The Simison lab investigates the processes that generate, maintain, and reduce biodiversity. In particular, we are interested in the process of speciation. We use comparative genomics techniques such as RADseq, Ultra Conserved Elements, transcriptomics, and whole genomes to study the role of admixture and introgression in speciation. We are currently focusing on the globally invasive red eared slider turtle system (Trachemys scripta elegans) native to North America. But, we also study the slider turtles of the Caribbean and Mesoamerica. As part of this research, we hope to better understand the genetic consequences of hybridization between native and invasive species and apply this information to improve the efficacy of conservation efforts associated with the protection of native species from invasives.


  • James F. Parham Ph.D. John D. Cooper Archaeological and Paleontological Center, Department of Geological Sciences, California State University, Fullerton.
  • David R, Lindberg Ph.D. UC Museum of Paleontology and Integrative Biology, UC Berkeley
  • Norah Saarman Ph.D. Postdoc, UC Santa Barbara
  • Jeffrey L. Boore, Ph.D., Chief Executive Officer of Genome Project Solutions, Inc. and Adj. Professor, Integrative Biology, UC Berkeley

Peer Reviewed Publications:


  • Henrik Krehenwinkel, Susanne Meese, Christoph Mayer, Jasmin Ruch, Jutta Schneider, Trine Bilde, Sven Künzel, Jim Henderson, Joe Russack, Warren Brian Simison, Rosemary Gillespie, Gabriele Uhl (IN PRESS). Cost effective microsatellite isolation and genotyping by next generation sequencing. Molecular Ecology Resources (2019).


  • Peter W. Fritsch, W. Brian Simison, Boni C. Cruz, Edward L. Schneider, Douglas D. Allshouse (ACCEPTED). A remarkable new species of Vaccinium (Ericaceae) from San Bruno Mountain, California. Madroño - A West American Journal of Botany.
  • Fernandez-Silva, I., J.B. Henderson, L.A. Rocha, and W.B. Simison. 2018. “Whole- Genome Assembly of the Coral Reef Pearlscale Pygmy Angelfish (Centropyge Vrolikii).” Scientific Reports 8 (1).


  • Krehenwinkel, Henrik, Madeline Wolf, Jun Ying Lim, Andrew J. Rominger, W. B. Simison, and Rosemary G. Gillespie. 2017. “Estimating and Mitigating Amplification Bias in Qualitative and Quantitative Arthropod Metabarcoding.” Scientific Reports.
  • Saarman, N.P., K.M. Kober, W.B. Simison, and G.H. Pogson. 2017. “Sequence-Based Analysis of Thermal Adaptation and Protein Energy Landscapes in an Invasive Bluemussel (Mytilus Galloprovincialis).” Genome Biology and Evolution 9 (10).
  • Hamilton, Healy, Norah Saarman, Graham Short, Anna B. Sellas, Beth Moore, Tinya Hoang, Christopher L. Grace, Martin Gomon, Karen Crow, and W. Brian Simison. 2017. “Molecular Phylogeny and Patterns of Diversification in Syngnathid Fishes.” Molecular Phylogenetics and Evolution 107: 388–403.
  • Cotoras, D.D., G.G.R. Murray, J. Kapp, R.G. Gillespie, C. Griswold, W.B. Simison, R.E. Green, and B. Shapiro. 2017. “Ancient DNA Resolves the History of Tetragnatha (Araneae, Tetragnathidae) Spiders on Rapa Nui.” Genes 8 (12).
  • Bernal, M.A., M.R. Gaither, W.B. Simison, and L.A. Rocha. 2017. “Introgression and Selection Shaped the Evolutionary History of Sympatric Sister-Species of Coral Reef Fishes (Genus: Haemulon).” Molecular Ecology 26 (2).


  • Joshua Hallas, W. Brian Simison and Terrence M Gosliner (2016). Dating and biogeographical patterns in the sea slug genus Acanthodoris Gray, 1850 (Mollusca, Gastropoda, Nudibranchia). Molecular Hhylogenetics and Evolution 97, 19-31.
  • Peter W. Fritsch, Boni C. Cruz, W. Brian Simison, Alexandra J. Campbell, and Jennifer K. Harris (2016). Early Phylogenetic Divergence of Gynodioecious Species Warrants the Recognition of Subseries in Styrax Series Valvatae.
  • Systematic Botany 40(4):1081-1092. 2015 doi:
  • ​Peter Fritsch, X Yao, W. Brian Simison, Boni Cruz, T Chen (2016). Perkinsiodendron, A new genus in the styracaceae based on morphology and DNA sequences. J. Bot. Res. Inst. Texas 10 (1), 109 – 117.
  • Ricardo Faustino de Lima, W. Brian Simison, Eden Maloney, Robert Drewes (2016). Reassessing the conservation status of Crocidura thomensis, endemic to São Tomé Island. Oryx. 1-4. DOI:
  • Healy Hamilton; Norah Saarman, ; Graham Short,.; Anna B Sellas.; Beth Moore,; Tinya Hoang,; Christopher L Grace; Martin Gomon; Karen Crow; W. Brian Simison (2016 – In Press). Molecular Phylogeny and Patterns of Diversification in Syngnathid Fishes. Molecular Phylogenetics and Evolution.
  • Thomas Pape et al., W Brian Simison (34 authors) (2016 – In Press). Taxonomy: Species can be named from photos. Nature. DOI:
  • ​Moisés A. Bernal, Michelle R. Gaither, W. Brian Simison, Luiz A. Rocha (2016 – accepted). Introgression and selection shaped the evolutionary history of sympatric sister-species of coral reef fishes (genus: Haemulon). Molecular Ecology.


