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5. Plasticity of Gene Expression and Thermal Tolerance: Implications for Climate Change Vulnerability in a Tropical Forest Lizard

Author

Rosso, Adam A., primary, Casement, Brianna, additional, Chung, Albert K., additional, Curlis, John David, additional, Folfas, Edita, additional, Gallegos, Maria A., additional, Neel, Lauren K., additional, Nicholson, Daniel J., additional, Williams, Claire E., additional, McMillan, W. Owen, additional, Logan, Michael L., additional, and Cox, Christian L., additional

Published
2024
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10. Everything Flows

Author

Nicholson, Daniel J. and Dupré, John

Subjects
explanation, identity, individuality, metaphysics of science, organism, persistence, philosophy of biology, process ontology, substance ontology, symbiosis, Evolution, Biology, life sciences
Abstract

This collection of essays explores the metaphysical thesis that the living world is not ontologically made up of substantial particles or things, as has often been assumed, but is rather constituted by processes. The biological domain is organized as an interdependent hierarchy of processes, which are stabilized and actively maintained at different timescales. Even entities that intuitively appear to be paradigms of things, such as organisms, are actually better understood as processes. Unlike previous attempts to articulate processual views of biology, which have tended to use Alfred North Whitehead’s panpsychist metaphysics as a foundation, this book takes a naturalistic approach to metaphysics. It submits that the main motivations for replacing an ontology of substances with one of processes are to be looked for in the empirical findings of science. Biology provides compelling reasons for thinking that the living realm is fundamentally dynamic and that the existence of things is always conditional on the existence of processes. The phenomenon of life cries out for theories that prioritize processes over things, and it suggests that the central explanandum of biology is not change but rather stability—or, more precisely, stability attained through constant change. This multicontributor volume brings together philosophers of science and metaphysicians interested in exploring the consequences of a processual philosophy of biology. The contributors draw on an extremely wide range of biological case studies and employ a process perspective to cast new light on a number of traditional philosophical problems such as identity, persistence, and individuality.

Published
2018

17. Sustained Drought, but Not Short-Term Warming, Alters the Gut Microbiomes of Wild Anolis Lizards

Author

Williams, Claire E., primary, Kueneman, Jordan G., additional, Nicholson, Daniel J., additional, Rosso, Adam A., additional, Folfas, Edita, additional, Casement, Brianna, additional, Gallegos-Koyner, Maria A., additional, Neel, Lauren K., additional, Curlis, John David, additional, McMillan, W. Owen, additional, Cox, Christian L., additional, and Logan, Michael L., additional

Published
2022
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21. Climate anomalies and competition reduce establishment success during island colonization

Author

Nicholson, Daniel J., Knell, Robert J., McCrea, Rachel S., Neel, Lauren K., Curlis, John David, Williams, Claire E., Chung, Albert K., McMillan, William Owen, Garner, Trenton W. J., Cox, Christian L., Logan, Michael L., Nicholson, Daniel J., Knell, Robert J., McCrea, Rachel S., Neel, Lauren K., Curlis, John David, Williams, Claire E., Chung, Albert K., McMillan, William Owen, Garner, Trenton W. J., Cox, Christian L., and Logan, Michael L.

Abstract

Understanding the factors that facilitate or constrain establishment of populations in novel environments is crucial for conservation biology and the study of adaptive radiation. Important questions include: (1) Does the timing of colonization relative to stochastic events, such as climatic perturbations, impact the probability of successful establishment? (2) To what extent does community context (e.g., the presence of competitors) change the probability of establishment? (3) How do sources of intrapopulation variance, such as sex differences, affect success at an individual level during the process of establishment? Answers to these questions are rarely pursued in a field‐experimental context or on the same time scales (months to years) as the processes of colonization and establishment. We introduced slender anole lizards (Anolis apletophallus) to eight islands in the Panama Canal and tracked them over multiple generations to investigate the factors that mediate establishment success. All islands were warmer than the mainland (ancestral) environment, and some islands had a native competitor. We transplanted half of these populations only 4 months before the onset of a severe regional drought and the other half 2 years (two generations) before the drought. We found that successful establishment depended on both the intensity of interspecific competition and the timing of colonization relative to the drought. The islands that were colonized shortly before the drought went functionally extinct by the second generation, and regardless of time before the drought, the populations on islands with interspecific competition declined continuously over the study period. Furthermore, the effect of the competitor interacted with sex, with males suffering, and females benefitting, from the presence of a native competitor. Our results reveal that community context and the timing of colonization relative to climactic events can combine to determine establishment succes

