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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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2
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Budd GE, Mann RP. Two Notorious Nodes: A Critical Examination of Relaxed Molecular Clock Age Estimates of the Bilaterian Animals and Placental Mammals. Syst Biol 2024; 73:223-234. [PMID: 37695319 PMCID: PMC11129587 DOI: 10.1093/sysbio/syad057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 08/30/2023] [Accepted: 09/08/2023] [Indexed: 09/12/2023] Open
Abstract
The popularity of relaxed clock Bayesian inference of clade origin timings has generated several recent publications with focal results considerably older than the fossils of the clades in question. Here, we critically examine two such clades: the animals (with a focus on the bilaterians) and the mammals (with a focus on the placentals). Each example displays a set of characteristic pathologies which, although much commented on, are rarely corrected for. We conclude that in neither case does the molecular clock analysis provide any evidence for an origin of the clade deeper than what is suggested by the fossil record. In addition, both these clades have other features (including, in the case of the placental mammals, proximity to a large mass extinction) that allow us to generate precise expectations of the timings of their origins. Thus, in these instances, the fossil record can provide a powerful test of molecular clock methodology, and why it goes astray, and we have every reason to think these problems are general. [Cambrian explosion; mammalian evolution; molecular clocks.].
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Affiliation(s)
- Graham E Budd
- Department of Earth Sciences, Palaeobiology Programme, Uppsala University, Villavägen 16 SE 75236, Sweden
| | - Richard P Mann
- Department of Statistics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK
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3
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Sallam M, Khalil R. Contemporary Insights into Hepatitis C Virus: A Comprehensive Review. Microorganisms 2024; 12:1035. [PMID: 38930417 PMCID: PMC11205832 DOI: 10.3390/microorganisms12061035] [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: 04/30/2024] [Revised: 05/15/2024] [Accepted: 05/20/2024] [Indexed: 06/28/2024] Open
Abstract
Hepatitis C virus (HCV) remains a significant global health challenge. Approximately 50 million people were living with chronic hepatitis C based on the World Health Organization as of 2024, contributing extensively to global morbidity and mortality. The advent and approval of several direct-acting antiviral (DAA) regimens significantly improved HCV treatment, offering potentially high rates of cure for chronic hepatitis C. However, the promising aim of eventual HCV eradication remains challenging. Key challenges include the variability in DAA access across different regions, slightly variable response rates to DAAs across diverse patient populations and HCV genotypes/subtypes, and the emergence of resistance-associated substitutions (RASs), potentially conferring resistance to DAAs. Therefore, periodic reassessment of current HCV knowledge is needed. An up-to-date review on HCV is also necessitated based on the observed shifts in HCV epidemiological trends, continuous development and approval of therapeutic strategies, and changes in public health policies. Thus, the current comprehensive review aimed to integrate the latest knowledge on the epidemiology, pathophysiology, diagnostic approaches, treatment options and preventive strategies for HCV, with a particular focus on the current challenges associated with RASs and ongoing efforts in vaccine development. This review sought to provide healthcare professionals, researchers, and policymakers with the necessary insights to address the HCV burden more effectively. We aimed to highlight the progress made in managing and preventing HCV infection and to highlight the persistent barriers challenging the prevention of HCV infection. The overarching goal was to align with global health objectives towards reducing the burden of chronic hepatitis, aiming for its eventual elimination as a public health threat by 2030.
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Affiliation(s)
- Malik Sallam
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan
- Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman 11942, Jordan
| | - Roaa Khalil
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan
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4
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Piwczyński M, Granjon L, Trzeciak P, Carlos Brito J, Oana Popa M, Daba Dinka M, Johnston NP, Boratyński Z. Unraveling phylogenetic relationships and species boundaries in the arid adapted Gerbillus rodents (Muridae: Gerbillinae) by RAD-seq data. Mol Phylogenet Evol 2023; 189:107913. [PMID: 37659480 DOI: 10.1016/j.ympev.2023.107913] [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: 02/20/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/04/2023]
Abstract
Gerbillus is one of the most speciose genera among rodents, with ca. 51 recognized species. Previous attempts to reconstruct the evolutionary history of Gerbillus mainly relied on the mitochondrial cyt-b marker as a source of phylogenetic information. In this study, we utilize RAD-seq genomic data from 37 specimens representing 11 species to reconstruct the phylogenetic tree for Gerbillus, applying concatenation and coalescence methods. We identified four highly supported clades corresponding to the traditionally recognized subgenera: Dipodillus, Gerbillus, Hendecapleura and Monodia. Only two uncertain branches were detected in the resulting trees, with one leading to diversification of the main lineages in the genus, recognized by quartet sampling analysis as uncertain due to possible introgression. We also examined species boundaries for four pairs of sister taxa, including potentially new species from Morocco, using SNAPP. The results strongly supported a speciation model in which all taxa are treated as separate species. The dating analyses confirmed the Plio-Pleistocene diversification of the genus, with the uncertain branch coinciding with the beginning of aridification of the Sahara at the the Plio-Pleistocene boundary. This study aligns well with the earlier analyses based on the cyt-b marker, reaffirming its suitability as an adequate marker for estimating genetic diversity in Gerbillus.
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Affiliation(s)
- Marcin Piwczyński
- Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Lwowska 1, PL-87-100 Toruń, Poland.
| | - Laurent Granjon
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Université de Montpellier, Montpellier, France
| | - Paulina Trzeciak
- Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Lwowska 1, PL-87-100 Toruń, Poland
| | - José Carlos Brito
- CIBIO-InBio, Research Center in Biodiversity and Genetic Resources, University of Porto, Campus de Vairão, Rua Padre Armando Quintas 7, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Madalina Oana Popa
- Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Lwowska 1, PL-87-100 Toruń, Poland; "Stejarul" Research Centre for Biological Sciences, National Institute of Research and Development for Biological Sciences, Alexandru cel Bun 6, RO-610004, Piatra Neamţ, Romania
| | - Mergi Daba Dinka
- Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Lwowska 1, PL-87-100 Toruń, Poland
| | - Nikolas P Johnston
- School of Life Sciences, University of Technology Sydney, 15 Broadway, Ultimo, NSW 2007, Australia; Centre for Sustainable Ecosystem Solutions, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Northfields Ave, Wollongong, NSW 2500, Australia
| | - Zbyszek Boratyński
- CIBIO-InBio, Research Center in Biodiversity and Genetic Resources, University of Porto, Campus de Vairão, Rua Padre Armando Quintas 7, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
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5
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Luo A, Zhang C, Zhou QS, Ho SYW, Zhu CD. Impacts of Taxon-Sampling Schemes on Bayesian Tip Dating Under the Fossilized Birth-Death Process. Syst Biol 2023; 72:781-801. [PMID: 36919368 PMCID: PMC10405359 DOI: 10.1093/sysbio/syad011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/18/2023] [Accepted: 03/14/2023] [Indexed: 03/16/2023] Open
Abstract
Evolutionary timescales can be inferred by molecular-clock analyses of genetic data and fossil evidence. Bayesian phylogenetic methods such as tip dating provide a powerful framework for inferring evolutionary timescales, but the most widely used priors for tree topologies and node times often assume that present-day taxa have been sampled randomly or exhaustively. In practice, taxon sampling is often carried out so as to include representatives of major lineages, such as orders or families. We examined the impacts of different densities of diversified sampling on Bayesian tip dating on unresolved fossilized birth-death (FBD) trees, in which fossil taxa are topologically constrained but their exact placements are averaged out. We used synthetic data generated by simulations of nucleotide sequence evolution, fossil occurrences, and diversified taxon sampling. Our analyses under the diversified-sampling FBD process show that increasing taxon-sampling density does not necessarily improve divergence-time estimates. However, when informative priors were specified for the root age or when tree topologies were fixed to those used for simulation, the performance of tip dating on unresolved FBD trees maintains its accuracy and precision or improves with taxon-sampling density. By exploring three situations in which models are mismatched, we find that including all relevant fossils, without pruning off those that are incompatible with the diversified-sampling FBD process, can lead to underestimation of divergence times. Our reanalysis of a eutherian mammal data set confirms some of the findings from our simulation study, and reveals the complexity of diversified taxon sampling in phylogenomic data sets. In highlighting the interplay of taxon-sampling density and other factors, the results of our study have practical implications for using Bayesian tip dating to infer evolutionary timescales across the Tree of Life. [Bayesian tip dating; eutherian mammals; fossilized birth-death process; phylogenomics; taxon sampling.].
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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
| | - 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
| | - Qing-Song Zhou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - 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
- International College, University of Chinese Academy of Sciences, Beijing, 100049, China
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6
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Clark JW, Donoghue PCJ. Constraining Whole-Genome Duplication Events in Geological Time. Methods Mol Biol 2023; 2545:139-154. [PMID: 36720811 DOI: 10.1007/978-1-0716-2561-3_7] [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] [Indexed: 02/02/2023]
Abstract
The timing of whole-genome duplication (WGD) events is crucial to understanding their role in evolution and underpins many hypotheses linking WGD to increased diversity and complexity. As such, means of estimating the timing of the WGD events relative to their macroevolutionary outcomes are of considerable importance. Molecular clock methods facilitate direct estimation of the absolute timing of WGD events, integrating information on the rate of sequence evolution between species while accommodating the uncertainty inherent to the fossil record. We present an explanation of the best practice for constructing fossil calibrations and estimating the age of WGD events via molecular clock methods in the program MCMCtree, with an example dataset based on a well-characterized WGD event within the flowering dogwoods (Cornus). The approach presented herein allows for the estimation of the age of WGD events and subsequent speciation events, allowing the relationship between WGD and the macroevolutionary outcomes to be explored. In our example, we show that in the case of flowering dogwoods, the WGD event long predates the end-Cretaceous mass extinction and that the two events may be independent.
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Affiliation(s)
- James W Clark
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, Bristol, UK.
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
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7
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Harris BJ, Clark JW, Schrempf D, Szöllősi GJ, Donoghue PCJ, Hetherington AM, Williams TA. Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants. Nat Ecol Evol 2022; 6:1634-1643. [PMID: 36175544 PMCID: PMC9630106 DOI: 10.1038/s41559-022-01885-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 08/12/2022] [Indexed: 11/16/2022]
Abstract
The origin of plants and their colonization of land fundamentally transformed the terrestrial environment. Here we elucidate the basis of this formative episode in Earth history through patterns of lineage, gene and genome evolution. We use new fossil calibrations, a relative clade age calibration (informed by horizontal gene transfer) and new phylogenomic methods for mapping gene family origins. Distinct rooting strategies resolve tracheophytes (vascular plants) and bryophytes (non-vascular plants) as monophyletic sister groups that diverged during the Cambrian, 515-494 million years ago. The embryophyte stem is characterized by a burst of gene innovation, while bryophytes subsequently experienced an equally dramatic episode of reductive genome evolution in which they lost genes associated with the elaboration of vasculature and the stomatal complex. Overall, our analyses reveal that extant tracheophytes and bryophytes are both highly derived from a more complex ancestral land plant. Understanding the origin of land plants requires tracing character evolution across a diversity of modern lineages.
