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Park T, Burin G, Lazo-Cancino D, Rees JPG, Rule JP, Slater GJ, Cooper N. Charting the course of pinniped evolution: insights from molecular phylogeny and fossil record integration. Evolution 2024; 78:1212-1226. [PMID: 38644688 DOI: 10.1093/evolut/qpae061] [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: 08/23/2023] [Revised: 04/02/2024] [Accepted: 04/19/2024] [Indexed: 04/23/2024]
Abstract
Pinnipeds (seals, sea lions, walruses, and their fossil relatives) are one of the most successful mammalian clades to live in the oceans. Despite a well-resolved molecular phylogeny and a global fossil record, a complete understanding of their macroevolutionary dynamics remains hampered by a lack of formal analyses that combine these 2 rich sources of information. We used a meta-analytic approach to infer the most densely sampled pinniped phylogeny to date (36 recent and 93 fossil taxa) and used phylogenetic paleobiological methods to study their diversification dynamics and biogeographic history. Pinnipeds mostly diversified at constant rates. Walruses, however, experienced rapid turnover in which extinction rates ultimately exceeded speciation rates from 12 to 6 Ma, possibly due to changing sea levels and/or competition with otariids (eared seals). Historical biogeographic analyses, including fossil data, allowed us to confidently identify the North Pacific and the North Atlantic (plus or minus Paratethys) as the ancestral ranges of Otarioidea (eared seals + walrus) and crown phocids (earless seals), respectively. Yet, despite the novel addition of stem pan-pinniped taxa, the region of origin for Pan-Pinnipedia remained ambiguous. These results suggest further avenues of study in pinnipeds and provide a framework for investigating other groups with substantial extinct and extant diversity.
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Affiliation(s)
- Travis Park
- School of Biological Sciences, Monash University, Melbourne, Australia
- Science Group, Natural History Museum London, London, United Kingdom
- Sciences, Museums Victoria, Melbourne, Australia
| | - Gustavo Burin
- Science Group, Natural History Museum London, London, United Kingdom
| | - Daniela Lazo-Cancino
- Laboratorio de Mastozoología, Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Joseph P G Rees
- Science Group, Natural History Museum London, London, United Kingdom
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - James P Rule
- School of Biological Sciences, Monash University, Melbourne, Australia
- Science Group, Natural History Museum London, London, United Kingdom
| | - Graham J Slater
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, United States
| | - Natalie Cooper
- Science Group, Natural History Museum London, London, United Kingdom
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2
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Barido-Sottani J, Schwery O, Warnock RCM, Zhang C, Wright AM. Practical guidelines for Bayesian phylogenetic inference using Markov Chain Monte Carlo (MCMC). OPEN RESEARCH EUROPE 2024; 3:204. [PMID: 38481771 PMCID: PMC10933576 DOI: 10.12688/openreseurope.16679.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 06/10/2024] [Indexed: 06/06/2024]
Abstract
Phylogenetic estimation is, and has always been, a complex endeavor. Estimating a phylogenetic tree involves evaluating many possible solutions and possible evolutionary histories that could explain a set of observed data, typically by using a model of evolution. Modern statistical methods involve not just the estimation of a tree, but also solutions to more complex models involving fossil record information and other data sources. Markov Chain Monte Carlo (MCMC) is a leading method for approximating the posterior distribution of parameters in a mathematical model. It is deployed in all Bayesian phylogenetic tree estimation software. While many researchers use MCMC in phylogenetic analyses, interpreting results and diagnosing problems with MCMC remain vexing issues to many biologists. In this manuscript, we will offer an overview of how MCMC is used in Bayesian phylogenetic inference, with a particular emphasis on complex hierarchical models, such as the fossilized birth-death (FBD) model. We will discuss strategies to diagnose common MCMC problems and troubleshoot difficult analyses, in particular convergence issues. We will show how the study design, the choice of models and priors, but also technical features of the inference tools themselves can all be adjusted to obtain the best results. Finally, we will also discuss the unique challenges created by the incorporation of fossil information in phylogenetic inference, and present tips to address them.
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Affiliation(s)
- Joëlle Barido-Sottani
- Institut de Biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, Île-de-France, 75005, France
| | - Orlando Schwery
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, Louisiana, 70402, USA
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, 24061, USA
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA
| | - Rachel C. M. Warnock
- GeoZentrum Nordbayern, Department of Geography and Geosciences, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Bavaria, 91054, Germany
| | - Chi Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - April Marie Wright
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, Louisiana, 70402, USA
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3
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Flannery-Sutherland JT, Crossan CD, Myers CE, Hendy AJW, Landman NH, Witts JD. Late Cretaceous ammonoids show that drivers of diversification are regionally heterogeneous. Nat Commun 2024; 15:5382. [PMID: 38937471 PMCID: PMC11211348 DOI: 10.1038/s41467-024-49462-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 06/05/2024] [Indexed: 06/29/2024] Open
Abstract
Palaeontologists have long sought to explain the diversification of individual clades to whole biotas at global scales. Advances in our understanding of the spatial distribution of the fossil record through geological time, however, has demonstrated that global trends in biodiversity were a mosaic of regionally heterogeneous diversification processes. Drivers of diversification must presumably have also displayed regional variation to produce the spatial disparities observed in past taxonomic richness. Here, we analyse the fossil record of ammonoids, pelagic shelled cephalopods, through the Late Cretaceous, characterised by some palaeontologists as an interval of biotic decline prior to their total extinction at the Cretaceous-Paleogene boundary. We regionally subdivide this record to eliminate the impacts of spatial sampling biases and infer regional origination and extinction rates corrected for temporal sampling biases using Bayesian methods. We then model these rates using biotic and abiotic drivers commonly inferred to influence diversification. Ammonoid diversification dynamics and responses to this common set of diversity drivers were regionally heterogeneous, do not support ecological decline, and demonstrate that their global diversification signal is influenced by spatial disparities in sampling effort. These results call into question the feasibility of seeking drivers of diversity at global scales in the fossil record.
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Affiliation(s)
- Joseph T Flannery-Sutherland
- School of Geography, Earth and Environmental Science, University of Birmingham, Birmingham, UK.
- Palaeobiology Research Group, School of Earth Sciences, University of Bristol, Bristol, UK.
| | - Cameron D Crossan
- Palaeobiology Research Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | - Corinne E Myers
- Department of Earth and Planetary Sciences, University of New Mexico, Albuquerque, NM, USA
| | - Austin J W Hendy
- Natural History Museum of Los Angeles County, Los Angeles, CA, USA
| | - Neil H Landman
- Division of Paleontology (Invertebrates), American Museum of Natural History, New York, NY, USA
| | - James D Witts
- Palaeobiology Research Group, School of Earth Sciences, University of Bristol, Bristol, UK
- Department of Earth Sciences, Natural History Museum, London, UK
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4
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Didier G, Laurin M. Testing extinction events and temporal shifts in diversification and fossilization rates through the skyline Fossilized Birth-Death (FBD) model: The example of some mid-Permian synapsid extinctions. Cladistics 2024; 40:282-306. [PMID: 38651531 DOI: 10.1111/cla.12577] [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: 12/31/2023] [Revised: 02/23/2024] [Accepted: 03/07/2024] [Indexed: 04/25/2024] Open
Abstract
In the last decade, the Fossilized Birth-Death (FBD) process has yielded interesting clues about the evolution of biodiversity through time. To facilitate such studies, we extend our method to compute the probability density of phylogenetic trees of extant and extinct taxa in which the only temporal information is provided by the fossil ages (i.e. without the divergence times) in order to deal with the piecewise constant FBD process, known as the "skyline FBD", which allows rates to change between pre-defined time intervals, as well as modelling extinction events at the bounds of these intervals. We develop approaches based on this method to assess hypotheses about the diversification process and to answer questions such as "Does a mass extinction occur at this time?" or "Is there a change in the fossilization rate between two given periods?". Our software can also yield Bayesian and maximum-likelihood estimates of the parameters of the skyline FBD model under various constraints. These approaches are applied to a simulated dataset in order to test their ability to answer the questions above. Finally, we study an updated dataset of Permo-Carboniferous synapsids to get additional insights into the dynamics of biodiversity change in three clades (Ophiacodontidae, Edaphosauridae and Sphenacodontidae) in the Pennsylvanian (Late Carboniferous) and Cisuralian (Early Permian), and to assess support for end-Sakmarian (or Artinskian) and end-Cisuralian mass extinction events discussed in previous studies.
