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Beausoleil MO, Carrión PL, Podos J, Camacho C, Rabadán-González J, Richard R, Lalla K, Raeymaekers JAM, Knutie SA, De León LF, Chaves JA, Clayton DH, Koop JAH, Sharpe DMT, Gotanda KM, Huber SK, Barrett RDH, Hendry AP. The fitness landscape of a community of Darwin's finches. Evolution 2023; 77:2533-2546. [PMID: 37671423 DOI: 10.1093/evolut/qpad160] [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: 04/05/2023] [Revised: 06/22/2023] [Accepted: 08/31/2023] [Indexed: 09/07/2023]
Abstract
Divergent natural selection should lead to adaptive radiation-that is, the rapid evolution of phenotypic and ecological diversity originating from a single clade. The drivers of adaptive radiation have often been conceptualized through the concept of "adaptive landscapes," yet formal empirical estimates of adaptive landscapes for natural adaptive radiations have proven elusive. Here, we use a 17-year dataset of Darwin's ground finches (Geospiza spp.) at an intensively studied site on Santa Cruz (Galápagos) to estimate individual apparent lifespan in relation to beak traits. We use these estimates to model a multi-species fitness landscape, which we also convert to a formal adaptive landscape. We then assess the correspondence between estimated fitness peaks and observed phenotypes for each of five phenotypic modes (G. fuliginosa, G. fortis [small and large morphotypes], G. magnirostris, and G. scandens). The fitness and adaptive landscapes show 5 and 4 peaks, respectively, and, as expected, the adaptive landscape was smoother than the fitness landscape. Each of the five phenotypic modes appeared reasonably close to the corresponding fitness peak, yet interesting deviations were also documented and examined. By estimating adaptive landscapes in an ongoing adaptive radiation, our study demonstrates their utility as a quantitative tool for exploring and predicting adaptive radiation.
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Affiliation(s)
| | - Paola Lorena Carrión
- Redpath Museum and Department of Biology, McGill University, Montréal, Québec, Canada
| | - Jeffrey Podos
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, United States
| | - Carlos Camacho
- Department of Ecology and Evolution, Estación Biológica de Doñana-CSIC, Sevilla, Spain
| | | | - Roxanne Richard
- Redpath Museum and Department of Biology, McGill University, Montréal, Québec, Canada
| | - Kristen Lalla
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Québec, Canada
| | | | - Sarah A Knutie
- Department of Ecology and Evolutionary Biology, Institute for Systems Genomics, University of Connecticut, Storrs, CT, United States
| | - Luis F De León
- Department of Biology, University of Massachusetts Boston, Boston, MA, United States
| | - Jaime A Chaves
- Department of Biology, San Francisco State University, San Francisco, CA, United States
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Dale H Clayton
- School of Biological Sciences, University of Utah, Salt Lake City, UT, United States
| | - Jennifer A H Koop
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, United States
| | - Diana M T Sharpe
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Kiyoko M Gotanda
- Redpath Museum and Department of Biology, McGill University, Montréal, Québec, Canada
- Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada
- Department of Zoology, University of Cambridge, United Kingdom
- Département de biologie, Université de Sherbrooke, Québec, Canada
| | - Sarah K Huber
- Virginia Institute of Marine Science, William and Mary, Gloucester Point, VA, United States
| | - Rowan D H Barrett
- Redpath Museum and Department of Biology, McGill University, Montréal, Québec, Canada
| | - Andrew P Hendry
- Redpath Museum and Department of Biology, McGill University, Montréal, Québec, Canada
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2
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Topper A, Kolodny O. Crossing the valley of non-intimidating conspicuousness: evolution of warning coloration through the lens of fitness landscapes. Evolution 2023; 77:335-341. [PMID: 36626813 DOI: 10.1093/evolut/qpac044] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 11/03/2022] [Accepted: 11/23/2022] [Indexed: 01/12/2023]
Abstract
