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1. Index

Author

Forsdick, Charles, Leak, Andrew, and Phillips, Richard

Published
2019

17. List of figures

Author

Forsdick, Charles, Leak, Andrew, and Phillips, Richard

Published
2019

18. List of tables

Author

Forsdick, Charles, Leak, Andrew, and Phillips, Richard

Published
2019

23. [Untitled]

Author

Forsdick, Charles, Leak, Andrew, and Phillips, Richard

Published
2019

24. Acknowledgements

Author

Forsdick, Charles, Leak, Andrew, and Phillips, Richard

Published
2019

25. Title Page

Author

Forsdick, Charles, Leak, Andrew, and Phillips, Richard

Published
2019

26. Half Title

Author

Forsdick, Charles, Leak, Andrew, and Phillips, Richard

Published
2019

27. Copyright Page

Author

Forsdick, Charles, Leak, Andrew, and Phillips, Richard

Published
2019

28. Cover

Author

Forsdick, Charles, Leak, Andrew, and Phillips, Richard

Published
2019

29. Latitudinal patterns in stabilizing density dependence of forest communities.

Author

Holík, Jan, Howe, Robert, Hubbell, Stephen, Itoh, Akira, Johnson, Daniel, Kenfack, David, Král, Kamil, Larson, Andrew, Lutz, James, Makana, Jean-Remy, Malhi, Yadvinder, McMahon, Sean, McShea, William, Mohamad, Mohizah, Nasardin, Musalmah, Nathalang, Anuttara, Norden, Natalia, Oliveira, Alexandre, Parmigiani, Renan, Perez, Rolando, Phillips, Richard, Pongpattananurak, Nantachai, Sun, I-Fang, Swanson, Mark, Tan, Sylvester, Thomas, Duncan, Thompson, Jill, Uriarte, Maria, Wolf, Amy, Yao, Tze, Zimmerman, Jess, Zuleta, Daniel, Hartig, Florian, Hülsmann, Lisa, Chisholm, Ryan, Comita, Liza, Visser, Marco, de Souza Leite, Melina, Aguilar, Salomon, Anderson-Teixeira, Kristina, Bourg, Norman, Brockelman, Warren, Bunyavejchewin, Sarayudh, Castaño, Nicolas, Chang-Yang, Chia-Hao, Chuyong, George, Clay, Keith, Davies, Stuart, Duque, Alvaro, Ediriweera, Sisira, Ewango, Corneille, and Gilbert, Gregory|Greg

Subjects
Seedlings, Tropical Climate, Forests, Trees, Biodiversity, Ecosystem
Abstract

Numerous studies have shown reduced performance in plants that are surrounded by neighbours of the same species1,2, a phenomenon known as conspecific negative density dependence (CNDD)3. A long-held ecological hypothesis posits that CNDD is more pronounced in tropical than in temperate forests4,5, which increases community stabilization, species coexistence and the diversity of local tree species6,7. Previous analyses supporting such a latitudinal gradient in CNDD8,9 have suffered from methodological limitations related to the use of static data10-12. Here we present a comprehensive assessment of latitudinal CNDD patterns using dynamic mortality data to estimate species-site-specific CNDD across 23 sites. Averaged across species, we found that stabilizing CNDD was present at all except one site, but that average stabilizing CNDD was not stronger toward the tropics. However, in tropical tree communities, rare and intermediate abundant species experienced stronger stabilizing CNDD than did common species. This pattern was absent in temperate forests, which suggests that CNDD influences species abundances more strongly in tropical forests than it does in temperate ones13. We also found that interspecific variation in CNDD, which might attenuate its stabilizing effect on species diversity14,15, was high but not significantly different across latitudes. Although the consequences of these patterns for latitudinal diversity gradients are difficult to evaluate, we speculate that a more effective regulation of population abundances could translate into greater stabilization of tropical tree communities and thus contribute to the high local diversity of tropical forests.

