The Past Sure Is Tense: On Interpreting Phylogenetic Divergence Time Estimates Σ(-᷅_-᷄๑)

Talk given @ Evolution 2017 (Portland) #evol2017

Mapping schematic.

<p>A basic schematic of the results of mapping and synthesis. A) Three source trees with completely overlapping taxon sets (left) mapped into a graph (right). The colored edges in the graph correspond to the source trees on the left, with graph nodes represented as gray circles. Internal graph nodes represent least inclusive common ancestors (LICAs), and are labelled with their descendant terminal taxa. B) A grey taxonomy hierarchy and additional green source tree added to the black, blue, and orange trees from A. The relationships presented in the black, blue, and orange trees are in light grey to cut down on clutter. C) A synthetic tree resulting from preferring source blue, green, and taxonomic source trees.</p

The cumulative difference across all nodes in the height, lower 95% HPD, and higher 95% HPD of each node comparing the UCLN estimates to the strict clock estimates from the individual empirical dating analyses.

<p>A value lower than 0 results when the cumulative difference in the clock values of height or HPD are younger than the associated UCLN values.</p

Assessment of dating error for the clock (CL) and UCLN (UC) analyses of the simulated <i>ucln</i> data.

<p>All measures involve distance from the true node age, and are cumulative sums across all nodes. Height is the inferred node age. Lower and Higher regard the 95% HPD node age bounds. Nodes (%) indicates the percent of true node ages contained within the HPD interval. Error is the total error involved, equivalent to Low + High.</p

Results from a simulation comparing total difference between true and estimated ages for three random genes under a clock (RC) and UCLN (RU) and three genes chosen with SortaDate under a clock (SC) and UCLN (SU).

<p>Results are from 100 simulations of distinct parameter values. See details in the text.</p

Graph of Angiosperm Tree of Life with average effective parents.

<p>A graph showing the mapping of the Angiosperm Tree of Life project bootstrap dataset of 100 trees that includes 640 taxa with chloroplast, mitochondrial, and ribosomal data <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003223#pcbi.1003223-Soltis1" target="_blank">[23]</a>. Larger node size indicates higher node support. Node color indicates the average subgraph destabilization () of each node, with blue nodes having relatively small values of , orange nodes with values between and red to pink nodes with values of .</p

Gene tree properties for the BIR, CAR, and CARY datasets.

<p>Left: relationship between root-to-tip variance and tree length for simulated (<i>clock</i> and <i>ucln</i>) and empirical (<i>data</i>) datasets. Each simulation condition consists of 100 simulated datasets. Contours represent densities, while grey dots represent raw empirical values. Right: tip-specific root-to-tip variance for empirical datasets. Here, 0 represents the mean root-to-tip across all genes and all lineages. Red dots indicate outgroup taxa.</p

Winnowing criteria used for sorting genes for use in divergence-time inference analyses.

<p>The order presented here is arbitrary.</p

A comparison of strict clock and UCLN estimates of node ages for the simulated <i>clock</i> and <i>ucln</i> datasets.

<p>Each simulation condition consists of three genes. Red and pink are scenarios where the generating and inference models are identical, while green and blue are where the models are mismatched. Bars represent 95% HPD intervals and overlay the true simulated tree.</p

Graph of Angiosperm Tree of Life with nodes having the highest amount of conflict highlighted.

<p>A graph showing the mapping of the Angiosperm Tree of Life project bootstrap dataset of 100 trees that includes 640 taxa with chloroplast, mitochondrial, and ribosomal data <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003223#pcbi.1003223-Soltis1" target="_blank">[23]</a>. Large purple nodes are those corresponding to nodes in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003223#pcbi-1003223-t002" target="_blank">Table 2</a>.</p