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1. NeRF-Accelerated Ecological Monitoring in Mixed-Evergreen Redwood Forest

Author

Korycki, Adam, Yeaton, Cory, Gilbert, Gregory S., Josephson, Colleen, and McGuire, Steve

Subjects
Computer Science - Computer Vision and Pattern Recognition, Computer Science - Robotics
Abstract

Forest mapping provides critical observational data needed to understand the dynamics of forest environments. Notably, tree diameter at breast height (DBH) is a metric used to estimate forest biomass and carbon dioxide sequestration. Manual methods of forest mapping are labor intensive and time consuming, a bottleneck for large-scale mapping efforts. Automated mapping relies on acquiring dense forest reconstructions, typically in the form of point clouds. Terrestrial laser scanning (TLS) and mobile laser scanning (MLS) generate point clouds using expensive LiDAR sensing, and have been used successfully to estimate tree diameter. Neural radiance fields (NeRFs) are an emergent technology enabling photorealistic, vision-based reconstruction by training a neural network on a sparse set of input views. In this paper, we present a comparison of MLS and NeRF forest reconstructions for the purpose of trunk diameter estimation in a mixed-evergreen Redwood forest. In addition, we propose an improved DBH-estimation method using convex-hull modeling. Using this approach, we achieved 1.68 cm RMSE, which consistently outperformed standard cylinder modeling approaches. Our code contributions and forest datasets are freely available at https://github.com/harelab-ucsc/RedwoodNeRF.

Published
2024

2. Airborne DNA reveals predictable spatial and seasonal dynamics of fungi

Author

Abrego, Nerea, Furneaux, Brendan, Hardwick, Bess, Somervuo, Panu, Palorinne, Isabella, Aguilar-Trigueros, Carlos A., Andrew, Nigel R., Babiy, Ulyana V., Bao, Tan, Bazzano, Gisela, Bondarchuk, Svetlana N., Bonebrake, Timothy C., Brennan, Georgina L., Bret-Harte, Syndonia, Bässler, Claus, Cagnolo, Luciano, Cameron, Erin K., Chapurlat, Elodie, Creer, Simon, D’Acqui, Luigi P., de Vere, Natasha, Desprez-Loustau, Marie-Laure, Dongmo, Michel A. K., Jacobsen, Ida B. Dyrholm, Fisher, Brian L., Flores de Jesus, Miguel, Gilbert, Gregory S., Griffith, Gareth W., Gritsuk, Anna A., Gross, Andrin, Grudd, Håkan, Halme, Panu, Hanna, Rachid, Hansen, Jannik, Hansen, Lars Holst, Hegbe, Apollon D. M. T., Hill, Sarah, Hogg, Ian D., Hultman, Jenni, Hyde, Kevin D., Hynson, Nicole A., Ivanova, Natalia, Karisto, Petteri, Kerdraon, Deirdre, Knorre, Anastasia, Krisai-Greilhuber, Irmgard, Kurhinen, Juri, Kuzmina, Masha, Lecomte, Nicolas, Lecomte, Erin, Loaiza, Viviana, Lundin, Erik, Meire, Alexander, Mešić, Armin, Miettinen, Otto, Monkhouse, Norman, Mortimer, Peter, Müller, Jörg, Nilsson, R. Henrik, Nonti, Puani Yannick C., Nordén, Jenni, Nordén, Björn, Norros, Veera, Paz, Claudia, Pellikka, Petri, Pereira, Danilo, Petch, Geoff, Pitkänen, Juha-Matti, Popa, Flavius, Potter, Caitlin, Purhonen, Jenna, Pätsi, Sanna, Rafiq, Abdullah, Raharinjanahary, Dimby, Rakos, Niklas, Rathnayaka, Achala R., Raundrup, Katrine, Rebriev, Yury A., Rikkinen, Jouko, Rogers, Hanna M. K., Rogovsky, Andrey, Rozhkov, Yuri, Runnel, Kadri, Saarto, Annika, Savchenko, Anton, Schlegel, Markus, Schmidt, Niels Martin, Seibold, Sebastian, Skjøth, Carsten, Stengel, Elisa, Sutyrina, Svetlana V., Syvänperä, Ilkka, Tedersoo, Leho, Timm, Jebidiah, Tipton, Laura, Toju, Hirokazu, Uscka-Perzanowska, Maria, van der Bank, Michelle, van der Bank, F. Herman, Vandenbrink, Bryan, Ventura, Stefano, Vignisson, Solvi R., Wang, Xiaoyang, Weisser, Wolfgang W., Wijesinghe, Subodini N., Wright, S. Joseph, Yang, Chunyan, Yorou, Nourou S., Young, Amanda, Yu, Douglas W., Zakharov, Evgeny V., Hebert, Paul D. N., Roslin, Tomas, and Ovaskainen, Otso

Published
2024
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3. Global Spore Sampling Project: A global, standardized dataset of airborne fungal DNA

Author

Ovaskainen, Otso, Abrego, Nerea, Furneaux, Brendan, Hardwick, Bess, Somervuo, Panu, Palorinne, Isabella, Andrew, Nigel R., Babiy, Ulyana V., Bao, Tan, Bazzano, Gisela, Bondarchuk, Svetlana N., Bonebrake, Timothy C., Brennan, Georgina L., Bret-Harte, Syndonia, Bässler, Claus, Cagnolo, Luciano, Cameron, Erin K., Chapurlat, Elodie, Creer, Simon, D’Acqui, Luigi P., de Vere, Natasha, Desprez-Loustau, Marie-Laure, Dongmo, Michel A. K., Dyrholm Jacobsen, Ida B., Fisher, Brian L., Flores de Jesus, Miguel, Gilbert, Gregory S., Griffith, Gareth W., Gritsuk, Anna A., Gross, Andrin, Grudd, Håkan, Halme, Panu, Hanna, Rachid, Hansen, Jannik, Hansen, Lars Holst, Hegbe, Apollon D. M. T., Hill, Sarah, Hogg, Ian D., Hultman, Jenni, Hyde, Kevin D., Hynson, Nicole A., Ivanova, Natalia, Karisto, Petteri, Kerdraon, Deirdre, Knorre, Anastasia, Krisai-Greilhuber, Irmgard, Kurhinen, Juri, Kuzmina, Masha, Lecomte, Nicolas, Lecomte, Erin, Loaiza, Viviana, Lundin, Erik, Meire, Alexander, Mešić, Armin, Miettinen, Otto, Monkhause, Norman, Mortimer, Peter, Müller, Jörg, Nilsson, R. Henrik, Nonti, Puani Yannick C., Nordén, Jenni, Nordén, Björn, Paz, Claudia, Pellikka, Petri, Pereira, Danilo, Petch, Geoff, Pitkänen, Juha-Matti, Popa, Flavius, Potter, Caitlin, Purhonen, Jenna, Pätsi, Sanna, Rafiq, Abdullah, Raharinjanahary, Dimby, Rakos, Niklas, Rathnayaka, Achala R., Raundrup, Katrine, Rebriev, Yury A., Rikkinen, Jouko, Rogers, Hanna M. K., Rogovsky, Andrey, Rozhkov, Yuri, Runnel, Kadri, Saarto, Annika, Savchenko, Anton, Schlegel, Markus, Schmidt, Niels Martin, Seibold, Sebastian, Skjøth, Carsten, Stengel, Elisa, Sutyrina, Svetlana V., Syvänperä, Ilkka, Tedersoo, Leho, Timm, Jebidiah, Tipton, Laura, Toju, Hirokazu, Uscka-Perzanowska, Maria, van der Bank, Michelle, Herman van der Bank, F., Vandenbrink, Bryan, Ventura, Stefano, Vignisson, Solvi R., Wang, Xiaoyang, Weisser, Wolfgang W., Wijesinghe, Subodini N., Joseph Wright, S., Yang, Chunyan, Yorou, Nourou S., Young, Amanda, Yu, Douglas W., Zakharov, Evgeny V., Hebert, Paul D. N., and Roslin, Tomas

Published
2024
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4. 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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5. Linking seed size and number to trait syndromes in trees

Author

Bogdziewicz, Michal, Acuña, Marie‐Claire Aravena, Andrus, Robert, Ascoli, Davide, Bergeron, Yves, Brveiller, Daniel, Boivin, Thomas, Bonal, Raul, Caignard, Thomas, Cailleret, Maxime, Calama, Rafael, Calderon, Sergio Donoso, Camarero, J Julio, Chang‐Yang, Chia‐Hao, Chave, Jerome, Chianucci, Francesco, Cleavitt, Natalie L, Courbaud, Benoit, Cutini, Andrea, Curt, Thomas, Das, Adrian J, Davi, Hendrik, Delpierre, Nicolas, Delzon, Sylvain, Dietze, Michael, Dormont, Laurent, Farfan‐Rios, William, Gehring, Catherine A, Gilbert, Gregory S, Gratzer, Georg, Greenberg, Cathryn H, Guignabert, Arthur, Guo, Qinfeng, Hacket‐Pain, Andrew, Hampe, Arndt, Han, Qingmin, Hoshizaki, Kazuhiko, Ibanez, Ines, Johnstone, Jill F, Journé, Valentin, Kitzberger, Thomas, Knops, Johannes MH, Kunstler, Georges, Kobe, Richard, Lageard, Jonathan GA, LaMontagne, Jalene M, Ledwon, Mateusz, Leininger, Theodor, Limousin, Jean‐Marc, Lutz, James A, Macias, Diana, Marell, Anders, McIntire, Eliot JB, Moran, Emily, Motta, Renzo, Myers, Jonathan A, Nagel, Thomas A, Naoe, Shoji, Noguchi, Mahoko, Oguro, Michio, Kurokawa, Hiroko, Ourcival, Jean‐Marc, Parmenter, Robert, Perez‐Ramos, Ignacio M, Piechnik, Lukasz, Podgórski, Tomasz, Poulsen, John, Qiu, Tong, Redmond, Miranda D, Reid, Chantal D, Rodman, Kyle C, Šamonil, Pavel, Holik, Jan, Scher, C Lane, Van Marle, Harald Schmidt, Seget, Barbara, Shibata, Mitsue, Sharma, Shubhi, Silman, Miles, Steele, Michael A, Straub, Jacob N, Sun, I‐Fang, Sutton, Samantha, Swenson, Jennifer J, Thomas, Peter A, Uriarte, Maria, Vacchiano, Giorgio, Veblen, Thomas T, Wright, Boyd, Wright, S Joseph, Whitham, Thomas G, Zhu, Kai, Zimmerman, Jess K, Zywiec, Magdalna, and Clark, James S

Subjects
fecundity, functional traits, leaf economics, life history strategies, size syndrome, tree recruitment, Ecology
Published
2023

6. Seed Disinfestation Practices to Control Seed-Borne Fungi and Bacteria in Home Production of Sprouts

Author

Gilbert, Gregory S, Diaz, Alyssa, and Bregoff, Haylee A

Subjects
Prevention, Zero Hunger, seed microbiology, bacteria, fungi, seed disinfection, seed sterilization, seed sprouts, food safety, hypochlorous acid, sodium hypochlorite, home sprout production, Food Sciences
Abstract

Concern over microbial contamination limits the adoption of home production of sprouts as a nutritious and sustainable food. Simple, accessible approaches to seed disinfection could support safe home seed sprouting. Here, we quantify bacterial and fungal contamination of seeds of 14 plant cultivars sold for home sprout production and test a range of chemical and physical methods for seed disinfestation appropriate for home use. Most seeds are contaminated with a variety of bacteria and fungi, and those microbes are usually limited to the seed surface. Heat treatments are not effective for seed disinfection because the high temperatures needed to effectively reduce microbial contamination also reduce seed germination. Two chlorine-based chemical disinfectants-dilute household bleach (0.6% sodium hypochlorite) and freshly generated hypochlorous acid (800 ppm chlorine)-were the most effective disinfection agents tested (up to a 5-log reduction in bacteria) that also did not harm seed germination.