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Affiliation(s)
- Brogan J Harris
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - James W Clark
- School of Biological Sciences, University of Bristol, Bristol, UK
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | - Dominik Schrempf
- Department of Biological Physics, Eötvös Loránd University, Budapest, Hungary
| | - Gergely J Szöllősi
- Department of Biological Physics, Eötvös Loránd University, Budapest, Hungary
- MTA-ELTE 'Lendület' Evolutionary Genomics Research Group, Budapest, Hungary
- Institute of Evolution, Centre for Ecological Research, Budapest, Hungary
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | | | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, UK.
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
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8
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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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9
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Beck RM, Voss RS, Jansa SA. Craniodental Morphology and Phylogeny of Marsupials. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2022. [DOI: 10.1206/0003-0090.457.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Robin M.D. Beck
- School of Science, Engineering and Environment University of Salford, U.K. School of Biological, Earth & Environmental Sciences University of New South Wales, Australia Division of Vertebrate Zoology (Mammalogy) American Museum of Natural History
| | - Robert S. Voss
- Division of Vertebrate Zoology (Mammalogy) American Museum of Natural History
| | - Sharon A. Jansa
- Bell Museum and Department of Ecology, Evolution, and Behavior University of Minnesota
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10
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Cai C, Tihelka E, Giacomelli M, Lawrence JF, Ślipiński A, Kundrata R, Yamamoto S, Thayer MK, Newton AF, Leschen RAB, Gimmel ML, Lü L, Engel MS, Bouchard P, Huang D, Pisani D, Donoghue PCJ. Integrated phylogenomics and fossil data illuminate the evolution of beetles. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211771. [PMID: 35345430 PMCID: PMC8941382 DOI: 10.1098/rsos.211771] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/15/2022] [Indexed: 05/03/2023]
Abstract
Beetles constitute the most biodiverse animal order with over 380 000 described species and possibly several million more yet unnamed. Recent phylogenomic studies have arrived at considerably incongruent topologies and widely varying estimates of divergence dates for major beetle clades. Here, we use a dataset of 68 single-copy nuclear protein-coding (NPC) genes sampling 129 out of the 193 recognized extant families as well as the first comprehensive set of fully justified fossil calibrations to recover a refined timescale of beetle evolution. Using phylogenetic methods that counter the effects of compositional and rate heterogeneity, we recover a topology congruent with morphological studies, which we use, combined with other recent phylogenomic studies, to propose several formal changes in the classification of Coleoptera: Scirtiformia and Scirtoidea sensu nov., Clambiformia ser. nov. and Clamboidea sensu nov., Rhinorhipiformia ser. nov., Byrrhoidea sensu nov., Dryopoidea stat. res., Nosodendriformia ser. nov. and Staphyliniformia sensu nov., and Erotyloidea stat. nov., Nitiduloidea stat. nov. and Cucujoidea sensu nov., alongside changes below the superfamily level. Our divergence time analyses recovered a late Carboniferous origin of Coleoptera, a late Palaeozoic origin of all modern beetle suborders and a Triassic-Jurassic origin of most extant families, while fundamental divergences within beetle phylogeny did not coincide with the hypothesis of a Cretaceous Terrestrial Revolution.
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Affiliation(s)
- Chenyang Cai
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Erik Tihelka
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Mattia Giacomelli
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - John F. Lawrence
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Adam Ślipiński
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Robin Kundrata
- Department of Zoology, Faculty of Science, Palacký University, 17. listopadu 50, 771 46 Olomouc, Czech Republic
| | - Shûhei Yamamoto
- Hokkaido University Museum, Hokkaido University, Kita 8, Nishi 5, Kita-ku, Sapporo 060-0808, Japan
| | - Margaret K. Thayer
- Negaunee Integrative Research Center, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
| | - Alfred F. Newton
- Negaunee Integrative Research Center, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
| | - Richard A. B. Leschen
- Manaaki Whenua Landcare Research, New Zealand Arthropod Collection, Private Bag 92170, Auckland, New Zealand
| | - Matthew L. Gimmel
- Invertebrate Zoology Department, Santa Barbara Museum of Natural History, 2559 Puesta del Sol Road, Santa Barbara, CA 93105, USA
| | - Liang Lü
- College of Life Science, Hebei Normal University, Shijiazhuang 050024, People's Republic of China
| | - Michael S. Engel
- Division of Entomology, Natural History Museum, and Department of Ecology & Evolutionary Biology, University of Kansas, 1501 Crestline Drive – Suite 140, Lawrence, KS 66045, USA
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Patrice Bouchard
- Division of Entomology, Natural History Museum, and Department of Ecology & Evolutionary Biology, University of Kansas, 1501 Crestline Drive – Suite 140, Lawrence, KS 66045, USA
| | - Diying Huang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China
| | - Davide Pisani
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Philip C. J. Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
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11
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Álvarez-Carretero S, Tamuri AU, Battini M, Nascimento FF, Carlisle E, Asher RJ, Yang Z, Donoghue PCJ, Dos Reis M. A species-level timeline of mammal evolution integrating phylogenomic data. Nature 2022; 602:263-267. [PMID: 34937052 DOI: 10.1038/s41586-021-04341-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 12/13/2021] [Indexed: 11/09/2022]
Abstract
High-throughput sequencing projects generate genome-scale sequence data for species-level phylogenies1-3. However, state-of-the-art Bayesian methods for inferring timetrees are computationally limited to small datasets and cannot exploit the growing number of available genomes4. In the case of mammals, molecular-clock analyses of limited datasets have produced conflicting estimates of clade ages with large uncertainties5,6, and thus the timescale of placental mammal evolution remains contentious7-10. Here we develop a Bayesian molecular-clock dating approach to estimate a timetree of 4,705 mammal species integrating information from 72 mammal genomes. We show that increasingly larger phylogenomic datasets produce diversification time estimates with progressively smaller uncertainties, facilitating precise tests of macroevolutionary hypotheses. For example, we confidently reject an explosive model of placental mammal origination in the Palaeogene8 and show that crown Placentalia originated in the Late Cretaceous with unambiguous ordinal diversification in the Palaeocene/Eocene. Our Bayesian methodology facilitates analysis of complete genomes and thousands of species within an integrated framework, making it possible to address hitherto intractable research questions on species diversifications. This approach can be used to address other contentious cases of animal and plant diversifications that require analysis of species-level phylogenomic datasets.
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Affiliation(s)
- Sandra Álvarez-Carretero
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Asif U Tamuri
- Centre for Advanced Research Computing, University College London, London, UK
- EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Matteo Battini
- School of Earth Sciences, University of Bristol, Bristol, UK
| | - Fabrícia F Nascimento
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - Emily Carlisle
- School of Earth Sciences, University of Bristol, Bristol, UK
| | - Robert J Asher
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | | | - Mario Dos Reis
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.
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12
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Liu J, Lindstrom AJ, Marler TE, Gong X. Not that young: combining plastid phylogenomic, plate tectonic and fossil evidence indicates a Palaeogene diversification of Cycadaceae. ANNALS OF BOTANY 2022; 129:217-230. [PMID: 34520529 PMCID: PMC8796677 DOI: 10.1093/aob/mcab118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/10/2021] [Indexed: 05/10/2023]
Abstract
BACKGROUND AND AIMS Previous molecular dating studies revealed historical mass extinctions and recent radiations of extant cycads, but debates still exist between palaeobotanists and evolutionary biologists regarding the origin and evolution of Cycadaceae. METHODS Using whole plastomic data, we revisited the phylogeny of this family and found the Palawan endemic Cycas clade was strongly related to all lineages from Southeast Eurasia, coinciding with a plate drift event occurring in the Early Oligocene. By integrating fossil and biogeographical calibrations as well as molecular data from protein-coding genes, we established different calibration schemes and tested competing evolutionary timelines of Cycadaceae. KEY RESULTS We found recent dispersal cannot explain the distribution of Palawan Cycas, yet the scenario including the tectonic calibration yielded a mean crown age of extant Cycadaceae of ~69-43 million years ago by different tree priors, consistent with multiple Palaeogene fossils assigned to this family. Biogeographical analyses incorporating fossil distributions revealed East Asia as the ancestral area of Cycadaceae. CONCLUSIONS Our findings challenge the previously proposed Middle-Late Miocene diversification of cycads and an Indochina origin for Cycadaceae and highlight the importance of combining phylogenetic clades, tectonic events and fossils for rebuilding the evolutionary history of lineages that have undergone massive extinctions.
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Affiliation(s)
- Jian Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- For correspondence. Email , or
| | - Anders J Lindstrom
- Global Biodiversity Conservancy, 144/124 Moo3, Soi Bua Thong, Bangsalae, Sattahip, Chonburi 20250, Thailand
- For correspondence. Email , or
| | - Thomas E Marler
- Western Pacific Tropical Research Center, University of Guam, UOG Station, Mangilao, GU 96923, USA
| | - Xun Gong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- For correspondence. Email , or
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13
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Dos Reis M. Dating Microbial Evolution with MCMCtree. Methods Mol Biol 2022; 2569:3-22. [PMID: 36083441 DOI: 10.1007/978-1-0716-2691-7_1] [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] [Indexed: 05/24/2023]
Abstract
This protocol explains how to use the program MCMCtree to estimate divergence times in microbial phylogenies. The main advantage of MCMCtree is the implementation of an approximation to the molecular data likelihood that dramatically speeds up computation during Bayesian MCMC sampling of divergence times and evolutionary rates. The approximation allows the analysis of large phylogenies with hundreds of taxa and molecular alignments with thousands or millions of sites. Two examples are used to illustrate Bayesian clock dating with MCMCtree. The first is a phylogeny of (mostly) microbial eukaryotes and prokaryotes encompassing the major groups of life on Earth, and for which fossil information, to calibrate the nodes of the phylogeny, is available. The second is a phylogeny of influenza viruses with known sampling times. An overview of Bayesian MCMC sampling is given as well as practical advice on issues such as construction of the time and rate prior and assessment of convergence of MCMC chains. Strategies for estimating times in microbial phylogenies for which neither fossil information nor sampling times are known are discussed.