Published
2022

22. What was Theoretical Biology? A Topic-Modelling Analysis of a Multilingual Corpus of Monographs and Journals, 1914-1945

Author

B��hm, Alexander, Reiners-Selbach, Stefan, Baedke, Jan, F��bregas Tejeda, Alejandro, Nicholson, Daniel J., Geierhos, Michaela, Trilcke, Peer, Börner, Ingo, Seifert, Sabine, Busch, Anna, and Helling, Patrick

Subjects
Forschung, ��bersetzung, Entdeckung, theoretical biology, DHd2022, Visualisierung, topic modelling, interactive visualization, Übersetzung, Inhaltsanalyse, Text
Abstract

Over the course of the twentieth century, theoretical biology changed beyond all recognition. Although the field today is synonymous with mathematical biology, when it first emerged it had a far more philosophical agenda. Regrettably, this early period of theoretical biology has been almost completely forgotten and its existence is seldom acknowledged—let alone carefully examined. Our aim is to rescue this multilingual corpus of monographs, book series and journal articles from the dustbin of history. Our guiding question is: What did theoretical biology look like in the early 20th century? We utilize LDA topic modelling (after machine translating where necessary), top2vec and document embeddings to create an interactive tool for the exploration of this corpus, which allows analyzing the development of early theoretical biology. Moreover, we calculate mathematization scores for the documents in our corpus to map the field's increasing emphasis on formal modeling. Ein Beitrag zur 8. Tagung des Verbands "Digital Humanities im deutschsprachigen Raum" - DHd 2022 Kulturen des digitalen Gedächtnisses.

Published
2022
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26. Habitat structure mediates vulnerability to climate change through its effects on thermoregulatory behavior

Author

Neel, Lauren K., primary, Logan, Michael L., additional, Nicholson, Daniel J., additional, Miller, Christina, additional, Chung, Albert K., additional, Maayan, Inbar, additional, Degon, Zach, additional, DuBois, Madeline, additional, Curlis, John David, additional, Taylor, Quinn, additional, Keegan, Kaitlin M., additional, McMillan, W. O., additional, Losos, Jonathan B., additional, and Cox, Christian L., additional

Published
2021
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27. Sex-biased parasitism and expression of a sexual signal

Author

Rosso, Adam A, primary, Nicholson, Daniel J, additional, Logan, Michael L, additional, Chung, Albert K, additional, Curlis, John David, additional, Degon, Zachariah M, additional, Knell, Robert J, additional, Garner, Trenton W J, additional, McMillan, W Owen, additional, and Cox, Christian L, additional

Published
2020
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28. Ectoparasite extinction in simplified lizard assemblages during experimental island invasion

Author

Cox, Christian L., primary, Alexander, Sean, additional, Casement, Brianna, additional, Chung, Albert K., additional, Curlis, John David, additional, Degon, Zachariah, additional, Dubois, Madeline, additional, Falvey, Cleo, additional, Graham, Zackary A., additional, Folfas, Edita, additional, Gallegos Koyner, Maria A., additional, Neel, Lauren K., additional, Nicholson, Daniel J., additional, Perez, Dylan J. Padilla, additional, Ortiz-Ross, Xochitl, additional, Rosso, Adam A., additional, Taylor, Quinn, additional, Thurman, Timothy J., additional, Williams, Claire E., additional, McMillan, W. Owen, additional, and Logan, Michael L., additional

Published
2020
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29. Supplemental Methods and Results from Ectoparasite extinction in simplified lizard assemblages during experimental island invasion

Author

Cox, Christian L., Alexander, Sean, Casement, Brianna, Chung, Albert K., Curlis, John David, Degon, Zachariah, Dubois, Madeline, Falvey, Cleo, Graham, Zackary A., Folfas, Edita, Koyner, Maria A. Gallegos, Neel, Lauren K., Nicholson, Daniel J., Perez, Dylan J. Padilla, Ross, Xochitl Ortiz, Rosso, Adam A., Taylor, Quinn, Thurman, Timothy J., Williams, Claire E., W. Owen McMillan, and Logan, Michael L.

