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273 results on '"Chisholm, Ryan A."'

2. Regression Copulas for Multivariate Responses

Author

Klein, Nadja, Smith, Michael Stanley, Nott, David, and Chisholm, Ryan

Subjects
Statistics - Methodology
Abstract

We propose a novel distributional regression model for a multivariate response vector based on a copula process over the covariate space. It uses the implicit copula of a Gaussian multivariate regression, which we call a ``regression copula''. To allow for large covariate vectors their coefficients are regularized using a novel multivariate extension of the horseshoe prior. Bayesian inference and distributional predictions are evaluated using efficient variational inference methods, allowing application to large datasets. An advantage of the approach is that the marginal distributions of the response vector can be estimated separately and accurately, resulting in predictive distributions that are marginally-calibrated. Two substantive applications of the methodology highlight its efficacy in multivariate modeling. The first is the econometric modeling and prediction of half-hourly regional Australian electricity prices. Here, our approach produces more accurate distributional forecasts than leading benchmark methods. The second is the evaluation of multivariate posteriors in likelihood-free inference (LFI) of a model for tree species abundance data, extending a previous univariate regression copula LFI method. In both applications, we demonstrate that our new approach exhibits a desirable marginal calibration property.

Published
2024

3. 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

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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13. Assessing the spatial scale of synchrony in forest tree population dynamics.

Author

Chisholm, Ryan A., Fung, Tak, Anderson-Teixeira, Kristina J., Bourg, Norman A., Brockelman, Warren Y., Bunyavejchewin, Sarayudh, Chang-Yang, Chia-Hao, Chen, Yu-Yun, Chuyong, George B., Condit, Richard, Dattaraja, Handanakere S., Davies, Stuart J., Ediriweera, Sisira, Ewango, Corneille E. N., Fernando, Edwino S., Gunatilleke, I. A. U. Nimal, Gunatilleke, C. V. Savitri, Hao, Zhanqing, Howe, Robert W., and Kenfack, David

Subjects
*PEARSON correlation (Statistics), *BIOTIC communities, *SEED dispersal, *TREE growth, *POPULATION dynamics, *FOREST dynamics
Abstract

Populations of forest trees exhibit large temporal fluctuations, but little is known about the synchrony of these fluctuations across space, including their sign, magnitude, causes and characteristic scales. These have important implications for metapopulation persistence and theoretical community ecology. Using data from permanent forest plots spanning local, regional and global spatial scales, we measured spatial synchrony in tree population growth rates over sub-decadal and decadal timescales and explored the relationship of synchrony to geographical distance. Synchrony was high at local scales of less than 1 km, with estimated Pearson correlations of approximately 0.6–0.8 between species' population growth rates across pairs of quadrats. Synchrony decayed by approximately 17–44% with each order of magnitude increase in distance but was still detectably positive at distances of 100 km and beyond. Dispersal cannot explain observed large-scale synchrony because typical seed dispersal distances (<100 m) are far too short to couple the dynamics of distant forests on decadal timescales. We attribute the observed synchrony in forest dynamics primarily to the effect of spatially synchronous environmental drivers (the Moran effect), in particular climate, although pests, pathogens and anthropogenic drivers may play a role for some species. [ABSTRACT FROM AUTHOR]

Published
2024
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14. High beta diversity of gaps contributes to plot‐level tree diversity in a tropical forest.

Author

Kong, Fanhua, He, Fangliang, and Chisholm, Ryan A.

Subjects
FOREST biodiversity, TROPICAL forests, SPECIES diversity, COMMUNITY forests, FOREST canopy gaps, SPECIES
Abstract

Canopy gaps are widely recognized as being crucial for maintaining the diversity of forest tree communities. But empirical studies have found mixed results because the differences in diversity between individual gaps and non‐gaps are often small and statistically undetectable. One overlooked factor, however, is how small individual gap versus non‐gap differences may accumulate across sites and potentially have a large effect on forest diversity at the plot scale. Our study investigated sapling richness, density, and composition in 124 treefall gaps, and 200 non‐gap sites in the 50‐ha tropical forest plot at Barro Colorado Island (BCI), Panama. Additionally, we analyzed species accumulation curves to understand how species richness increases with increasing stem numbers. We observed that sapling richness and density were only slightly higher in gaps 7 years after formation and statistically indistinguishable from non‐gaps after 12 years. However, species accumulation curves across multiple gaps were substantially higher than those across non‐gaps. Species composition showed small differences between individual gaps and non‐gaps but differed significantly between collections of gaps and non‐gaps. Specifically, 55 species specialized in 7‐year‐old gaps compared with 24 in non‐gaps; of these, 23 gap‐specialized species and zero non‐gap species were pioneers. Our results indicate that tree species richness is higher in gaps because of both higher stem density and the presence of gap‐specialized species. Our study has finally provided compelling evidence to support the idea that gaps enhance the overall diversity of tropical forest tree communities. [ABSTRACT FROM AUTHOR]