The initial evolution of conspicuous aposematism is a longstanding evolutionary paradox: while the benefits of conspicuousness in aposematic signals have been demonstrated, they rely on predators being familiar with the conspicuous signals and avoiding them. In a system dominated by naïve predators, the appearance of conspicuousness would be expected to increase detection and attack rate by the predators. Hence, it is unclear how such signals could become established in a naïve community. We suggest that this problem may usefully be framed in the terms of fitness landscapes, an idea used for conceptualizing the mapping between genotype/phenotype and fitness. The evolution of conspicuousness can be thought of as a special case of valley crossing, which concerns the transition of populations between fitness peaks, when such a transition imposes an initial decrease in fitness. Crypsis may be regarded as a local fitness peak, hindering predators' ability to detect prey; for an unpalatable species, conspicuous aposematism may constitute a higher-still fitness peak, preventing predation attempts altogether and allowing access to niches unavailable to species encumbered by the necessity to remain concealed from predators. However, in order to reach this higher peak, the population must first cross the valley of non-intimidating conspicuousness, in which the prey is conspicuous but the predators are not yet deterred. Using terms borrowed from the concept of fitness landscapes, we categorize several solutions suggested previously in the literature as either concerning changes in the fitness landscape or as illuminating possible ridges connecting the two peaks, which emerge from unconsidered dimensions of the fitness landscape. We suggest that considering this question through the lens of fitness landscapes not only facilitates useful categorization of previously suggested solutions but may also prove useful for thinking about novel ones.
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Affiliation(s)
- Akiva Topper
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Oren Kolodny
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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Jones KE, Dickson BV, Angielczyk KD, Pierce SE. Adaptive landscapes challenge the "lateral-to-sagittal" paradigm for mammalian vertebral evolution. Curr Biol 2021; 31:1883-1892.e7. [PMID: 33657406 DOI: 10.1016/j.cub.2021.02.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [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: 10/20/2020] [Revised: 01/08/2021] [Accepted: 02/03/2021] [Indexed: 11/28/2022]
Abstract
The evolution of mammals from their extinct forerunners, the non-mammalian synapsids, is one of the most iconic locomotor transitions in the vertebrate fossil record. In the limb skeleton, the synapsid-mammal transition is traditionally characterized by a shift from a sprawling limb posture, resembling that of extant reptiles and amphibians, to more adducted limbs, as seen in modern-day mammals. Based on proposed postural similarities between early synapsids and extant reptiles, this change is thought to be accompanied by a shift from ancestral reptile-like lateral bending to mammal-like sagittal bending of the vertebral column. To test this "lateral-to-sagittal" evolutionary paradigm, we used combinatorial optimization to produce functionally informed adaptive landscapes and determined the functional trade-offs associated with evolutionary changes in vertebral morphology. We show that the synapsid adaptive landscape is different from both extant reptiles and mammals, casting doubt on the reptilian model for early synapsid axial function, or indeed for the ancestral condition of amniotes more broadly. Further, the synapsid-mammal transition is characterized by not only increasing sagittal bending in the posterior column but also high stiffness and increasing axial twisting in the anterior column. Therefore, we refute the simplistic lateral-to-sagittal hypothesis and instead suggest the synapsid-mammal locomotor transition involved a more complex suite of functional changes linked to increasing regionalization of the backbone. These results highlight the importance of fossil taxa for understanding major evolutionary transitions.
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Affiliation(s)
- Katrina E Jones
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA; Department of Earth and Environmental Sciences, University of Manchester, Williamson Building, Oxford Road, Manchester M13 9PL, UK.