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Affiliation(s)
- Mario Dos Reis
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.
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14
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Zhang H, Wang S, Luo H. A Computational Protocol for Dating the Evolution of Cyanobacteria. Methods Mol Biol 2022; 2569:23-40. [PMID: 36083442 DOI: 10.1007/978-1-0716-2691-7_2] [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] [Indexed: 05/24/2023]
Abstract
Cyanobacteria are known to play important roles in driving biological and geochemical innovations in ancient Earth. The origin of Cyanobacteria is the key to understanding these evolutionary events and thus has gained much interest to biologists and geobiologists. Recent development of the molecular dating approaches provides us an opportunity to assess the timeline of Cyanobacteria evolution based on relaxed clock models. The implementation of Bayesian phylogenetic approaches accommodates the uncertainties from different sources, such as fossil calibrations and topological structure of the phylogenomic tree, and provides us converged estimates of posterior mean ages. In this chapter, by taking Cyanobacteria as an example, we introduce a refined strategy to perform molecular dating analysis, as well as a practical method to evaluate the precision of dating analysis.
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Affiliation(s)
- Hao Zhang
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Sishuo Wang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Haiwei Luo
- School of Life Sciences, Earth and Environmental Sciences Programme, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
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15
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Didier G, Laurin M. Distributions of extinction times from fossil ages and tree topologies: the example of mid-Permian synapsid extinctions. PeerJ 2021; 9:e12577. [PMID: 34966586 PMCID: PMC8667717 DOI: 10.7717/peerj.12577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 11/09/2021] [Indexed: 11/20/2022] Open
Abstract
Given a phylogenetic tree that includes only extinct, or a mix of extinct and extant taxa, where at least some fossil data are available, we present a method to compute the distribution of the extinction time of a given set of taxa under the Fossilized-Birth-Death model. Our approach differs from the previous ones in that it takes into account (i) the possibility that the taxa or the clade considered may diversify before going extinct and (ii) the whole phylogenetic tree to estimate extinction times, whilst previous methods do not consider the diversification process and deal with each branch independently. Because of this, our method can estimate extinction times of lineages represented by a single fossil, provided that they belong to a clade that includes other fossil occurrences. We assess and compare our new approach with a standard previous one using simulated data. Results show that our method provides more accurate confidence intervals. This new approach is applied to the study of the extinction time of three Permo-Carboniferous synapsid taxa (Ophiacodontidae, Edaphosauridae, and Sphenacodontidae) that are thought to have disappeared toward the end of the Cisuralian (early Permian), or possibly shortly thereafter. The timing of extinctions of these three taxa and of their component lineages supports the idea that the biological crisis in the late Kungurian/early Roadian consisted of a progressive decline in biodiversity throughout the Kungurian.
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Affiliation(s)
| | - Michel Laurin
- CNRS/MNHN/UPMC, Sorbonne Université, Muséum National d’Histoire Naturelle, CR2P (“Centre de Recherches sur la Paléobiodiversité et les Paléoenvironnements” UMR 7207), Paris, France
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16
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Evolution and dispersal of snakes across the Cretaceous-Paleogene mass extinction. Nat Commun 2021; 12:5335. [PMID: 34521829 PMCID: PMC8440539 DOI: 10.1038/s41467-021-25136-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 07/22/2021] [Indexed: 02/08/2023] Open
Abstract
Mass extinctions have repeatedly shaped global biodiversity. The Cretaceous-Paleogene (K-Pg) mass extinction caused the demise of numerous vertebrate groups, and its aftermath saw the rapid diversification of surviving mammals, birds, frogs, and teleost fishes. However, the effects of the K-Pg extinction on the evolution of snakes-a major clade of predators comprising over 3,700 living species-remains poorly understood. Here, we combine an extensive molecular dataset with phylogenetically and stratigraphically constrained fossil calibrations to infer an evolutionary timescale for Serpentes. We reveal a potential diversification among crown snakes associated with the K-Pg mass extinction, led by the successful colonisation of Asia by the major extant clade Afrophidia. Vertebral morphometrics suggest increasing morphological specialisation among marine snakes through the Paleogene. The dispersal patterns of snakes following the K-Pg underscore the importance of this mass extinction event in shaping Earth's extant vertebrate faunas.
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17
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Incorporating Topological and Age Uncertainty into Event-Based Biogeography of Sand Spiders Supports Paleo-Islands in Galapagos and Ancient Connections among Neotropical Dry Forests. DIVERSITY 2021. [DOI: 10.3390/d13090418] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Event-based biogeographic methods, such as dispersal-extinction-cladogenesis, have become increasingly popular for attempting to reconstruct the biogeographic history of organisms. Such methods employ distributional data of sampled species and a dated phylogenetic tree to estimate ancestral distribution ranges. Because the input tree is often a single consensus tree, uncertainty in topology and age estimates are rarely accounted for, even when they may affect the outcome of biogeographic estimates. Even when such uncertainties are taken into account for estimates of ancestral ranges, they are usually ignored when researchers compare competing biogeographic hypotheses. We explore the effect of incorporating this uncertainty in a biogeographic analysis of the 21 species of sand spiders (Sicariidae: Sicarius) from Neotropical xeric biomes, based on a total-evidence phylogeny including a complete sampling of the genus. Using a custom R script, we account for uncertainty in ages and topology by estimating ancestral ranges over a sample of trees from the posterior distribution of a Bayesian analysis, and for uncertainty in biogeographic estimates by using stochastic maps. This approach allows for counting biogeographic events such as dispersal among areas, counting lineages through time per area, and testing biogeographic hypotheses, while not overestimating the confidence in a single topology. Including uncertainty in ages indicates that Sicarius dispersed to the Galapagos Islands when the archipelago was formed by paleo-islands that are now submerged; model comparison strongly favors a scenario where dispersal took place before the current islands emerged. We also investigated past connections among currently disjunct Neotropical dry forests; failing to account for topological uncertainty underestimates possible connections among the Caatinga and Andean dry forests in favor of connections among Caatinga and Caribbean + Mesoamerican dry forests. Additionally, we find that biogeographic models including a founder-event speciation parameter (“+J”) are more prone to suffer from the overconfidence effects of estimating ancestral ranges using a single topology. This effect is alleviated by incorporating topological and age uncertainty while estimating stochastic maps, increasing the similarity in the inference of biogeographic events between models with or without a founder-event speciation parameter. We argue that incorporating phylogenetic uncertainty in biogeographic hypothesis-testing is valuable and should be a commonplace approach in the presence of rogue taxa or wide confidence intervals in age estimates, and especially when using models including founder-event speciation.
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18
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A global phylogeny of turtles reveals a burst of climate-associated diversification on continental margins. Proc Natl Acad Sci U S A 2021; 118:2012215118. [PMID: 33558231 DOI: 10.1073/pnas.2012215118] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Living turtles are characterized by extraordinarily low species diversity given their age. The clade's extensive fossil record indicates that climate and biogeography may have played important roles in determining their diversity. We investigated this hypothesis by collecting a molecular dataset for 591 individual turtles that, together, represent 80% of all turtle species, including representatives of all families and 98% of genera, and used it to jointly estimate phylogeny and divergence times. We found that the turtle tree is characterized by relatively constant diversification (speciation minus extinction) punctuated by a single threefold increase. We also found that this shift is temporally and geographically associated with newly emerged continental margins that appeared during the Eocene-Oligocene transition about 30 million years before present. In apparent contrast, the fossil record from this time period contains evidence for a major, but regional, extinction event. These seemingly discordant findings appear to be driven by a common global process: global cooling and drying at the time of the Eocene-Oligocene transition. This climatic shift led to aridification that drove extinctions in important fossil-bearing areas, while simultaneously exposing new continental margin habitat that subsequently allowed for a burst of speciation associated with these newly exploitable ecological opportunities.
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19
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Su D, Yang L, Shi X, Ma X, Zhou X, Hedges SB, Zhong B. Large-Scale Phylogenomic Analyses Reveal the Monophyly of Bryophytes and Neoproterozoic Origin of Land Plants. Mol Biol Evol 2021; 38:3332-3344. [PMID: 33871608 PMCID: PMC8321542 DOI: 10.1093/molbev/msab106] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The relationships among the four major embryophyte lineages (mosses, liverworts, hornworts, vascular plants) and the timing of the origin of land plants are enigmatic problems in plant evolution. Here, we resolve the monophyly of bryophytes by improving taxon sampling of hornworts and eliminating the effect of synonymous substitutions. We then estimate the divergence time of crown embryophytes based on three fossil calibration strategies, and reveal that maximum calibration constraints have a major effect on estimating the time of origin of land plants. Moreover, comparison of priors and posteriors provides a guide for evaluating the optimal calibration strategy. By considering the reliability of fossil calibrations and the influences of molecular data, we estimate that land plants originated in the Precambrian (980–682 Ma), much older than widely recognized. Our study highlights the important contribution of molecular data when faced with contentious fossil evidence, and that fossil calibrations used in estimating the timescale of plant evolution require critical scrutiny.
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Affiliation(s)
- Danyan Su
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Lingxiao Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xuan Shi
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoya Ma
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaofan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - S Blair Hedges
- Center for Biodiversity, Temple University, Philadelphia, PA, USA
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, China
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20
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Fu P, Sun S, Twyford AD, Li B, Zhou R, Chen S, Gao Q, Favre A. Lineage-specific plastid degradation in subtribe Gentianinae (Gentianaceae). Ecol Evol 2021; 11:3286-3299. [PMID: 33841784 PMCID: PMC8019047 DOI: 10.1002/ece3.7281] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 12/24/2020] [Accepted: 01/04/2021] [Indexed: 01/03/2023] Open
Abstract
The structure and sequence of plastid genomes is highly conserved across most land plants, except for a minority of lineages that show gene loss and genome degradation. Understanding the early stages of plastome degradation may provide crucial insights into the repeatability and predictability of genomic evolutionary trends. We investigated these trends in subtribe Gentianinae of the Gentianaceae, which encompasses ca. 450 species distributed around the world, particularly in alpine and subalpine environments. We sequenced, assembled, and annotated the plastomes of 41 species, representing all six genera in subtribe Gentianinae and all main sections of the species-rich genus Gentiana L. We reconstructed the phylogeny, estimated divergence times, investigated the phylogenetic distribution of putative gene losses, and related these to substitution rate shifts and species' habitats. We obtained a strongly supported topology consistent with earlier studies, with all six genera in Gentianinae recovered as monophyletic and all main sections of Gentiana having full support. While closely related species have very similar plastomes in terms of size and structure, independent gene losses, particularly of the ndh complex, have occurred in multiple clades across the phylogeny. Gene loss was usually associated with a shift in the boundaries of the small single-copy and inverted repeat regions. Substitution rates were variable between clades, with evidence for both elevated and decelerated rate shifts. Independent lineage-specific loss of ndh genes occurred at a wide range of times, from Eocene to Pliocene. Our study illustrates that diverse degradation patterns shape the evolution of the plastid in this species-rich plant group.
