Literature DB >> 30690622

Priors and Posteriors in Bayesian Timing of Divergence Analyses: The Age of Butterflies Revisited.

Nicolas Chazot1,2,3, Niklas Wahlberg1, André Victor Lucci Freitas4, Charles Mitter5, Conrad Labandeira5,6,7,8, Jae-Cheon Sohn9, Ranjit Kumar Sahoo10, Noemy Seraphim11, Rienk de Jong12, Maria Heikkilä13.   

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.
© The Author(s) 2019. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Entities:  

Keywords:  Butterflies; Early Cretaceous; Papilionoidea; fossils; host plants; marginal prior; time-calibration

Mesh:

Year:  2019        PMID: 30690622      PMCID: PMC6893297          DOI: 10.1093/sysbio/syz002

Source DB:  PubMed          Journal:  Syst Biol        ISSN: 1063-5157            Impact factor:   15.683


  39 in total

1.  Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales).

Authors:  Hervé Sauquet; Simon Y W Ho; Maria A Gandolfo; Gregory J Jordan; Peter Wilf; David J Cantrill; Michael J Bayly; Lindell Bromham; Gillian K Brown; Raymond J Carpenter; Daphne M Lee; Daniel J Murphy; J M Kale Sniderman; Frank Udovicic
Journal:  Syst Biol       Date:  2011-12-26       Impact factor: 15.683

2.  Taxon sampling effects in molecular clock dating: an example from the African Restionaceae.

Authors:  H Peter Linder; Christopher R Hardy; Frank Rutschmann
Journal:  Mol Phylogenet Evol       Date:  2005-01-21       Impact factor: 4.286

3.  Fossil-calibrated molecular phylogenies reveal that leaf-mining moths radiated millions of years after their host plants.

Authors:  C Lopez-Vaamonde; N Wikström; C Labandeira; H C J Godfray; S J Goodman; J M Cook
Journal:  J Evol Biol       Date:  2006-07       Impact factor: 2.411

4.  RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.

Authors:  Alexandros Stamatakis
Journal:  Bioinformatics       Date:  2006-08-23       Impact factor: 6.937

5.  BUTTERFLIES AND PLANTS: A PHYLOGENETIC STUDY.

Authors:  Niklas Janz; Sören Nylin
Journal:  Evolution       Date:  1998-04       Impact factor: 3.694

6.  Systematics and evolutionary history of butterflies in the "Taygetis clade" (Nymphalidae: Satyrinae: Euptychiina): towards a better understanding of Neotropical biogeography.

Authors:  Pável F Matos-Maraví; Carlos Peña; Keith R Willmott; André V L Freitas; Niklas Wahlberg
Journal:  Mol Phylogenet Evol       Date:  2012-09-18       Impact factor: 4.286

7.  The impact of calibration and clock-model choice on molecular estimates of divergence times.

Authors:  Sebastián Duchêne; Robert Lanfear; Simon Y W Ho
Journal:  Mol Phylogenet Evol       Date:  2014-06-06       Impact factor: 4.286

8.  The Past Sure is Tense: On Interpreting Phylogenetic Divergence Time Estimates.

Authors:  Joseph W Brown; Stephen A Smith
Journal:  Syst Biol       Date:  2018-03-01       Impact factor: 15.683

9.  Incompatible Ages for Clearwing Butterflies Based on Alternative Secondary Calibrations.

Authors:  Ivonne J Garzón-Orduña; Karina L Silva-Brandão; Keith R Willmott; André V L Freitas; Andrew V Z Brower
Journal:  Syst Biol       Date:  2015-05-25       Impact factor: 15.683

10.  VoSeq: a voucher and DNA sequence web application.

Authors:  Carlos Peña; Tobias Malm
Journal:  PLoS One       Date:  2012-06-12       Impact factor: 3.240

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  20 in total

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Authors:  Jurriaan M de Vos; Hannah Augustijnen; Livio Bätscher; Kay Lucek
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2020-07-13       Impact factor: 6.237

2.  Recalibration of the insect evolutionary time scale using Monte San Giorgio fossils suggests survival of key lineages through the End-Permian Extinction.

Authors:  Matteo Montagna; K Jun Tong; Giulia Magoga; Laura Strada; Andrea Tintori; Simon Y W Ho; Nathan Lo
Journal:  Proc Biol Sci       Date:  2019-10-09       Impact factor: 5.349

3.  Genomics-guided refinement of butterfly taxonomy.

Authors:  Jing Zhang; Qian Cong; Jinhui Shen; Paul A Opler; Nick V Grishin
Journal:  Taxon Rep Int Lepid Surv       Date:  2021-05-29

4.  Genomics-based higher classification of the species-rich Hairstreaks (Lepidoptera: Lycaenidae: Eumaeini).

Authors:  Robert K Robbins; Qian Cong; Jing Zhang; Jinhui Shen; Robert C Busby; Christophe Faynel; Marcelo Duarte; Ananda R P Martins; Carlos Prieto; Gerardo Lamas; Nick V Grishin
Journal:  Syst Entomol       Date:  2022-03-08       Impact factor: 4.841

5.  Stepwise evolution of a butterfly supergene via duplication and inversion.

Authors:  Kang-Wook Kim; Rishi De-Kayne; Ian J Gordon; Kennedy Saitoti Omufwoko; Dino J Martins; Richard Ffrench-Constant; Simon H Martin
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2022-06-13       Impact factor: 6.671

Review 6.  A Revised Phylogenetic Classification for Viola (Violaceae).

Authors:  Thomas Marcussen; Harvey E Ballard; Jiří Danihelka; Ana R Flores; Marcela V Nicola; John M Watson
Journal:  Plants (Basel)       Date:  2022-08-27

7.  Genomic evidence suggests further changes of butterfly names.

Authors:  Jing Zhang; Qian Cong; Jinhui Shen; Paul A Opler; Nick V Grishin
Journal:  Taxon Rep Int Lepid Surv       Date:  2020-11-06

8.  Chromosome Level Assembly of the Comma Butterfly (Polygonia c-album).

Authors:  Maria de la Paz Celorio-Mancera; Pasi Rastas; Rachel A Steward; Soren Nylin; Christopher W Wheat
Journal:  Genome Biol Evol       Date:  2021-05-07       Impact factor: 3.416

9.  Rampant Genome-Wide Admixture across the Heliconius Radiation.

Authors:  Krzysztof M Kozak; Mathieu Joron; W Owen McMillan; Chris D Jiggins
Journal:  Genome Biol Evol       Date:  2021-07-06       Impact factor: 3.416

10.  Miocene Climate and Habitat Change Drove Diversification in Bicyclus, Africa's Largest Radiation of Satyrine Butterflies.

Authors:  Kwaku Aduse-Poku; Erik van Bergen; Szabolcs Sáfián; Steve C Collins; Rampal S Etienne; Leonel Herrera-Alsina; Paul M Brakefield; Oskar Brattström; David J Lohman; Niklas Wahlberg
Journal:  Syst Biol       Date:  2022-04-19       Impact factor: 9.160

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