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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

Rooting artefacts in clock trees. (a) Analysis of relationships among extant taxa under a non-clock model. (b) Ditto under a strict-clock model. (c) Ditto under a relaxed-clock model (independent gamma rates). (d) Ditto under a relaxed-clock model (independent gamma rates), enforcing the topological constraint that Boreoeutheria (Euarchontoglires + Laurasiatheria) are monophyletic. The non-clock tree (a) can be rooted by appropriate choice of outgroup, so that placental superorders (coloured bars) are monophyletic. Clock models produce rooted trees without the need for specifying an outgroup. However, both strict (b) and relaxed clocks (c) result in topological artefacts close to the root when no rooting constraints are enforced. This can be solved in the relaxed-clock analysis by adding a single topological constraint close to the root of the tree (d). (Online version in colour.)
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RSTB20150136F2: Rooting artefacts in clock trees. (a) Analysis of relationships among extant taxa under a non-clock model. (b) Ditto under a strict-clock model. (c) Ditto under a relaxed-clock model (independent gamma rates). (d) Ditto under a relaxed-clock model (independent gamma rates), enforcing the topological constraint that Boreoeutheria (Euarchontoglires + Laurasiatheria) are monophyletic. The non-clock tree (a) can be rooted by appropriate choice of outgroup, so that placental superorders (coloured bars) are monophyletic. Clock models produce rooted trees without the need for specifying an outgroup. However, both strict (b) and relaxed clocks (c) result in topological artefacts close to the root when no rooting constraints are enforced. This can be solved in the relaxed-clock analysis by adding a single topological constraint close to the root of the tree (d). (Online version in colour.)

Mentions: Non-clock trees based on molecular data and combined data can readily be rooted, so that the four mammalian superorders are monophyletic (figure 2a). Unconstrained strict-clock and relaxed-clock analyses, however, produce rooted trees with various apparent topological artefacts owing to incorrect rooting (figure 2b,c). Depending on the exact model used, the clock trees may be rooted between Euarchontoglires and Laurasiatheria, or within one of these two superorders (often within Rodentia or Eulipotyphla (hedgehogs, shrews and moles)). The artefacts occur both in strict-clock trees and in relaxed-clock trees. Adding a single rooting constraint in the relaxed-clock analyses, forcing Boreoeutheria (Euarchontoglires + Laurasiatheria) to be monophyletic, is sufficient to stabilize the rooting and retrieve a tree topology of extant taxa that is fully congruent with the non-clock tree, and consistent with monophyly of all four mammalian superorders (figure 2d). Such a rooting constraint was used for extant taxa in all subsequent relaxed-clock analyses; fossil taxa were allowed to attach to any part of the extant tree.Figure 2.


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)

Rooting artefacts in clock trees. (a) Analysis of relationships among extant taxa under a non-clock model. (b) Ditto under a strict-clock model. (c) Ditto under a relaxed-clock model (independent gamma rates). (d) Ditto under a relaxed-clock model (independent gamma rates), enforcing the topological constraint that Boreoeutheria (Euarchontoglires + Laurasiatheria) are monophyletic. The non-clock tree (a) can be rooted by appropriate choice of outgroup, so that placental superorders (coloured bars) are monophyletic. Clock models produce rooted trees without the need for specifying an outgroup. However, both strict (b) and relaxed clocks (c) result in topological artefacts close to the root when no rooting constraints are enforced. This can be solved in the relaxed-clock analysis by adding a single topological constraint close to the root of the tree (d). (Online version in colour.)
© Copyright Policy - open-access
Related In: Results  -  Collection

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

RSTB20150136F2: Rooting artefacts in clock trees. (a) Analysis of relationships among extant taxa under a non-clock model. (b) Ditto under a strict-clock model. (c) Ditto under a relaxed-clock model (independent gamma rates). (d) Ditto under a relaxed-clock model (independent gamma rates), enforcing the topological constraint that Boreoeutheria (Euarchontoglires + Laurasiatheria) are monophyletic. The non-clock tree (a) can be rooted by appropriate choice of outgroup, so that placental superorders (coloured bars) are monophyletic. Clock models produce rooted trees without the need for specifying an outgroup. However, both strict (b) and relaxed clocks (c) result in topological artefacts close to the root when no rooting constraints are enforced. This can be solved in the relaxed-clock analysis by adding a single topological constraint close to the root of the tree (d). (Online version in colour.)
Mentions: Non-clock trees based on molecular data and combined data can readily be rooted, so that the four mammalian superorders are monophyletic (figure 2a). Unconstrained strict-clock and relaxed-clock analyses, however, produce rooted trees with various apparent topological artefacts owing to incorrect rooting (figure 2b,c). Depending on the exact model used, the clock trees may be rooted between Euarchontoglires and Laurasiatheria, or within one of these two superorders (often within Rodentia or Eulipotyphla (hedgehogs, shrews and moles)). The artefacts occur both in strict-clock trees and in relaxed-clock trees. Adding a single rooting constraint in the relaxed-clock analyses, forcing Boreoeutheria (Euarchontoglires + Laurasiatheria) to be monophyletic, is sufficient to stabilize the rooting and retrieve a tree topology of extant taxa that is fully congruent with the non-clock tree, and consistent with monophyly of all four mammalian superorders (figure 2d). Such a rooting constraint was used for extant taxa in all subsequent relaxed-clock analyses; fossil taxa were allowed to attach to any part of the extant tree.Figure 2.

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