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Affiliation(s)
- Peng‐Cheng Fu
- School of Life ScienceLuoyang Normal UniversityLuoyangChina
| | - Shan‐Shan Sun
- School of Life ScienceLuoyang Normal UniversityLuoyangChina
| | - Alex D. Twyford
- Ashworth LaboratoriesInstitute of Evolutionary BiologyThe University of EdinburghEdinburghUK
- Royal Botanic Garden EdinburghEdinburghUK
| | - Bei‐Bei Li
- School of Life ScienceLuoyang Normal UniversityLuoyangChina
| | - Rui‐Qi Zhou
- School of Life ScienceLuoyang Normal UniversityLuoyangChina
| | - Shi‐Long Chen
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningChina
- Qinghai Provincial Key Laboratory of Crop Molecular BreedingXiningChina
| | - Qing‐Bo Gao
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningChina
- Qinghai Provincial Key Laboratory of Crop Molecular BreedingXiningChina
| | - Adrien Favre
- Senckenberg Research Institute and Natural History MuseumFrankfurt am MainGermany
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21
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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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22
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Tao Q, Barba-Montoya J, Huuki LA, Durnan MK, Kumar S. Relative Efficiencies of Simple and Complex Substitution Models in Estimating Divergence Times in Phylogenomics. Mol Biol Evol 2021; 37:1819-1831. [PMID: 32119075 PMCID: PMC7253201 DOI: 10.1093/molbev/msaa049] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The conventional wisdom in molecular evolution is to apply parameter-rich models of nucleotide and amino acid substitutions for estimating divergence times. However, the actual extent of the difference between time estimates produced by highly complex models compared with those from simple models is yet to be quantified for contemporary data sets that frequently contain sequences from many species and genes. In a reanalysis of many large multispecies alignments from diverse groups of taxa, we found that the use of the simplest models can produce divergence time estimates and credibility intervals similar to those obtained from the complex models applied in the original studies. This result is surprising because the use of simple models underestimates sequence divergence for all the data sets analyzed. We found three fundamental reasons for the observed robustness of time estimates to model complexity in many practical data sets. First, the estimates of branch lengths and node-to-tip distances under the simplest model show an approximately linear relationship with those produced by using the most complex models applied on data sets with many sequences. Second, relaxed clock methods automatically adjust rates on branches that experience considerable underestimation of sequence divergences, resulting in time estimates that are similar to those from complex models. And, third, the inclusion of even a few good calibrations in an analysis can reduce the difference in time estimates from simple and complex models. The robustness of time estimates to model complexity in these empirical data analyses is encouraging, because all phylogenomics studies use statistical models that are oversimplified descriptions of actual evolutionary substitution processes.
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Affiliation(s)
- Qiqing Tao
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA.,Department of Biology, Temple University, Philadelphia, PA
| | - Jose Barba-Montoya
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA.,Department of Biology, Temple University, Philadelphia, PA
| | - Louise A Huuki
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
| | - Mary Kathleen Durnan
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA.,Department of Biology, Temple University, Philadelphia, PA
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA.,Department of Biology, Temple University, Philadelphia, PA.,Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
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23
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Salvi D, Pinho C, Mendes J, Harris DJ. Fossil-calibrated time tree of Podarcis wall lizards provides limited support for biogeographic calibration models. Mol Phylogenet Evol 2021; 161:107169. [PMID: 33798673 DOI: 10.1016/j.ympev.2021.107169] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/17/2021] [Accepted: 03/25/2021] [Indexed: 11/15/2022]
Abstract
Podarcis wall lizards are endemic to the Mediterranean Basin where they represent the predominant reptile group. Despite being extensively used as model organisms in evolutionary and ecological studies their phylogeny and historical biogeography are still incompletely resolved. Moreover, molecular clock calibrations used in wall lizard phylogeography are based on the assumption of vicariant speciation triggered by the abrupt Mediterranean Sea level rise at the end of the Messinian salinity crisis (MSC). However, the validity of this biogeographic calibration remains untested. In this study we inferred a robust time tree based on multilocus data and fossil calibrations using both gene concatenation and species-tree approaches and including models with gene-flow. We found five deeply divergent, geographically coherent, and well-supported clades comprising species from i) Iberian Peninsula and North Africa; ii) Western Mediterranean islands, iii) Sicilian and Maltese islands; and iv-v) Balkan region and Aegean islands. The mitochondrial tree shows some inconsistencies with the species tree that warrant future investigation. Diversification of main clades is estimated in a short time frame during the Middle Miocene and might have been associated with a period of global climate cooling with the establishment of a marked climatic zonation in Europe. Cladogenetic events within the main clades are scattered throughout the time tree, from the Late Miocene to the Early Pleistocene, suggesting that speciation events in wall lizards reflect a complex interplay between regional topography, climate and geological history rather than a shared major climatic or paleogeographic event. Our absolute time estimates, as well as a relative dating approach, demonstrate that the assumption of a causal link between sea-level rise at the end of the MSC and the diversification of many island endemics is not justified. This study reinforces the notion that multiple dispersal and vicariant events, at different time frames, are required to explain current allopatric distributions and to account for the historical assembly of Mediterranean biota, and cautions against the use of biogeographic calibrations based on the assumption of vicariance.
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Affiliation(s)
- Daniele Salvi
- University of L'Aquila, Department of Health, Life and Environmental Sciences, 67100 Coppito, L'Aquila, Italy; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.
| | - Catarina Pinho
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.
| | - Joana Mendes
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - D James Harris
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.
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24
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Carruthers T, Scotland RW. The implications of interrelated assumptions on estimates of divergence times and rates of diversification. Syst Biol 2021; 70:1181-1199. [PMID: 33760070 DOI: 10.1093/sysbio/syab021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 03/16/2021] [Accepted: 03/22/2021] [Indexed: 11/15/2022] Open
Abstract
Phylogenies are increasingly being used as a basis to provide insight into macroevolutionary history. Here, we use simulation experiments and empirical analyses to evaluate methods that use phylogenies as a basis to make estimates of divergence times and rates of diversification. This is the first study to present a comprehensive assessment of the key variables that underpin analyses in this field - including substitution rates, speciation rates, and extinction, plus character sampling and taxon sampling. We show that in unrealistically simplistic cases (where substitution rates and speciation rates are constant, and where there is no extinction), increased character and taxon sampling lead to more accurate and precise parameter estimates. By contrast, in more complex but realistic cases (where substitution rates, speciation rates, and extinction rates vary), gains in accuracy and precision from increased character and taxon sampling are far more limited. The lack of accuracy and precision even occurs when using methods that are designed to account for more complex cases, such as relaxed clocks, fossil calibrations, and models that allow speciation rates and extinction rates to vary. The problem also persists when analysing genomic scale datasets. These results suggest two interrelated problems that occur when the processes that generated the data are more complex. First, methodological assumptions are more likely to be violated. Second, limitations in the information content of the data become more important.
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Affiliation(s)
- Tom Carruthers
- Royal Botanic Gardens Kew, Richmond, London, TW9 3AE, United Kingdom
| | - Robert W Scotland
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, United Kingdom
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25
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Heads M, Grehan JR. The Galápagos Islands: biogeographic patterns and geology. Biol Rev Camb Philos Soc 2021; 96:1160-1185. [PMID: 33749122 DOI: 10.1111/brv.12696] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 02/06/2021] [Accepted: 02/09/2021] [Indexed: 11/29/2022]
Abstract
In the traditional biogeographic model, the Galápagos Islands appeared a few million years ago in a sea where no other islands existed and were colonized from areas outside the region. However, recent work has shown that the Galápagos hotspot is 139 million years old (Early Cretaceous), and so groups are likely to have survived at the hotspot by dispersal of populations onto new islands from older ones. This process of metapopulation dynamics means that species can persist indefinitely in an oceanic region, as long as new islands are being produced. Metapopulations can also undergo vicariance into two metapopulations, for example at active island arcs that are rifted by transform faults. We reviewed the geographic relationships of Galápagos groups and found 10 biogeographic patterns that are shared by at least two groups. Each of the patterns coincides spatially with a major tectonic structure; these structures include: the East Pacific Rise; west Pacific and American subduction zones; large igneous plateaus in the Pacific; Alisitos terrane (Baja California), Guerrero terrane (western Mexico); rifting of North and South America; formation of the Caribbean Plateau by the Galápagos hotspot, and its eastward movement; accretion of Galápagos hotspot tracks; Andean uplift; and displacement on the Romeral fault system. All these geological features were active in the Cretaceous, suggesting that geological change at that time caused vicariance in widespread ancestors. The present distributions are explicable if ancestors survived as metapopulations occupying both the Galápagos hotspot and other regions before differentiating, more or less in situ.
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Affiliation(s)
- Michael Heads
- Buffalo Museum of Science, 1020 Humboldt Parkway, Buffalo, NY, 14211-1293, U.S.A
| | - John R Grehan
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, 3215 Hull Rd, Gainesville, FL, 32611, U.S.A
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26
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Hassanin A, Veron G, Ropiquet A, Jansen van Vuuren B, Lécu A, Goodman SM, Haider J, Nguyen TT. Evolutionary history of Carnivora (Mammalia, Laurasiatheria) inferred from mitochondrial genomes. PLoS One 2021; 16:e0240770. [PMID: 33591975 PMCID: PMC7886153 DOI: 10.1371/journal.pone.0240770] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/06/2021] [Indexed: 11/18/2022] Open
Abstract
The order Carnivora, which currently includes 296 species classified into 16 families, is distributed across all continents. The phylogeny and the timing of diversification of members of the order are still a matter of debate. Here, complete mitochondrial genomes were analysed to reconstruct the phylogenetic relationships and to estimate divergence times among species of Carnivora. We assembled 51 new mitogenomes from 13 families, and aligned them with available mitogenomes by selecting only those showing more than 1% of nucleotide divergence and excluding those suspected to be of low-quality or from misidentified taxa. Our final alignment included 220 taxa representing 2,442 mitogenomes. Our analyses led to a robust resolution of suprafamilial and intrafamilial relationships. We identified 21 fossil calibration points to estimate a molecular timescale for carnivorans. According to our divergence time estimates, crown carnivorans appeared during or just after the Early Eocene Climatic Optimum; all major groups of Caniformia (Cynoidea/Arctoidea; Ursidae; Musteloidea/Pinnipedia) diverged from each other during the Eocene, while all major groups of Feliformia (Nandiniidae; Feloidea; Viverroidea) diversified more recently during the Oligocene, with a basal divergence of Nandinia at the Eocene/Oligocene transition; intrafamilial divergences occurred during the Miocene, except for the Procyonidae, as Potos separated from other genera during the Oligocene.
