1
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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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2
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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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3
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Suvorov A, Kim BY, Wang J, Armstrong EE, Peede D, D'Agostino ERR, Price DK, Waddell P, Lang M, Courtier-Orgogozo V, David JR, Petrov D, Matute DR, Schrider DR, Comeault AA. Widespread introgression across a phylogeny of 155 Drosophila genomes. Curr Biol 2022; 32:111-123.e5. [PMID: 34788634 PMCID: PMC8752469 DOI: 10.1016/j.cub.2021.10.052] [Citation(s) in RCA: 91] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/29/2021] [Accepted: 10/22/2021] [Indexed: 01/12/2023]
Abstract
Genome-scale sequence data have invigorated the study of hybridization and introgression, particularly in animals. However, outside of a few notable cases, we lack systematic tests for introgression at a larger phylogenetic scale across entire clades. Here, we leverage 155 genome assemblies from 149 species to generate a fossil-calibrated phylogeny and conduct multilocus tests for introgression across 9 monophyletic radiations within the genus Drosophila. Using complementary phylogenomic approaches, we identify widespread introgression across the evolutionary history of Drosophila. Mapping gene-tree discordance onto the phylogeny revealed that both ancient and recent introgression has occurred across most of the 9 clades that we examined. Our results provide the first evidence of introgression occurring across the evolutionary history of Drosophila and highlight the need to continue to study the evolutionary consequences of hybridization and introgression in this genus and across the tree of life.
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Affiliation(s)
- Anton Suvorov
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Bernard Y Kim
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Jeremy Wang
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | | | - David Peede
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | | | - Donald K Price
- School of Life Sciences, University of Nevada, Las Vegas, NV 89119, USA
| | - Peter Waddell
- School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Michael Lang
- CNRS, Institut Jacques Monod, Université de Paris, Paris 75013, France
| | | | - Jean R David
- Laboratoire Evolution, Génomes, Comportement, Ecologie (EGCE) CNRS, IRD, Univ. Paris-sud, Université Paris-Saclay, Gif sur Yvette 91190, France; Institut de Systématique, Evolution, Biodiversité, CNRS, MNHN, UPMC, EPHE, Muséum National d'Histoire Naturelle, Sorbonne Universités, Paris 75005, France
| | - Dmitri Petrov
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Daniel R Matute
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Daniel R Schrider
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Aaron A Comeault
- Molecular Ecology & Evolution Group, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2DGA, UK.
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4
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May MR, Contreras DL, Sundue MA, Nagalingum NS, Looy CV, Rothfels CJ. Inferring the Total-Evidence Timescale of Marattialean Fern Evolution in the Face of Model Sensitivity. Syst Biol 2021; 70:1232-1255. [PMID: 33760075 PMCID: PMC8513765 DOI: 10.1093/sysbio/syab020] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 03/09/2021] [Accepted: 03/22/2021] [Indexed: 11/24/2022] Open
Abstract
Phylogenetic divergence-time estimation has been revolutionized by two recent developments: 1) total-evidence dating (or "tip-dating") approaches that allow for the incorporation of fossils as tips in the analysis, with their phylogenetic and temporal relationships to the extant taxa inferred from the data and 2) the fossilized birth-death (FBD) class of tree models that capture the processes that produce the tree (speciation, extinction, and fossilization) and thus provide a coherent and biologically interpretable tree prior. To explore the behavior of these methods, we apply them to marattialean ferns, a group that was dominant in Carboniferous landscapes prior to declining to its modest extant diversity of slightly over 100 species. We show that tree models have a dramatic influence on estimates of both divergence times and topological relationships. This influence is driven by the strong, counter-intuitive informativeness of the uniform tree prior, and the inherent nonidentifiability of divergence-time models. In contrast to the strong influence of the tree models, we find minor effects of differing the morphological transition model or the morphological clock model. We compare the performance of a large pool of candidate models using a combination of posterior-predictive simulation and Bayes factors. Notably, an FBD