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A mixed relaxed clock model.

Lartillot N, Phillips MJ, Ronquist F - Philos. Trans. R. Soc. Lond., B, Biol. Sci. (2016)

Bottom Line: In this context, the classical pure Brownian relaxed clock appears to be overly rigid, leading to biases in divergence time estimation.By contrast, the use of a mixed clock leads to more recent and more reasonable estimates for the crown ages of placental orders and superorders.Altogether, the mixed clock introduced here represents a first step towards empirically more adequate models of the patterns of rate variation across phylogenetic trees.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Claude Bernard Lyon 1, F-69622 Villeurbanne Cedex, France nicolas.lartillot@univ-lyon1.fr.

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Inferred history of long-term rate variation (Brownian component of the mixed clock) using the tip-dating approach.
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RSTB20150132F3: Inferred history of long-term rate variation (Brownian component of the mixed clock) using the tip-dating approach.

Mentions: Strikingly, however, although half of the total rate variation inferred over the tree is attributed to the autocorrelated component, divergence times inferred under the mixed clock (figure 2) are much more similar to those estimated under a pure uncorrelated clock (d = 3.3, electronic supplementary material, figure S7) than to those inferred under a pure Brownian clock (d = 9.2, electronic supplementary material, figure S8). In addition, as in the case of the pure white noise clock, the posterior median ages under the mixed clock are similar to the prior median ages (d = 6.1 between prior and posterior median ages, versus d = 6.4 under the white noise clock and d = 13.1 under the Brownian clock; figure 3). The size of the credible intervals under the mixed clock (15.6) is intermediate between those obtained under the Brownian clock (15.2) and those returned by the white noise clock (16.7).Figure 2.


A mixed relaxed clock model.

Lartillot N, Phillips MJ, Ronquist F - Philos. Trans. R. Soc. Lond., B, Biol. Sci. (2016)

Inferred history of long-term rate variation (Brownian component of the mixed clock) using the tip-dating approach.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4920333&req=5

RSTB20150132F3: Inferred history of long-term rate variation (Brownian component of the mixed clock) using the tip-dating approach.
Mentions: Strikingly, however, although half of the total rate variation inferred over the tree is attributed to the autocorrelated component, divergence times inferred under the mixed clock (figure 2) are much more similar to those estimated under a pure uncorrelated clock (d = 3.3, electronic supplementary material, figure S7) than to those inferred under a pure Brownian clock (d = 9.2, electronic supplementary material, figure S8). In addition, as in the case of the pure white noise clock, the posterior median ages under the mixed clock are similar to the prior median ages (d = 6.1 between prior and posterior median ages, versus d = 6.4 under the white noise clock and d = 13.1 under the Brownian clock; figure 3). The size of the credible intervals under the mixed clock (15.6) is intermediate between those obtained under the Brownian clock (15.2) and those returned by the white noise clock (16.7).Figure 2.

Bottom Line: In this context, the classical pure Brownian relaxed clock appears to be overly rigid, leading to biases in divergence time estimation.By contrast, the use of a mixed clock leads to more recent and more reasonable estimates for the crown ages of placental orders and superorders.Altogether, the mixed clock introduced here represents a first step towards empirically more adequate models of the patterns of rate variation across phylogenetic trees.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Claude Bernard Lyon 1, F-69622 Villeurbanne Cedex, France nicolas.lartillot@univ-lyon1.fr.

No MeSH data available.


Related in: MedlinePlus