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Voje KL. Fitting and evaluating univariate and multivariate models of within-lineage evolution. PALEOBIOLOGY 2023; 49:747-764. [PMID: 37859727 PMCID: PMC7615219 DOI: 10.1017/pab.2023.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
The nature of phenotypic evolution within lineages is central to many unresolved questions in paleontology and evolutionary biology. Analyses of evolutionary time-series of ancestor-descendant populations in the fossil record are likely to make important contributions to many of these debates. However, the limited number of models that have been applied to these types of data may restrict our ability to interpret phenotypic evolution in the fossil record. Using uni- and multivariate models of trait evolution that make different assumptions regarding the dynamics of the adaptive landscape, I evaluate contrasting hypotheses to explain evolution of size in the radiolarian Eucyrtidium calvertense and armor in the stickleback Gaserosteus doryssus. Body size evolution in E. calvertense is best explained by a model where the lineage evolves as a consequence of a shift in the adaptive landscape that coincides with the initiation of neosympatry with its sister lineage. Multivariate evolution of armor traits in a stickleback lineage (Gasterosteus doryssus) show evidence of adaptation towards independent optima on the adaptive landscape at the same time as traits change in a correlated fashion. The fitted models are available in a the R package evoTS, which builds on the commonly used paleoTS framework.
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Grabowski M, Pienaar J, Voje KL, Andersson S, Fuentes-González J, Kopperud BT, Moen DS, Tsuboi M, Uyeda J, Hansen TF. A Cautionary Note on "A Cautionary Note on the Use of Ornstein Uhlenbeck Models in Macroevolutionary Studies". Syst Biol 2023; 72:955-963. [PMID: 37229537 PMCID: PMC10405355 DOI: 10.1093/sysbio/syad012] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 01/08/2023] [Accepted: 03/16/2023] [Indexed: 05/27/2023] Open
Abstract
Models based on the Ornstein-Uhlenbeck process have become standard for the comparative study of adaptation. Cooper et al. (2016) have cast doubt on this practice by claiming statistical problems with fitting Ornstein-Uhlenbeck models to comparative data. Specifically, they claim that statistical tests of Brownian motion may have too high Type I error rates and that such error rates are exacerbated by measurement error. In this note, we argue that these results have little relevance to the estimation of adaptation with Ornstein-Uhlenbeck models for three reasons. First, we point out that Cooper et al. (2016) did not consider the detection of distinct optima (e.g. for different environments), and therefore did not evaluate the standard test for adaptation. Second, we show that consideration of parameter estimates, and not just statistical significance, will usually lead to correct inferences about evolutionary dynamics. Third, we show that bias due to measurement error can be corrected for by standard methods. We conclude that Cooper et al. (2016) have not identified any statistical problems specific to Ornstein-Uhlenbeck models, and that their cautions against their use in comparative analyses are unfounded and misleading. [adaptation, Ornstein-Uhlenbeck model, phylogenetic comparative method.].
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Affiliation(s)
- Mark Grabowski
- Research Centre in Evolutionary Anthropology and Palaeoecology, Liverpool John Moores University, Liverpool, UK
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - Jason Pienaar
- Department of Biological Sciences and the Institutes of Environment, Florida International University Miami, Miami, FL, USA
| | - Kjetil L Voje
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Staffan Andersson
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Jesualdo Fuentes-González
- Department of Biological Sciences and the Institutes of Environment, Florida International University Miami, Miami, FL, USA
| | - Bjørn T Kopperud
- GeoBio-Center LMU, Ludwig-Maximilians-Universität München, Richard-Wagner Straße 10, 80333 Munich, Germany
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner Straße 10, 80333 Munich, Germany
| | - Daniel S Moen
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | | | - Josef Uyeda
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Thomas F Hansen
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
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Rolland J, Henao-Diaz LF, Doebeli M, Germain R, Harmon LJ, Knowles LL, Liow LH, Mank JE, Machac A, Otto SP, Pennell M, Salamin N, Silvestro D, Sugawara M, Uyeda J, Wagner CE, Schluter D. Conceptual and empirical bridges between micro- and macroevolution. Nat Ecol Evol 2023; 7:1181-1193. [PMID: 37429904 DOI: 10.1038/s41559-023-02116-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 06/13/2023] [Indexed: 07/12/2023]
Abstract
Explaining broad molecular, phenotypic and species biodiversity patterns necessitates a unifying framework spanning multiple evolutionary scales. Here we argue that although substantial effort has been made to reconcile microevolution and macroevolution, much work remains to identify the links between biological processes at play. We highlight four major questions of evolutionary biology whose solutions require conceptual bridges between micro and macroevolution. We review potential avenues for future research to establish how mechanisms at one scale (drift, mutation, migration, selection) translate to processes at the other scale (speciation, extinction, biogeographic dispersal) and vice versa. We propose ways in which current comparative methods to infer molecular evolution, phenotypic evolution and species diversification could be improved to specifically address these questions. We conclude that researchers are in a better position than ever before to build a synthesis to understand how microevolutionary dynamics unfold over millions of years.
