1
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Marion AFP, Condamine FL, Guinot G. Sequential trait evolution did not drive deep-time diversification in sharks. Evolution 2024; 78:1405-1425. [PMID: 38745524 DOI: 10.1093/evolut/qpae070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 04/23/2024] [Accepted: 05/13/2024] [Indexed: 05/16/2024]
Abstract
Estimating how traits evolved and impacted diversification across the tree of life represents a critical topic in ecology and evolution. Although there has been considerable research in comparative biology, large parts of the tree of life remain underexplored. Sharks are an iconic clade of marine vertebrates, and key components of marine ecosystems since the early Mesozoic. However, few studies have addressed how traits evolved or whether they impacted their extant diversity patterns. Our study aimed to fill this gap by reconstructing the largest time-calibrated species-level phylogeny of sharks and compiling an exhaustive database for ecological (diet, habitat) and biological (reproduction, maximum body length) traits. Using state-of-the-art models of evolution and diversification, we outlined the major character shifts and modes of trait evolution across shark species. We found support for sequential models of trait evolution and estimated a small to medium-sized lecithotrophic and coastal-dwelling most recent common ancestor for extant sharks. However, our exhaustive hidden traits analyses do not support trait-dependent diversification for any examined traits, challenging previous works. This suggests that the role of traits in shaping sharks' diversification dynamics might have been previously overestimated and should motivate future macroevolutionary studies to investigate other drivers of diversification in this clade.
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Affiliation(s)
- Alexis F P Marion
- Institut des Sciences de l'Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | - Fabien L Condamine
- Institut des Sciences de l'Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | - Guillaume Guinot
- Institut des Sciences de l'Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
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2
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Verboom GA, Boucher FC, Ackerly DD, Wootton LM, Freyman WA. Species Selection Regime and Phylogenetic Tree Shape. Syst Biol 2020; 69:774-794. [DOI: 10.1093/sysbio/syz076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/08/2019] [Accepted: 11/11/2019] [Indexed: 11/12/2022] Open
Abstract
Abstract
Species selection, the effect of heritable traits in generating between-lineage diversification rate differences, provides a valuable conceptual framework for understanding the relationship between traits, diversification, and phylogenetic tree shape. An important challenge, however, is that the nature of real diversification landscapes—curves or surfaces which describe the propensity of species-level lineages to diversify as a function of one or more traits—remains poorly understood. Here, we present a novel, time-stratified extension of the QuaSSE model in which speciation/extinction rate is specified as a static or temporally shifting Gaussian or skewed-Gaussian function of the diversification trait. We then use simulations to show that the generally imbalanced nature of real phylogenetic trees, as well as their generally greater than expected frequency of deep branching events, are typical outcomes when diversification is treated as a dynamic, trait-dependent process. Focusing on four basic models (Gaussian-speciation with and without background extinction; skewed-speciation; Gaussian-extinction), we also show that particular features of the species selection regime produce distinct tree shape signatures and that, consequently, a combination of tree shape metrics has the potential to reveal the species selection regime under which a particular lineage diversified. We evaluate this idea empirically by comparing the phylogenetic trees of plant lineages diversifying within climatically and geologically stable environments of the Greater Cape Floristic Region, with those of lineages diversifying in environments that have experienced major change through the Late Miocene-Pliocene. Consistent with our expectations, the trees of lineages diversifying in a dynamic context are less balanced, show a greater concentration of branching events close to the present, and display stronger diversification rate-trait correlations. We suggest that species selection plays an important role in shaping phylogenetic trees but recognize the need for an explicit probabilistic framework within which to assess the likelihoods of alternative diversification scenarios as explanations of a particular tree shape. [Cape flora; diversification landscape; environmental change; gamma statistic; species selection; time-stratified QuaSSE model; trait-dependent diversification; tree imbalance.]