Published
2024
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20. Two centuries of biodiversity discovery and loss in Singapore

Author

Chisholm, Ryan A., primary, Kristensen, Nadiah P., additional, Rheindt, Frank E., additional, Chong, Kwek Yan, additional, Ascher, John S., additional, Lim, Kelvin K. P., additional, Ng, Peter K. L., additional, Yeo, Darren C. J., additional, Meier, Rudolf, additional, Tan, Heok Hui, additional, Giam, Xingli, additional, Yeoh, Yi Shuen, additional, Seah, Wei Wei, additional, Berman, Laura M., additional, Tan, Hui Zhen, additional, Sadanandan, Keren R., additional, Theng, Meryl, additional, Jusoh, Wan F. A., additional, Jain, Anuj, additional, Huertas, Blanca, additional, Tan, David J. X., additional, Ng, Alicia C. R., additional, Teo, Aloysius, additional, Yiwen, Zeng, additional, Cho, Tricia J. Y., additional, and Sin, Y. C. Keita, additional

Published
2023
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47. ForestGEO: understanding forest diversity and dynamics through a global observatory network

Author

Davies, Stuart J., Abiem, Iveren, Abu Salim, Kamariah, Aguilar, Salomón, Allen, David, Alonso, Alfonso, Anderson-Teixeira, Kristina, Andrade, Ana, Arellano, Gabriel, Ashton, Peter S., Baker, Patrick J., Baker, Matthew E., Baltzer, Jennifer L., Basset, Yves, Bissiengou, Pulchérie, Bohlman, Stephanie, Bourg, Norman A., Brockelman, Warren Y., Bunyavejchewin, Sarayudh, Burslem, David F.R.P., Cao, Min, Cárdenas, Dairon, Chang, Li-Wan, Chang-Yang, Chia-Hao, Chao, Kuo-Jung, Chao, Wei-Chun, Chapman, Hazel, Chen, Yu-Yun, Chisholm, Ryan A., Chu, Chengjin, Chuyong, George, Clay, Keith, Comita, Liza S., Condit, Richard, Cordell, Susan, Dattaraja, Handanakere S., de Oliveira, Alexandre Adalardo, den Ouden, Jan, Detto, Matteo, Dick, Christopher, Du, Xiaojun, Duque, Álvaro, Ediriweera, Sisira, Ellis, Erle C., Engone Obiang, Nestor Laurier, Esufali, Shameema, Ewango, Corneille E.N., Fernando, Edwino S., Filip, Jonah, Fischer, Gunter A., Foster, Robin, Giambelluca, Thomas, Giardina, Christian, Gilbert, Gregory S., Gonzalez-Akre, Erika, Gunatilleke, I.A.U.N., Gunatilleke, C.V.S., Hao, Zhanqing, Hau, Billy C.H., He, Fangliang, Ni, Hongwei, Howe, Robert W., Hubbell, Stephen P., Huth, Andreas, Inman-Narahari, Faith, Itoh, Akira, Janík, David, Jansen, Patrick A., Jiang, Mingxi, Johnson, Daniel J., Jones, F. Andrew, Kanzaki, Mamoru, Kenfack, David, Kiratiprayoon, Somboon, Král, Kamil, Krizel, Lauren, Lao, Suzanne, Larson, Andrew J., Li, Yide, Li, Xiankun, Litton, Creighton M., Liu, Yu, Liu, Shirong, Lum, Shawn K.Y., Luskin, Matthew S., Lutz, James A., Luu, Hong Truong, Ma, Keping, Makana, Jean-Remy, Malhi, Yadvinder, Martin, Adam, McCarthy, Caly, McMahon, Sean M., McShea, William J., Memiaghe, Hervé, Mi, Xiangcheng, Mitre, David, Mohamad, Mohizah, Monks, Logan, Muller-Landau, Helene C., Musili, Paul M., Myers, Jonathan A., Nathalang, Anuttara, Ngo, Kang Min, Norden, Natalia, Novotny, Vojtech, O'Brien, Michael J., Orwig, David, Ostertag, Rebecca, Papathanassiou, Konstantinos, Parker, Geoffrey G., Pérez, Rolando, Perfecto, Ivette, Phillips, Richard P., Pongpattananurak, Nantachai, Pretzsch, Hans, Ren, Haibo, Reynolds, Glen, Rodriguez, Lillian J., Russo, Sabrina E., Sack, Lawren, Sang, Weiguo, Shue, Jessica, Singh, Anudeep, Song, Guo-Zhang