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Affiliation(s)
- Jonathan Rolland
- CNRS, UMR5174, Laboratoire Evolution et Diversité Biologique, Université Toulouse 3 Paul Sabatier, Toulouse, France.
| | - L Francisco Henao-Diaz
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Michael Doebeli
- Department of Zoology, and Department of Mathematics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rachel Germain
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Luke J Harmon
- Dept. of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | | | - Judith E Mank
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Antonin Machac
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Prague, Czech Republic
| | - Sarah P Otto
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matt Pennell
- Departments of Quantitative and Computational Biology and Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Daniele Silvestro
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | - Mauro Sugawara
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Mário Schenberg Institute, São Paulo, Brazil
| | - Josef Uyeda
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Catherine E Wagner
- Department of Botany, and Program in Ecology and Evolution, University of Wyoming, Laramie, WY, USA
| | - Dolph Schluter
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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Tamagnini D, Canestrelli D, Meloro C, Raia P, Maiorano L. New Avenues for Old Travellers: Phenotypic Evolutionary Trends Meet Morphodynamics, and Both Enter the Global Change Biology Era. Evol Biol 2021. [DOI: 10.1007/s11692-021-09545-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AbstractEvolutionary trends (ETs) are traditionally defined as substantial changes in the state of traits through time produced by a persistent condition of directional evolution. ETs might also include directional responses to ecological, climatic or biological gradients and represent the primary evolutionary pattern at high taxonomic levels and over long-time scales. The absence of a well-supported operative definition of ETs blurred the definition of conceptual differences between ETs and other key concepts in evolution such as convergence, parallel evolution, and divergence. Also, it prevented the formulation of modern guidelines for studying ETs and evolutionary dynamics related to them. In phenotypic evolution, the theory of morphodynamics states that the interplay between evolutionary factors such as phylogeny, evo-devo constraints, environment, and biological function determines morphological evolution. After introducing a new operative definition, here we provide a morphodynamics-based framework for studying phenotypic ETs, discussing how understanding the impact of these factors on ETs improves the explanation of links between biological patterns and processes underpinning directional evolution. We envisage that adopting a quantitative, pattern-based, and multifactorial approach will pave the way to new potential applications for this field of evolutionary biology. In this framework, by exploiting the catalysing effect of climate change on evolution, research on ETs induced by global change might represent an ideal arena for validating hypotheses about the predictability of evolution.
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The Evolution of 'Ecological Release' into the 21st Century. Trends Ecol Evol 2020; 36:206-215. [PMID: 33223276 DOI: 10.1016/j.tree.2020.10.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/22/2020] [Accepted: 10/26/2020] [Indexed: 11/22/2022]
Abstract
Ecological release, originally conceived as niche expansion following a reduction in interspecific competition, may prompt invasion success, morphological evolution, speciation, and other ecological and evolutionary outcomes. However, the concept has not been recently reviewed. Here, we trace the study of 'ecological release' from its inception through the present day and find that current definitions are broad and highly varied. Viewing this development as a potential impediment to clear communication and hypothesis testing, we suggest a consensus definition for ecological release: niche expansions and shifts when a constraining interspecific interaction is reduced or removed. In rationalizing this definition, we highlight the various ways ecological release can unfold and address its potential evolutionary consequences.
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Khodaei L. Digest: Fossils, evolutionary models, and diatoms. Evolution 2019; 74:210-211. [PMID: 31702054 DOI: 10.1111/evo.13869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 10/14/2019] [Indexed: 11/28/2022]
Abstract
Adaptation to new environments by organisms has been and is of much interest in scientific research. Does the diatom lineage Stephanodiscus niagarae/yellowstonensis follow models compatible with adaptation to a new environment? Voje (2019) shows that in this lineage, none of the current models tested-decelerated evolution, Ornstein-Uhlenbeck, and random walk-fully explained how multiple traits-valve diameter, the number of costae, and spines per valve-evolved. More accurate models are needed to understand the evolutionary history of these diatoms.
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Affiliation(s)
- Lucas Khodaei
- Biological and Geological Sciences Building (BGS), Department of Biology, Western University, London, Ontario, Canada
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