Robert Cooper
Robert Cooper
1015 Life Science Circle
Blacksburg, VA 24061
- B.S. - University of California, Santa Cruz (2012)
- M.S. - University of California, Los Angeles (2015)
- Ph.D. - University of California, Los Angeles (2021)
Areas of interest:
Conservation, Genomics, Bioinformatics, Invasive Species Biology, Ecological Modeling
My lab applies genomic and computational tools to understand major threats to native biodiversity, including the introduction of invasive species, habitat destruction, fragmentation, and climate change. We work closely with managers at the state and federal level to identify and address pressing challenges in wildlife conservation. Much of our work has focused on the endangered California tiger salamander which is threatened both by habitat conversion and non-native hybridization with the invasive barred tiger salamander. In this system we have employed gene-expression studies to understand difference in thermal tolerance, constructed experimental ponds with varied hydrology, and built genetically-informed demographic models to simulate population viability in the face of invasive hybridization. These salamanders have large genomes 10 times the size of the human genome, with highly repetitive regions, making them an especially tricky non-model system to study genetically. As a result we employ a wide range of techniques to understand their biology. My lab also develops new genomic techniques to address conservation needs, including rapid genotyping assays to scan large populations for non-native alleles.
Cooper, R.D., Messerman, A.F., Searcy, C.A., Toffelmier, Grether, G.F., Shaffer, H.B. (In Press). Using integral projection models to guide conservation management of invasive-native species hybrid zones. In press. Ecological Applications.
McGuire, J.A., Richmond, J.Q., Escalona, M., Marimuthu, M.P., Nguyen, O., Sacco, S., Beraut, E., Toffelmier, E., Cooper, R.D., Westphal, M. and Fisher, R.N., Wang, I.J., H.B. Shaffer, Genome Resources—A chromosome-Level genome assembly for the long-nosed leopard lizard, Gambelia wislizenii, the first reference genome for the lizard family crotaphytidae, Journal of Heredity.https://doi.org/10.1093/jhered/esaf053
Richmond, J.Q., Escalona, M., Marimuthu, M.P., Nguyen, O., Sacco, S., Beraut, E., Toffelmier, E., Karin, B.R., Cooper, R.D., Fisher, R.N. and Wang, I.J.,, H.B. Shaffer, A chromosome-level reference genome assembly for Gilbert’s skink Plestiodon gilberti, Journal of Heredity. https://doi.org/10.1093/jhered/esaf040
Grismer, J.L., Escalona, M., Miller, C., Marimuthu, M.P., Nguyen, O., Beraut, E., Sacco, S., Toffelmier, E., Cooper, R.D., Wang, I.J., R.N. Fisher, H.B. Shaffer, Reference genome of the Gophersnake, Pituophis catenifer (Serpentes: Colubridae), Journal of Heredity. https://doi.org/10.1093/jhered/esaf024
Cooper, R.D., Luckau, T.K., Toffelmier, E., Cook, D.G., Martinelli, S., Shaffer, H.B. (2024). A novel genetic tool to enable rapid detection of rare non-native alleles. Scientific Reports. doi: 10.1038/s41598-024-76149-8.
Cooper, R.D., Shaffer, H.B. (2024). Managing invasive hybrids with pond hydroperiod manipulation in an endangered salamander system. Conservation Biology, 38, e14167. https://doi.org/10.1111/cobi.14167.
Megía-Palma, R., Paranjpe, D., Blaimont, P., Cooper, R., & Sinervo, B. (2022). Natural parasites in conjunction with behavioral and color traits explain male agonistic behaviors in Sceloporus occidentalis. Current Zoology. https://doi.org/10.1093/cz/zoac095.
Cooper, R.D., Shaffer, H.B. (2021). Allele Specific Expression and Gene Regulation Help Explain Transgressive Thermal Tolerance in Non-native Hybrids of the Endangered California Tiger Salamander (Ambystoma californiense). Mol. Ecol. https://doi.org/10.1111/mec.15779
Cooper, R. D. (2021). The Ecology, Evolution, and Management of Recent Non-Native Hybridization of the Endangered California Tiger Salamander (Ambystoma californiense). University of California, Los Angeles; 2021.
Megía-Palma, R., Paranjpe, D., Blaimont, P., Cooper, R., & Sinervo, B. (2020). To cool or not to cool? Intestinal coccidians disrupt the behavioral hypothermia of lizards in response to tick infestation. Ticks and Tick-Borne Diseases, 101275. doi: 10.1016/j.ttbdis.2019.101275
Aburto-Oropeza , O., Johnson, A.F., Agha, M., Allen, E.B., Allen, M.F., González, J.A., Arenas Moreno, D.M., Beas-Luna, R., Butterfield, S., Caetano, G., Caselle, J.E., Gaytán, G.C.,. Castorani, M.C.N , Cat, L.A., Cavanaugh, K., Chambers, J.Q., Cooper, R.D., et al. (2018). Harnessing cross-border resources to confront climate change. Environ. Sci. Policy 87, 128–132.
Megía-Palma, Rodrigo, Paranjpe, D., Reguera, S., Martínez, J., Cooper, R. D., Blaimont, P., … Sinervo, B. (2018). Multiple color patches and parasites in Sceloporus occidentalis: differential relationships by sex and infection. Current Zoology, 64(6), 703–711. doi: 10.1093/cz/zoy007
Megía-Palma R et al. 2015. Phylogeny of the reptilian Eimeria: are Choleoeimeria and Acroeimeria valid generic names? Zoologica Scripta 44:684–692.
Agha M, Augustine B, Lovich JE, Delaney D, Sinervo B, Murphy MO, Ennen JR, Briggs JR, Cooper R, Price SJ. 2015. Using motion-sensor camera technology to infer seasonal activity and thermal niche of the desert tortoise (Gopherus agassizii). Journal of thermal biology 49:119–126.
Paranjpe DA, Medina D, Cooper R, Sinervo B. 2014. Blood parasites and the side-blotched lizards: do the parasites drive negative frequency dependent cycles of three throat color morphs? Pages E160–E160 Integrative And Comparative Biology. Oxford Univ. Press Inc. Journals Dept., 2001 Evans Rd, Cary, NC. 27513 USA.
Paranjpe DA, Bastiaans E, Patten A, Cooper RD, Sinervo B. 2013. Evidence of maternal effects on temperature preference in side-blotched lizards: implications for evolutionary response to climate change. Ecology and Evolution 3:1977–1991.
Paranjpe DA, Cooper RD, Patten A, Sinervo B. 2012. Measuring thermal profile of reptiles in laboratory and field. Pages 460–462 Proceedings of measuring behavior. Noldus Information Technology Utrecht, the Netherlands.