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Affiliation(s)
- Alexandre Hassanin
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, UA, Paris, France
| | - Géraldine Veron
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, UA, Paris, France
| | - Anne Ropiquet
- Faculty of Science and Technology, Department of Natural Sciences, Middlesex University, London, United Kingdom
| | - Bettine Jansen van Vuuren
- Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg, South Africa
| | - Alexis Lécu
- Parc zoologique de Paris, Muséum national d’Histoire naturelle, Paris, France
| | - Steven M. Goodman
- Field Museum of Natural History, Chicago, IL, United States of America
| | - Jibran Haider
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, UA, Paris, France
- Department of Wildlife Management, Pir Mehr Ali Shah, Arid Agriculture University Rawalpindi, Rawalpindi, Pakistan
- Forest Parks & Wildlife Department Gilgit-Baltistan, Skardu, Pakistan
| | - Trung Thanh Nguyen
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, UA, Paris, France
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27
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Carruthers T, Sanderson MJ, Scotland RW. The Implications of Lineage-Specific Rates for Divergence Time Estimation. Syst Biol 2021; 69:660-670. [PMID: 31808929 PMCID: PMC7302051 DOI: 10.1093/sysbio/syz080] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 11/28/2019] [Accepted: 12/01/2019] [Indexed: 11/29/2022] Open
Abstract
Rate variation adds considerable complexity to divergence time estimation in molecular phylogenies. Here, we evaluate the impact of lineage-specific rates—which we define as among-branch-rate-variation that acts consistently across the entire genome. We compare its impact to residual rates—defined as among-branch-rate-variation that shows a different pattern of rate variation at each sampled locus, and gene-specific rates—defined as variation in the average rate across all branches at each sampled locus. We show that lineage-specific rates lead to erroneous divergence time estimates, regardless of how many loci are sampled. Further, we show that stronger lineage-specific rates lead to increasing error. This contrasts to residual rates and gene-specific rates, where sampling more loci significantly reduces error. If divergence times are inferred in a Bayesian framework, we highlight that error caused by lineage-specific rates significantly reduces the probability that the 95% highest posterior density includes the correct value, and leads to sensitivity to the prior. Use of a more complex rate prior—which has recently been proposed to model rate variation more accurately—does not affect these conclusions. Finally, we show that the scale of lineage-specific rates used in our simulation experiments is comparable to that of an empirical data set for the angiosperm genus Ipomoea. Taken together, our findings demonstrate that lineage-specific rates cause error in divergence time estimates, and that this error is not overcome by analyzing genomic scale multilocus data sets. [Divergence time estimation; error; rate variation.]
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Affiliation(s)
- Tom Carruthers
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Michael J Sanderson
- Department of Ecology and Evolutionary Biology, University of Arizona, 1041 East Lowell, Tucson, AZ 85721-0088, USA
| | - Robert W Scotland
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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28
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Bláha M, Patoka J, Japoshvili B, Let M, Buřič M, Kouba A, Mumladze L. Genetic diversity, phylogenetic position and morphometric analysis of Astacus colchicus (Decapoda, Astacidae): a new insight into Eastern European crayfish fauna. Integr Zool 2020; 16:368-378. [PMID: 32978865 DOI: 10.1111/1749-4877.12493] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The phylogeny of European crayfish fauna, especially with respect to Eastern European species, is still far from being completely resolved. To fill this gap, we analyzed most of the European crayfish species focusing on the phylogenetic position of the endemic crayfish Astacus colchicus, inhabiting Georgia. Three mitochondrial and one nuclear marker were used to study evolutionary relationships among European crayfish species, resulting in the unique phylogenetic position of A. colchicus indicating independent species status to A. astacus. Phylogenetic analyses revealed a deep molecular divergence of A. colchicus in comparison to A. astacus (6.5-10.9% in mtDNA and 1.1% in nDNA) as well as to Pontastacus leptodactylus and P. pachypus (5.5-10.0% in mtDNA and 1.4-2.4% in nDNA). Absent ventral process on second male pleopod and abdominal somites II and III with pleura rounded lacking prominent spines clearly indicate taxonomic assignment to the genus Astacus; however, the species is distributed almost in the middle of Ponto-Caspian area typical by occurrence of the genus Pontastacus. Several morphological indices linked to head length, carapace, and total body length and width were found to demonstrate apparent differences between A. colchicus and A. astacus. Although this study provides a novel insight into European crayfish phylogeography, we also point out the gaps in comprehensive study of the P. leptodactylus species complex, which could reveal details about the potential species status of particular species and subspecies within this genus.
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Affiliation(s)
- Martin Bláha
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Vodňany, Czech Republic
| | - Jiří Patoka
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Praha, Czech Republic
| | | | - Marek Let
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Vodňany, Czech Republic
| | - Miloš Buřič
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Vodňany, Czech Republic
| | - Antonín Kouba
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Vodňany, Czech Republic
| | - Levan Mumladze
- Institute of Zoology of Ilia State University, Tbilisi, Georgia
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29
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Mello B, Tao Q, Barba-Montoya J, Kumar S. Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches. Mol Ecol Resour 2020; 21:122-136. [PMID: 32881388 DOI: 10.1111/1755-0998.13249] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 08/14/2020] [Accepted: 08/19/2020] [Indexed: 12/11/2022]
Abstract
Simultaneous molecular dating of population and species divergences is essential in many biological investigations, including phylogeography, phylodynamics and species delimitation studies. In these investigations, multiple sequence alignments consist of both intra- and interspecies samples (mixed samples). As a result, the phylogenetic trees contain interspecies, interpopulation and within-population divergences. Bayesian relaxed clock methods are often employed in these analyses, but they assume the same tree prior for both inter- and intraspecies branching processes and require specification of a clock model for branch rates (independent vs. autocorrelated rates models). We evaluated the impact of a single tree prior on Bayesian divergence time estimates by analysing computer-simulated data sets. We also examined the effect of the assumption of independence of evolutionary rate variation among branches when the branch rates are autocorrelated. Bayesian approach with coalescent tree priors generally produced excellent molecular dates and highest posterior densities with high coverage probabilities. We also evaluated the performance of a non-Bayesian method, RelTime, which does not require the specification of a tree prior or a clock model. RelTime's performance was similar to that of the Bayesian approach, suggesting that it is also suitable to analyse data sets containing both populations and species variation when its computational efficiency is needed.
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Affiliation(s)
- Beatriz Mello
- Department of Genetics, Federal University of Rio de Janeiro, Brazil.,Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
| | - Qiqing Tao
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA.,Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jose Barba-Montoya
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA.,Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA.,Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
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30
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Peña V, Vieira C, Braga JC, Aguirre J, Rösler A, Baele G, De Clerck O, Le Gall L. Radiation of the coralline red algae (Corallinophycidae, Rhodophyta) crown group as inferred from a multilocus time-calibrated phylogeny. Mol Phylogenet Evol 2020; 150:106845. [DOI: 10.1016/j.ympev.2020.106845] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 04/21/2020] [Accepted: 04/21/2020] [Indexed: 01/20/2023]
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31
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Budd GE, Mann RP. Survival and selection biases in early animal evolution and a source of systematic overestimation in molecular clocks. Interface Focus 2020; 10:20190110. [PMID: 32637066 PMCID: PMC7333906 DOI: 10.1098/rsfs.2019.0110] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2020] [Indexed: 12/21/2022] Open
Abstract
Important evolutionary events such as the Cambrian Explosion have inspired many attempts at explanation: why do they happen when they do? What shapes them, and why do they eventually come to an end? However, much less attention has been paid to the idea of a 'null hypothesis'-that certain features of such diversifications arise simply through their statistical structure. Such statistical features also appear to influence our perception of the timing of these events. Here, we show in particular that study of unusually large clades leads to systematic overestimates of clade ages from some types of molecular clocks, and that the size of this effect may be enough to account for the puzzling mismatches seen between these molecular clocks and the fossil record. Our analysis of the fossil record of the late Ediacaran to Cambrian suggests that it is likely to be recording a true evolutionary radiation of the bilaterians at this time, and that explanations involving various sorts of cryptic origins for the bilaterians do not seem to be necessary.
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Affiliation(s)
- Graham E. Budd
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, Uppsala 752 36, Sweden
| | - Richard P. Mann
- Department of Statistics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK
- The Alan Turing Institute, London NW1 2DB, UK
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32
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Beavan AJS, Donoghue PCJ, Beaumont MA, Pisani D. Performance of A Priori and A Posteriori Calibration Strategies in Divergence Time Estimation. Genome Biol Evol 2020; 12:1087-1098. [PMID: 32442306 PMCID: PMC7486956 DOI: 10.1093/gbe/evaa105] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2020] [Indexed: 11/25/2022] Open
Abstract
Relaxed molecular clock methods allow the use of genomic data to estimate divergence times across the tree of life. This is most commonly achieved in Bayesian analyses where the molecular clock is calibrated a priori through the integration of fossil information. Alternatively, fossil calibrations can be used a posteriori, to transform previously estimated relative divergence times that were inferred without considering fossil information, into absolute divergence times. However, as branch length is the product of the rate of evolution and the duration in time of the considered branch, the extent to which a posteriori calibrated, relative divergence time methods can disambiguate time and rate, is unclear. Here, we use forward evolutionary simulations and compare a priori and a posteriori calibration strategies using different molecular clock methods and models. Specifically, we compare three Bayesian methods, the strict clock, uncorrelated clock and autocorrelated clock, and the non-Bayesian algorithm implemented in RelTime. We simulate phylogenies with multiple, independent substitution rate changes and show that correct timescales cannot be inferred without the use of calibrations. Under our simulation conditions, a posteriori calibration strategies almost invariably inferred incorrect rate changes and divergence times. The a priori integration of fossil calibrations is fundamental in these cases to improve the accuracy of the estimated divergence times. Relative divergence times and absolute timescales derived by calibrating relative timescales to geological time a posteriori appear to be less reliable than a priori calibrated, timescales.
