Why extinction estimates from extant phylogenies are so often zero.
| Autor: | Louca S; Department of Biology, University of Oregon, 1210 University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, 5289 University of Oregon, Eugene, OR 97403, USA. Electronic address: louca.research@gmail.com., Pennell MW; Biodiversity Research Centre, University of British Columbia, 2212 Main Mall, Vancouver, BC V6T1Z4, Canada; Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T1Z4, Canada. Electronic address: pennell@zoology.ubc.ca. |
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| Jazyk: | angličtina |
| Zdroj: | Current biology : CB [Curr Biol] 2021 Jul 26; Vol. 31 (14), pp. 3168-3173.e4. Date of Electronic Publication: 2021 May 20. |
| DOI: | 10.1016/j.cub.2021.04.066 |
| Abstrakt: | Time-calibrated phylogenies of extant species ("extant timetrees") are widely used to estimate historical speciation and extinction rates by fitting stochastic birth-death models. 1 These approaches have long been controversial, as many phylogenetic studies report zero extinction in many taxa, contradicting the high extinction rates seen in the fossil record and the fact that the majority of species ever to have existed are now extinct. 2-9 To date, the causes of this discrepancy remain unresolved. Here, we provide a novel and simple explanation for these "zero-inflated" extinction estimates, based on the recent discovery that there exist many alternative "congruent" diversification scenarios that cannot be distinguished based solely on extant timetrees. 10 Due to such congruencies, estimation methods tend to converge to some scenario congruent to (i.e., statistically indistinguishable from) the true diversification scenario, but not necessarily to the true diversification scenario itself. This congruent scenario may exhibit negative extinction rates, a biologically meaningless but mathematically feasible situation, in which case estimators will tend to stick to the boundary of zero extinction. Based on this explanation, we make multiple testable predictions, which we confirm using analyses of simulated trees and 121 empirical trees. In contrast to other proposed mechanisms for erroneous extinction rate estimates, 5 , 11-14 our proposed mechanism specifically explains the zero inflation of previous extinction rate estimates in the absence of detectable model violations, even for large trees. Not only do our results likely resolve a long-standing mystery in phylogenetics, they demonstrate that model congruencies can have severe consequences in practice. Competing Interests: Declaration of interests The authors declare no competing interests. (Copyright © 2021 Elsevier Inc. All rights reserved.) |
| Databáze: | MEDLINE |
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