| | - Blake V Dickson
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA; Department of Evolutionary Anthropology, Duke University, Biological Sciences Building, 130 Science Drive, Durham, NC 27708, USA
| | - Kenneth D Angielczyk
- Negaunee Integrative Research Center, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605-2496, USA
| | - Stephanie E Pierce
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
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Weaver LN, Grossnickle DM. Functional diversity of small-mammal postcrania is linked to both substrate preference and body size. Curr Zool 2020; 66:539-553. [PMID: 33293932 PMCID: PMC7705507 DOI: 10.1093/cz/zoaa057] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 09/14/2020] [Indexed: 01/18/2023] Open
Abstract
Selective pressures favor morphologies that are adapted to distinct ecologies, resulting in trait partitioning among ecomorphotypes. However, the effects of these selective pressures vary across taxa, especially because morphology is also influenced by factors such as phylogeny, body size, and functional trade-offs. In this study, we examine how these factors impact functional diversification in mammals. It has been proposed that trait partitioning among mammalian ecomorphotypes is less pronounced at small body sizes due to biomechanical, energetic, and environmental factors that favor a “generalist” body plan, whereas larger taxa exhibit more substantial functional adaptations. We title this the Divergence Hypothesis (DH) because it predicts greater morphological divergence among ecomorphotypes at larger body sizes. We test DH by using phylogenetic comparative methods to examine the postcranial skeletons of 129 species of taxonomically diverse, small-to-medium-sized (<15 kg) mammals, which we categorize as either “tree-dwellers” or “ground-dwellers.” In some analyses, the morphologies of ground-dwellers and tree-dwellers suggest greater between-group differentiation at larger sizes, providing some evidence for DH. However, this trend is neither particularly strong nor supported by all analyses. Instead, a more pronounced pattern emerges that is distinct from the predictions of DH: within-group phenotypic disparity increases with body size in both ground-dwellers and tree-dwellers, driven by morphological outliers among “medium”-sized mammals. Thus, evolutionary increases in body size are more closely linked to increases in within-locomotor-group disparity than to increases in between-group disparity. We discuss biomechanical and ecological factors that may drive these evolutionary patterns, and we emphasize the significant evolutionary influences of ecology and body size on phenotypic diversity.
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Affiliation(s)
- Lucas N Weaver
- Department of Biology, Life Sciences Building, University of Washington, Seattle, WA 98195, USA
| | - David M Grossnickle
- Department of Biology, Life Sciences Building, University of Washington, Seattle, WA 98195, USA
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Cervera H, Lalić J, Elena SF. Efficient escape from local optima in a highly rugged fitness landscape by evolving RNA virus populations. Proc Biol Sci 2017; 283:rspb.2016.0984. [PMID: 27534955 DOI: 10.1098/rspb.2016.0984] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [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: 05/04/2016] [Accepted: 07/26/2016] [Indexed: 12/25/2022] Open
Abstract
Predicting viral evolution has proven to be a particularly difficult task, mainly owing to our incomplete knowledge of some of the fundamental principles that drive it. Recently, valuable information has been provided about mutation and recombination rates, the role of genetic drift and the distribution of mutational, epistatic and pleiotropic fitness effects. However, information about the topography of virus' adaptive landscapes is still scarce, and to our knowledge no data has been reported so far on how its ruggedness may condition virus' evolvability. Here, we show that populations of an RNA virus move efficiently on a rugged landscape and scape from the basin of attraction of a local optimum. We have evolved a set of Tobacco etch virus genotypes located at increasing distances from a local adaptive optimum in a highly rugged fitness landscape, and we observed that few evolved lineages remained trapped in the local optimum, while many others explored distant regions of the landscape. Most of the diversification in fitness among the evolved lineages was explained by adaptation, while historical contingency and chance events contribution was less important. Our results demonstrate that the ruggedness of adaptive landscapes is not an impediment for RNA viruses to efficiently explore remote parts of it.
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Affiliation(s)
- Héctor Cervera
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Ingeniero Fausto Elio s/n, 46022 València, Spain
| | - Jasna Lalić
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Ingeniero Fausto Elio s/n, 46022 València, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Ingeniero Fausto Elio s/n, 46022 València, Spain The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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Abstract
Strong disruptive ecological selection can initiate speciation, even in the absence of physical isolation of diverging populations. Species evolving under disruptive ecological selection are expected to be ecologically distinct but, at least initially, genetically weakly differentiated. Strong selection and the associated fitness advantages of narrowly adapted individuals, coupled with assortative mating, are predicted to overcome the homogenizing effects of gene flow. Theoretical plausibility is, however, contrasted by limited evidence for the existence of rugged adaptive landscapes in nature. We found evidence for multiple, disruptive ecological selection regimes that have promoted divergence in the sympatric, incipient radiation of 'sharpfin' sailfin silverside fishes in ancient Lake Matano (Sulawesi, Indonesia). Various modes of ecological specialization have led to adaptive morphological differences between the species, and differently adapted morphs display significant but incomplete reproductive isolation. Individual fitness and variation in morphological key characters show that disruptive selection shapes a rugged adaptive landscape in this small but complex incipient lake fish radiation.
