1
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Marion AFP, Condamine FL, Guinot G. Sequential trait evolution did not drive deep-time diversification in sharks. Evolution 2024; 78:1405-1425. [PMID: 38745524 DOI: 10.1093/evolut/qpae070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 04/23/2024] [Accepted: 05/13/2024] [Indexed: 05/16/2024]
Abstract
Estimating how traits evolved and impacted diversification across the tree of life represents a critical topic in ecology and evolution. Although there has been considerable research in comparative biology, large parts of the tree of life remain underexplored. Sharks are an iconic clade of marine vertebrates, and key components of marine ecosystems since the early Mesozoic. However, few studies have addressed how traits evolved or whether they impacted their extant diversity patterns. Our study aimed to fill this gap by reconstructing the largest time-calibrated species-level phylogeny of sharks and compiling an exhaustive database for ecological (diet, habitat) and biological (reproduction, maximum body length) traits. Using state-of-the-art models of evolution and diversification, we outlined the major character shifts and modes of trait evolution across shark species. We found support for sequential models of trait evolution and estimated a small to medium-sized lecithotrophic and coastal-dwelling most recent common ancestor for extant sharks. However, our exhaustive hidden traits analyses do not support trait-dependent diversification for any examined traits, challenging previous works. This suggests that the role of traits in shaping sharks' diversification dynamics might have been previously overestimated and should motivate future macroevolutionary studies to investigate other drivers of diversification in this clade.
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Affiliation(s)
- Alexis F P Marion
- Institut des Sciences de l'Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | - Fabien L Condamine
- Institut des Sciences de l'Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | - Guillaume Guinot
- Institut des Sciences de l'Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
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2
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Lecocq de Pletincx N, Cerdà X, Kiran K, Karaman C, Taheri A, Aron S. Ecological diversification preceded geographical expansion during the evolutionary radiation of Cataglyphis desert ants. iScience 2024; 27:109852. [PMID: 38779477 PMCID: PMC11109030 DOI: 10.1016/j.isci.2024.109852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/20/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
Biological diversity often arises as organisms adapt to new ecological conditions (i.e., ecological opportunities) or colonize suitable areas (i.e., spatial opportunities). Cases of geographical expansion followed by local ecological divergence are well described; they result in clades comprising ecologically heterogeneous subclades. Here, we show that the desert ant genus Cataglyphis likely originated in open grassland habitats in the Middle East ∼18 million years ago and became a taxon of diverse species specializing in prey of different masses. The genus then colonized the Mediterranean Basin around 9 million years ago. The result was the rapid accumulation of species, and the appearance of local assemblages containing species from different lineages that still displayed ancestral foraging specialties. These findings highlight that, in Cataglyphis, ecological diversification preceded geographical expansion, resulting in a clade composed of ecologically homogeneous subclades.
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Affiliation(s)
- Nathan Lecocq de Pletincx
- Evolutionary Biology and Ecology, Faculty of Sciences, Université Libre de Bruxelles, CP 160/12, av. FD Roosevelt, 1050 Brussels, Belgium
| | - Xim Cerdà
- Department of Ethology and Biodiversity Conservation, Estación Biológica de Doñana, CSIC, Sevilla, Spain
| | - Kadri Kiran
- Department of Biology, Faculty of Sciences, Trakya University, Edirne 22030, Türkiye
| | - Celal Karaman
- Department of Biology, Faculty of Sciences, Trakya University, Edirne 22030, Türkiye
| | - Ahmed Taheri
- Laboratory of Plant Biotechnology, Ecology and Ecosystem Valorization, Faculty of Sciences of El Jadida, University Chouaïb Doukkali, El Jadida, Morocco
| | - Serge Aron
- Evolutionary Biology and Ecology, Faculty of Sciences, Université Libre de Bruxelles, CP 160/12, av. FD Roosevelt, 1050 Brussels, Belgium
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3
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van Holstein LA, Foley RA. Diversity-dependent speciation and extinction in hominins. Nat Ecol Evol 2024; 8:1180-1190. [PMID: 38632435 PMCID: PMC11166571 DOI: 10.1038/s41559-024-02390-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 03/08/2024] [Indexed: 04/19/2024]
Abstract
The search for drivers of hominin speciation and extinction has tended to focus on the impact of climate change. Far less attention has been paid to the role of interspecific competition. However, research across vertebrates more broadly has shown that both processes are often correlated with species diversity, suggesting an important role for interspecific competition. Here we ask whether hominin speciation and extinction conform to the expected patterns of negative and positive diversity dependence, respectively. We estimate speciation and extinction rates from fossil occurrence data with preservation variability priors in a validated Bayesian framework and test whether these rates are correlated with species diversity. We supplement these analyses with calculations of speciation rate across a phylogeny, again testing whether these are correlated with diversity. Our results are consistent with clade-wide diversity limits that governed speciation in hominins overall but that were not quite reached by the Australopithecus and Paranthropus subclade before its extinction. Extinction was not correlated with species diversity within the Australopithecus and Paranthropus subclade or within hominins overall; this is concordant with climate playing a greater part in hominin extinction than speciation. By contrast, Homo is characterized by positively diversity-dependent speciation and negatively diversity-dependent extinction-both exceedingly rare patterns across all forms of life. The genus Homo expands the set of reported associations between diversity and macroevolution in vertebrates, underscoring that the relationship between diversity and macroevolution is complex. These results indicate an important, previously underappreciated and comparatively unusual role of biotic interactions in Homo macroevolution, and speciation in particular. The unusual and unexpected patterns of diversity dependence in Homo speciation and extinction may be a consequence of repeated Homo range expansions driven by interspecific competition and made possible by recurrent innovations in ecological strategies. Exploring how hominin macroevolution fits into the general vertebrate macroevolutionary landscape has the potential to offer new perspectives on longstanding questions in vertebrate evolution and shed new light on evolutionary processes within our own lineage.
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Affiliation(s)
- Laura A van Holstein
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Cambridge, UK.
| | - Robert A Foley
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Cambridge, UK
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4
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Zarzyczny KM, Rius M, Williams ST, Fenberg PB. The ecological and evolutionary consequences of tropicalisation. Trends Ecol Evol 2024; 39:267-279. [PMID: 38030539 DOI: 10.1016/j.tree.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023]
Abstract
Tropicalisation is a marine phenomenon arising from contemporary climate change, and is characterised by the range expansion of tropical/subtropical species and the retraction of temperate species. Tropicalisation occurs globally and can be detected in both tropical/temperate transition zones and temperate regions. The ecological consequences of tropicalisation range from single-species impacts (e.g., altered behaviour) to whole ecosystem changes (e.g., phase shifts in intertidal and subtidal habitats). Our understanding of the evolutionary consequences of tropicalisation is limited, but emerging evidence suggests that tropicalisation could induce phenotypic change as well as shifts in the genotypic composition of both expanding and retracting species. Given the rapid rate of contemporary climate change, research on tropicalisation focusing on shifts in ecosystem functioning, biodiversity change, and socioeconomic impacts is urgently needed.
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Affiliation(s)
- Karolina M Zarzyczny
- School of Ocean and Earth Science, National Oceanography Centre, University of Southampton, Southampton SO14 3ZH, UK; Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Marc Rius
- Centre for Advanced Studies of Blanes (CEAB), Consejo Superior de Investigaciones Científicas (CSIC), Accés a la Cala Sant Francesc 14, Blanes 17300, Spain; Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park, 2006 Johannesburg, South Africa
| | | | - Phillip B Fenberg
- School of Ocean and Earth Science, National Oceanography Centre, University of Southampton, Southampton SO14 3ZH, UK; Natural History Museum, Cromwell Road, London SW7 5BD, UK
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5
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Drury JP, Clavel J, Tobias JA, Rolland J, Sheard C, Morlon H. Limited ecological opportunity influences the tempo of morphological evolution in birds. Curr Biol 2024; 34:661-669.e4. [PMID: 38218182 DOI: 10.1016/j.cub.2023.12.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/27/2023] [Accepted: 12/18/2023] [Indexed: 01/15/2024]
Abstract
According to classic models of lineage diversification and adaptive radiation, phenotypic evolution should accelerate in the context of ecological opportunity and slow down when niches become saturated.1,2 However, only weak support for these ideas has been found in nature, perhaps because most analyses make the biologically unrealistic assumption that clade members contribute equally to reducing ecological opportunity, even when they occur in different continents or specialize on different habitats and diets. To view this problem through a different lens, we adapted a new phylogenetic modeling approach that accounts for the fact that competition for ecological opportunity only occurs between species that coexist and share similar habitats and diets. Applying this method to trait data for nearly all extant species of landbirds,3 we find a widespread signature of decelerating trait evolution in lineages adapted to similar habitats or diets. The strength of this pattern was consistent across latitudes when comparing tropical and temperate assemblages. Our results provide little support for the idea that increased diversity and tighter packing of niches accentuates evolutionary slowdowns in the tropics and instead suggest that limited ecological opportunity can be an important factor determining the rate of morphological diversification at a global scale.
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Affiliation(s)
- Jonathan P Drury
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK.
| | - Julien Clavel
- Université Claude Bernard Lyon 1, LEHNA UMR 5023, CNRS, ENTPE, F-69622 Villeurbanne, France
| | - Joseph A Tobias
- Department of Life Sciences, Imperial College London, Ascot SL5 7PY, UK
| | - Jonathan Rolland
- CNRS, UMR5174, Laboratoire Evolution et Diversité Biologique, Université Toulouse 3 Paul Sabatier, Bâtiment 4R1, 118 Route de Narbonne, 31062 Toulouse, France
| | - Catherine Sheard
- School of Earth Sciences, University of Bristol, Bristol BS8 1RL, UK; School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, UK
| | - Hélène Morlon
- Institut de Biologie - École Normale Supérieure, Université PSL, CNRS, INSERM, 75005 Paris, France
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6
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Overcast I, Noguerales V, Meramveliotakis E, Andújar C, Arribas P, Creedy TJ, Emerson BC, Vogler AP, Papadopoulou A, Morlon H. Inferring the ecological and evolutionary determinants of community genetic diversity. Mol Ecol 2023; 32:6093-6109. [PMID: 37221561 DOI: 10.1111/mec.16958] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 05/25/2023]
Abstract
Understanding the relative contributions of ecological and evolutionary processes to the structuring of ecological communities is needed to improve our ability to predict how communities may respond to future changes in an increasingly human-modified world. Metabarcoding methods make it possible to gather population genetic data for all species within a community, unlocking a new axis of data to potentially unveil the origins and maintenance of biodiversity at local scales. Here, we present a new eco-evolutionary simulation model for investigating community assembly dynamics using metabarcoding data. The model makes joint predictions of species abundance, genetic variation, trait distributions and phylogenetic relationships under a wide range of parameter settings (e.g. high speciation/low dispersal or vice versa) and across a range of community states, from pristine and unmodified to heavily disturbed. We first demonstrate that parameters governing metacommunity and local community processes leave detectable signatures in simulated biodiversity data axes. Next, using a simulation-based machine learning approach we show that neutral and non-neutral models are distinguishable and that reasonable estimates of several model parameters within the local community can be obtained using only community-scale genetic data, while phylogenetic information is required to estimate those describing metacommunity dynamics. Finally, we apply the model to soil microarthropod metabarcoding data from the Troodos mountains of Cyprus, where we find that communities in widespread forest habitats are structured by neutral processes, while high-elevation and isolated habitats act as an abiotic filter generating non-neutral community structure. We implement our model within the ibiogen R package, a package dedicated to the investigation of island, and more generally community-scale, biodiversity using community-scale genetic data.