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Affiliation(s)
| | - Michel Laurin
- CR2P ("Centre de Recherches sur la Paléobiodiversité et les Paléoenvironnements"; UMR 7207), CNRS/MNHN/UPMC, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France
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5
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Zhao W, Gao J, Hall D, Andersson BA, Bruxaux J, Tomlinson KW, Drouzas AD, Suyama Y, Wang XR. Evolutionary radiation of the Eurasian Pinus species under pervasive gene flow. THE NEW PHYTOLOGIST 2024. [PMID: 38515228 DOI: 10.1111/nph.19694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 03/04/2024] [Indexed: 03/23/2024]
Abstract
Evolutionary radiation, a pivotal aspect of macroevolution, offers valuable insights into evolutionary processes. The genus Pinus is the largest genus in conifers withc . $$ c. $$ 90% of the extant species emerged in the Miocene, which signifies a case of rapid diversification. Despite this remarkable history, our understanding of the mechanisms driving radiation within this expansive genus has remained limited. Using exome capture sequencing and a fossil-calibrated phylogeny, we investigated the divergence history, niche diversification, and introgression among 13 closely related Eurasian species spanning climate zones from the tropics to the boreal Arctic. We detected complex introgression among lineages in subsection Pinus at all stages of the phylogeny. Despite this widespread gene exchange, each species maintained its genetic identity and showed clear niche differentiation. Demographic analysis unveiled distinct population histories among these species, which further influenced the nucleotide diversity and efficacy of purifying and positive selection in each species. Our findings suggest that radiation in the Eurasian pines was likely fueled by interspecific recombination and further reinforced by their adaptation to distinct environments. Our study highlights the constraints and opportunities for evolutionary change, and the expectations of future adaptation in response to environmental changes in different lineages.
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Affiliation(s)
- Wei Zhao
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, SE-90187, Sweden
| | - Jie Gao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
| | - David Hall
- Forestry Research Institute of Sweden (Skogforsk), Sävar, SE-91833, Sweden
| | - Bea Angelica Andersson
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, SE-90187, Sweden
| | - Jade Bruxaux
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, SE-90187, Sweden
| | - Kyle W Tomlinson
- Center for Integrative Conservation & Yunnan Key Laboratory for Conservation of Tropical Rainforests and Asian Elephant, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
| | - Andreas D Drouzas
- Laboratory of Systematic Botany and Phytogeography, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Yoshihisa Suyama
- Graduate School of Agricultural Science, Tohoku University, Miyagi, 989-6711, Japan
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, SE-90187, Sweden
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
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6
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Brocklehurst N, Field DJ. Tip dating and Bayes factors provide insight into the divergences of crown bird clades across the end-Cretaceous mass extinction. Proc Biol Sci 2024; 291:20232618. [PMID: 38351798 PMCID: PMC10865003 DOI: 10.1098/rspb.2023.2618] [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: 11/20/2023] [Accepted: 01/05/2024] [Indexed: 02/16/2024] Open
Abstract
The origin of crown birds (Neornithes) remains contentious owing to conflicting divergence time hypotheses obtained from alternative sources of data. The fossil record suggests limited diversification of Neornithes in the Late Mesozoic and a substantial radiation in the aftermath of the Cretaceous-Palaeogene (K-Pg) mass extinction, approximately 66 Ma. Molecular clock studies, however, have yielded estimates for neornithine origins ranging from the Early Cretaceous (130 Ma) to less than 10 Myr before the K-Pg. We use Bayes factors to compare the fit of node ages from different molecular clock studies to an independent morphological dataset. Our results allow us to reject scenarios of crown bird origins deep in the Early Cretaceous, as well as an origin of crown birds within the last 10 Myr of the Cretaceous. The scenario best supported by our analyses is one where Neornithes originated between the Early and Late Cretaceous (ca 100 Ma), while numerous divergences within major neoavian clades either span or postdate the K-Pg. This study affirms the importance of the K-Pg on the diversification of modern birds, and the potential of combined-evidence tip-dating analyses to illuminate recalcitrant 'rocks versus clocks' debates.
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Affiliation(s)
- Neil Brocklehurst
- Department of Earth Sciences, University of Cambridge, Cambridge, UK
| | - Daniel J. Field
- Department of Earth Sciences, University of Cambridge, Cambridge, UK
- Museum of Zoology, University of Cambridge, Cambridge, UK
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7
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Bobe R, Aldeias V, Alemseged Z, Anemone RL, Archer W, Aumaître G, Bamford MK, Biro D, Bourlès DL, Doyle Boyd M, Braun DR, Capelli C, d’Oliveira Coelho J, Habermann JM, Head JJ, Keddadouche K, Kupczik K, Lebatard AE, Lüdecke T, Macôa A, Martínez FI, Mathe J, Mendes C, Paulo LM, Pinto M, Presnyakova D, Püschel TA, Regala FT, Sier M, Ferreira da Silva MJ, Stalmans M, Carvalho S. The first Miocene fossils from coastal woodlands in the southern East African Rift. iScience 2023; 26:107644. [PMID: 37701811 PMCID: PMC10494320 DOI: 10.1016/j.isci.2023.107644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 03/20/2023] [Accepted: 08/11/2023] [Indexed: 09/14/2023] Open
Abstract
The Miocene was a key time in the evolution of African ecosystems witnessing the origin of the African apes and the isolation of eastern coastal forests through an expanding arid corridor. Until recently, however, Miocene sites from the southeastern regions of the continent were unknown. Here, we report the first Miocene fossil teeth from the shoulders of the Urema Rift in Gorongosa National Park, Mozambique. We provide the first 1) radiometric ages of the Mazamba Formation, 2) reconstructions of paleovegetation in the region based on pedogenic carbonates and fossil wood, and 3) descriptions of fossil teeth. Gorongosa is unique in the East African Rift in combining marine invertebrates, marine vertebrates, reptiles, terrestrial mammals, and fossil woods in coastal paleoenvironments. The Gorongosa fossil sites offer the first evidence of woodlands and forests on the coastal margins of southeastern Africa during the Miocene, and an exceptional assemblage of fossils including new species.
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Affiliation(s)
- René Bobe
- Gorongosa National Park, Sofala, Mozambique
- Primate Models for Behavioural Evolution Lab, Institute of Human Sciences, School of Anthropology, University of Oxford, Oxford OX2 6PN, UK
- Interdisciplinary Center for Archaeology and Evolution of Human Behavior (ICArEHB), Universidade do Algarve, 8005-139 Faro, Portugal
| | - Vera Aldeias
- Interdisciplinary Center for Archaeology and Evolution of Human Behavior (ICArEHB), Universidade do Algarve, 8005-139 Faro, Portugal
| | - Zeresenay Alemseged
- Department of Organismal Biology & Anatomy, University of Chicago, Chicago, IL 60637, USA
| | - Robert L. Anemone
- University of North Carolina at Greensboro, Department of Anthropology, Greensboro, NC 27402-6170, USA
| | - Will Archer
- Max Planck Partner Group, Department of Archaeology and Anthropology, National Museum, Bloemfontein, South Africa
- Department of Geology, University of the Free State, Bloemfontein, South Africa
| | | | - Marion K. Bamford
- Evolutionary Studies Institute and School of Geosciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Dora Biro
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK
| | | | - Melissa Doyle Boyd
- Department of Earth and Planetary Sciences, Rutgers University, Piscataway, NJ 08854, USA
| | - David R. Braun
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, George Washington University, Washington, DC 20052, USA
- Technological Primate Research Group, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Cristian Capelli
- Dipartimento delle Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, 43124 Parma, Italy
| | - João d’Oliveira Coelho
- Primate Models for Behavioural Evolution Lab, Institute of Human Sciences, School of Anthropology, University of Oxford, Oxford OX2 6PN, UK
- Centre for Functional Ecology, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Jörg M. Habermann
- GeoZentrum Nordbayern, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Jason J. Head
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | | | - Kornelius Kupczik
- Departamento de Antropología, Facultad de Ciencias Sociales, Universidad de Chile, Santiago, Chile
| | - Anne-Elisabeth Lebatard
- Centre Européen de Recherche et d'Enseignement de Géosciences de l'Environnement, CEREGE - UM 34 Aix-Marseille Université, CNRS, IRD, Collège de France, INRAE, OSU Institut Pythéas, Technopole Environnement Arbois - Méditerranée, Domaine du Petit Arbois, Avenue Louis Philibert, Les Milles-Aix en Provence BP80, 13545 AIX en Provence, Cedex 04, France
| | - Tina Lüdecke
- Primate Models for Behavioural Evolution Lab, Institute of Human Sciences, School of Anthropology, University of Oxford, Oxford OX2 6PN, UK
- Emmy Noether Group for Hominin Meat Consumption, Max Planck Institute for Chemistry, 55128 Mainz, Germany
- Senckenberg Biodiversity and Climate Research Centre, 60325 Frankfurt, Germany
| | - Amélia Macôa
- Departamento de Arqueologia e Antropologia, Faculdade de Letras e Ciências Sociais, Universidade Eduardo Mondlane, Maputo, Mozambique
| | - Felipe I. Martínez
- Escuela de Antropología, Facultad de Ciencias Sociales, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jacinto Mathe
- Primate Models for Behavioural Evolution Lab, Institute of Human Sciences, School of Anthropology, University of Oxford, Oxford OX2 6PN, UK
| | - Clara Mendes
- Departamento de Arqueologia e Antropologia, Faculdade de Letras e Ciências Sociais, Universidade Eduardo Mondlane, Maputo, Mozambique
| | - Luis Meira Paulo
- AESDA – Associação de Estudos Subterrâneos e Defesa do Ambiente, Torres Vedras, Portugal
| | - Maria Pinto
- AESDA – Associação de Estudos Subterrâneos e Defesa do Ambiente, Torres Vedras, Portugal
| | - Darya Presnyakova
- CNRS Aix-Marseille Université, Marseille, France
- Department of Early Prehistory and Quaternary Ecology, University of Tübingen, 72074 Tübingen, Germany
| | - Thomas A. Püschel
- Primate Models for Behavioural Evolution Lab, Institute of Human Sciences, School of Anthropology, University of Oxford, Oxford OX2 6PN, UK