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Affiliation(s)
- G Anthony Verboom
- Bolus Herbarium and Department of Biological Sciences, University of Cape Town, Private Bag, Rondebosch 7700, South Africa
| | - Florian C Boucher
- Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
- Université Grenoble Alpes, CNRS, Laboratoire d’Ecologie Alpine (LECA), 2233 Rue de la Piscine, FR-38000 Grenoble, France
| | - David D Ackerly
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
- Department of Environmental Sciences, Policy, and Management, University of California, Berkeley, CA 94720, USA
| | - Lara M Wootton
- Bolus Herbarium and Department of Biological Sciences, University of Cape Town, Private Bag, Rondebosch 7700, South Africa
| | - William A Freyman
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN 55108, USA
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3
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Burbrink FT, Ruane S, Kuhn A, Rabibisoa N, Randriamahatantsoa B, Raselimanana AP, Andrianarimalala MSM, Cadle JE, Lemmon AR, Lemmon EM, Nussbaum RA, Jones LN, Pearson R, Raxworthy CJ. The Origins and Diversification of the Exceptionally Rich Gemsnakes (Colubroidea: Lamprophiidae: Pseudoxyrhophiinae) in Madagascar. Syst Biol 2019; 68:918-936. [DOI: 10.1093/sysbio/syz026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 04/05/2019] [Accepted: 04/09/2019] [Indexed: 11/14/2022] Open
Abstract
Abstract
Processes leading to spectacular diversity of both form and species on islands have been well-documented under island biogeography theory, where distance from source and island size are key factors determining immigration and extinction resistance. But far less understood are the processes governing in situ diversification on the world’s mega islands, where large and isolated land masses produced morphologically distinct radiations from related taxa on continental regions. Madagascar has long been recognized as a natural laboratory due to its isolation, lack of influence from adjacent continents, and diversification of spectacular vertebrate radiations. However, only a handful of studies have examined rate shifts of in situ diversification for this island. Here, we examine rates of diversification in the Malagasy snakes of the family Pseudoxyrhophiinae (gemsnakes) to understand if rates of speciation were initially high, enhanced by diversification into distinct biomes, and associated with key dentition traits. Using a genomic sequence-capture data set for 366 samples, we determine that all previously described and newly discovered species are delimitable and therefore useful candidates for understanding diversification trajectories through time. Our analysis detected no shifts in diversification rate between clades or changes in biome or dentition type. Remarkably, we demonstrate that rates of diversification of the gemsnake radiation, which originated in Madagascar during the early Miocene, remained steady throughout the Neogene. However, we do detect a significant slowdown in diversification during the Pleistocene. We also comment on the apparent paradox where most living species originated in the Pleistocene, despite diversification rates being substantially higher during the earlier 15 myr.
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Affiliation(s)
- Frank T Burbrink
- Department of Herpetology, The American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
| | - Sara Ruane
- Department of Biological Sciences, 206 Boyden Hall, Rutgers University-Newark, 195 University Ave, Newark, NJ 07102, USA
| | - Arianna Kuhn
- Department of Herpetology, The American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
- Department of Biology, The Graduate School and University Center, The City University of New York, 365 Fifth Ave., New York, NY 10016, USA
| | - Nirhy Rabibisoa
- Mention Sciences de la Vie et de l’Environnement, Faculté des Sciences, de Technologies et de l’Environnement, Université de Mahajanga, Campus Universitaire d’Ambondrona, BP 652, Mahajanga 401, Madagascar
| | - Bernard Randriamahatantsoa
- Mention Sciences de la Vie et de l’Environnement, Faculté des Sciences, de Technologies et de l’Environnement, Université de Mahajanga, Campus Universitaire d’Ambondrona, BP 652, Mahajanga 401, Madagascar
| | - Achille P Raselimanana
- Mention: Zoologie et Biodiversité Animale, Faculté des Sciences, Université d’Antananarivo, BP 906, Antananarivo 101, Madagascar
| | - Mamy S M Andrianarimalala
- Mention: Zoologie et Biodiversité Animale, Faculté des Sciences, Université d’Antananarivo, BP 906, Antananarivo 101, Madagascar
| | - John E Cadle
- Department of Biology, East Georgia State College, Swainsboro, GA 30401, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4102, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306-4295, USA
| | - Ronald A Nussbaum
- Division of Reptiles and Amphibians, Museum of Zoology, Research Museums Center, 3600 Varsity Drive, University of Michigan, Ann Arbor, MI 48108, USA
| | - Leonard N Jones
- Department of Biology, University of Washington, Seattle, WA 98195-1800, USA
| | - Richard Pearson
- Centre for Biodiversity & Environment Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Christopher J Raxworthy
- Department of Herpetology, The American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
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4
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Bravo GA, Antonelli A, Bacon CD, Bartoszek K, Blom MPK, Huynh S, Jones G, Knowles LL, Lamichhaney S, Marcussen T, Morlon H, Nakhleh LK, Oxelman B, Pfeil B, Schliep A, Wahlberg N, Werneck FP, Wiedenhoeft J, Willows-Munro S, Edwards SV. Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics. PeerJ 2019; 7:e6399. [PMID: 30783571 PMCID: PMC6378093 DOI: 10.7717/peerj.6399] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 01/07/2019] [Indexed: 12/23/2022] Open
Abstract
Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress.
