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Closing the gap between rocks and clocks using total-evidence dating.

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

Bottom Line: Failure to account for diversified sampling results in dramatic DRA, but this can be addressed using existing techniques.The major reason seems to be that current models do not account for dependencies among morphological characters, causing distorted topology and branch length estimates.Finally, diversification and fossil sampling priors that do not incorporate all the available background information can contribute to DRA, but these priors can also be used to compensate for DRA.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, 104 05 Stockholm, Sweden fredrik.ronquist@nrm.se.

No MeSH data available.


Related in: MedlinePlus

The influence of diversification and fossil sampling parameter priors. (a) Divergence time estimates (posterior densities) for crown Placentalia under different priors on diversification and fossil sampling parameters. (b) Ditto for crown Rodentia. (c) Ditto for crown Chiroptera. Ideally, with a large tree and a rich fossil sample, there will be enough information to infer diversification and fossil sampling parameters under an uninformative prior, but the signal in the eutherian data is not strong enough to resist DRA under such conditions. Instead, an uninformative prior results in a poorly defined, bimodal deep-root scenario in the posterior (solid line). It is sufficient to introduce a moderate extra penalty for unobserved ghost lineages to shift the posterior to a well-defined solution with a minimal gap between rocks and clocks. Such penalties may involve assumptions of low extinction rates, high fossil sampling probabilities, high net diversification or any combination of these (various dashed lines); the result is similar under all these scenarios. Bimodal distributions correspond to cases where there are alternative likely placements for key fossils.
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RSTB20150136F5: The influence of diversification and fossil sampling parameter priors. (a) Divergence time estimates (posterior densities) for crown Placentalia under different priors on diversification and fossil sampling parameters. (b) Ditto for crown Rodentia. (c) Ditto for crown Chiroptera. Ideally, with a large tree and a rich fossil sample, there will be enough information to infer diversification and fossil sampling parameters under an uninformative prior, but the signal in the eutherian data is not strong enough to resist DRA under such conditions. Instead, an uninformative prior results in a poorly defined, bimodal deep-root scenario in the posterior (solid line). It is sufficient to introduce a moderate extra penalty for unobserved ghost lineages to shift the posterior to a well-defined solution with a minimal gap between rocks and clocks. Such penalties may involve assumptions of low extinction rates, high fossil sampling probabilities, high net diversification or any combination of these (various dashed lines); the result is similar under all these scenarios. Bimodal distributions correspond to cases where there are alternative likely placements for key fossils.

Mentions: Detailed analysis of divergence time estimates for three key clades under these models (figure 5) shows that the vague prior is associated with a posterior that is both diffuse and bimodal. The multiple peaks in the distribution are caused by different topological placements of key fossils. For instance, the age estimate for crown placentals (figure 5a) is affected by the position of Eomaia, which can be placed either within or outside of Placentalia, and both solutions have significant posterior probability.Figure 5.


Closing the gap between rocks and clocks using total-evidence dating.

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

The influence of diversification and fossil sampling parameter priors. (a) Divergence time estimates (posterior densities) for crown Placentalia under different priors on diversification and fossil sampling parameters. (b) Ditto for crown Rodentia. (c) Ditto for crown Chiroptera. Ideally, with a large tree and a rich fossil sample, there will be enough information to infer diversification and fossil sampling parameters under an uninformative prior, but the signal in the eutherian data is not strong enough to resist DRA under such conditions. Instead, an uninformative prior results in a poorly defined, bimodal deep-root scenario in the posterior (solid line). It is sufficient to introduce a moderate extra penalty for unobserved ghost lineages to shift the posterior to a well-defined solution with a minimal gap between rocks and clocks. Such penalties may involve assumptions of low extinction rates, high fossil sampling probabilities, high net diversification or any combination of these (various dashed lines); the result is similar under all these scenarios. Bimodal distributions correspond to cases where there are alternative likely placements for key fossils.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4920337&req=5

RSTB20150136F5: The influence of diversification and fossil sampling parameter priors. (a) Divergence time estimates (posterior densities) for crown Placentalia under different priors on diversification and fossil sampling parameters. (b) Ditto for crown Rodentia. (c) Ditto for crown Chiroptera. Ideally, with a large tree and a rich fossil sample, there will be enough information to infer diversification and fossil sampling parameters under an uninformative prior, but the signal in the eutherian data is not strong enough to resist DRA under such conditions. Instead, an uninformative prior results in a poorly defined, bimodal deep-root scenario in the posterior (solid line). It is sufficient to introduce a moderate extra penalty for unobserved ghost lineages to shift the posterior to a well-defined solution with a minimal gap between rocks and clocks. Such penalties may involve assumptions of low extinction rates, high fossil sampling probabilities, high net diversification or any combination of these (various dashed lines); the result is similar under all these scenarios. Bimodal distributions correspond to cases where there are alternative likely placements for key fossils.
Mentions: Detailed analysis of divergence time estimates for three key clades under these models (figure 5) shows that the vague prior is associated with a posterior that is both diffuse and bimodal. The multiple peaks in the distribution are caused by different topological placements of key fossils. For instance, the age estimate for crown placentals (figure 5a) is affected by the position of Eomaia, which can be placed either within or outside of Placentalia, and both solutions have significant posterior probability.Figure 5.

Bottom Line: Failure to account for diversified sampling results in dramatic DRA, but this can be addressed using existing techniques.The major reason seems to be that current models do not account for dependencies among morphological characters, causing distorted topology and branch length estimates.Finally, diversification and fossil sampling priors that do not incorporate all the available background information can contribute to DRA, but these priors can also be used to compensate for DRA.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, 104 05 Stockholm, Sweden fredrik.ronquist@nrm.se.

No MeSH data available.


Related in: MedlinePlus