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Illustrating phylogenetic placement of fossils using RoguePlots: An example from ichneumonid parasitoid wasps (Hymenoptera, Ichneumonidae) and an extensive morphological matrix
The fossil record constitutes the primary source of information about the evolutionary history of extant and extinct groups, and many analyses of macroevolution rely on fossils that are accurately placed within phylogenies. To avoid misinterpretation of the fossil record, especially by non-palaeonto...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6445432/ https://www.ncbi.nlm.nih.gov/pubmed/30939174 http://dx.doi.org/10.1371/journal.pone.0212942 |
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author | Klopfstein, Seraina Spasojevic, Tamara |
author_facet | Klopfstein, Seraina Spasojevic, Tamara |
author_sort | Klopfstein, Seraina |
collection | PubMed |
description | The fossil record constitutes the primary source of information about the evolutionary history of extant and extinct groups, and many analyses of macroevolution rely on fossils that are accurately placed within phylogenies. To avoid misinterpretation of the fossil record, especially by non-palaeontologists, the proper assessment and communication of uncertainty in fossil placement is crucial. We here use Bayesian morphological phylogenetics to evaluate the classifications of fossil parasitoid wasps (Hymenoptera, Ichneumonidae) and introduce ‘RoguePlots’ to illustrate placement uncertainty on the phylogeny of extant taxa. Based on an extensive, newly constructed morphological matrix of 222 characters in 24 fossil and 103 extant taxa, we test three different aspects of models of morphological evolution. We find that a model that includes ordered characters, among-character rate variation, and a state-space restricted to observed states achieves the highest marginal likelihoods. The individual RoguePlots reveal large differences in confidence in the placement of the different fossils and allow some refinements to their classification: Polyhelictes bipolarus and Ichninsum appendicrassum are moved from an uncertain subfamily placement to Pimplinae, Plectiscidea lanhami is transferred to Allomacrus in Cylloceriinae (Allomacrus lanhami, comb. nov.), Lithotorus cressoni is moved from Diplazontinae to Orthocentrinae, and we note uncertainty in the generic placements of Rhyssella? vera and Xanthopimpla? messelensis. We discuss potential artefacts that might result in biased posterior probabilities in Bayesian morphological phylogenetic analyses, pertaining to character and taxon sampling, fossilization biases, and model misspecification. Finally, we suggest future directions both in ichneumonid palaeontology and in the way RoguePlots can improve both assessment and representation of placement uncertainty, both in fossils and other rogue taxa. |
format | Online Article Text |
id | pubmed-6445432 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-64454322019-04-17 Illustrating phylogenetic placement of fossils using RoguePlots: An example from ichneumonid parasitoid wasps (Hymenoptera, Ichneumonidae) and an extensive morphological matrix Klopfstein, Seraina Spasojevic, Tamara PLoS One Research Article The fossil record constitutes the primary source of information about the evolutionary history of extant and extinct groups, and many analyses of macroevolution rely on fossils that are accurately placed within phylogenies. To avoid misinterpretation of the fossil record, especially by non-palaeontologists, the proper assessment and communication of uncertainty in fossil placement is crucial. We here use Bayesian morphological phylogenetics to evaluate the classifications of fossil parasitoid wasps (Hymenoptera, Ichneumonidae) and introduce ‘RoguePlots’ to illustrate placement uncertainty on the phylogeny of extant taxa. Based on an extensive, newly constructed morphological matrix of 222 characters in 24 fossil and 103 extant taxa, we test three different aspects of models of morphological evolution. We find that a model that includes ordered characters, among-character rate variation, and a state-space restricted to observed states achieves the highest marginal likelihoods. The individual RoguePlots reveal large differences in confidence in the placement of the different fossils and allow some refinements to their classification: Polyhelictes bipolarus and Ichninsum appendicrassum are moved from an uncertain subfamily placement to Pimplinae, Plectiscidea lanhami is transferred to Allomacrus in Cylloceriinae (Allomacrus lanhami, comb. nov.), Lithotorus cressoni is moved from Diplazontinae to Orthocentrinae, and we note uncertainty in the generic placements of Rhyssella? vera and Xanthopimpla? messelensis. We discuss potential artefacts that might result in biased posterior probabilities in Bayesian morphological phylogenetic analyses, pertaining to character and taxon sampling, fossilization biases, and model misspecification. Finally, we suggest future directions both in ichneumonid palaeontology and in the way RoguePlots can improve both assessment and representation of placement uncertainty, both in fossils and other rogue taxa. Public Library of Science 2019-04-02 /pmc/articles/PMC6445432/ /pubmed/30939174 http://dx.doi.org/10.1371/journal.pone.0212942 Text en © 2019 Klopfstein, Spasojevic http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Klopfstein, Seraina Spasojevic, Tamara Illustrating phylogenetic placement of fossils using RoguePlots: An example from ichneumonid parasitoid wasps (Hymenoptera, Ichneumonidae) and an extensive morphological matrix |
title | Illustrating phylogenetic placement of fossils using RoguePlots: An example from ichneumonid parasitoid wasps (Hymenoptera, Ichneumonidae) and an extensive morphological matrix |
title_full | Illustrating phylogenetic placement of fossils using RoguePlots: An example from ichneumonid parasitoid wasps (Hymenoptera, Ichneumonidae) and an extensive morphological matrix |
title_fullStr | Illustrating phylogenetic placement of fossils using RoguePlots: An example from ichneumonid parasitoid wasps (Hymenoptera, Ichneumonidae) and an extensive morphological matrix |
title_full_unstemmed | Illustrating phylogenetic placement of fossils using RoguePlots: An example from ichneumonid parasitoid wasps (Hymenoptera, Ichneumonidae) and an extensive morphological matrix |
title_short | Illustrating phylogenetic placement of fossils using RoguePlots: An example from ichneumonid parasitoid wasps (Hymenoptera, Ichneumonidae) and an extensive morphological matrix |
title_sort | illustrating phylogenetic placement of fossils using rogueplots: an example from ichneumonid parasitoid wasps (hymenoptera, ichneumonidae) and an extensive morphological matrix |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6445432/ https://www.ncbi.nlm.nih.gov/pubmed/30939174 http://dx.doi.org/10.1371/journal.pone.0212942 |
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