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Affiliation(s)
- Gustavo A. Bravo
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Alexandre Antonelli
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
- Gothenburg Botanical Garden, Göteborg, Sweden
| | - Christine D. Bacon
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Krzysztof Bartoszek
- Department of Computer and Information Science, Linköping University, Linköping, Sweden
| | - Mozes P. K. Blom
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Stella Huynh
- Institut de Biologie, Université de Neuchâtel, Neuchâtel, Switzerland
| | - Graham Jones
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Sangeet Lamichhaney
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Thomas Marcussen
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Hélène Morlon
- Institut de Biologie, Ecole Normale Supérieure de Paris, Paris, France
| | - Luay K. Nakhleh
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Bengt Oxelman
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Bernard Pfeil
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Alexander Schliep
- Department of Computer Science and Engineering, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
| | | | - Fernanda P. Werneck
- Coordenação de Biodiversidade, Programa de Coleções Científicas Biológicas, Instituto Nacional de Pesquisa da Amazônia, Manaus, AM, Brazil
| | - John Wiedenhoeft
- Department of Computer Science and Engineering, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
- Department of Computer Science, Rutgers University, Piscataway, NJ, USA
| | - Sandi Willows-Munro
- School of Life Sciences, University of Kwazulu-Natal, Pietermaritzburg, South Africa
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Gothenburg Centre for Advanced Studies in Science and Technology, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
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5
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García-Navas V, Rodríguez-Rey M. The Evolution of Climatic Niches and its Role in Shaping Diversity Patterns in Diprotodontid Marsupials. J MAMM EVOL 2018. [DOI: 10.1007/s10914-018-9435-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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6
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Chen X, Lemmon AR, Lemmon EM, Pyron RA, Burbrink FT. Using phylogenomics to understand the link between biogeographic origins and regional diversification in ratsnakes. Mol Phylogenet Evol 2017; 111:206-218. [DOI: 10.1016/j.ympev.2017.03.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 01/07/2017] [Accepted: 03/20/2017] [Indexed: 11/15/2022]
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7
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Halliday TJD, Upchurch P, Goswami A. Resolving the relationships of Paleocene placental mammals. Biol Rev Camb Philos Soc 2017; 92:521-550. [PMID: 28075073 PMCID: PMC6849585 DOI: 10.1111/brv.12242] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 10/28/2015] [Accepted: 11/04/2015] [Indexed: 01/25/2023]
Abstract
The 'Age of Mammals' began in the Paleocene epoch, the 10 million year interval immediately following the Cretaceous-Palaeogene mass extinction. The apparently rapid shift in mammalian ecomorphs from small, largely insectivorous forms to many small-to-large-bodied, diverse taxa has driven a hypothesis that the end-Cretaceous heralded an adaptive radiation in placental mammal evolution. However, the affinities of most Paleocene mammals have remained unresolved, despite significant advances in understanding the relationships of the extant orders, hindering efforts to reconstruct robustly the origin and early evolution of placental mammals. Here we present the largest cladistic analysis of Paleocene placentals to date, from a data matrix including 177 taxa (130 of which are Palaeogene) and 680 morphological characters. We improve the resolution of the relationships of several enigmatic Paleocene clades, including families of 'condylarths'. Protungulatum is resolved as a stem eutherian, meaning that no crown-placental mammal unambiguously pre-dates the Cretaceous-Palaeogene boundary. Our results support an Atlantogenata-Boreoeutheria split at the root of crown Placentalia, the presence of phenacodontids as closest relatives of Perissodactyla, the validity of Euungulata, and the placement of Arctocyonidae close to Carnivora. Periptychidae and Pantodonta are resolved as sister taxa, Leptictida and Cimolestidae are found to be stem eutherians, and Hyopsodontidae is highly polyphyletic. The inclusion of Paleocene taxa in a placental phylogeny alters interpretations of relationships and key events in mammalian evolutionary history. Paleocene mammals are an essential source of data for understanding fully the biotic dynamics associated with the end-Cretaceous mass extinction. The relationships presented here mark a critical first step towards accurate reconstruction of this important interval in the evolution of the modern fauna.
