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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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Luiselli J, Overcast I, Rominger A, Ruffley M, Morlon H, Rosindell J. Detecting the ecological footprint of selection. PLoS One 2024; 19:e0302794. [PMID: 38848435 DOI: 10.1371/journal.pone.0302794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 04/12/2024] [Indexed: 06/09/2024] Open
Abstract
The structure of communities is influenced by many ecological and evolutionary processes, but the way these manifest in classic biodiversity patterns often remains unclear. Here we aim to distinguish the ecological footprint of selection-through competition or environmental filtering-from that of neutral processes that are invariant to species identity. We build on existing Massive Eco-evolutionary Synthesis Simulations (MESS), which uses information from three biodiversity axes-species abundances, genetic diversity, and trait variation-to distinguish between mechanistic processes. To correctly detect and characterise competition, we add a new and more realistic form of competition that explicitly compares the traits of each pair of individuals. Our results are qualitatively different to those of previous work in which competition is based on the distance of each individual's trait to the community mean. We find that our new form of competition is easier to identify in empirical data compared to the alternatives. This is especially true when trait data are available and used in the inference procedure. Our findings hint that signatures in empirical data previously attributed to neutrality may in fact be the result of pairwise-acting selective forces. We conclude that gathering more different types of data, together with more advanced mechanistic models and inference as done here, could be the key to unravelling the mechanisms of community assembly and question the relative roles of neutral and selective processes.
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Affiliation(s)
- Juliette Luiselli
- Département de Biologie, École Normale Supérieure-PSL, Paris, France
- INSA-Lyon, Inria, CNRS, Université Claude Bernard Lyon 1, ECL, Université Lumière Lyon 2, LIRIS UMR5205, Lyon, France
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire, United Kingdom
| | - Isaac Overcast
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- School of Biology and Ecology, University of Maine, Orono, ME, United States of America
| | - Andrew Rominger
- School of Biology and Ecology, University of Maine, Orono, ME, United States of America
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, HI, United States of America
| | - Megan Ruffley
- Department of Plant Biology, Carnegie Institution for Science, Washington, DC, United States of America
| | - Hélène Morlon
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - James Rosindell
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire, United Kingdom
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3
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Barrero A, Traba J, Tarjuelo R. Increased density of conspecifics caused niche contraction in a multispecific passerine assemblage. Ecology 2024; 105:e4296. [PMID: 38527496 DOI: 10.1002/ecy.4296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 11/27/2023] [Accepted: 02/09/2024] [Indexed: 03/27/2024]
Abstract
Competition is a prominent mechanism driving population dynamics and structuring community assemblage, which can be investigated by linking shifts in species' ecological niche and the densities of sympatric species because the ecological release from competitive constraints is a density-dependent process. In this work we determine how a steppe passerine community segregates their ecological niches and evaluate the role of competition in inducing changes in the ecological niche of species. We built multidimensional ecological niches (with Gaussian kernel density estimators) using data on the habitat features used by 10 bird species collected from seven sites in the natural steppes of Central Spain over 2 consecutive years. We computed distance and niche similarity metrics to explore the ecological niche partitioning of the bird community. Next, we ran multivariate linear regression models to evaluate the effects of conspecific and heterospecific density (as proxies of intraspecific and interspecific competition, respectively) on niche breadth and/or position of the three most abundant species. We found low niche overlap in the community assemblage but varying levels of niche similarity among pairs of species, which could increase the likelihood of current competition operating in the community. However, we found no effect of heterospecific density on niche breadth or position, although conspecific density was negatively related to niche breadth. Contrary to predictions of competition theory, increased density of conspecifics caused niche contraction. Our results from a multispecies system contribute to advanced knowledge of the biotic mechanisms structuring wildlife communities within the framework of ecological niche theory.
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Affiliation(s)
- Adrián Barrero
- Terrestrial Ecology Group, Department of Ecology, Universidad Autónoma de Madrid (TEG-UAM), Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global, Universidad Autónoma de Madrid (CIBC-UAM), Madrid, Spain
| | - Juan Traba
- Terrestrial Ecology Group, Department of Ecology, Universidad Autónoma de Madrid (TEG-UAM), Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global, Universidad Autónoma de Madrid (CIBC-UAM), Madrid, Spain
| | - Rocío Tarjuelo
- Instituto Universitario de Investigación en Gestión Forestal Sostenible (iuFOR), Universidad de Valladolid, Palencia, Spain
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4
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Zou Y, Yang J, Zhou J, Liu G, Shen L, Zhou Z, Su Z, Gu X. Anciently duplicated genes continuously recruited to heart expression in vertebrate evolution are associated with heart chamber increase. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024. [PMID: 38361319 DOI: 10.1002/jez.b.23248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/17/2024]
Abstract
Although gene/genome duplications in the early stage of vertebrates have been thought to provide major resources of raw genetic materials for evolutionary innovations, it is unclear whether they continuously contribute to the evolution of morphological complexity during the course of vertebrate evolution, such as the evolution from two heart chambers (fishes) to four heart chambers (mammals and birds). We addressed this issue by our heart RNA-Seq experiments combined with published data, using 13 vertebrates and one invertebrate (sea squirt, as an outgroup). Our evolutionary transcriptome analysis showed that number of ancient paralogous genes expressed in heart tends to increase with the increase of heart chamber number along the vertebrate phylogeny, in spite that most of them were duplicated at the time near to the origin of vertebrates or even more ancient. Moreover, those paralogs expressed in heart exert considerably different functions from heart-expressed singletons: the former are functionally enriched in cardiac muscle and muscle contraction-related categories, whereas the latter play more basic functions of energy generation like aerobic respiration. These findings together support the notion that recruiting anciently paralogous genes that are expressed in heart is associated with the increase of chamber number in vertebrate evolution.