- Ecology and Evolutionary Biology Division, School of Biological Sciences, University of Reading, Reading RG6 6LA, UK
| | - Frederico Tátá Regala
- Interdisciplinary Center for Archaeology and Evolution of Human Behavior (ICArEHB), Universidade do Algarve, 8005-139 Faro, Portugal
| | - Mark Sier
- CENIEH, 09002 Burgos, Spain
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht 3584 CS, the Netherlands
| | - Maria Joana Ferreira da Silva
- CIBIO, Centro de Investigação Em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
- ONE - Organisms and Environment Group, Cardiff University, School of Biosciences, Sir Martin Evans Building, c5:15, Cardiff CF10 3AX, UK
| | | | - Susana Carvalho
- Gorongosa National Park, Sofala, Mozambique
- Primate Models for Behavioural Evolution Lab, Institute of Human Sciences, School of Anthropology, University of Oxford, Oxford OX2 6PN, UK
- Interdisciplinary Center for Archaeology and Evolution of Human Behavior (ICArEHB), Universidade do Algarve, 8005-139 Faro, Portugal
- Centre for Functional Ecology, University of Coimbra, 3000-456 Coimbra, Portugal
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8
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Barido-Sottani J, Żyła D, Heath TA. Estimating the Age of Poorly Dated Fossil Specimens and Deposits Using a Total-Evidence Approach and the Fossilized Birth-Death Process. Syst Biol 2023; 72:466-475. [PMID: 36382797 PMCID: PMC10275547 DOI: 10.1093/sysbio/syac073] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/04/2022] [Indexed: 02/02/2024] Open
Abstract
Bayesian total-evidence approaches under the fossilized birth-death model enable biologists to combine fossil and extant data while accounting for uncertainty in the ages of fossil specimens, in an integrative phylogenetic analysis. Fossil age uncertainty is a key feature of the fossil record as many empirical data sets may contain a mix of precisely dated and poorly dated fossil specimens or deposits. In this study, we explore whether reliable age estimates for fossil specimens can be obtained from Bayesian total-evidence phylogenetic analyses under the fossilized birth-death model. Through simulations based on the example of the Baltic amber deposit, we show that estimates of fossil ages obtained through such an analysis are accurate, particularly when the proportion of poorly dated specimens remains low and the majority of fossil specimens have precise dates. We confirm our results using an empirical data set of living and fossil penguins by artificially increasing the age uncertainty around some fossil specimens and showing that the resulting age estimates overlap with the recorded age ranges. Our results are applicable to many empirical data sets where classical methods of establishing fossil ages have failed, such as the Baltic amber and the Gobi Desert deposits. [Bayesian phylogenetic inference; fossil age estimates; fossilized birth-death; Lagerstätte; total-evidence.].
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Affiliation(s)
- Joëlle Barido-Sottani
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, 2200 Osborne Drive, Ames, IA 50011, USA
- Institut de Biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, 46 rue d’Ulm, 75005 Paris, France
| | - Dagmara Żyła
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, 2200 Osborne Drive, Ames, IA 50011, USA
- Department of Invertebrate Zoology and Parasitology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
- Museum of Nature Hamburg, Leibniz Institute for the Analysis of Biodiversity Change, Martin-Luther-King Platz 3, 20146 Hamburg, Germany
| | - Tracy A Heath
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, 2200 Osborne Drive, Ames, IA 50011, USA
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9
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Dalmasso A, Peláez-Campomanes P, López-Antoñanzas R. Relative performance of Bayesian morphological clock and parsimony methods for phylogenetic reconstructions: Insights from the case of Myomiminae and Dryomyinae glirid rodents. Cladistics 2022; 38:702-710. [PMID: 36043995 DOI: 10.1111/cla.12516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/19/2022] [Accepted: 08/02/2022] [Indexed: 01/31/2023] Open
Abstract
Extinct organisms provide crucial information about the origin and time of origination of extant groups. The importance of morphological phylogenetics for rigorously dating the tree of life is now widely recognized and has been revitalized by methodological developments such as the application of tip-dating Bayesian approaches. Traditionally, molecular clocks have been node calibrated. However, node calibrations are often unsatisfactory because they do not allow the fossil age to inform about phylogenetic hypothesis. The introduction of tip calibrations allow fossil species to be included alongside their living relatives, and the absence of molecular sequence data for these taxa to be remedied by supplementing the sequence alignments for living taxa with phenotype character matrices for both living and fossil taxa. Therefore, only phylogenetic analyses that take into account morphological characters can incorporate both fossil and extant species. Herein we present an unprecedented morphological dataset for a vast group of glirid rodents, to which different phylogenetic methodologies have been applied. We have compared the tree topologies resulting from traditional parsimony and Bayesian phylogenetic approaches and calculate stratigraphic congruence indices for each. Bayesian tip-dated clock methods seem to outperform parsimony with our dataset. The strict consensus tree recovered by tip dating invalidates the classic classification and allows dates to be proposed for the divergence and origin of the different clades.
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Affiliation(s)
- Andrea Dalmasso
- Laboratoire de Paléontologie, Institut des Sciences de l'Évolution (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE), Université de Montpellier, Montpellier, France
| | | | - Raquel López-Antoñanzas
- Laboratoire de Paléontologie, Institut des Sciences de l'Évolution (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE), Université de Montpellier, Montpellier, France.,Departamento de Paleobiología, Museo Nacional de Ciencias Naturales-CSIC, Madrid, Spain
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10
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Beaulieu JM, O'Meara BC. Fossils Do Not Substantially Improve, and May Even Harm, Estimates of Diversification Rate Heterogeneity. Syst Biol 2022; 72:50-61. [PMID: 35861420 DOI: 10.1093/sysbio/syac049] [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: 11/19/2021] [Revised: 07/04/2022] [Accepted: 07/06/2022] [Indexed: 11/14/2022] Open
Abstract
The fossilized birth-death (FBD) model is a naturally appealing way of directly incorporating fossil information when estimating diversification rates. However, an important yet often overlooked property of the original FBD derivation is that it distinguishes between two types of sampled lineages. Here we first discuss and demonstrate the impact of severely undersampling, and even not including fossils that represent samples of lineages that also had sampled descendants. We then explore the benefits of including fossils, generally, by implementing and then testing two-types of FBD models, including one that converts a fossil set into stratigraphic ranges, in more complex likelihood-based models that assume multiple rate classes across the tree. Under various simulation scenarios, including a scenario that exists far outside the set of models we evaluated, including fossils rarely outperforms analyses that exclude them altogether. At best, the inclusion of fossils improves precision but does not influence bias. Similarly, we found that converting the fossil set to stratigraphic ranges, which is one way to remedy the effects of undercounting the number of k-type fossils, results in turnover rates and extinction fraction estimates that are generally underestimated. While fossils remain essential for understanding diversification through time, in the specific case of understanding diversification given an existing, largely modern tree, they are not especially beneficial.
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Affiliation(s)
- Jeremy M Beaulieu
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701 USA
| | - Brian C O'Meara
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, 37996-1610 USA
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11
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Abstract
Phylogenetic models have long assumed that lineages diverge independently. Processes of diversification that are of interest in biogeography, epidemiology, and genome evolution violate this assumption by affecting multiple evolutionary lineages. To relax the assumption of independent divergences and infer patterns of divergences predicted by such processes, we introduce a way of conceptualizing, modeling, and inferring phylogenetic trees. We apply the approach to genomic data from geckos distributed across the Philippines and find support for patterns of shared divergences predicted by repeated fragmentation of the archipelago by interglacial rises in sea level. Many processes of biological diversification can simultaneously affect multiple evolutionary lineages. Examples include multiple members of a gene family diverging when a region of a chromosome is duplicated, multiple viral strains diverging at a “super-spreading” event, and a geological event fragmenting whole communities of species. It is difficult to test for patterns of shared divergences predicted by such processes because all phylogenetic methods assume that lineages diverge independently. We introduce a Bayesian phylogenetic approach to relax the assumption of independent, bifurcating divergences by expanding the space of topologies to include trees with shared and multifurcating divergences. This allows us to jointly infer phylogenetic relationships, divergence times, and patterns of divergences predicted by processes of diversification that affect multiple evolutionary lineages simultaneously or lead to more than two descendant lineages. Using simulations, we find that the method accurately infers shared and multifurcating divergence events when they occur and performs as well as current phylogenetic methods when divergences are independent and bifurcating. We apply our approach to genomic data from two genera of geckos from across the Philippines to test if past changes to the islands’ landscape caused bursts of speciation. Unlike previous analyses restricted to only pairs of gecko populations, we find evidence for patterns of shared divergences. By generalizing the space of phylogenetic trees in a way that is independent from the likelihood model, our approach opens many avenues for future research into processes of diversification across the life sciences.
