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Smith TJ, Sansom RS, Pisani D, Donoghue PCJ. Fossilization can mislead analyses of phenotypic disparity. Proc Biol Sci 2023; 290:20230522. [PMID: 37554036 PMCID: PMC10410227 DOI: 10.1098/rspb.2023.0522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 07/20/2023] [Indexed: 08/10/2023] Open
Abstract
Analyses of morphological disparity can incorporate living and fossil taxa to facilitate the exploration of how phenotypic variation changes through time. However, taphonomic processes introduce non-random patterns of data loss in fossil data and their impact on perceptions of disparity is unclear. To address this, we characterize how measures of disparity change when simulated and empirical data are degraded through random and structured data loss. We demonstrate that both types of data loss can distort the disparity of clades, and that the magnitude and direction of these changes varies between the most commonly employed distance metrics and disparity indices. The inclusion of extant taxa and exceptionally preserved fossils mitigates these distortions and clarifies the full extent of the data lost, most of which would otherwise go uncharacterized. This facilitates the use of ancestral state estimation and evolutionary simulations to further control for the effects of data loss. Where the addition of such reference taxa is not possible, we urge caution in the extrapolation of general patterns in disparity from datasets that characterize subsets of phenotype, which may represent no more than the traits that they sample.
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Affiliation(s)
- Thomas J. Smith
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - Robert S. Sansom
- Department of Earth and Environmental Sciences, University of Manchester, Williamson Building, Oxford Road, Manchester M13 9PL, UK
| | - Davide Pisani
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Philip C. J. Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
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2
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Decoupled Patterns of Diversity and Disparity Characterize an Ecologically Specialized Lineage of Neotropical Cricetids. Evol Biol 2023. [DOI: 10.1007/s11692-022-09596-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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3
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Leventhal S, Jamison-Todd S, Simpson C. Aggregate Trait Evolvability and Macroevolution in Two Sister Species of the Bryozoan Stylopoma. Evol Biol 2022. [DOI: 10.1007/s11692-022-09588-8] [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
AbstractThe study of trait evolution in modular animals is more complicated than that in solitary animals, because a single genotype of a modular colony can express an enormous range of phenotypic variation. Furthermore, traits can occur either at the module level or at the colony level. However, it is unclear how the traits at the colony level evolve. We test whether colony-level aggregate traits, defined as the summary statistics of a phenotypic distribution, can evolve. To quantify this evolutionary potential, we use parent-offspring pairs in two sister species of the bryozoan Stylopoma, grown and bred in a common garden breeding experiment. We find that the medians of phenotypic distributions are evolvable between generations of colonies. We also find that the structure of this evolutionary potential differs between these two species. Ancestral species align more closely with the direction of species divergence than the descendent species. This result indicates that aggregate trait evolvability can itself evolve.
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4
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Jardine PE, Palazzesi L, Tellería MC, Barreda VD. Why does pollen morphology vary? Evolutionary dynamics and morphospace occupation in the largest angiosperm order (Asterales). THE NEW PHYTOLOGIST 2022; 234:1075-1087. [PMID: 35147224 DOI: 10.1111/nph.18024] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Morphological diversity (disparity) is a key component of biodiversity and increasingly a focus of botanical research. Despite the wide range of morphologies represented by pollen grains, to date there are few studies focused on the controls on pollen disparity and morphospace occupation, and fewer still considering these parameters in a phylogenetic framework. Here, we analyse morphospace occupation, disparity and rates of morphological evolution in Asterales pollen, in a phylogenetic context. We use a dataset comprising 113 taxa from across the Asterales phylogeny, with pollen morphology described using 28 discrete characters. The Asterales pollen morphospace is phylogenetically structured around groups of related taxa, consistent with punctuated bursts of morphological evolution at key points in the Asterales phylogeny. There is no substantial difference in disparity among these groups of taxa, despite large differences in species richness and biogeographic range. There is also mixed evidence for whole-genome duplication as a driver of Asterales pollen morphological evolution. Our results highlight the importance of evolutionary history for structuring pollen morphospace. Our study is consistent with others that have shown a decoupling of biodiversity parameters, and reinforces the need to focus on disparity as a key botanical metric in its own right.
