Published papers (first author name linked to paper access; Koskella lab members in bold type)
Koskella, B., Hernandez, C. A., & Wheatley, R. M. (2022). Understanding the Impacts of Bacteriophage Viruses: From Laboratory Evolution to Natural Ecosystems. Annual Review of Virology, 9.
Mehlferber, E. C., Song, M. J., Pelaez, J. N., Jaenisch, J., Coate, J. E., Koskella, B., & Rothfels, C. J. (2022). Polyploidy and microbiome associations mediate similar responses to pathogens in Arabidopsis. Current Biology. (online early)
Mehlferber, E. C., McCue, K. F., Ferrel, J. E., Koskella, B., & Khanna, R. (2022). Temporally Selective Modification of the Tomato Rhizosphere and Root Microbiome by Volcanic Ash Fertilizer Containing Micronutrients. Applied and Environmental Microbiology, e00049-22.
Meyer, K. M., Porch, R., Muscettola, I. E., Vasconcelos, A. L. S., Sherman, J. K., Metcalf, C. J. E., Lindow, S. E. & Koskella, B. (2022). Plant neighborhood shapes diversity and reduces interspecific variation of the phyllosphere microbiome. The ISME journal, 1-12.
**Behind the paper can be found here: https://ecoevocommunity.nature.com/posts/plant-neighbors-leave-a-lingering-presence-in-the-microbiome. Chosen for Microbiome Digest Bik’s Picks: https://microbiomedigest.com/2022/01/14/january-14-2022/
Debray, R., Socolar, Y., Kaulbach, G., Guzman, A., Hernandez, C. A., Curley, R., Dhond, A., Bowles, T. & Koskella, B. (2022). Water stress and disruption of mycorrhizas induce parallel shifts in phyllosphere microbiome composition. New Phytologist, 234(6), 2018-2031
Dewald-Wang, E. A., Parr, N., Tiley, K., Lee, A., & Koskella, B. (2022). Multiyear time-shift study of bacteria and phage dynamics in the phyllosphere. The American Naturalist, 199(1), 126-140.
Debray, R., Herbert, R. A., Jaffe, A. L., Crits-Christoph, A., Power, M. E., & Koskella, B. (2021). Priority effects in microbiome assembly. Nature Reviews Microbiology, 1-13.
Hernandez, C. A., Salazar, A. J., & Koskella, B. (2020). Bacteriophage-Mediated Reduction of Bacterial Speck on Tomato Seedlings. PHAGE, 1(4), 205-212.
McDonald, J. E., Marchesi, J. R., & Koskella, B. (2020). Application of ecological and evolutionary theory to microbiome community dynamics across systems. Proceedings of the Royal Society B, 287(1941), 20202886.
Koskella, B. (2020). The phyllosphere. Current Biology, 30(19), R1143-R1146.
Koskella, B., & Bergelson, J. (2020). The study of host–microbiome (co) evolution across levels of selection. Philosophical Transactions of the Royal Society B, 375(1808), 20190604.
Simmons, E. L., Bond, M. C., Koskella, B., Drescher, K., Bucci, V., & Nadell, C. D. (2020). Biofilm structure promotes coexistence of phage-resistant and phage-susceptible bacteria. Msystems, 5(3).
Mutalik VK, Adler BA, Rishi HS, Piya D, Zhong C, Koskella B, Calendar, R., Novichkov, P., Price, M.N., Deutschbauer, A.M. and Arkin, A.P. (2020) High-throughput mapping of the phage resistance landscape in E. coli. PLoS Biol 18(10): e3000877. https://doi.org/10.1371/journal.pbio.3000877
Morella, N. M., Weng, F. C. H., Joubert, P. M., Metcalf, C. J. E., Lindow, S., & Koskella, B. (2020). Successive passaging of a plant-associated microbiome reveals robust habitat and host genotype-dependent selection. PNAS, 117 (2), 1148-1159.