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12
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Sakamoto M. Estimating bite force in extinct dinosaurs using phylogenetically predicted physiological cross-sectional areas of jaw adductor muscles. PeerJ 2022; 10:e13731. [PMID: 35846881 PMCID: PMC9285543 DOI: 10.7717/peerj.13731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/23/2022] [Indexed: 01/17/2023] Open
Abstract
I present a Bayesian phylogenetic predictive modelling (PPM) framework that allows the prediction of muscle parameters (physiological cross-sectional area, A Phys) in extinct archosaurs from skull width (W Sk) and phylogeny. This approach is robust to phylogenetic uncertainty and highly versatile given its ability to base predictions on simple, readily available predictor variables. The PPM presented here has high prediction accuracy (up to 95%), with downstream biomechanical modelling yielding bite force estimates that are in line with previous estimates based on muscle parameters from reconstructed muscles. This approach does not replace muscle reconstructions but one that provides a powerful means to predict A Phys from skull geometry and phylogeny to the same level of accuracy as that measured from reconstructed muscles in species for which soft tissue data are unavailable or difficult to obtain.
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13
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Jamson KM, Moon BC, Fraass AJ. Diversity dynamics of microfossils from the Cretaceous to the Neogene show mixed responses to events. PALAEONTOLOGY 2022; 65:e12615. [PMID: 36248238 PMCID: PMC9540813 DOI: 10.1111/pala.12615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 10/29/2021] [Accepted: 03/14/2022] [Indexed: 06/16/2023]
Abstract
Microfossils have a ubiquitous and well-studied fossil record with temporally and spatially fluctuating diversity, but how this arises and how major events affect speciation and extinction is uncertain. We present one of the first applications of PyRate to a micropalaeontological global occurrence dataset, reconstructing diversification rates within a Bayesian framework from the Mesozoic to the Neogene in four microfossil groups: planktic foraminiferans, calcareous nannofossils, radiolarians and diatoms. Calcareous and siliceous groups demonstrate opposed but inconsistent responses in diversification. Radiolarian origination increases from c. 104 Ma, maintaining high rates into the Cenozoic. Calcareous microfossil diversification rates significantly declines across the Cretaceous-Palaeogene boundary, while rates in siliceous microfossil groups remain stable until the Paleocene-Eocene transition. Diversification rates in the Cenozoic are largely stable in calcareous groups, whereas the Palaeogene is a turbulent time for diatoms. Diversification fluctuations are driven by climate change and fluctuations in sea surface temperatures, leading to different responses in the groups generating calcareous or siliceous microfossils. Extinctions are apparently induced by changes in anoxia, acidification and stratification; speciation tends to be associated with upwelling, productivity and ocean circulation. These results invite further micropalaeontological quantitative analysis and study of the effects of major transitions in the fossil record. Despite extensive occurrence data, regional diversification events were not recovered; neither were some global events. These unexpected results show the need to consider multiple spatiotemporal levels of diversity and diversification analyses and imply that occurrence datasets of different clades may be more appropriate for testing some hypotheses than others.
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Affiliation(s)
- Katie M. Jamson
- Palaeobiology Research GroupSchool of Earth SciencesUniversity of BristolWills Memorial Building, Queens RoadBristolBS8 1RJUK
- Present address:
School of Earth & Ocean SciencesUniversity of VictoriaBob Wright Centre A405VictoriaBCV8W 2Y2Canada
| | - Benjamin C. Moon
- Palaeobiology Research GroupSchool of Earth SciencesUniversity of BristolWills Memorial Building, Queens RoadBristolBS8 1RJUK
| | - Andrew J. Fraass
- Palaeobiology Research GroupSchool of Earth SciencesUniversity of BristolWills Memorial Building, Queens RoadBristolBS8 1RJUK
- The Academy of Natural Sciences of Drexel University1900 Benjamin Franklin ParkwayPhiladelphiaPA19103USA
- Present address:
School of Earth & Ocean SciencesUniversity of VictoriaBob Wright Centre A405VictoriaBCV8W 2Y2Canada
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14
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Andréoletti J, Zwaans A, Warnock RCM, Aguirre-Fernández G, Barido-Sottani J, Gupta A, Stadler T, Manceau M. The Occurrence Birth-Death Process for combined-evidence analysis in macroevolution and epidemiology. Syst Biol 2022; 71:1440-1452. [PMID: 35608305 PMCID: PMC9558841 DOI: 10.1093/sysbio/syac037] [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: 11/26/2021] [Revised: 05/02/2022] [Accepted: 05/06/2022] [Indexed: 11/28/2022] Open
Abstract
Phylodynamic models generally aim at jointly inferring phylogenetic relationships, model parameters, and more recently, the number of lineages through time, based on molecular sequence data. In the fields of epidemiology and macroevolution, these models can be used to estimate, respectively, the past number of infected individuals (prevalence) or the past number of species (paleodiversity) through time. Recent years have seen the development of “total-evidence” analyses, which combine molecular and morphological data from extant and past sampled individuals in a unified Bayesian inference framework. Even sampled individuals characterized only by their sampling time, that is, lacking morphological and molecular data, which we call occurrences, provide invaluable information to estimate the past number of lineages. Here, we present new methodological developments around the fossilized birth–death process enabling us to (i) incorporate occurrence data in the likelihood function; (ii) consider piecewise-constant birth, death, and sampling rates; and (iii) estimate the past number of lineages, with or without knowledge of the underlying tree. We implement our method in the RevBayes software environment, enabling its use along with a large set of models of molecular and morphological evolution, and validate the inference workflow using simulations under a wide range of conditions. We finally illustrate our new implementation using two empirical data sets stemming from the fields of epidemiology and macroevolution. In epidemiology, we infer the prevalence of the coronavirus disease 2019 outbreak on the Diamond Princess ship, by taking into account jointly the case count record (occurrences) along with viral sequences for a fraction of infected individuals. In macroevolution, we infer the diversity trajectory of cetaceans using molecular and morphological data from extant taxa, morphological data from fossils, as well as numerous fossil occurrences. The joint modeling of occurrences and trees holds the promise to further bridge the gap between traditional epidemiology and pathogen genomics, as well as paleontology and molecular phylogenetics. [Birth–death model; epidemiology; fossils; macroevolution; occurrences; phylogenetics; skyline.]
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Affiliation(s)
- Jérémy Andréoletti
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Antoine Zwaans
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Rachel C M Warnock
- GeoZentrum Nordbayern,Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | | | - Joëlle Barido-Sottani
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, USA
| | - Ankit Gupta
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Marc Manceau
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
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15
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Crouch NMA, Edie SM, Collins KS, Bieler R, Jablonski D. Calibrating phylogenies assuming bifurcation or budding alters inferred macroevolutionary dynamics in a densely sampled phylogeny of bivalve families. Proc Biol Sci 2021; 288:20212178. [PMID: 34847770 PMCID: PMC8634622 DOI: 10.1098/rspb.2021.2178] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 11/10/2021] [Indexed: 01/07/2023] Open
Abstract
Analyses of evolutionary dynamics depend on how phylogenetic data are time-scaled. Most analyses of extant taxa assume a purely bifurcating model, where nodes are calibrated using the daughter lineage with the older first occurrence in the fossil record. This contrasts with budding, where nodes are calibrated using the younger first occurrence. Here, we use the extensive fossil record of bivalve molluscs for a large-scale evaluation of how branching models affect macroevolutionary analyses. We time-calibrated 91% of nodes, ranging in age from 2.59 to 485 Ma, in a phylogeny of 97 extant bivalve families. Allowing budding-based calibrations minimizes conflict between the tree and observed fossil record, and reduces the summed duration of inferred 'ghost lineages' from 6.76 billion years (Gyr; bifurcating model) to 1.00 Gyr (budding). Adding 31 extinct paraphyletic families raises ghost lineage totals to 7.86 Gyr (bifurcating) and 1.92 Gyr (budding), but incorporates more information to date divergences between lineages. Macroevolutionary analyses under a bifurcating model conflict with other palaeontological evidence on the magnitude of the end-Palaeozoic extinction, and strongly reduce Cenozoic diversification. Consideration of different branching models is essential when node-calibrating phylogenies, and for a major clade with a robust fossil record, a budding model appears more appropriate.
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Affiliation(s)
- Nicholas M. A. Crouch
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Stewart M. Edie
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | | | - Rüdiger Bieler
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, USA
| | - David Jablonski
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL 60637, USA
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16
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Canitz J, Sikes DS, Knee W, Baumann J, Haftaro P, Steinmetz N, Nave M, Eggert AK, Hwang W, Nehring V. Cryptic diversity within the Poecilochirus carabi mite species complex phoretic on Nicrophorus burying beetles: Phylogeny, biogeography, and host specificity. Mol Ecol 2021; 31:658-674. [PMID: 34704311 DOI: 10.1111/mec.16248] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 01/09/2023]
Abstract
Coevolution is often considered a major driver of speciation, but evidence for this claim is not always found because diversity might be cryptic. When morphological divergence is low, molecular data are needed to uncover diversity. This is often the case in mites, which are known for their extensive and often cryptic diversity. We studied mites of the genus Poecilochirus that are phoretic on burying beetles (Silphidae: Nicrophorus). Poecilochirus taxonomy is poorly understood. Most studies on this genus focus on the evolutionary ecology of Poecilochirus carabi sensu lato, a complex of at least two biological species. Based on molecular data of 230 specimens from 43 locations worldwide, we identified 24 genetic clusters that may represent species. We estimate that these mites began to diversify during the Paleogene, when the clade containing P. subterraneus branched off and the remaining mites diverged into two further clades. One clade resembles P. monospinosus. The other clade contains 17 genetic clusters resembling P. carabi s.l.. Among these are P. carabi sensu stricto, P. necrophori, and potentially many additional cryptic species. Our analyses suggest that these clades were formed in the Miocene by large-scale geographic separation; co-speciation of mites with the host beetles can be largely ruled out. Diversification also seems to have happened on a smaller scale, potentially due to adaptation to specific hosts or local abiotic conditions, causing some clusters to specialize on certain beetle species. Our results suggest that biodiversity in this genus was generated by multiple interacting forces shaping the tangled webs of life.