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Affiliation(s)
- Thomas J. D. Halliday
- Department of Earth SciencesUniversity College LondonGower StreetLondonWC1E 6BTU.K.
- Department of Genetics, Evolution and EnvironmentUniversity College LondonGower StreetLondonWC1E 6BTU.K.
| | - Paul Upchurch
- Department of Earth SciencesUniversity College LondonGower StreetLondonWC1E 6BTU.K.
| | - Anjali Goswami
- Department of Earth SciencesUniversity College LondonGower StreetLondonWC1E 6BTU.K.
- Department of Genetics, Evolution and EnvironmentUniversity College LondonGower StreetLondonWC1E 6BTU.K.
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8
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Hunt G, Slater G. Integrating Paleontological and Phylogenetic Approaches to Macroevolution. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2016. [DOI: 10.1146/annurev-ecolsys-112414-054207] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
With proliferation of molecular phylogenies and advances in statistical modeling, phylogeneticists can now address macroevolutionary questions that had traditionally been the purview of paleontology. Interest has focused on three areas at the intersection of phylogenetic and paleontological research: time-scaling phylogenies, understanding trait evolution, and modeling species diversification. Fossil calibrations have long been crucial for scaling phylogenies to absolute time, but recent advances allow more equal integration of extinct taxa. Simulation and empirical studies have shown that fossil data can markedly improve inferences about trait evolution, especially for models with heterogeneous temporal dynamics and in clades for which the living forms are unrepresentative remnants of their larger clade. Recent years have also seen a productive cross-disciplinary conversation about the nature and uncertainties of inferring diversification dynamics. Challenges remain, but the present time represents a flowering of interest in integrating these two views on the history of life.
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Affiliation(s)
- Gene Hunt
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Graham Slater
- Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois 60637
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9
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Phylogeny and Divergence Times of Lemurs Inferred with Recent and Ancient Fossils in the Tree. Syst Biol 2016; 65:772-91. [DOI: 10.1093/sysbio/syw035] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 03/30/2016] [Indexed: 01/14/2023] Open
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10
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Serb JM. Reconciling Morphological and Molecular Approaches in Developing a Phylogeny for the Pectinidae (Mollusca: Bivalvia). SCALLOPS - BIOLOGY, ECOLOGY, AQUACULTURE, AND FISHERIES 2016. [DOI: 10.1016/b978-0-444-62710-0.00001-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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11
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Ng J, Smith SD. How traits shape trees: new approaches for detecting character state-dependent lineage diversification. J Evol Biol 2014; 27:2035-45. [PMID: 25066512 DOI: 10.1111/jeb.12460] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 07/07/2014] [Accepted: 07/08/2014] [Indexed: 12/30/2022]
Abstract
Biologists have long sought to understand the processes underlying disparities in clade size across the tree of life and the extent to which such clade size differences can be attributed to the evolution of particular traits. The association of certain character states with species-rich clades suggests that trait evolution can lead to increased diversification, but such a pattern could also arise due other processes, such as directional trait evolution. Recent advances in phylogenetic comparative methods have provided new statistical approaches for distinguishing between these intertwined and potentially confounded macroevolutionary processes. Here, we review the historical development of methods for detecting state-dependent diversification and explore what new methods have revealed about classic examples of traits that affect diversification, including evolutionary dead ends, key innovations and geographic traits. Applications of these methods thus far collectively suggest that trait diversity commonly arises through the complex interplay between transition, speciation and extinction rates and that long hypothesized evolutionary dead ends and key innovations are instead often cases of directional trends in trait evolution.