**Highlighted here: Copeland, C., & Schulze-Lefert, P. (2020. Leaf-derived bacterial communities adapt to the local environment. PNAS. 117(2), 808-810. and covered here: https://news.berkeley.edu/2019/12/06/how-do-you-cultivate-a-healthy-plant-microbiome/ and here: https://plantae.org/research/what-were-reading-this-week/successive-passaging-of-plant-associated-microbiome-reveals-robust-habitat-and-host-genotype-dependent-selection-pnas/** (bioRxiv, 627794)
Smets, W., & Koskella, B. (2020). Microbiome: insect herbivory drives plant phyllosphere dysbiosis. Current biology, 30(9), R412-R414.
Hernandez, C. A., & Koskella, B. (2019). Phage resistance evolution in vitro is not reflective of in vivo outcome in a plant‐bacteria‐phage system. Evolution 73(12): 2461-2475.
**Highlighted here: Wagner, K. S., & Rajkov, J. (2019). Digest: Lab versus nature: Disease resistance evolution differs between environments. Evolution 73(12), 2540-2541.**
Bass, D., Stentiford, G. D., Wang, H. C., Koskella, B., & Tyler, C. R. (2019). The Pathobiome in Animal and Plant Diseases. Trends in ecology & evolution 34(11): 996-1008
**Chosen as CEFAS (Centre for Environment Fisheries and Aquaculture Science) paper of the year**
Metcalf, C. J., & Koskella, B. (2019). Protective microbiomes can limit the evolution of host pathogen defense. Evolution Letters 3: 534-543; bioRxiv, 665265.
Metcalf, C. J. E., Henry, L. P., Rebolleda-Gomez, M., & Koskella, B. (2019). Why evolve reliance on the microbiome for timing of ontogeny? mBio 10(5); bioRxiv, 665182.
Lin, D. M., Koskella, B. L., Ritz, N. L., Lin, D., Carroll-Portillo, A., & Lin, H. C. (2019). Transplanting Fecal Virus-Like Particles Reduces High-Fat Diet-Induced Small Intestinal Bacterial Overgrowth in Mice. Frontiers in Cellular and Infection Microbiology, 9, 348.
Cavicchioli, R., Ripple, W. J., Timmis, K. N., Azam, F., Bakken, L. R., Baylis, M., ….Koskella, B... & Crowther, T. W. (2019). Scientists’ warning to humanity: microorganisms and climate change. Nature Reviews Microbiology, 1.
Dickinson, A. W., Power, A., Hansen, M.G., Brandt, K.K., Piliposian, G., Appleby, P., O’Neill, P.A., Jones, R.T., Sierocinski, P., Koskella, B. and Vos, M. (2019). Heavy metal pollution and co-selection for antibiotic resistance: A microbial palaeontology approach. Environment international, 132, 105117.
Morella, N. M., Zhang, X., & Koskella, B. (2019). Tomato seed-associated bacteria confer protection of seedlings against foliar speck caused by Pseudomonas syringae. Phytobiomes Journal, 3 (3), 177-190.
Koskella, B. (2019). New approaches to characterizing bacteria–phage interactions in microbial communities and microbiomes. Environmental microbiology reports, 11(1), 15-16.
Koskella, B. (2018). Resistance gained, resistance lost: An explanation for host–parasite coexistence. PLoS biology, 16(9), e3000013.
Berg, M., & Koskella, B. (2018). Nutrient-and Dose-Dependent Microbiome-Mediated Protection against a Plant Pathogen. Current Biology, 28(15), 2487-2492.
Koskella, B., & Taylor, T. B. (2018). Multifaceted Impacts of Bacteriophages in the Plant Microbiome. Annual review of phytopathology, 56, 361-380.
Morella, N. M., Yang, S. C., Hernandez, C. A., & Koskella, B. (2018). Rapid Quantification of Bacteriophages and Their Bacterial Hosts in Vitro and in Vivo using Droplet Digital PCR. Journal of virological methods, 259, 18-24.
Morella, N. M., Gomez, A. L., Wang, G., Leung, M. S., & Koskella, B. (2018). The impact of bacteriophages on phyllosphere bacterial abundance and composition. Molecular ecology 27(8), 2025-2038.
Best, A., Ashby, B., White, A., Bowers, R., Buckling, A., Koskella, B., & Boots, M. (2017). Host–parasite fluctuating selection in the absence of specificity. Proc. R. Soc. B. 284(1866), 20171615.
Koskella, B., Hall, L. J., & Metcalf, C. J. E. (2017). The microbiome beyond the horizon of ecological and evolutionary theory. Nature ecology & evolution, 1(11), 1606.