Published
2024

30. Mycorrhizal feedbacks influence global forest structure and diversity.

Author

Delavaux, Camille, LaManna, Joseph, Myers, Jonathan, Phillips, Richard, Aguilar, Salomón, Allen, David, Alonso, Alfonso, Anderson-Teixeira, Kristina, Baker, Matthew, Baltzer, Jennifer, Bissiengou, Pulchérie, Bonfim, Mariana, Bourg, Norman, Brockelman, Warren, Burslem, David, Chang, Li-Wan, Chen, Yang, Chiang, Jyh-Min, Chu, Chengjin, Clay, Keith, Cordell, Susan, Cortese, Mary, den Ouden, Jan, Dick, Christopher, Ediriweera, Sisira, Ellis, Erle, Feistner, Anna, Freestone, Amy, Giambelluca, Thomas, Giardina, Christian, He, Fangliang, Holík, Jan, Howe, Robert, Huaraca Huasca, Walter, Hubbell, Stephen, Inman, Faith, Jansen, Patrick, Johnson, Daniel, Kral, Kamil, Larson, Andrew, Litton, Creighton, Lutz, James, Malhi, Yadvinder, McGuire, Krista, McMahon, Sean, McShea, William, Memiaghe, Hervé, Nathalang, Anuttara, Norden, Natalia, Novotny, Vojtech, OBrien, Michael, Orwig, David, Ostertag, Rebecca, Parker, Geoffrey, Pérez, Rolando, Reynolds, Glen, Russo, Sabrina, Sack, Lawren, Šamonil, Pavel, Sun, I-Fang, Swanson, Mark, Thompson, Jill, Uriarte, Maria, Vandermeer, John, Wang, Xihua, Ware, Ian, Weiblen, George, Wolf, Amy, Wu, Shu-Hui, Zimmerman, Jess, Lauber, Thomas, Maynard, Daniel, Crowther, Thomas, Averill, Colin, and Gilbert, Gregory|Greg

Subjects
Mycorrhizae, Feedback, Symbiosis, Plants, Soil
Abstract

One mechanism proposed to explain high species diversity in tropical systems is strong negative conspecific density dependence (CDD), which reduces recruitment of juveniles in proximity to conspecific adult plants. Although evidence shows that plant-specific soil pathogens can drive negative CDD, trees also form key mutualisms with mycorrhizal fungi, which may counteract these effects. Across 43 large-scale forest plots worldwide, we tested whether ectomycorrhizal tree species exhibit weaker negative CDD than arbuscular mycorrhizal tree species. We further tested for conmycorrhizal density dependence (CMDD) to test for benefit from shared mutualists. We found that the strength of CDD varies systematically with mycorrhizal type, with ectomycorrhizal tree species exhibiting higher sapling densities with increasing adult densities than arbuscular mycorrhizal tree species. Moreover, we found evidence of positive CMDD for tree species of both mycorrhizal types. Collectively, these findings indicate that mycorrhizal interactions likely play a foundational role in global forest diversity patterns and structure.

Published
2023

33. Synchronous timing of return to breeding sites in a long-distance migratory seabird with ocean-scale variation in migration schedules

Author

van Bemmelen, Rob S. A., Moe, Børge, Schekkerman, Hans, Hansen, Sveinn Are, Snell, Katherine R. S., Humphreys, Elizabeth M., Mäntylä, Elina, Hallgrimsson, Gunnar Thor, Gilg, Olivier, Ehrich, Dorothée, Calladine, John, Hammer, Sjúrður, Harris, Sarah, Lang, Johannes, Vignisson, Sölvi Rúnar, Kolbeinsson, Yann, Nuotio, Kimmo, Sillanpää, Matti, Sittler, Benoît, Sokolov, Aleksandr, Klaassen, Raymond H. G., Phillips, Richard A., and Tulp, Ingrid

Published
2024
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34. Diversity of Culicoides in the middle belt of Ghana with Implications on the transmission of Mansonella perstans; a molecular approach

Author

Debrah, Linda Batsa, Arthur, Joseph F., Yeboah, Augustine, Owusu, Dorcas O., Adankwah, Ernest, Acheampong, Isaac, Minadzi, Difery, Lamptey, Millicent, Opoku, Vera Serwaa, Aniagyei, Wilfred, Vivekanandan, Monika M., Abass, Mohammed K., Gawusu, Amidu, Wanji, Samuel, Debrah, Alexander Y., Jacobsen, Marc, and Phillips, Richard O.

Published
2024
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35. Latitudinal patterns in stabilizing density dependence of forest communities

Author

Hülsmann, Lisa, Chisholm, Ryan A., Comita, Liza, Visser, Marco D., de Souza Leite, Melina, Aguilar, Salomon, Anderson-Teixeira, Kristina J., Bourg, Norman A., Brockelman, Warren Y., Bunyavejchewin, Sarayudh, Castaño, Nicolas, Chang-Yang, Chia-Hao, Chuyong, George B., Clay, Keith, Davies, Stuart J., Duque, Alvaro, Ediriweera, Sisira, Ewango, Corneille, Gilbert, Gregory S., Holík, Jan, Howe, Robert W., Hubbell, Stephen P., Itoh, Akira, Johnson, Daniel J., Kenfack, David, Král, Kamil, Larson, Andrew J., Lutz, James A., Makana, Jean-Remy, Malhi, Yadvinder, McMahon, Sean M., McShea, William J., Mohamad, Mohizah, Nasardin, Musalmah, Nathalang, Anuttara, Norden, Natalia, Oliveira, Alexandre A., Parmigiani, Renan, Perez, Rolando, Phillips, Richard P., Pongpattananurak, Nantachai, Sun, I-Fang, Swanson, Mark E., Tan, Sylvester, Thomas, Duncan, Thompson, Jill, Uriarte, Maria, Wolf, Amy T., Yao, Tze Leong, Zimmerman, Jess K., Zuleta, Daniel, and Hartig, Florian