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Affiliation(s)
- Yangyun Zou
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jingwen Yang
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- Brown Center for Immunotherapy, School of Medicine, Indiana University, Indianapolis, Indiana, USA
| | - Jingqi Zhou
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- School of Public Health, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Gangbiao Liu
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Libing Shen
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Zhan Zhou
- Innovation Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Zhixi Su
- Singlera Genomics Ltd., Shanghai, China
| | - Xun Gu
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa, USA
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5
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Payne ARD, Mannion PD, Lloyd GT, Davis KE. Decoupling speciation and extinction reveals both abiotic and biotic drivers shaped 250 million years of diversity in crocodile-line archosaurs. Nat Ecol Evol 2024; 8:121-132. [PMID: 38049481 PMCID: PMC10781641 DOI: 10.1038/s41559-023-02244-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/26/2023] [Indexed: 12/06/2023]
Abstract
Whereas living representatives of Pseudosuchia, crocodylians, number fewer than 30 species, more than 700 pseudosuchian species are known from their 250-million-year fossil record, displaying far greater ecomorphological diversity than their extant counterparts. With a new time-calibrated tree of >500 species, we use a phylogenetic framework to reveal that pseudosuchian evolutionary history and diversification dynamics were directly shaped by the interplay of abiotic and biotic processes over hundreds of millions of years, supported by information theory analyses. Speciation, but not extinction, is correlated with higher temperatures in terrestrial and marine lineages, with high sea level associated with heightened extinction in non-marine taxa. Low lineage diversity and increased speciation in non-marine species is consistent with opportunities for niche-filling, whereas increased competition may have led to elevated extinction rates. In marine lineages, competition via increased lineage diversity appears to have driven both speciation and extinction. Decoupling speciation and extinction, in combination with ecological partitioning, reveals a more complex picture of pseudosuchian evolution than previously understood. As the number of species threatened with extinction by anthropogenic climate change continues to rise, the fossil record provides a unique window into the drivers that led to clade success and those that may ultimately lead to extinction.
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Affiliation(s)
- Alexander R D Payne
- Department of Biology, University of York, York, UK
- Leverhulme Centre for Anthropocene Biodiversity, University of York, York, UK
| | - Philip D Mannion
- Department of Earth Sciences, University College London, London, UK
| | | | - Katie E Davis
- Department of Biology, University of York, York, UK.
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6
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Lambert S, Voznica J, Morlon H. Deep Learning from Phylogenies for Diversification Analyses. Syst Biol 2023; 72:1262-1279. [PMID: 37556735 DOI: 10.1093/sysbio/syad044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 06/20/2023] [Accepted: 08/08/2023] [Indexed: 08/11/2023] Open
Abstract
Birth-death (BD) models are widely used in combination with species phylogenies to study past diversification dynamics. Current inference approaches typically rely on likelihood-based methods. These methods are not generalizable, as a new likelihood formula must be established each time a new model is proposed; for some models, such a formula is not even tractable. Deep learning can bring solutions in such situations, as deep neural networks can be trained to learn the relation between simulations and parameter values as a regression problem. In this paper, we adapt a recently developed deep learning method from pathogen phylodynamics to the case of diversification inference, and we extend its applicability to the case of the inference of state-dependent diversification models from phylogenies associated with trait data. We demonstrate the accuracy and time efficiency of the approach for the time-constant homogeneous BD model and the Binary-State Speciation and Extinction model. Finally, we illustrate the use of the proposed inference machinery by reanalyzing a phylogeny of primates and their associated ecological role as seed dispersers. Deep learning inference provides at least the same accuracy as likelihood-based inference while being faster by several orders of magnitude, offering a promising new inference approach for the deployment of future models in the field.
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Affiliation(s)
- Sophia Lambert
- Institut de Biologie de l'École Normale Supérieure, École Normale Supérieure, CNRS, INSERM, Université Paris Sciences et Lettres, 46 Rue d'Ulm, 75005 Paris, France
- Institute of Ecology and Evolution, Department of Biology, 5289 University of Oregon, Eugene, OR 97403, USA
| | - Jakub Voznica
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, 25-28 Rue du Dr Roux, 75015 Paris, France
- Unité de Biologie Computationnelle, USR 3756 CNRS, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Hélène Morlon
- Institut de Biologie de l'École Normale Supérieure, École Normale Supérieure, CNRS, INSERM, Université Paris Sciences et Lettres, 46 Rue d'Ulm, 75005 Paris, France
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7
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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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8
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Rolland J, Henao-Diaz LF, Doebeli M, Germain R, Harmon LJ, Knowles LL, Liow LH, Mank JE, Machac A, Otto SP, Pennell M, Salamin N, Silvestro D, Sugawara M, Uyeda J, Wagner CE, Schluter D. Conceptual and empirical bridges between micro- and macroevolution. Nat Ecol Evol 2023; 7:1181-1193. [PMID: 37429904 DOI: 10.1038/s41559-023-02116-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 06/13/2023] [Indexed: 07/12/2023]
Abstract
Explaining broad molecular, phenotypic and species biodiversity patterns necessitates a unifying framework spanning multiple evolutionary scales. Here we argue that although substantial effort has been made to reconcile microevolution and macroevolution, much work remains to identify the links between biological processes at play. We highlight four major questions of evolutionary biology whose solutions require conceptual bridges between micro and macroevolution. We review potential avenues for future research to establish how mechanisms at one scale (drift, mutation, migration, selection) translate to processes at the other scale (speciation, extinction, biogeographic dispersal) and vice versa. We propose ways in which current comparative methods to infer molecular evolution, phenotypic evolution and species diversification could be improved to specifically address these questions. We conclude that researchers are in a better position than ever before to build a synthesis to understand how microevolutionary dynamics unfold over millions of years.