  • Michael F Palopoli, Daniel J Fergus, Samuel Minot, Dorothy T. Pei, W. Brian Simison, Iria Fernandez-Silva, Megan S Thoemmes, Robert R. Dunn, Michelle Trautwein (2015). Global divergence of the human follicle mite Demodex folliculorum: Persistent associations between host ancestry and mite lineages, Proceedings of the National Academy of Sciences 112 (52), 15958-15963.
  • James F. Parham, Theodore J. Papenfuss, James R. Buskirk, Gabriela Parra-Olea, Jei-Ying Chen, and W. Brian Simison (2015). Trachemys ornata or not ornata: Reassessment of a Taxonomic Revision for Mexican Trachemys. Proceedings of the California Academy of Sciences. Series 4, Volume 62, Part 2, No. 12, pp. 359–367.
  • Michelle R. Gaither, Moisés A. Bernal, Richard R. Coleman, Brian W. Bowen, Shelley A. Jones, W. Brian Simison, Luiz A. Rocha. (2015). Genomic signatures of geographic isolation and natural selection in coral reef fishes. Molecular Ecology. DOI: 10.1111/mec.13129.
  • Nicholas Crawford, James F Parham, Anna B Sellas, Brant C Faircloth, Travis C Glenn, Theodore J Papenfuss, James B. Henderson, Madison H Hansen, W. Brian Simison (2015). A phylogenomic analysis of turtles. Mol. Phy. & Evol.


  • Luiz Rocha, …, W. Brian Simison, et al. (128 authors). (2014) Specimen collection: an essential tool. Science 344 (6186), 814.


  • W Brian Simison, Anna B Sellas, Kevin A Feldheim, James F Parham (2013). Isolation and characterization of microsatellite markers for identifying hybridization and genetic pollution associated with red-eared slider turtles (Trachemys scripta elegans). Conservation Genetics Resources, 1-2.
  • James F Parham, Theodore J Papenfuss, Peter Paul van Dijk, Byron S Wilson, Cristian Marte, Lourdes R Schettino, W Brian Simison (2013). Genetic introgression and hybridization in Antillean freshwater turtles Trachemys revealed by coalescent analyses of mitochondrial and cloned nuclear markers. Mol Phylogenet Evol. 2013 Jan 23;67(1):176-187. doi: 10.1016/j.ympev.2013.01.004.
  • Dana Carrison-Stone, Robert Van Syoc, Gary Williams, W. Brian Simison (2013). Two new species of the gorgonian inhabiting barnacle, Conopea (Crustacea, Cirripedia, Thoracica), from the Gulf of Guinea. ZooKeys 270: 1–20, doi: 10.3897/zookeys.270.3736.


  • Christine L. Huffard, Norah Saarman, Healy Hamilton, W.Brian. Simison (2010). The evolution of conspicuous facultative mimicry in octopus: an example of secondary adaptation? Biological Journal of the Linnean Society, 101:68-77.
  • W.B. Simison and Boore, J. (2008). Molluscan evolutionary genomics. In Phylogeny and Evolution of the Mollusca. (W. F. Ponder & D. R. Lindberg, eds.), University of California Press, Berkeley, CA.
  • W.B. Simison, Lindberg, D. R. and Boore, J. (2006). Rolling circle amplification of metazoan mitochondrial genomes. Molecular Phylogenetics and Evolution, 39:562-567.
  • W.B. Simison (2006). Patterns of endemism for nearshore gastropod molluscs: A new view of the Gulf of California. Journal of Molluscan Studies, 72: 53-63.
  • Shi, H., J.F. Parham, W.B. Simison, J. Wang, S. Gong, and B. Fu. (2005).A report on the wild hybridization between two species of threatened Asian box turtles (Testudines: Cuora) on Hainan Island, China. Amphibia-Reptilia 26(3):377-381 Espoz, Carmen, Lindberg, D. R., Castilla, J. C., and Simison, W. B. (2004). Intertidal limpets of Chile and Peru. Revista Chilena de Historia Natural. 77(2):257-283.
  • W.B. Simison, Lindberg, David R. (2003). On the identity of Lottia strigatella (Carpenter, 1864) (Patellogastropoda:Lottidae). The Veliger, 46:1-19.
  • W.B. Simison (2002). Plate Tectonics. Encyclopedia of Global Environmental Change. The Earth System: Physical & Chemical Dimensions of Global Environmental Change. 1:605-606.
  • J.F. Parham, W.B. Simison, K.H. Kozak, C.R. Feldman (2001). New Chinese turtles: Endangered or invalid? A reassessment of two species using mitochondrial DNA, allozyme electrophoresis and known-locality specimens. Animal Conservation, 4:357-457.
  • W.B. Simison, D.R. Lindberg (1999). Morphological and molecular resolution of a putative cryptic species complex: A case study of Notoacmea fascicularis (Menke, 1851) (Gastropoda: Patellogastropoda). Journal of Molluscan Studies, 65:99-109.

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The Fish Speciation Genome Project (P. I.: Iria Fernandez-Silva) seeks to address key evolutionary questions.

Dr Brian Simison, Anna Sellas and their colleague

Exploring the endemic flora and fauna of an African island nation

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Contact Info

Center for Comparative Genomics
(415) 379-5297

Curriculum Vitae