Published
2024
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38. Global assessment of marine plastic exposure risk for oceanic birds.

Author

Clark, Bethany, Carneiro, Ana, Pearmain, Elizabeth, Rouyer, Marie-Morgane, Clay, Thomas, Cowger, Win, Phillips, Richard, Manica, Andrea, Hazin, Carolina, Eriksen, Marcus, González-Solís, Jacob, Adams, Josh, Albores-Barajas, Yuri, Alfaro-Shigueto, Joanna, Alho, Maria, Araujo, Deusa, Arcos, José, Arnould, John, Barbosa, Nadito, Barbraud, Christophe, Beard, Annalea, Beck, Jessie, Bell, Elizabeth, Bennet, Della, Berlincourt, Maud, Biscoito, Manuel, Bjørnstad, Oskar, Bolton, Mark, Booth Jones, Katherine, Borg, John, Bourgeois, Karen, Bretagnolle, Vincent, Bried, Joël, Briskie, James, Brooke, M, Brownlie, Katherine, Bugoni, Leandro, Calabrese, Licia, Campioni, Letizia, Carey, Mark, Carle, Ryan, Carlile, Nicholas, Carreiro, Ana, Catry, Paulo, Catry, Teresa, Cecere, Jacopo, Ceia, Filipe, Cherel, Yves, Choi, Chang-Yong, Cianchetti-Benedetti, Marco, Clarke, Rohan, Cleeland, Jaimie, Colodro, Valentina, Congdon, Bradley, Danielsen, Jóhannis, De Pascalis, Federico, Deakin, Zoe, Dehnhard, Nina, DellOmo, Giacomo, Delord, Karine, Descamps, Sébastien, Dilley, Ben, Dinis, Herculano, Dubos, Jerome, Dunphy, Brendon, Emmerson, Louise, Fagundes, Ana, Fayet, Annette, Felis, Jonathan, Fischer, Johannes, Freeman, Amanda, Fromant, Aymeric, Gaibani, Giorgia, García, David, Gjerdrum, Carina, Gomes, Ivandra, Forero, Manuela, Granadeiro, José, Grecian, W, Grémillet, David, Guilford, Tim, Hallgrimsson, Gunnar, Halpin, Luke, Hansen, Erpur, Hedd, April, Helberg, Morten, Helgason, Halfdan, Henry, Leeann, Hereward, Hannah, Hernandez-Montero, Marcos, Hindell, Mark, Hodum, Peter, Imperio, Simona, Jaeger, Audrey, Jessopp, Mark, Jodice, Patrick, Jones, Carl, Jones, Christopher, Jónsson, Jón, and Kane, Adam

Subjects
Animals, Plastics, Waste Products, Environmental Monitoring, Oceans and Seas, Birds, Indian Ocean
Abstract

Plastic pollution is distributed patchily around the worlds oceans. Likewise, marine organisms that are vulnerable to plastic ingestion or entanglement have uneven distributions. Understanding where wildlife encounters plastic is crucial for targeting research and mitigation. Oceanic seabirds, particularly petrels, frequently ingest plastic, are highly threatened, and cover vast distances during foraging and migration. However, the spatial overlap between petrels and plastics is poorly understood. Here we combine marine plastic density estimates with individual movement data for 7137 birds of 77 petrel species to estimate relative exposure risk. We identify high exposure risk areas in the Mediterranean and Black seas, and the northeast Pacific, northwest Pacific, South Atlantic and southwest Indian oceans. Plastic exposure risk varies greatly among species and populations, and between breeding and non-breeding seasons. Exposure risk is disproportionately high for Threatened species. Outside the Mediterranean and Black seas, exposure risk is highest in the high seas and Exclusive Economic Zones (EEZs) of the USA, Japan, and the UK. Birds generally had higher plastic exposure risk outside the EEZ of the country where they breed. We identify conservation and research priorities, and highlight that international collaboration is key to addressing the impacts of marine plastic on wide-ranging species.