model with epoch-specific speciation and extinction rates was strongly favored by Bayes factors. Our best-fitting model infers stem and crown divergences for the Marattiales in the mid-Devonian and Late Cretaceous, respectively, with elevated speciation rates in the Mississippian and elevated extinction rates in the Cisuralian leading to a peak diversity of ${\sim}$2800 species at the end of the Carboniferous, representing the heyday of the Psaroniaceae. This peak is followed by the rapid decline and ultimate extinction of the Psaroniaceae, with their descendants, the Marattiaceae, persisting at approximately stable levels of diversity until the present. This general diversification pattern appears to be insensitive to potential biases in the fossil record; despite the preponderance of available fossils being from Pennsylvanian coal balls, incorporating fossilization-rate variation does not improve model fit. In addition, by incorporating temporal data directly within the model and allowing for the inference of the phylogenetic position of the fossils, our study makes the surprising inference that the clade of extant Marattiales is relatively young, younger than any of the fossils historically thought to be congeneric with extant species. This result is a dramatic demonstration of the dangers of node-based approaches to divergence-time estimation, where the assignment of fossils to particular clades is made a priori (earlier node-based studies that constrained the minimum ages of extant genera based on these fossils resulted in much older age estimates than in our study) and of the utility of explicit models of morphological evolution and lineage diversification. [Bayesian model comparison; Carboniferous; divergence-time estimation; fossil record; fossilized birth-death; lineage diversification; Marattiales; models of morphological evolution; Psaronius; RevBayes.].
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Affiliation(s)
- Michael R May
- Department of Integrative Biology, University of California, Berkeley, 3040 Valley Life Sciences Building #3140, Berkeley, CA 94720, USA
- University Herbarium, University of California, Berkeley, 1001 Valley Life Sciences Building #2465, Berkeley, CA 94720, USA
| | - Dori L Contreras
- Department of Paleontology, Perot Museum of Nature and Science, 2201 N. Field Street, Dallas TX 75201, USA
| | - Michael A Sundue
- Department of Plant Biology, University of Vermont, 111 Jeffords Hall, 63 Carrigan Drive, Burlington, VT 05405, USA
- The Pringle Herbarium, University of Vermont, 305 Jeffords Hall, 63 Carrigan Drive, Burlington, VT 05405, USA
| | - Nathalie S Nagalingum
- Department of Botany, California Academy of Sciences, Golden Gate Park, 55 Music Concourse Drive, San Francisco, CA 94118, USA
| | - Cindy V Looy
- Department of Integrative Biology, University of California, Berkeley, 3040 Valley Life Sciences Building #3140, Berkeley, CA 94720, USA
- University Herbarium, University of California, Berkeley, 1001 Valley Life Sciences Building #2465, Berkeley, CA 94720, USA
- Museum of Paleontology, University of California, 1101 Valley Life Sciences Building, Berkeley, CA 94720, USA
| | - Carl J Rothfels
- Department of Integrative Biology, University of California, Berkeley, 3040 Valley Life Sciences Building #3140, Berkeley, CA 94720, USA
- University Herbarium, University of California, Berkeley, 1001 Valley Life Sciences Building #2465, Berkeley, CA 94720, USA
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5
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Jouault C, Maréchal A, Condamine FL, Wang B, Nel A, Legendre F, Perrichot V. Including fossils in phylogeny: a glimpse into the evolution of the superfamily Evanioidea (Hymenoptera: Apocrita) under tip-dating and the fossilized birth–death process. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab034] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Abstract
Using a fossilized birth–death model, a new phylogeny of the superfamily Evanioidea (including ensign wasps, nightshade wasps and hatchet wasps) is proposed, with estimates of divergence times for its constitutive families and for corroborating the monophyly of Evanioidea. Additionally, our Bayesian analyses demonstrate the monophyly of †Anomopterellidae, †Othniodellithidae, †Andreneliidae, Aulacidae, Gasteruptiida and Evaniidae, whereas †Praeaulacidae and †Baissidae appear to be paraphyletic. Vectevania vetula and Hyptiogastrites electrinus are transferred to Aulacidae. We estimate the divergence time of Evanioidea to be in the Late Triassic (~203 Mya). Additionally, three new othniodellithid wasps are described and figured from mid-Cretaceous Burmese amber as the new genus Keratodellitha, with three new species: Keratodellitha anubis sp. nov., Keratodellitha basilisci sp. nov. and Keratodellitha kirin sp. nov. We also document a temporal shift in relative species richness between Ichneumonoidea and Evanioidea.