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Affiliation(s)
- Jobst Pfaender
- Sektion Ichthyologie, Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, Bonn 53113, Germany Museum für Naturkunde Berlin, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Invalidenstraße 43, Berlin 10115, Germany
| | - Renny K Hadiaty
- Ichthyology Laboratory, Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jl. Raya Bogor Km 46, Cibinong 16911, Indonesia
| | - Ulrich K Schliewen
- Department of Ichthyology, SNSB - Bavarian State Collection of Zoology (ZSM), Münchhausenstr. 21, München 81247, Germany
| | - Fabian Herder
- Sektion Ichthyologie, Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, Bonn 53113, Germany
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Abstract
Most studies on the evolution of antibiotic resistance are focused on selection for resistance at lethal antibiotic concentrations, which has allowed the detection of mutant strains that show strong phenotypic traits. However, solely focusing on lethal concentrations of antibiotics narrowly limits our perspective of antibiotic resistance evolution. New high-resolution competition assays have shown that resistant bacteria are selected at relatively low concentrations of antibiotics. This finding is important because sublethal concentrations of antibiotics are found widely in patients undergoing antibiotic therapies, and in nonmedical conditions such as wastewater treatment plants, and food and water used in agriculture and farming. To understand the impacts of sublethal concentrations on selection, we measured 30 adaptive landscapes for a set of TEM β-lactamases containing all combinations of the four amino acid substitutions that exist in TEM-50 for 15 β-lactam antibiotics at multiple concentrations. We found that there are many evolutionary pathways within this collection of landscapes that lead to nearly every TEM-genotype that we studied. While it is known that the pathways change depending on the type of β-lactam, this study demonstrates that the landscapes including fitness optima also change dramatically as the concentrations of antibiotics change. Based on these results we conclude that the presence of multiple concentrations of β-lactams in an environment result in many different adaptive landscapes through which pathways to nearly every genotype are available. Ultimately this may increase the diversity of genotypes in microbial populations.
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Affiliation(s)
- Portia M Mira
- School of Natural Sciences, University of California, Merced
| | - Juan C Meza
- School of Natural Sciences, University of California, Merced
| | - Anna Nandipati
- School of Natural Sciences, University of California, Merced
| | - Miriam Barlow
- School of Natural Sciences, University of California, Merced
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8
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Laughlin DC, Messier J. Fitness of multidimensional phenotypes in dynamic adaptive landscapes. Trends Ecol Evol 2015; 30:487-96. [PMID: 26122484 DOI: 10.1016/j.tree.2015.06.003] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [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: 03/31/2015] [Revised: 05/28/2015] [Accepted: 06/04/2015] [Indexed: 10/23/2022]
Abstract
Phenotypic traits influence species distributions, but ecology lacks established links between multidimensional phenotypes and fitness for predicting species responses to environmental change. The common focus on single traits rather than multiple trait combinations limits our understanding of their adaptive value, and intraspecific trait covariation has been neglected in ecology despite its importance in evolutionary theory and its likely impact on species distributions. Here, we extend the adaptive landscape framework to ecological sorting of multidimensional phenotypes across environments and discuss how two analytical approaches can be used to quantify fitness as a function of the interaction between the phenotype and the environment. We encourage ecologists to consider how phenotypic integration will constrain species responses to environmental change.
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Affiliation(s)
- Daniel C Laughlin
- Environmental Research Institute and School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand.
| | - Julie Messier
- Ecology and Evolutionary Biology, University of Arizona, 1041 E. Lowell Street, Tucson, AZ 85721, USA
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