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O'Connell RD, Doak DF, Horvitz CC, Pascarella JB, Morris WF. Nonlinear life table response experiment analysis: Decomposing nonlinear and nonadditive population growth responses to changes in environmental drivers. Ecol Lett 2024; 27:e14417. [PMID: 38549264 DOI: 10.1111/ele.14417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 04/02/2024]
Abstract
Life table response experiments (LTREs) decompose differences in population growth rate between environments into separate contributions from each underlying demographic rate. However, most LTRE analyses make the unrealistic assumption that the relationships between demographic rates and environmental drivers are linear and independent, which may result in diminished accuracy when these assumptions are violated. We extend regression LTREs to incorporate nonlinear (second-order) terms and compare the accuracy of both approaches for three previously published demographic datasets. We show that the second-order approach equals or outperforms the linear approach for all three case studies, even when all of the underlying vital rate functions are linear. Nonlinear vital rate responses to driver changes contributed most to population growth rate responses, but life history changes also made substantial contributions. Our results suggest that moving from linear to second-order LTRE analyses could improve our understanding of population responses to changing environments.
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Affiliation(s)
- Ryan D O'Connell
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Daniel F Doak
- Environmental Studies Program, University of Colorado, Boulder, Colorado, USA
| | - Carol C Horvitz
- Department of Biology, University of Miami, Coral Gables, Florida, USA
| | - John B Pascarella
- Department of Biological Sciences, Sam Houston State University, Huntsville, Texas, USA
| | - William F Morris
- Department of Biology, Duke University, Durham, North Carolina, USA
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Raybin JG, Wai RB, Ginsberg NS. Nonadditive Interactions Unlock Small-Particle Mobility in Binary Colloidal Monolayers. ACS Nano 2023; 17:8303-8314. [PMID: 37093781 PMCID: PMC10173694 DOI: 10.1021/acsnano.2c12668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We examine the organization and dynamics of binary colloidal monolayers composed of micron-scale silica particles interspersed with smaller-diameter silica particles that serve as minority component impurities. These binary monolayers are prepared at the surface of ionic liquid droplets over a range of size ratios (σ = 0.16-0.66) and are studied with low-dose minimally perturbative scanning electron microscopy (SEM). The high resolution of SEM imaging provides direct tracking of all particle coordinates over time, enabling a complete description of the microscopic state. In these bidisperse size mixtures, particle interactions are nonadditive because interfacial pinning to the droplet surface causes the equators of differently sized particles to lie in separate planes. By varying the size ratio, we control the extent of nonadditivity in order to achieve phase behavior inaccessible to additive 2D systems. Across the range of size ratios, we tune the system from a mobile small-particle phase (σ < 0.24) to an interstitial solid (0.24 < σ < 0.33) and furthermore to a disordered glass (σ > 0.33). These distinct phase regimes are classified through measurements of hexagonal ordering of the large-particle host lattice and the lattice's capacity for small-particle transport. Altogether, we explain these structural and dynamic trends by considering the combined influence of interparticle interactions and the colloidal packing geometry. Our measurements are reproduced in molecular dynamics simulations of 2D nonadditive disks, suggesting an efficient method for describing confined systems with reduced dimensionality representations.
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Affiliation(s)
- Jonathan G Raybin
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Rebecca B Wai
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Naomi S Ginsberg
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Department of Physics, University of California, Berkeley, California 94720, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Kavli Energy NanoScience Institute, Berkeley, California 94720, United States
- STROBE, NSF Science & Technology Center, Berkeley, California 94720, United States
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Cornelissen JHC, Grootemaat S, Verheijen LM, Cornwell WK, van Bodegom PM, van der Wal R, Aerts R. Are litter decomposition and fire linked through plant species traits? New Phytol 2017; 216:653-669. [PMID: 28892160 DOI: 10.1111/nph.14766] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 07/19/2017] [Indexed: 06/07/2023]
Abstract
Contents 653 I. 654 II. 657 III. 659 IV. 661 V. 662 VI. 663 VII. 665 665 References 665 SUMMARY: Biological decomposition and wildfire are connected carbon release pathways for dead plant material: slower litter decomposition leads to fuel accumulation. Are decomposition and surface fires also connected through plant community composition, via the species' traits? Our central concept involves two axes of trait variation related to decomposition and fire. The 'plant economics spectrum' (PES) links biochemistry traits to the litter decomposability of different fine organs. The 'size and shape spectrum' (SSS) includes litter particle size and shape and their consequent effect on fuel bed structure, ventilation and flammability. Our literature synthesis revealed that PES-driven decomposability is largely decoupled from predominantly SSS-driven surface litter flammability across species; this finding needs empirical testing in various environmental settings. Under certain conditions, carbon release will be dominated by decomposition, while under other conditions litter fuel will accumulate and fire may dominate carbon release. Ecosystem-level feedbacks between decomposition and fire, for example via litter amounts, litter decomposition stage, community-level biotic interactions and altered environment, will influence the trait-driven effects on decomposition and fire. Yet, our conceptual framework, explicitly comparing the effects of two plant trait spectra on litter decomposition vs fire, provides a promising new research direction for better understanding and predicting Earth surface carbon dynamics.