Published
2023

7. Globally, tree fecundity exceeds productivity gradients

Author

Journé, Valentin, Andrus, Robert, Aravena, Marie‐Claire, Ascoli, Davide, Berretti, Roberta, Berveiller, Daniel, Bogdziewicz, Michal, Boivin, Thomas, Bonal, Raul, Caignard, Thomas, Calama, Rafael, Camarero, Jesús Julio, Chang‐Yang, Chia‐Hao, Courbaud, Benoit, Courbet, Francois, Curt, Thomas, Das, Adrian J, Daskalakou, Evangelia, Davi, Hendrik, Delpierre, Nicolas, Delzon, Sylvain, Dietze, Michael, Calderon, Sergio Donoso, Dormont, Laurent, Espelta, Josep Maria, Fahey, Timothy J, Farfan‐Rios, William, Gehring, Catherine A, Gilbert, Gregory S, Gratzer, Georg, Greenberg, Cathryn H, Guo, Qinfeng, Hacket‐Pain, Andrew, Hampe, Arndt, Han, Qingmin, Lambers, Janneke Hille Ris, Hoshizaki, Kazuhiko, Ibanez, Ines, Johnstone, Jill F, Kabeya, Daisuke, Kays, Roland, Kitzberger, Thomas, Knops, Johannes MH, Kobe, Richard K, Kunstler, Georges, Lageard, Jonathan GA, LaMontagne, Jalene M, Leininger, Theodor, Limousin, Jean‐Marc, Lutz, James A, Macias, Diana, McIntire, Eliot JB, Moore, Christopher M, Moran, Emily, Motta, Renzo, Myers, Jonathan A, Nagel, Thomas A, Noguchi, Kyotaro, Ourcival, Jean‐Marc, Parmenter, Robert, Pearse, Ian S, Perez‐Ramos, Ignacio M, Piechnik, Lukasz, Poulsen, John, Poulton‐Kamakura, Renata, Qiu, Tong, Redmond, Miranda D, Reid, Chantal D, Rodman, Kyle C, Rodriguez‐Sanchez, Francisco, Sanguinetti, Javier D, Scher, C Lane, Van Marle, Harald Schmidt, Seget, Barbara, Sharma, Shubhi, Silman, Miles, Steele, Michael A, Stephenson, Nathan L, Straub, Jacob N, Swenson, Jennifer J, Swift, Margaret, Thomas, Peter A, Uriarte, Maria, Vacchiano, Giorgio, Veblen, Thomas T, Whipple, Amy V, Whitham, Thomas G, Wright, Boyd, Wright, S Joseph, Zhu, Kai, Zimmerman, Jess K, Zlotin, Roman, Zywiec, Magdalena, and Clark, James S

Subjects
Climate Change Impacts and Adaptation, Biological Sciences, Ecology, Environmental Sciences, Regenerative Medicine, Biodiversity, Climate, Fertility, Forests, Seeds, Trees, climate, competition, forest regeneration, seed consumption, species interactions, tree fecundity, Ecological Applications, Evolutionary Biology, Ecological applications, Environmental management
Abstract

Lack of tree fecundity data across climatic gradients precludes the analysis of how seed supply contributes to global variation in forest regeneration and biotic interactions responsible for biodiversity. A global synthesis of raw seedproduction data shows a 250-fold increase in seed abundance from cold-dry to warm-wet climates, driven primarily by a 100-fold increase in seed production for a given tree size. The modest (threefold) increase in forest productivity across the same climate gradient cannot explain the magnitudes of these trends. The increase in seeds per tree can arise from adaptive evolution driven by intense species interactions or from the direct effects of a warm, moist climate on tree fecundity. Either way, the massive differences in seed supply ramify through food webs potentially explaining a disproportionate role for species interactions in the wet tropics.

Published
2022

8. Mycorrhizal feedbacks influence global forest structure and diversity

Author

Delavaux, Camille S., LaManna, Joseph A., Myers, Jonathan A., Phillips, Richard P., Aguilar, Salomón, Allen, David, Alonso, Alfonso, Anderson-Teixeira, Kristina J., Baker, Matthew E., Baltzer, Jennifer L., Bissiengou, Pulchérie, Bonfim, Mariana, Bourg, Norman A., Brockelman, Warren Y., Burslem, David F. R. P., 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 C., Feistner, Anna, Freestone, Amy L., Giambelluca, Thomas, Giardina, Christian P., Gilbert, Gregory S., He, Fangliang, Holík, Jan, Howe, Robert W., Huaraca Huasca, Walter, Hubbell, Stephen P., Inman, Faith, Jansen, Patrick A., Johnson, Daniel J., Kral, Kamil, Larson, Andrew J., Litton, Creighton M., Lutz, James A., Malhi, Yadvinder, McGuire, Krista, McMahon, Sean M., McShea, William J., Memiaghe, Hervé, Nathalang, Anuttara, Norden, Natalia, Novotny, Vojtech, O’Brien, Michael J., Orwig, David A., Ostertag, Rebecca, Parker, Geoffrey G. (‘Jess’), Pérez, Rolando, Reynolds, Glen, Russo, Sabrina E., Sack, Lawren, Šamonil, Pavel, Sun, I-Fang, Swanson, Mark E., Thompson, Jill, Uriarte, Maria, Vandermeer, John, Wang, Xihua, Ware, Ian, Weiblen, George D., Wolf, Amy, Wu, Shu-Hui, Zimmerman, Jess K., Lauber, Thomas, Maynard, Daniel S., Crowther, Thomas W., and Averill, Colin

Published
2023
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9. Masting is uncommon in trees that depend on mutualist dispersers in the context of global climate and fertility gradients

Author

Qiu, Tong, Aravena, Marie-Claire, Ascoli, Davide, Bergeron, Yves, Bogdziewicz, Michal, Boivin, Thomas, Bonal, Raul, Caignard, Thomas, Cailleret, Maxime, Calama, Rafael, Calderon, Sergio Donoso, Camarero, J. Julio, Chang-Yang, Chia-Hao, Chave, Jerome, Chianucci, Francesco, Courbaud, Benoit, Cutini, Andrea, Das, Adrian J., Delpierre, Nicolas, Delzon, Sylvain, Dietze, Michael, Dormont, Laurent, Espelta, Josep Maria, Fahey, Timothy J., Farfan-Rios, William, Franklin, Jerry F., Gehring, Catherine A., Gilbert, Gregory S., Gratzer, Georg, Greenberg, Cathryn H., Guignabert, Arthur, Guo, Qinfeng, Hacket-Pain, Andrew, Hampe, Arndt, Han, Qingmin, Holik, Jan, Hoshizaki, Kazuhiko, Ibanez, Ines, Johnstone, Jill F., Journé, Valentin, Kitzberger, Thomas, Knops, Johannes M. H., Kunstler, Georges, Kurokawa, Hiroko, Lageard, Jonathan G. A., LaMontagne, Jalene M., Lefevre, Francois, Leininger, Theodor, Limousin, Jean-Marc, Lutz, James A., Macias, Diana, Marell, Anders, McIntire, Eliot J. B., Moore, Christopher M., Moran, Emily, Motta, Renzo, Myers, Jonathan A., Nagel, Thomas A., Naoe, Shoji, Noguchi, Mahoko, Oguro, Michio, Parmenter, Robert, Pearse, Ian S., Perez-Ramos, Ignacio M., Piechnik, Lukasz, Podgorski, Tomasz, Poulsen, John, Redmond, Miranda D., Reid, Chantal D., Rodman, Kyle C., Rodriguez-Sanchez, Francisco, Samonil, Pavel, Sanguinetti, Javier D., Scher, C. Lane, Seget, Barbara, Sharma, Shubhi, Shibata, Mitsue, Silman, Miles, Steele, Michael A., Stephenson, Nathan L., Straub, Jacob N., Sutton, Samantha, Swenson, Jennifer J., Swift, Margaret, Thomas, Peter A., Uriarte, Maria, Vacchiano, Giorgio, Whipple, Amy V., Whitham, Thomas G., Wion, Andreas P., Wright, S. Joseph, Zhu, Kai, Zimmerman, Jess K., Zywiec, Magdalena, and Clark, James S.

Published
2023
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10. North American tree migration paced by climate in the West, lagging in the East

Author

Sharma, Shubhi, Andrus, Robert, Bergeron, Yves, Bogdziewicz, Michal, Bragg, Don C, Brockway, Dale, Cleavitt, Natalie L, Courbaud, Benoit, Das, Adrian J, Dietze, Michael, Fahey, Timothy J, Franklin, Jerry F, Gilbert, Gregory S, Greenberg, Cathryn H, Guo, Qinfeng, Lambers, Janneke Hille Ris, Ibanez, Ines, Johnstone, Jill F, Kilner, Christopher L, Knops, Johannes MH, Koenig, Walter D, Kunstler, Georges, LaMontagne, Jalene M, Macias, Diana, Moran, Emily, Myers, Jonathan A, Parmenter, Robert, Pearse, Ian S, Poulton-Kamakura, Renata, Redmond, Miranda D, Reid, Chantal D, Rodman, Kyle C, Scher, C Lane, Schlesinger, William H, Steele, Michael A, Stephenson, Nathan L, Swenson, Jennifer J, Swift, Margaret, Veblen, Thomas T, Whipple, Amy V, Whitham, Thomas G, Wion, Andreas P, Woodall, Christopher W, Zlotin, Roman, and Clark, James S

Subjects
Climate Action, Climate Change, Ecosystem, Fertility, Geography, North America, Trees, Uncertainty, climate change, forest regeneration, seed production, tree migration
Abstract

Tree fecundity and recruitment have not yet been quantified at scales needed to anticipate biogeographic shifts in response to climate change. By separating their responses, this study shows coherence across species and communities, offering the strongest support to date that migration is in progress with regional limitations on rates. The southeastern continent emerges as a fecundity hotspot, but it is situated south of population centers where high seed production could contribute to poleward population spread. By contrast, seedling success is highest in the West and North, serving to partially offset limited seed production near poleward frontiers. The evidence of fecundity and recruitment control on tree migration can inform conservation planning for the expected long-term disequilibrium between climate and forest distribution.