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Affiliation(s)
- Phillip E Jardine
- Institute of Geology and Palaeontology, University of Münster, Münster, 48149, Germany
| | - Luis Palazzesi
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1405DJR, Buenos Aires, Argentina
- Sección Paleopalinología, Museo Argentino de Ciencias Naturales 'Bernardino Rivadavia', C1405DJR, Buenos Aires, Argentina
| | - M Cristina Tellería
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1405DJR, Buenos Aires, Argentina
- Laboratorio de Sistemática y Biología Evolutiva, Museo de La Plata, B1900FWA, La Plata, Argentina
| | - Viviana D Barreda
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1405DJR, Buenos Aires, Argentina
- Sección Paleopalinología, Museo Argentino de Ciencias Naturales 'Bernardino Rivadavia', C1405DJR, Buenos Aires, Argentina
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5
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Mongiardino Koch N. Exploring adaptive landscapes across deep time: A case study using echinoid body size. Evolution 2021; 75:1567-1581. [PMID: 33782962 DOI: 10.1111/evo.14219] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 03/10/2021] [Accepted: 03/15/2021] [Indexed: 11/30/2022]
Abstract
Adaptive landscapes are a common way of conceptualizing the phenotypic evolution of lineages across deep time. Although multiple approaches exist to implement this concept into operational models of trait evolution, inferring adaptive landscapes from comparative datasets remains challenging. Here, I explore the macroevolutionary dynamics of echinoid body size using data from over 5000 specimens and a phylogenetic framework incorporating a dense fossil sampling and spanning approximately 270 million years. Furthermore, I implement a novel approach of exploring alternative parameterizations of adaptive landscapes that succeeds in finding simpler, yet better-fitting models. Echinoid body size has been constrained to evolve within a single adaptive optimum for much of the clade's history. However, most of the morphological disparity of echinoids was generated by multiple regime shifts that drove the repeated evolution of miniaturized and gigantic forms. Events of body size innovation occurred predominantly in the Late Cretaceous and were followed by a drastic slowdown following the Cretaceous-Paleogene mass extinction. The discovery of these patterns is contingent upon directly sampling fossil taxa. The macroevolution of echinoid body size is therefore characterized by a late increase in disparity (likely linked to an expansion of ecospace), generated by active processes driving lineages toward extreme morphologies.
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De Mendoza RS, Gómez RO, Tambussi CP. The lacrimal/ectethmoid region of waterfowl (Aves, Anseriformes): Phylogenetic signal and major evolutionary patterns. J Morphol 2020; 281:1486-1500. [PMID: 32936967 DOI: 10.1002/jmor.21265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/02/2020] [Accepted: 09/02/2020] [Indexed: 11/08/2022]
Abstract
Waterfowl (Aves, Anseriformes) constitute an ancient global radiation, and understanding the pattern and timing of their evolution requires a well-corroborated phylogeny including extant species and fossils. Following the molecular advances in avian systematics, however, morphology has often been held as misleading, yet congruence with molecular data has been shown to vary considerably among different skeletal parts. Here, we explore phylogenetic signal in discrete characters of the lacrimal/ectethmoid region of waterfowl, which is highly variable among species and constitutes a rich source of data. We do so by combining cladistic and multivariate approaches, and using phylogenetic comparative methods. We quantitatively recognize three major morphological types among lacrimal bones, and discuss homoplasy and potential synapomorphies of major clades using a molecular backbone tree. Our results clearly indicate that the lacrimal bone carries substantial phylogenetic signal and could be of systematic value at different levels of the phylogeny of waterfowl, feeding the exploration of other regions of the skull with this combined approach.
