The DOI matches its Crossref record; 47 of the 47 references it cites were found in a registry or an index.
Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record
Open accessAbstract
The branching times of molecular phylogenies allow us to infer speciation and extinction dynamics even when fossils are absent. Troublingly, phylogenetic approaches usually return estimates of zero extinction, conflicting with fossil evidence. Phylogenies and fossils do agree, however, that there are often limits to diversity. Here, we present a general approach to evaluate the likelihood of a phylogeny under a model that accommodates diversity-dependence and extinction. We find, by likelihood maximization, that extinction is estimated most precisely if the rate of increase in the number of lineages in the phylogeny saturates towards the present or first decreases and then increases. We demonstrate the utility and limits of our approach by applying it to the phylogenies for two cases where a fossil record exists (Cetacea and Cenozoic macroperforate planktonic foraminifera) and to three radiations lacking fossil evidence ( Dendroica , Plethodon and Heliconius ). We propose that the diversity-dependence model with extinction be used as the standard model for macro-evolutionary dynamics because of its biological realism and flexibility.
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Alfaro, M. E., Santini, F., Brock, C., Alamillo, H., Dornburg, A., Rabosky, D. L., Carnevale, G., & Harmon, L. J. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0811087106 · Cited by 833
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Rabosky, D. L. (2010) · Evolution · doi:10.1111/j.1558-5646.2009.00926.x · Cited by 589
Niche Construction: The Neglected Process in Evolution (MPB-37)
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The Shifting Balance of Diversity Among Major Marine Animal Groups
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Density-Dependent Cladogenesis in Birds
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Mega-evolutionary dynamics of the adaptive radiation of birds
Cooney, C. R., Bright, J. A., Capp, E. J. R., Chira, A. M., Hughes, E. C., Moody, C. J. A., Nouri, L. O., Varley, Z. K., & Thomas, G. H. (2017) · Nature · doi:10.1038/nature21074 · Cited by 356
Metadata
- Authors
- Etienne, R. S., Haegeman, B., Stadler, T., Aze, T., Pearson, P. N., Purvis, A., & Phillimore, A. B.
- Venue
- Proceedings of the Royal Society B: Biological Sciences
- Publisher
- The Royal Society
- Published
- 2011-10-12
- Volume
- 279
- Issue
- 1732
- Pages
- 1300-1309
- ISSN
- 0080-4649 (ISSN-L)
- 0962-8452
- 1471-2954
- OpenAlex
- W2126833785
- Cited by
- 342
- References
- 47
- FWCI
- 17.43
- Type
- journal article
- Language
- en
- Open access
- green
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- Etienne, R. S., Haegeman, B., Stadler, T., Aze, T., Pearson, P. N., Purvis, A., & Phillimore, A. B. (2012). Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record. Proceedings of the Royal Society B: Biological Sciences. https://doi.org/10.1098/rspb.2011.1439
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