Published
2022

11. Limits to reproduction and seed size-number trade-offs that shape forest dominance and future recovery

Author

Qiu, Tong, Andrus, Robert, Aravena, Marie-Claire, Ascoli, Davide, Bergeron, Yves, Berretti, Roberta, Berveiller, Daniel, Bogdziewicz, Michal, Boivin, Thomas, Bonal, Raul, Bragg, Don C, Caignard, Thomas, Calama, Rafael, Camarero, J Julio, Chang-Yang, Chia-Hao, Cleavitt, Natalie L, Courbaud, Benoit, Courbet, Francois, Curt, Thomas, Das, Adrian J, Daskalakou, Evangelia, Davi, Hendrik, Delpierre, Nicolas, Delzon, Sylvain, Dietze, Michael, Calderon, Sergio Donoso, Dormont, Laurent, Espelta, Josep, Fahey, Timothy J, Farfan-Rios, William, Gehring, Catherine A, Gilbert, Gregory S, Gratzer, Georg, Greenberg, Cathryn H, Guo, Qinfeng, Hacket-Pain, Andrew, Hampe, Arndt, Han, Qingmin, Hille Ris Lambers, Janneke, Hoshizaki, Kazuhiko, Ibanez, Ines, Johnstone, Jill F, Journé, Valentin, Kabeya, Daisuke, Kilner, Christopher L, Kitzberger, Thomas, Knops, Johannes MH, Kobe, Richard K, Kunstler, Georges, Lageard, Jonathan GA, LaMontagne, Jalene M, Ledwon, Mateusz, Lefevre, Francois, Leininger, Theodor, Limousin, Jean-Marc, Lutz, James A, Macias, Diana, McIntire, Eliot JB, Moore, Christopher M, Moran, Emily, Motta, Renzo, Myers, Jonathan A, Nagel, Thomas A, Noguchi, Kyotaro, Ourcival, Jean-Marc, Parmenter, Robert, Pearse, Ian S, Perez-Ramos, Ignacio M, Piechnik, Lukasz, Poulsen, John, Poulton-Kamakura, Renata, Redmond, Miranda D, Reid, Chantal D, Rodman, Kyle C, Rodriguez-Sanchez, Francisco, Sanguinetti, Javier D, Scher, C Lane, Schlesinger, William H, Schmidt Van Marle, Harald, Seget, Barbara, Sharma, Shubhi, Silman, Miles, Steele, Michael A, Stephenson, Nathan L, Straub, Jacob N, Sun, I-Fang, Sutton, Samantha, Swenson, Jennifer J, Swift, Margaret, Thomas, Peter A, Uriarte, Maria, Vacchiano, Giorgio, Veblen, Thomas T, Whipple, Amy V, Whitham, Thomas G, Wion, Andreas P, Wright, Boyd, Wright, S Joseph, Zhu, Kai, and Zimmerman, Jess K

Subjects
Agricultural, Veterinary and Food Sciences, Biological Sciences, Ecology, Contraception/Reproduction, Fertility, Forests, Reproduction, Seeds, Trees
Abstract

The relationships that control seed production in trees are fundamental to understanding the evolution of forest species and their capacity to recover from increasing losses to drought, fire, and harvest. A synthesis of fecundity data from 714 species worldwide allowed us to examine hypotheses that are central to quantifying reproduction, a foundation for assessing fitness in forest trees. Four major findings emerged. First, seed production is not constrained by a strict trade-off between seed size and numbers. Instead, seed numbers vary over ten orders of magnitude, with species that invest in large seeds producing more seeds than expected from the 1:1 trade-off. Second, gymnosperms have lower seed production than angiosperms, potentially due to their extra investments in protective woody cones. Third, nutrient-demanding species, indicated by high foliar phosphorus concentrations, have low seed production. Finally, sensitivity of individual species to soil fertility varies widely, limiting the response of community seed production to fertility gradients. In combination, these findings can inform models of forest response that need to incorporate reproductive potential.

Published
2022

12. Is there tree senescence? The fecundity evidence

Author

Qiu, Tong, Aravena, Marie-Claire, Andrus, Robert, Ascoli, Davide, Bergeron, Yves, Berretti, Roberta, Bogdziewicz, Michal, Boivin, Thomas, Bonal, Raul, Caignard, Thomas, Calama, Rafael, Camarero, J Julio, Clark, Connie J, Courbaud, Benoit, Delzon, Sylvain, Calderon, Sergio Donoso, Farfan-Rios, William, Gehring, Catherine A, Gilbert, Gregory S, Greenberg, Cathryn H, Guo, Qinfeng, Lambers, Janneke Hille Ris, Hoshizaki, Kazuhiko, Ibanez, Ines, Journé, Valentin, Kilner, Christopher L, Kobe, Richard K, Koenig, Walter D, Kunstler, Georges, LaMontagne, Jalene M, Ledwon, Mateusz, Lutz, James A, Motta, Renzo, Myers, Jonathan A, Nagel, Thomas A, Nuñez, Chase L, Pearse, Ian S, Piechnik, Łukasz, Poulsen, John R, Poulton-Kamakura, Renata, Redmond, Miranda D, Reid, Chantal D, Rodman, Kyle C, Scher, C Lane, Van Marle, Harald Schmidt, Seget, Barbara, Sharma, Shubhi, Silman, Miles, Swenson, Jennifer J, Swift, Margaret, Uriarte, Maria, Vacchiano, Giorgio, Veblen, Thomas T, Whipple, Amy V, Whitham, Thomas G, Wion, Andreas P, Wright, S Joseph, Zhu, Kai, Zimmerman, Jess K, Żywiec, Magdalena, and Clark, James S

Subjects
Fertility, Forests, Models, Biological, Regeneration, Trees, tree fecundity, tree senescence, tree life history, allometric scaling, crown architecture
Abstract

Despite its importance for forest regeneration, food webs, and human economies, changes in tree fecundity with tree size and age remain largely unknown. The allometric increase with tree diameter assumed in ecological models would substantially overestimate seed contributions from large trees if fecundity eventually declines with size. Current estimates are dominated by overrepresentation of small trees in regression models. We combined global fecundity data, including a substantial representation of large trees. We compared size-fecundity relationships against traditional allometric scaling with diameter and two models based on crown architecture. All allometric models fail to describe the declining rate of increase in fecundity with diameter found for 80% of 597 species in our analysis. The strong evidence of declining fecundity, beyond what can be explained by crown architectural change, is consistent with physiological decline. A downward revision of projected fecundity of large trees can improve the next generation of forest dynamic models.

Published
2021

13. Arbuscular mycorrhizal trees influence the latitudinal beta-diversity gradient of tree communities in forests worldwide.

Author

Zhong, Yonglin, Chu, Chengjin, Myers, Jonathan A, Gilbert, Gregory S, Lutz, James A, Stillhard, Jonas, Zhu, Kai, Thompson, Jill, Baltzer, Jennifer L, He, Fangliang, LaManna, Joseph A, Davies, Stuart J, Aderson-Teixeira, Kristina J, Burslem, David FRP, Alonso, Alfonso, Chao, Kuo-Jung, Wang, Xugao, Gao, Lianming, Orwig, David A, Yin, Xue, Sui, Xinghua, Su, Zhiyao, Abiem, Iveren, Bissiengou, Pulchérie, Bourg, Norm, Butt, Nathalie, Cao, Min, Chang-Yang, Chia-Hao, Chao, Wei-Chun, Chapman, Hazel, Chen, Yu-Yun, Coomes, David A, Cordell, Susan, de Oliveira, Alexandre A, Du, Hu, Fang, Suqin, Giardina, Christian P, Hao, Zhanqing, Hector, Andrew, Hubbell, Stephen P, Janík, David, Jansen, Patrick A, Jiang, Mingxi, Jin, Guangze, Kenfack, David, Král, Kamil, Larson, Andrew J, Li, Buhang, Li, Xiankun, Li, Yide, Lian, Juyu, Lin, Luxiang, Liu, Feng, Liu, Yankun, Liu, Yu, Luan, Fuchen, Luo, Yahuang, Ma, Keping, Malhi, Yadvinder, McMahon, Sean M, McShea, William, Memiaghe, Hervé, Mi, Xiangcheng, Morecroft, Mike, Novotny, Vojtech, O'Brien, Michael J, Ouden, Jan den, Parker, Geoffrey G, Qiao, Xiujuan, Ren, Haibao, Reynolds, Glen, Samonil, Pavel, Sang, Weiguo, Shen, Guochun, Shen, Zhiqiang, Song, Guo-Zhang Michael, Sun, I-Fang, Tang, Hui, Tian, Songyan, Uowolo, Amanda L, Uriarte, María, Wang, Bin, Wang, Xihua, Wang, Youshi, Weiblen, George D, Wu, Zhihong, Xi, Nianxun, Xiang, Wusheng, Xu, Han, Xu, Kun, Ye, Wanhui, Yu, Mingjian, Zeng, Fuping, Zhang, Minhua, Zhang, Yingming, Zhu, Li, and Zimmerman, Jess K

Subjects
Mycorrhizae, Trees, Soil Microbiology, Biodiversity, Plant Dispersal, Forests, Host Microbial Interactions
Abstract

Arbuscular mycorrhizal (AM) and ectomycorrhizal (EcM) associations are critical for host-tree performance. However, how mycorrhizal associations correlate with the latitudinal tree beta-diversity remains untested. Using a global dataset of 45 forest plots representing 2,804,270 trees across 3840 species, we test how AM and EcM trees contribute to total beta-diversity and its components (turnover and nestedness) of all trees. We find AM rather than EcM trees predominantly contribute to decreasing total beta-diversity and turnover and increasing nestedness with increasing latitude, probably because wide distributions of EcM trees do not generate strong compositional differences among localities. Environmental variables, especially temperature and precipitation, are strongly correlated with beta-diversity patterns for both AM trees and all trees rather than EcM trees. Results support our hypotheses that latitudinal beta-diversity patterns and environmental effects on these patterns are highly dependent on mycorrhizal types. Our findings highlight the importance of AM-dominated forests for conserving global forest biodiversity.

Published
2021

14. Host evolutionary relationships explain tree mortality caused by a generalist pest–pathogen complex

Author

Lynch, Shannon Colleen, Eskalen, Akif, and Gilbert, Gregory S

Subjects
Microbiology, Biological Sciences, Aetiology, 2.2 Factors relating to the physical environment, Infection, biological invasions, Euwallacea, Fusarium dieback, host specificity, infectious diseases, invasive plant pests, invasive shot hole borers, phylogenetic signal, Medicinal and Biomolecular Chemistry, Evolutionary Biology, Genetics, Ecology, Evolutionary biology
Abstract

The phylogenetic signal of transmissibility (competence) and attack severity among hosts of generalist pests is poorly understood. In this study, we examined the phylogenetic effects on hosts differentially affected by an emergent generalist beetle-pathogen complex in California and South Africa. Host types (non-competent, competent and killed-competent) are based on nested types of outcomes of interactions between host plants, the beetles and the fungal pathogens. Phylogenetic dispersion analysis of each host type revealed that the phylogenetic preferences of beetle attack and fungal growth were a nonrandom subset of all available tree and shrub species. Competent hosts were phylogenetically narrower by 62 Myr than the set of all potential hosts, and those with devastating impacts were the most constrained by 107 Myr. Our results show a strong phylogenetic signal in the relative effects of a generalist pest-pathogen complex on host species, demonstrating that the strength of multi-host pest impacts in plants can be predicted by host evolutionary relationships. This study presents a unifying theoretical approach to identifying likely disease outcomes across multiple host-pest combinations.