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Affiliation(s)
- Julia Canitz
- Institute for Biology I, University of Freiburg, Freiburg, Germany.,Senckenberg German Entomological Institute, Müncheberg, Germany
| | - Derek S Sikes
- University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, Alaska, USA
| | - Wayne Knee
- Canadian National Collection of Insects, Arachnids, and Nematodes, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Julia Baumann
- Institute of Biology, University of Graz, Graz, Austria
| | - Petra Haftaro
- Institute for Biology I, University of Freiburg, Freiburg, Germany
| | - Nadine Steinmetz
- Institute for Biology I, University of Freiburg, Freiburg, Germany
| | - Martin Nave
- Institute for Biology I, University of Freiburg, Freiburg, Germany
| | - Anne-Katrin Eggert
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Wenbe Hwang
- Department of Ecology and Environmental Resources, National University of Tainan, Tainan, Taiwan
| | - Volker Nehring
- Institute for Biology I, University of Freiburg, Freiburg, Germany
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17
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Upham NS, Esselstyn JA, Jetz W. Molecules and fossils tell distinct yet complementary stories of mammal diversification. Curr Biol 2021; 31:4195-4206.e3. [PMID: 34329589 DOI: 10.1016/j.cub.2021.07.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/05/2021] [Accepted: 07/07/2021] [Indexed: 11/25/2022]
Abstract
Reconstructing the tempo at which biodiversity arose is a fundamental goal of evolutionary biologists, yet the relative merits of evolutionary-rate estimates are debated based on whether they are derived from the fossil record or time-calibrated phylogenies (timetrees) of living species. Extinct lineages unsampled in timetrees are known to "pull" speciation rates downward, but the temporal scale at which this bias matters is unclear. To investigate this problem, we compare mammalian diversification-rate signatures in a credible set of molecular timetrees (n = 5,911 species, ∼70% from DNA) to those in fossil genus durations (n = 5,320). We use fossil extinction rates to correct or "push" the timetree-based (pulled) speciation-rate estimates, finding a surge of speciation during the Paleocene (∼66-56 million years ago, Ma) between the Cretaceous-Paleogene (K-Pg) boundary and the Paleocene-Eocene Thermal Maximum (PETM). However, about two-thirds of the K-Pg-to-PETM originating taxa did not leave modern descendants, indicating that this rate signature is likely undetectable from extant lineages alone. For groups without substantial fossil records, thankfully all is not lost. Pushed and pulled speciation rates converge starting ∼10 Ma and are equal at the present day when recent evolutionary processes can be estimated without bias using species-specific "tip" rates of speciation. Clade-wide moments of tip rates also enable enriched inference, as the skewness of tip rates is shown to approximate a clade's extent of past diversification-rate shifts. Molecular timetrees need fossil-correction to address deep-time questions, but they are sufficient for shallower time questions where extinctions are fewer.
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Affiliation(s)
- Nathan S Upham
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06511, USA; Center for Biodiversity and Global Change, Yale University, New Haven, CT 06511, USA; School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Jacob A Esselstyn
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Walter Jetz
- Department of Ecology & 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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18
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Ogilvie HA, Mendes FK, Vaughan TG, Matzke NJ, Stadler T, Welch D, Drummond AJ. Novel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales. Syst Biol 2021; 71:208-220. [PMID: 34228807 PMCID: PMC8677526 DOI: 10.1093/sysbio/syab054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/23/2021] [Accepted: 06/29/2021] [Indexed: 11/13/2022] Open
Abstract
Evolutionary models account for either population- or species-level processes but usually not both. We introduce a new model, the FBD-MSC, which makes it possible for the first time to integrate both the genealogical and fossilization phenomena, by means of the multispecies coalescent (MSC) and the fossilized birth–death (FBD) processes. Using this model, we reconstruct the phylogeny representing all extant and many fossil Caninae, recovering both the relative and absolute time of speciation events. We quantify known inaccuracy issues with divergence time estimates using the popular strategy of concatenating molecular alignments and show that the FBD-MSC solves them. Our new integrative method and empirical results advance the paradigm and practice of probabilistic total evidence analyses in evolutionary biology.[Caninae; fossilized birth–death; molecular clock; multispecies coalescent; phylogenetics; species trees.]
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Affiliation(s)
- Huw A Ogilvie
- Department of Computer Science, Rice University, Houston TX, 77005, USA
| | - Fábio K Mendes
- Centre for Computational Evolution, The University of Auckland, Auckland, 1010, New Zealand.,School of Biological Sciences, The University of Auckland, Auckland, 1010, New Zealand
| | - Timothy G Vaughan
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, 4058, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - Nicholas J Matzke
- Centre for Computational Evolution, The University of Auckland, Auckland, 1010, New Zealand.,School of Biological Sciences, The University of Auckland, Auckland, 1010, New Zealand
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, 4058, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - David Welch
- Centre for Computational Evolution, The University of Auckland, Auckland, 1010, New Zealand.,School of Computer Science, The University of Auckland, Auckland, 1010, New Zealand
| | - Alexei J Drummond
- Centre for Computational Evolution, The University of Auckland, Auckland, 1010, New Zealand.,School of Computer Science, The University of Auckland, Auckland, 1010, New Zealand.,School of Biological Sciences, The University of Auckland, Auckland, 1010, New Zealand
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19
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Irish JD, Grabowski M. Relative tooth size, Bayesian inference, and Homo naledi. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 176:262-282. [PMID: 34190335 DOI: 10.1002/ajpa.24353] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 05/04/2021] [Accepted: 06/08/2021] [Indexed: 01/29/2023]
Abstract
OBJECTIVES Size-corrected tooth crown measurements were used to estimate phenetic affinities among Homo naledi (~335-236 ka) and 11 other Plio-Pleistocene and recent species. To assess further their efficacy, and identify dental evolutionary trends, the data were then quantitatively coded for phylogenetic analyses. Results from both methods contribute additional characterization of H. naledi relative to other hominins. MATERIALS AND METHODS After division by their geometric mean, scaled mesiodistal and buccolingual dimensions were used in tooth size apportionment analysis to compare H. naledi with Australopithecus africanus, A. afarensis, Paranthropus robustus, P. boisei, H. habilis, H. ergaster, H. erectus, H. heidelbergensis, H. neanderthalensis, H. sapiens, and Pan troglodytes. These data produce equivalently scaled samples unaffected by interspecific size differences. The data were then gap-weighted for Bayesian inference. RESULTS Congruence in interspecific relationships is evident between methods, and with many inferred from earlier systematic studies. However, the present results place H. naledi as a sister taxon to H. habilis, based on a symplesiomorphic pattern of relative tooth size. In the preferred Bayesian phylogram, H. naledi is nested within a clade comprising all Homo species, but it shares some characteristics with australopiths and, particularly, early Homo. DISCUSSION Phylogenetic analyses of relative tooth size yield information about evolutionary dental trends not previously reported in H. naledi and the other hominins. Moreover, with an appropriate model these data recovered plausible evolutionary relationships. Together, the findings support recent study suggesting H. naledi originated long before the geological date of the Dinaledi Chamber, from which the specimens under study were recovered.
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Affiliation(s)
- Joel D Irish
- Research Centre in Evolutionary Anthropology and Palaeoecology, School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK.,The Centre for the Exploration of the Deep Human Journey, University of the Witwatersrand, Johannesburg, South Africa
| | - Mark Grabowski
- Research Centre in Evolutionary Anthropology and Palaeoecology, School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK.,Centre for Ecology and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
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20
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Silvestro D, Bacon CD, Ding W, Zhang Q, Donoghue PCJ, Antonelli A, Xing Y. Fossil data support a pre-Cretaceous origin of flowering plants. Nat Ecol Evol 2021; 5:449-457. [PMID: 33510432 DOI: 10.1038/s41559-020-01387-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 12/17/2020] [Indexed: 01/30/2023]
Abstract
Flowering plants (angiosperms) are the most diverse of all land plants, becoming abundant in the Cretaceous and achieving dominance in the Cenozoic. However, the exact timing of their origin remains a controversial topic, with molecular clocks generally placing their origin much further back in time than the oldest unequivocal fossils. To resolve this discrepancy, we developed a Bayesian method to estimate the ages of angiosperm families on the basis of the fossil record (a newly compiled dataset of ~15,000 occurrences in 198 families) and their living diversity. Our results indicate that several families originated in the Jurassic, strongly rejecting a Cretaceous origin for the group. We report a marked increase in lineage accumulation from 125 to 72 million years ago, supporting Darwin's hypothesis of a rapid Cretaceous angiosperm diversification. Our results demonstrate that a pre-Cretaceous origin of angiosperms is supported not only by molecular clock approaches but also by analyses of the fossil record that explicitly correct for incomplete sampling.
