Michael Nachman

Michael Nachman

Professor

Email: mnachman@berkeley.edu
Phone: (510) 642-1792
Lab Webpage: https://www.nachmanlab.org/

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Research Description

Research in the Nachman lab addresses a range of basic questions in population, evolutionary, and ecological genetics and genomics. Most work is on mammals with particular emphasis on house mice. We are broadly interested in the genetic basis of evolutionary change, including the genetics of adaptation and the genetic basis of speciation. For example, we are interested in uncovering signatures of selection in patterns of DNA sequence variation across the genome and in linking specific genetic changes to specific adaptive phenotypes. We are also interested in the genetic basis of reproductive isolation between populations and closely related species that hybridize in nature.  Our research utilizes a wide range of methods and approaches including field studies, genetic crosses in the laboratory, tools of molecular biology, genomics, and computational analyses of large datasets.

Selected Publications

Ballinger, M.A., K.L. Mack, S.M. Durkin, E.A. Riddell, and M.W. Nachman, 2023. Environmentally robust cis-regulatory changes underlie rapid climatic adaptation. Proc. Nat. Acad. Sci. USA.  DOI 10.1073/pnas.2214614120.

Agwamba, K.D., and M.W. Nachman, 2023.  The demographic history of house mice (Mus musculus domesticus) in eastern North America, G3 Genes, genomes, and genetics: jkac332.

Bittner, N.K.J., K.L. Mack, and M.W. Nachman, 2022. Convergent patterns of gene expression and protein evolution associated with adaptation to desert environments in rodents. Genome Biology and Evolution, 14(11) https://doi.org/10.1093/gbe/evac155

Ballinger, M.A. and M.W. Nachman, 2022. The contribution of genetic and environmental effects to Bergmann’s rule and Allen’s rule in house mice. The American Naturalist, 199: 691-704.

Banker, S.E., F. Bonhomme, and M.W. Nachman, 2022. Bidirectional introgression between Mus musculus domesticus and Mus spretus. Genome Biology and Evolution 14(1): evab288.

Beckman, E.J., F. Martins, T.A. Suzuki, K. Bi, S. Keeble, J.M. Good, A. Chavez, M.A. Ballinger, K. Agwamba, and M.W. Nachman, 2022. The genomic basis of high-elevation adaptation in wild house mice (Mus musculus domesticus) from South America.  Genetics 220(2): iyab226.

Bittner, N.K.J., K.L. Mack, and M.W. Nachman, 2021.  Gene expression plasticity and desert adaptation in house mice.  Evolution 75: 1477-1491.

Ferris, K.G., A.S. Chavez, T.A. Suzuki, E.J. Beckman, M. Phifer-Rixey, K. Bi, and M.W. Nachman, 2021.  The genomics of rapid climatic adaptation and parallel evolution in North American house mice.  PLOS Genetics (17)4: e1009495.

Suzuki, T.A., F.M. Martins, M. Phifer-Rixey, and M.W. Nachman, 2020. The gut microbiota and Bergmann’s rule in wild house mice.  Molecular Ecology 29: 2300-2311.

Suzuki, T.A.S., F.M. Martins, and M.W. Nachman, 2019. Altitudinal variation of the gut microbiota in wild house mice.  Molecular Ecology 28: 2378-2390.

Mack, K.L., M. Phifer-Rixey, B. Harr, and M.W. Nachman, 2019.  Gene expression networks across multiple tissues are associated with rates of molecular evolution in wild house mice.  Gene 10: 225.

Suzuki, T.A.S., M. Phifer-Rixey, K.L. Mack, M.J. Sheehan, T-T. Lin, K. Bi, and M.W. Nachman, 2019.  Host genetic determinants of the gut microbiota of wild mice, Molecular Ecology 28: 3197-3207.

Moeller, A.H, J.C. Gomes-Neto, S. Mantz, H. Kittana, R.R. Segura Munoz, R.J. Schmaltz, A.E. Ramer-Tait, and M.W. Nachman, 2019.  Experimental evidence for adaptation to species-specific gut microbiota in house mice.  mSphere 4: e00387-19.