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Affiliation(s)
- Alan J S Beavan
- School of Biological Sciences, University of Bristol, United Kingdom
| | | | - Mark A Beaumont
- School of Biological Sciences, University of Bristol, United Kingdom
| | - Davide Pisani
- School of Biological Sciences, University of Bristol, United Kingdom
- School of Earth Sciences, University of Bristol, United Kingdom
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33
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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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34
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Wolfe JM, Breinholt JW, Crandall KA, Lemmon AR, Lemmon EM, Timm LE, Siddall ME, Bracken-Grissom HD. A phylogenomic framework, evolutionary timeline and genomic resources for comparative studies of decapod crustaceans. Proc Biol Sci 2020; 286:20190079. [PMID: 31014217 DOI: 10.1098/rspb.2019.0079] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Comprising over 15 000 living species, decapods (crabs, shrimp and lobsters) are the most instantly recognizable crustaceans, representing a considerable global food source. Although decapod systematics have received much study, limitations of morphological and Sanger sequence data have yet to produce a consensus for higher-level relationships. Here, we introduce a new anchored hybrid enrichment kit for decapod phylogenetics designed from genomic and transcriptomic sequences that we used to capture new high-throughput sequence data from 94 species, including 58 of 179 extant decapod families, and 11 of 12 major lineages. The enrichment kit yields 410 loci (greater than 86 000 bp) conserved across all lineages of Decapoda, more clade-specific molecular data than any prior study. Phylogenomic analyses recover a robust decapod tree of life strongly supporting the monophyly of all infraorders, and monophyly of each of the reptant, 'lobster' and 'crab' groups, with some results supporting pleocyemate monophyly. We show that crown decapods diverged in the Late Ordovician and most crown lineages diverged in the Triassic-Jurassic, highlighting a cryptic Palaeozoic history, and post-extinction diversification. New insights into decapod relationships provide a phylogenomic window into morphology and behaviour, and a basis to rapidly and cheaply expand sampling in this economically and ecologically significant invertebrate clade.
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Affiliation(s)
- Joanna M Wolfe
- 1 Division of Invertebrate Zoology and Sackler Institute of Comparative Genomics, American Museum of Natural History , New York, NY 10024 , USA.,2 Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology , Cambridge, MA 02139 , USA.,3 Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University , Cambridge, MA 02138 , USA
| | - Jesse W Breinholt
- 4 Florida Museum of Natural History, University of Florida , Gainesville, FL 32611 , USA.,5 RAPiD Genomics , Gainesville, FL 32601 , USA
| | - Keith A Crandall
- 6 Computational Biology Institute, The George Washington University , Ashburn, VA 20147 , USA.,7 Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution , Washington, DC 20012 , USA
| | - Alan R Lemmon
- 8 Department of Scientific Computing, Florida State University , Dirac Science Library, Tallahassee, FL 32306 , USA
| | - Emily Moriarty Lemmon
- 9 Department of Biological Science, Florida State University , Tallahassee, FL 32306 , USA
| | - Laura E Timm
- 10 Department of Biological Sciences, Florida International University , North Miami, FL 33181 , USA
| | - Mark E Siddall
- 1 Division of Invertebrate Zoology and Sackler Institute of Comparative Genomics, American Museum of Natural History , New York, NY 10024 , USA
| | - Heather D Bracken-Grissom
- 10 Department of Biological Sciences, Florida International University , North Miami, FL 33181 , USA
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35
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Powell CLE, Waskin S, Battistuzzi FU. Quantifying the Error of Secondary vs. Distant Primary Calibrations in a Simulated Environment. Front Genet 2020; 11:252. [PMID: 32265987 PMCID: PMC7099002 DOI: 10.3389/fgene.2020.00252] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/02/2020] [Indexed: 12/25/2022] Open
Abstract
Using calibrations to obtain absolute divergence times is standard practice in molecular clock studies. While the use of primary (e.g., fossil) calibrations is preferred, this approach can be limiting because of their rarity in fast-growing datasets. Thus, alternatives need to be explored, such as the use of secondary (molecularly-derived) calibrations that can anchor a timetree in a larger number of nodes. However, the use of secondary calibrations has been discouraged in the past because of concerns in the error rates of the node estimates they produce with an apparent high precision. Here, we quantify the amount of errors in estimates produced by the use of secondary calibrations relative to true times and primary calibrations placed on distant nodes. We find that, overall, the inaccuracies in estimates based on secondary calibrations are predictable and mirror errors associated with primary calibrations and their confidence intervals. Additionally, we find comparable error rates in estimated times from secondary calibrations and distant primary calibrations, although the precision of estimates derived from distant primary calibrations is roughly twice as good as that of estimates derived from secondary calibrations. This suggests that increasing dataset size to include primary calibrations may produce divergence times that are about as accurate as those from secondary calibrations, albeit with a higher precision. Overall, our results suggest that secondary calibrations may be useful to explore the parameter space of plausible evolutionary scenarios when compared to time estimates obtained with distant primary calibrations.
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Affiliation(s)
| | - Sydney Waskin
- Department of Biological Sciences, Oakland University, Rochester, MI, United States
| | - Fabia Ursula Battistuzzi
- Department of Biological Sciences, Oakland University, Rochester, MI, United States
- Center for Data Science and Big Data Analytics, Oakland University, Rochester, MI, United States
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36
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Carruthers T, Muñoz-Rodríguez P, Wood JRI, Scotland RW. The temporal dynamics of evolutionary diversification in Ipomoea. Mol Phylogenet Evol 2020; 146:106768. [PMID: 32081764 DOI: 10.1016/j.ympev.2020.106768] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 02/11/2020] [Accepted: 02/12/2020] [Indexed: 10/25/2022]
Abstract
Molecular phylogenies are used as a basis for making inferences about macroevolutionary history. However, a robust phylogeny does not contain the information that is necessary to make many of these inferences. Complex methodologies that incorporate important assumptions about the nature of evolutionary history are therefore required. Here, we explore the implications of these assumptions for making inferences about the macroevolutionary history of Ipomoea - a large pantropical genus of flowering plants that contains the sweet potato (Ipomoea batatas), a crop of global economic importance. We focus on assumptions that underlie inferences of divergence times, and diversification parameters (speciation rates, extinction rates, and net diversification rates). These are among the most fundamental variables in macroevolutionary research. We use a series of novel approaches to explore the implications of these assumptions for inferring the age of Ipomoea, the ages of major clades within Ipomoea, whether there are significant differences in diversification parameters among clades within Ipomoea, and whether the storage root of I. batatas evolved in pre-human times. We show that inferring an age estimate for Ipomoea and major clades within Ipomoea is highly problematic. Inferred divergence times are sensitive to uncertain fossil calibrations and differing assumptions about among-branch-substitution-rate-variation. Despite this uncertainty, we are able to make robust inferences about patterns of variation in diversification parameters within Ipomoea, and that the storage root of I. batatas evolved in pre-human times. Taken together, this study presents novel and generalizable insights into the implications of methodological assumptions for making inferences about macroevolutionary history. Further, by presenting novel findings relating to the temporal dynamics of evolution in Ipomoea, as well as more specifically to I. batatas, this study makes a valuable contribution to our understanding of tropical plant evolution, and the evolutionary context in which economically important crops evolve.
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Affiliation(s)
- Tom Carruthers
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, United Kingdom
| | - Pablo Muñoz-Rodríguez
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, United Kingdom
| | - John R I Wood
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, United Kingdom
| | - Robert W Scotland
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, United Kingdom.
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37
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Copilaş-Ciocianu D, Borko Š, Fišer C. The late blooming amphipods: Global change promoted post-Jurassic ecological radiation despite Palaeozoic origin. Mol Phylogenet Evol 2020; 143:106664. [DOI: 10.1016/j.ympev.2019.106664] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 10/19/2019] [Accepted: 10/24/2019] [Indexed: 01/04/2023]
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38
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Magalhaes ILF, Azevedo GHF, Michalik P, Ramírez MJ. The fossil record of spiders revisited: implications for calibrating trees and evidence for a major faunal turnover since the Mesozoic. Biol Rev Camb Philos Soc 2020; 95:184-217. [PMID: 31713947 DOI: 10.1111/brv.12559] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/06/2019] [Accepted: 09/10/2019] [Indexed: 01/24/2023]
Abstract
Studies in evolutionary biology and biogeography increasingly rely on the estimation of dated phylogenetic trees using molecular clocks. In turn, the calibration of such clocks is critically dependent on external evidence (i.e. fossils) anchoring the ages of particular nodes to known absolute ages. In recent years, a plethora of new fossil spiders, especially from the Mesozoic, have been described, while the number of studies presenting dated spider phylogenies based on fossil calibrations increased sharply. We critically evaluate 44 of these studies, which collectively employed 67 unique fossils in 180 calibrations. Approximately 54% of these calibrations are problematic, particularly regarding unsupported assignment of fossils to extant clades (44%) and crown (rather than stem) dating (9%). Most of these cases result from an assumed equivalence between taxonomic placement of fossils and their phylogenetic position. To overcome this limitation, we extensively review the literature on fossil spiders, with a special focus on putative synapomorphies and the phylogenetic placement of fossil species with regard to their importance for calibrating higher taxa (families and above) in the spider tree of life. We provide a curated list including 41 key fossils intended to be a basis for future estimations of dated spider phylogenies. In a second step, we use a revised set of 23 calibrations to estimate a new dated spider tree of life based on transcriptomic data. The revised placement of key fossils and the new calibrated tree are used to resolve a long-standing debate in spider evolution - we tested whether there has been a major turnover in the spider fauna between the Mesozoic and Cenozoic. At least 17 (out of 117) extant families have been recorded from the Cretaceous, implying that at least 41 spider lineages in the family level or above crossed the Cretaeous-Paleogene (K-Pg) boundary. The putative phylogenetic affinities of families known only from the Mesozoic suggest that at least seven Cretaceous families appear to have no close living relatives and might represent extinct lineages. There is no unambiguous fossil evidence of the retrolateral tibial apophysis clade (RTA-clade) in the Mesozoic, although molecular clock analyses estimated the major lineages within this clade to be at least ∼100 million years old. Our review of the fossil record supports a major turnover showing that the spider faunas in the Mesozoic and the Cenozoic are very distinct at high taxonomic levels, with the Mesozoic dominated by Palpimanoidea and Synspermiata, while the Cenozoic is dominated by Araneoidea and RTA-clade spiders.
