Stanford Advisors

All Publications

  • A global test of ecoregions. Nature ecology & evolution Smith, J. R., Letten, A. D., Ke, P., Anderson, C. B., Hendershot, J. N., Dhami, M. K., Dlott, G. A., Grainger, T. N., Howard, M. E., Morrison, B. M., Routh, D., San Juan, P. A., Mooney, H. A., Mordecai, E. A., Crowther, T. W., Daily, G. C. 2018


    A foundational paradigm in biological and Earth sciences is that our planet is divided into distinct ecoregions and biomes demarking unique assemblages of species. This notion has profoundly influenced scientific research and environmental policy. Given recent advances in technology and data availability, however, we are now poised to ask whether ecoregions meaningfully delimit biological communities. Using over 200 million observations of plants, animals and fungi we show compelling evidence that ecoregions delineate terrestrial biodiversity patterns. We achieve this by testing two competing hypotheses: the sharp-transition hypothesis, positing that ecoregion borders divide differentiated biotic communities; and the gradual-transition hypothesis, proposing instead that species turnover is continuous and largely independent of ecoregion borders. We find strong support for the sharp-transition hypothesis across all taxa, although adherence to ecoregion boundaries varies across taxa. Although plant and vertebrate species are tightly linked to sharp ecoregion boundaries, arthropods and fungi show weaker affiliations to this set of ecoregion borders. Our results highlight the essential value of ecological data for setting conservation priorities and reinforce the importance of protecting habitats across as many ecoregions as possible. Specifically, we conclude that ecoregion-based conservation planning can guide investments that simultaneously protect species-, community- and ecosystem-level biodiversity, key for securing Earth's life support systems into the future.

    View details for PubMedID 30397301

  • Coexistence theory and the frequency-dependence of priority effects. Nature ecology & evolution Ke, P., Letten, A. D. 2018


    Priority effects are commonly used to describe a broad suite of phenomena capturing the influence of species arrival order on the diversity, composition and function of ecological communities. Several studies have suggested reframing priority effects around the stabilizing and equalizing concepts of coexistence theory. We show that the only compatible priority effects are those characterized by positive frequency-dependence, irrespective of whether they emerge in equilibrium or non-equilibrium systems.

    View details for PubMedID 30297744

  • Ontogenetic antagonism-mutualism coupling: perspectives on resilience of stage-structured communities OIKOS Ke, P., Nakazawa, T. 2018; 127 (3): 353–63

    View details for DOI 10.1111/oik.04702

    View details for Web of Science ID 000426652500003

  • Statistical recipe for quantifying microbial functional diversity from EcoPlate metabolic profiling ECOLOGICAL RESEARCH Miki, T., Yokokawa, T., Ke, P., Hsieh, I., Hsieh, C., Kume, T., Yoneya, K., Matsui, K. 2018; 33 (1): 249–60
  • Species coexistence through simultaneous fluctuation-dependent mechanisms. Proceedings of the National Academy of Sciences of the United States of America Letten, A. D., Dhami, M. K., Ke, P. J., Fukami, T. 2018


    Understanding the origins and maintenance of biodiversity remains one of biology's grand challenges. From theory and observational evidence, we know that variability in environmental conditions through time is likely critical to the coexistence of competing species. Nevertheless, experimental tests of fluctuation-driven coexistence are rare and have typically focused on just one of two potential mechanisms, the temporal storage effect, to the neglect of the theoretically equally plausible mechanism known as relative nonlinearity of competition. We combined experiments and simulations in a system of nectar yeasts to quantify the relative contribution of the two mechanisms to coexistence. Resource competition models parameterized from single-species assays predicted the outcomes of mixed-culture competition experiments with 83% accuracy. Model simulations revealed that both mechanisms have measurable effects on coexistence and that relative nonlinearity can be equal or greater in magnitude to the temporal storage effect. In addition, we show that their effect on coexistence can be both antagonistic and complementary. These results falsify the common assumption that relative nonlinearity is of negligible importance, and in doing so reveal the importance of testing coexistence mechanisms in combination.

    View details for PubMedID 29895689

  • Linking modern coexistence theory and contemporary niche theory ECOLOGICAL MONOGRAPHS Letten, A. D., Ke, P., Fukami, T. 2017; 87 (2): 161-177

    View details for DOI 10.1002/ecm.1242

    View details for Web of Science ID 000400406300001

  • The soil microbial community predicts the importance of plant traits in plant-soil feedback NEW PHYTOLOGIST Ke, P., Miki, T., Ding, T. 2015; 206 (1): 329-341


    Reciprocal interaction between plant and soil (plant-soil feedback, PSF) can determine plant community structure. Understanding which traits control interspecific variation of PSF strength is crucial for plant ecology. Studies have highlighted either plant-mediated nutrient cycling (litter-mediated PSF) or plant-microbe interaction (microbial-mediated PSF) as important PSF mechanisms, each attributing PSF variation to different traits. However, this separation neglects the complex indirect interactions between the two mechanisms. We developed a model coupling litter- and microbial-mediated PSFs to identify the relative importance of traits in controlling PSF strength, and its dependency on the composition of root-associated microbes (i.e. pathogens and/or mycorrhizal fungi). Results showed that although plant carbon: nitrogen (C : N) ratio and microbial nutrient acquisition traits were consistently important, the importance of litter decomposability varied. Litter decomposability was not a major PSF determinant when pathogens are present. However, its importance increased with the relative abundance of mycorrhizal fungi as nutrient released from the mycorrhizal-enhanced litter production to the nutrient-depleted soils result in synergistic increase of soil nutrient and mycorrhizal abundance. Data compiled from empirical studies also supported our predictions. We propose that the importance of litter decomposability depends on the composition of root-associated microbes. Our results provide new perspectives in plant invasion and trait-based ecology.

    View details for DOI 10.1111/nph.13215

    View details for Web of Science ID 000350347500033

    View details for PubMedID 25521190

  • Incorporating the soil environment and microbial community into plant competition theory. Frontiers in microbiology Ke, P., Miki, T. 2015; 6: 1066-?

    View details for DOI 10.3389/fmicb.2015.01066

    View details for PubMedID 26500621