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Affiliation(s)
- Isaac Overcast
- Institut de Biologie de l'ENS (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Department of Vertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Víctor Noguerales
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Spain
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | | | - Carmelo Andújar
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Spain
| | - Paula Arribas
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Spain
| | - Thomas J Creedy
- Department of Life Sciences, Natural History Museum, London, UK
| | - Brent C Emerson
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Spain
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, UK
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Anna Papadopoulou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Hélène Morlon
- Institut de Biologie de l'ENS (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
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7
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Helmstetter AJ, Zenil-Ferguson R, Sauquet H, Otto SP, Méndez M, Vallejo-Marin M, Schönenberger J, Burgarella C, Anderson B, de Boer H, Glémin S, Käfer J. Trait-dependent diversification in angiosperms: Patterns, models and data. Ecol Lett 2023; 26:640-657. [PMID: 36829296 DOI: 10.1111/ele.14170] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 02/26/2023]
Abstract
Variation in species richness across the tree of life, accompanied by the incredible variety of ecological and morphological characteristics found in nature, has inspired many studies to link traits with species diversification. Angiosperms are a highly diverse group that has fundamentally shaped life on earth since the Cretaceous, and illustrate how species diversification affects ecosystem functioning. Numerous traits and processes have been linked to differences in species richness within this group, but we know little about their relative importance and how they interact. Here, we synthesised data from 152 studies that used state-dependent speciation and extinction (SSE) models on angiosperm clades. Intrinsic traits related to reproduction and morphology were often linked to diversification but a set of universal drivers did not emerge as traits did not have consistent effects across clades. Importantly, SSE model results were correlated to data set properties - trees that were larger, older or less well-sampled tended to yield trait-dependent outcomes. We compared these properties to recommendations for SSE model use and provide a set of best practices to follow when designing studies and reporting results. Finally, we argue that SSE model inferences should be considered in a larger context incorporating species' ecology, demography and genetics.
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Affiliation(s)
- Andrew J Helmstetter
- Fondation pour la recherche sur la biodiversité-CEntre de Synthèse et d'Analyse sur la Biodiversité, Montpellier, France
| | | | - Hervé Sauquet
- National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Sydney, New South Wales, Australia
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Sarah P Otto
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marcos Méndez
- Area of Biodiversity and Conservation, Universidad Rey Juan Carlos, Móstoles, Madrid, Spain
| | | | - Jürg Schönenberger
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | | | - Bruce Anderson
- Department of Botany and Zoology, University of Stellenbosch, Matieland, South Africa
| | - Hugo de Boer
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Sylvain Glémin
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- CNRS, Ecosystèmes Biodiversité Evolution (Université de Rennes), Rennes, France
| | - Jos Käfer
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
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8
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Hodge JR, Price SA. Biotic Interactions and the Future of Fishes on Coral Reefs: The Importance of Trait-Based Approaches. Integr Comp Biol 2022; 62:1734-1747. [PMID: 36138511 DOI: 10.1093/icb/icac147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/24/2022] [Accepted: 09/06/2022] [Indexed: 01/05/2023] Open
Abstract
Biotic interactions govern the structure and function of coral reef ecosystems. As environmental conditions change, reef-associated fish populations can persist by tracking their preferred niche or adapting to new conditions. Biotic interactions will affect how these responses proceed and whether they are successful. Yet, our understanding of these effects is currently limited. Ecological and evolutionary theories make explicit predictions about the effects of biotic interactions, but many remain untested. Here, we argue that large-scale functional trait datasets enable us to investigate how biotic interactions have shaped the assembly of contemporary reef fish communities and the evolution of species within them, thus improving our ability to predict future changes. Importantly, the effects of biotic interactions on these processes have occurred simultaneously within dynamic environments. Functional traits provide a means to integrate the effects of both ecological and evolutionary processes, as well as a way to overcome some of the challenges of studying biotic interactions. Moreover, functional trait data can enhance predictive modeling of future reef fish distributions and evolvability. We hope that our vision for an integrative approach, focused on quantifying functionally relevant traits and how they mediate biotic interactions in different environmental contexts, will catalyze new research on the future of reef fishes in a changing environment.
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Affiliation(s)
- Jennifer R Hodge
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Samantha A Price
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
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9
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Bird Communities in a Changing World: The Role of Interspecific Competition. DIVERSITY 2022. [DOI: 10.3390/d14100857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Significant changes in the environment have the potential to affect bird species abundance and distribution, both directly, through a modification of the landscape, habitats, and climate, and indirectly, through a modification of biotic interactions such as competitive interactions. Predicting and mitigating the consequences of global change thus requires not only a sound understanding of the role played by biotic interactions in current ecosystems, but also the recognition and study of the complex and intricate effects that result from the perturbation of these ecosystems. In this review, we emphasize the role of interspecific competition in bird communities by focusing on three main predictions derived from theoretical and empirical considerations. We provide numerous examples of population decline and displacement that appeared to be, at least in part, driven by competition, and were amplified by environmental changes associated with human activities. Beyond a shift in relative species abundance, we show that interspecific competition may have a negative impact on species richness, ecosystem services, and endangered species. Despite these findings, we argue that, in general, the role played by interspecific competition in current communities remains poorly understood due to methodological issues and the complexity of natural communities. Predicting the consequences of global change in these communities is further complicated by uncertainty regarding future environmental conditions and the speed and efficacy of plastic and evolutionary responses to fast-changing environments. Possible directions of future research are highlighted.
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10
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Affiliation(s)
- Scott L. Nuismer
- Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844
| | - Bob Week
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan 48824
| | - Luke J. Harmon
- Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844
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11
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Pavón-Vázquez CJ, Brennan IG, Skeels A, Keogh JS. Competition and geography underlie speciation and morphological evolution in Indo-Australasian monitor lizards. Evolution 2022; 76:476-495. [PMID: 34816437 DOI: 10.1111/evo.14403] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 10/06/2021] [Accepted: 10/16/2021] [Indexed: 01/21/2023]
Abstract
How biotic and abiotic factors act together to shape biological diversity is a major question in evolutionary biology. The recent availability of large datasets and development of new methodological approaches provide new tools to evaluate the predicted effects of ecological interactions and geography on lineage diversification and phenotypic evolution. Here, we use a near complete phylogenomic-scale phylogeny and a comprehensive morphological dataset comprising more than a thousand specimens to assess the role of biotic and abiotic processes in the diversification of monitor lizards (Varanidae). This charismatic group of lizards shows striking variation in species richness among its clades and multiple instances of endemic radiation in Indo-Australasia (i.e., the Indo-Australian Archipelago and Australia), one of Earth's most biogeographically complex regions. We found heterogeneity in diversification dynamics across the family. Idiosyncratic biotic and geographic conditions appear to have driven diversification and morphological evolution in three endemic Indo-Australasian radiations. Furthermore, incumbency effects partially explain patterns in the biotic exchange between Australia and New Guinea. Our results offer insight into the dynamic history of Indo-Australasia, the evolutionary significance of competition, and the long-term consequences of incumbency effects.
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Affiliation(s)
- Carlos J Pavón-Vázquez
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia.,Current Address: Department of Biological Sciences, New York City College of Technology, City University of New York, Brooklyn, New York, 11201
| | - Ian G Brennan
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Alexander Skeels
- Landscape Ecology, Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zürich, CH-8092, Switzerland.,Swiss Federal Research Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, CH-8903, Switzerland
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
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12
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Drury JP, Clavel J, Tobias JA, Rolland J, Sheard C, Morlon H. Tempo and mode of morphological evolution are decoupled from latitude in birds. PLoS Biol 2021; 19:e3001270. [PMID: 34428214 PMCID: PMC8384433 DOI: 10.1371/journal.pbio.3001270] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 05/07/2021] [Indexed: 12/17/2022] Open
Abstract
The latitudinal diversity gradient is one of the most striking patterns in nature, yet its implications for morphological evolution are poorly understood. In particular, it has been proposed that an increased intensity of species interactions in tropical biota may either promote or constrain trait evolution, but which of these outcomes predominates remains uncertain. Here, we develop tools for fitting phylogenetic models of phenotypic evolution in which the impact of species interactions-namely, competition-can vary across lineages. Deploying these models on a global avian trait dataset to explore differences in trait divergence between tropical and temperate lineages, we find that the effect of latitude on the mode and tempo of morphological evolution is weak and clade- or trait dependent. Our results indicate that species interactions do not disproportionately impact morphological evolution in tropical bird families and question the validity of previously reported patterns of slower trait evolution in the tropics.