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Affiliation(s)
- Jonathan Rolland
- CNRS, UMR5174, Laboratoire Evolution et Diversité Biologique, Université Toulouse 3 Paul Sabatier, Toulouse, France.
| | - L Francisco Henao-Diaz
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Michael Doebeli
- Department of Zoology, and Department of Mathematics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rachel Germain
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Luke J Harmon
- Dept. of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | | | - Judith E Mank
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Antonin Machac
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Prague, Czech Republic
| | - Sarah P Otto
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matt Pennell
- Departments of Quantitative and Computational Biology and Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Daniele Silvestro
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | - Mauro Sugawara
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Mário Schenberg Institute, São Paulo, Brazil
| | - Josef Uyeda
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Catherine E Wagner
- Department of Botany, and Program in Ecology and Evolution, University of Wyoming, Laramie, WY, USA
| | - Dolph Schluter
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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9
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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: 2] [Impact Index Per Article: 2.0] [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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10
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Zhang K, Zhang Y, Deng M, Wang P, Yue X, Wang P, Li W. Monthly dynamics of microbial communities and variation of nitrogen-cycling genes in an industrial-scale expanded granular sludge bed reactor. Front Microbiol 2023; 14:1125709. [PMID: 36876106 PMCID: PMC9978346 DOI: 10.3389/fmicb.2023.1125709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 01/18/2023] [Indexed: 02/18/2023] Open
Abstract
Introduction The expanded granular sludge bed (EGSB) is a major form of anaerobic digestion system during wastewater treatment. Yet, the dynamics of microbial and viral communities and members functioning in nitrogen cycling along with monthly changing physicochemical properties have not been well elucidated. Methods Here, by collecting the anaerobic activated sludge samples from a continuously operating industrial-scale EGSB reactor, we conducted 16S rRNA gene amplicon sequencing and metagenome sequencing to reveal the microbial community structure and variation with the ever-changing physicochemical properties along within a year. Results We observed a clear monthly variation of microbial community structures, while COD, the ratio of volatile suspended solids (VSS) to total suspended solids (TSS) (VSS/TSS ratio), and temperature were predominant factors in shaping community dissimilarities examined by generalized boosted regression modeling (GBM) analysis. Meanwhile, a significant correlation was found between the changing physicochemical properties and microbial communities (p <0.05). The alpha diversity (Chao1 and Shannon) was significantly higher (p <0.05) in both winter (December, January, and February) and autumn (September, October, and November) with higher organic loading rate (OLR), higher VSS/TSS ratio, and lower temperature, resulting higher biogas production and nutrition removal efficiency. Further, 18 key genes covering nitrate reduction, denitrification, nitrification, and nitrogen fixation pathways were discovered, the total abundance of which was significantly associated with the changing environmental factors (p <0.05). Among these pathways, the dissimilatory nitrate reduction to ammonia (DNRA) and denitrification had the higher abundance contributed by the top highly abundant genes narGH, nrfABCDH, and hcp. The COD, OLR, and temperature were primary factors in affecting DNRA and denitrification by GBM evaluation. Moreover, by metagenome binning, we found the DNRA populations mainly belonged to Proteobacteria, Planctomycetota, and Nitrospirae, while the denitrifying bacteria with complete denitrification performance were all Proteobacteria. Besides, we detected 3,360 non-redundant viral sequences with great novelty, in which Siphoviridae, Podoviridae, and Myoviridae were dominant viral families. Interestingly, viral communities likewise depicted clear monthly variation and had significant associations with the recovered populations (p <0.05). Discussion Our work highlights the monthly variation of microbial and viral communities during the continuous operation of EGSB affected by the predominant changing COD, OLR, and temperature, while DNRA and denitrification pathways dominated in this anaerobic system. The results also provide a theoretical basis for the optimization of the engineered system.
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Affiliation(s)
- Kun Zhang
- School of Eco-environment Technology, Guangdong Industry Polytechnic, Guangzhou, China
| | - Yanling Zhang
- School of Mechanics and Construction Engineering, Jinan University, Guangzhou, China
| | - Maocheng Deng
- School of Food and Bioengineering, Guangdong Industry Polytechnic, Guangzhou, China
| | - Pengcheng Wang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.,China National Electric Apparatus Research Institute Co., Ltd., Guangzhou, China
| | - Xiu Yue
- School of Eco-environment Technology, Guangdong Industry Polytechnic, Guangzhou, China
| | - Pandeng Wang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Wenjun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
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11
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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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12
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Iron acquisition strategies in pseudomonads: mechanisms, ecology, and evolution. Biometals 2022:10.1007/s10534-022-00480-8. [PMID: 36508064 PMCID: PMC10393863 DOI: 10.1007/s10534-022-00480-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
AbstractIron is important for bacterial growth and survival, as it is a common co-factor in essential enzymes. Although iron is very abundant in the earth crust, its bioavailability is low in most habitats because ferric iron is largely insoluble under aerobic conditions and at neutral pH. Consequently, bacteria have evolved a plethora of mechanisms to solubilize and acquire iron from environmental and host stocks. In this review, I focus on Pseudomonas spp. and first present the main iron uptake mechanisms of this taxa, which involve the direct uptake of ferrous iron via importers, the production of iron-chelating siderophores, the exploitation of siderophores produced by other microbial species, and the use of iron-chelating compounds produced by plants and animals. In the second part of this review, I elaborate on how these mechanisms affect interactions between bacteria in microbial communities, and between bacteria and their hosts. This is important because Pseudomonas spp. live in diverse communities and certain iron-uptake strategies might have evolved not only to acquire this essential nutrient, but also to gain relative advantages over competitors in the race for iron. Thus, an integrative understanding of the mechanisms of iron acquisition and the eco-evolutionary dynamics they drive at the community level might prove most useful to understand why Pseudomonas spp., in particular, and many other bacterial species, in general, have evolved such diverse iron uptake repertoires.