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Affiliation(s)
- Ricardo S De Mendoza
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.,División Paleontología Vertebrados, Museo de La Plata, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Argentina
| | - Raúl O Gómez
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.,Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria, Buenos Aires, Argentina
| | - Claudia P Tambussi
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.,Centro de Investigaciones en Ciencias de la Tierra (CICTERRA), Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba, X5016GCA, Argentina
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7
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Affiliation(s)
- David Jablonski
- Department of Geophysical Sciences University of Chicago Chicago Illinois
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Jablonski D. Approaches to Macroevolution: 2. Sorting of Variation, Some Overarching Issues, and General Conclusions. Evol Biol 2017; 44:451-475. [PMID: 29142334 PMCID: PMC5661022 DOI: 10.1007/s11692-017-9434-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 10/04/2017] [Indexed: 11/08/2022]
Abstract
Approaches to macroevolution require integration of its two fundamental components, within a hierarchical framework. Following a companion paper on the origin of variation, I here discuss sorting within an evolutionary hierarchy. Species sorting-sometimes termed species selection in the broad sense, meaning differential origination and extinction owing to intrinsic biological properties-can be split into strict-sense species selection, in which rate differentials are governed by emergent, species-level traits such as geographic range size, and effect macroevolution, in which rates are governed by organism-level traits such as body size; both processes can create hitchhiking effects, indirectly causing the proliferation or decline of other traits. Several methods can operationalize the concept of emergence, so that rigorous separation of these processes is increasingly feasible. A macroevolutionary tradeoff, underlain by the intrinsic traits that influence evolutionary dynamics, causes speciation and extinction rates to covary in many clades, resulting in evolutionary volatility of some clades and more subdued behavior of others; the few clades that break the tradeoff can achieve especially prolific diversification. In addition to intrinsic biological traits at multiple levels, extrinsic events can drive the waxing and waning of clades, and the interaction of traits and events are difficult but important to disentangle. Evolutionary trends can arise in many ways, and at any hierarchical level; descriptive models can be fitted to clade trajectories in phenotypic or functional spaces, but they may not be diagnostic regarding processes, and close attention must be paid to both leading and trailing edges of apparent trends. Biotic interactions can have negative or positive effects on taxonomic diversity within a clade, but cannot be readily extrapolated from the nature of such interactions at the organismic level. The relationships among macroevolutionary currencies through time (taxonomic richness, morphologic disparity, functional variety) are crucial for understanding the nature of evolutionary diversification. A novel approach to diversity-disparity analysis shows that taxonomic diversifications can lag behind, occur in concert with, or precede, increases in disparity. Some overarching issues relating to both the origin and sorting of clades and phenotypes include the macroevolutionary role of mass extinctions, the potential differences between plant and animal macroevolution, whether macroevolutionary processes have changed through geologic time, and the growing human impact on present-day macroevolution. Many challenges remain, but progress is being made on two of the key ones: (a) the integration of variation-generating mechanisms and the multilevel sorting processes that act on that variation, and (b) the integration of paleontological and neontological approaches to historical biology.
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Affiliation(s)
- David Jablonski
- Department of Geophysical Sciences, University of Chicago, 5734 South Ellis Avenue, Chicago, IL 60637 USA
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9
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Jablonski D. Approaches to Macroevolution: 1. General Concepts and Origin of Variation. Evol Biol 2017; 44:427-450. [PMID: 29142333 PMCID: PMC5661017 DOI: 10.1007/s11692-017-9420-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Accepted: 05/26/2017] [Indexed: 12/11/2022]
Abstract
Approaches to macroevolution require integration of its two fundamental components, i.e. the origin and the sorting of variation, in a hierarchical framework. Macroevolution occurs in multiple currencies that are only loosely correlated, notably taxonomic diversity, morphological disparity, and functional variety. The origin of variation within this conceptual framework is increasingly understood in developmental terms, with the semi-hierarchical structure of gene regulatory networks (GRNs, used here in a broad sense incorporating not just the genetic circuitry per se but the factors controlling the timing and location of gene expression and repression), the non-linear relation between magnitude of genetic change and the phenotypic results, the evolutionary potential of co-opting existing GRNs, and developmental responsiveness to nongenetic signals (i.e. epigenetics and plasticity), all requiring modification of standard microevolutionary models, and rendering difficult any simple definition of evolutionary novelty. The developmental factors underlying macroevolution create anisotropic probabilities-i.e., an uneven density distribution-of evolutionary change around any given phenotypic starting point, and the potential for coordinated changes among traits that can accommodate change via epigenetic mechanisms. From this standpoint, "punctuated equilibrium" and "phyletic gradualism" simply represent two cells in a matrix of evolutionary models of phenotypic change, and the origin of trends and evolutionary novelty are not simply functions of ecological opportunity. Over long timescales, contingency becomes especially important, and can be viewed in terms of macroevolutionary lags (the temporal separation between the origin of a trait or clade and subsequent diversification); such lags can arise by several mechanisms: as geological or phylogenetic artifacts, or when diversifications require synergistic interactions among traits, or between traits and external events. The temporal and spatial patterns of the origins of evolutionary novelties are a challenge to macroevolutionary theory; individual events can be described retrospectively, but a general model relating development, genetics, and ecology is needed. An accompanying paper (Jablonski in Evol Biol 2017) reviews diversity dynamics and the sorting of variation, with some general conclusions.