Morkovsky, L., V. Janousek, J. Reif, J. Ridl, J. Paces, L. Choleva, K. Janko, M.W. Nachman, and R. Reifova, 2018. Genomic islands of differentiation in two songbird species reveal candidate genes for hybrid female sterility.  Molecular Ecology 27: 949-958.

Emerling, C.A., F. Delsuc, and M.W. Nachman, 2018.  Chitinase (CHIA) genes provide genomic footprints of a post-Cretaceous dietary radiation in placental mammals.  Science Advances 4(5): eaar6478

Phifer-Rixey, M., K. Bi, K.G. Ferris, M.J. Sheehan, D. Lin, K.L. Mack, S.M. Keeble, T.A. Suzuki, J.M. Good, and M.W. Nachman, 2018. The genomic basis of environmental adaptation in house mice. PLOS Genetics 14 (9): e1007672.

Mack, K.L., M.A. Ballinger, M. Phiofer-Rixey, and M.W. Nachman, 2018. Gene regulation underlies environmental adaptation in house mice.  Genome Research, 28: 1636-1645.

Moeller, A.H., T.A. Suzuki, M. Phifer-Rixey, and M.W. Nachman, 2018, Transmission modes of the mammalian gut microbiota.  Science 362: 453-457.

Mack, K.L., and M.W. Nachman, 2017. Gene regulation and speciation.  Trends in Genetics 33: 68-80.

Moeller, A.H., T.A. Suzuki, D. Lin, E.A. Lacey, S.K. Wasser, and M.W. Nachman, 2017. Dispersal limitation promotes the diversification of the mammalian gut microbiota.  Proc. Nat. Acad. Sci. USA 114: 13768-13773.

Mack, K.L., Campbell, P., and M.W. Nachman, 2016. Gene regulation and speciation in house mice.  Genome Research 26: 451-461.

Holmes, M.W., T.H. Hammond, G.O.U. Wogan, R.E. Walsh, K. LaBarbera, E.A. Wommack, F.M. Martins, J.C. Crawford, K.L. Mack, L.M. Bloch, and M.W. Nachman, 2016.  Natural history collections as windows on evolutionary processes.  Molecular Ecology 25: 864-881.

Sheehan, M.J., V. Lee, R. Corbett-Detig, K. Bi, R.J. Beynon, J.L. Hurst, and M.W. Nachman, 2016. Selection on coding and regulatory variation maintains individuality in major urinary protein scent marks in wild mice. PLOS Genetics 12(3): e1005891.

Suzuki, T.A., and M.W. Nachman, 2016. Spatial heterogeneity of gut microbial composition along the gastrointestinal tract in natural populations of house mice. PLOS One 11(9) e0163720.

Phifer-Rixey, M., and M.W. Nachman, 2015.  The natural history of model organisms: Insights into mammalian biology from the wild house mouse Mus musculus. eLife 4:e05959

Suzuki, T.A. and M.W. Nachman, 2015. Speciation and reduced hybrid female fertility in house mice. Evolution, 69: 2468-2481.

Campbell, P., and M.W. Nachman, 2014. X-Y interactions underlie sperm head abnormality in hybrid male house mice. Genetics 196: 1231-1240. 

Sheehan, M.J. and M.W. Nachman, 2014. Morphological and population genomic evidence that human faces have evolved to signal individual identity. Nature Communication 5: 4800. 

Carneiro, M., F.W. Albert, S. Afonso, R. J. Pereira, H. Burbano, R. Campos, J. Melo-Ferreira, J. A. Blanco-Aguiar, R. Villafuerte, M. W. Nachman, J. M. Good, and N. Ferrand, 2014. The genomic architecture of population divergence between subspecies of the European rabbit. PLOS Genetics 10(8):e1003519. 

Phifer-Rixey, M., M. Bomhoff, and M.W. Nachman, 2014. Genome-wide patterns of differentiation among house mouse subspecies inferred from transcriptome sequencing. Genetics 198: 283-297. 