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Affiliation(s)
- J Ng
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
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12
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Boucher FC, Thuiller W, Davies TJ, Lavergne S. Neutral biogeography and the evolution of climatic niches. Am Nat 2014; 183:573-84. [PMID: 24739191 PMCID: PMC4001461 DOI: 10.1086/675506] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Recent debate on whether climatic niches are conserved through time has focused on how phylogenetic niche conservatism can be measured by deviations from a Brownian motion model of evolutionary change. However, there has been no evaluation of this methodological approach. In particular, the fact that climatic niches are usually obtained from distribution data and are thus heavily influenced by biogeographic factors has largely been overlooked. Our main objective here was to test whether patterns of climatic niche evolution that are frequently observed might arise from neutral dynamics rather than from adaptive scenarios. We developed a model inspired by neutral biodiversity theory, where individuals disperse, compete, and undergo speciation independently of climate. We then sampled the climatic niches of species according to their geographic position and showed that even when species evolve independently of climate, their niches can nonetheless exhibit evolutionary patterns strongly differing from Brownian motion. Indeed, climatic niche evolution is better captured by a model of punctuated evolution with constraints due to landscape boundaries, two features that are traditionally interpreted as evidence for selective processes acting on the niche. We therefore suggest that deviation from Brownian motion alone should not be used as evidence for phylogenetic niche conservatism but that information on phenotypic traits directly linked to physiology is required to demonstrate that climatic niches have been conserved through time.
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Affiliation(s)
- Florian C. Boucher
- Laboratoire d’Ecologie Alpine, UMR 5533 CNRS-Université de Grenoble, Grenoble, France ;
| | - Wilfried Thuiller
- Laboratoire d’Ecologie Alpine, UMR 5533 CNRS-Université de Grenoble, Grenoble, France ;
| | | | - Sébastien Lavergne
- Laboratoire d’Ecologie Alpine, UMR 5533 CNRS-Université de Grenoble, Grenoble, France ;
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13
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Pyron RA, Burbrink FT. Phylogenetic estimates of speciation and extinction rates for testing ecological and evolutionary hypotheses. Trends Ecol Evol 2013; 28:729-36. [PMID: 24120478 DOI: 10.1016/j.tree.2013.09.007] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 09/03/2013] [Accepted: 09/15/2013] [Indexed: 10/26/2022]
Abstract
Phylogenies are used to estimate rates of speciation and extinction, reconstruct historical diversification scenarios, and link these to ecological and evolutionary factors, such as climate or organismal traits. Recent models can now estimate the effects of binary, multistate, continuous, and biogeographic characters on diversification rates. Others test for diversity dependence (DD) in speciation and extinction, which has become recognized as an important process in numerous clades. A third class incorporates flexible time-dependent functions, enabling reconstruction of major periods of both expanding and contracting diversity. Although there are some potential problems (particularly for estimating extinction), these methods hold promise for answering many classic questions in ecology and evolution, such as the origin of adaptive radiations, and the latitudinal gradient in species richness.
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Affiliation(s)
- R Alexander Pyron
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, DC 20052, USA.
