Accounting for Calibration Uncertainty in Phylogenetic Estimation of Evolutionary Divergence Times

Ho, Simon Y. W.; Phillips, Matthew J.

doi:10.1093/sysbio/syp035

Cited by 816 publications

(786 citation statements)

References 89 publications

(153 reference statements)

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“…Unfortunately, this means that there are no hard upper constraints to divergence times which can lead to arbitrarily old age estimates (especially near the root of the tree) while the substitution rate takes on low values [64]. Even when each node has a prior age distribution associated with it, as is the case here, a more explicit prior on the age of root is desirable [64]. We therefore also ran analyses in which we placed a normally distributed prior on the age of the root node of the tree (which represents the divergence between Sphecidae and Crabronidae þ bees).…”

Section: (I) Phylogenetic Analysesmentioning

confidence: 99%

Bees diversified in the age of eudicots

2013

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Reliable estimates on the ages of the major bee clades are needed to further understand the evolutionary history of bees and their close association with flowering plants. Divergence times have been estimated for a few groups of bees, but no study has yet provided estimates for all major bee lineages. To date the origin of bees and their major clades, we first perform a phylogenetic analysis of bees including representatives from every extant family, subfamily and almost all tribes, using sequence data from seven genes. We then use this phylogeny to place 14 time calibration points based on information from the fossil record for an uncorrelated relaxed clock divergence time analysis taking into account uncertainties in phylogenetic relationships and the fossil record. We explore the effect of placing a hard upper age bound near the root of the tree and the effect of different topologies on our divergence time estimates. We estimate that crown bees originated approximately 123 Ma (million years ago) (113-132 Ma), concurrently with the origin or diversification of the eudicots, a group comprising 75 per cent of angiosperm species. All of the major bee clades are estimated to have originated during the Middle to Late Cretaceous, which is when angiosperms became the dominant group of land plants.

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Section: (I) Phylogenetic Analysesmentioning

confidence: 99%

Bees diversified in the age of eudicots

2013

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“…Simultaneous phylogenetic reconstruction and dating of the rbcL data set was performed using BEAST ver. 1.5.3 (Drummond and and employed a soft lower bound (see Yang and Rannala, 2006; also see Ho and Phillips, 2009) to constrain the divergence time between Liliaceae and Smilacaceae. This constraint was set using a lognormal distribution based on the age of Smilax wilcoxensis (offset 48.6, mean 52 and the 95% high probability density (HPD) 48.6-65 Ma, which covered the whole Paleocene and the early Eocene).…”

Section: Dating the Times Of Divergencementioning

confidence: 99%

Evolutionary events in Lilium (including Nomocharis, Liliaceae) are temporally correlated with orogenies of the Q–T plateau and the Hengduan Mountains

Gao

Harris

Zhou

et al. 2013

Molecular Phylogenetics and Evolution

136

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“…The fossil calibrating information was incorporated in the form of lognormal prior age distributions in line with the recommendations of Ho (2007) and Ho and Phillips (2009). Each of the fossil-based minimum clade ages was set as the zero offset of the lognormal distribution to represent the minimum bound.…”

Section: Beast Analysismentioning

confidence: 99%

Evolutionary and biogeographic history of weasel-like carnivorans (Musteloidea)

Sato

Wolsan

Prevosti

et al. 2012

Molecular Phylogenetics and Evolution

140

122

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We analyzed a concatenated (8492 bp) nuclear-mitochondrial DNA data set from 44 musteloids The early offshoots of this radiation largely evolved into badger and marten ecological niches (Taxidiinae, Melinae, Mellivorinae, Guloninae, and Helictidinae), whereas the later divergences have adapted to other niches including those of weasels, polecats, minks, and otters (Mustelinae, Ictonychinae, and Lutrinae). Notably, and contrary to traditional beliefs, the morphological adaptations of badgers, martens, weasels, polecats, and minks each evolved independently more than once within Mustelidae. Ictonychinae (which is most closely related to Lutrinae) arose approximately 9.5-8.9 MYA, most likely in Asia, where it diverged into the Old World and Poecilogale, respectively, we propose that Pekania and Poecilictis be treated as valid genera and that -Martes‖ pennanti and -Ictonyx‖ libyca, respectively, be assigned to these genera.

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Accounting for Calibration Uncertainty in Phylogenetic Estimation of Evolutionary Divergence Times

Cited by 816 publications

References 89 publications

Bees diversified in the age of eudicots

Bees diversified in the age of eudicots

Evolutionary events in Lilium (including Nomocharis, Liliaceae) are temporally correlated with orogenies of the Q–T plateau and the Hengduan Mountains

Evolutionary and biogeographic history of weasel-like carnivorans (Musteloidea)

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