List of software for ancestral reconstruction.

List of software for ancestral reconstruction.</p

Graphical representation of an asymmetrical five-state 2-parameter Markov chain model.

<p>Graphical representation of an asymmetrical five-state 2-parameter Markov chain model.</p

Ancestral Reconstruction - Fig 5

<p><b>Plots of 200 trajectories of each of: Brownian motion with drift 0 and <i>σ</i>² = 1 (black); Ornstein–Uhlenbeck with <i>σ</i>² = 1 and <i>α</i> = −4 (green); and Ornstein–Uhlenbeck with <i>σ</i>² = 1 and <i>α</i> = −40 (orange)</b>.</p

Ancestral Reconstruction - Fig 2

<p><b>A general two-state Markov chain representing the rate of jumps from allele <i>a</i> to allele <i>A</i>.</b> The different types of jumps are allowed to have different rates.</p

Phylogeny of a hypothetical genus of plants with pollination states of either “bees”, “hummingbirds”, or “wind” denoted by pictues at the tips.

<p>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.</p

Example of a four-state 1 parameter Markov chain model.

<p>Note that in this diagram, transitions between states <i>A</i> and <i>D</i> have been disallowed; it is conventional to not draw the arrow rather than to draw it with a rate of 0.</p

Phylogeny of seven regional strains of <i>Drosophila pseudoobscura</i>, as inferred by Sturtevant and Dobzhansky [64].

<p>Displayed sequences do not correspond to the original paper, but were derived from the notation in the authors' companion paper [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004763#pcbi.1004763.ref008" target="_blank">8</a>] 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.</p

Estimated genome-wide selection coefficients (fitness costs) in the HCV genome.

(A) Selection coefficients (1/replication cycle) along the HCV genome, colored by mutation type (syn = synonymous; nonsynon = nonsynonymous); each dot represents the average at each position across 195 patient samples, and lines represent the sliding window average for 50 bases. (B) Selection coefficients (1/replication cycle) stratified by nucleotide and syn/nonsyn status, colored by mutation type. (C) Estimated mutation frequencies stratified by starting nucleotide and syn/nonsyn status, colored by mutation type. Comparison of (B) and (C) shows higher estimated selection coefficients at A and T sites than at C and G sites, even though mutation frequencies were higher at A and T sites compared to C and G sites.</p

Comparisons between HCV mutation rates estimated from Gellers et al. (2016)’s <i>in vitro</i> dataset and our <i>in vivo</i> dataset using nonsense mutation frequencies (A).

Correlation between estimated in vivo and in vitro mutation rates are shown in B. (PNG)</p

Mutation rates estimated from the dataset obtained from Geller et al. (2016).

(PDF)</p