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Affiliation(s)
- Johannes H C Cornelissen
- Systems Ecology, Department of Ecological Science, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, the Netherlands
| | - Saskia Grootemaat
- Systems Ecology, Department of Ecological Science, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, the Netherlands
- Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Lieneke M Verheijen
- Systems Ecology, Department of Ecological Science, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, the Netherlands
| | - William K Cornwell
- Ecology and Evolution Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Peter M van Bodegom
- Institute of Environmental Sciences CML, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands
| | - René van der Wal
- School of Biological Science, University of Aberdeen, 23 St Machar Drive, Aberdeen, AB24 3UU, UK
| | - Rien Aerts
- Systems Ecology, Department of Ecological Science, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, the Netherlands
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Abstract
In generalizability theory (G theory), one-facet models are specified to be additive, which is equivalent to the assumption that subject-by-facet interaction effects are absent. In this article, the authors first derive estimators of variance components (VCs) for nonadditive models and show that, in some cases, they are different from their counterparts in additive models. The authors then demonstrate and later confirm with a simulation study that when the subject-by-facet interaction exists, but the additive-model formulas are used, the VC of subjects is underestimated. Consequently, generalizability coefficients are also underestimated. Thus, depending on the nature of interaction effects, an appropriate model, either additive or nonadditive, should be used in applications of G theory. The nonadditive G theory developed in this article generalizes current G theory and uses data at hand to determine when additive or nonadditive models should be used to estimate VCs. Finally, the implications of the findings are discussed in light of an analysis of real data.
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Wise MJ, Rausher MD. Costs of resistance and correlational selection in the multiple-herbivore community of Solanum carolinense. Evolution 2016; 70:2411-2420. [PMID: 27501350 DOI: 10.1111/evo.13035] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/12/2016] [Accepted: 07/24/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Michael J Wise
- Department of Biology, Duke University, Box 90338, Durham, North Carolina, 27708. .,Current Address: Department of Biology, Roanoke College, 221 College Lane, Salem, Virginia, 24153.
| | - Mark D Rausher
- Department of Biology, Duke University, Box 90338, Durham, North Carolina, 27708
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Ko YA, Saha-Chaudhuri P, Park SK, Vokonas PS, Mukherjee B. Novel likelihood ratio tests for screening gene-gene and gene-environment interactions with unbalanced repeated-measures data. Genet Epidemiol 2013; 37:581-91. [PMID: 23798480 DOI: 10.1002/gepi.21744] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 03/29/2013] [Accepted: 05/20/2013] [Indexed: 01/24/2023]
Abstract
There has been extensive literature on modeling gene-gene interaction (GGI) and gene-environment interaction (GEI) in case-control studies with limited literature on statistical methods for GGI and GEI in longitudinal cohort studies. We borrow ideas from the classical two-way analysis of variance literature to address the issue of robust modeling of interactions in repeated-measures studies. While classical interaction models proposed by Tukey and Mandel have interaction structures as a function of main effects, a newer class of models, additive main effects and multiplicative interaction (AMMI) models, do not have similar restrictive assumptions on the interaction structure. AMMI entails a singular value decomposition of the cell residual matrix after fitting the additive main effects and has been shown to perform well across various interaction structures. We consider these models for testing GGI and GEI from two perspectives: likelihood ratio test based on cell means and a regression-based approach using individual observations. Simulation results indicate that both approaches for AMMI models lead to valid tests in terms of maintaining the type I error rate, with the regression approach having better power properties. The performance of these models was evaluated across different interaction structures and 12 common epistasis patterns. In summary, AMMI model is robust with respect to misspecified interaction structure and is a useful screening tool for interaction even in the absence of main effects. We use the proposed methods to examine the interplay between the hemochromatosis gene and cumulative lead exposure on pulse pressure in the Normative Aging Study.
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Affiliation(s)
- Yi-An Ko
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109-2029, USA.
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Abstract
Arc repressor mutants containing from three to 15 multiple-alanine substitutions have spectral properties expected for native Arc proteins, form heterodimers with wild-type Arc, denature cooperatively with Tms equal to or greater than wild type, and, in some cases, fold as much as 30-fold faster and unfold as much as 50-fold slower than wild type. Two of the mutants, containing a total of 14 different substitutions, also footprint operator DNA in vitro. The stability of some of the proteins with multiple-alanine mutations is significantly greater than that predicted from the sum of the single substitutions, suggesting that a subset of the wild-type residues in Arc may interact in an unfavorable fashion. Overall, these results show that almost half of the residues in Arc can be replaced by alanine en masse without compromising the ability of this small, homodimeric protein to fold into a stable, native-like structure.
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Affiliation(s)
- B M Brown
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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