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13
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Esquerré D, Brennan IG, Donnellan S, Keogh JS. Evolutionary models demonstrate rapid and adaptive diversification of Australo-Papuan pythons. Biol Lett 2022; 18:20220360. [PMID: 36541096 PMCID: PMC9768648 DOI: 10.1098/rsbl.2022.0360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022] Open
Abstract
Lineages may diversify when they encounter available ecological niches. Adaptive divergence by ecological opportunity often appears to follow the invasion of a new environment with open ecological space. This evolutionary process is hypothesized to explain the explosive diversification of numerous Australian vertebrate groups following the collision of the Eurasian and Australian plates 25 Mya. One of these groups is the pythons, which demonstrate their greatest phenotypic and ecological diversity in Australo-Papua (Australia and New Guinea). Here, using an updated and near complete time-calibrated phylogenomic hypothesis of the group, we show that following invasion of this region, pythons experienced a sudden burst of speciation rates coupled with multiple instances of accelerated phenotypic evolution in head and body shape and body size. These results are consistent with adaptive radiation theory with an initial rapid niche-filling phase and later slow-down approaching niche saturation. We discuss these findings in the context of other Australo-Papuan adaptive radiations and the importance of incorporating adaptive diversification systems that are not extraordinarily species-rich but ecomorphologically diverse to understand how biodiversity is generated.
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Affiliation(s)
- Damien Esquerré
- Division of Ecology and Evolution, Research School of Biology, The Australian National University 0200, Canberra, ACT, Australia
| | - Ian G. Brennan
- Division of Ecology and Evolution, Research School of Biology, The Australian National University 0200, Canberra, ACT, Australia
| | - Stephen Donnellan
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, SA 5000, Australia
| | - J. Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University 0200, Canberra, ACT, Australia
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14
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de Brito V, Betancur-R R, Burns MD, Buser TJ, Conway KW, Fontenelle JP, Kolmann MA, McCraney WT, Thacker CE, Bloom DD. Patterns of Phenotypic Evolution Associated with Marine/Freshwater Transitions in Fishes. Integr Comp Biol 2022; 62:406-423. [PMID: 35675320 DOI: 10.1093/icb/icac085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/01/2022] [Accepted: 06/01/2022] [Indexed: 11/12/2022] Open
Abstract
Evolutionary transitions between marine and freshwater ecosystems have occurred repeatedly throughout the phylogenetic history of fishes. The theory of ecological opportunity predicts that lineages that colonize species-poor regions will have greater potential for phenotypic diversification than lineages invading species-rich regions. Thus, transitions between marine and freshwaters may promote phenotypic diversification in trans-marine/freshwater fish clades. We used phylogenetic comparative methods to analyze body size data in nine major fish clades that have crossed the marine/freshwater boundary. We explored how habitat transitions, ecological opportunity, and community interactions influenced patterns of phenotypic diversity. Our analyses indicated that transitions between marine and freshwater habitats did not drive body size evolution, and there are few differences in body size between marine and freshwater lineages. We found that body size disparity in freshwater lineages is not correlated with the number of independent transitions to freshwaters. We found a positive correlation between body size disparity and overall species richness of a given area, and a negative correlation between body size disparity and diversity of closely related species. Our results indicate that the diversity of incumbent freshwater species does not restrict phenotypic diversification, but the diversity of closely related taxa can limit body size diversification. Ecological opportunity arising from colonization of novel habitats does not seem to have a major effect in the trajectory of body size evolution in trans-marine/freshwater clades. Moreover, competition with closely related taxa in freshwaters has a greater effect than competition with distantly related incumbent species.