Published
2021

15. Continent-wide tree fecundity driven by indirect climate effects.

Author

Clark, James S, Andrus, Robert, Aubry-Kientz, Melaine, Bergeron, Yves, Bogdziewicz, Michal, Bragg, Don C, Brockway, Dale, Cleavitt, Natalie L, Cohen, Susan, Courbaud, Benoit, Daley, Robert, Das, Adrian J, Dietze, Michael, Fahey, Timothy J, Fer, Istem, Franklin, Jerry F, Gehring, Catherine A, Gilbert, Gregory S, Greenberg, Cathryn H, Guo, Qinfeng, HilleRisLambers, Janneke, Ibanez, Ines, Johnstone, Jill, Kilner, Christopher L, Knops, Johannes, Koenig, Walter D, Kunstler, Georges, LaMontagne, Jalene M, Legg, Kristin L, Luongo, Jordan, Lutz, James A, Macias, Diana, McIntire, Eliot JB, Messaoud, Yassine, Moore, Christopher M, Moran, Emily, Myers, Jonathan A, Myers, Orrin B, Nunez, Chase, Parmenter, Robert, Pearse, Sam, Pearson, Scott, Poulton-Kamakura, Renata, Ready, Ethan, Redmond, Miranda D, Reid, Chantal D, Rodman, Kyle C, Scher, C Lane, Schlesinger, William H, Schwantes, Amanda M, Shanahan, Erin, Sharma, Shubhi, Steele, Michael A, Stephenson, Nathan L, Sutton, Samantha, Swenson, Jennifer J, Swift, Margaret, Veblen, Thomas T, Whipple, Amy V, Whitham, Thomas G, Wion, Andreas P, Zhu, Kai, and Zlotin, Roman

Subjects
Trees, Seasons, Fertility, Geography, Models, Theoretical, North America, Climate Change, Models, Theoretical
Abstract

Indirect climate effects on tree fecundity that come through variation in size and growth (climate-condition interactions) are not currently part of models used to predict future forests. Trends in species abundances predicted from meta-analyses and species distribution models will be misleading if they depend on the conditions of individuals. Here we find from a synthesis of tree species in North America that climate-condition interactions dominate responses through two pathways, i) effects of growth that depend on climate, and ii) effects of climate that depend on tree size. Because tree fecundity first increases and then declines with size, climate change that stimulates growth promotes a shift of small trees to more fecund sizes, but the opposite can be true for large sizes. Change the depresses growth also affects fecundity. We find a biogeographic divide, with these interactions reducing fecundity in the West and increasing it in the East. Continental-scale responses of these forests are thus driven largely by indirect effects, recommending management for climate change that considers multiple demographic rates.

Published
2021

16. Parasitism to mutualism continuum for Joshua trees inoculated with different communities of arbuscular mycorrhizal fungi from a desert elevation gradient.

Author

Harrower, Jennifer T and Gilbert, Gregory S

Subjects
General Science & Technology
Abstract

Most desert plants form symbiotic relationships with arbuscular mycorrhizal fungi (AMF), yet fungal identity and impacts on host plants remain largely unknown. Despite widespread recognition of the importance of AMF relationships for plant functioning, we do not know how fungal community structure changes across a desert climate gradient, nor the impacts of different fungal communities on host plant species. Because climate change can shape the distribution of species through effects on species interactions, knowing how the ranges of symbiotic partners are geographically structured and the outcomes of those species interactions informs theory and improves management recommendations. Here we used high throughput sequencing to examine the AMF community of Joshua trees along a climate gradient in Joshua Tree National Park. We then used a range of performance measures and abiotic factors to evaluate how different AMF communities may affect Joshua tree fitness. We found that fungal communities change with elevation resulting in a spectrum of interaction outcomes from mutualism to parasitism that changed with the developmental stage of the plant. Nutrient accumulation and the mycorrhizal growth response of Joshua tree seedlings inoculated with fungi from the lowest (warmest) elevations was first negative, but after 9 months had surpassed that of plants with other fungal treatments. This indicates that low elevation fungi are costly for the plant to initiate symbiosis, yet confer benefits over time. The strong relationship between AMF community and plant growth suggests that variation in AMF community may have long term consequences for plant populations along an elevation gradient.

Published
2021

33. Soil microbes drive phylogenetic diversity-productivity relationships in a subtropical forest.

Author

Liang, Minxia, Liu, Xubing, Parker, Ingrid M, Johnson, David, Zheng, Yi, Luo, Shan, Gilbert, Gregory S, and Yu, Shixiao

Subjects
Regression Analysis, Soil Microbiology, Biodiversity, Tropical Climate, Phylogeny, Forests, Seedlings
Abstract

The relationship between plant diversity and productivity and the mechanisms underpinning that relationship remain poorly resolved in species-rich forests. We combined extensive field observations and experimental manipulations in a subtropical forest to test how species richness (SR) and phylogenetic diversity (PD) interact with putative root-associated pathogens and how these interactions mediate diversity-productivity relationships. We show that (i) both SR and PD were positively correlated with biomass for both adult trees and seedlings across multiple spatial scales, but productivity was best predicted by PD; (ii) significant positive relationships between PD and productivity were observed in nonsterile soil only; and (iii) root fungal diversity was positively correlated with plant PD and SR, while the relative abundance of putative pathogens was negatively related to plant PD. Our findings highlight the key role of soil pathogenic fungi in tree diversity-productivity relationships and suggest that increasing PD may counteract negative effects of plant-soil feedback.

Published
2019

34. Linking Aboveground Traits to Root Traits and Local Environment: Implications of the Plant Economics Spectrum

Author

Shen, Yong, Gilbert, Gregory S, Li, Wenbin, Fang, Miao, Lu, Huanping, and Yu, Shixiao

Subjects
Agricultural, Veterinary and Food Sciences, Biological Sciences, Ecology, Agriculture, Land and Farm Management, Crop and Pasture Production, Forestry Sciences, functional traits, light, plant economics spectrum, soil fertility, subtropical forest, woody seedling, Plant Biology, Crop and pasture production, Plant biology
Abstract

The plant economics spectrum proposes that ecological traits are functionally coordinated and adapt along environmental gradients. However, empirical evidence is mixed about whether aboveground and root traits are consistently linked and which environmental factors drive functional responses. Here we measure the strength of relationships between aboveground and root traits, and examine whether community-weighted mean trait values are adapted along gradients of light and soil fertility, based on the seedling censuses of 57 species in a subtropical forest. We found that aboveground traits were good predictors of root traits; specific leaf area, dry matter, nitrogen and phosphorus content were strongly correlated with root tissue density and specific root length. Traits showed patterns of adaptation along the gradients of soil fertility and light; species with fast resource-acquisitive strategies were more strongly associated with high soil phosphorus, potassium, openness, and with low nitrogen, organic matter conditions. This demonstrates the potential to estimate belowground traits from known aboveground traits in seedling communities, and suggests that soil fertility is one of the main factors driving functional responses. Our results extend our understanding of how ecological strategies shape potential responses of plant communities to environmental change.

Published
2019

35. Adapterama II: universal amplicon sequencing on Illumina platforms (TaggiMatrix).

Author

Glenn, Travis C, Pierson, Todd W, Bayona-Vásquez, Natalia J, Kieran, Troy J, Hoffberg, Sandra L, Thomas Iv, Jesse C, Lefever, Daniel E, Finger, John W, Gao, Bei, Bian, Xiaoming, Louha, Swarnali, Kolli, Ramya T, Bentley, Kerin E, Rushmore, Julie, Wong, Kelvin, Shaw, Timothy I, Rothrock, Michael J, McKee, Anna M, Guo, Tai L, Mauricio, Rodney, Molina, Marirosa, Cummings, Brian S, Lash, Lawrence H, Lu, Kun, Gilbert, Gregory S, Hubbell, Stephen P, and Faircloth, Brant C

Subjects
Fusion primers, Hierarchical indexing, Internal tagging, Libraries, MiSeq, Multiplexing, Next generation sequencing, PCR, Quadruple indexing, Biotechnology, Biological Sciences, Medical and Health Sciences
Abstract

Next-generation sequencing (NGS) of amplicons is used in a wide variety of contexts. In many cases, NGS amplicon sequencing remains overly expensive and inflexible, with library preparation strategies relying upon the fusion of locus-specific primers to full-length adapter sequences with a single identifying sequence or ligating adapters onto PCR products. In Adapterama I, we presented universal stubs and primers to produce thousands of unique index combinations and a modifiable system for incorporating them into Illumina libraries. Here, we describe multiple ways to use the Adapterama system and other approaches for amplicon sequencing on Illumina instruments. In the variant we use most frequently for large-scale projects, we fuse partial adapter sequences (TruSeq or Nextera) onto the 5' end of locus-specific PCR primers with variable-length tag sequences between the adapter and locus-specific sequences. These fusion primers can be used combinatorially to amplify samples within a 96-well plate (8 forward primers + 12 reverse primers yield 8 × 12 = 96 combinations), and the resulting amplicons can be pooled. The initial PCR products then serve as template for a second round of PCR with dual-indexed iTru or iNext primers (also used combinatorially) to make full-length libraries. The resulting quadruple-indexed amplicons have diversity at most base positions and can be pooled with any standard Illumina library for sequencing. The number of sequencing reads from the amplicon pools can be adjusted, facilitating deep sequencing when required or reducing sequencing costs per sample to an economically trivial amount when deep coverage is not needed. We demonstrate the utility and versatility of our approaches with results from six projects using different implementations of our protocols. Thus, we show that these methods facilitate amplicon library construction for Illumina instruments at reduced cost with increased flexibility. A simple web page to design fusion primers compatible with iTru primers is available at: http://baddna.uga.edu/tools-taggi.html. A fast and easy to use program to demultiplex amplicon pools with internal indexes is available at: https://github.com/lefeverde/Mr_Demuxy.

Published
2019

37. Best practices: social research methods to inform biological conservation

Author

Crandall, Sharifa G, Ohayon, Jennifer L, de Wit, Luz A, Hammond, JE, Melanson, Kate L, Moritsch, Monica M, Davenport, Rob, Ruiz, Diana, Keitt, Bradford, Holmes, Nick D, Packard, Heath G, Bury, Jeffrey, Gilbert, Gregory S, and Parker, Ingrid M

Subjects
Environmental Sciences, Human Society, Life on Land, Sociology, social research, methodology, conservation, biodiversity, islands, Studies in Human Society, Environmental sciences, Human society
Published
2018

38. Use of sonic tomography to detect and quantify wood decay in living trees.

Author

Gilbert, Gregory S, Ballesteros, Javier O, Barrios-Rodriguez, Cesar A, Bonadies, Ernesto F, Cedeño-Sánchez, Marjorie L, Fossatti-Caballero, Nohely J, Trejos-Rodríguez, Mariam M, Pérez-Suñiga, José Moises, Holub-Young, Katharine S, Henn, Laura AW, Thompson, Jennifer B, García-López, Cesar G, Romo, Amanda C, Johnston, Daniel C, Barrick, Pablo P, Jordan, Fulvia A, Hershcovich, Shiran, Russo, Natalie, Sánchez, Juan David, Fábrega, Juan Pablo, Lumpkin, Raleigh, McWilliams, Hunter A, Chester, Kathleen N, Burgos, Alana C, Wong, E Beatriz, Diab, Jonathan H, Renteria, Sonia A, Harrower, Jennifer T, Hooton, Douglas A, Glenn, Travis C, Faircloth, Brant C, and Hubbell, Stephen P

Subjects
Argus PiCUS 3 Sonic Tomograph, ImageJ, acoustic tomography, tropical trees, Crop and Pasture Production
Abstract

Premise of the studyField methodology and image analysis protocols using acoustic tomography were developed and evaluated as a tool to estimate the amount of internal decay and damage of living trees, with special attention to tropical rainforest trees with irregular trunk shapes.Methods and resultsLiving trunks of a diversity of tree species in tropical rainforests in the Republic of Panama were scanned using an Argus Electronic PiCUS 3 Sonic Tomograph and evaluated for the amount and patterns of internal decay. A protocol using ImageJ analysis software was used to quantify the proportions of intact and compromised wood. The protocols provide replicable estimates of internal decay and cavities for trees of varying shapes, wood density, and bark thickness.ConclusionsSonic tomography, coupled with image analysis, provides an efficient, noninvasive approach to evaluate decay patterns and structural integrity of even irregularly shaped living trees.

