DOI: 10.5061/dryad.h065g
title: Data from: Supertrees based on the subtree prune-and-regraft distance

description: Supertree methods reconcile a set of phylogenetic trees into a single
 structure that is often interpreted as a branching history of species. A
 key challenge is combining conflicting evolutionary histories that are due
 to artifacts of phylogenetic reconstruction and phenomena such as lateral
 gene transfer (LGT). Although they often work well in practice, existing
 supertree approaches use optimality criteria that do not reflect
 underlying processes, have known biases and may be unduly influenced by
 LGT. We present the first method to construct supertrees by using the
 subtree prune-and-regraft (SPR) distance as an optimality criterion.
 Although calculating the rooted SPR distance between a pair of trees is
 NP-hard, our new maximum agreement forest-based methods can reconcile
 trees with hundreds of taxa and &gt; 50 transfers in fractions of a
 second, which enables repeated calculations during the course of an
 iterative search. Our approach can accommodate trees in which uncertain
 relationships have been collapsed to multifurcating nodes. Using a series
 of simulated benchmark datasets, we show that SPR supertrees are more
 similar to correct species histories under plausible rates of LGT than
 supertrees based on parsimony or Robinson-Foulds distance criteria. We
 successfully constructed an SPR supertree from a phylogenomic dataset of
 40,631 gene trees that covered 244 genomes representing several major
 bacterial phyla. Our SPR-based approach also allowed direct inference of
 highways of gene transfer between bacterial classes and genera; a small
 number of these highways connect genera in different phyla and can
 highlight specific genes implicated in long-distance LGT.
description: Supplemetary Figure
 1Supplementary Figure 1.
 Inferred LGT events between 13 bacterial classes. (a) LGT heatmap. The
 colour side bars indicate class. The row and column order is the same. The
 number of transfers is shown in a white-yellow-red colour scale with
 darker colours indicating a higher proportion of transfer events. Colour
 intensity is relative to the largest number of transfers in a row.
 Relationships with fewer than 5% of the maximum transfer events for a row
 or only a single transfer event were filtered out. (b) LGT affinity graph
 of the bacterial classes. Each node of the graph represents a bacterial
 class scaled relative to the number of represented taxa (2-75). Two genera
 are connected by an edge if the number of inferred LGT events between them
 exceeds 5% of their shared genes. The shade of an edge is proportional to
 this ratio of LGT events to shared genes; black edges indicate
 relationships with at least as many LGT events as shared genes. The
 thickness of an edge scales relative to the actual number of inferred
 transfers (30-1414) with thicker edges indicating more
 transfers.suppfigure1.pdfSupplemetary Figure 2Supplementary Figure 2: The LGT affinity neighbourhood of genus Clostridium. Each node of the graph represents a bacterial genus coloured by class and scaled relative to the number of represented taxa (1-13). Two genera are connected by an edge if the number of inferred LGT events between them exceeds 5% of their shared genes. The shade of an edge is proportional to this ratio of LGT events to shared genes; black edges indicate relationships with at least as many LGT events as shared genes. The thickness of an edge scales relative to the actual number of inferred transfers (2-125) with thicker edges indicating more transfers.suppfigure2.pdfSupplemetary Figure 3Supplementary Figure 3: A comparison of the accuracy of SPR, RF and MRP supertrees as measured by the minimal SPR distance between simulated species histories and any rooting of the supertree under varying rates of random or divergence-biased simulated LGT events.suppfigure3.pdfSupplemetary Figure 4Supplementary Figure 4: One application of the cluster reduction. The subtrees on leaves 1, 2, 3, and 4 are not identical but cover the same leaf set. Thus, they can be split from the trees and solved independently. The original locations of the removed subtrees are represented by a new leaf a1 and their roots are labelled ρ1. It is preferable to cut ρ1 in any sub-MAF as we can then cut the equivalent edge above a1.suppfigure4.pdfEvolSimParamsExample EvolSimulator configuration file used to generate simulated trees and datasets.Eukaryotic SupertreesEukaryotic supertrees described in the main manuscript.Eukaryotic_Supertrees.zipBacterial_trees_and_supertreesTrees and supertrees built from 244 bacterial genomes.