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Affiliation(s)
- Victor de Brito
- Department of Biological Sciences, Western Michigan University, 1903 W Michigan Ave, Kalamazoo, MI 49008-5410, USA
| | - Ricardo Betancur-R
- Department of Biology, University of Oklahoma, 730 Van Vleet Oval, Room 314, Norman, OK 73019, USA
| | - Michael D Burns
- Cornell Lab of Ornithology, Cornell Museum of Vertebrates, Cornell University, 159 Sapsucker Woods Road, Ithaca, NY 14850-1923, USA
| | - Thaddaeus J Buser
- Department of BioSciences, Rice University, W100 George R. Brown Hall, 6100 Main Street, Houston, TX 77005, USA
| | - Kevin W Conway
- Department of Ecology and Conservation Biology and Biodiversity Research and Teaching Collections, Texas A&M University, College Station, TX 77843, USA
| | - João Pedro Fontenelle
- Institute of Forestry and Conservation, University of Toronto, 33 Willcocks St., Toronto, ON M5S 3E8, Canada
| | - Matthew A Kolmann
- Museum of Paleontology, Biological Sciences Building, University of Michigan, 1105 North University Ave, Ann Arbor, MI 48109-1085, USA
| | - W Tyler McCraney
- Department of Ecology and Evolutionary Biology, University of California, 612 Charles E. Young Drive South, Los Angeles, CA 90095-7246, USA
| | - Christine E Thacker
- Research and Collections, Section of Ichthyology, Natural History Museum of Los Angeles County, 900 Exposition Blvd., Los Angeles, CA 90007, USA.,Vertebrate Zoology, Santa Barbara Museum of Natural History, 2559 Puesta del Sol, Santa Barbara, CA 93105, USA
| | - Devin D Bloom
- Department of Biological Sciences, Western Michigan University, 1903 W Michigan Ave, Kalamazoo, MI 49008-5410, USA.,Institute of the Environment and Sustainability, Western Michigan University, 1903 W Michigan Ave, Kalamazoo, MI 49008-5419, USA
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15
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Morlon H, Robin S, Hartig F. Studying speciation and extinction dynamics from phylogenies: addressing identifiability issues. Trends Ecol Evol 2022; 37:497-506. [PMID: 35246322 DOI: 10.1016/j.tree.2022.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/20/2021] [Accepted: 02/07/2022] [Indexed: 11/18/2022]
Abstract
A lot of what we know about past speciation and extinction dynamics is based on statistically fitting birth-death processes to phylogenies of extant species. Despite their wide use, the reliability of these tools is regularly questioned. It was recently demonstrated that vast 'congruent' sets of alternative diversification histories cannot be distinguished (i.e., are not identifiable) using extant phylogenies alone, reanimating the debate about the limits of phylogenetic diversification analysis. Here, we summarize what we know about the identifiability of the birth-death process and how identifiability issues can be addressed. We conclude that extant phylogenies, when combined with appropriate prior hypotheses and regularization techniques, can still tell us a lot about past diversification dynamics.
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Affiliation(s)
- Hélène Morlon
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France.
| | - Stéphane Robin
- UMR MIA-Paris, AgroParisTech, INRA, Paris-Saclay University, 75005 Paris, France; Centre d'Ecologie et des Sciences de la Conservation (CESCO), Muséum National d'Histoire Naturelle, CNRS, Sorbonne University, Paris, France
| | - Florian Hartig
- Theoretical Ecology, University of Regensburg, Regensburg, Germany
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16
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Quintero I, Suchard MA, Jetz W. Macroevolutionary dynamics of climatic niche space. Proc Biol Sci 2022; 289:20220091. [PMID: 35611527 PMCID: PMC9130784 DOI: 10.1098/rspb.2022.0091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
How and why lineages evolve along with niche space as they diversify and adapt to different environments is fundamental to evolution. Progress has been hampered by the difficulties of linking a robust empirical characterization of species niches with flexible evolutionary models that describe their evolution. Consequently, the relative influence of abiotic and biotic factors remains poorly understood. Here, we characterize species' two-dimensional temperature and precipitation niche space occupied (i.e. species niche envelope) as complex geometries and assess their evolution across all Aves using a model that captures heterogeneous evolutionary rates on time-calibrated phylogenies. We find that extant birds coevolved from warm, mesic climatic niches into colder and drier environments and responded to the Cretaceous-Palaeogene (K-Pg) boundary with a dramatic increase in disparity. Contrary to expectations of subsiding rates of niche evolution, our results show that overall rates have increased steadily, with some lineages experiencing exceptionally high evolutionary rates, associated with the colonization of novel niche spaces, and others showing niche stasis. Both competition- and environmental change-driven niche evolution transpire and result in highly heterogeneous rates near the present. Our findings highlight the growing ecological and conservation insights arising from the model-based integration of comprehensive environmental and phylogenetic information.
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Affiliation(s)
- Ignacio Quintero
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France,Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
| | - Marc A. Suchard
- Department of Human Genetics, University of California, Los Angeles, 695 Charles E. Young Dr., Los Angeles, CA 90095, USA,Department of Biostatistics, University of California, Los Angeles, 695 Charles E. Young Dr., Los Angeles, CA 90095, USA
| | - Walter Jetz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA,Center for Biodiversity and Global Change, Yale University, New Haven, CT 06511, USA
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17
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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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18
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Levis NA, Ragsdale EJ. Linking Molecular Mechanisms and Evolutionary Consequences of Resource Polyphenism. Front Integr Neurosci 2022; 16:805061. [PMID: 35210995 PMCID: PMC8861301 DOI: 10.3389/fnint.2022.805061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/10/2022] [Indexed: 11/13/2022] Open
Abstract
Resource polyphenism—the occurrence of environmentally induced, discrete, and intraspecific morphs showing differential niche use—is taxonomically widespread and fundamental to the evolution of ecological function where it has arisen. Despite longstanding appreciation for the ecological and evolutionary significance of resource polyphenism, only recently have its proximate mechanisms begun to be uncovered. Polyphenism switches, especially those influencing and influenced by trophic interactions, offer a route to integrating proximate and ultimate causation in studies of plasticity, and its potential influence on evolution more generally. Here, we use the major events in generalized polyphenic development as a scaffold for linking the molecular mechanisms of polyphenic switching with potential evolutionary outcomes of polyphenism and for discussing challenges and opportunities at each step in this process. Not only does the study of resource polyphenism uncover interesting details of discrete plasticity, it also illuminates and informs general principles at the intersection of development, ecology, and evolution.