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Affiliation(s)
- Jonathan P. Drury
- Department of Biosciences, Durham University, Durham, United Kingdom
| | - Julien Clavel
- Natural History Museum, London, United Kingdom
- Univ. Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023, LEHNA, Villeurbanne, France
| | - Joseph A. Tobias
- Department of Life Sciences, Imperial College London, Ascot, United Kingdom
| | - Jonathan Rolland
- Zoology Department, University of British Columbia, Vancouver, Canada
| | - Catherine Sheard
- School of Earth Sciences, University of Bristol, Bristol, United Kingdom
| | - Hélène Morlon
- Institut de Biologie, École Normale Supérieure, CNRS UMR 8197, Paris, France
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13
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Bastide P, Ho LST, Baele G, Lemey P, Suchard MA. Efficient Bayesian inference of general Gaussian models on large phylogenetic trees. Ann Appl Stat 2021. [DOI: 10.1214/20-aoas1419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
| | - Lam Si Tung Ho
- Department of Mathematics and Statistics, Dalhousie University
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven
| | - Marc A. Suchard
- Departments of Biostatistics, Biomathematics, and Human Genetics, University of California, Los Angeles
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14
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Character displacement drives trait divergence in a continental fauna. Proc Natl Acad Sci U S A 2021; 118:2021209118. [PMID: 33963076 DOI: 10.1073/pnas.2021209118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Coexisting (sympatric) pairs of closely related species are often characterized by exaggerated trait differences. This widespread pattern is consistent with adaptation for reduced similarity due to costly interactions (i.e., "character displacement")-a classic hypothesis in evolutionary theory. But it is equally consistent with a community assembly bias in which lineages with greater trait differences are more likely to establish overlapping ranges in the first place (i.e., "species sorting"), as well as with null expectations of trait divergence through time. Few comparative analyses have explicitly modeled these alternatives, and it remains unclear whether trait divergence is a general prerequisite for sympatry or a consequence of interactions between sympatric species. Here, we develop statistical models that allow us to distinguish the signature of these processes based on patterns of trait divergence in closely related lineage pairs. We compare support for each model using a dataset of bill shape differences in 207 pairs of New World terrestrial birds representing 30 avian families. We find that character displacement models are overwhelmingly supported over species sorting and null expectations, indicating that exaggerated bill shape differences in sympatric pairs result from enhanced divergent selection in sympatry. We additionally detect a latitudinal gradient in character displacement, which appears strongest in the tropics. Our analysis implicates costly species interactions as powerful drivers of trait divergence in a major vertebrate fauna. These results help substantiate a long-standing but equivocally supported linchpin of evolutionary theory.
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15
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Gallinat AS, Pearse WD. Phylogenetic generalized linear mixed modeling presents novel opportunities for eco‐evolutionary synthesis. OIKOS 2021. [DOI: 10.1111/oik.08048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Amanda S. Gallinat
- Dept of Biology and Ecology Center, Utah State Univ. Logan UT USA
- Dept of Geography, Univ. of Wisconsin‐Milwaukee Milwaukee WI USA
| | - William D. Pearse
- Dept of Biology and Ecology Center, Utah State Univ. Logan UT USA
- Dept of Life Sciences, Imperial College London Silwood Park Campus Ascot Berkshire UK
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16
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Eliason CM, McCullough JM, Andersen MJ, Hackett SJ. Accelerated Brain Shape Evolution Is Associated with Rapid Diversification in an Avian Radiation. Am Nat 2021; 197:576-591. [PMID: 33908824 DOI: 10.1086/713664] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractNiche expansion is a critical step in the speciation process. Large brains linked to improved cognitive ability may enable species to expand their niches and forage in new ways, thereby promoting speciation. Despite considerable work on ecological divergence in brain size and its importance in speciation, relatively little is known about how brain shape relates to behavioral, ecological, and taxonomic diversity at macroevolutionary scales. This is due in part to inherent challenges with quantifying brain shape across many species. Here we present a novel, semiautomated approach for rapidly phenotyping brain shape using semilandmarks derived from X-ray computed microtomography scans. We then test its utility by parsing evolutionary trends within a diverse radiation of birds: kingfishers (Aves: Alcedinidae). Multivariate comparative analyses reveal that rates of brain shape evolution (but not beak shape) are positively correlated with lineage diversification rates. Distinct brain shapes are further associated with changes in body size and foraging behavior, suggesting both allometric and ecological constraints on brain shape evolution. These results are in line with the idea of brains acting as a "master regulator" of critical processes governing speciation, such as dispersal, foraging behavior, and dietary niche.
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17
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Duchen P, Alfaro ML, Rolland J, Salamin N, Silvestro D. On the Effect of Asymmetrical Trait Inheritance on Models of Trait Evolution. Syst Biol 2021; 70:376-388. [PMID: 32681798 PMCID: PMC7875446 DOI: 10.1093/sysbio/syaa055] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 06/30/2020] [Accepted: 07/09/2020] [Indexed: 11/25/2022] Open
Abstract
Current phylogenetic comparative methods modeling quantitative trait evolution generally assume that, during speciation, phenotypes are inherited identically between the two daughter species. This, however, neglects the fact that species consist of a set of individuals, each bearing its own trait value. Indeed, because descendent populations after speciation are samples of a parent population, we can expect their mean phenotypes to randomly differ from one another potentially generating a "jump" of mean phenotypes due to asymmetrical trait inheritance at cladogenesis. Here, we aim to clarify the effect of asymmetrical trait inheritance at speciation on macroevolutionary analyses, focusing on model testing and parameter estimation using some of the most common models of quantitative trait evolution. We developed an individual-based simulation framework in which the evolution of phenotypes is determined by trait changes at the individual level accumulating across generations, and cladogenesis occurs then by separation of subsets of the individuals into new lineages. Through simulations, we assess the magnitude of phenotypic jumps at cladogenesis under different modes of trait inheritance at speciation. We show that even small jumps can strongly alter both the results of model selection and parameter estimations, potentially affecting the biological interpretation of the estimated mode of evolution of a trait. Our results call for caution when interpreting analyses of trait evolution, while highlighting the importance of testing a wide range of alternative models. In the light of our findings, we propose that future methodological advances in comparative methods should more explicitly model the intraspecific variability around species mean phenotypes and how it is inherited at speciation.
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Affiliation(s)
- Pablo Duchen
- Department of Computational Biology, University of Lausanne, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Michael L Alfaro
- University of California Los Angeles (UCLA). College Life Sciences - Ecology and Evolutionary Biology. Los Angeles, CA, USA
| | - Jonathan Rolland
- Department of Computational Biology, University of Lausanne, Quartier Sorge, 1015 Lausanne, Switzerland
- Department of Zoology, University of British Columbia, #4200-6270 University Blvd, Vancouver, BC, Canada
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Daniele Silvestro
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland Nicolas Salamin and Daniele Silvestro contributed equally to this article
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18
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Pouchon C, Lavergne S, Fernández Á, Alberti A, Aubert S, Mavárez J. Phylogenetic signatures of ecological divergence and leapfrog adaptive radiation in Espeletia. AMERICAN JOURNAL OF BOTANY 2021; 108:113-128. [PMID: 33426651 DOI: 10.1002/ajb2.1591] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 09/21/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Events of accelerated species diversification represent one of Earth's most celebrated evolutionary outcomes. Northern Andean high-elevation ecosystems, or páramos, host some plant lineages that have experienced the fastest diversification rates, likely triggered by ecological opportunities created by mountain uplifts, local climate shifts, and key trait innovations. However, the mechanisms behind rapid speciation into the new adaptive zone provided by these opportunities have long remained unclear. METHODS We address this issue by studying the Venezuelan clade of Espeletia, a species-rich group of páramo-endemics showing a dazzling ecological and morphological diversity. We performed several comparative analyses to study both lineage and trait diversification, using an updated molecular phylogeny of this plant group. RESULTS We showed that sets of either vegetative or reproductive traits have conjointly diversified in Espeletia along different vegetation belts, leading to adaptive syndromes. Diversification in vegetative traits occurred earlier than in reproductive ones. The rate of species and morphological diversification showed a tendency to slow down over time, probably due to diversity dependence. We also found that closely related species exhibit significantly more overlap in their geographic distributions than distantly related taxa, suggesting that most events of ecological divergence occurred at close geographic proximity within páramos. CONCLUSIONS These results provide compelling support for a scenario of small-scale ecological divergence along multiple ecological niche dimensions, possibly driven by competitive interactions between species, and acting sequentially over time in a leapfrog pattern.
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Affiliation(s)
- Charles Pouchon
- Laboratoire d'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000, Grenoble, France
| | - Sébastien Lavergne
- Laboratoire d'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000, Grenoble, France
| | - Ángel Fernández
- Herbario IVIC. Instituto Venezolano de Investigaciones Científicas, Apartado 20632, Caracas, 1020-A, Venezuela
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France
| | - Serge Aubert
- Laboratoire d'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000, Grenoble, France
- Université Grenoble Alpes, CNRS, Université Savoie Mont Blanc, SAJF, Station Alpine Joseph Fourier, 38000, Grenoble, France
| | - Jesús Mavárez
- Laboratoire d'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000, Grenoble, France
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19
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Stayton CT. Are our phylomorphospace plots so terribly tangled? An investigation of disorder in data simulated under adaptive and nonadaptive models. Curr Zool 2020; 66:565-574. [PMID: 33293934 PMCID: PMC7705511 DOI: 10.1093/cz/zoaa045] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/17/2020] [Indexed: 01/02/2023] Open
Abstract
Contemporary methods for visualizing phenotypic evolution, such as phylomorphospaces, often reveal patterns which depart strongly from a naïve expectation of consistently divergent branching and expansion. Instead, branches regularly crisscross as convergence, reversals, or other forms of homoplasy occur, forming patterns described as “birds’ nests”, “flies in vials”, or less elegantly, “a mess”. In other words, the phenotypic tree of life often appears highly tangled. Various explanations are given for this, such as differential degrees of developmental constraint, adaptation, or lack of adaptation. However, null expectations for the magnitude of disorder or “tangling” have never been established, so it is unclear which or even whether various evolutionary factors are required to explain messy patterns of evolution. I simulated evolution along phylogenies under a number of varying parameters (number of taxa and number of traits) and models (Brownian motion, Ornstein–Uhlenbeck (OU)-based, early burst, and character displacement (CD)] and quantified disorder using 2 measures. All models produce substantial amounts of disorder. Disorder increases with tree size and the number of phenotypic traits. OU models produced the largest amounts of disorder—adaptive peaks influence lineages to evolve within restricted areas, with concomitant increases in crossing of branches and density of evolution. Large early changes in trait values can be important in minimizing disorder. CD consistently produced trees with low (but not absent) disorder. Overall, neither constraints nor a lack of adaptation is required to explain messy phylomorphospaces—both stochastic and deterministic processes can act to produce the tantalizingly tangled phenotypic tree of life.
