Stanford Advisors


2018-19 Courses


All Publications


  • Intensive farming drives long-term shifts in avian community composition. Nature Hendershot, J. N., Smith, J. R., Anderson, C. B., Letten, A. D., Frishkoff, L. O., Zook, J. R., Fukami, T., Daily, G. C. 2020; 579 (7799): 393–96

    Abstract

    Agricultural practices constitute both the greatest cause of biodiversity loss and the greatest opportunity for conservation1,2, given the shrinking scope of protected areas in many regions. Recent studies have documented the high levels of biodiversity-across many taxa and biomes-that agricultural landscapes can support over the short term1,3,4. However, little is known about the long-term effects of alternative agricultural practices on ecological communities4,5 Here we document changes in bird communities in intensive-agriculture, diversified-agriculture and natural-forest habitats in 4 regions of Costa Rica over a period of 18 years. Long-term directional shifts in bird communities were evident in intensive- and diversified-agricultural habitats, but were strongest in intensive-agricultural habitats, where the number of endemic and International Union for Conservation of Nature (IUCN) Red List species fell over time. All major guilds, including those involved in pest control, pollination and seed dispersal, were affected. Bird communities in intensive-agricultural habitats proved more susceptible to changes in climate, with hotter and drier periods associated with greater changes in community composition in these settings. These findings demonstrate that diversified agriculture can help to alleviate the long-term loss of biodiversity outside natural protected areas1.

    View details for DOI 10.1038/s41586-020-2090-6

    View details for PubMedID 32188954

  • Land-use change has host-specific influences on avian gut microbiomes. The ISME journal San Juan, P. A., Hendershot, J. N., Daily, G. C., Fukami, T. 2019

    Abstract

    Human modification of the environment, particularly through land-use change, often reduces animal species diversity. However, the effect of land-use change on the gut microbiome of wildlife in human-dominated landscapes is not well understood despite its potential consequences for host health. We sought to quantify the effect of land-use change on wild bird gut microbiomes in a countryside landscape in Costa Rica, comprising a range of habitat types, ranging from primary and secondary forests to diversified and monoculture farms. We collected 280 fresh fecal samples from individuals belonging to six common species of saltator, thrushes, and warblers at 24 sites across this land-use gradient. Through 16S rRNA community profiling, we found that bacterial species composition responded to host species identity more strongly than to habitat type. In addition, we found evidence that habitat type affected microbial composition only for two of the six bird species. Our findings indicate that some host species and their microbiota may be more vulnerable to human disturbances than others.

    View details for DOI 10.1038/s41396-019-0535-4

    View details for PubMedID 31624349

  • 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

    Abstract

    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

  • Consistently inconsistent drivers of patterns of microbial diversity and abundance at macroecological scales. Ecology Hendershot, J. N., Read, Q. D., Henning, J. A., Sanders, N. J., Classen, A. T. 2017

    Abstract

    Macroecology seeks to understand broad-scale patterns in the diversity and abundance of organisms, but macroecologists typically study aboveground macroorganisms. Belowground organisms regulate numerous ecosystem functions, yet we lack understanding of what drives their diversity. Here, we examine the controls on belowground diversity along latitudinal and elevational gradients. We performed a global meta-analysis of 325 soil communities across 20 studies conducted along temperature and soil pH gradients. Belowground taxa, whether bacterial or fungal, observed along a given gradient of temperature or soil pH were equally likely to show a linear increase, linear decrease, humped pattern, trough-shaped pattern, or no pattern in diversity along the gradient. Land-use intensity weakly affected the diversity-temperature relationship, but no other factor did so. Our study highlights disparities among diversity patterns of soil microbial communities. Belowground diversity may be controlled by the associated climatic and historical contexts of particular gradients, by factors not typically measured in community-level studies, or by processes operating at scales that do not match the temporal and spatial scales under study. Because these organisms are responsible for a suite of key processes, understanding the drivers of their distribution and diversity is fundamental to understanding the functioning of ecosystems.

    View details for DOI 10.1002/ecy.1829

    View details for PubMedID 28380683

  • The biogeography of ecoregions: Descriptive power across regions and taxa JOURNAL OF BIOGEOGRAPHY Smith, J. R., Hendershot, J., Nova, N., Daily, G. C. 2020

    View details for DOI 10.1111/jbi.13871

    View details for Web of Science ID 000533465200001

  • Constraints on microbial communities, decomposition and methane production in deep peat deposits PLOS ONE Kluber, L. A., Johnston, E. R., Allen, S. A., Hendershot, J., Hanson, P. J., Schadt, C. W. 2020; 15 (2): e0223744

    Abstract

    Peatlands play outsized roles in the global carbon cycle. Despite occupying a rather small fraction of the terrestrial biosphere (~3%), these ecosystems account for roughly one third of the global soil carbon pool. This carbon is largely comprised of undecomposed deposits of plant material (peat) that may be meters thick. The fate of this deep carbon stockpile with ongoing and future climate change is thus of great interest and has large potential to induce positive feedback to climate warming. Recent in situ warming of an ombrotrophic peatland indicated that the deep peat microbial communities and decomposition rates were resistant to elevated temperatures. In this experiment, we sought to understand how nutrient and pH limitations may interact with temperature to limit microbial activity and community composition. Anaerobic microcosms of peat collected from 1.5 to 2 meters in depth were incubated at 6°C and 15°C with elevated pH, nitrogen (NH4Cl), and/or phosphorus (KH2PO4) in a full factorial design. The production of CO2 and CH4 was significantly greater in microcosms incubated at 15°C, although the structure of the microbial community did not differ between the two temperatures. Increasing the pH from ~3.5 to ~5.5 altered microbial community structure, however increases in CH4 production were non-significant. Contrary to expectations, N and P additions did not increase CO2 and CH4 production, indicating that nutrient availability was not a primary constraint in microbial decomposition of deep peat. Our findings indicate that temperature is a key factor limiting the decomposition of deep peat, however other factors such as the availability of O2 or alternative electron donors and high concentrations of phenolic compounds, may also exert constraints. Continued experimental peat warming studies will be necessary to assess if the deep peat carbon bank is susceptible to increased temperatures over the longer time scales.

    View details for DOI 10.1371/journal.pone.0223744

    View details for Web of Science ID 000534623800006

    View details for PubMedID 32027653

    View details for PubMedCentralID PMC7004313

  • Publisher Correction: Intensive farming drives long-term shifts in avian community composition. Nature Hendershot, J. N., Smith, J. R., Anderson, C. B., Letten, A. D., Frishkoff, L. O., Zook, J. R., Fukami, T. n., Daily, G. C. 2020; 581 (7808): E6

    Abstract

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

    View details for DOI 10.1038/s41586-020-2310-0

    View details for PubMedID 32433608

  • A global test of ecoregions (vol 2, pg 1889, 2018) NATURE ECOLOGY & EVOLUTION Smith, J. R., Letten, A. D., Ke, P., Anderson, C. B., Hendershot, J., Dhami, M. K., Dlott, G. A., Grainger, T. N., Howard, M. E., Morrison, B. L., Routh, D., San Juan, P. A., Mooney, H. A., Mordecai, E. A., Crowther, T. W., Daily, G. C. 2019; 3 (4): 708
  • Author Correction: 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., Juan, P. A., Mooney, H. A., Mordecai, E. A., Crowther, T. W., Daily, G. C. 2019

    Abstract

    The original paper was published without unique DOIs for GBIF occurrence downloads. These have now been inserted as references 70-76, and the error has been corrected in the PDF and HTML versions of the article.

    View details for PubMedID 30858593