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19
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Zimmer RK, Ferrier GA, Zimmer CA. Chemosensory Exploitation and Predator-Prey Arms Races. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.752327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Thousands of armed predatory species, distributed widely across the metazoan tree-of-life, consume only hard-shell or exoskeleton-bearing organisms (called “durophagy”). Prey armor clearly has evolved in response to selection by predators, but there is little evidence of the contrary, counter-adaptation by predators. Evolved consumer responses to prey, in general, might be more readily expressed in ways other than morphological traits, including via sensory cues. Here, we explored the chemosensory basis for durophagy in a model predator-prey system, and identified intimate associations between durophagous predators and their shelled prey. Barnacles (Balanus glandula and Semibalanus cariosus) bear hard shells and secrete, respectively, a 199 or 201 kDa glycoprotein ortholog (named “MULTIFUNCin”), with expression limited to the body armor (epidermis, cuticle, and live shell). To test for effects of MULTIFUNCin on predators, we constructed faux prey to mimic meaningful physical and chemical characteristics of live barnacles. In separate experiments, each consumer species was presented MULTIFUNCin, purified from either B. glandula or S. cariosus, at a typical armor concentration. All six predatory species (sea star, Pisaster ochraceus; whelks, Acanthinucella spirata, Nucella emarginata, N. ostrina, N. canaliculata, and N. lamellosa) attacked and ate MULTIFUNCin-infused faux prey significantly more than controls. Akin to barnacles, secretion of glycoprotein-rich extracellular matrices is common among armored prey species—from marine sponges to terrestrial vertebrates. Our results, therefore, suggest that chemosensory exploitation of glycoproteins could be widespread, with notable consequences for life on land and in the sea.
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20
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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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21
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White KA, McEntire KD, Buan NR, Robinson L, Barbar E. Charting a New Frontier Integrating Mathematical Modeling in Complex Biological Systems from Molecules to Ecosystems. Integr Comp Biol 2021; 61:2255-2266. [PMID: 34283225 DOI: 10.1093/icb/icab165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 07/09/2021] [Accepted: 07/16/2021] [Indexed: 11/14/2022] Open
Affiliation(s)
| | | | - Nicole R Buan
- University of Nebraska-Lincoln, Department of Biochemistry
| | | | - Elisar Barbar
- Oregon State University, Department of Biochemistry and Biophysics
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22
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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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23
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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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24
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Pannetier T, Martinez C, Bunnefeld L, Etienne RS. Branching patterns in phylogenies cannot distinguish diversity-dependent diversification from time-dependent diversification. Evolution 2020; 75:25-38. [PMID: 33205832 PMCID: PMC7898657 DOI: 10.1111/evo.14124] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 10/06/2020] [Accepted: 10/10/2020] [Indexed: 01/08/2023]
Abstract
One of the primary goals of macroevolutionary biology has been to explain general trends in long‐term diversity patterns, including whether such patterns correspond to an upscaling of processes occurring at lower scales. Reconstructed phylogenies often show decelerated lineage accumulation over time. This pattern has often been interpreted as the result of diversity‐dependent (DD) diversification, where the accumulation of species causes diversification to decrease through niche filling. However, other processes can also produce such a slowdown, including time dependence without diversity dependence. To test whether phylogenetic branching patterns can be used to distinguish these two mechanisms, we formulated a time‐dependent, but diversity‐independent model that matches the expected diversity through time of a DD model. We simulated phylogenies under each model and studied how well likelihood methods could recover the true diversification mode. Standard model selection criteria always recovered diversity dependence, even when it was not present. We correct for this bias by using a bootstrap method and find that neither model is decisively supported. This implies that the branching pattern of reconstructed trees contains insufficient information to detect the presence or absence of diversity dependence. We advocate that tests encompassing additional data, for example, traits or range distributions, are needed to evaluate how diversity drives macroevolutionary trends.
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Affiliation(s)
- Théo Pannetier
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, 9712 CP, The Netherlands.,Biological and Environmental Sciences, University of Stirling, Stirling, FK9 4LA, United Kingdom
| | - César Martinez
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, 9712 CP, The Netherlands
| | - Lynsey Bunnefeld
- Biological and Environmental Sciences, University of Stirling, Stirling, FK9 4LA, United Kingdom
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, 9712 CP, The Netherlands
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25
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Folk RA, Siniscalchi CM, Soltis DE. Angiosperms at the edge: Extremity, diversity, and phylogeny. PLANT, CELL & ENVIRONMENT 2020; 43:2871-2893. [PMID: 32926444 DOI: 10.1111/pce.13887] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/21/2020] [Accepted: 08/13/2020] [Indexed: 05/26/2023]
Abstract
A hallmark of flowering plants is their ability to invade some of the most extreme and dynamic habitats, including cold and dry biomes, to a far greater extent than other land plants. Recent work has provided insight to the phylogenetic distribution and evolutionary mechanisms which have enabled this success, yet needed is a synthesis of evolutionary perspectives with plant physiological traits, morphology, and genomic diversity. Linking these disparate components will not only lead to better understand the evolutionary parallelism and diversification of plants with these two strategies, but also to provide the framework needed for directing future research. We summarize the primary physiological and structural traits involved in response to cold- and drought stress, outline the phylogenetic distribution of these adaptations, and describe the recurring association of these changes with rapid diversification events that occurred in multiple lineages over the past 15 million years. Across these threefold facets of dry-cold correlation (traits, phylogeny, and time) we stress the contrast between (a) the amazing diversity of solutions flowering plants have developed in the face of extreme environments and (b) a broad correlation between cold and dry adaptations that in some cases may hint at deep common origins.