Published
2023

39. Leaf angle as a leaf and canopy trait: Rejuvenating its role in ecology with new technology

Author

Yang, Xi, Li, Rong, Jablonski, Andrew, Stovall, Atticus, Kim, Jongmin, Yi, Koong, Ma, Yixin, Beverly, Daniel, Phillips, Richard, Novick, Kim, Xu, Xiangtao, and Lerdau, Manuel

Subjects
Plant Biology, Biological Sciences, Ecology, Affordable and Clean Energy, Ecosystem, Photosynthesis, Plant Leaves, Water, Technology, Trees, canopy optimization, leaf economics spectrum, light environment, photosynthesis, radiative transfer, Ecological Applications, Evolutionary Biology, Ecological applications, Environmental management
Abstract

Life on Earth depends on the conversion of solar energy to chemical energy by plants through photosynthesis. A fundamental challenge in optimizing photosynthesis is to adjust leaf angles to efficiently use the intercepted sunlight under the constraints of heat stress, water loss and competition. Despite the importance of leaf angle, until recently, we have lacked data and frameworks to describe and predict leaf angle dynamics and their impacts on leaves to the globe. We review the role of leaf angle in studies of ecophysiology, ecosystem ecology and earth system science, and highlight the essential yet understudied role of leaf angle as an ecological strategy to regulate plant carbon-water-energy nexus and to bridge leaf, canopy and earth system processes. Using two models, we show that leaf angle variations have significant impacts on not only canopy-scale photosynthesis, energy balance and water use efficiency but also light competition within the forest canopy. New techniques to measure leaf angles are emerging, opening opportunities to understand the rarely-measured intraspecific, interspecific, seasonal and interannual variations of leaf angles and their implications to plant biology and earth system science. We conclude by proposing three directions for future research.

Published
2023

40. Bacterial diversity in Buruli ulcer lesions in Ghana

Author

Ackam, Nancy, Opoku-Boadi, Abigail, Agbavor, Bernadette, Adjei, Jonathan Kofi, Agbanyo, Abigail, Oppong, Michael Ntiamoah, Wiafe-Akenten, Charity, Sylverken, Augustina, Obiri-Danso, Kwasi, Wansbrough-Jones, Mark, Amoako, Yaw Ampem, and Phillips, Richard Odame

Published
2024
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41. Implementation of an integrated control programme for neglected tropical diseases of the skin in Ghana: The essential role of the laboratory

Author

Agbanyo, Abigail, Agbavor, Bernadette, Gyabaah, Solomon, Oppong, Michael Ntiamoah, Dornu, Olivia, Antwi, Philemon Boasiako, Loglo, Aloysius Dzigbordi, Abass, Kabiru Mohammed, Amofa, George, Kotey, Nana Konama, Quao, Benedict, Frimpong, Michael, Asiedu, Kingsley, Amoako, Yaw Ampem, and Phillips, Richard Odame

Published
2024
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48. One for One, or All for All: Equilibria and Optimality of Collaboration in Federated Learning

Author

Blum, Avrim, Haghtalab, Nika, Phillips, Richard Lanas, and Shao, Han

Subjects
Computer Science - Machine Learning, Computer Science - Data Structures and Algorithms, Computer Science - Computer Science and Game Theory
Abstract

In recent years, federated learning has been embraced as an approach for bringing about collaboration across large populations of learning agents. However, little is known about how collaboration protocols should take agents' incentives into account when allocating individual resources for communal learning in order to maintain such collaborations. Inspired by game theoretic notions, this paper introduces a framework for incentive-aware learning and data sharing in federated learning. Our stable and envy-free equilibria capture notions of collaboration in the presence of agents interested in meeting their learning objectives while keeping their own sample collection burden low. For example, in an envy-free equilibrium, no agent would wish to swap their sampling burden with any other agent and in a stable equilibrium, no agent would wish to unilaterally reduce their sampling burden. In addition to formalizing this framework, our contributions include characterizing the structural properties of such equilibria, proving when they exist, and showing how they can be computed. Furthermore, we compare the sample complexity of incentive-aware collaboration with that of optimal collaboration when one ignores agents' incentives.