Carneiro, M., S.J.E. Baird, S. Afonso, E. Ramirez, P. Tarroso, H. Teotonio, R. Villafuerte, M.W. Nachman, and N. Ferrand, 2013. Steep clines within a highly permeable genome across a hybrid zone between two subspecies of the European rabbit. Molecular Ecology 22: 2511-2525. 

Campbell, P., J.M. Good, and M.W. Nachman, 2013. Meiotic sex chromosome inactivation is disrupted in sterile hybrid male house mice. Genetics 193: 819-828. 

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(4): 1271-1281. 

Phifer-Rixey, M., F. Bonhomme, P. Boursot, G.A. Churchill, J. Pialek, P.K. Tucker, and M.W. Nachman, 2012. Adaptative evoluton and effective population size in wild house mice. Molecular Biology and Evolution 29(10): 2949-2955. 

Janousek, V., L. Wang, K. Luzynski, P. Dufkova, M.M. Vyskocilova, M.W. Nachman, P. Munclinger, M. Macholan, J. Pialek, and P.K. Tucker, 2012. Genome-wide architecture of reproductive isolation in a naturally occurring hybrid zone between Mus musculus and M. m. domesticus. Molecular Ecology 21(12): 3032-3047. 

Carnerio, M., F.W. Albert, J. Melo-Ferreira, N. Galtier, P. Gayral, J.A. Blanco-Aguiar, R. Villafuerte, M.W. Nachman, N. Ferrand, 2012. Evidence for widespread positive and purifying selection across the European rabbit (Oryctolagus cuniculus) genome. Molecular Biology and Evolution 29(7): 1837-1849. 

Nachman, M.W. and B.A. Payseur, 2012. Recombination rate variation and speciation: theoretical predictions and empirical results from rabbits and mice. Philosophical Transactions of the Royal Society B 367: 409-421. 

Geraldes, A., P. Basset, K.L. Smith, and M.W. Nachman, 2011. Higher differentiation among subspecies of the house mouse (Mus musculus) in genomic regions with low recombination. Molecular Ecology 20(22): 4722-4736. 

Song, Y., S. Endepols, N. Klemann, D. Richter, F.-R. Matuschka, C.-H. Shih, M.W. Nachman, and M.H. Kohn, 2011. Adaptive introgression of anticoagulant rodent poison resistance by hybridization between Old World mice. Current Biology 21: 1296-1301. 

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. 

Yang, H., J.R. Wang, J.P. Didion, R.J. Buus, T.A. Bell, C.E. Welsh, F. Bonhomme, H.T. Yu, M.W. Nachman, J. Pialek, P.K. Tucker, P. Boursot, L. McMillan, G.A. Churchill, and F. Pardo-Manuel de Villena, 2011.  Subspecific origin and haplotype diversity in the laboratory mouse.  Nature Genetics 43: 648-655. 

Wang, L., K. Luzynski, J. Pool, V. Janoušek, P. Dufková, M. Vyskocilová, K.C. Teeter, M.W. Nachman, P. Munclinger, M. Macholán, J. Piálek, and P.K. Tucker, 2011. Measures of linkage disequilibrium among neighboring SNPs indicate asymmetries across the house mouse hybrid zone. Molecular Ecology 20: 2985-3000. 

Reifova, R., J. Reif, M. Antczak, and M.W. Nachman, 2011. Ecological character displacement in the face of gene flow: evidence from two species of nightingales.  BMC Evolutionary Biology 11: 138. 

Carneiro, M., S. Afonso, A. Geraldes, H. Garreau, G. Bolet, S. Boucher, A. Tircazes, G. Queney, M.W. Nachman, and N. Ferrand, 2011. The genetic structure of domestic rabbits. Molecular Biology and Evolution 28(6): 1801-1816. 

Good, J.M., D. Vanderpool, K.L. Smith, and M.W. Nachman, 2011. Extraordinary sequence divergence at Tsga8, an X-linked gene involved in mouse spermiogensis. Molecular Biology and Evolution 28(5): 1675-1686.