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Affiliation(s)
- C Tristan Stayton
- Department of Biology, Bucknell University, 337 Biology Building, Lewisburg, PA, 17837, USA
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20
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Fielding AP, Pantel JH. Eco-Evolutionary Feedbacks and the Maintenance of Metacommunity Diversity in a Changing Environment. Genes (Basel) 2020; 11:E1433. [PMID: 33260620 PMCID: PMC7761218 DOI: 10.3390/genes11121433] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 11/23/2020] [Accepted: 11/26/2020] [Indexed: 11/16/2022] Open
Abstract
The presence and strength of resource competition can influence how organisms adaptively respond to environmental change. Selection may thus reflect a balance between two forces, adaptation to an environmental optimum and evolution to avoid strong competition. While this phenomenon has previously been explored in the context of single communities, its implications for eco-evolutionary dynamics at the metacommunity scale are largely unknown. We developed a simulation model for the evolution of a quantitative trait that influences both an organism's carrying capacity and its intra- and interspecific competitive ability. In the model, multiple species inhabit a three-patch landscape, and we investigated the effect of varying the connectivity level among patches, the presence and pace of directional environmental change, and the strength of competition between the species. Our model produced some patterns previously observed in evolving metacommunity models, such as species sorting and community monopolization. However, we found that species sorting was diminished even at low rates of dispersal and was influenced by competition strength, and that monopolization was observed only when environmental change was very rapid. We also detected an eco-evolutionary feedback loop between local phenotypic evolution at one site and competition at another site, which maintains species diversity in some conditions. The existence of a feedback loop maintained by dispersal indicates that eco-evolutionary dynamics in communities operate at a landscape scale.
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Affiliation(s)
- Aidan P. Fielding
- Department of Biology, The College of William and Mary, P.O. Box 8795, Williamsburg, VA 23187-8795, USA;
| | - Jelena H. Pantel
- Department of Biology, The College of William and Mary, P.O. Box 8795, Williamsburg, VA 23187-8795, USA;
- Department of Computer Science, Mathematics, and Environmental Science, The American University of Paris, 6 rue du Colonel Combes, 75007 Paris, France
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21
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Chira AM, Cooney CR, Bright JA, Capp EJR, Hughes EC, Moody CJA, Nouri LO, Varley ZK, Thomas GH. The signature of competition in ecomorphological traits across the avian radiation. Proc Biol Sci 2020; 287:20201585. [PMID: 33171084 PMCID: PMC7735287 DOI: 10.1098/rspb.2020.1585] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Competition for shared resources represents a fundamental driver of biological diversity. However, the tempo and mode of phenotypic evolution in deep-time has been predominantly investigated using trait evolutionary models which assume that lineages evolve independently from each other. Consequently, the role of species interactions in driving macroevolutionary dynamics remains poorly understood. Here, we quantify the prevalence for signatures of competition between related species in the evolution of ecomorphological traits across the bird radiation. We find that mechanistic trait models accounting for the effect of species interactions on phenotypic divergence provide the best fit for the data on at least one trait axis in 27 out of 59 clades ranging between 21 and 195 species. Where it occurs, the signature of competition generally coincides with positive species diversity-dependence, driven by the accumulation of lineages with similar ecologies, and we find scarce evidence for trait-dependent or negative diversity-dependent phenotypic evolution. Overall, our results suggest that the footprint of interspecific competition is often eroded in long-term patterns of phenotypic diversification, and that other selection pressures may predominantly shape ecomorphological diversity among extant species at macroevolutionary scales.
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Affiliation(s)
- A M Chira
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.,Department of Biology, Washington University in St Louis, St Louis, MO, USA
| | - C R Cooney
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - J A Bright
- Department of Biological and Marine Sciences, University of Hull, Hull, UK
| | - E J R Capp
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - E C Hughes
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - C J A Moody
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - L O Nouri
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Z K Varley
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - G H Thomas
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.,Bird Group, Department of Life Sciences, The Natural History Museum, Tring, Hertfordshire, UK
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22
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Hembry DH, Weber MG. Ecological Interactions and Macroevolution: A New Field with Old Roots. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-011720-121505] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Linking interspecific interactions (e.g., mutualism, competition, predation, parasitism) to macroevolution (evolutionary change on deep timescales) is a key goal in biology. The role of species interactions in shaping macroevolutionary trajectories has been studied for centuries and remains a cutting-edge topic of current research. However, despite its deep historical roots, classic and current approaches to this topic are highly diverse. Here, we combine historical and contemporary perspectives on the study of ecological interactions in macroevolution, synthesizing ideas across eras to build a zoomed-out picture of the big questions at the nexus of ecology and macroevolution. We discuss the trajectory of this important and challenging field, dividing research into work done before the 1970s, research between 1970 and 2005, and work done since 2005. We argue that in response to long-standing questions in paleobiology, evidence accumulated to date has demonstrated that biotic interactions (including mutualism) can influence lineage diversification and trait evolution over macroevolutionary timescales, and we outline major open questions for future research in the field.
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Affiliation(s)
- David H. Hembry
- Department of Entomology, Cornell University, Ithaca, New York 14853, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Marjorie G. Weber
- Department of Plant Biology; Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, Michigan 48824, USA
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23
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Jarzyna MA, Quintero I, Jetz W. Global functional and phylogenetic structure of avian assemblages across elevation and latitude. Ecol Lett 2020; 24:196-207. [PMID: 33124188 DOI: 10.1111/ele.13631] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/06/2020] [Accepted: 10/05/2020] [Indexed: 02/06/2023]
Abstract
Mountain systems are exceptionally species rich, yet the associated elevational gradients in functional and phylogenetic diversity and their consistency across latitude remain little understood. Here, we document how avian functional and phylogenetic diversity and structure vary along all major elevational gradients worldwide and uncover strong latitudinal differences. Assemblages in warm tropical lowlands and cold temperate highlands are marked by high functional overdispersion and distinctiveness, whereas tropical highlands and temperate lowlands appear strongly functionally clustered and redundant. We additionally find strong geographic variation in the interplay of phylogenetic and functional structure, with strongest deviations between the two in temperate highlands. This latitudinal and elevational variation in assemblage functional structure is underpinned by nuanced shifts in the position, shape and composition of multivariate trait space. We find that, independent of latitude, high-elevation assemblages emerge as exceptionally susceptible to functional change.
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Affiliation(s)
- Marta A Jarzyna
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 318 W. 12th Avenue, 300 Aronoff Laboratory, Columbus, OH, 43210, USA.,Translational Data Analytics Institute, The Ohio State University, 1760 Neil Avenue, 175 Pomerene Hall, Columbus, OH, 43210, USA.,Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
| | - Ignacio Quintero
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA.,Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Walter Jetz
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA.,Center for Biodiversity and Global Change, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
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24
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Xu L, Van Doorn S, Hildenbrandt H, Etienne RS. Inferring the Effect of Species Interactions on Trait Evolution. Syst Biol 2020; 70:463-479. [PMID: 32960972 PMCID: PMC8048392 DOI: 10.1093/sysbio/syaa072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 09/01/2020] [Accepted: 09/08/2020] [Indexed: 11/18/2022] Open
Abstract
Models of trait evolution form an important part of macroevolutionary biology. The Brownian motion model and Ornstein–Uhlenbeck models have become classic (null) models of character evolution, in which species evolve independently. Recently, models incorporating species interactions have been developed, particularly involving competition where abiotic factors pull species toward an optimal trait value and competitive interactions drive the trait values apart. However, these models assume a fitness function rather than derive it from population dynamics and they do not consider dynamics of the trait variance. Here, we develop a general coherent trait evolution framework where the fitness function is based on a model of population dynamics, and therefore it can, in principle, accommodate any type of species interaction. We illustrate our framework with a model of abundance-dependent competitive interactions against a macroevolutionary background encoded in a phylogenetic tree. We develop an inference tool based on Approximate Bayesian Computation and test it on simulated data (of traits at the tips). We find that inference performs well when the diversity predicted by the parameters equals the number of species in the phylogeny. We then fit the model to empirical data of baleen whale body lengths, using three different summary statistics, and compare it to a model without population dynamics and a model where competition depends on the total metabolic rate of the competitors. We show that the unweighted model performs best for the least informative summary statistic, while the model with competition weighted by the total metabolic rate fits the data slightly better than the other two models for the two more informative summary statistics. Regardless of the summary statistic used, the three models substantially differ in their predictions of the abundance distribution. Therefore, data on abundance distributions will allow us to better distinguish the models from one another, and infer the nature of species interactions. Thus, our framework provides a conceptual approach to reveal species interactions underlying trait evolution and identifies the data needed to do so in practice. [Approximate Bayesian computation; competition; phylogeny; population dynamics; simulations; species interaction; trait evolution.]
