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. 2016 Jul 12;12(7):e1004763.
doi: 10.1371/journal.pcbi.1004763. eCollection 2016 Jul.

Ancestral Reconstruction

Jeffrey B Joy  1   2 , Richard H Liang  1 , Rosemary M McCloskey  1 , T Nguyen  1 , Art F Y Poon  1   2
Affiliations

Ancestral Reconstruction

Jeffrey B Joy et al. PLoS Comput Biol. .
No abstract available

PubMed Disclaimer

Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Phylogeny of a hypothetical genus of plants with pollination states of either “bees”, “hummingbirds”, or “wind” denoted by pictues at the tips.
Pollination state nodes in the phylogenetic tree inferred under maximum parsimony are coloured on the branches leading into them (yellow represents “bee” pollination, red representing “hummingbird” pollination, and black representing “wind” pollination, dual coloured branches are equally parsimonious for the two states coloured). Assignment of “hummingbird” as the root state (because of prior knowledge from the fossil record) leads to the pattern of ancestral states represented by symbols at the nodes of the phylogeny, the state requiring the fewest number of changes to give rise to the pattern observed at the tips is circled at each node.
Fig 2
Fig 2
A general two-state Markov chain representing the rate of jumps from allele a to allele A. The different types of jumps are allowed to have different rates.
Fig 3
Fig 3. Example of a four-state 1 parameter Markov chain model.
Note that in this diagram, transitions between states A and D have been disallowed; it is conventional to not draw the arrow rather than to draw it with a rate of 0.
Fig 4
Fig 4. Graphical representation of an asymmetrical five-state 2-parameter Markov chain model.
Fig 5
Fig 5
Plots of 200 trajectories of each of: Brownian motion with drift 0 and σ2 = 1 (black); Ornstein–Uhlenbeck with σ2 = 1 and α = −4 (green); and Ornstein–Uhlenbeck with σ2 = 1 and α = −40 (orange).
Fig 6
Fig 6. Phylogeny of seven regional strains of Drosophila pseudoobscura, as inferred by Sturtevant and Dobzhansky [64].
Displayed sequences do not correspond to the original paper, but were derived from the notation in the authors' companion paper [8] as follows: A (63A–65B), B (65C–68D), C (69A–70A), D (70B–70D), E (71A–71B), F (71A–73C), G (74A–74C), H (75A–75C), I (76A–76B), J (76C–77B), K (78A–79D), L (80A–81D). Inversions inferred by the authors are highlighted in blue along branches.
See this image and copyright information in PMC

References

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