Published
2021

49. WILDS: A Benchmark of in-the-Wild Distribution Shifts

Author

Koh, Pang Wei, Sagawa, Shiori, Marklund, Henrik, Xie, Sang Michael, Zhang, Marvin, Balsubramani, Akshay, Hu, Weihua, Yasunaga, Michihiro, Phillips, Richard Lanas, Gao, Irena, Lee, Tony, David, Etienne, Stavness, Ian, Guo, Wei, Earnshaw, Berton A., Haque, Imran S., Beery, Sara, Leskovec, Jure, Kundaje, Anshul, Pierson, Emma, Levine, Sergey, Finn, Chelsea, and Liang, Percy

Subjects
Computer Science - Machine Learning
Abstract

Distribution shifts -- where the training distribution differs from the test distribution -- can substantially degrade the accuracy of machine learning (ML) systems deployed in the wild. Despite their ubiquity in the real-world deployments, these distribution shifts are under-represented in the datasets widely used in the ML community today. To address this gap, we present WILDS, a curated benchmark of 10 datasets reflecting a diverse range of distribution shifts that naturally arise in real-world applications, such as shifts across hospitals for tumor identification; across camera traps for wildlife monitoring; and across time and location in satellite imaging and poverty mapping. On each dataset, we show that standard training yields substantially lower out-of-distribution than in-distribution performance. This gap remains even with models trained by existing methods for tackling distribution shifts, underscoring the need for new methods for training models that are more robust to the types of distribution shifts that arise in practice. To facilitate method development, we provide an open-source package that automates dataset loading, contains default model architectures and hyperparameters, and standardizes evaluations. Code and leaderboards are available at https://wilds.stanford.edu.

Published
2020

50. The three major axes of terrestrial ecosystem function

Author

Migliavacca, Mirco, Musavi, Talie, Mahecha, Miguel D, Nelson, Jacob A, Knauer, Jürgen, Baldocchi, Dennis D, Perez-Priego, Oscar, Christiansen, Rune, Peters, Jonas, Anderson, Karen, Bahn, Michael, Black, T Andrew, Blanken, Peter D, Bonal, Damien, Buchmann, Nina, Caldararu, Silvia, Carrara, Arnaud, Carvalhais, Nuno, Cescatti, Alessandro, Chen, Jiquan, Cleverly, Jamie, Cremonese, Edoardo, Desai, Ankur R, El-Madany, Tarek S, Farella, Martha M, Fernández-Martínez, Marcos, Filippa, Gianluca, Forkel, Matthias, Galvagno, Marta, Gomarasca, Ulisse, Gough, Christopher M, Göckede, Mathias, Ibrom, Andreas, Ikawa, Hiroki, Janssens, Ivan A, Jung, Martin, Kattge, Jens, Keenan, Trevor F, Knohl, Alexander, Kobayashi, Hideki, Kraemer, Guido, Law, Beverly E, Liddell, Michael J, Ma, Xuanlong, Mammarella, Ivan, Martini, David, Macfarlane, Craig, Matteucci, Giorgio, Montagnani, Leonardo, Pabon-Moreno, Daniel E, Panigada, Cinzia, Papale, Dario, Pendall, Elise, Penuelas, Josep, Phillips, Richard P, Reich, Peter B, Rossini, Micol, Rotenberg, Eyal, Scott, Russell L, Stahl, Clement, Weber, Ulrich, Wohlfahrt, Georg, Wolf, Sebastian, Wright, Ian J, Yakir, Dan, Zaehle, Sönke, and Reichstein, Markus

Subjects
Life on Land, Carbon Cycle, Carbon Dioxide, Climate, Datasets as Topic, Ecosystem, Humidity, Plants, Principal Component Analysis, Water Cycle, General Science & Technology
Abstract

The leaf economics spectrum1,2 and the global spectrum of plant forms and functions3 revealed fundamental axes of variation in plant traits, which represent different ecological strategies that are shaped by the evolutionary development of plant species2. Ecosystem functions depend on environmental conditions and the traits of species that comprise the ecological communities4. However, the axes of variation of ecosystem functions are largely unknown, which limits our understanding of how ecosystems respond as a whole to anthropogenic drivers, climate and environmental variability4,5. Here we derive a set of ecosystem functions6 from a dataset of surface gas exchange measurements across major terrestrial biomes. We find that most of the variability within ecosystem functions (71.8%) is captured by three key axes. The first axis reflects maximum ecosystem productivity and is mostly explained by vegetation structure. The second axis reflects ecosystem water-use strategies and is jointly explained by variation in vegetation height and climate. The third axis, which represents ecosystem carbon-use efficiency, features a gradient related to aridity, and is explained primarily by variation in vegetation structure. We show that two state-of-the-art land surface models reproduce the first and most important axis of ecosystem functions. However, the models tend to simulate more strongly correlated functions than those observed, which limits their ability to accurately predict the full range of responses to environmental changes in carbon, water and energy cycling in terrestrial ecosystems7,8.

Published
2021

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