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Affiliation(s)
| | | | - Fabien L Condamine
- CNRS, UMR 5554 Institut des Sciences de l’Évolution de Montpellier, Place Eugène Bataillon, Montpellier, France
| | - Bo Wang
- 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, China
| | - André Nel
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, Muséum national d’Histoire naturelle, CNRS, SU, EPHE, Université des Antilles, Paris, France
| | - Frédéric Legendre
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, Muséum national d’Histoire naturelle, CNRS, SU, EPHE, Université des Antilles, Paris, France
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6
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Featherstone LA, Di Giallonardo F, Holmes EC, Vaughan TG, Duchêne S. Infectious disease phylodynamics with occurrence data. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13620] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Leo A. Featherstone
- Department of Microbiology and Immunology Peter Doherty Institute for Infection and Immunity University of Melbourne Melbourne Vic. Australia
| | | | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and BiosecurityThe University of Sydney Sydney NSW Australia
- Charles Perkins Centre School of Life and Environmental Sciences The University of Sydney Sydney NSW Australia
- School of Medical Sciences The University of Sydney Sydney NSW Australia
| | - Timothy G. Vaughan
- Department of Biosystems Science and Engineering ETH Zurich Basel Switzerland
- Swiss Institute of Bioinformatics (SIB) Lausanne Switzerland
| | - Sebastián Duchêne
- Department of Microbiology and Immunology Peter Doherty Institute for Infection and Immunity University of Melbourne Melbourne Vic. Australia
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7
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Marjanović D. The Making of Calibration Sausage Exemplified by Recalibrating the Transcriptomic Timetree of Jawed Vertebrates. Front Genet 2021; 12:521693. [PMID: 34054911 PMCID: PMC8149952 DOI: 10.3389/fgene.2021.521693] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/22/2021] [Indexed: 01/20/2023] Open
Abstract
Molecular divergence dating has the potential to overcome the incompleteness of the fossil record in inferring when cladogenetic events (splits, divergences) happened, but needs to be calibrated by the fossil record. Ideally but unrealistically, this would require practitioners to be specialists in molecular evolution, in the phylogeny and the fossil record of all sampled taxa, and in the chronostratigraphy of the sites the fossils were found in. Paleontologists have therefore tried to help by publishing compendia of recommended calibrations, and molecular biologists unfamiliar with the fossil record have made heavy use of such works (in addition to using scattered primary sources and copying from each other). Using a recent example of a large node-dated timetree inferred from molecular data, I reevaluate all 30 calibrations in detail, present the current state of knowledge on them with its various uncertainties, rerun the dating analysis, and conclude that calibration dates cannot be taken from published compendia or other secondary or tertiary sources without risking strong distortions to the results, because all such sources become outdated faster than they are published: 50 of the (primary) sources I cite to constrain calibrations were published in 2019, half of the total of 280 after mid-2016, and 90% after mid-2005. It follows that the present work cannot serve as such a compendium either; in the slightly longer term, it can only highlight known and overlooked problems. Future authors will need to solve each of these problems anew through a thorough search of the primary paleobiological and chronostratigraphic literature on each calibration date every time they infer a new timetree, and that literature is not optimized for that task, but largely has other objectives.