Published
2016

39. Phylogenetic congruence between subtropical trees and their associated fungi

Author

Liu, Xubing, Liang, Minxia, Etienne, Rampal S, Gilbert, Gregory S, and Yu, Shixiao

Subjects
Microbiology, Plant Biology, Biological Sciences, Ecology, 2.2 Factors relating to the physical environment, Aetiology, Infection, congruent phylogenies, DNA sequencing, foliar pathogens, fungi, molecular phylogeny, network, soil pathogens, subtropical trees, Evolutionary Biology, Evolutionary biology, Ecological applications
Abstract

Recent studies have detected phylogenetic signals in pathogen-host networks for both soil-borne and leaf-infecting fungi, suggesting that pathogenic fungi may track or coevolve with their preferred hosts. However, a phylogenetically concordant relationship between multiple hosts and multiple fungi in has rarely been investigated. Using next-generation high-throughput DNA sequencing techniques, we analyzed fungal taxa associated with diseased leaves, rotten seeds, and infected seedlings of subtropical trees. We compared the topologies of the phylogenetic trees of the soil and foliar fungi based on the internal transcribed spacer (ITS) region with the phylogeny of host tree species based on matK, rbcL, atpB, and 5.8S genes. We identified 37 foliar and 103 soil pathogenic fungi belonging to the Ascomycota and Basidiomycota phyla and detected significantly nonrandom host-fungus combinations, which clustered on both the fungus phylogeny and the host phylogeny. The explicit evidence of congruent phylogenies between tree hosts and their potential fungal pathogens suggests either diffuse coevolution among the plant-fungal interaction networks or that the distribution of fungal species tracked spatially associated hosts with phylogenetically conserved traits and habitat preferences. Phylogenetic conservatism in plant-fungal interactions within a local community promotes host and parasite specificity, which is integral to the important role of fungi in promoting species coexistence and maintaining biodiversity of forest communities.

Published
2016

40. Global Spore Sampling Project:A global, standardized dataset of airborne fungal DNA

Author

Ovaskainen, Otso, Abrego, Nerea, Furneaux, Brendan, Hardwick, Bess, Somervuo, Panu, Palorinne, Isabella, Andrew, Nigel R, Babiy, Ulyana V, Bao, Tan, Bazzano, Gisela, Bondarchuk, Svetlana N, Bonebrake, Timothy C, Brennan, Georgina L, Bret-Harte, Syndonia, Bässler, Claus, Cagnolo, Luciano, Cameron, Erin K, Chapurlat, Elodie, Creer, Simon, D'Acqui, Luigi P, de Vere, Natasha, Desprez-Loustau, Marie-Laure, Dongmo, Michel A K, Dyrholm Jacobsen, Ida B, Fisher, Brian L, Flores de Jesus, Miguel, Gilbert, Gregory S, Griffith, Gareth W, Gritsuk, Anna A, Gross, Andrin, Grudd, Håkan, Halme, Panu, Hanna, Rachid, Hansen, Jannik, Hansen, Lars Holst, Hegbe, Apollon D M T, Hill, Sarah, Hogg, Ian D, Hultman, Jenni, Hyde, Kevin D, Hynson, Nicole A, Ivanova, Natalia, Karisto, Petteri, Kerdraon, Deirdre, Knorre, Anastasia, Krisai-Greilhuber, Irmgard, Kurhinen, Juri, Kuzmina, Masha, Lecomte, Nicolas, Lecomte, Erin, Loaiza, Viviana, Lundin, Erik, Meire, Alexander, Mešić, Armin, Miettinen, Otto, Monkhause, Norman, Mortimer, Peter, Müller, Jörg, Nilsson, R Henrik, Nonti, Puani Yannick C, Nordén, Jenni, Nordén, Björn, Paz, Claudia, Pellikka, Petri, Pereira, Danilo, Petch, Geoff, Pitkänen, Juha-Matti, Popa, Flavius, Potter, Caitlin, Purhonen, Jenna, Pätsi, Sanna, Rafiq, Abdullah, Raharinjanahary, Dimby, Rakos, Niklas, Rathnayaka, Achala R, Raundrup, Katrine, Rebriev, Yury A, Rikkinen, Jouko, Rogers, Hanna M K, Rogovsky, Andrey, Rozhkov, Yuri, Runnel, Kadri, Saarto, Annika, Savchenko, Anton, Schlegel, Markus, Schmidt, Niels Martin, Seibold, Sebastian, Skjøth, Carsten, Stengel, Elisa, Sutyrina, Svetlana V, Syvänperä, Ilkka, Tedersoo, Leho, Timm, Jebidiah, Tipton, Laura, Toju, Hirokazu, Uscka-Perzanowska, Maria, van der Bank, Michelle, Herman van der Bank, F, Vandenbrink, Bryan, Ventura, Stefano, Vignisson, Solvi R, Wang, Xiaoyang, Weisser, Wolfgang W, Wijesinghe, Subodini N, Joseph Wright, S, Yang, Chunyan, Yorou, Nourou S, Young, Amanda, Yu, Douglas W, Zakharov, Evgeny V, Hebert, Paul D N, Roslin, Tomas, Ovaskainen, Otso, Abrego, Nerea, Furneaux, Brendan, Hardwick, Bess, Somervuo, Panu, Palorinne, Isabella, Andrew, Nigel R, Babiy, Ulyana V, Bao, Tan, Bazzano, Gisela, Bondarchuk, Svetlana N, Bonebrake, Timothy C, Brennan, Georgina L, Bret-Harte, Syndonia, Bässler, Claus, Cagnolo, Luciano, Cameron, Erin K, Chapurlat, Elodie, Creer, Simon, D'Acqui, Luigi P, de Vere, Natasha, Desprez-Loustau, Marie-Laure, Dongmo, Michel A K, Dyrholm Jacobsen, Ida B, Fisher, Brian L, Flores de Jesus, Miguel, Gilbert, Gregory S, Griffith, Gareth W, Gritsuk, Anna A, Gross, Andrin, Grudd, Håkan, Halme, Panu, Hanna, Rachid, Hansen, Jannik, Hansen, Lars Holst, Hegbe, Apollon D M T, Hill, Sarah, Hogg, Ian D, Hultman, Jenni, Hyde, Kevin D, Hynson, Nicole A, Ivanova, Natalia, Karisto, Petteri, Kerdraon, Deirdre, Knorre, Anastasia, Krisai-Greilhuber, Irmgard, Kurhinen, Juri, Kuzmina, Masha, Lecomte, Nicolas, Lecomte, Erin, Loaiza, Viviana, Lundin, Erik, Meire, Alexander, Mešić, Armin, Miettinen, Otto, Monkhause, Norman, Mortimer, Peter, Müller, Jörg, Nilsson, R Henrik, Nonti, Puani Yannick C, Nordén, Jenni, Nordén, Björn, Paz, Claudia, Pellikka, Petri, Pereira, Danilo, Petch, Geoff, Pitkänen, Juha-Matti, Popa, Flavius, Potter, Caitlin, Purhonen, Jenna, Pätsi, Sanna, Rafiq, Abdullah, Raharinjanahary, Dimby, Rakos, Niklas, Rathnayaka, Achala R, Raundrup, Katrine, Rebriev, Yury A, Rikkinen, Jouko, Rogers, Hanna M K, Rogovsky, Andrey, Rozhkov, Yuri, Runnel, Kadri, Saarto, Annika, Savchenko, Anton, Schlegel, Markus, Schmidt, Niels Martin, Seibold, Sebastian, Skjøth, Carsten, Stengel, Elisa, Sutyrina, Svetlana V, Syvänperä, Ilkka, Tedersoo, Leho, Timm, Jebidiah, Tipton, Laura, Toju, Hirokazu, Uscka-Perzanowska, Maria, van der Bank, Michelle, Herman van der Bank, F, Vandenbrink, Bryan, Ventura, Stefano, Vignisson, Solvi R, Wang, Xiaoyang, Weisser, Wolfgang W, Wijesinghe, Subodini N, Joseph Wright, S, Yang, Chunyan, Yorou, Nourou S, Young, Amanda, Yu, Douglas W, Zakharov, Evgeny V, Hebert, Paul D N, and Roslin, Tomas

Abstract

Novel methods for sampling and characterizing biodiversity hold great promise for re-evaluating patterns of life across the planet. The sampling of airborne spores with a cyclone sampler, and the sequencing of their DNA, have been suggested as an efficient and well-calibrated tool for surveying fungal diversity across various environments. Here we present data originating from the Global Spore Sampling Project, comprising 2,768 samples collected during two years at 47 outdoor locations across the world. Each sample represents fungal DNA extracted from 24 m 3 of air. We applied a conservative bioinformatics pipeline that filtered out sequences that did not show strong evidence of representing a fungal species. The pipeline yielded 27,954 species-level operational taxonomic units (OTUs). Each OTU is accompanied by a probabilistic taxonomic classification, validated through comparison with expert evaluations. To examine the potential of the data for ecological analyses, we partitioned the variation in species distributions into spatial and seasonal components, showing a strong effect of the annual mean temperature on community composition.

Published
2024

43. Exploring Models in the Biology Classroom

Author

Bryce, Caleb M, Baliga, Vikram B, De Nesnera, Kristin L, Fiack, Duran, Goetz, Kimberly, Tarjan, L Maxine, Wade, Catherine E, Yovovich, Veronica, Baumgart, Sarah, Bard, Donald G, Ash, Doris, Parker, Ingrid M, and Gilbert, Gregory S

Subjects
Quality Education, Next Generation Science Standards, model-based learning, inquiry-based science, scientific practice, student learning, inquiry-based learning, Education
Abstract

Models are simplified representations of more complex systems that help scientists structure the knowledge they acquire. As such, they are ubiquitous and invaluable in scientific research and communication. Because science education strives to make classroom activities more closely reflect science in practice, models have become integral teaching and learning tools woven throughout the Next Generation Science Standards (NGSS). Although model-based learning and curriculum are not novel in educational theory, only recently has modeling taken center stage in K–12 national standards for science, technology, engineering, and mathematics (STEM) classes. We present a variety of examples to outline the importance of various types of models and the practice of modeling in biological research, as well as the emphasis of NGSS on their use in both classroom learning and assessment. We then suggest best practices for creating and modifying models in the context of student-driven inquiry and demonstrate that even subtle incorporation of modeling into existing science curricula can help achieve student learning outcomes, particularly for English-language learners. In closing, we express the value of models and modeling in life beyond the classroom and research laboratory, and highlight the critical importance of “model literacy” for the next generation of scientists, engineers, and problem-solvers.

Published
2016

44. Persistence of Neighborhood Demographic Influences over Long Phylogenetic Distances May Help Drive Post-Speciation Adaptation in Tropical Forests.

Author

Wills, Christopher, Harms, Kyle E, Wiegand, Thorsten, Punchi-Manage, Ruwan, Gilbert, Gregory S, Erickson, David, Kress, W John, Hubbell, Stephen P, Gunatilleke, CV Savitri, and Gunatilleke, IAU Nimal

Subjects
Trees, Conservation of Natural Resources, Tropical Climate, Population Density, Acclimatization, Phylogeny, Species Specificity, Geography, Algorithms, Models, Biological, Panama, Sri Lanka, Genes, Chloroplast, Forests, General Science & Technology
Abstract

Studies of forest dynamics plots (FDPs) have revealed a variety of negative density-dependent (NDD) demographic interactions, especially among conspecific trees. These interactions can affect growth rate, recruitment and mortality, and they play a central role in the maintenance of species diversity in these complex ecosystems. Here we use an equal area annulus (EAA) point-pattern method to comprehensively analyze data from two tropical FDPs, Barro Colorado Island in Panama and Sinharaja in Sri Lanka. We show that these NDD interactions also influence the continued evolutionary diversification of even distantly related tree species in these FDPs. We examine the details of a wide range of these interactions between individual trees and the trees that surround them. All these interactions, and their cumulative effects, are strongest among conspecific focal and surrounding tree species in both FDPs. They diminish in magnitude with increasing phylogenetic distance between heterospecific focal and surrounding trees, but do not disappear or change the pattern of their dependence on size, density, frequency or physical distance even among the most distantly related trees. The phylogenetic persistence of all these effects provides evidence that interactions between tree species that share an ecosystem may continue to promote adaptive divergence even after the species' gene pools have become separated. Adaptive divergence among taxa would operate in stark contrast to an alternative possibility that has previously been suggested, that distantly related species with dispersal-limited distributions and confronted with unpredictable neighbors will tend to converge on common strategies of resource use. In addition, we have also uncovered a positive density-dependent effect: growth rates of large trees are boosted in the presence of a smaller basal area of surrounding trees. We also show that many of the NDD interactions switch sign rapidly as focal trees grow in size, and that their cumulative effect can strongly influence the distributions and species composition of the trees that surround the focal trees during the focal trees' lifetimes.