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Affiliation(s)
- Liang Xu
- Faculty of Science and Engineering, Groningen Institute for Evolutionary Life Sciences, University of Groningen, PO Box 11103, Groningen 9700 CC, The Netherlands
| | - Sander Van Doorn
- Faculty of Science and Engineering, Groningen Institute for Evolutionary Life Sciences, University of Groningen, PO Box 11103, Groningen 9700 CC, The Netherlands
| | - Hanno Hildenbrandt
- Faculty of Science and Engineering, Groningen Institute for Evolutionary Life Sciences, University of Groningen, PO Box 11103, Groningen 9700 CC, The Netherlands
| | - Rampal S Etienne
- Faculty of Science and Engineering, Groningen Institute for Evolutionary Life Sciences, University of Groningen, PO Box 11103, Groningen 9700 CC, The Netherlands
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25
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Gaboriau T, Mendes FK, Joly S, Silvestro D, Salamin N. A multi‐platform package for the analysis of intra‐ and interspecific trait evolution. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13458] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Théo Gaboriau
- Department of Computational Biology University of Lausanne Lausanne Switzerland
| | - Fábio K. Mendes
- School of Computer Science The University of Auckland Auckland New Zealand
- School of Biological Sciences The University of Auckland Auckland New Zealand
| | - Simon Joly
- Institut Recherche en Biologie Végétale Montréal QC Canada
- Montreal Botanical Garden Montreal QC Canada
| | - Daniele Silvestro
- Department of Biology University of Fribourg Fribourg Switzerland
- Department of Biological and Environmental Sciences University of Gothenburg and Global Gothenburg Biodiversity Centre Gothenburg Sweden
| | - Nicolas Salamin
- Department of Computational Biology University of Lausanne Lausanne Switzerland
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26
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Brennan IG, Lemmon AR, Lemmon EM, Portik DM, Weijola V, Welton L, Donnellan SC, Keogh JS. Phylogenomics of Monitor Lizards and the Role of Competition in Dictating Body Size Disparity. Syst Biol 2020; 70:120-132. [PMID: 32521014 DOI: 10.1093/sysbio/syaa046] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/22/2020] [Accepted: 05/27/2020] [Indexed: 12/13/2022] Open
Abstract
Organismal interactions drive the accumulation of diversity by influencing species ranges, morphology, and behavior. Interactions vary from agonistic to cooperative and should result in predictable patterns in trait and range evolution. However, despite a conceptual understanding of these processes, they have been difficult to model, particularly on macroevolutionary timescales and across broad geographic spaces. Here, we investigate the influence of biotic interactions on trait evolution and community assembly in monitor lizards (Varanus). Monitors are an iconic radiation with a cosmopolitan distribution and the greatest size disparity of any living terrestrial vertebrate genus. Between the colossal Komodo dragon Varanus komodoensis and the smallest Australian dwarf goannas, Varanus length and mass vary by multiple orders of magnitude. To test the hypothesis that size variation in this genus was driven by character displacement, we extended existing phylogenetic comparative methods which consider lineage interactions to account for dynamic biogeographic history and apply these methods to Australian monitors and marsupial predators. Incorporating both exon-capture molecular and morphological data sets we use a combined evidence approach to estimate the relationships among living and extinct varaniform lizards. Our results suggest that communities of Australian Varanus show high functional diversity as a result of continent-wide interspecific competition among monitors but not with faunivorous marsupials. We demonstrate that patterns of trait evolution resulting from character displacement on continental scales are recoverable from comparative data and highlight that these macroevolutionary patterns may develop in parallel across widely distributed sympatric groups.[Character displacement; comparative methods; phylogenetics; trait evolution; Varanus.].
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Affiliation(s)
- Ian G Brennan
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Alan R Lemmon
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Daniel M Portik
- Department of Ecology and Evolution, University of Arizona, Biosciences West Rm 310, 1041 E. Lowell St, Tucson, AZ 85745 USA
| | - Valter Weijola
- Zoological Museum, Biodiversity Unit, FI-20014 University of Turku, Finland
| | - Luke Welton
- Univeristy of Kansas Biodiversity Institute & Natural History Museum, 1345 Jayhawk Blvd, Lawrence, KS 66045, USA
| | - Stephen C Donnellan
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia.,South Australian Museum, North Terrace, Adelaide SA 5000 Australia
| | - J Scott Keogh
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
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27
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Drury JP, Cowen MC, Grether GF. Competition and hybridization drive interspecific territoriality in birds. Proc Natl Acad Sci U S A 2020; 117:12923-12930. [PMID: 32457140 PMCID: PMC7293658 DOI: 10.1073/pnas.1921380117] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Costly interactions between species that arise as a by-product of ancestral similarities in communication signals are expected to persist only under specific evolutionary circumstances. Territorial aggression between species, for instance, is widely assumed to persist only when extrinsic barriers prevent niche divergence or selection in sympatry is too weak to overcome gene flow from allopatry. However, recent theoretical and comparative studies have challenged this view. Here we present a large-scale, phylogenetic analysis of the distribution and determinants of interspecific territoriality. We find that interspecific territoriality is widespread in birds and strongly associated with hybridization and resource overlap during the breeding season. Contrary to the view that territoriality only persists between species that rarely breed in the same areas or where niche divergence is constrained by habitat structure, we find that interspecific territoriality is positively associated with breeding habitat overlap and unrelated to habitat structure. Furthermore, our results provide compelling evidence that ancestral similarities in territorial signals are maintained and reinforced by selection when interspecific territoriality is adaptive. The territorial signals linked to interspecific territoriality in birds depend on the evolutionary age of interacting species, plumage at shallow (within-family) timescales, and song at deeper (between-family) timescales. Evidently, territorial interactions between species have persisted and shaped phenotypic diversity on a macroevolutionary timescale.
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Affiliation(s)
- Jonathan P Drury
- Department of Biosciences, Durham University, DH1 3LE Durham, United Kingdom;
| | - Madeline C Cowen
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA 90095
| | - Gregory F Grether
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA 90095
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28
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Morlon H, Rolland J, Condamine FL. Response to technical comment 'A cautionary note for users of linear diversification dependencies'. Ecol Lett 2020; 23:1172-1174. [PMID: 32419323 DOI: 10.1111/ele.13513] [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: 03/05/2020] [Revised: 03/06/2020] [Accepted: 03/20/2020] [Indexed: 11/27/2022]
Abstract
The comment by Gamisch (2020) draws the attention of users of the R-package RPANDA (Methods Ecol. Evol., 7, 2016, 589) on situations when properly interpreting the results of linear diversification dependencies requires caution. Here we provide clarifications to help users interpreting their results when using any type of functional diversification dependencies with time or the environment.
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Affiliation(s)
- Hélène Morlon
- Institut de Biologie de l'ENS (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Jonathan Rolland
- Department of Zoology, University of British Columbia, University Blvd, #4200-6270, Vancouver, B.C, Canada.,Department of Computational Biology, University of Lausanne, Quartier Sorge, 1015, Lausanne, Switzerland
| | - Fabien L Condamine
- Institut des Sciences de l'Évolution de Montpellier, Université de Montpellier , Place Eugène Bataillon, 34095, Montpellier, France
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29
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Billaud O, Moen DS, Parsons TL, Morlon H. Estimating Diversity Through Time Using Molecular Phylogenies: Old and Species-Poor Frog Families are the Remnants of a Diverse Past. Syst Biol 2020; 69:363-383. [PMID: 31682272 DOI: 10.1093/sysbio/syz057] [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: 11/01/2017] [Revised: 07/08/2019] [Accepted: 08/26/2019] [Indexed: 01/27/2023] Open
Abstract
Estimating how the number of species in a given group varied in the deep past is of key interest to evolutionary biologists. However, current phylogenetic approaches for obtaining such estimates have limitations, such as providing unrealistic diversity estimates at the origin of the group. Here, we develop a robust probabilistic approach for estimating diversity through time curves and uncertainty around these estimates from phylogenetic data. We show with simulations that under various realistic scenarios of diversification, this approach performs better than previously proposed approaches. We also characterize the effect of tree size and undersampling on the performance of the approach. We apply our method to understand patterns of species diversity in anurans (frogs and toads). We find that Archaeobatrachia-a species-poor group of old frog clades often found in temperate regions-formerly had much higher diversity and net diversification rate, but the group declined in diversity as younger, nested clades diversified. This diversity decline seems to be linked to a decline in speciation rate rather than an increase in extinction rate. Our approach, implemented in the R package RPANDA, should be useful for evolutionary biologists interested in understanding how past diversity dynamics have shaped present-day diversity. It could also be useful in other contexts, such as for analyzing clade-clade competitive effects or the effect of species richness on phenotypic divergence.
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Affiliation(s)
- O Billaud
- Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, École Normale Supérieure, Paris Sciences et Lettres (PSL) Research University, F-75005 Paris, France
| | - D S Moen
- Department of Integrative Biology, Oklahoma State University, 517 Life Sciences West, Stillwater, OK 74078, USA
| | - T L Parsons
- Laboratoire de Probabilités, Statistique et Modélisation (LPSM), Sorbonne Université, CNRS UMR 8001, Paris, France
| | - H Morlon
- Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, École Normale Supérieure, Paris Sciences et Lettres (PSL) Research University, F-75005 Paris, France
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30
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Lewitus E, Aristide L, Morlon H. Characterizing and Comparing Phylogenetic Trait Data from Their Normalized Laplacian Spectrum. Syst Biol 2020; 69:234-248. [PMID: 31529071 DOI: 10.1093/sysbio/syz061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 09/02/2019] [Accepted: 09/10/2019] [Indexed: 11/13/2022] Open
Abstract
The dissection of the mode and tempo of phenotypic evolution is integral to our understanding of global biodiversity. Our ability to infer patterns of phenotypes across phylogenetic clades is essential to how we infer the macroevolutionary processes governing those patterns. Many methods are already available for fitting models of phenotypic evolution to data. However, there is currently no comprehensive nonparametric framework for characterizing and comparing patterns of phenotypic evolution. Here, we build on a recently introduced approach for using the phylogenetic spectral density profile (SDP) to compare and characterize patterns of phylogenetic diversification, in order to provide a framework for nonparametric analysis of phylogenetic trait data. We show how to construct the SDP of trait data on a phylogenetic tree from the normalized graph Laplacian. We demonstrate on simulated data the utility of the SDP to successfully cluster phylogenetic trait data into meaningful groups and to characterize the phenotypic patterning within those groups. We furthermore demonstrate how the SDP is a powerful tool for visualizing phenotypic space across traits and for assessing whether distinct trait evolution models are distinguishable on a given empirical phylogeny. We illustrate the approach in two empirical data sets: a comprehensive data set of traits involved in song, plumage, and resource-use in tanagers, and a high-dimensional data set of endocranial landmarks in New World monkeys. Considering the proliferation of morphometric and molecular data collected across the tree of life, we expect this approach will benefit big data analyses requiring a comprehensive and intuitive framework.
