Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees

Abstract

Accurate gene tree-species tree reconciliation is fundamental to inferring the evolutionary history of a gene family. However, although it has long been appreciated that population-related effects such as incomplete lineage sorting (ILS) can dramatically affect the gene tree, many of the most popular reconciliation methods consider discordance only due to gene duplication and loss (and sometimes horizontal gene transfer). Methods that do model ILS are either highly parameterized or consider a restricted set of histories, thus limiting their applicability and accuracy. To address these challenges, we present a novel algorithm DLCpar for inferring a most parsimonious (MP) history of a gene family in the presence of duplications, losses, and ILS. Our algorithm relies on a new reconciliation structure, the labeled coalescent tree (LCT), that simultaneously describes coalescent and duplication-loss history. We show that the LCT representation enables an exhaustive and efficient search over the space of reconciliations, and, for most gene families, the least common ancestor (LCA) mapping is an optimal solution for the species mapping between the gene tree and species tree in an MP LCT. Applying our algorithm to a variety of clades, including flies, fungi, and primates, as well as to simulated phylogenies, we achieve high accuracy, comparable to sophisticated probabilistic reconciliation methods, at reduced run time and with far fewer parameters. These properties enable inferences of the complex evolution of gene families across a broad range of species and large data sets.

OrthoFinder: phylogenetic orthology inference for comparative genomics

“…For example, there are a range of methods for identifying orthogroups of genes from user supplied gene sequences [8-10, 12, 22]and a wide variety of gene tree inference methods that can infer trees from these orthogroups [23][24][25][26][27]. Similarly, there is a range of methods for inferring orthologs from gene trees that also vary in terms of scalability and accuracy [28][29][30][31].…”

Cophylogenetic Reconciliation with ILP

“…Therefore, we define binary variables t ph for any two p ∈ V P and h ∈ V H . For these variables it holds that c ph ≥ 1 ⇔ t ph = 1, which is ensured by Constraints (20) and (21), and t ph = 1 ⇒ t p = t h is implemented by Constraints (22) and (23).…”

“…In particular, we compare the results with those of Jane 4 [14], Treemap 3b [5], [2], NOTUNG 2.8 Beta [13], and Ranger-DTL [12]. It should be mentioned that a few other reconciliation tools have not been used for comparison for the following reasons: (i) Mowgli [9] because it requires fully dated cladograms as input, (ii) CoRe-Sym [8] and the ILP approach presented in [15] because of the exceptionally long runtimes (> 1h) for trees of practical size, and (iii) the reconciliation tools DLCoalRecon [21] and DLCpar [22] because they utilize a disparate event model based on duplication, loss, and coalescence.…”

“…Jane uses a genetic algorithm, for determining a node timing, i.e., an order of the nodes of the phylogenetic trees, in combination with a dynamic programming algorithm, that computes a reconciliation for the trees under the determined node order. The algorithms DLCoalRecon [21] and DLCpar [22] are tailored for the analysis of gene/species tree problems and create reconciliations based on the DLCoal model, which includes duplication, loss, and coalescence. Coalescence was previously used for species tree inference from multiple gene trees [23], [24].…”

On the computational complexity of the maximum parsimony reconciliation problem in the duplication-loss-coalescence model

“…Wu et al [3] gave the first maximum parsimony algorithm for the DLC reconciliation problem. That algorithm has worst-case exponential time, leaving open the question of whether the problem can be solved in polynomial time.…”