Published
2016

46. Author Correction: Continent-wide tree fecundity driven by indirect climate effects

Author

Clark, James S., Andrus, Robert, Aubry-Kientz, Melaine, Bergeron, Yves, Bogdziewicz, Michal, Bragg, Don C., Brockway, Dale, Cleavitt, Natalie L., Cohen, Susan, Courbaud, Benoit, Daley, Robert, Das, Adrian J., Dietze, Michael, Fahey, Timothy J., Fer, Istem, Franklin, Jerry F., Gehring, Catherine A., Gilbert, Gregory S., Greenberg, Cathryn H., Guo, Qinfeng, HilleRisLambers, Janneke, Ibanez, Ines, Johnstone, Jill, Kilner, Christopher L., Knops, Johannes, Koenig, Walter D., Kunstler, Georges, LaMontagne, Jalene M., Legg, Kristin L., Luongo, Jordan, Lutz, James A., Macias, Diana, McIntire, Eliot J. B., Messaoud, Yassine, Moore, Christopher M., Moran, Emily, Myers, Jonathan A., Myers, Orrin B., Nunez, Chase, Parmenter, Robert, Pearse, Sam, Pearson, Scott, Poulton-Kamakura, Renata, Ready, Ethan, Redmond, Miranda D., Reid, Chantal D., Rodman, Kyle C., Scher, C. Lane, Schlesinger, William H., Schwantes, Amanda M., Shanahan, Erin, Sharma, Shubhi, Steele, Michael A., Stephenson, Nathan L., Sutton, Samantha, Swenson, Jennifer J., Swift, Margaret, Veblen, Thomas T., Whipple, Amy V., Whitham, Thomas G., Wion, Andreas P., Zhu, Kai, and Zlotin, Roman

Published
2021
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47. Masting is uncommon in trees that depend on mutualist dispersers in the context of global climate and fertility gradients

Author

National Science Foundation (US), Belmont Forum, NASA Astrobiology Institute (US), Pennsylvania State University, Gordon and Betty Moore Foundation, Polish Academy of Sciences, Junta de Andalucía, European Commission, US Forest Service, Qiu, Tong [0000-0003-4499-437X], Aravena, Marie-Claire [0000-0002-4493-4396], Ascoli, Davide [0000-0002-2671-5122], Bergeron, Yves [0000-0003-3707-3687], Bogdziewicz, Michal [0000-0002-6777-9034], Boivin, Thomas [0000-0003-1694-2425], Bonal, Raúl [0000-0002-6084-1771], Caignard, Thomas [0000-0001-5009-4613], Calama Sainz, Rafael Argimiro [0000-0002-2598-9594], Calderon, Sergio Donoso [0000-0002-6324-9351], Camarero, Jesús Julio [0000-0003-2436-2922], Chang-Yang, Chia-Hao [0000-0003-3635-4946], Chave, Jérôme [0000-0002-7766-1347], Chianucci, F. [0000-0002-5688-2060], Courbaud, Benoit [0000-0002-3050-9559], Cutini, A. [0000-0002-7033-2399], Das, Adrian J. [0000-0002-3937-2616], Delpierre, Nicolas [0000-0003-0906-9402], Delzon, Sylvain [0000-0003-3442-1711], Dietze, Michael [0000-0002-2324-2518], Dormont, Laurent [0000-0002-2021-0625], Espelta, Josep Maria [0000-0002-0242-4988], Fahey, Timothy J. [0000-0003-1283-1162], Farfan-Rios, William [0000-0002-3196-0317], Gehring, Catherine [0000-0002-9393-9556], Gilbert, Gregory S. [0000-0002-5195-9903], Gratzer, Georg [0000-0002-6355-6562], Greenberg, Cathryn H. [0000-0002-2831-0989], Guignabert, Arthur [0000-0002-1512-6760], Guo, Qinfeng [0000-0002-4375-4916], Hacket-Pain, Andrew [0000-0003-3676-1568], Hampe, Arndt [0000-0003-2551-9784], Han, Qingmin [0000-0001-6063-6068], Holik, Jan [0000-0002-7949-9689], Hoshizaki, Kazuhiko [0000-0001-7654-9129], Ibáñez, Inés [0000-0002-1054-0727], Johnstone, Jill F. [0000-0001-6131-9339], Journé, Valentin [0000-0001-7324-7002], Kitzberger, T. [0000-0002-9754-4121], Knops, Johannes M.H. [0000-0002-9647-9209], Kunstler, Georges [0000-0002-2544-1940], Kurokawa, Hiroko [0000-0001-8778-8045], Lageard, Jonathan G. A. [0000-0001-8971-0444], LaMontagne, Jalene M. [0000-0001-7713-8591], Lefèvre, François [0000-0003-2242-7251], Leininger, Theodor [0000-0002-4939-3656], Limousin, Jean-Marc [0000-0002-2734-2495], Lutz, James A. [0000-0002-2560-0710], Marell, Anders [0000-0002-3328-4834], McIntire, Eliot J B [0000-0002-6914-8316], Moore, Christopher M. [0000-0001-5783-9833], Moran, Emily [0000-0003-4624-1910], Motta, Renzo [0000-0002-1631-3840], Myers, Jonathan A. [0000-0002-2058-8468], Nagel, Thomas A. [0000-0002-4207-9218], Naoe, Shoji [0000-0002-0605-4187], Noguchi, Mahoko [0000-0002-3393-5131], Oguro, Michio [0000-0003-0974-7971], Parmenter, Robert [0000-0002-2099-6824], Pearse, Ian S. [0000-0001-7098-0495], Pérez-Ramos, Ignacio Manuel [0000-0003-2332-7818], Piechnik, Lukasz [0000-0002-3958-7393], Podgórski, Tomasz [0000-0001-6858-7838], Poulsen, John [0000-0002-1532-9808], Redmond, Miranda D. [0000-0002-4657-7943], Reid, Chantal D. [0000-0002-3811-4076], Rodman, Kyle C. [0000-0001-9538-8412], Rodríguez-Sánchez, Francisco [0000-0002-7981-1599], Šamonil, Pavel [0000-0002-7722-8797], Seget, Barbara [0000-0002-7872-926X], Silman, Miles [0000-0003-4152-2844], Stephenson, Nathan L. [0000-0003-0208-7229], Straub, Jacob N. [0009-0000-3720-7564], Swenson, Jennifer [0000-0002-2069-667X], Swift, Margaret [0000-0001-7913-1879], Thomas, Peter A. [0000-0003-3115-3301], Uriarte, María [0000-0002-0484-0758], Vacchiano, Giorgio [0000-0001-8100-0659], Whipple, Amy V. [0000-0003-3956-7832], Whitham, Thomas G. [0000-0002-1262-4342], Wion, Andreas P. [0000-0002-0701-2843], Wright, S. Joseph [0000-0003-4260-5676], Zhu, Kai [0000-0003-1587-3317], Zimmerman, Jess K. [0000-0002-8179-0731], Zywiec, Magdalena [0000-0002-5992-4051], Clark, James S. [0000-0002-5677-9733], Qiu, Tong, Aravena, Marie-Claire, Ascoli, Davide, Bergeron, Yves, Bogdziewicz, Michal, Boivin, Thomas, Bonal, Raúl, Caignard, Thomas, Cailleret, Maxime, Calama Sainz, Rafael Argimiro, Calderon, Sergio Donoso, Camarero, Jesús Julio, Chang-Yang, Chia-Hao, Chave, Jérôme, Chianucci, F., Courbaud, Benoit, Cutini, A., Das, Adrian J., Delpierre, Nicolas, Delzon, Sylvain, Dietze, Michael, Dormont, Laurent, Espelta, Josep María, Fahey, Timothy J., Farfan-Rios, William, Franklin, Jerry F., Gehring, Catherine, Gilbert, Gregory S., Gratzer, Georg, Greenberg, Cathryn H., Guignabert, Arthur, Guo, Qinfeng, Hacket-Pain, Andrew, Hampe, Arndt, Han, Qingmin, Holik, Jan, Hoshizaki, Kazuhiko, Ibáñez, Inés, Johnstone, Jill F., Journé, Valentin, Kitzberger, Thomas, Knops, Johannes M. H., Kunstler, Georges, Kurokawa, Hiroko, Lageard, Jonathan G. A., LaMontagne, Jalene M., Lefèvre, François, Leininger, Theodor, Limousin, Jean-Marc, Lutz, James A., Macías, Diana, Marell, Anders, McIntire, Eliot J B, Moore, Christopher