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Affiliation(s)
- Daniele Silvestro
- Department of Biology, University of Fribourg, Fribourg, Switzerland.
- Swiss Institute of Bioinformatics, Fribourg, Switzerland.
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden.
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Wenna Ding
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Qiuyue Zhang
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | | | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Yaowu Xing
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
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21
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Parins-Fukuchi C. Morphological and phylogeographic evidence for budding speciation: an example in hominins. Biol Lett 2021; 17:20200754. [PMID: 33465331 PMCID: PMC7876604 DOI: 10.1098/rsbl.2020.0754] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/21/2020] [Indexed: 02/03/2023] Open
Abstract
Parametric phylogenetic approaches that attempt to delineate between distinct 'modes' of speciation (splitting cladogenesis, budding cladogenesis and anagenesis) between fossil taxa have become increasingly popular among comparative biologists. But it is not yet well understood how clearly morphological data from fossil taxa speak to detailed questions of speciation mode when compared with the lineage diversification models that serve as their basis. In addition, the congruence of inferences made using these approaches with geographical patterns has not been explored. Here, I extend a previously introduced maximum-likelihood approach for the examination of ancestor-descendant relationships to accommodate budding speciation and apply it to a dataset of fossil hominins. I place these results in a phylogeographic context to better understand spatial dynamics underlying the hypothesized speciation patterns. The spatial patterns implied by the phylogeny hint at the complex demographic processes underlying the spread and diversification of hominins throughout the Pleistocene. I also find that inferences of budding are driven primarily by stratigraphic, versus morphological, data and discuss the ramifications for interpretations of speciation process in hominins specifically and from phylogenetic data in general.
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Affiliation(s)
- Caroline Parins-Fukuchi
- Division of the Physical Sciences, Department of Geophysical Sciences, University of Chicago, Chicago, IL, USA
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22
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Sanders MT, Merle D, Laurin M, Bonillo C, Puillandre N. Raising names from the dead: A time-calibrated phylogeny of frog shells (Bursidae, Tonnoidea, Gastropoda) using mitogenomic data. Mol Phylogenet Evol 2020; 156:107040. [PMID: 33310060 DOI: 10.1016/j.ympev.2020.107040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/04/2020] [Accepted: 12/08/2020] [Indexed: 12/23/2022]
Abstract
With 59 Recent species, Bursidae, known as «frog shells», are a small but widely distributed group of tropical and subtropical gastropods that are most diverse in the Indo-West Pacific. The present study is aimed at reconstructing phylogenetic relationships of bursid gastropods based on extensive and representative taxon sampling. Five genetic markers (cytochrome c oxidase subunit I (cox1), 16 s and 12 s rRNA mitochondrial genes, 28 s rRNA and Histone H3 nuclear gene) were sequenced for over 30 species in every known genus but Crossata. Furthermore, we sequenced the complete mt-genome of 9 species (10 specimens) (Aspa marginata, Marsupina bufo, Korrigania quirihorai, Korrigania fijiensis, Tutufa rubeta, Bursa lamarckii, Lampasopsis rhodostoma (twice), Bufonaria perelegans and Bursa aff. tuberosissima). Our analysis recovered Bursidae as a monophyletic group, whereas the genus Bursa was found to be polyphyletic. The genera Talisman and Dulcerana are resurrected and the genera Alanbeuella gen. nov. and Korrigania gen. nov. are described. Dating analysis using 21 extinct taxa for node and simplified tip calibrations was performed, showing a diversification of the group in two phases. Diversification may be linked to tectonic events leading to biodiversity relocation from the western Tethys toward the Indo-Pacific.
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Affiliation(s)
- Malcolm T Sanders
- Centre de Recherche en Paléontologie - Paris CR2P - UMR 7207 - CNRS, Muséum national d'Histoire naturelle, Sorbonne Université, 8 rue Buffon, CP 38, 75005 Paris, France; Institut de Systématique, Évolution, Biodiversité ISYEB - Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP26, F-75005 Paris, France.
| | - Didier Merle
- Centre de Recherche en Paléontologie - Paris CR2P - UMR 7207 - CNRS, Muséum national d'Histoire naturelle, Sorbonne Université, 8 rue Buffon, CP 38, 75005 Paris, France
| | - Michel Laurin
- Centre de Recherche en Paléontologie - Paris CR2P - UMR 7207 - CNRS, Muséum national d'Histoire naturelle, Sorbonne Université, 8 rue Buffon, CP 38, 75005 Paris, France
| | - Céline Bonillo
- Service de systématique moléculaire SSM - UMS 2700 - MNHN, CNRS, Muséum national d'Histoire naturelle, Sorbonne Université. 57 rue Cuvier, CP26, 75005 Paris, France
| | - Nicolas Puillandre
- Institut de Systématique, Évolution, Biodiversité ISYEB - Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP26, F-75005 Paris, France
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23
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Fraser D, Soul LC, Tóth AB, Balk MA, Eronen JT, Pineda-Munoz S, Shupinski AB, Villaseñor A, Barr WA, Behrensmeyer AK, Du A, Faith JT, Gotelli NJ, Graves GR, Jukar AM, Looy CV, Miller JH, Potts R, Lyons SK. Investigating Biotic Interactions in Deep Time. Trends Ecol Evol 2020; 36:61-75. [PMID: 33067015 DOI: 10.1016/j.tree.2020.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/31/2020] [Accepted: 09/02/2020] [Indexed: 11/16/2022]
Abstract
Recent renewed interest in using fossil data to understand how biotic interactions have shaped the evolution of life is challenging the widely held assumption that long-term climate changes are the primary drivers of biodiversity change. New approaches go beyond traditional richness and co-occurrence studies to explicitly model biotic interactions using data on fossil and modern biodiversity. Important developments in three primary areas of research include analysis of (i) macroevolutionary rates, (ii) the impacts of and recovery from extinction events, and (iii) how humans (Homo sapiens) affected interactions among non-human species. We present multiple lines of evidence for an important and measurable role of biotic interactions in shaping the evolution of communities and lineages on long timescales.
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Affiliation(s)
- Danielle Fraser
- Palaeobiology, Canadian Museum of Nature, Ottawa, ON, Canada; Biology and Earth Sciences, Carleton University, Ottawa, ON, Canada; Department of Paleobiology and Evolution of Terrestrial Ecosystems Program, Smithsonian Institution, National Museum of Natural History, Washington, DC , USA.
| | - Laura C Soul
- Department of Paleobiology and Evolution of Terrestrial Ecosystems Program, Smithsonian Institution, National Museum of Natural History, Washington, DC , USA
| | - Anikó B Tóth
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, NSW, Australia
| | - Meghan A Balk
- Department of Paleobiology and Evolution of Terrestrial Ecosystems Program, Smithsonian Institution, National Museum of Natural History, Washington, DC , USA; BIO5 Institute, University of Arizona, Tucson, AZ, USA
| | - Jussi T Eronen
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland; Helsinki Institute of Sustainability Science, Faculty of Biological and Environmental Sciences, Ecosystems and Environment Research Programme, University of Helsinki, Helsinki, Finland; BIOS research Unit, Helsinki, Finland
| | - Silvia Pineda-Munoz
- Department of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | | | - Amelia Villaseñor
- Department of Anthropology, University of Arkansas, Fayetteville, AR, USA
| | - W Andrew Barr
- Department of Paleobiology and Evolution of Terrestrial Ecosystems Program, Smithsonian Institution, National Museum of Natural History, Washington, DC , USA; Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC, USA
| | - Anna K Behrensmeyer
- Department of Paleobiology and Evolution of Terrestrial Ecosystems Program, Smithsonian Institution, National Museum of Natural History, Washington, DC , USA
| | - Andrew Du
- Department of Anthropology and Geography, Colorado State University, Fort Collins, CO, USA
| | - J Tyler Faith
- Natural History Museum of Utah, University of Utah, Salt Lake City, UT,USA; Department of Anthropology, University of Utah, Salt Lake City, UT, USA
| | | | - Gary R Graves
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA; Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Advait M Jukar
- Department of Paleobiology and Evolution of Terrestrial Ecosystems Program, Smithsonian Institution, National Museum of Natural History, Washington, DC , USA
| | - Cindy V Looy
- Department of Integrative Biology, Museum of Paleontology, University and Jepson Herbaria, University of California-Berkeley, Berkeley, CA , USA
| | - Joshua H Miller
- Department of Geology, University of Cincinnati, Cincinnati, OH, USA
| | - Richard Potts
- Human Origins Program, National Museum of Natural History, Smithsonian Institution, Washington, DC , USA
| | - S Kathleen Lyons
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
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24
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King B, Rücklin M. Tip dating with fossil sites and stratigraphic sequences. PeerJ 2020; 8:e9368. [PMID: 32617191 PMCID: PMC7323711 DOI: 10.7717/peerj.9368] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/26/2020] [Indexed: 11/24/2022] Open
Abstract
Tip dating, a method of phylogenetic analysis in which fossils are included as terminals and assigned an age, is becoming increasingly widely used in evolutionary studies. Current implementations of tip dating allow fossil ages to be assigned as a point estimate, or incorporate uncertainty through the use of uniform tip age priors. However, the use of tip age priors has the unwanted effect of decoupling the ages of fossils from the same fossil site. Here we introduce a new Markov Chain Monte Carlo (MCMC) proposal, which allows fossils from the same site to have linked ages, while still incorporating uncertainty in the age of the fossil site itself. We also include an extension, allowing fossil sites to be ordered in a stratigraphic column with age bounds applied only to the top and bottom of the sequence. These MCMC proposals are implemented in a new open-source BEAST2 package, palaeo. We test these new proposals on a dataset of early vertebrate fossils, concentrating on the effects on two sites with multiple acanthodian fossil taxa but wide age uncertainty, the Man On The Hill (MOTH) site from northern Canada, and the Turin Hill site from Scotland, both of Lochkovian (Early Devonian) age. The results show an increased precision of age estimates when fossils have linked tip ages compared to when ages are unlinked, and in this example leads to support for a younger age for the MOTH site compared with the Turin Hill site. There is also a minor effect on the tree topology of acanthodians. These new MCMC proposals should be widely applicable to studies that employ tip dating, particularly when the terminals are coded as individual specimens.
