TreeShrink: fast and accurate detection of outlier long branches in - PowerPoint PPT Presentation

TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees 1 Paper Presentation Xilin Yu University of Illinois Urbana-Champaign Nov 27th, 2018 1 Uyen Mai and Siavash Mirarab Xilin Yu (University of Illinois Urbana-Champaign) TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic Nov 27th, 2018 1 / 19

Table of Contents Background 1 The k-shrink Problem 2 Statistical Test Methods 3 Experiments and Evaluation 4 Discussion and Conclusion 5 Xilin Yu (University of Illinois Urbana-Champaign) TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic Nov 27th, 2018 2 / 19

Background Problem: errors from early steps propogate to downstream Possible sign of errors: unexpectedly long branches in inferred tree Common species filtering methods Rogue taxon removal (RTR, e.g., RogueNaRok) Rooted filtering based on branch length (e.g., Rooted Pruning) No clear definition of outlier (errorneous sequences) causing unexpectedly long branches causing discordance in gene trees large edit distance to the rest – causing underalignment low probability of generation by the profile HMM on the set Xilin Yu (University of Illinois Urbana-Champaign) TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic Nov 27th, 2018 4 / 19

The k-shrink Problem Definition The diameter of a tree is the maximum distance between any two leaves. Definition (The k-shrink problem ) Given a tree on n leaves with branch lengths and k ∈ [ n ], for every i ∈ [ k ], find a set of i leaves whose removal reduces the tree diameter maximally. Definition 1 A diameter pair of vertices is any pair of vertices whose distance is equal to the diameter of the tree. 2 A reasonable removal is a removal of a leaf that belongs to some diameter pair. 3 A reasonable k-removing set is a set of k leaves s.t. there is an ordering x 1 , . . . , x k s.t. the removal of x i is reasonable after removing all of x 1 , . . . , x i − 1 . Xilin Yu (University of Illinois Urbana-Champaign) TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic Nov 27th, 2018 6 / 19

Polytime Algorithm for the k-shrink Problem Suppose for simplicity, there is only one diameter pair for the tree and any tree obtained by restrciting it to a subset of leaves. DAG of reasonable k-removal sets Xilin Yu (University of Illinois Urbana-Champaign) TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic Nov 27th, 2018 7 / 19

Polytime Algorithm for the k-shrink Problem Theorem Any k-removing set that maximally reduces the tree diameter is a reasonable k-removing set. Theorem There are k + 1 reasonble k-removing sets. The above implies O ( k 2 ) nodes in the graph to search. Poly sized graph + poly time to find each node gives poly time algorithm. The paper shows that the above holds for general trees as well. Xilin Yu (University of Illinois Urbana-Champaign) TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic Nov 27th, 2018 8 / 19

Notations for Statistics d i = minimum tree diameter after removing i leaves. OPT i = set of i leafs to remove to achieve d i . ν i = d i − 1 d i , ∆ i = log ν i the signature of a leaf x is max ∆ i such that x ∈ OPT i Outliers are those with abnormally large signature Xilin Yu (University of Illinois Urbana-Champaign) TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic Nov 27th, 2018 10 / 19

Three Statistical Tests Tests # of trees # of density sequences to remove functions Per-gene 1 1 sequence whose signature has cumulative density ≥ 1 − α All-gene multiple 1 sequence from gene trees in which signature has cumulative density ≥ 1 − α Per-species multiple n sequence from gene trees in which signature has cumulative density ≥ 1 − α for that species α = false positive tolarence parameter Xilin Yu (University of Illinois Urbana-Champaign) TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic Nov 27th, 2018 11 / 19

Experiments Data Set Data Sequences Genes Outgroups Plants 104 852 4 Mammal 37 424 1 Insects 144 1478 9 Cannon 78 213 5 Rouse 26 393 4 Frogs 164 95 8 HIV 648 1 7+2 Methods Treeshrink (with 20 different α values) 1 RogueNaRok (with 20 different weights) 2 Rooted filtering (with 20 cut offs using different number of deviations) 3 Evaluation criterion: gene tree discordance and taxon occupancy Xilin Yu (University of Illinois Urbana-Champaign) TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic Nov 27th, 2018 13 / 19

Evaluation Xilin Yu (University of Illinois Urbana-Champaign) TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic Nov 27th, 2018 14 / 19

Discussion and Conclusion 1 The k-shrink problem is solvable in polynomial time. 2 The per-species test is most effective among the three tests, but it also demands more data. 3 Treeshrink works better than rooted filtering on majority of data sets in the test. 4 Treeshrink and RogueNaRok have different target and can complement each other. 5 Treeshrink is scalable: 10 6 sequences in 28 minutes. Xilin Yu (University of Illinois Urbana-Champaign) TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic Nov 27th, 2018 19 / 19

TreeShrink: fast and accurate detection of outlier long branches in - PowerPoint PPT Presentation

TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees 1 Paper Presentation Xilin Yu University of Illinois Urbana-Champaign Nov 27th, 2018 1 Uyen Mai and Siavash Mirarab Xilin Yu (University of

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