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Here, we are using tip calibration and morphological data, and we use these plots to show that the assumption of an infinite sites plot may not hold true with tip calibration. The root constraint may provide an upper bound, and so shorten the upper older confidence intervals. In contrast, and unlike node dating analyses, internal nodes are not constrained, so the expected positive relationship between node age and uncertainty may not be applicable Fig.

We only applied eight node calibrations, so perhaps more node constraints would produce ages more congruent with molecular divergence estimates.

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However, even with node constraints Fig. A potential problem here could be specific problems with clock models in MrBayes: The spike in rates near the base may be due to divergence of major clades, and it has been suggested that these high rates can influence divergence times Beck and Lee This spike does not appear attributable to fossils near the base, as it alters when using different time constraints even when identical fossils are included Fig. Additionally, factors such as increasing character conflict as datasets increase in size may explain difficulties in achieving convergence with larger character matrices.

Therefore, we do not believe that these reflect specific software idiosyncrasies or bugs. Therefore, the current tree priors may not accurately capture variations in sampling and so may be a problem for the dating analyses, and could potentially be improved to reflect variable sampling through time. However, the fact that there are problems with dating in models with no fossils Tables 1 and 2 suggests that it is unlikely that variable sampling is the key or sole explanation of problems with morphological clock models.

It may be that smaller clades show more uniform rates of morphological evolution across all branches, whereas among Placentalia as a whole, there are substantially different rates of morphological change within different subclades, or at different times. Effective priors on the nodes appear to be quite old Fig. The effective priors differ between the uniform tree prior and fossilized birth—death tree prior analyses, but the data still produce ancient ages in the posterior Fig. Therefore, morphometric data from dentition of basal Placentalia Late Cretaceous—Early Paleogene could be used, as the data would have not yet reached saturation and would provide the appropriate temporal resolution D.

When sampling and diversification rates are considered alongside occurrence dates, independently of the morphological clock, the dates produced are more congruent with the fossil record. Here, we employ a method that incorporates branching, extinction, and sampling estimates Bapst alone independent of the morphological clock or character change to act as time priors on nodes and to coalesce on a time of common ancestry for Placentalia.

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This method can increase the congruence between the fossil record and molecular clocks Fig. Clearly, these estimates are sensitive to prior assumptions Fig. S3 , as the lower sampling rate input gives an older age estimate, mainly due to the greater uncertainty in the model. However, this argument may become circular: The morphological clock, in its current form, cannot close the gap between the fossil record and molecular clock estimates for the date of origin of Placentalia. Our results suggest that morphological dating analyses as currently used tend to estimate ancient divergence estimates for clades when based on morphological data.

Morphological dating approaches cannot reconcile molecular estimates and a literal reading of the fossil record. We are very grateful to D. Polly and an anonymous reviewer for suggestions that greatly improved the manuscript. We are also grateful to J.

Donoghue for help and suggestions during this study. We also thank the Bristol Palaeobiology group for general suggestions. National Center for Biotechnology Information , U. Evolution; International Journal of Organic Evolution.

Dating placentalia: Morphological clocks fail to close the molecular fossil gap

Published online Apr 6. Puttick , 1 Gavin H. Thomas , 2 and Michael J. Author information Article notes Copyright and License information Disclaimer. Evolution published by Wiley Periodicals, Inc. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. This article has been cited by other articles in PMC. Morphological clock ages indicate an ancient origin for Placentalia when using a uniform distribution on the root constraint Table S3.

Abstract Dating the origin of Placentalia has been a contentious issue for biologists and paleontologists. Mammalia, molecular clock, morphological clock, placentalia, tip dating. Phylogenies Overall, we performed three main analyses of the morphological clock with different modes of time calibration: Table 1 Summary of the main analyses using the different phylogenies and dating methods. Main phylogeny Topology Major analyses Taxa included 1 Unconstrained fixed tree Nonclock phylogeny estimated with no topological constraints prior to dating analyses. Open in a separate window.

CAL3 Phylogeny dating methods can incorporate estimates of speciation, extinction, and fossil sampling rates, either independently of the morphological clock e.

Table 2 Morphological clock ages indicate an ancient origin for Placentalia. Table 3 Topological constraints have little effect on the age estimates for Placentalia. Root Placentals Marsupials Dos Reis Discussion The ages for deep nodes in the phylogeny of Mammalia presented here do not close the gap between the fossil record and molecular estimates of the age of origin of Placentalia. Conclusions The morphological clock, in its current form, cannot close the gap between the fossil record and molecular clock estimates for the date of origin of Placentalia.

Supporting information Figure S1. Click here for additional data file. Taxonomic occurrences of mammalia recorded in , Fossilworks, the Evolution of Terrestrial Ecosystems database, and the Paleobiology Database. The fossil record of North American mammals: Quantitative analysis of the timing of the origin and diversification of extant placental orders.

Protungulatum, confirmed cretaceous occurrence of an otherwise paleocene eutherian placental? Identifying hidden rate changes in the evolution of a binary morphological character: Ancient dates or accelerated rates? Morphological clocks and the antiquity of placental mammals. Early origins of modern birds and mammals: Exploring macroevolution using modern and fossil data.

The extinction of the dinosaurs.

Mosaicism, modules, and the evolution of birds: Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals. Evolutionary and preservational constraints on origins of biologic groups: No known hominin species matches the expected dental morphology of the last common ancestor of Neanderthals and modern humans.

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A radiation of arboreal basal eutherian mammals beginning in the Late Cretaceous of India. Constraints on clade ages from fossil outgroups. New postcranial bones of the extinct mammalian family Nyctitheriidae Paleogene, UK: Primitive euarchontans with scansorial locomotion.

Early Palaeogene Louisinidae Macroscelidea, Mammalia , their relationships and north European diversity. The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times.

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