Abstract

Supplemental Methods and Results

Published
2020
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30. Sex-specific microhabitat use is associated with sex-biased thermal physiology in Anolis lizards

Author

Logan, Michael L., primary, Neel, Lauren K., additional, Nicholson, Daniel J., additional, Stokes, Andrew J., additional, Miller, Christina L., additional, Chung, Albert K., additional, Curlis, John David, additional, Keegan, Kaitlin M., additional, Rosso, Adam A., additional, Maayan, Inbar, additional, Folfas, Edite, additional, Williams, Claire E., additional, Casement, Brianna, additional, Koyner, Maria A. Gallegos, additional, Perez, Dylan J. Padilla, additional, Falvey, Cleo H., additional, Alexander, Sean M., additional, Charles, Kristin L., additional, Graham, Zackary A., additional, McMillan, W. Owen, additional, Losos, Jonathan B., additional, and Cox, Christian L., additional

Published
2020
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31. Everything Flows : Towards a Processual Philosophy of Biology

Author

NIcholson, Daniel J., University of Exeter, Dupré, John, NIcholson, Daniel J., University of Exeter, and Dupré, John

Subjects
Conference papers and proceedings, Biology--Philosophy--Congresses, Process philosophy--Congresses, Biology--Philosophy, Process philosophy
Abstract

This is an open access title available under the terms of a CC BY-NC-ND 4.0 International licence. It is free to read at Oxford Scholarship Online and offered as a free PDF download from OUP and selected open access locations. Everything Flows explores the metaphysical thesis that the living world is not made up of substantial particles or things, as has often been supposed, but is rather constituted by processes. The biological domain is organised as an interdependent hierarchy of processes, which are stabilized and actively maintained at different timescales. Even entities that intuitively appear to be paradigms of things, such as organisms, are actually better understood as processes. Unlike previous attempts to articulate processual views of biology, which have tended to use Alfred North Whitehead's panpsychist metaphysics as a foundation, this book takes a naturalistic approach to metaphysics. It submits that the main motivations for replacing an ontology of substances with one of processes are to be found in the empirical findings of science. Biology provides compelling reasons for thinking that the living realm is fundamentally dynamic, and that the existence of things is always conditional on the existence of processes. The phenomenon of life cries out for theories that prioritise processes over things, and it suggests that the central explanandum of biology is not change but rather stability, or more precisely, stability attained through constant change. This edited volume brings together philosophers of science and metaphysicians interested in exploring the prospects of a processual philosophy of biology. The contributors draw on an extremely wide range of biological case studies, and employ a process perspective to cast new light on a number of traditional philosophical problems, such as identity, persistence, and individuality.

Published
2018

33. Genidentity and Biological Processes

Author

Nicholson, Daniel J., Dupré, John, Nicholson, Daniel J., and Dupré, John

Abstract

A crucial question for a process view of life is how to identify a process and how to follow it through time. The genidentity view (first proposed by Kurt Lewin and later elaborated by Hans Reichenbach) can contribute decisively to this project. It says that the identity through time of an entity X is given by a well-identified series of continuous states of affairs. Genidentity helps address the problem of diachronic identity in the living world. This chapter describes the centrality of the concept of genidentity for David Hull and proposes an extension of Hull’s view to the ubiquitous phenomenon of symbiosis. Finally, using immunology as a key example, it shows that the genidentity view suggests that the main interest of a process approach is epistemological rather than ontological and that its principal claim is one of priority, namely that processes precede and define things, and not vice versa.

Published
2018

39. Estimation of the S/G ratios of the lignins in three widely used North American hardwoods.

Author

NICHOLSON, DANIEL J., GUILFORD, CANDACE R., ABIOLA, ADEBUKOLA B., BOSE, SAMAR K., and FRANCIS, RAYMOND C.

Abstract

Sugar maple (Acer saccharum), aspen (Populus tremuloides), and white birch (Betula papyrifera) are three hardwoods that are widely used by the North American pulp and paper industry. Because of their abundance, these species are also likely to be used by some of the biorefinery processes that are being developed. A significant amount of evidence indicates that the syringyl to guaiacyl (S/G) ratio of the lignin in a hardwood is a governing parameter regarding its ease of delignification. Credible data also show that among poplars the S/G ratio of the lignin significantly influences the ease of saccharification of the carbohydrate polymers to sugar monomers. Although the S/G ratio appears to be a key parameter for hardwoods, values accepted by most practitioners are not available for the three species. In this investigation, those ratios were estimated by an extensive literature review followed by S/G determination by nitrobenzene oxidation (NBO) and methoxyl analyses of organosolv lignin (OSL) from the ethanol/water/sulfuric acid pulping process. The S/G values were approximately 1.4 for sugar maple, and 2.0 for aspen and white birch. Data are also included showing that sugar maple and white birch were equally reactive in kraft pulping. Thus, it is unclear whether or not the S/G ratio is indeed a governing parameter in this delignification process. Application: The results from this investigation suggest that S/G ratio alone cannot explain the different rates of delignification by kraft liquor typically observed among hardwoods. Mills might benefit from including more sugar maple in their cooking furnish, if possible. [ABSTRACT FROM AUTHOR]