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14
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Slater GJ, Harmon LJ. Unifying fossils and phylogenies for comparative analyses of diversification and trait evolution. Methods Ecol Evol 2013. [DOI: 10.1111/2041-210x.12091] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Graham J. Slater
- Department of Paleobiology and Division of Mammals; National Museum of Natural History; Smithsonian Institution; MRC 121, P.O. Box 37012; Washington; DC; 20013-7012; USA
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15
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Slater GJ. Phylogenetic evidence for a shift in the mode of mammalian body size evolution at the Cretaceous-Palaeogene boundary. Methods Ecol Evol 2013. [DOI: 10.1111/2041-210x.12084] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Graham J. Slater
- Department of Paleobiology; National Museum of Natural History; Smithsonian Institution; MRC 121, P.O. Box 37012; Washington; DC; 20013-7012; USA
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16
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Maruvka YE, Shnerb NM, Kessler DA, Ricklefs RE. Model for macroevolutionary dynamics. Proc Natl Acad Sci U S A 2013; 110:E2460-9. [PMID: 23781101 PMCID: PMC3703965 DOI: 10.1073/pnas.1220014110] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The highly skewed distribution of species among genera, although challenging to macroevolutionists, provides an opportunity to understand the dynamics of diversification, including species formation, extinction, and morphological evolution. Early models were based on either the work by Yule [Yule GU (1925) Philos Trans R Soc Lond B Biol Sci 213:21-87], which neglects extinction, or a simple birth-death (speciation-extinction) process. Here, we extend the more recent development of a generic, neutral speciation-extinction (of species)-origination (of genera; SEO) model for macroevolutionary dynamics of taxon diversification. Simulations show that deviations from the homogeneity assumptions in the model can be detected in species-per-genus distributions. The SEO model fits observed species-per-genus distributions well for class-to-kingdom-sized taxonomic groups. The model's predictions for the appearance times (the time of the first existing species) of the taxonomic groups also approximately match estimates based on molecular inference and fossil records. Unlike estimates based on analyses of phylogenetic reconstruction, fitted extinction rates for large clades are close to speciation rates, consistent with high rates of species turnover and the relatively slow change in diversity observed in the fossil record. Finally, the SEO model generally supports the consistency of generic boundaries based on morphological differences between species and provides a comparator for rates of lineage splitting and morphological evolution.
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Affiliation(s)
- Yosef E. Maruvka
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115
- Department of Physics, Bar-Ilan University, Ramat-Gan 52900, Israel; and
| | - Nadav M. Shnerb
- Department of Physics, Bar-Ilan University, Ramat-Gan 52900, Israel; and
| | - David A. Kessler
- Department of Physics, Bar-Ilan University, Ramat-Gan 52900, Israel; and
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Fritz SA, Schnitzler J, Eronen JT, Hof C, Böhning-Gaese K, Graham CH. Diversity in time and space: wanted dead and alive. Trends Ecol Evol 2013; 28:509-16. [PMID: 23726658 DOI: 10.1016/j.tree.2013.05.004] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 04/24/2013] [Accepted: 05/01/2013] [Indexed: 11/26/2022]
Abstract
Current patterns of biological diversity are influenced by both historical and present-day factors, yet research in ecology and evolution is largely split between paleontological and neontological studies. Responding to recent calls for integration, we provide a conceptual framework that capitalizes on data and methods from both disciplines to investigate fundamental processes. We highlight the opportunities arising from a combined approach with four examples: (i) which mechanisms generate spatial and temporal variation in diversity; (ii) how traits evolve; (iii) what determines the temporal dynamics of geographical ranges and ecological niches; and (iv) how species-environment and biotic interactions shape community structure. Our framework provides conceptual guidelines for combining paleontological and neontological perspectives to unravel the fundamental processes shaping life on Earth.
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Affiliation(s)
- Susanne A Fritz
- Biodiversity and Climate Research Centre (BiK-F) and Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt, Germany.
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18
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Condamine FL, Rolland J, Morlon H. Macroevolutionary perspectives to environmental change. Ecol Lett 2013; 16 Suppl 1:72-85. [DOI: 10.1111/ele.12062] [Citation(s) in RCA: 183] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 10/10/2012] [Accepted: 12/04/2012] [Indexed: 11/28/2022]
Affiliation(s)
- Fabien L. Condamine
- CNRS; UMR 7641 Centre de Mathématiques Appliquées (École Polytechnique); Route de Saclay; 91128 Palaiseau; France
| | - Jonathan Rolland
- CNRS; UMR 7641 Centre de Mathématiques Appliquées (École Polytechnique); Route de Saclay; 91128 Palaiseau; France
| | - Hélène Morlon
- CNRS; UMR 7641 Centre de Mathématiques Appliquées (École Polytechnique); Route de Saclay; 91128 Palaiseau; France
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