M., Sukumar, Raman, Sun, I-Fang, Suresh, Hebbalalu S., Swenson, Nathan G., Tan, Sylvester, Thomas, Sean C., Thomas, Duncan, Thompson, Jill, Turner, Benjamin L., Uowolo, Amanda, Uriarte, María, Valencia, Renato, Vandermeer, John, Vicentini, Alberto, Visser, Marco, Vrska, Tomas, Wang, Xugao, Wang, Xihua, Weiblen, George D., Whitfeld, Timothy J.S., Wolf, Amy, Wright, S. Joseph, Xu, Han, Yao, Tze Leong, Yap, Sandra L., Ye, Wanhui, Yu, Mingjian, Zhang, Minhua, Zhu, Daoguang, Zhu, Li, Zimmerman, Jess K., Zuleta, Daniel, Davies, Stuart J., Abiem, Iveren, Abu Salim, Kamariah, Aguilar, Salomón, Allen, David, Alonso, Alfonso, Anderson-Teixeira, Kristina, Andrade, Ana, Arellano, Gabriel, Ashton, Peter S., Baker, Patrick J., Baker, Matthew E., Baltzer, Jennifer L., Basset, Yves, Bissiengou, Pulchérie, Bohlman, Stephanie, Bourg, Norman A., Brockelman, Warren Y., Bunyavejchewin, Sarayudh, Burslem, David F.R.P., Cao, Min, Cárdenas, Dairon, Chang, Li-Wan, Chang-Yang, Chia-Hao, Chao, Kuo-Jung, Chao, Wei-Chun, Chapman, Hazel, Chen, Yu-Yun, Chisholm, Ryan A., Chu, Chengjin, Chuyong, George, Clay, Keith, Comita, Liza S., Condit, Richard, Cordell, Susan, Dattaraja, Handanakere S., de Oliveira, Alexandre Adalardo, den Ouden, Jan, Detto, Matteo, Dick, Christopher, Du, Xiaojun, Duque, Álvaro, Ediriweera, Sisira, Ellis, Erle C., Engone Obiang, Nestor Laurier, Esufali, Shameema, Ewango, Corneille E.N., Fernando, Edwino S., Filip, Jonah, Fischer, Gunter A., Foster, Robin, Giambelluca, Thomas, Giardina, Christian, Gilbert, Gregory S., Gonzalez-Akre, Erika, Gunatilleke, I.A.U.N., Gunatilleke, C.V.S., Hao, Zhanqing, Hau, Billy C.H., He, Fangliang, Ni, Hongwei, Howe, Robert W., Hubbell, Stephen P., Huth, Andreas, Inman-Narahari, Faith, Itoh, Akira, Janík, David, Jansen, Patrick A., Jiang, Mingxi, Johnson, Daniel J., Jones, F. Andrew, Kanzaki, Mamoru, Kenfack, David, Kiratiprayoon, Somboon, Král, Kamil, Krizel, Lauren, Lao, Suzanne, Larson, Andrew J., Li, Yide, Li, Xiankun, Litton, Creighton M., Liu, Yu, Liu, Shirong, Lum, Shawn K.Y., Luskin, Matthew S., Lutz, James A., Luu, Hong Truong, Ma, Keping, Makana, Jean-Remy, Malhi, Yadvinder, Martin, Adam, McCarthy, Caly, McMahon, Sean M., McShea, William J., Memiaghe, Hervé, Mi, Xiangcheng, Mitre, David, Mohamad, Mohizah, Monks, Logan, Muller-Landau, Helene C., Musili, Paul M., Myers, Jonathan A., Nathalang, Anuttara, Ngo, Kang Min, Norden, Natalia, Novotny, Vojtech, O'Brien, Michael J., Orwig, David, Ostertag, Rebecca, Papathanassiou, Konstantinos, Parker, Geoffrey G., Pérez, Rolando, Perfecto, Ivette, Phillips, Richard P., Pongpattananurak, Nantachai, Pretzsch, Hans, Ren, Haibo, Reynolds, Glen, Rodriguez, Lillian J., Russo, Sabrina E., Sack, Lawren, Sang, Weiguo, Shue, Jessica, Singh, Anudeep, Song, Guo-Zhang M., Sukumar, Raman, Sun, I-Fang, Suresh, Hebbalalu S., Swenson, Nathan G., Tan, Sylvester, Thomas, Sean C., Thomas, Duncan, Thompson, Jill, Turner, Benjamin L., Uowolo, Amanda, Uriarte, María, Valencia, Renato, Vandermeer, John, Vicentini, Alberto, Visser, Marco, Vrska, Tomas, Wang, Xugao, Wang, Xihua, Weiblen, George D., Whitfeld, Timothy J.S., Wolf, Amy, Wright, S. Joseph, Xu, Han, Yao, Tze Leong, Yap, Sandra L., Ye, Wanhui, Yu, Mingjian, Zhang, Minhua, Zhu, Daoguang, Zhu, Li, Zimmerman, Jess K., and Zuleta, Daniel