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25
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Barido-Sottani J, van Tiel NMA, Hopkins MJ, Wright DF, Stadler T, Warnock RCM. Ignoring Fossil Age Uncertainty Leads to Inaccurate Topology and Divergence Time Estimates in Time Calibrated Tree Inference. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00183] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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26
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Guindon S. Rates and Rocks: Strengths and Weaknesses of Molecular Dating Methods. Front Genet 2020; 11:526. [PMID: 32536940 PMCID: PMC7267027 DOI: 10.3389/fgene.2020.00526] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 04/30/2020] [Indexed: 12/19/2022] Open
Abstract
I present here an in-depth, although non-exhaustive, review of two topics in molecular dating. Clock models, which describe the evolution of the rate of evolution, are considered first. Some of the shortcomings of popular approaches-uncorrelated clock models in particular-are presented and discussed. Autocorrelated models are shown to be more reasonable from a biological perspective. Some of the most recent autocorrelated models also rely on a coherent treatment of instantaneous and average substitution rates while previous models are based on implicit approximations. Second, I provide a brief overview of the processes involved in collecting and preparing fossil data. I then review the main techniques that use this data for calibrating the molecular clock. I argue that, in its current form, the fossilized birth-death process relies on assumptions about the mechanisms underlying fossilization and the data collection process that may negatively impact the date estimates. Node-dating approaches make better use of the data available, even though they rest on paleontologists' intervention to prepare raw fossil data. Altogether, this study provides indications that may help practitioners in selecting appropriate methods for molecular dating. It will also hopefully participate in defining the contour of future methodological developments in the field.
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Affiliation(s)
- Stéphane Guindon
- Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier, CNRS and Université Montpellier (UMR 5506), Montpellier, France
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27
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Extant timetrees are consistent with a myriad of diversification histories. Nature 2020; 580:502-505. [PMID: 32322065 DOI: 10.1038/s41586-020-2176-1] [Citation(s) in RCA: 213] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 03/10/2020] [Indexed: 11/09/2022]
Abstract
Time-calibrated phylogenies of extant species (referred to here as 'extant timetrees') are widely used for estimating diversification dynamics1. However, there has been considerable debate surrounding the reliability of these inferences2-5 and, to date, this critical question remains unresolved. Here we clarify the precise information that can be extracted from extant timetrees under the generalized birth-death model, which underlies most existing methods of estimation. We prove that, for any diversification scenario, there exists an infinite number of alternative diversification scenarios that are equally likely to have generated any given extant timetree. These 'congruent' scenarios cannot possibly be distinguished using extant timetrees alone, even in the presence of infinite data. Importantly, congruent diversification scenarios can exhibit markedly different and yet similarly plausible dynamics, which suggests that many previous studies may have over-interpreted phylogenetic evidence. We introduce identifiable and easily interpretable variables that contain all available information about past diversification dynamics, and demonstrate that these can be estimated from extant timetrees. We suggest that measuring and modelling these identifiable variables offers a more robust way to study historical diversification dynamics. Our findings also make it clear that palaeontological data will continue to be crucial for answering some macroevolutionary questions.
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28
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The probability distribution of the reconstructed phylogenetic tree with occurrence data. J Theor Biol 2020; 488:110115. [DOI: 10.1016/j.jtbi.2019.110115] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 12/09/2019] [Accepted: 12/11/2019] [Indexed: 11/20/2022]
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29
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Luo A, Duchêne DA, Zhang C, Zhu CD, Ho SYW. A Simulation-Based Evaluation of Tip-Dating Under the Fossilized Birth-Death Process. Syst Biol 2020; 69:325-344. [PMID: 31132125 PMCID: PMC7175741 DOI: 10.1093/sysbio/syz038] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 05/13/2019] [Accepted: 05/17/2019] [Indexed: 11/25/2022] Open
Abstract
Bayesian molecular dating is widely used to study evolutionary timescales. This procedure usually involves phylogenetic analysis of nucleotide sequence data, with fossil-based calibrations applied as age constraints on internal nodes of the tree. An alternative approach is tip-dating, which explicitly includes fossil data in the analysis. This can be done, for example, through the joint analysis of molecular data from present-day taxa and morphological data from both extant and fossil taxa. In the context of tip-dating, an important development has been the fossilized birth-death process, which allows non-contemporaneous tips and sampled ancestors while providing a model of lineage diversification for the prior on the tree topology and internal node times. However, tip-dating with fossils faces a number of considerable challenges, especially, those associated with fossil sampling and evolutionary models for morphological characters. We conducted a simulation study to evaluate the performance of tip-dating using the fossilized birth-death model. We simulated fossil occurrences and the evolution of nucleotide sequences and morphological characters under a wide range of conditions. Our analyses of these data show that the number and the maximum age of fossil occurrences have a greater influence than the degree of among-lineage rate variation or the number of morphological characters on estimates of node times and the tree topology. Tip-dating with the fossilized birth-death model generally performs well in recovering the relationships among extant taxa but has difficulties in correctly placing fossil taxa in the tree and identifying the number of sampled ancestors. The method yields accurate estimates of the ages of the root and crown group, although the precision of these estimates varies with the probability of fossil occurrence. The exclusion of morphological characters results in a slight overestimation of node times, whereas the exclusion of nucleotide sequences has a negative impact on inference of the tree topology. Our results provide an overview of the performance of tip-dating using the fossilized birth-death model, which will inform further development of the method and its application to key questions in evolutionary biology.
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Affiliation(s)
- Arong Luo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - David A Duchêne
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Chi Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
- Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Chao-Dong Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
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30
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Budd GE, Mann RP. The dynamics of stem and crown groups. SCIENCE ADVANCES 2020; 6:eaaz1626. [PMID: 32128421 PMCID: PMC7030935 DOI: 10.1126/sciadv.aaz1626] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 12/03/2019] [Indexed: 05/22/2023]
Abstract
The fossil record of the origins of major groups such as animals and birds has generated considerable controversy, especially when it conflicts with timings based on molecular clock estimates. Here, we model the diversity of "stem" (basal) and "crown" (modern) members of groups using a "birth-death model," the results of which qualitatively match many large-scale patterns seen in the fossil record. Typically, the stem group diversifies rapidly until the crown group emerges, at which point its diversity collapses, followed shortly by its extinction. Mass extinctions can disturb this pattern and create long stem groups such as the dinosaurs. Crown groups are unlikely to emerge either cryptically or just before mass extinctions, in contradiction to popular hypotheses such as the "phylogenetic fuse". The patterns revealed provide an essential context for framing ecological and evolutionary explanations for how major groups originate, and strengthen our confidence in the reliability of the fossil record.
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Affiliation(s)
- Graham E. Budd
- Department of Earth Sciences, Palaeobiology Programme, Uppsala University, Uppsala, Sweden
- Corresponding author.
| | - Richard P. Mann
- Department of Statistics, School of Mathematics, University of Leeds, Leeds, UK
- The Alan Turing Institute, London, UK
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31
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Carruthers T, Scotland RW. Insights from Empirical Analyses and Simulations on Using Multiple Fossil Calibrations with Relaxed Clocks to Estimate Divergence Times. Mol Biol Evol 2020; 37:1508-1529. [DOI: 10.1093/molbev/msz310] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Abstract
Relaxed clock methods account for among-branch-rate-variation when estimating divergence times by inferring different rates for individual branches. In order to infer different rates for individual branches, important assumptions are required. This is because molecular sequence data do not provide direct information about rates but instead provide direct information about the total number of substitutions along any branch, which is a product of the rate and time for that branch. Often, the assumptions required for estimating rates for individual branches depend heavily on the implementation of multiple fossil calibrations in a single phylogeny. Here, we show that the basis of these assumptions is often critically undermined. First, we highlight that the temporal distribution of the fossil record often violates key assumptions of methods that use multiple fossil calibrations with relaxed clocks. With respect to “node calibration” methods, this conclusion is based on our inference that different fossil calibrations are unlikely to reflect the relative ages of different clades. With respect to the fossilized birth–death process, this conclusion is based on our inference that the fossil recovery rate is often highly heterogeneous. We then demonstrate that methods of divergence time estimation that use multiple fossil calibrations are highly sensitive to assumptions about the fossil record and among-branch-rate-variation. Given the problems associated with these assumptions, our results highlight that using multiple fossil calibrations with relaxed clocks often does little to improve the accuracy of divergence time estimates.