Morella, N. M., & Koskella, B. (2017). the value of a comparative Approach to Understand the complex interplay between Microbiota and Host immunity. Frontiers in immunology, 8, 1114.
Lin, D. M., Koskella, B., & Lin, H. C. (2017). Phage therapy: An alternative to antibiotics in the age of multi-drug resistance. World journal of gastrointestinal pharmacology and therapeutics, 8(3), 162.
Koskella, B., Meaden, S., Crowther, W.J., Leimu, R., and Metcalf, C.J.E. (2017) A signature of tree health? Shift in the microbiome and the ecological drivers of horse chestnut bleeding canker disease. New Phytologist, 215: 737-746.
Giraud, T., Koskella, B. and Laine, A.-L. (2017). Introduction: microbial local adaptation: insights from natural populations, genomics and experimental evolution. Molecular Ecology, 26: 1703–1710.
Meaden, S., & Koskella, B. (2017). Adaptation of the pathogen, Pseudomonas syringae, during experimental evolution on a native vs. alternative host plant. Molecular Ecology, 26: 1790–1801.
Meaden, S., Metcalf, C. J. E., & Koskella, B. (2016). The effects of host age and spatial location on bacterial community composition in the English Oak tree (Quercus robur). Environmental microbiology reports, 8(5), 649-658.
Penczykowski, R. M., Laine, A. L., & Koskella, B. (2016). Understanding the ecology and evolution of host–parasite interactions across scales. Evolutionary Applications, 9: 37-52.
Rihtman, B., Meaden, S., Clokie, M. R., Koskella, B., & Millard, A. D. (2016). Assessing Illumina technology for the high-throughput sequencing of bacteriophage genomes. PeerJ, 4, e2055.
Koskella, B. and Parr, N. (2015). The evolution of bacterial resistance against bacteriophages in the horse chestnut phyllosphere is general across both space and time. Phil Trans R Soc B, 370: 20140297.
Koskella, B. and Vos, M. (2015). Adaptation in Natural Microbial Populations. Annual Review of Ecology, Evolution, and Systematics, 46: 503.
Meaden, S., Paszkiewicz, K., & Koskella, B. (2015). The cost of phage resistance in a plant pathogenic bacterium is context‐dependent. Evolution, 69: 1321-1328.
Cunniffe N. J., Koskella B., Metcalf C. J., Parnell S. , Gottwald T.R. & Gilligan C. A.(2015) Thirteen challenges in modelling plant diseases. Epidemics 10: 6-10.
Lin, D., & Koskella, B. (2014). Friend and foe: factors influencing the movement of the bacterium Helicobacter pylori along the parasitism‐mutualism continuum. Evolutionary Applications 8: 9-22.
Koskella, B. & Brockhurst, M.A. 2014. Bacteria–phage coevolution as a driver of ecological and evolutionary processes in microbial communities. FEMS Microbiol Rev 38: 916–931,.
Koskella B. 2014. Bacteria-Phage Interactions across Time and Space: Merging Local Adaptation and Time-Shift Experiments to Understand Phage Evolution. Am Nat 184: S9-S21.
Lively C. M., Roode J. C., Duffy M. A., Graham A. L. & Koskella B. 2014. Interesting Open Questions in Disease Ecology and Evolution. Am Nat 184: S1-S8.
Díaz-Muñoz S. L. and Koskella B. (2014) Bacteria-Phage Interactions in Natural Environments Advances in Applied Microbiology 89: 135-183.
Meaden, S. and Koskella, B. 2013. Exploring the risks of phage application in the environment. Frontiers in Microbiology 4, 358.
Koskella, B. 2013. Phage-Mediated Selection on Microbiota of a Long-Lived Host. Current Biology 23, 1256–1260.
Brockhurst, M.A. and Koskella, B. 2013. Experimental coevolution of species interactions. Trends in Ecology & Evolution 28(6): 367-75.