M., Moran, Emily, Motta, Renzo, Myers, Jonathan A., Nagel, Thomas A., Naoe, Shoji, Noguchi, Mahoko, Oguro, Michio, Parmenter, Robert, Pearse, Ian S., Pérez-Ramos, Ignacio Manuel, Piechnik, Lukasz, Podgórski, Tomasz, Poulsen, John, Redmond, Miranda D., Reid, Chantal D., Rodman, Kyle C., Rodríguez-Sánchez, Francisco, Šamonil, Pavel, Sanguinetti, Javier D., Scher, C. Lane, Seget, Barbara, Sharma, Shubhi, Shibata, M., Silman, Miles, Steele, Michael A., Stephenson, Nathan L., Straub, Jacob N., Sutton, Samantha, Swenson, Jennifer, Swift, Margaret, Thomas, Peter A., Uriarte, María, Vacchiano, Giorgio, Whipple, Amy V., Whitham, Thomas G., Wion, Andreas P., Wright, S. Joseph, Zhu, Kai, Zimmerman, Jess K., Zywiec, Magdalena, Clark, James S., National Science Foundation (US), Belmont Forum, NASA Astrobiology Institute (US), Pennsylvania State University, Gordon and Betty Moore Foundation, Polish Academy of Sciences, Junta de Andalucía, European Commission, US Forest Service, Qiu, Tong [0000-0003-4499-437X], Aravena, Marie-Claire [0000-0002-4493-4396], Ascoli, Davide [0000-0002-2671-5122], Bergeron, Yves [0000-0003-3707-3687], Bogdziewicz, Michal [0000-0002-6777-9034], Boivin, Thomas [0000-0003-1694-2425], Bonal, Raúl [0000-0002-6084-1771], Caignard, Thomas [0000-0001-5009-4613], Calama Sainz, Rafael Argimiro [0000-0002-2598-9594], Calderon, Sergio Donoso [0000-0002-6324-9351], Camarero, Jesús Julio [0000-0003-2436-2922], Chang-Yang, Chia-Hao [0000-0003-3635-4946], Chave, Jérôme [0000-0002-7766-1347], Chianucci, F. [0000-0002-5688-2060], Courbaud, Benoit [0000-0002-3050-9559], Cutini, A. [0000-0002-7033-2399], Das, Adrian J. [0000-0002-3937-2616], Delpierre, Nicolas [0000-0003-0906-9402], Delzon, Sylvain [0000-0003-3442-1711], Dietze, Michael [0000-0002-2324-2518], Dormont, Laurent [0000-0002-2021-0625], Espelta, Josep Maria [0000-0002-0242-4988], Fahey, Timothy J. [0000-0003-1283-1162], Farfan-Rios, William [0000-0002-3196-0317], Gehring, Catherine [0000-0002-9393-9556], Gilbert, Gregory S. [0000-0002-5195-9903], Gratzer, Georg [0000-0002-6355-6562], Greenberg, Cathryn H. [0000-0002-2831-0989], Guignabert, Arthur [0000-0002-1512-6760], Guo, Qinfeng [0000-0002-4375-4916], Hacket-Pain, Andrew [0000-0003-3676-1568], Hampe, Arndt [0000-0003-2551-9784], Han, Qingmin [0000-0001-6063-6068], Holik, Jan [0000-0002-7949-9689], Hoshizaki, Kazuhiko [0000-0001-7654-9129], Ibáñez, Inés [0000-0002-1054-0727], Johnstone, Jill F. [0000-0001-6131-9339], Journé, Valentin [0000-0001-7324-7002], Kitzberger, T. [0000-0002-9754-4121], Knops, Johannes M.H. [0000-0002-9647-9209], Kunstler, Georges [0000-0002-2544-1940], Kurokawa, Hiroko [0000-0001-8778-8045], Lageard, Jonathan G. A. [0000-0001-8971-0444], LaMontagne, Jalene M. [0000-0001-7713-8591], Lefèvre, François [0000-0003-2242-7251], Leininger, Theodor [0000-0002-4939-3656], Limousin, Jean-Marc [0000-0002-2734-2495], Lutz, James A. [0000-0002-2560-0710], Marell, Anders [0000-0002-3328-4834], McIntire, Eliot J B [0000-0002-6914-8316], Moore, Christopher M. [0000-0001-5783-9833], Moran, Emily [0000-0003-4624-1910], Motta, Renzo [0000-0002-1631-3840], Myers, Jonathan A. [0000-0002-2058-8468], Nagel, Thomas A. [0000-0002-4207-9218], Naoe, Shoji [0000-0002-0605-4187], Noguchi, Mahoko [0000-0002-3393-5131], Oguro, Michio [0000-0003-0974-7971], Parmenter, Robert [0000-0002-2099-6824], Pearse, Ian S. [0000-0001-7098-0495], Pérez-Ramos, Ignacio Manuel [0000-0003-2332-7818], Piechnik, Lukasz [0000-0002-3958-7393], Podgórski, Tomasz [0000-0001-6858-7838], Poulsen, John [0000-0002-1532-9808], Redmond, Miranda D. [0000-0002-4657-7943], Reid, Chantal D. [0000-0002-3811-4076], Rodman, Kyle C. [0000-0001-9538-8412], Rodríguez-Sánchez, Francisco [0000-0002-7981-1599], Šamonil, Pavel [0000-0002-7722-8797], Seget, Barbara [0000-0002-7872-926X], Silman, Miles [0000-0003-4152-2844], Stephenson, Nathan L. [0000-0003-0208-7229], Straub, Jacob N. [0009-0000-3720-7564], Swenson, Jennifer [0000-0002-2069-667X], Swift, Margaret [0000-0001-7913-1879], Thomas, Peter A. [0000-0003-3115-3301], Uriarte, María [0000-0002-0484-0758], Vacchiano, Giorgio [0000-0001-8100-0659], Whipple, Amy V. [0000-0003-3956-7832], Whitham, Thomas G. [0000-0002-1262-4342], Wion, Andreas P. [0000-0002-0701-2843], Wright, S. Joseph [0000-0003-4260-5676], Zhu, Kai [0000-0003-1587-3317], Zimmerman, Jess K. [0000-0002-8179-0731], Zywiec, Magdalena [0000-0002-5992-4051], Clark, James S. [0000-0002-5677-9733], Qiu, Tong, Aravena, Marie-Claire, Ascoli, Davide, Bergeron, Yves, Bogdziewicz, Michal, Boivin, Thomas, Bonal, Raúl, Caignard, Thomas, Cailleret, Maxime, Calama Sainz, Rafael Argimiro, Calderon, Sergio Donoso, Camarero, Jesús Julio, Chang-Yang, Chia-Hao, Chave, Jérôme, Chianucci, F., Courbaud, Benoit, Cutini, A., Das, Adrian J., Delpierre, Nicolas, Delzon, Sylvain, Dietze, Michael, Dormont, Laurent, Espelta, Josep María, Fahey, Timothy J., Farfan-Rios, William, Franklin, Jerry F., Gehring, Catherine, Gilbert, Gregory S., Gratzer, Georg, Greenberg, Cathryn H., Guignabert, Arthur, Guo, Qinfeng, Hacket-Pain, Andrew, Hampe, Arndt, Han, Qingmin, Holik, Jan, Hoshizaki, Kazuhiko, Ibáñez, Inés, Johnstone, Jill F., Journé, Valentin, Kitzberger, Thomas, Knops, Johannes M. H., Kunstler, Georges, Kurokawa, Hiroko, Lageard, Jonathan G. A., LaMontagne, Jalene M., Lefèvre, François, Leininger, Theodor, Limousin, Jean-Marc, Lutz, James A., Macías, Diana, Marell, Anders, McIntire, Eliot J B, Moore, Christopher M., Moran, Emily, Motta, Renzo, Myers, Jonathan A., Nagel, Thomas A., Naoe, Shoji, Noguchi, Mahoko, Oguro, Michio, Parmenter, Robert, Pearse, Ian S., Pérez-Ramos, Ignacio Manuel, Piechnik, Lukasz, Podgórski, Tomasz, Poulsen, John, Redmond, Miranda D., Reid, Chantal D., Rodman, Kyle C., Rodríguez-Sánchez, Francisco, Šamonil, Pavel, Sanguinetti, Javier D., Scher, C. Lane, Seget, Barbara, Sharma, Shubhi, Shibata, M., Silman, Miles, Steele, Michael A., Stephenson, Nathan L., Straub, Jacob N., Sutton, Samantha, Swenson, Jennifer, Swift, Margaret, Thomas, Peter A., Uriarte, María, Vacchiano, Giorgio, Whipple, Amy V., Whitham, Thomas G., Wion, Andreas P., Wright, S. Joseph, Zhu, Kai, Zimmerman, Jess K., Zywiec, Magdalena, and Clark, James S.