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Affiliation(s)
- David Jablonski
- Department of Geophysical Sciences, University of Chicago, 5734 South Ellis Avenue, Chicago, IL 60637 USA
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10
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Phylogenetic Paleoecology: Tree-Thinking and Ecology in Deep Time. Trends Ecol Evol 2017; 32:452-463. [DOI: 10.1016/j.tree.2017.03.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/04/2017] [Accepted: 03/06/2017] [Indexed: 01/26/2023]
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11
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Knoll AH, Nowak MA. The timetable of evolution. SCIENCE ADVANCES 2017; 3:e1603076. [PMID: 28560344 PMCID: PMC5435417 DOI: 10.1126/sciadv.1603076] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 03/21/2017] [Indexed: 05/06/2023]
Abstract
The integration of fossils, phylogeny, and geochronology has resulted in an increasingly well-resolved timetable of evolution. Life appears to have taken root before the earliest known minimally metamorphosed sedimentary rocks were deposited, but for a billion years or more, evolution played out beneath an essentially anoxic atmosphere. Oxygen concentrations in the atmosphere and surface oceans first rose in the Great Oxygenation Event (GOE) 2.4 billion years ago, and a second increase beginning in the later Neoproterozoic Era [Neoproterozoic Oxygenation Event (NOE)] established the redox profile of modern oceans. The GOE facilitated the emergence of eukaryotes, whereas the NOE is associated with large and complex multicellular organisms. Thus, the GOE and NOE are fundamental pacemakers for evolution. On the time scale of Earth's entire 4 billion-year history, the evolutionary dynamics of the planet's biosphere appears to be fast, and the pace of evolution is largely determined by physical changes of the planet. However, in Phanerozoic ecosystems, interactions between new functions enabled by the accumulation of characters in a complex regulatory environment and changing biological components of effective environments appear to have an important influence on the timing of evolutionary innovations. On the much shorter time scale of transient environmental perturbations, such as those associated with mass extinctions, rates of genetic accommodation may have been limiting for life.
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Affiliation(s)
- Andrew H. Knoll
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Martin A. Nowak
- Program for Evolutionary Dynamics, Department of Organismic and Evolutionary Biology, Department of Mathematics, Harvard University, Cambridge, MA 02138, USA
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12
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Mongiardino Koch N, Ceccarelli FS, Ojanguren-Affilastro AA, Ramírez MJ. Discrete and morphometric traits reveal contrasting patterns and processes in the macroevolutionary history of a clade of scorpions. J Evol Biol 2017; 30:814-825. [DOI: 10.1111/jeb.13050] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 02/05/2017] [Accepted: 02/06/2017] [Indexed: 02/01/2023]
Affiliation(s)
| | - F. S. Ceccarelli
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”; Buenos Aires Argentina
- Departamento de Biología de la Conservación; Centro de Investigación Científica y de Educación Superior de Ensenada; Ensenada Baja California México
| | | | - M. J. Ramírez
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”; Buenos Aires Argentina
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13
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Sherratt E, Alejandrino A, Kraemer AC, Serb JM, Adams DC. Trends in the sand: Directional evolution in the shell shape of recessing scallops (Bivalvia: Pectinidae). Evolution 2016; 70:2061-73. [DOI: 10.1111/evo.12995] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Revised: 06/06/2016] [Accepted: 06/21/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Emma Sherratt
- Department of Ecology, Evolution, and Organismal Biology Iowa State University Ames Iowa 50011
- Division of Evolution, Ecology and Genetics The Australian National University Canberra ACT 2601 Australia
| | - Alvin Alejandrino
- Department of Ecology, Evolution, and Organismal Biology Iowa State University Ames Iowa 50011
| | - Andrew C. Kraemer
- Department of Ecology, Evolution, and Organismal Biology Iowa State University Ames Iowa 50011
| | - Jeanne M. Serb
- Department of Ecology, Evolution, and Organismal Biology Iowa State University Ames Iowa 50011
| | - Dean C. Adams
- Department of Ecology, Evolution, and Organismal Biology Iowa State University Ames Iowa 50011
- Department of Statistics Iowa State University Ames Iowa 50011
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Lloyd GT. Estimating morphological diversity and tempo with discrete character-taxon matrices: implementation, challenges, progress, and future directions. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12746] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Graeme T. Lloyd
- Department of Biological Sciences; Faculty of Science; Macquarie University; NSW 2109 Australia
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15
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Goswami A, Mannion PD, Benton MJ. Radiation and extinction: investigating clade dynamics in deep time. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12763] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Anjali Goswami
- Department of Genetics, Evolution & Environment; University College London; Darwin Building Gower Street London WC1E 6BT UK
- Department of Earth Sciences; University College London; Gower Street London WC1E 6BT UK
| | - Philip D. Mannion
- Department of Earth Science and Engineering; Imperial College London; South Kensington Campus London SW7 2AZ UK
| | - Michael J. Benton
- School of Earth Sciences; University of Bristol; Wills Memorial Building Queens Road Clifton BS8 1RJ UK
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