Koskella, B., Meaden, S. 2013. Understanding Bacteriophage Specificity in Natural Microbial Communities. Viruses 5: 806-823. PDF
Antonovics, J., Boots, M., Ebert, D., Koskella, B., Poss, M., and Sadd, B.M. 2012. The origin of specificity by means of natural selection: evolved and non-host resistance in host-pathogen interactions. Evolution 67: 1-9. PDF
Koskella, B., Lin, D.M., Buckling, A. and Thompson, J.N. 2012. The costs of evolving resistance in heterogeneous parasite environments. Proceedings of the Royal Society B. 279: 1896-1903. –> Evaluated by Faculty 1000 as Recommended (6) and featured in Current Biology (22[5]: R142-R145). PDF
Koskella, B., Taylor, T., Bates, J., & Buckling, A. 2011. Using experimental evolution to explore natural patterns between bacterial motility and resistance to bacteriophage. ISME 5: 1809-1817. PDF
Koskella, B., Vergara, D., & Lively, C.M. 2011. Experimental evolution of sexual host populations in response to sterilizing parasites. Evolutionary Ecology Research, 13:315–322. PDF
Koskella, B., Thompson, J.N., Preston, G.M. & Buckling, A. 2011. Local biotic environment shapes the spatial scale of bacteriophage adaptation to bacteria. The American Naturalist, 177(4):440-51. –> Evaluated by Faculty 1000 as Exceptional (10) and highlighted as Editor’s Choice in Science, 332 (6027): 284-285. PDF
Koskella, B. and C.M. Lively. 2009. Evidence for negative frequency-dependent selection during experimental coevolution of a freshwater snail and a sterilizing trematode. Evolution, 63(9): 2213-2221. –> Awarded theSociety for the Study of Evolution Fisher Prize for outstanding Ph.D. dissertation paper in Evolution. PDF
Dybdahl, M. F., Jokela, J., Delph, L. F., Koskella, B., and Lively, C. M. 2008. Hybrid fitness in a locally adapted parasite. The American Naturalist, 172(6):772-782. PDF
Greischar, M. and B. Koskella. 2007. A synthesis of experimental work on parasite local adaptation. Ecology Letters 10, 418–434. PDF
Koskella, B. and C.M. Lively. 2007. Advice of the rose: Experimental coevolution of a trematode parasite and its snail host. Evolution 61: 152–159. PDF
Koskella, B., Giraud, T. and M.E. Hood. 2006. Pathogen relatedness affects the outcome of within- host competition. The American Naturalist 168: 121-126 (4.725, 18). PDF
Lynch, M., Koskella, B. and S. Schaack. 2006. Mutation pressure and the evolution of organelle genomic architecture. Science 311: 1727-30 (31.201, 146). PDF
Hood, M.E., Antonovics, J. and B. Koskella. 2004. Shared forces of sex chromosome evolution in haploid-mating and diploid-mating organisms: Microbotryum violaceum and Other Model Organisms. Genetics 168: 141–146. PDF
Book chapters
Koskella, B. and Taylor, T. B. The potential role of bacteriophages in shaping plant-bacterial interactions, in Plant-Bacterial Interactions, Murillo, J., Jackson, R. W., Arnold, D., and Vinatzer, B. (eds). Horizon Scientific Press, Norwich UK. (author version here)
Morgan, A.D. & Koskella, B. 2010. Co-evolution between host and pathogen. In: Tibayrenc, M. (ed.) Genetics and Evolution of Infectious Diseases. Elsevier. PDF
Neiman, M. & Koskella, B. 2009. Sex and the red queen. In: Schön, I., Martens, K. & Van Dijk P. (eds.) Lost sex. Springer Academic publishers, Heidelberg, Germany. PDF
Koskella Lab at UC Berkeley 
I am a graduate student of Anthropology, interested in population ecology, behavioral ecology and conservation. I came to your website looking for the freely accessible textbook you mentioned in your course syllabus for INTEGBI 172 Coevolution: from genes to ecosystem. I really liked the course structure and it would be of immense help if you could suggest some readings (in case the book is not coming soon!) as I’m not enrolled in the course.
Hi Snata,
The textbook is not quite ready for public consumption (but I hope it will be within the next year, at least in beta version). However. I am happy to share the reading list I assigned for the course the last time I taught it:
Janzen, D. H. (1980). When is it coevolution. Evolution, 34(3), 611-612.
