Evolution through segmental duplications and losses: a Super-Reconciliation approach

Abstract

The classical gene and species tree reconciliation, used to infer the history of gene gain and loss explaining the evolution of gene families, assumes an independent evolution for each family. While this assumption is reasonable for genes that are far apart in the genome, it is not appropriate for genes grouped into syntenic blocks, which are more plausibly the result of a concerted evolution. Here, we introduce the Super-Reconciliation problem which consists in inferring a history of segmental duplication and loss events (involving a set of neighboring genes) leading to a set of present-day syntenies from a single ancestral one. In other words, we extend the traditional Duplication-Loss reconciliation problem of a single gene tree, to a set of trees, accounting for segmental duplications and losses. Existency of a Super-Reconciliation depends on individual gene tree consistency. In addition, ignoring rearrangements implies that existency also depends on gene order consistency. We first show that the problem of reconstructing a most parsimonious Super-Reconciliation, if any, is NP-hard and give an exact exponential-time algorithm to solve it. Alternatively, we show that accounting for rearrangements in the evolutionary model, but still only minimizing segmental duplication and loss events, leads to an exact polynomial-time algorithm. We finally assess time efficiency of the former exponential time algorithm for the Duplication-Loss model on simulated datasets, and give a proof of concept on the opioid receptor genes.

FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models

“…Species trees are important models that can be used to address many biological questions, for example how is biodiversity created/maintained and how do species adapt to their environments ( Cracraft et al , 2004 ). There is also a vast literature regarding gene tree reconciliation , where gene trees are compared to an established species tree in order to understand how genes evolved (for some of the recent literature on this question, see Delabre et al , 2020 ; Dondi et al , 2019 ; El-Mabrouk and Noutahi, 2019 ; Hasić and Tannier, 2019 ; Jacox et al , 2016 ; Kundu and Bansal, 2018 ; Lai et al , 2017 ; Muhammad et al , 2018 ). However, in most cases, species trees are not known in advance and instead must be estimated.…”

Predicting the Evolution of Syntenies—An Algorithmic Review

“…In [94,95], the DL-reconciliation of a gene tree has been generalized to the DLreconciliation of a "synteny tree" (defined bellow) accounting for segmental duplications and losses. In this study, a synteny X is an ordered sequence of genes belonging to a genome s(X).…”

“…If this holds, the syntenies are said to be order-consistent. As explained in [95], this can be verified in linear time by representing the gene orders as a directed graph and verifying if it is acyclic. For example, the syntenies {A 1 , A 2 , B 1 , B 2 } in Figure 5(1)-( 3) are order-consistent, while the syntenies {A 3 , A 4 , B 3 , B 4 } in Figure 5(4) are not order-consistent,…”

“…In the case of gene families likely containing multiple copies in the same synteny, a way of doing can be to keep a single copy in each synteny. This is actually required for the super-reconciliation model considered in [94,95], as tandem duplications are not allowed in this model. Formally, given a set of gene trees represented as MUL-trees, i.e., trees with potentially repeated leaf-labels, the problem is to prune them in an appropriate way, keeping a single copy of each label.…”

“…In [94,95], this problem is handled by a two-step algorithm: First label the internal nodes of T as duplications or speciation following the LCA-mapping (Figure 5(3), left), and then infer an optimal scenario of losses in agreement with this event-labeled treẽ T (Figure 5(3), right). This two-steps method has been shown exact, i.e., leading to a super-reconciliation of minimum cost (DL-distance).…”