Published
2016

43. Sex-specific microhabitat use is associated with sex-biased thermal physiology in Anolislizards

Author

Logan, Michael L., Neel, Lauren K., Nicholson, Daniel J., Stokes, Andrew J., Miller, Christina L., Chung, Albert K., Curlis, John David, Keegan, Kaitlin M., Rosso, Adam A., Maayan, Inbar, Folfas, Edite, Williams, Claire E., Casement, Brianna, Gallegos Koyner, Maria A., Padilla Perez, Dylan J., Falvey, Cleo H., Alexander, Sean M., Charles, Kristin L., Graham, Zackary A., McMillan, W. Owen, Losos, Jonathan B., and Cox, Christian L.

Abstract

If fitness optima for a given trait differ between males and females in a population, sexual dimorphism may evolve. Sex-biased trait variation may affect patterns of habitat use, and if the microhabitats used by each sex have dissimilar microclimates, this can drive sex-specific selection on thermal physiology. Nevertheless, tests of differences between the sexes in thermal physiology are uncommon, and studies linking these differences to microhabitat use or behavior are even rarer. We examined microhabitat use and thermal physiology in two ectothermic congeners that are ecologically similar but differ in their degree of sexual size dimorphism. Brown anoles (Anolis sagrei) exhibit male-biased sexual size dimorphism and live in thermally heterogeneous habitats, whereas slender anoles (Anolis apletophallus) are sexually monomorphic in body size and live in thermally homogeneous habitats. We hypothesized that differences in habitat use between the sexes would drive sexual divergence in thermal physiology in brown anoles, but not slender anoles, because male and female brown anoles may be exposed to divergent microclimates. We found that male and female brown anoles, but not slender anoles, used perches with different thermal characteristics and were sexually dimorphic in thermal tolerance traits. However, field-active body temperatures and behavior in a laboratory thermal arena did not differ between females and males in either species. Our results suggest that sexual dimorphism in thermal physiology can arise from phenotypic plasticity or sex-specific selection on traits that are linked to thermal tolerance, rather than from direct effects of thermal environments experienced by males and females.

Published
2021
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45. A high-quality genome for the slender anole (Anolis apletophallus): an emerging model for field studies of tropical ecology and evolution.

Author

Pirani, Renata M, Arias, Carlos F, Charles, Kristin, Chung, Albert K, Curlis, John David, Nicholson, Daniel J, Vargas, Marta, Cox, Christian L, McMillan, W Owen, and Logan, Michael L

Subjects
*ANOLES, *ADAPTIVE radiation, *FIELD research, *GENOMES, *LIZARDS, *COMPARATIVE genomics
Abstract

The slender anole, Anolis apletophallus , is a small arboreal lizard of the rainforest understory of central and eastern Panama. This species has been the subject of numerous ecological and evolutionary studies over the past 60 years as a result of attributes that make it especially amenable to field and laboratory science. Slender anoles are highly abundant, short-lived (nearly 100% annual turnover), easy to manipulate in both the lab and field, and are ubiquitous in the forests surrounding the Smithsonian Tropical Research Institute in Panama, where researchers have access to high-quality laboratory facilities. Here, we present a high-quality genome for the slender anole, which is an important new resource for studying this model species. We assembled and annotated the slender anole genome by combining 3 technologies: Oxford Nanopore, 10× Genomics Linked-Reads, and Dovetail Omni-C. We compared this genome with the recently published brown anole (Anolis sagrei) and the canonical green anole (Anolis carolinensis) genomes. Our genome is the first assembled for an Anolis lizard from mainland Central or South America, the regions that host the majority of diversity in the genus. This new reference genome is one of the most complete genomes of any anole assembled to date and should facilitate deeper studies of slender anole evolution, as well as broader scale comparative genomic studies of both mainland and island species. In turn, such studies will further our understanding of the well-known adaptive radiation of Anolis lizards. [ABSTRACT FROM AUTHOR]

Published
2024
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