Grant, P. R., & Grant, B. R. (2006). Evolution of character displacement in Darwin’s finches. science, 313(5784), 224-226 / Stuart, Y. E., & Losos, J. B. (2013). Ecological character displacement: glass half full or half empty?. Trends in ecology & evolution, 28(7), 402-408.
Lively, C. M., & Dybdahl, M. F. (2000). Parasite adaptation to locally common host genotypes. Nature, 405(6787), 679-681 / Scanlan, P. D., Hall, A. R., Blackshields, G., Friman, V. P., Davis, M. R., Goldberg, J. B., & Buckling, A. (2015). Coevolution with bacteriophages drives genome-wide host evolution and constrains the acquisition of abiotic-beneficial mutations. Molecular biology and evolution, 32(6), 1425-1435.
Hu, S., Dilcher, D. L., Jarzen, D. M., & Taylor, D. W. (2008). Early steps of angiosperm–pollinator coevolution. Proceedings of the National Academy of Sciences, 105(1), 240-245 / Schiestl, F. P., & Dötterl, S. (2012). The evolution of floral scent and olfactory preferences in pollinators: Coevolution or pre-existing bias? Evolution, 66(7), 2042-2055.
Kapan, D. D. (2001). Three-butterfly system provides a field test of Müllerian mimicry. Nature, 409(6818), 338-340 / Langmore, N. E., Stevens, M., Maurer, G., Heinsohn, R., Hall, M. L., Peters, A., & Kilner, R. M. (2011). Visual mimicry of host nestlings by cuckoos. Proceedings of the Royal Society of London B: Biological Sciences, 278(1717), 2455-2463.
Koskella, B., & Lively, C. M. (2009). Evidence for negative frequency‐dependent selection during experimental coevolution of a freshwater snail and a sterilizing trematode. Evolution, 63(9), 2213-2221 / Brockhurst, M. A., & Koskella, B. (2013). Experimental coevolution of species interactions. Trends in ecology & evolution, 28(6), 367-375.
Iwao, K., & Rausher, M. D. (1997). Evolution of plant resistance to multiple herbivores: quantifying diffuse coevolution. American Naturalist, 316-335 / Agrawal, A. A., Hastings, A. P., Johnson, M. T., Maron, J. L., & Salminen, J. P. (2012). Insect herbivores drive real-time ecological and evolutionary change in plant populations. Science, 338(6103), 113-116.
Currie, C. R., Wong, B., Stuart, A. E., Schultz, T. R., Rehner, S. A., Mueller, U. G., … & Straus, N. A. (2003). Ancient tripartite coevolution in the attine ant-microbe symbiosis. Science, 299(5605), 386-388 / Ellers, J., Toby Kiers, E., Currie, C. R., McDonald, B. R., & Visser, B. (2012). Ecological interactions drive evolutionary loss of traits. Ecology letters, 15(10), 1071-1082.
Anderson, B., & Johnson, S. D. (2008). The geographical mosaic of coevolution in a plant–pollinator mutualism. Evolution, 62(1), 220-225 / Hembry, D. H., Yoder, J. B., & Goodman, K. R. (2014). Coevolution and the diversification of life. The American Naturalist, 184(4), 425-438.
Gaba, S., & Ebert, D. (2009). Time-shift experiments as a tool to study antagonistic coevolution. Trends in Ecology & Evolution, 24(4), 226-232 / Betts, A., Kaltz, O., & Hochberg, M. E. (2014). Contrasted coevolutionary dynamics between a bacterial pathogen and its bacteriophages. Proceedings of the National Academy of Sciences, 111(30), 11109-11114.
Buckling, A., & Rainey, P. B. (2002). The role of parasites in sympatric and allopatric host diversification. Nature, 420(6915), 496-499 / Estes, J. A., Terborgh, J., Brashares, J. S., Power, M. E., Berger, J., Bond, W. J., … & Marquis, R. J. (2011). Trophic downgrading of planet Earth. science, 333(6040), 301-306.
Brown, J. K. (2015). Durable resistance of crops to disease: a Darwinian perspective. Annual review of phytopathology, 53, 513-539 / Anisimova, M. (2015). Darwin and Fisher meet at biotech: on the potential of computational molecular evolution in industry. BMC evolutionary biology, 15(1), 1.
Happy reading!
Britt