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Affiliation(s)
- Ivan L F Magalhaes
- División Aracnología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" - CONICET, Av. Ángel Gallardo 470, Buenos Aires, C1405DJR, Argentina
| | - Guilherme H F Azevedo
- División Aracnología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" - CONICET, Av. Ángel Gallardo 470, Buenos Aires, C1405DJR, Argentina
| | - Peter Michalik
- Zoologisches Institut und Museum, Universität Greifswald, Loitzer Straβe 26, Greifswald, D-17489, Germany
| | - Martín J Ramírez
- División Aracnología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" - CONICET, Av. Ángel Gallardo 470, Buenos Aires, C1405DJR, Argentina
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39
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Chazot N, Wahlberg N, Freitas AVL, Mitter C, Labandeira C, Sohn JC, Sahoo RK, Seraphim N, de Jong R, Heikkilä M. Priors and Posteriors in Bayesian Timing of Divergence Analyses: The Age of Butterflies Revisited. Syst Biol 2020; 68:797-813. [PMID: 30690622 PMCID: PMC6893297 DOI: 10.1093/sysbio/syz002] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 01/11/2019] [Accepted: 01/15/2019] [Indexed: 11/14/2022] Open
Abstract
The need for robust estimates of times of divergence is essential for downstream analyses, yet assessing this robustness is still rare. We generated a time-calibrated genus-level phylogeny of butterflies (Papilionoidea), including 994 taxa, up to 10 gene fragments and an unprecedented set of 12 fossils and 10 host-plant node calibration points. We compared marginal priors and posterior distributions to assess the relative importance of the former on the latter. This approach revealed a strong influence of the set of priors on the root age but for most calibrated nodes posterior distributions shifted from the marginal prior, indicating significant information in the molecular data set. Using a very conservative approach we estimated an origin of butterflies at 107.6 Ma, approximately equivalent to the latest Early Cretaceous, with a credibility interval ranging from 89.5 Ma (mid Late Cretaceous) to 129.5 Ma (mid Early Cretaceous). In addition, we tested the effects of changing fossil calibration priors, tree prior, different sets of calibrations and different sampling fractions but our estimate remained robust to these alternative assumptions. With 994 genera, this tree provides a comprehensive source of secondary calibrations for studies on butterflies.
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Affiliation(s)
- Nicolas Chazot
- Department of Biology, Lunds Universitet, Sölvegatan 37, 223 62 Lund, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, 405 30 Gothenburg, Sweden.,Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Gothenburg, Sweden
| | - Niklas Wahlberg
- Department of Biology, Lunds Universitet, Sölvegatan 37, 223 62 Lund, Sweden
| | - André Victor Lucci Freitas
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Caixa Postal 6109, Barão Geraldo 13083-970, Campinas, São Paulo, Brazil
| | - Charles Mitter
- Department of Entomology, University of Maryland, 4291 Fieldhouse Dr, College Park, MD 20742, USA
| | - Conrad Labandeira
- Department of Entomology, University of Maryland, 4291 Fieldhouse Dr, College Park, MD 20742, USA.,Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, 10th St. & Constitution Ave., Washington, DC 20013, USA.,Department of Entomology and BEES Program, University of Maryland, 4291 Fieldhouse Dr, College Park, MD 20741, USA.,Key Lab of Insect Evolution and Environmental Change, School of Life Sciences, Capital Normal University, XinJieKouWai St., Beijing 100048, China
| | - Jae-Cheon Sohn
- Department of Science Education, Gongju National University of Education, Gongju, 27, Ungjin-ro, Gongju-si, Chungnam 32553, Republic of Korea
| | - Ranjit Kumar Sahoo
- IISER-TVM Centre for Research and Education in Ecology and Evolution (ICREEE), School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695 551, India
| | - Noemy Seraphim
- Instituto Federal de Educação, Ciência e Tecnologia de São Paulo, Campus Campinas, CTI Renato Archer - Av. Comendador Aladino Selmi, s/n - Amarais, Campinas, São Paulo 13069-901, Brazil
| | - Rienk de Jong
- Department of Entomology, Naturalis Biodiversity Center, PO Box 9517, 2300 RA Leiden, The Netherlands
| | - Maria Heikkilä
- Finnish Museum of Natural History LUOMUS, Zoology Unit, University of Helsinki, P.O. Box 17, Helsinki FI-00014, Finland
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40
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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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41
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Duan L, Harris A, Su C, Zhang ZR, Arslan E, Ertuğrul K, Loc PK, Hayashi H, Wen J, Chen HF. Chloroplast Phylogenomics Reveals the Intercontinental Biogeographic History of the Liquorice Genus (Leguminosae: Glycyrrhiza). FRONTIERS IN PLANT SCIENCE 2020; 11:793. [PMID: 32636856 PMCID: PMC7318913 DOI: 10.3389/fpls.2020.00793] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 05/18/2020] [Indexed: 05/09/2023]
Abstract
The liquorice genus, Glycyrrhiza L. (Leguminosae), is a medicinal herb with great economic importance and an intriguing intercontinental disjunct distribution in Eurasia, North Africa, the Americas, and Australia. Glycyrrhiza, along with Glycyrrhizopsis Boiss. and Meristotropis Fisch. & C.A.Mey., comprise Glycyrrhiza s.l. Here we reconstructed the phylogenetic relationships and biogeographic history in Glycyrrhiza s.l. using sequence data of whole chloroplast genomes. We found that Glycyrrhiza s.l. is sister to the tribe Wisterieae and is divided into four main clades. Clade I, corresponds to Glycyrrhizopsis and is sister to Glycyrrhiza sensu Meng. Meristotropis is embedded within Glycyrrhiza sensu Meng, and these two genera together form Clades II-IV. Based on biogeographic analyses and divergence time dating, Glycyrrhiza s.l. originated during the late Eocene and its most recent common ancestor (MRCA) was distributed in the interior of Eurasia and the circum-Mediterranean region. A vicariance event, which was possibly a response to the uplifting of the Turkish-Iranian Plateau, may have driven the divergence between Glycyrrhiza sensu Meng and Glycyrrhizopsis in the Middle Miocene. The third and fourth main uplift events of the Qinghai-Tibetan Plateau may have led to rapid evolutionary diversification within Glycyrrhiza sensu Meng. Subsequently, the MRCA of Clade II might have migrated to North America (G. lepidota) via the Bering land bridge during the early Pliocene, and reached temperate South America (G. astragalina) by long-distance dispersal (LDD). Within Clade III, the ancestor of G. acanthocarpa arrived at southern Australia through LDD after the late Pliocene, whereas all other species (the SPEY clade) migrated to the interior of Eurasia and the Mediterranean region in the early Pleistocene. The MRCA of Clade IV was restricted in the interior of Eurasia, but its descendants have become widespread in temperate regions of the Old World Northern Hemisphere during the last million years.
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Affiliation(s)
- Lei Duan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, United States
- *Correspondence: Lei Duan,
| | - A.J. Harris
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Chun Su
- College of Life Science, Northwest A&F University, Yangling, China
| | - Zhi-Rong Zhang
- Germplasm Bank of Wild Species in Southwest China, Kunming Institution of Botany, Chinese Academy of Sciences, Kunming, China
| | - Emine Arslan
- Department of Biology, Faculty of Science, Selçuk University, Konya, Turkey
| | - Kuddisi Ertuğrul
- Department of Biology, Faculty of Science, Selçuk University, Konya, Turkey
| | - Phan Ke Loc
- Department of Botany and HNU, Faculty of Biology, VNU Hanoi University of Science (HUS), Hanoi, Vietnam
| | - Hiroaki Hayashi
- Laboratory of Natural Products Chemistry, College of Pharmaceutical Sciences, Ritsumeikan University, Kyoto, Japan
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, United States
- Jun Wen,
| | - Hong-Feng Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Hong-Feng Chen,
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42
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van Santen M, Linder HP. The assembly of the Cape flora is consistent with an edaphic rather than climatic filter. Mol Phylogenet Evol 2020; 142:106645. [DOI: 10.1016/j.ympev.2019.106645] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 12/14/2022]
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43
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O'Reilly JE, Donoghue PCJ. The Effect of Fossil Sampling on the Estimation of Divergence Times with the Fossilized Birth-Death Process. Syst Biol 2020; 69:124-138. [PMID: 31127936 DOI: 10.1093/sysbio/syz037] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 05/17/2019] [Indexed: 08/25/2023] Open
Abstract
Timescales are of fundamental importance to evolutionary biology as they facilitate hypothesis tests of historical evolutionary processes. Through the incorporation of fossil occurrence data, the fossilized birth-death (FBD) process provides a framework for estimating divergence times using more paleontological data than traditional node calibration approaches have allowed. The inclusion of more data can refine evolutionary timescale estimates, but for many taxonomic groups it is computationally infeasible to include all available fossil occurrence data. Here, we utilize both empirical data and a simulation framework to identify approaches to subsampling fossil occurrence data that result in the most accurate estimates of divergence times. To achieve this we assess the performance of the FBD-Skyline model when implementing multiple approaches to incorporating subsampled fossil occurrence data. Our results demonstrate that it is necessary to account for all available fossil occurrence data to achieve the most accurate estimates of clade age. We show that this can be achieved if an empirical Bayes approach, accounting for fossil sampling through time, is applied to the FBD process. Random subsampling of occurrence data can lead to estimates of clade age that are incompatible with fossil evidence if no control over the affinities of fossil occurrences is enforced. Our results call into question the accuracy of previous divergence time studies incorporating the FBD process that have used only a subsample of all available fossil occurrence data.