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Affiliation(s)
- Eric Lewitus
- Ecole Normale Superieure Paris Sciences et Lettres (PSL) Research University, Institut de Biologie de l'Ecole Normale Superieure (IBENS) CNRS UMR 8197 INSERM U1024 46rue d'Ulm,F-75005, Paris, France.,Henry M. Jackson Foundation in support of the US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Leandro Aristide
- Ecole Normale Superieure Paris Sciences et Lettres (PSL) Research University, Institut de Biologie de l'Ecole Normale Superieure (IBENS) CNRS UMR 8197 INSERM U1024 46rue d'Ulm,F-75005, Paris, France
| | - Hélène Morlon
- Ecole Normale Superieure Paris Sciences et Lettres (PSL) Research University, Institut de Biologie de l'Ecole Normale Superieure (IBENS) CNRS UMR 8197 INSERM U1024 46rue d'Ulm,F-75005, Paris, France
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31
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Segar ST, Fayle TM, Srivastava DS, Lewinsohn TM, Lewis OT, Novotny V, Kitching RL, Maunsell SC. The Role of Evolution in Shaping Ecological Networks. Trends Ecol Evol 2020; 35:454-466. [PMID: 32294426 DOI: 10.1016/j.tree.2020.01.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 01/12/2020] [Accepted: 01/20/2020] [Indexed: 11/17/2022]
Abstract
The structure of ecological networks reflects the evolutionary history of their biotic components, and their dynamics are strongly driven by ecoevolutionary processes. Here, we present an appraisal of recent relevant research, in which the pervasive role of evolution within ecological networks is manifest. Although evolutionary processes are most evident at macroevolutionary scales, they are also important drivers of local network structure and dynamics. We propose components of a blueprint for further research, emphasising process-based models, experimental evolution, and phenotypic variation, across a range of distinct spatial and temporal scales. Evolutionary dimensions are required to advance our understanding of foundational properties of community assembly and to enhance our capability of predicting how networks will respond to impending changes.
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Affiliation(s)
- Simon T Segar
- Biology Centre, Czech Academy of Sciences, Institute of Entomology, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic; University of South Bohemia in Ceske Budejovice, Faculty of Science, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic; Department of Crop and Environment Sciences, Harper Adams University, Newport, Shropshire, TF10 8NB, UK.
| | - Tom M Fayle
- Biology Centre, Czech Academy of Sciences, Institute of Entomology, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic; University of South Bohemia in Ceske Budejovice, Faculty of Science, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic; Institute for Tropical Biology and Conservation,Universiti Malaysia Sabah,Kota Kinabalu, Sabah, Malaysia
| | - Diane S Srivastava
- Department of Zoology & Biodiversity Research Centre, University of British Columbia6270 University Blvd Vancouver BC, Canada V6T 1Z4
| | - Thomas M Lewinsohn
- Departamento Biologia Animal, Instituto de Biologia, University of Campinas, Campinas 13083-870, São Paulo, Brazil; Wissenschaftskolleg zu Berlin, Berlin 14193, Germany
| | - Owen T Lewis
- Department of Zoology, South Parks Road, Oxford, OX1 3PS, UK
| | - Vojtech Novotny
- Biology Centre, Czech Academy of Sciences, Institute of Entomology, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic; University of South Bohemia in Ceske Budejovice, Faculty of Science, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic
| | - Roger L Kitching
- Environmental Futures Research Institute,Griffith University, Brisbane, Queensland 4111, Australia
| | - Sarah C Maunsell
- Department of Organismic and EvolutionaryBiology, Harvard University, Cambridge, MA, 02138, USA
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32
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Origin of Elevational Replacements in a Clade of Nearly Flightless Birds: Most Diversity in Tropical Mountains Accumulates via Secondary Contact Following Allopatric Speciation. NEOTROPICAL DIVERSIFICATION: PATTERNS AND PROCESSES 2020. [DOI: 10.1007/978-3-030-31167-4_23] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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33
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Quintero I, Landis MJ. Interdependent Phenotypic and Biogeographic Evolution Driven by Biotic Interactions. Syst Biol 2019; 69:739-755. [DOI: 10.1093/sysbio/syz082] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 12/06/2019] [Accepted: 12/10/2019] [Indexed: 11/13/2022] Open
Abstract
Abstract
Biotic interactions are hypothesized to be one of the main processes shaping trait and biogeographic evolution during lineage diversification. Theoretical and empirical evidence suggests that species with similar ecological requirements either spatially exclude each other, by preventing the colonization of competitors or by driving coexisting populations to extinction, or show niche divergence when in sympatry. However, the extent and generality of the effect of interspecific competition in trait and biogeographic evolution has been limited by a dearth of appropriate process-generating models to directly test the effect of biotic interactions. Here, we formulate a phylogenetic parametric model that allows interdependence between trait and biogeographic evolution, thus enabling a direct test of central hypotheses on how biotic interactions shape these evolutionary processes. We adopt a Bayesian data augmentation approach to estimate the joint posterior distribution of trait histories, range histories, and coevolutionary process parameters under this analytically intractable model. Through simulations, we show that our model is capable of distinguishing alternative scenarios of biotic interactions. We apply our model to the radiation of Darwin’s finches—a classic example of adaptive divergence—and find limited support for in situ trait divergence in beak size, but stronger evidence for convergence in traits such as beak shape and tarsus length and for competitive exclusion throughout their evolutionary history. These findings are more consistent with presympatric, rather than postsympatric, niche divergence. Our modeling framework opens new possibilities for testing more complex hypotheses about the processes underlying lineage diversification. More generally, it provides a robust probabilistic methodology to model correlated evolution of continuous and discrete characters. [Bayesian; biotic interactions; competition; data augmentation; historical biogeography; trait evolution.]
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Affiliation(s)
- Ignacio Quintero
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
- Département de Biologie, Institut de Biologie de l’ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Michael J Landis
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
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34
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Wang A, Peng Y, Harder LD, Huang J, Yang D, Zhang D, Liao W. The nature of interspecific interactions and co-diversification patterns, as illustrated by the fig microcosm. THE NEW PHYTOLOGIST 2019; 224:1304-1315. [PMID: 31494940 PMCID: PMC6856861 DOI: 10.1111/nph.16176] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 09/02/2019] [Indexed: 05/05/2023]
Abstract
Interactions between mutualists, competitors, and antagonists have contrasting ecological effects that, sustained over generations, can influence micro- and macroevolution. Dissimilar benefits and costs for these interactions should cause contrasting co-diversification patterns between interacting clades, with prevalent co-speciation by mutualists, association loss by competitors, and host switching by antagonists. We assessed these expectations for a local assemblage of 26 fig species (Moraceae: Ficus), 26 species of mutualistic (pollinating), and 33 species of parasitic (galling) wasps (Chalcidoidea). Using newly acquired gene sequences, we inferred the phylogenies for all three clades. We then compared the three possible pairs of phylogenies to assess phylogenetic congruence and the relative frequencies of co-speciation, association duplication, switching, and loss. The paired phylogenies of pollinators with their mutualists and competitors were significantly congruent, unlike that of figs and their parasites. The distributions of macroevolutionary events largely agreed with expectations for mutualists and antagonists. By contrast, that for competitors involved relatively frequent association switching, as expected, but also unexpectedly frequent co-speciation. The latter result likely reflects the heterogeneous nature of competition among fig wasps. These results illustrate the influence of different interspecific interactions on co-diversification, while also revealing its dependence on specific characteristics of those interactions.
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Affiliation(s)
- Ai‐Ying Wang
- State Key Laboratory of Earth Surface Processes and Resource EcologyMinistry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringBeijing Normal UniversityBeijingChina
| | - Yan‐Qiong Peng
- CAS Key Laboratory of Tropical Forest EcologyXishuangbanna Tropical Botanical GardenChinese Academy of SciencesKunmingChina
| | - Lawrence D. Harder
- Department of Biological SciencesUniversity of Calgary2500 University Drive NWCalgaryABCanada
| | - Jian‐Feng Huang
- CAS Key Laboratory of Tropical Forest EcologyXishuangbanna Tropical Botanical GardenChinese Academy of SciencesKunmingChina
| | - Da‐Rong Yang
- CAS Key Laboratory of Tropical Forest EcologyXishuangbanna Tropical Botanical GardenChinese Academy of SciencesKunmingChina
| | - Da‐Yong Zhang
- State Key Laboratory of Earth Surface Processes and Resource EcologyMinistry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringBeijing Normal UniversityBeijingChina
| | - Wan‐Jin Liao
- State Key Laboratory of Earth Surface Processes and Resource EcologyMinistry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringBeijing Normal UniversityBeijingChina
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35
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Aristide L, Morlon H. Understanding the effect of competition during evolutionary radiations: an integrated model of phenotypic and species diversification. Ecol Lett 2019; 22:2006-2017. [PMID: 31507039 DOI: 10.1111/ele.13385] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/12/2019] [Accepted: 08/19/2019] [Indexed: 02/05/2023]
Abstract
Competition can drive macroevolutionary change, for example during adaptive radiations. However, we still lack a clear understanding of how it shapes diversification processes and patterns. To better understand the macroevolutionary consequences of competition, as well as the signal left on phylogenetic data, we developed a model linking trait evolution and species diversification in an ecological context. We find four main results: first, competition spurs trait diversity but not necessarily species richness; second, competition produces slowdowns in species diversification even in the absence of explicit ecological limits, but not in phenotypic diversification even in the presence of such limits; third, early burst patterns do not provide a reliable way of testing for adaptive radiations; and fourth, looking for phylogenetic signal in trait data and support for phenotypic models incorporating competition is a better alternative. Our results clarify the macroevolutionary consequences of competition and could help design more powerful tests of adaptive radiations in nature.