Abstract

ForestGEO is a network of scientists and long-term forest dynamics plots (FDPs) spanning the Earth's major forest types. ForestGEO's mission is to advance understanding of the diversity and dynamics of forests and to strengthen global capacity for forest science research. ForestGEO is unique among forest plot networks in its large-scale plot dimensions, censusing of all stems ≥1 cm in diameter, inclusion of tropical, temperate and boreal forests, and investigation of additional biotic (e.g., arthropods) and abiotic (e.g., soils) drivers, which together provide a holistic view of forest functioning. The 71 FDPs in 27 countries include approximately 7.33 million living trees and about 12,000 species, representing 20% of the world's known tree diversity. With >1300 published papers, ForestGEO researchers have made significant contributions in two fundamental areas: species coexistence and diversity, and ecosystem functioning. Specifically, defining the major biotic and abiotic controls on the distribution and coexistence of species and functional types and on variation in species' demography has led to improved understanding of how the multiple dimensions of forest diversity are structured across space and time and how this diversity relates to the processes controlling the role of forests in the Earth system. Nevertheless, knowledge gaps remain that impede our ability to predict how forest diversity and function will respond to climate change and other stressors. Meeting these global research challenges requires major advances in standardizing taxonomy of tropical species, resolving the main drivers of forest dynamics, and integrating plot-based ground and remote sensing observations to scale up estimates of forest diversity and function, coupled with improved predictive models. However, they cannot be met without greater financial commitment to sustain the long-term research of ForestGEO and other forest plot networks, greatly expanded scientific capacity across the

Published
2021

50. Validation and extension of the Tea Bag Index to collect decomposition data from termite-rich ecosystems

Author

Teo, Aloysius, Kristensen, Nadiah P., Keuskamp, Joost A., Evans, Theodore A., Foo, Maosheng, Chisholm, Ryan A., Ecology and Biodiversity, Sub Ecology and Biodiversity, Ecology and Biodiversity, and Sub Ecology and Biodiversity

Subjects
0106 biological sciences, Termite-exclusion, Carbon mineralization, Soil Science, 04 agricultural and veterinary sciences, Citizen science, Tropical forest, 010603 evolutionary biology, 01 natural sciences, Full sample, Litter decomposition, nervous system diseases, nervous system, Statistics, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Recalcitrant fraction, Ecosystem, Ecology, Evolution, Behavior and Systematics, Litter bag
Abstract

The Tea Bag Index (TBI) is a standardised and cheap method to quantify microbial-driven decomposition by measuring the mass loss of tea within tea bags. Termites are known to damage the bags to access the content, rendering the method less suitable for termite-rich ecosystems. Extension of the TBI to accommodate and incorporate the influence of termites would broaden its applicability to include termite-rich ecosystems, such as tropical forests. We extended the original TBI by applying physical and chemical termite-exclusion methods. Tea mass loss and the proportion of tea bags detected by termites in the original TBI were also recorded to infer the role of termites in litter decomposition. TBI estimates derived from the original and extended TBI were compared, benchmarked against global estimates, and validated with time-series mass loss data. Using the original TBI, we found that termites damaged up to 80 % of tea bags and consumed the recalcitrant fraction of tea in several of them, leaving only 20 % of tea bags from which TBI estimates could be retrieved. The physical termite-exclusion treatment completely eliminated termite-infringement, thus preserving the full sample size for estimating TBI parameters. The chemical termite-exclusion treatment also successfully excluded termites, but potentially inhibited microbial decomposition and made TBI estimates unreliable. In the absence of termite-infringement, both the TBI estimates and time-series analysis revealed a low decomposition rate compared to other measurements in tropical and temperate regions. We propose an extended TBI, in which the physical termite-exclusion treatment is used to preserve the retrieval rate of TBI parameters and reliably measure microbial-driven decomposition, while the original TBI is used to incorporate the contribution of termites in driving litter mass loss. By characterising both termite- and microbial-driven decomposition, the extended TBI will provide a comprehensive understanding of decomposition and its drivers in termite-rich ecosystems, and permit global comparisons.

Published
2020

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