Abstract

The benefits of masting (volatile, quasi-synchronous seed production at lagged intervals) include satiation of seed predators, but these benefits come with a cost to mutualist pollen and seed dispersers. If the evolution of masting represents a balance between these benefits and costs, we expect mast avoidance in species that are heavily reliant on mutualist dispersers. These effects play out in the context of variable climate and site fertility among species that vary widely in nutrient demand. Meta-analyses of published data have focused on variation at the population scale, thus omitting periodicity within trees and synchronicity between trees. From raw data on 12 million tree-years worldwide, we quantified three components of masting that have not previously been analysed together: (i) volatility, defined as the frequency-weighted year-to-year variation; (ii) periodicity, representing the lag between high-seed years; and (iii) synchronicity, indicating the tree-to-tree correlation. Results show that mast avoidance (low volatility and low synchronicity) by species dependent on mutualist dispersers explains more variation than any other effect. Nutrient-demanding species have low volatility, and species that are most common on nutrient-rich and warm/wet sites exhibit short periods. The prevalence of masting in cold/dry sites coincides with climatic conditions where dependence on vertebrate dispersers is less common than in the wet tropics. Mutualist dispersers neutralize the benefits of masting for predator satiation, further balancing the effects of climate, site fertility and nutrient demands.

Published
2023

48. Linking seed size and number to trait syndromes in trees

Author

National Science Foundation (US), Belmont Forum, NASA Astrobiology Institute (US), Gordon and Betty Moore Foundation, National Science Centre (Poland), Polish National Agency for Academic Exchange, US Forest Service, Bogdziewicz, Michal [0000-0002-6777-9034], Aravena, Marie-Claire [0000-0002-4493-4396], Andrus, Robert [0000-0003-0968-8377], Ascoli, Davide [0000-0002-0546-4467], Bergeron, Yves [0000-0003-3707-3687], Bonal, Raul [0000-0002-6084-1771], Caignard, Thomas [0000-0001-5009-4613], Calama, Rafael [0000-0002-2598-9594], Calderon, Sergio Donoso [0000-0002-4599-4702], Camarero, J Julio [0000-0003-2436-2922], Chang-Yang, Chia-Hao [0000-0003-3635-4946], Cleavitt, Natalie L [0000-0003-0425-2486], Courbaud, Benoit [0000-0002-3050-9559], Curt, Thomas [0000-0002-2654-3009], Davi, Hendrik [0000-0001-8828-3145], Delpierre, Nicolas [0000-0003-0906-9402], Delzon, Sylvain [0000-0003-3442-1711], Dietze, Michael [0000-0002-2324-2518], Dormont, Laurent [0000-0002-2021-0625], Farfan-Rios, William [0000-0002-3196-0317], Gehring, Catherine [0000-0002-9393-9556], Gilbert, Gregory S. [0000-0002-5195-9903], Gratzer, Georg [0000-0002-6355-6562], Greenberg, Cathryn H. [0000-0002-2831-0989], Guignabert, Arthur [0000-0002-1512-6760], Guo,Qinfeng [0000-0002-4375-4916], Hacket-Pain, Andrew [0000-0003-3676-1568], Hampe, Arndt [0000-0003-2551-9784], Han, Qingmin [0000-0001-6063-6068], Hoshizaki, Kazuhiko [0000-0001-7654-9129], Ibáñez, Inés [0000-0002-1054-0727], Johnstone, Jill F. [0000-0001-6131-9339], Journé, Valentin [0000-0001-7324-7002], Kitzberger, Thomas [0000-0002-9754-4121], Knops, Johannes M. H. [0000-0002-9647-9209], Kunstler, Georges [0000-0002-2544-1940], Kobe, Richard K. [0000-0002-0943-9613], Lageard, Jonathan G. A. [0000-0001-8971-0444], LaMontagne, Jalene M. [0000-0001-7713-8591], Ledwon, Mateusz [0000-0003-3017-6376], Leininger, Theodor [0000-0002-4939-3656], Limousin, Jean-Marc [0000-0002-2734-2495], Lutz, James A. [0000-0002-2560-0710], Moran, Emily [0000-0003-4624-1910], Motta, Renzo [0000-0002-1631-3840], Myers, Jonathan A. [0000-0002-2058-8468], Nagel, Thomas A. [0000-0002-4207-9218], Shoji, N. [0000-0002-0605-4187], Michio Oguro, Mahoko Noguchi [0000-0002-3393-5131], Ourcival, Jean-Marc [0000-0002-3557-3496], Parmenter, Robert [0000-0002-2099-6824], Perez-Ramos, Ignacio M. [0000-0003-2332-7818], Piechnik, Lukasz [0000-0002-3958-7393], Poulsen, John [0000-0002-1532-9808], Qiu, Tong [0000-0003-4499-437X], Redmond, Miranda D. [0000-0002-4657-7943], Reid, Chantal D. [0000-0002-3811-4076], Rodman, Kyle C. [0000-0001-9538-8412], Scher, C. Lane [0000-0003-3689-5769], Seget, Barbara [0000-0002-7872-926X], Silman, Miles [0000-0003-4152-2844], Sun, I-Fang [0000-0001-9749-8324], Sutton, Samantha [0000-0002-1491-7763], Swenson, Jennifer J. [0000-0002-2069-667X], Thomas, Peter A. [0000-0003-3115-3301], Uriarte, Maria [0000-0002-0484-0758], Vacchiano, Giorgio [0000-0001-8100-0659], Veblen, Thomas T. [0000-0002-3037-640X], Wright, Boyd [0000-0002-6322-4904], Wright, S. Joseph [0000-0003-4260-5676], Zhu, Kai [0000-0003-1587-3317], Zimmerman, Jess K. [0000-0002-8179-0731], Zywiec, Magdalena [0000-0002-5992-4051], Bogdziewicz, Michal, Aravena, Marie-Claire, Andrus, Robert, Ascoli, Davide, Bergeron, Yves, Brveille, Daniel, Boivin, Thomas, Bonal, Raúl, Caignard, Thomas, Cailleret, Maxime, Calama Sainz, Rafael Argimiro, Calderon, Sergio Donoso, Camarero, Jesús Julio, Chang-Yang, Chia-Hao, Chave, Jérôme, Chianucci, F., Cleavitt, Natalie L, Courbaud, Benoit, Cutini, A., Curt, Thomas, Das, Adrian J., Davi, Hendrik, Delpierre, Nicolas, Delzon, Sylvain, Dietze, Michael, Dormont, Laurent, Farfan-Rios, William, Gehring, Catherine, Gilbert, Gregory S., Gratzer, Georg, Greenberg, Cathryn H., Guignabert, Arthur, Guo, Qinfeng, Hacket-Pain, Andrew, Hampe, Arndt, Han, Qingmin, Hoshizaki, Kazuhiko, Ibáñez, Inés, Johnstone, Jill F., Journé, Valentin, Kitzberger, Thomas, Knops, Johannes M. H., Kunstler, Georges, Kobe, Richard K., Lageard, Jonathan G. A., LaMontagne, Jalene M., Ledwon, Mateusz, Leininger, Theodor, Limousin, Jean-Marc, Lutz, James A., Macías, Diana, McIntire, Eliot J B, Moran, Emily, Motta, Renzo, Myers, Jonathan A., Nagel, Thomas A., Shoji, N., Michio Oguro, Mahoko Noguchi, Kurokawa, Hiroko, Ourcival, Jean-Marc, Parmenter, Robert, Pérez-Ramos, Ignacio Manuel, Piechnik, Lukasz, Poulsen, John, Podgórski, Tomasz, Qiu, Tong, Redmond, Miranda D., Reid, Chantal D., Rodman, Kyle C., Šamonil, Pavel, Holik, Jan, Scher, C. Lane, van Marle, Harald S., Seget, Barbara, Shibata, M., Sharma, Shubhi, Silman, Miles, Steele, Michael A., Straub, Jacob N., Sun, I-Fang, Sutton, Samantha, Swenson, Jennifer J., Thomas, Peter A., Uriarte, Maria, Vacchiano, Giorgio, Veblen, Thomas T., Wright, Boyd, Wright, S. Joseph, Whitham, Thomas G., Zhu, Kai, Zimmerman, Jess K., Zywiec, Magdalena, Clark, James S., National Science Foundation (US), Belmont Forum, NASA Astrobiology Institute (US), Gordon and Betty Moore Foundation, National Science Centre (Poland), Polish National Agency for Academic Exchange, US Forest Service, Bogdziewicz, Michal [0000-0002-6777-9034], Aravena, Marie-Claire [0000-0002-4493-4396], Andrus, Robert [0000-0003-0968-8377], Ascoli, Davide [0000-0002-0546-4467], Bergeron, Yves [0000-0003-3707-3687], Bonal, Raul [0000-0002-6084-1771], Caignard, Thomas [0000-0001-5009-4613], Calama, Rafael [0000-0002-2598-9594], Calderon, Sergio Donoso [0000-0002-4599-4702], Camarero, J Julio [0000-0003-2436-2922], Chang-Yang, Chia-Hao [0000-0003-3635-4946], Cleavitt, Natalie L [0000-0003-0425-2486], Courbaud, Benoit [0000-0002-3050-9559], Curt, Thomas [0000-0002-2654-3009], Davi, Hendrik [0000-0001-8828-3145], Delpierre, Nicolas [0000-0003-0906-9402], Delzon, Sylvain [0000-0003-3442-1711], Dietze, Michael [0000-0002-2324-2518], Dormont, Laurent [0000-0002-2021-0625], Farfan-Rios, William [0000-0002-3196-0317], Gehring, Catherine [0000-0002-9393-9556], Gilbert, Gregory S. [0000-0002-5195-9903], Gratzer, Georg [0000-0002-6355-6562], Greenberg, Cathryn H. [0000-0002-2831-0989], Guignabert, Arthur [0000-0002-1512-6760], Guo,Qinfeng [0000-0002-4375-4916], Hacket-Pain, Andrew [0000-0003-3676-1568], Hampe, Arndt [0000-0003-2551-9784], Han, Qingmin [0000-0001-6063-6068], Hoshizaki, Kazuhiko [0000-0001-7654-9129], Ibáñez, Inés [0000-0002-1054-0727], Johnstone, Jill F. [0000-0001-6131-9339], Journé, Valentin [0000-0001-7324-7002], Kitzberger, Thomas [0000-0002-9754-4121], Knops, Johannes M. H. [0000-0002-9647-9209], Kunstler, Georges [0000-0002-2544-1940], Kobe, Richard K. [0000-0002-0943-9613], Lageard, Jonathan G. A. [0000-0001-8971-0444], LaMontagne, Jalene M. [0000-0001-7713-8591], Ledwon, Mateusz [0000-0003-3017-6376], Leininger, Theodor [0000-0002-4939-3656], Limousin, Jean-Marc [0000-0002-2734-2495], Lutz, James A. [0000-0002-2560-0710], Moran, Emily [0000-0003-4624-1910], Motta, Renzo [0000-0002-1631-3840], Myers, Jonathan A. [0000-0002-2058-8468], Nagel, Thomas A. [0000-0002-4207-9218], Shoji, N. [0000-0002-0605-4187], Michio Oguro, Mahoko Noguchi [0000-0002-3393-5131], Ourcival, Jean-Marc [0000-0002-3557-3496], Parmenter, Robert [0000-0002-2099-6824], Perez-Ramos, Ignacio M. [0000-0003-2332-7818], Piechnik, Lukasz [0000-0002-3958-7393], Poulsen, John [0000-0002-1532-9808], Qiu, Tong [0000-0003-4499-437X], Redmond, Miranda D. [0000-0002-4657-7943], Reid, Chantal D. [0000-0002-3811-4076], Rodman, Kyle C. [0000-0001-9538-8412], Scher, C. Lane [0000-0003-3689-5769], Seget, Barbara [0000-0002-7872-926X], Silman, Miles [0000-0003-4152-2844], Sun, I-Fang [0000-0001-9749-8324], Sutton, Samantha [0000-0002-1491-7763], Swenson, Jennifer J. [0000-0002-2069-667X], Thomas, Peter A. [0000-0003-3115-3301], Uriarte, Maria [0000-0002-0484-0758], Vacchiano, Giorgio [0000-0001-8100-0659], Veblen, Thomas T. [0000-0002-3037-640X], Wright, Boyd [0000-0002-6322-4904], Wright, S. Joseph [0000-0003-4260-5676], Zhu, Kai [0000-0003-1587-3317], Zimmerman, Jess K. [0000-0002-8179-0731], Zywiec, Magdalena [0000-0002-5992-4051], Bogdziewicz, Michal, Aravena, Marie-Claire, Andrus, Robert, Ascoli, Davide, Bergeron, Yves, Brveille, Daniel, Boivin, Thomas, Bonal, Raúl, Caignard, Thomas, Cailleret, Maxime, Calama Sainz, Rafael Argimiro, Calderon, Sergio Donoso, Camarero, Jesús Julio, Chang-Yang, Chia-Hao, Chave, Jérôme, Chianucci, F., Cleavitt, Natalie L, Courbaud, Benoit, Cutini, A., Curt, Thomas, Das, Adrian J., Davi, Hendrik, Delpierre, Nicolas, Delzon, Sylvain, Dietze, Michael, Dormont, Laurent, Farfan-Rios, William, Gehring, Catherine, Gilbert, Gregory S., Gratzer, Georg, Greenberg, Cathryn H., Guignabert, Arthur, Guo, Qinfeng, Hacket-Pain, Andrew, Hampe, Arndt, Han, Qingmin, Hoshizaki, Kazuhiko, Ibáñez, Inés, Johnstone, Jill F., Journé, Valentin, Kitzberger, Thomas, Knops, Johannes M. H., Kunstler, Georges, Kobe, Richard K., Lageard, Jonathan G. A., LaMontagne, Jalene M., Ledwon, Mateusz, Leininger, Theodor, Limousin, Jean-Marc, Lutz, James A., Macías, Diana, McIntire, Eliot J B, Moran, Emily, Motta, Renzo, Myers, Jonathan A., Nagel, Thomas A., Shoji, N., Michio Oguro, Mahoko Noguchi, Kurokawa, Hiroko, Ourcival, Jean-Marc, Parmenter, Robert, Pérez-Ramos, Ignacio Manuel, Piechnik, Lukasz, Poulsen, John, Podgórski, Tomasz, Qiu, Tong, Redmond, Miranda D., Reid, Chantal D., Rodman, Kyle C., Šamonil, Pavel, Holik, Jan, Scher, C. Lane, van Marle, Harald S., Seget, Barbara, Shibata, M., Sharma, Shubhi, Silman, Miles, Steele, Michael A., Straub, Jacob N., Sun, I-Fang, Sutton, Samantha, Swenson, Jennifer J., Thomas, Peter A., Uriarte, Maria, Vacchiano, Giorgio, Veblen, Thomas T., Wright, Boyd, Wright, S. Joseph, Whitham, Thomas G., Zhu, Kai, Zimmerman, Jess K., Zywiec, Magdalena, and Clark, James S.

Abstract

Aim Our understanding of the mechanisms that maintain forest diversity under changing climate can benefit from knowledge about traits that are closely linked to fitness. We tested whether the link between traits and seed number and seed size is consistent with two hypotheses, termed the leaf economics spectrum and the plant size syndrome, or whether reproduction represents an independent dimension related to a seed size–seed number trade-off. Location Most of the data come from Europe, North and Central America and East Asia. A minority of the data come from South America, Africa and Australia. Time period 1960–2022. Major taxa studied Trees. Methods We gathered 12 million observations of the number of seeds produced in 784 tree species. We estimated the number of seeds produced by individual trees and scaled it up to the species level. Next, we used principal components analysis and generalized joint attribute modelling (GJAM) to map seed number and size on the tree traits spectrum. Results Incorporating seed size and number into trait analysis while controlling for environment and phylogeny with GJAM exposes relationships in trees that might otherwise remain hidden. Production of the large total biomass of seeds [product of seed number and seed size; hereafter, species seed productivity (SSP)] is associated with high leaf area, low foliar nitrogen, low specific leaf area (SLA) and dense wood. Production of high seed numbers is associated with small seeds produced by nutrient-demanding species with softwood, small leaves and high SLA. Trait covariation is consistent with opposing strategies: one fast-growing, early successional, with high dispersal, and the other slow-growing, stress-tolerant, that recruit in shaded conditions. Main conclusions Earth system models currently assume that reproductive allocation is indifferent among plant functional types. Easily measurable seed size is a strong predictor of the seed number and species seed productivity. The connectio

Published
2023

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