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Affiliation(s)
- Ryan A Folk
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, USA
| | - Carolina M Siniscalchi
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Department of Biology, University of Florida, Gainesville, Florida, USA
- Biodiversity Institute, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
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26
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Condamine FL, Silvestro D, Koppelhus EB, Antonelli A. The rise of angiosperms pushed conifers to decline during global cooling. Proc Natl Acad Sci U S A 2020; 117:28867-28875. [PMID: 33139543 PMCID: PMC7682372 DOI: 10.1073/pnas.2005571117] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Competition among species and entire clades can impact species diversification and extinction, which can shape macroevolutionary patterns. The fossil record shows successive biotic turnovers such that a dominant group is replaced by another. One striking example involves the decline of gymnosperms and the rapid diversification and ecological dominance of angiosperms in the Cretaceous. It is generally believed that angiosperms outcompeted gymnosperms, but the macroevolutionary processes and alternative drivers explaining this pattern remain elusive. Using extant time trees and vetted fossil occurrences for conifers, we tested the hypotheses that clade competition or climate change led to the decline of conifers at the expense of angiosperms. Here, we find that both fossil and molecular data show high congruence in revealing 1) low diversification rates, punctuated by speciation pulses, during warming events throughout the Phanerozoic and 2) that conifer extinction increased significantly in the Mid-Cretaceous (100 to 110 Ma) and remained high ever since. Their extinction rates are best explained by the rise of angiosperms, rejecting alternative models based on either climate change or time alone. Our results support the hypothesis of an active clade replacement, implying that direct competition with angiosperms increased the extinction of conifers by pushing their remaining species diversity and dominance out of the warm tropics. This study illustrates how entire branches on the Tree of Life may actively compete for ecological dominance under changing climates.
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Affiliation(s)
- Fabien L Condamine
- CNRS, UMR 5554 Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier), 34095 Montpellier, France;
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Daniele Silvestro
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, SE-405 30 Gothenburg, Sweden
| | - Eva B Koppelhus
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, SE-405 30 Gothenburg, Sweden
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, United Kingdom
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, United Kingdom
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27
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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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28
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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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29
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Nürk NM, Linder HP, Onstein RE, Larcombe MJ, Hughes CE, Piñeiro Fernández L, Schlüter PM, Valente L, Beierkuhnlein C, Cutts V, Donoghue MJ, Edwards EJ, Field R, Flantua SGA, Higgins SI, Jentsch A, Liede‐Schumann S, Pirie MD. Diversification in evolutionary arenas-Assessment and synthesis. Ecol Evol 2020; 10:6163-6182. [PMID: 32607221 PMCID: PMC7319112 DOI: 10.1002/ece3.6313] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 03/30/2020] [Accepted: 04/06/2020] [Indexed: 12/23/2022] Open
Abstract
Understanding how and why rates of evolutionary diversification vary is a key issue in evolutionary biology, ecology, and biogeography. Evolutionary rates are the net result of interacting processes summarized under concepts such as adaptive radiation and evolutionary stasis. Here, we review the central concepts in the evolutionary diversification literature and synthesize these into a simple, general framework for studying rates of diversification and quantifying their underlying dynamics, which can be applied across clades and regions, and across spatial and temporal scales. Our framework describes the diversification rate (d) as a function of the abiotic environment (a), the biotic environment (b), and clade-specific phenotypes or traits (c); thus, d ~ a,b,c. We refer to the four components (a-d) and their interactions collectively as the "Evolutionary Arena." We outline analytical approaches to this framework and present a case study on conifers, for which we parameterize the general model. We also discuss three conceptual examples: the Lupinus radiation in the Andes in the context of emerging ecological opportunity and fluctuating connectivity due to climatic oscillations; oceanic island radiations in the context of island formation and erosion; and biotically driven radiations of the Mediterranean orchid genus Ophrys. The results of the conifer case study are consistent with the long-standing scenario that low competition and high rates of niche evolution promote diversification. The conceptual examples illustrate how using the synthetic Evolutionary Arena framework helps to identify and structure future directions for research on evolutionary radiations. In this way, the Evolutionary Arena framework promotes a more general understanding of variation in evolutionary rates by making quantitative results comparable between case studies, thereby allowing new syntheses of evolutionary and ecological processes to emerge.
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Affiliation(s)
- Nicolai M. Nürk
- Department of Plant SystematicsBayreuth Center of Ecology and Environmental Research (BayCEER)University of BayreuthBayreuthGermany
| | - H. Peter Linder
- Department of Systematic & Evolutionary BotanyUniversity of ZurichZurichSwitzerland
| | - Renske E. Onstein
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
| | | | - Colin E. Hughes
- Department of Systematic & Evolutionary BotanyUniversity of ZurichZurichSwitzerland
| | - Laura Piñeiro Fernández
- Department of Systematic & Evolutionary BotanyUniversity of ZurichZurichSwitzerland
- Department of BotanyUniversity of HohenheimStuttgartGermany
| | | | - Luis Valente
- Naturalis Biodiversity CenterUnderstanding Evolution GroupLeidenThe Netherlands
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
| | - Carl Beierkuhnlein
- Department of BiogeographyBayreuth Center of Ecology and Environmental Research (BayCEER)University of BayreuthBayreuthGermany
| | - Vanessa Cutts
- School of GeographyUniversity of NottinghamNottinghamUK
| | - Michael J. Donoghue
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticut
| | - Erika J. Edwards
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticut
| | - Richard Field
- School of GeographyUniversity of NottinghamNottinghamUK
| | | | | | - Anke Jentsch
- Department of Disturbance EcologyBayreuth Center of Ecology and Environmental Research (BayCEER)University of BayreuthBayreuthGermany