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Affiliation(s)
- David Marjanović
- Department of Evolutionary Morphology, Science Programme “Evolution and Geoprocesses”, Museum für Naturkunde – Leibniz Institute for Evolutionary and Biodiversity Research, Berlin, Germany
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8
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Spasojevic T, Broad GR, Sääksjärvi IE, Schwarz M, Ito M, Korenko S, Klopfstein S. Mind the Outgroup and Bare Branches in Total-Evidence Dating: a Case Study of Pimpliform Darwin Wasps (Hymenoptera, Ichneumonidae). Syst Biol 2021; 70:322-339. [PMID: 33057674 PMCID: PMC7875445 DOI: 10.1093/sysbio/syaa079] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 10/02/2020] [Accepted: 10/02/2020] [Indexed: 01/16/2023] Open
Abstract
Taxon sampling is a central aspect of phylogenetic study design, but it has received limited attention in the context of total-evidence dating, a widely used dating approach that directly integrates molecular and morphological information from extant and fossil taxa. We here assess the impact of commonly employed outgroup sampling schemes and missing morphological data in extant taxa on age estimates in a total-evidence dating analysis under the uniform tree prior. Our study group is Pimpliformes, a highly diverse, rapidly radiating group of parasitoid wasps of the family Ichneumonidae. We analyze a data set comprising 201 extant and 79 fossil taxa, including the oldest fossils of the family from the Early Cretaceous and the first unequivocal representatives of extant subfamilies from the mid-Paleogene. Based on newly compiled molecular data from ten nuclear genes and a morphological matrix that includes 222 characters, we show that age estimates become both older and less precise with the inclusion of more distant and more poorly sampled outgroups. These outgroups not only lack morphological and temporal information but also sit on long terminal branches and considerably increase the evolutionary rate heterogeneity. In addition, we discover an artifact that might be detrimental for total-evidence dating: "bare-branch attraction," namely high attachment probabilities of certain fossils to terminal branches for which morphological data are missing. Using computer simulations, we confirm the generality of this phenomenon and show that a large phylogenetic distance to any of the extant taxa, rather than just older age, increases the risk of a fossil being misplaced due to bare-branch attraction. After restricting outgroup sampling and adding morphological data for the previously attracting, bare branches, we recover a Jurassic origin for Pimpliformes and Ichneumonidae. This first age estimate for the group not only suggests an older origin than previously thought but also that diversification of the crown group happened well before the Cretaceous-Paleogene boundary. Our case study demonstrates that in order to obtain robust age estimates, total-evidence dating studies need to be based on a thorough and balanced sampling of both extant and fossil taxa, with the aim of minimizing evolutionary rate heterogeneity and missing morphological information. [Bare-branch attraction; ichneumonids; fossils; morphological matrix; phylogeny; RoguePlots.].
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Affiliation(s)
- Tamara Spasojevic
- Abteilung Wirbellose Tiere Invertebrates, Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse 15, 3005 Bern, Switzerland
- Institute of Ecology and Evolution, Department of Biology, University of Bern, 3012 Bern, Switzerland
- Department of Entomology, National Museum of Natural History, Washington, DC 20560, USA
| | - Gavin R Broad
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | | | | | - Masato Ito
- Graduate School of Agricultural Science, Department of Agrobioscience, Kobe University, 657-8501 Japan
| | - Stanislav Korenko
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 21 Prague 6, Suchdol, Czech Republic
| | - Seraina Klopfstein
- Abteilung Wirbellose Tiere Invertebrates, Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse 15, 3005 Bern, Switzerland
- Institute of Ecology and Evolution, Department of Biology, University of Bern, 3012 Bern, Switzerland
- Abteilung für Biowissenschaften, Naturhistorisches Museum Basel, 4051 Basel, Switzerland
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9
