Strong support for a heterogeneous speciation decline model in Dinosauria: a response to claims made by Bonsor <italic toggle="yes">et al</italic>. (2020)
Through phylogenetic modelling, we previously presented strong support for diversification decline in the three major subclades of dinosaurs (Sakamoto et al. 2016 Proc. Natl Acad. Sci. USA 113, 5036–5040. (doi:10.1073/pnas.1521478113)). Recently, our support for this model has been criticized (Bonso...
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| Format: | Article |
| Language: | English |
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The Royal Society
2021-08-01
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| Series: | Royal Society Open Science |
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| Online Access: | https://royalsocietypublishing.org/doi/10.1098/rsos.202143 |
| _version_ | 1818572834166800384 |
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| author | Manabu Sakamoto Michael J. Benton Chris Venditti |
| author_facet | Manabu Sakamoto Michael J. Benton Chris Venditti |
| author_sort | Manabu Sakamoto |
| collection | DOAJ |
| description | Through phylogenetic modelling, we previously presented strong support for diversification decline in the three major subclades of dinosaurs (Sakamoto et al. 2016 Proc. Natl Acad. Sci. USA 113, 5036–5040. (doi:10.1073/pnas.1521478113)). Recently, our support for this model has been criticized (Bonsor et al. 2020 R. Soc. Open Sci. 7, 201195. (doi:10.1098/rsos.201195)). Here, we highlight that these criticisms seem to largely stem from a misunderstanding of our study: contrary to Bonsor et al.'s claims, our model accounts for heterogeneity in diversification dynamics, was selected based on deviance information criterion (DIC) scores (not parameter significance), and intercepts were estimated to account for uncertainties in the root age of the phylogenetic tree. We also demonstrate that their new analyses are not comparable to our models: they fit simple, Dinosauria-wide models as a direct comparison to our group-wise models, and their additional trees are subclades that are limited in taxonomic coverage and temporal span, i.e. severely affected by incomplete sampling. We further present results of new analyses on larger, better-sampled trees (N = 961) of dinosaurs, showing support for the time-quadratic model. Disagreements in how we interpret modelled diversification dynamics are to be expected, but criticisms should be based on sound logic and understanding of the model under discussion. |
| first_indexed | 2024-12-15T00:02:56Z |
| format | Article |
| id | doaj.art-e81125d871a44813a3c18140dfc29361 |
| institution | Directory Open Access Journal |
| issn | 2054-5703 |
| language | English |
| last_indexed | 2024-12-15T00:02:56Z |
| publishDate | 2021-08-01 |
| publisher | The Royal Society |
| record_format | Article |
| series | Royal Society Open Science |
| spelling | doaj.art-e81125d871a44813a3c18140dfc293612022-12-21T22:42:51ZengThe Royal SocietyRoyal Society Open Science2054-57032021-08-018810.1098/rsos.202143Strong support for a heterogeneous speciation decline model in Dinosauria: a response to claims made by Bonsor <italic toggle="yes">et al</italic>. (2020)Manabu Sakamoto0Michael J. Benton1Chris Venditti2School of Life Sciences, University of Lincoln, Lincoln, UKSchool of Earth Sciences, University of Bristol, Bristol, UKSchool of Biological Sciences, University of Reading, Reading, UKThrough phylogenetic modelling, we previously presented strong support for diversification decline in the three major subclades of dinosaurs (Sakamoto et al. 2016 Proc. Natl Acad. Sci. USA 113, 5036–5040. (doi:10.1073/pnas.1521478113)). Recently, our support for this model has been criticized (Bonsor et al. 2020 R. Soc. Open Sci. 7, 201195. (doi:10.1098/rsos.201195)). Here, we highlight that these criticisms seem to largely stem from a misunderstanding of our study: contrary to Bonsor et al.'s claims, our model accounts for heterogeneity in diversification dynamics, was selected based on deviance information criterion (DIC) scores (not parameter significance), and intercepts were estimated to account for uncertainties in the root age of the phylogenetic tree. We also demonstrate that their new analyses are not comparable to our models: they fit simple, Dinosauria-wide models as a direct comparison to our group-wise models, and their additional trees are subclades that are limited in taxonomic coverage and temporal span, i.e. severely affected by incomplete sampling. We further present results of new analyses on larger, better-sampled trees (N = 961) of dinosaurs, showing support for the time-quadratic model. Disagreements in how we interpret modelled diversification dynamics are to be expected, but criticisms should be based on sound logic and understanding of the model under discussion.https://royalsocietypublishing.org/doi/10.1098/rsos.202143dinosaursphylogenetic comparative methodsgeneralized linear mixed modeldiversification ratediversification decline |
| spellingShingle | Manabu Sakamoto Michael J. Benton Chris Venditti Strong support for a heterogeneous speciation decline model in Dinosauria: a response to claims made by Bonsor <italic toggle="yes">et al</italic>. (2020) Royal Society Open Science dinosaurs phylogenetic comparative methods generalized linear mixed model diversification rate diversification decline |
| title | Strong support for a heterogeneous speciation decline model in Dinosauria: a response to claims made by Bonsor <italic toggle="yes">et al</italic>. (2020) |
| title_full | Strong support for a heterogeneous speciation decline model in Dinosauria: a response to claims made by Bonsor <italic toggle="yes">et al</italic>. (2020) |
| title_fullStr | Strong support for a heterogeneous speciation decline model in Dinosauria: a response to claims made by Bonsor <italic toggle="yes">et al</italic>. (2020) |
| title_full_unstemmed | Strong support for a heterogeneous speciation decline model in Dinosauria: a response to claims made by Bonsor <italic toggle="yes">et al</italic>. (2020) |
| title_short | Strong support for a heterogeneous speciation decline model in Dinosauria: a response to claims made by Bonsor <italic toggle="yes">et al</italic>. (2020) |
| title_sort | strong support for a heterogeneous speciation decline model in dinosauria a response to claims made by bonsor italic toggle yes et al italic 2020 |
| topic | dinosaurs phylogenetic comparative methods generalized linear mixed model diversification rate diversification decline |
| url | https://royalsocietypublishing.org/doi/10.1098/rsos.202143 |
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