| | - Sigrid Liede‐Schumann
- Department of Plant SystematicsBayreuth Center of Ecology and Environmental Research (BayCEER)University of BayreuthBayreuthGermany
| | - Michael D. Pirie
- Johannes Gutenberg‐UniversitätMainzGermany
- University MuseumUniversity of BergenBergenNorway
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30
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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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31
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Kennedy SR, Prost S, Overcast I, Rominger AJ, Gillespie RG, Krehenwinkel H. High-throughput sequencing for community analysis: the promise of DNA barcoding to uncover diversity, relatedness, abundances and interactions in spider communities. Dev Genes Evol 2020; 230:185-201. [PMID: 32040713 PMCID: PMC7127999 DOI: 10.1007/s00427-020-00652-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 01/29/2020] [Indexed: 12/19/2022]
Abstract
Large-scale studies on community ecology are highly desirable but often difficult to accomplish due to the considerable investment of time, labor and, money required to characterize richness, abundance, relatedness, and interactions. Nonetheless, such large-scale perspectives are necessary for understanding the composition, dynamics, and resilience of biological communities. Small invertebrates play a central role in ecosystems, occupying critical positions in the food web and performing a broad variety of ecological functions. However, it has been particularly difficult to adequately characterize communities of these animals because of their exceptionally high diversity and abundance. Spiders in particular fulfill key roles as both predator and prey in terrestrial food webs and are hence an important focus of ecological studies. In recent years, large-scale community analyses have benefitted tremendously from advances in DNA barcoding technology. High-throughput sequencing (HTS), particularly DNA metabarcoding, enables community-wide analyses of diversity and interactions at unprecedented scales and at a fraction of the cost that was previously possible. Here, we review the current state of the application of these technologies to the analysis of spider communities. We discuss amplicon-based DNA barcoding and metabarcoding for the analysis of community diversity and molecular gut content analysis for assessing predator-prey relationships. We also highlight applications of the third generation sequencing technology for long read and portable DNA barcoding. We then address the development of theoretical frameworks for community-level studies, and finally highlight critical gaps and future directions for DNA analysis of spider communities.
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Affiliation(s)
- Susan R Kennedy
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology, Onna, Okinawa, Japan
| | - Stefan Prost
- LOEWE-Centre for Translational Biodiversity Genomics, Senckenberg Museum, Frankfurt, Germany
- National Zoological Garden, South African National Biodiversity Institute, Pretoria, South Africa
| | - Isaac Overcast
- Graduate Center of the City University New York, New York, NY, USA
- Ecole Normale Supérieure, Paris, France
| | | | - Rosemary G Gillespie
- Environmental Sciences Policy and Management, University of California Berkeley, Berkeley, CA, USA
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32
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Rowsey DM, Keenan RM, Jansa SA. Dietary morphology of two island-endemic murid rodent clades is consistent with persistent, incumbent-imposed competitive interactions. Proc Biol Sci 2020; 287:20192746. [PMID: 32097592 DOI: 10.1098/rspb.2019.2746] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A lineage colonizing a geographic region with no competitors may exhibit rapid diversification due to greater ecological opportunity. The resultant species diversity of this primary-colonizing (incumbent) clade may limit subsequent lineages' ability to persist unless these non-incumbent lineages are ecologically distinct. We compare the diversity in diet-related mandibular morphology of two sympatric murid rodent clades endemic to Luzon Island, Philippines-incumbent Phloeomyini and secondary-colonizing Chrotomyini-to the mandibular morphological diversity of Sahul Hydromyini, the sister clade of Chrotomyini and the incumbent murid lineage on the supercontinent of Sahul. This three-clade comparison allows us to test the hypothesis that incumbent lineages can force persistent ecological distinction of subsequent colonists at the time of colonization and throughout the subsequent history of the two sympatric clades. We find that Chrotomyini forms a subset of the diversity of their clade plus Sahul Hydromyini that minimizes overlap with Phloeomyini. We also infer that this differentiation extends to the stem ancestor of Chrotomyini and Sahul Hydromyini, consistent with a biotic filter imposed by Phloeomyini. Our work illustrates that incumbency has the potential to have a profound influence on the ecomorphological diversity of colonizing lineages at the island scale even when the traits in question are evolving at similar rates among independently colonizing clades.
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Affiliation(s)
- Dakota M Rowsey
- Department of Ecology, Evolution, and Behavior & Bell Museum of Natural History, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN 55108, USA.,Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
| | - Ryan M Keenan
- Department of Fisheries, Wildlife, and Conservation Biology, University of Minnesota, 2003 Upper Buford Circle, St. Paul, MN 55108, USA
| | - Sharon A Jansa
- Department of Ecology, Evolution, and Behavior & Bell Museum of Natural History, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN 55108, USA
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33
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Condamine FL, Rolland J, Morlon H. Assessing the causes of diversification slowdowns: temperature‐dependent and diversity‐dependent models receive equivalent support. Ecol Lett 2019; 22:1900-1912. [DOI: 10.1111/ele.13382] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/20/2019] [Accepted: 08/12/2019] [Indexed: 12/30/2022]
Affiliation(s)
- Fabien L. Condamine
- CNRS, UMR 5554 Institut des Sciences de l'Evolution de Montpellier Place Eugène Bataillon 34095Montpellier France
- CNRS, UMR 7641 Centre de Mathématiques Appliquées (Ecole Polytechnique) route de Saclay 91128Palaiseau France
| | - Jonathan Rolland
- CNRS, UMR 7641 Centre de Mathématiques Appliquées (Ecole Polytechnique) route de Saclay 91128Palaiseau France
- Department of Computational Biology, Biophore University of Lausanne Lausanne 1015Switzerland
- Department of Zoology University of British Columbia University Blvd #4200‐6270Vancouver B.C Canada
| | - Hélène Morlon
- CNRS, UMR 7641 Centre de Mathématiques Appliquées (Ecole Polytechnique) route de Saclay 91128Palaiseau France
- IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University F‐75005Paris France
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