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Simões TR, Caldwell MW, Pierce SE. Sphenodontian phylogeny and the impact of model choice in Bayesian morphological clock estimates of divergence times and evolutionary rates. BMC Biol 2020; 18:191. [PMID: 33287835 PMCID: PMC7720557 DOI: 10.1186/s12915-020-00901-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/16/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The vast majority of all life that ever existed on earth is now extinct and several aspects of their evolutionary history can only be assessed by using morphological data from the fossil record. Sphenodontian reptiles are a classic example, having an evolutionary history of at least 230 million years, but currently represented by a single living species (Sphenodon punctatus). Hence, it is imperative to improve the development and implementation of probabilistic models to estimate evolutionary trees from morphological data (e.g., morphological clocks), which has direct benefits to understanding relationships and evolutionary patterns for both fossil and living species. However, the impact of model choice on morphology-only datasets has been poorly explored. RESULTS Here, we investigate the impact of a wide array of model choices on the inference of evolutionary trees and macroevolutionary parameters (divergence times and evolutionary rates) using a new data matrix on sphenodontian reptiles. Specifically, we tested different clock models, clock partitioning, taxon sampling strategies, sampling for ancestors, and variations on the fossilized birth-death (FBD) tree model parameters through time. We find a strong impact on divergence times and background evolutionary rates when applying widely utilized approaches, such as allowing for ancestors in the tree and the inappropriate assumption of diversification parameters being constant through time. We compare those results with previous studies on the impact of model choice to molecular data analysis and provide suggestions for improving the implementation of morphological clocks. Optimal model combinations find the radiation of most major lineages of sphenodontians to be in the Triassic and a gradual but continuous drop in morphological rates of evolution across distinct regions of the phenotype throughout the history of the group. CONCLUSIONS We provide a new hypothesis of sphenodontian classification, along with detailed macroevolutionary patterns in the evolutionary history of the group. Importantly, we provide suggestions to avoid overestimated divergence times and biased parameter estimates using morphological clocks. Partitioning relaxed clocks offers methodological limitations, but those can be at least partially circumvented to reveal a detailed assessment of rates of evolution across the phenotype and tests of evolutionary mosaicism.
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Affiliation(s)
- Tiago R Simões
- Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
| | - Michael W Caldwell
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Stephanie E Pierce
- Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
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10
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Matschiner M, Böhne A, Ronco F, Salzburger W. The genomic timeline of cichlid fish diversification across continents. Nat Commun 2020; 11:5895. [PMID: 33208747 PMCID: PMC7674422 DOI: 10.1038/s41467-020-17827-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 07/15/2020] [Indexed: 11/23/2022] Open
Abstract
Cichlid fishes are celebrated for their vast taxonomic, phenotypic, and ecological diversity; however, a central aspect of their evolution - the timeline of their diversification - remains contentious. Here, we generate draft genome assemblies of 14 species representing the global cichlid diversity and integrate these into a new phylogenomic hypothesis of cichlid and teleost evolution that we time-calibrate with 58 re-evaluated fossil constraints and a new Bayesian model accounting for fossil-assignment uncertainty. Our results support cichlid diversification long after the breakup of the supercontinent Gondwana and lay the foundation for precise temporal reconstructions of the exceptional continental cichlid adaptive radiations.
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Affiliation(s)
- Michael Matschiner
- Zoological Institute, University of Basel, Basel, Switzerland.
- Department of Palaeontology and Museum, University of Zurich, Zurich, Switzerland.
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.
| | - Astrid Böhne
- Zoological Institute, University of Basel, Basel, Switzerland
- Center for Molecular Biodiversity Research (ZMB), Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Fabrizia Ronco
- Zoological Institute, University of Basel, Basel, Switzerland
| | - Walter Salzburger
- Zoological Institute, University of Basel, Basel, Switzerland.
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.
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11
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Barido-Sottani J, van Tiel NMA, Hopkins MJ, Wright DF, Stadler T, Warnock RCM. Ignoring Fossil Age Uncertainty Leads to Inaccurate Topology and Divergence Time Estimates in Time Calibrated Tree Inference. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00183] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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12
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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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