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Affiliation(s)
- Joseph E O'Reilly
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
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44
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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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45
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Du Y, Wu S, Edwards SV, Liu L. The effect of alignment uncertainty, substitution models and priors in building and dating the mammal tree of life. BMC Evol Biol 2019; 19:203. [PMID: 31694538 PMCID: PMC6833305 DOI: 10.1186/s12862-019-1534-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 10/21/2019] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The flood of genomic data to help build and date the tree of life requires automation at several critical junctures, most importantly during sequence assembly and alignment. It is widely appreciated that automated alignment protocols can yield inaccuracies, but the relative impact of various sources error on phylogenomic analysis is not yet known. This study employs an updated mammal data set of 5162 coding loci sampled from 90 species to evaluate the effects of alignment uncertainty, substitution models, and fossil priors on gene tree, species tree, and divergence time estimation. Additionally, a novel coalescent likelihood ratio test is introduced for comparing competing species trees against a given set of gene trees. RESULTS The aligned DNA sequences of 5162 loci from 90 species were trimmed and filtered using trimAL and two filtering protocols. The final dataset contains 4 sets of alignments - before trimming, after trimming, filtered by a recently proposed pipeline, and further filtered by comparing ML gene trees for each locus with the concatenation tree. Our analyses suggest that the average discordance among the coalescent trees is significantly smaller than that among the concatenation trees estimated from the 4 sets of alignments or with different substitution models. There is no significant difference among the divergence times estimated with different substitution models. However, the divergence dates estimated from the alignments after trimming are more recent than those estimated from the alignments before trimming. CONCLUSIONS Our results highlight that alignment uncertainty of the updated mammal data set and the choice of substitution models have little impact on tree topologies yielded by coalescent methods for species tree estimation, whereas they are more influential on the trees made by concatenation. Given the choice of calibration scheme and clock models, divergence time estimates are robust to the choice of substitution models, but removing alignments deemed problematic by trimming algorithms can lead to more recent dates. Although the fossil prior is important in divergence time estimation, Bayesian estimates of divergence times in this data set are driven primarily by the sequence data.
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Affiliation(s)
- Yan Du
- Department of Statistics, University of Georgia, 310 Herty Drive, Athens, GA 30606 USA
| | - Shaoyuan Wu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu 221116 People’s Republic of China
| | - Scott V. Edwards
- Department of Organismic & Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138 USA
| | - Liang Liu
- Liang Liu, Department of Statistics and Institute of Bioinformatics, University of Georgia, 310 Herty Drive, Athens, GA 30606 USA
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46
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Montagna M, Tong KJ, Magoga G, Strada L, Tintori A, Ho SYW, Lo N. Recalibration of the insect evolutionary time scale using Monte San Giorgio fossils suggests survival of key lineages through the End-Permian Extinction. Proc Biol Sci 2019; 286:20191854. [PMID: 31594499 PMCID: PMC6790769 DOI: 10.1098/rspb.2019.1854] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 09/17/2019] [Indexed: 12/24/2022] Open
Abstract
Insects are a highly diverse group of organisms and constitute more than half of all known animal species. They have evolved an extraordinary range of traits, from flight and complete metamorphosis to complex polyphenisms and advanced eusociality. Although the rich insect fossil record has helped to chart the appearance of many phenotypic innovations, data are scarce for a number of key periods. One such period is that following the End-Permian Extinction, recognized as the most catastrophic of all extinction events. We recently discovered several 240-million-year-old insect fossils in the Mount San Giorgio Lagerstätte (Switzerland-Italy) that are remarkable for their state of preservation (including internal organs and soft tissues), and because they extend the records of their respective taxa by up to 200 million years. By using these fossils as calibrations in a phylogenomic dating analysis, we present a revised time scale for insect evolution. Our date estimates for several major lineages, including the hyperdiverse crown groups of Lepidoptera, Hemiptera: Heteroptera and Diptera, are substantially older than their currently accepted post-Permian origins. We found that major evolutionary innovations, including flight and metamorphosis, appeared considerably earlier than previously thought. These results have numerous implications for understanding the evolution of insects and their resilience in the face of extreme events such as the End-Permian Extinction.
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Affiliation(s)
- Matteo Montagna
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy
| | - K. Jun Tong
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Sydney, Australia
| | - Giulia Magoga
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy
| | - Laura Strada
- Dipartimento di Scienze della Terra ‘Ardito Desio’, Università degli Studi di Milano, Via Mangiagalli 34, 20133 Milano, Italy
| | - Andrea Tintori
- Dipartimento di Scienze della Terra ‘Ardito Desio’, Università degli Studi di Milano, Via Mangiagalli 34, 20133 Milano, Italy
| | - Simon Y. W. Ho
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Sydney, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Sydney, Australia
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47
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Cole TL, Ksepka DT, Mitchell KJ, Tennyson AJD, Thomas DB, Pan H, Zhang G, Rawlence NJ, Wood JR, Bover P, Bouzat JL, Cooper A, Fiddaman SR, Hart T, Miller G, Ryan PG, Shepherd LD, Wilmshurst JM, Waters JM. Mitogenomes Uncover Extinct Penguin Taxa and Reveal Island Formation as a Key Driver of Speciation. Mol Biol Evol 2019; 36:784-797. [PMID: 30722030 DOI: 10.1093/molbev/msz017] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The emergence of islands has been linked to spectacular radiations of diverse organisms. Although penguins spend much of their lives at sea, they rely on land for nesting, and a high proportion of extant species are endemic to geologically young islands. Islands may thus have been crucial to the evolutionary diversification of penguins. We test this hypothesis using a fossil-calibrated phylogeny of mitochondrial genomes (mitogenomes) from all extant and recently extinct penguin taxa. Our temporal analysis demonstrates that numerous recent island-endemic penguin taxa diverged following the formation of their islands during the Plio-Pleistocene, including the Galápagos (Galápagos Islands), northern rockhopper (Gough Island), erect-crested (Antipodes Islands), Snares crested (Snares) and royal (Macquarie Island) penguins. Our analysis also reveals two new recently extinct island-endemic penguin taxa from New Zealand's Chatham Islands: Eudyptes warhami sp. nov. and a dwarf subspecies of the yellow-eyed penguin, Megadyptes antipodes richdalei ssp. nov. Eudyptes warhami diverged from the Antipodes Islands erect-crested penguin between 1.1 and 2.5 Ma, shortly after the emergence of the Chatham Islands (∼3 Ma). This new finding of recently evolved taxa on this young archipelago provides further evidence that the radiation of penguins over the last 5 Ma has been linked to island emergence. Mitogenomic analyses of all penguin species, and the discovery of two new extinct penguin taxa, highlight the importance of island formation in the diversification of penguins, as well as the extent to which anthropogenic extinctions have affected island-endemic taxa across the Southern Hemisphere's isolated archipelagos.
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Affiliation(s)
- Theresa L Cole
- Department of Zoology, University of Otago, Dunedin, New Zealand.,Manaaki Whenua Landcare Research, Lincoln, Canterbury, New Zealand
| | | | - Kieren J Mitchell
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | | | - Daniel B Thomas
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Hailin Pan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,China National Genebank, BGI-Shenzhen, Shenzhen, Guangdong, China.,Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,China National Genebank, BGI-Shenzhen, Shenzhen, Guangdong, China.,Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Jamie R Wood
- Manaaki Whenua Landcare Research, Lincoln, Canterbury, New Zealand
| | - Pere Bover
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia.,ARAID Foundation, IUCA-Grupo Aragosaurus, Universidad de Zaragoza, Zaragoza, Spain
| | - Juan L Bouzat
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, USA
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | | | - Tom Hart
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Gary Miller
- Division of Pathology and Laboratory Medicine, University of Western Australia, Crawley, WA, Australia.,Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Peter G Ryan
- DST-NRF Centre of Excellence, FitzPatrick Institute of African Ornithology, University of Cape Town, Rondebosch, South Africa
| | - Lara D Shepherd
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | - Janet M Wilmshurst
- Manaaki Whenua Landcare Research, Lincoln, Canterbury, New Zealand.,School of Environment, University of Auckland, Auckland, New Zealand
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48
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Dates and rates in grape's plastomes: evolution in slow motion. Curr Genet 2019; 66:123-140. [PMID: 31201544 DOI: 10.1007/s00294-019-01004-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 06/02/2019] [Accepted: 06/05/2019] [Indexed: 01/08/2023]
Abstract
The family Vitaceae includes the domesticated grapevine (Vitis vinifera), one of the most economically important crops in the world. Despite the importance of Vitaceae, there is still considerable controversy surrounding their phylogenetic relationships and evolutionary timescales. Moreover, variation in rates of molecular evolution among Vitaceae remains mostly unexplored. The present research aims to fill these knowledge gaps through the analysis of plastome sequences. Thirteen newly sequenced grape plastomes are presented and their phylogenetic relationships examined. Divergence times and absolute substitution rates are inferred under different molecular clocks by the analysis of 95 non-coding plastid regions and 43 representative accessions of the major lineages of Vitaceae. Furthermore, the phylogenetic informativeness of non-coding plastid regions is investigated. We find strong evidence in favor of the random local clock model and rate heterogeneity within Vitaceae. Substitution rates decelerate in Ampelocissus, Ampelopsis, Nekemias, Parthenocissus, Rhoicissus, and Vitis, with genus Vitis showing the lowest values up to a minimum of ~ 4.65 × 10-11 s/s/y. We suggest that liana-like species of Vitaceae evolve slower than erect growth habit plants and we invoke the "rate of mitosis hypothesis" to explain the observed pattern of the substitution rates. We identify a reduced set of 20 non-coding regions able to accurately reconstruct the phylogeny of Vitaceae and we provide a detailed description of all 152 non-coding regions identified in the plastomes of subg. Vitis. These polymorphic regions will find their applications in phylogenetics, phylogeography, and population genetics as well in grapes identification through DNA barcoding techniques.
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Tamura K, Tao Q, Kumar S. Theoretical Foundation of the RelTime Method for Estimating Divergence Times from Variable Evolutionary Rates. Mol Biol Evol 2019; 35:1770-1782. [PMID: 29893954 PMCID: PMC5995221 DOI: 10.1093/molbev/msy044] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
RelTime estimates divergence times by relaxing the assumption of a strict molecular clock in a phylogeny. It shows excellent performance in estimating divergence times for both simulated and empirical molecular sequence data sets in which evolutionary rates varied extensively throughout the tree. RelTime is computationally efficient and scales well with increasing size of data sets. Until now, however, RelTime has not had a formal mathematical foundation. Here, we show that the basis of the RelTime approach is a relative rate framework (RRF) that combines comparisons of evolutionary rates in sister lineages with the principle of minimum rate change between evolutionary lineages and their respective descendants. We present analytical solutions for estimating relative lineage rates and divergence times under RRF. We also discuss the relationship of RRF with other approaches, including the Bayesian framework. We conclude that RelTime will be useful for phylogenies with branch lengths derived not only from molecular data, but also morphological and biochemical traits.
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Affiliation(s)
- Koichiro Tamura
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.,Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Qiqing Tao
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA.,Department of Biology, Temple University, Philadelphia, PA
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA.,Department of Biology, Temple University, Philadelphia, PA.,Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
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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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