Data set of Bonin et al. [11].

<p>The unrooted neighbor-joining trees are based on Nei-Li genetic distances calculated from A) the orignal character matrix with 328 markers (10 primer combinations), B) the original character matrix with 222 markers (the 5 primer combinations including replicates) and C) the AMARE masked character matrix with 158 markers. Bootstrap support values ≥50% (1000 bootstrap replicates) are labeled with • and are only shown for more basal splits. Each sample site is indicated by its own colour. A graphical overview of the replicates character matrix is shown below. In this matrix each row represents a replicate pair of a single individual and each column a bin. Light blue cells specify reproducible (0,0) bin states, dark blue cells reproducible (1,1) bin states and red cells unreproducible (0,1) bin states. Scale bar indicates Nei-Li distance.</p

Flow chart of AMARE.

<p>Flow chart of AMARE.</p

Overview of character matrices and quality estimates.

<p>Selected character matrices are indicated in <b>bold</b>, original character matrices in <i>italics</i>.</p>*<p> = Nei-Li distances were used for resolution score, principal coordinate and stemminess analyses.</p><p>♦ = Uncorrected distances were used for resolution score, principal coordinate and stemminess analyses.</p><p>▪ = percentage of variation explained by the first three axes of the principle coordinate analyses (PCoA).</p

AMARE replicate transformation.

<p>This example shows how AMARE transforms replicates into pairs (<i>i,j</i>) representing the observed state 0 (fragment absence) or 1 (fragment presence) within each bin.</p

<i>Ipomoea</i> data set of Holland et al. [31].

<p>The neighbor-joining trees are based on uncorrected genetic distances calculated from A) the original character matrix with 1425 markers and B) the AMARE masked character matrix with 406 markers. Bootstrap support values ≥50% (1000 bootstrap replicates) are labeled with •. Replicated individuals are indicated in green. <i>Ipomoea tiliacea</i> represents the root of the tree. A graphical overview of the replicates character matrix is shown below. In this matrix each row represents a replicate pair of a single individual and each column a bin. Light blue cells specify reproducible (0,0) bin states, dark blue cells reproducible (1,1) bin states and red cells unreproducible (0,1) bin states. Scale bar indicates uncorrected genetic distance.</p

Two sets of simulations.

<p>Given model topology for a) Topology A: stepwise elongation of two terminal branches () under different ancestral branch lengths () and b) Topology B: stepwise elongation of two internal branches () under different lengths of an intermediate branch (). Topology A was used to identify class II and III effects (following tree shape of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036593#pone-0036593-g001" target="_blank">Figure 1b</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036593#pone-0036593-g001" target="_blank">Figure 1c</a>), Topology B was used to identify class I effects (following tree shape of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036593#pone-0036593-g001" target="_blank">Figure 1a</a>).</p

Selected results of ML reconstuctions for under the mixed-distribution model (JC++I) and the distributed model (Jukes-Cantor+).

<p>Class III (“Felsenstein effect”), Class I (attraction due to symplesiomorphies), and Class II (random error probably due to signal erosion) inferred from 100 simulation repeats for each branch length combination and alignment length. Each individual plot corresponds to a fixed branch increase of (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036593#pone-0036593-g002" target="_blank">Figure 2</a>) and fixed reconstruction scheme with the models JC+ () or JC++I (; ). Branch length differences increase from left to right by increasing branch in discrete elongation steps (0.1–1.5). Four successive data points (belonging to one cell in the plot) correspond to four alignment lengths (2,000, 3,000, 4,000, 10,000 base pairs). Alignment corresponding branch lengths of are shown above each subfigure. The y-axis depicts the reconstruction success of the 100 simulation repeats (N) for a) Topology A (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036593#pone-0036593-g002" target="_blank">Figure 2a</a>) and b) Topology B (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036593#pone-0036593-g002" target="_blank">Figure 2b</a>).</p

<i>Ourisia</i> data set of Holland et al.[31].

<p>The neighbor-joining trees are based on uncorrected genetic distances calculated from A) the original character matrix with 2011 markers and B) the AMARE masked character matrix with 530 markers. Bootstrap support values ≥50% (1000 bootstrap replicates) are labeled with • and are only shown for more basal splits. Replicated individuals are indicated in green. The Australian species <i>Ourisia integrifolia</i> is sister to all New Zealand species and thus the root of the tree. A graphical overview of the replicates character matrix is shown below. In this matrix each row represents a replicate pair of a single individual and each column a bin. Light blue cells specify reproducible (0,0) bin states, dark blue cells reproducible (1,1) bin states and red cells unreproducible (0,1) bin states. Scale bar indicates uncorrected genetic distance.</p

Rooted neighbor-joining tree of the AMARE reduced character matrix of Dasmahapatra et al. [8].

<p>The AMARE reduced character matrix comprised 108 selected markers. The tree is based on Nei-Li genetic distances. Numbers represent % bootstrap support obtained from 1000 bootstrap replicates and are shown only when ≥50%. Replicated individuals are indicated in green. A graphical overview of the replicates character matrix is shown below. In this matrix each row represents a replicate pair of a single individual and each column a bin. Light blue cells specify reproducible (0,0) bin states, dark blue cells reproducible (1,1) bin states and red cells unreproducible (0,1) bin states. Scale bar indicates Nei-Li distance.</p

The used model parameter settings of ASRV for maximum likelihood analyses.

<p>Single settings included either or +I parameters (fixed or estimated). Simulated ASRV as well as model parameter setting for additional simulations/analyses of alignment length of 100,000 base positions are highlighted bold.</p