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Affiliation(s)
- Leandro Aristide
- École Normale Supérieure, Paris Sciences et Lettres (PSL) Research University, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS, UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005, Paris, France
| | - Hélène Morlon
- École Normale Supérieure, Paris Sciences et Lettres (PSL) Research University, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS, UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005, Paris, France
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36
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Chomicki G, Weber M, Antonelli A, Bascompte J, Kiers ET. The Impact of Mutualisms on Species Richness. Trends Ecol Evol 2019; 34:698-711. [DOI: 10.1016/j.tree.2019.03.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 03/11/2019] [Accepted: 03/18/2019] [Indexed: 11/28/2022]
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37
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Harmon LJ, Andreazzi CS, Débarre F, Drury J, Goldberg EE, Martins AB, Melián CJ, Narwani A, Nuismer SL, Pennell MW, Rudman SM, Seehausen O, Silvestro D, Weber M, Matthews B. Detecting the macroevolutionary signal of species interactions. J Evol Biol 2019; 32:769-782. [DOI: 10.1111/jeb.13477] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 03/26/2019] [Accepted: 04/04/2019] [Indexed: 02/04/2023]
Affiliation(s)
- Luke J. Harmon
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry Eawag Kastanienbaum Switzerland
- Department of Biological Sciences University of Idaho Moscow Idaho
| | | | - Florence Débarre
- Sorbonne Université, UPMC Univ Paris 06, CNRS, IRD, INRA, Université Paris Diderot, Institute of Ecology and Environmental Sciences (UMR7618) Paris France
| | | | - Emma E. Goldberg
- Department of Ecology, Evolution and Behavior University of Minnesota Saint Paul Minnesota
| | - Ayana B. Martins
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry Eawag Kastanienbaum Switzerland
- Instituto de Física ‘Gleb Wataghin’ Universidade Estadual de Campinas Campinas Brazil
| | - Carlos J. Melián
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry Eawag Kastanienbaum Switzerland
| | - Anita Narwani
- Department of Aquatic Ecology Swiss Federal Institute of Aquatic Science and Technology Eawag Dübendorf Switzerland
| | - Scott L. Nuismer
- Department of Biological Sciences University of Idaho Moscow Idaho
| | - Matthew W. Pennell
- Department of Zoology and Biodiversity Research Centre University of British Columbia Vancouver British Columbia
| | - Seth M. Rudman
- Department of Biology University of Pennsylvania Philadelphia Pennsylvania
| | - Ole Seehausen
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry Eawag Kastanienbaum Switzerland
- Institute of Ecology and Evolution University of Bern Bern Switzerland
| | - Daniele Silvestro
- Department of Biological and Environmental Sciences Global Gothenburg Biodiversity Centre University of Gothenburg Gothenburg Sweden
| | - Marjorie Weber
- Department of Plant Biology & Program in Ecology, Evolution, and Behavior Michigan State University East Lansing Michigan
| | - Blake Matthews
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry Eawag Kastanienbaum Switzerland
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution University of Bern Bern Switzerland
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38
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Skeels A, Cardillo M. Equilibrium and non‐equilibrium phases in the radiation of
Hakea
and the drivers of diversity in Mediterranean‐type ecosystems. Evolution 2019; 73:1392-1410. [DOI: 10.1111/evo.13769] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 03/05/2019] [Accepted: 04/29/2019] [Indexed: 01/10/2023]
Affiliation(s)
- Alexander Skeels
- Macroevolution and Macroecology Group Research School of Biology Australian National University Canberra 0200 Australia
| | - Marcel Cardillo
- Macroevolution and Macroecology Group Research School of Biology Australian National University Canberra 0200 Australia
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39
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Lewitus E, Morlon H. Detecting Environment-Dependent Diversification From Phylogenies: A Simulation Study and Some Empirical Illustrations. Syst Biol 2018; 67:576-593. [PMID: 29272547 DOI: 10.1093/sysbio/syx095] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 12/11/2017] [Indexed: 01/30/2023] Open
Abstract
Understanding the relative influence of various abiotic and biotic variables on diversification dynamics is a major goal of macroevolutionary studies. Recently, phylogenetic approaches have been developed that make it possible to estimate the role of various environmental variables on diversification using time-calibrated species trees, paleoenvironmental data, and maximum-likelihood techniques. These approaches have been effectively employed to estimate how speciation and extinction rates vary with key abiotic variables, such as temperature and sea level, and we can anticipate that they will be increasingly used in the future. Here we compile a series of biotic and abiotic paleodatasets that can be used as explanatory variables in these models and use simulations to assess the statistical properties of the approach when applied to these paleodatasets. We demonstrate that environment-dependent models perform well in recovering environment-dependent speciation and extinction parameters, as well as in correctly identifying the simulated environmental model when speciation is environment-dependent. We explore how the strength of the environment-dependency, tree size, missing taxa, and characteristics of the paleoenvironmental curves influence the performance of the models. Finally, using these models, we infer environment-dependent diversification in two empirical phylogenies: temperature-dependence in Cetacea and $\delta^{13}C$-dependence in Ruminantia. We illustrate how to evaluate the relative importance of abiotic and biotic variables in these two clades and interpret these results in light of macroevolutionary hypotheses. Given the important role paleoenvironments are presumed to have played in species evolution, our statistical assessment of how environment-dependent models behave is crucial for their utility in macroevolutionary analysis.
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Affiliation(s)
- Eric Lewitus
- IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France
| | - Hélène Morlon
- IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France
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40
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Hutchinson MC, Gaiarsa MP, Stouffer DB. Contemporary Ecological Interactions Improve Models of Past Trait Evolution. Syst Biol 2018; 67:861-872. [PMID: 29471501 DOI: 10.1093/sysbio/syy012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 02/10/2018] [Indexed: 11/12/2022] Open
Abstract
Despite the fact that natural selection underlies both traits and interactions, evolutionary models often neglect that ecological interactions may, and in many cases do, influence the evolution of traits. Herein, we explore the interdependence of ecological interactions and functional traits in the pollination associations of hawkmoths and flowering plants. Specifically, we develop an adaptation of the Ornstein-Uhlenbeck model of trait evolution that allows us to study the influence of plant corolla depth and observed hawkmoth-plant interactions on the evolution of hawkmoth proboscis length. Across diverse modelling scenarios, we find that the inclusion of contemporary interactions can provide a better description of trait evolution than the null expectation. Moreover, we show that the pollination interactions provide more-likely models of hawkmoth trait evolution when interactions are considered at increasingly fine-scale groups of hawkmoths. Finally, we demonstrate how the results of best-fit modeling approaches can implicitly support the association between interactions and trait evolution that our method explicitly examines. In showing that contemporary interactions can provide insight into the historical evolution of hawkmoth proboscis length, we demonstrate the clear utility of incorporating additional ecological information to models designed to study past trait evolution.
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Affiliation(s)
- Matthew C Hutchinson
- Centre for Integrative Ecology, School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand.,Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Marília P Gaiarsa
- Centre for Integrative Ecology, School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand.,Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, 11294, 05422-970 São Paulo, Brazil
| | - Daniel B Stouffer
- Centre for Integrative Ecology, School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
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41
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Sauquet H, Magallón S. Key questions and challenges in angiosperm macroevolution. THE NEW PHYTOLOGIST 2018; 219:1170-1187. [PMID: 29577323 DOI: 10.1111/nph.15104] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 02/05/2018] [Indexed: 05/26/2023]
Abstract
Contents Summary 1170 I. Introduction 1170 II. Six key questions 1172 III. Three key challenges 1177 IV. Conclusions 1181 Acknowledgements 1182 References 1183 SUMMARY: The origin and rapid diversification of angiosperms (flowering plants) represent one of the most intriguing topics in evolutionary biology. Despite considerable progress made in complementary fields over the last two decades (paleobotany, phylogenetics, ecology, evo-devo, genomics), many important questions remain. For instance, what has been the impact of mass extinctions on angiosperm diversification? Are the angiosperms an adaptive radiation? Has morphological evolution in angiosperms been gradual or pulsed? We propose that the recent and ongoing revolution in macroevolutionary methods provides an unprecedented opportunity to explore long-standing questions that probably hold important clues to understand present-day biodiversity. We present six key questions that explore the origin and diversification of angiosperms. We also identify three key challenges to address these questions: (1) the development of new integrative models that include diversification, multiple intrinsic and environmental traits, biogeography and the fossil record all at once, whilst accounting for sampling bias and heterogeneity of macroevolutionary processes through time and among lineages; (2) the need for large and standardized synthetic databases of morphological variation; and (3) continuous effort on sampling the fossil record, but with a revolution in current paleobotanical practice.
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Affiliation(s)
- Hervé Sauquet
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, NSW, 2000, Australia
- Laboratoire Écologie, Systématique, Évolution, Université Paris-Sud, CNRS, UMR 8079, Orsay, 91405, France
| | - Susana Magallón
- Instituto de Biología, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Coyoacán, México City, 04510, México
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42
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Chira AM, Cooney CR, Bright JA, Capp EJR, Hughes EC, Moody CJA, Nouri LO, Varley ZK, Thomas GH. Correlates of rate heterogeneity in avian ecomorphological traits. Ecol Lett 2018; 21:1505-1514. [PMID: 30133084 PMCID: PMC6175488 DOI: 10.1111/ele.13131] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/22/2018] [Accepted: 07/05/2018] [Indexed: 12/13/2022]
Abstract
Heterogeneity in rates of trait evolution is widespread, but it remains unclear which processes drive fast and slow character divergence across global radiations. Here, we test multiple hypotheses for explaining rate variation in an ecomorphological trait (beak shape) across a globally distributed group (birds). We find low support that variation in evolutionary rates of species is correlated with life history, environmental mutagenic factors, range size, number of competitors, or living on islands. Indeed, after controlling for the negative effect of species' age, 80% of variation in species‐specific evolutionary rates remains unexplained. At the clade level, high evolutionary rates are associated with unusual phenotypes or high species richness. Taken together, these results imply that macroevolutionary rates of ecomorphological traits are governed by both ecological opportunity in distinct adaptive zones and niche differentiation among closely related species.
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Affiliation(s)
- A M Chira
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - C R Cooney
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - J A Bright
- School of Geosciences, University of South Florida, Tampa, FL, USA
| | - E J R Capp
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - E C Hughes
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - C J A Moody
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - L O Nouri
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Z K Varley
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - G H Thomas
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK.,Bird Group, Department of Life Sciences, The Natural History Museum, Tring, Hertfordshire, UK
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43
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Lewitus E. Inferring Evolutionary Process From Neuroanatomical Data. Front Neuroanat 2018; 12:54. [PMID: 30100868 PMCID: PMC6072856 DOI: 10.3389/fnana.2018.00054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/06/2018] [Indexed: 01/09/2023] Open
Abstract
Brain evolution has interested neuroanatomists for over a century. These interests often fall on how free the brain is to evolve independently of the body, how free brain regions are to evolve independently of each other, and how different environmental and ecological factors affect the brain over evolutionary time. But despite major advances in phylogenetic methods, comparative neuroanatomists have tended to limit their macroevolutionary toolbox to regression-based analyses and ignored the scope of evolutionary process-based models at their disposal. This Review summarizes the history of comparative neuroanatomy and highlights the pitfalls of the methodologies traditionally used. It provides an overview of evolutionary process-based modeling approaches for investigating univariate and multivariate data, as well as more sophisticated methods that incorporate hypotheses about biotic and abiotic pressures that may drive brain evolution. The benefits of evolutionary process-based models, and shortcomings of regression-based ones, are illustrated with widely used neuroanatomical data. Ultimately, the intent of this Review is to be a guide for subsuming macroevolutionary methods not typically used in comparative neuroanatomy, in order to improve our understanding of how the brain evolves.
