loci that influence a yeast’s ability to infect a mammal. One of the more interesting findings was that yeast genotypes that were good at persisting in the mammalian brain were bad at persisting in non-brain tissues, and vice versa, suggesting a tradeoff in a yeast’s ability to infect particular tissues. Many more questions to follow.)
Keeble, S.GS, R. C. Firman, B. A. J. Sarver, N. L. Clark, L. W. Simmons, and M. D. Dean. 2021. Evolutionary, proteomic, and experimental investigations suggest the extracellular matrix of cumulus cells mediates fertilization outcomes. Biology of Reproduction ioab082. PDF
(We identified several abundant, rapidly evolving proteins from the extracellular matrix of cumulus cells – the layer of cells that surround the ovum – that have been shown to stabilize hyaluronic acid. In a separate experiment, we showed that the cumulus layer breaks down more slowly when derived from female mice raised in the presence of multiple males. We propose these are molecular mechanisms by which females modulate fertilization outcomes.)
Lough-Stevens, M. J.GS, C. GhioneGS, M. UrnessUG, A. HobbsUG, C. SweeneyUG, M. D. Dean. 2021. Male-derived copulatory plugs enhance implantation success in Mus musculus. Biology of Reproduction 104: 684-694. PDF
(We show that male-derived copulatory plugs influence the probability that females will be receptive to implantation four days after mating. We hypothesize that copulatory plugs contribute to some threshold level of stimulation required for females to enter this physiological state.)
Adams, N. E., M. D. Dean, and G. B. Pauly. 2018. Morphological divergence among populations of Xantusia riversiana, a Night Lizard endemic to the Channel Islands of California. Copeia 106: 550-562. PDF
(This paper originated during BISC499, Hands-on Research at the Natural History Museum. In collaboration with Greg Pauly, curator at the LA County Natural History Museum, and Nicole Adams, a student enrolled in the course, we showed that sex and island contribute to morphometric variation in the body plan of these extremely closely related lizards.)
Larson, E. D. Vanderpool, B. Sarver, C. Callahan, S. KeebleGS, L. ProvencioGS, M. KesslerUG, V. Stewart, E. Nordquist, M. D. Dean, J. Good. 2018. The evolution of polymorphic hybrid incompatibilities in house mice. Genetics 209: 845-859. PDF
(This paper explores incompatibility between two different species of house mice. Our specific role was to test whether the sperm of hybrid males “drive”, meaning sperm with one allele is preferentially transmitted compared to sperm carrying the other allele. We developed powerful methods drive, including high throughput sequencing from motile vs. immotille sperm to test for the preferential transmission of certain alleles.)
(This paper won the Editors’ Choice Award for an outstanding Population Genetics article published in Genetics in 2018)
Lough-StevensGS, M., N. G. SchultzGS, and M. D. Dean. 2018. The baubellum is more developmentally and evolutionarily labile than the baculum. Ecology and Evolution 8:1073–1083. PDF
(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.
Qu, J., E. Hodges, A. Molaro, P. Gagneux, M. D. Dean, G. J. Hannon, and A. D. Smith. 2017. Evolutionary expansion of DNA hypomethylation in the mammalian germline genome. Genome Research 28: 1-14. 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. In rodents, the evolution of methylation is dominated by birth of novel hypomethylated regions.)
Chang, P. L., E. KopaniaUG, S. KeebleGS, B. Sarver, E. Larson, A. Orth, K. Belkhir, P. Boursot, F. Bonhomme, J. M. Good, and 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
(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. KeebleGS, 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
(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.GS, E. Otárola-Castillo, and M. D. Dean. 2017. Dissection, microCT scanning, and morphometric analyses of the baculum. Journal of Visualized Experiments 55342. PDF Video
(This is a “methods” paper that details a novel morphometrics pipeline that defines semi-landmarks for morphometric analyses.)
Larson, E. L., S. KeebleGS, D. Vanderpool, M. D. Dean, and J. M. Good. 2016. The composite regulatory basis of the large X-effect in mouse speciation. Molecular Biology and Evolution 34: 282-295. PDF
(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. MangelsGS, and M. D. Dean. 2016. The molecular basis and reproductive function(s) of copulatory plugs. Molecular Reproduction and Development 83: 755-767. PDF
(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.GS, K. TsungUG, K. KwanGS, and M. D. Dean. 2016. Copulatory plugs inhibit the reproductive success of rival males. Journal of Evolutionary Biology 29: 2289-2296. PDF
(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. KeebleGS, 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
(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.PD, 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
(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.GS, M. Lough-StevensGS, E. AbreuHS, T. Orr, and M. D. Dean. 2016. The baculum was gained and lost multiple times during mammalian evolution. Integrative and Comparative Biology icw034. PDF
(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.GS, 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
(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.TC and M. D. Dean. 2015. To be, or not to be, related; how female guppies bias sperm usage. Molecular Ecology 24: 4039-4041. PDF
(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.GS, 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
(In some whale species, the males develop disproportionately 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.GS, B. YoungTC, S. KeebleGS, 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
(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.GS, E. Otárola-Castillo, P. Ralph, J. AlasHS, T. Daley, A. D. Smith, and M.
D. Dean. 2014. Sexual selection targets cetacean pelvic bones. Evolution 68: 3296-3306. PDF
(In this paper, we demonstrate that far from being “useless” structures, whale pelvic bones respond to sexual selection. Specifically, they are larger and more divergent in shape among species inferred to experience relatively strong sexual selection. This pattern is likely driven by the fact that whale pelvic bones serve as attachment sites to muscles that control the penis.
(Featured in the popular press: Science, National Geographic, Washington Post, Smithsonian Magazine, Discovery Magazine, Time, USC news, and many more)
Kessler, M.UG and M. D. Dean. 2014. Effective population size does not predict codon usage bias in mammals. Ecology and Evolution 4: 3887-3900. PDF
(It was long assumed that codon usage bias was the subject of weak selection, and that variation in codon usage bias was simply a reflection of a species’ effective population size [and thus the efficacy of weak selection]. In this paper, we show that even though selection shapes codon usage bias across mammals, variation does not correlate with effective population size, calling into question this the often cited interpretation of weak selection.)
Young, B.TC, 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 (featured on cover)
(Both theoretical and emprical evidence suggests that males subject to consistent sperm competition will invest disproportionately in sperm production, presumably to out-compete rival males. Here we show that in addition, such males invest not only in more sperm, but in higher quality sperm.)
Dean, M. D. 2013. Genetic disruption of the copulatory plug in mice leads to severely reduced fertility. PLoS Genetics 9:e1003185. PDF
(In this paper, we demonstrate that transglutaminase IV is necessary for males to produce a copulatory plug. Males where this gene is knocked out fail to produce a plug. In spite of their normal morphology, these males have a difficult time getting females pregnant, and this has led to a diversity of novel research directions in the lab.)
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
Public service announcement:
If you are interested in the types of papers listed above, there is a good chance you are interested in majoring in the “Ecology, Evolution, and Environment” emphasis, here. I am the leader of that emphasis… please feel free to contact me if you have questions (matthew.dean@usc.edu).
You are also likely to be interested in interacting with the Center for Ecological and Evolutionary Dynamics, here. I am the co-director of that center… please feel free to contact me if you have questions (matthew.dean@usc.edu).
(this page last updated Jan. 23 2024)