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Affiliation(s)
- Tom Carruthers
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Robert W Scotland
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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32
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Marshall CR. Using the Fossil Record to Evaluate Timetree Timescales. Front Genet 2019; 10:1049. [PMID: 31803226 PMCID: PMC6871265 DOI: 10.3389/fgene.2019.01049] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/30/2019] [Indexed: 12/11/2022] Open
Abstract
The fossil and geologic records provide the primary data used to established absolute timescales for timetrees. For the paleontological evaluation of proposed timetree timescales, and for node-based methods for constructing timetrees, the fossil record is used to bracket divergence times. Minimum brackets (minimum ages) can be established robustly using well-dated fossils that can be reliably assigned to lineages based on positive morphological evidence. Maximum brackets are much harder to establish, largely because it is difficult to establish definitive evidence that the absence of a taxon in the fossil record is real and not just due to the incompleteness of the fossil and rock records. Five primary methods have been developed to estimate maximum age brackets, each of which is discussed. The fact that the fossilization potential of a group typically decreases the closer one approaches its time of origin increases the challenge of estimating maximum age brackets. Additional complications arise: 1) because fossil data actually bracket the time of origin of the first relevant fossilizable morphology (apomorphy), not the divergence time itself; 2) due to the phylogenetic uncertainty in the placement of fossils; 3) because of idiosyncratic temporal and geographic gaps in the rock and fossil records; and 4) if the preservation potential of a group changed significantly during its history. In contrast, uncertainties in the absolute ages of fossils are typically relatively unimportant, even though the vast majority of fossil cannot be dated directly. These issues and relevant quantitative methods are reviewed, and their relative magnitudes assessed, which typically correlate with the age of the group, its geographic range, and species richness.
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Affiliation(s)
- Charles R. Marshall
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States
- University of California Museum of Paleontology, University of California, Berkeley, Berkeley, CA, United States
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33
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Matschiner M. Selective Sampling of Species and Fossils Influences Age Estimates Under the Fossilized Birth-Death Model. Front Genet 2019; 10:1064. [PMID: 31737047 PMCID: PMC6836569 DOI: 10.3389/fgene.2019.01064] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 10/03/2019] [Indexed: 01/24/2023] Open
Abstract
The fossilized birth-death (FBD) model allows the estimation of species divergence times from molecular and fossil information in a coherent framework of diversification and fossil sampling. Some assumptions of the FBD model, however, are difficult to meet in phylogenetic analyses of highly diverse groups. Here, I use simulations to assess the impact of extreme model violations, including diversified sampling of species and the exclusive use of the oldest fossils per clade, on divergence times estimated with the FBD model. My results demonstrate that selective sampling of fossils can produce dramatically overestimated divergence times when the FBD model is used for inference, due to an interplay of underestimates for the model parameters net diversification rate, turnover, and fossil-sampling proportion. In contrast, divergence times estimated with CladeAge, a method that uses information about the oldest fossils per clade together with estimates of sampling and diversification rates, are accurate under these conditions. Practitioners of Bayesian divergence-time estimation should therefore ensure that the dataset conforms to the expectations of the FBD model, or estimates of sampling and diversification rates should be obtained a priori so that CladeAge can be used for the inference.
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Affiliation(s)
- Michael Matschiner
- Department of Palaentology and Museum, University of Zurich, Zurich, Switzerland
- Centre of Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
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34
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Marcondes RS. Realistic scenarios of missing taxa in phylogenetic comparative methods and their effects on model selection and parameter estimation. PeerJ 2019; 7:e7917. [PMID: 31616606 PMCID: PMC6791351 DOI: 10.7717/peerj.7917] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 09/18/2019] [Indexed: 12/24/2022] Open
Abstract
Model-based analyses of continuous trait evolution enable rich evolutionary insight. These analyses require a phylogenetic tree and a vector of trait values for the tree's terminal taxa, but rarely do a tree and dataset include all taxa within a clade. Because the probability that a taxon is included in a dataset depends on ecological traits that have phylogenetic signal, missing taxa in real datasets should be expected to be phylogenetically clumped or correlated to the modelled trait. I examined whether those types of missing taxa represent a problem for model selection and parameter estimation. I simulated univariate traits under a suite of Brownian Motion and Ornstein-Uhlenbeck models, and assessed the performance of model selection and parameter estimation under absent, random, clumped or correlated missing taxa. I found that those analyses perform well under almost all scenarios, including situations with very sparsely sampled phylogenies. The only notable biases I detected were in parameter estimation under a very high percentage (90%) of correlated missing taxa. My results offer a degree of reassurance for studies of continuous trait evolution with missing taxa, but the problem of missing taxa in phylogenetic comparative methods still demands much further investigation. The framework I have described here might provide a starting point for future work.
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Affiliation(s)
- Rafael S. Marcondes
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States of America
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35
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Barido-Sottani J, Aguirre-Fernández G, Hopkins MJ, Stadler T, Warnock R. Ignoring stratigraphic age uncertainty leads to erroneous estimates of species divergence times under the fossilized birth-death process. Proc Biol Sci 2019; 286:20190685. [PMID: 31064306 PMCID: PMC6532507 DOI: 10.1098/rspb.2019.0685] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 04/12/2019] [Indexed: 12/12/2022] Open
Abstract
Fossil information is essential for estimating species divergence times, and can be integrated into Bayesian phylogenetic inference using the fossilized birth-death (FBD) process. An important aspect of palaeontological data is the uncertainty surrounding specimen ages, which can be handled in different ways during inference. The most common approach is to fix fossil ages to a point estimate within the known age interval. Alternatively, age uncertainty can be incorporated by using priors, and fossil ages are then directly sampled as part of the inference. This study presents a comparison of alternative approaches for handling fossil age uncertainty in analysis using the FBD process. Based on simulations, we find that fixing fossil ages to the midpoint or a random point drawn from within the stratigraphic age range leads to biases in divergence time estimates, while sampling fossil ages leads to estimates that are similar to inferences that employ the correct ages of fossils. Second, we show a comparison using an empirical dataset of extant and fossil cetaceans, which confirms that different methods of handling fossil age uncertainty lead to large differences in estimated node ages. Stratigraphic age uncertainty should thus not be ignored in divergence time estimation and instead should be incorporated explicitly.
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Affiliation(s)
- Joëlle Barido-Sottani
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA
| | | | - Melanie J. Hopkins
- Division of Paleontology, American Museum of Natural History, New York, NY, USA
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Rachel Warnock
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
- Palaeontological Institute and Museum, University of Zurich, Zurich, Switzerland
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36
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Barido‐Sottani J, Pett W, O’Reilly JE, Warnock RCM. FossilSim
: An
r
package for simulating fossil occurrence data under mechanistic models of preservation and recovery. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13170] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joëlle Barido‐Sottani
- Department of Biosystems Science & EngineeringEidgenössische Technische Hochschule Zürich Basel Switzerland
- Swiss Institute of Bioinformatics (SIB) Switzerland
| | - Walker Pett
- Department of Ecology, Evolution and Organismal BiologyIowa State University Ames Iowa
| | | | - Rachel C. M. Warnock
- Department of Biosystems Science & EngineeringEidgenössische Technische Hochschule Zürich Basel Switzerland
- Swiss Institute of Bioinformatics (SIB) Switzerland
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Silvestro D, Warnock RCM, Gavryushkina A, Stadler T. Closing the gap between palaeontological and neontological speciation and extinction rate estimates. Nat Commun 2018; 9:5237. [PMID: 30532040 PMCID: PMC6286320 DOI: 10.1038/s41467-018-07622-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 11/13/2018] [Indexed: 11/09/2022] Open
Abstract
Measuring the pace at which speciation and extinction occur is fundamental to understanding the origin and evolution of biodiversity. Both the fossil record and molecular phylogenies of living species can provide independent estimates of speciation and extinction rates, but often produce strikingly divergent results. Despite its implications, the theoretical reasons for this discrepancy remain unknown. Here, we reveal a conceptual and methodological basis able to reconcile palaeontological and molecular evidence: discrepancies are driven by different implicit assumptions about the processes of speciation and species evolution in palaeontological and neontological analyses. We present the "birth-death chronospecies" model that clarifies the definition of speciation and extinction processes allowing for a coherent joint analysis of fossil and phylogenetic data. Using simulations and empirical analyses we demonstrate not only that this model explains much of the apparent incongruence between fossils and phylogenies, but that differences in rate estimates are actually informative about the prevalence of different speciation modes.
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Affiliation(s)
- Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, 41319, Gothenburg, Sweden.
- Global Gothenburg Biodiversity Centre, 41319, Gothenburg, Sweden.
- Department of Computational Biology, University of Lausanne, Lausanne, 1015, Switzerland.
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland.
| | - Rachel C M Warnock
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
- Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, 4058, Basel, Switzerland
| | | | - Tanja Stadler
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
- Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, 4058, Basel, Switzerland
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