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Affiliation(s)
- Eric Lewitus
- Institut de Biologie de l'ENS, Paris Sciences et Lettres Université, Paris, France
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44
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Sukumaran J, Knowles LL. Trait-Dependent Biogeography: (Re)Integrating Biology into Probabilistic Historical Biogeographical Models. Trends Ecol Evol 2018; 33:390-398. [PMID: 29685579 DOI: 10.1016/j.tree.2018.03.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 03/26/2018] [Accepted: 03/27/2018] [Indexed: 11/29/2022]
Abstract
The development of process-based probabilistic models for historical biogeography has transformed the field by grounding it in modern statistical hypothesis testing. However, most of these models abstract away biological differences, reducing species to interchangeable lineages. We present here the case for reintegration of biology into probabilistic historical biogeographical models, allowing a broader range of questions about biogeographical processes beyond ancestral range estimation or simple correlation between a trait and a distribution pattern, as well as allowing us to assess how inferences about ancestral ranges themselves might be impacted by differential biological traits. We show how new approaches to inference might cope with the computational challenges resulting from the increased complexity of these trait-based historical biogeographical models.
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Affiliation(s)
- Jeet Sukumaran
- Department of Ecology and Evolutionary Biology, University of Michigan, 1109 Geddes Avenue, Ann Arbor, MI 48109-1079, USA.
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, 1109 Geddes Avenue, Ann Arbor, MI 48109-1079, USA
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45
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Lipshutz SE. Interspecific competition, hybridization, and reproductive isolation in secondary contact: missing perspectives on males and females. Curr Zool 2018; 64:75-88. [PMID: 29492041 PMCID: PMC5809030 DOI: 10.1093/cz/zox060] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 10/15/2017] [Indexed: 12/26/2022] Open
Abstract
Research on sexual selection and hybridization has focused on female mate choice and male-male competition. While the evolutionary outcomes of interspecific female preference have been well explored, we are now gaining a better understanding of the processes by which male-male competition between species in secondary contact promotes reproductive isolation versus hybridization. What is relatively unexplored is the interaction between female choice and male competition, as they can oppose one another or align with similar outcomes for reproductive isolation. The role of female-female competition in hybridization is also not well understood, but could operate similarly to male-male competition in polyandrous and other systems where costs to heterospecific mating are low for females. Reproductive competition between either sex of sympatric species can cause the divergence and/or convergence of sexual signals and recognition, which in turn influences the likelihood for interspecific mating. Future work on species interactions in secondary contact should test the relative influences of both mate choice and competition for mates on hybridization outcomes, and should not ignore the possibilities that females can compete over mating resources, and males can exercise mate choice.
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Affiliation(s)
- Sara E Lipshutz
- Department of Ecology and Evolutionary Biology, Division of Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
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46
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Adams DC, Nason JD. A phylogenetic comparative method for evaluating trait coevolution across two phylogenies for sets of interacting species. Evolution 2018; 72:234-243. [DOI: 10.1111/evo.13415] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 12/06/2017] [Indexed: 11/30/2022]
Affiliation(s)
- 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
| | - John D. Nason
- Department of Ecology, Evolution, and Organismal Biology Iowa State University Ames Iowa 50011
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47
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Drury JP, Tobias JA, Burns KJ, Mason NA, Shultz AJ, Morlon H. Contrasting impacts of competition on ecological and social trait evolution in songbirds. PLoS Biol 2018; 16:e2003563. [PMID: 29385141 PMCID: PMC5809094 DOI: 10.1371/journal.pbio.2003563] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 02/12/2018] [Accepted: 01/11/2018] [Indexed: 11/19/2022] Open
Abstract
Competition between closely related species has long been viewed as a powerful selective force that drives trait diversification, thereby generating phenotypic diversity over macroevolutionary timescales. However, although the impact of interspecific competition has been documented in a handful of iconic insular radiations, most previous studies have focused on traits involved in resource use, and few have examined the role of competition across large, continental radiations. Thus, the extent to which broad-scale patterns of phenotypic diversity are shaped by competition remain largely unclear, particularly for social traits. Here, we estimate the effect of competition between interacting lineages by applying new phylogenetic models that account for such interactions to an exceptionally complete dataset of resource-use traits and social signaling traits for the entire radiation of tanagers (Aves, Thraupidae), the largest family of songbirds. We find that interspecific competition strongly influences the evolution of traits involved in resource use, with a weaker effect on plumage signals, and very little effect on song. Our results provide compelling evidence that interspecific exploitative competition contributes to ecological trait diversification among coexisting species, even in a large continental radiation. In comparison, signal traits mediating mate choice and social competition seem to diversify under different evolutionary models, including rapid diversification in the allopatric stage of speciation.
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Affiliation(s)
- Jonathan P. Drury
- Department of Biosciences, Durham University, Stockton Road, Durham, United Kingdom
| | - Joseph A. Tobias
- Department of Life Sciences, Imperial College London, Ascot, United Kingdom
| | - Kevin J. Burns
- Department of Biology, San Diego State University, San Diego, California, United States of America
| | - Nicholas A. Mason
- Department of Ecology & Evolutionary Biology, Cornell University, Ithaca, New York
| | - Allison J. Shultz
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
| | - Hélène Morlon
- Institut de Biologie, École Normale Supérieure, CNRS UMR 8197, Paris, France
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48
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Simonet C, Scherrer R, Rego-Costa A, Etienne RS. Robustness of the approximate likelihood of the protracted speciation model. J Evol Biol 2017; 31:469-479. [PMID: 29274113 DOI: 10.1111/jeb.13233] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 11/22/2017] [Accepted: 12/04/2017] [Indexed: 11/29/2022]
Abstract
The protracted speciation model presents a realistic and parsimonious explanation for the observed slowdown in lineage accumulation through time, by accounting for the fact that speciation takes time. A method to compute the likelihood for this model given a phylogeny is available and allows estimation of its parameters (rate of initiation of speciation, rate of completion of speciation and extinction rate) and statistical comparison of this model to other proposed models of diversification. However, this likelihood computation method makes an approximation of the protracted speciation model to be mathematically tractable: it sometimes counts fewer species than one would do from a biological perspective. This approximation may have large consequences for likelihood-based inferences: it may render any conclusions based on this method completely irrelevant. Here, we study to what extent this approximation affects parameter estimations. We simulated phylogenies from which we reconstructed the tree of extant species according to the original, biologically meaningful protracted speciation model and according to the approximation. We then compared the resulting parameter estimates. We found that the differences were larger for high values of extinction rates and small values of speciation-completion rates. Indeed, a long speciation-completion time and a high extinction rate promote the appearance of cases to which the approximation applies. However, surprisingly, the deviation introduced is largely negligible over the parameter space explored, suggesting that this approximate likelihood can be applied reliably in practice to estimate biologically relevant parameters under the original protracted speciation model.
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Affiliation(s)
- C Simonet
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - R Scherrer
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - A Rego-Costa
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - R S Etienne
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
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49
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Moritz CC, Pratt RC, Bank S, Bourke G, Bragg JG, Doughty P, Keogh JS, Laver RJ, Potter S, Teasdale LC, Tedeschi LG, Oliver PM. Cryptic lineage diversity, body size divergence, and sympatry in a species complex of Australian lizards (
Gehyra
). Evolution 2017; 72:54-66. [DOI: 10.1111/evo.13380] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 09/15/2017] [Accepted: 10/02/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Craig C. Moritz
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis The Australian National University Building 116, Daley Road Acton ACT 2601 Australia
| | - Renae C. Pratt
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis The Australian National University Building 116, Daley Road Acton ACT 2601 Australia
| | - Sarah Bank
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis The Australian National University Building 116, Daley Road Acton ACT 2601 Australia
| | - Gayleen Bourke
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis The Australian National University Building 116, Daley Road Acton ACT 2601 Australia
| | - Jason G. Bragg
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis The Australian National University Building 116, Daley Road Acton ACT 2601 Australia
- National Herbarium of New South Wales The Royal Botanic Gardens and Domain Trust Sydney NSW Australia
| | - Paul Doughty
- Western Australian Museum Perth WA 6026 Australia
| | - J. Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis The Australian National University Building 116, Daley Road Acton ACT 2601 Australia
| | - Rebecca J. Laver
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis The Australian National University Building 116, Daley Road Acton ACT 2601 Australia
- School of BioSciences The University of Melbourne Parkville VIC 3010 Australia
- Department of Sciences Museum Victoria Carlton, Melbourne VIC 3001 Australia
| | - Sally Potter
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis The Australian National University Building 116, Daley Road Acton ACT 2601 Australia
- Australian Museum Research Institute, Australian Museum Sydney NSW Australia
| | - Luisa C. Teasdale
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis The Australian National University Building 116, Daley Road Acton ACT 2601 Australia
- School of BioSciences The University of Melbourne Parkville VIC 3010 Australia
- Department of Sciences Museum Victoria Carlton, Melbourne VIC 3001 Australia
- National Collections & Marine Infrastructure, Australian National Insect Collection CSIRO Black Mountain Laboratories Acton ACT 2601 Australia
| | - Leonardo G. Tedeschi
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis The Australian National University Building 116, Daley Road Acton ACT 2601 Australia
| | - Paul M. Oliver
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis The Australian National University Building 116, Daley Road Acton ACT 2601 Australia
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50
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Drury JP, Grether GF, Garland T, Morlon H. An Assessment of Phylogenetic Tools for Analyzing the Interplay Between Interspecific Interactions and Phenotypic Evolution. Syst Biol 2017; 67:413-427. [DOI: 10.1093/sysbio/syx079] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 09/21/2017] [Indexed: 11/14/2022] Open
Affiliation(s)
- J P Drury
- Département de Biologie, Institut de Biologie, École Normale Supérieure, CNRS UMR 8197, 46 rue d’Ulm 75005 Paris, France
- Department of Ecology & Evolutionary Biology, University of California, 621 Charles E. Young Dr. S, Los Angeles, CA 90095-1606, USA
| | - G F Grether
- Department of Ecology & Evolutionary Biology, University of California, 621 Charles E. Young Dr. S, Los Angeles, CA 90095-1606, USA
| | - T Garland
- Department of Evolution, Ecology, and Organismal Biology, University of California, 900 University Ave., Riverside, CA 92521, USA
| | - H Morlon
- Département de Biologie, Institut de Biologie, École Normale Supérieure, CNRS UMR 8197, 46 rue d’Ulm 75005 Paris, France
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