Models, algorithms, and programs for phylogeny reconciliation

International audienceGene sequences contain a gold mine of phylogenetic information. But unfortunately for taxonomists this information does not only tell the story of the species from which it was collected. Genes have their own complex histories which record speciation events, of course, but also many other events. Among them, gene duplications, transfers and losses are especially important to identify. These events are crucial to account for when reconstructing the history of species, and they play a fundamental role in the evolution of genomes, the diversification of organisms and the emergence of new cellular functions. We review reconciliations between gene and species trees, which are rigorous approaches for identifying duplications, transfers and losses that mark the evolution of a gene family. Existing reconciliation models and algorithms are reviewed and difficulties in modeling gene transfers are discussed. We also compare different reconciliation programs along with their advantages and disadvantages

Representing a set of reconciliations in a compact way

International audienceComparative genomic studies are often conducted by reconciliation analyses comparing gene and species trees. One of the issues with reconciliation approaches is that an exponential number of optimal scenarios is possible. The resulting complexity is masked by the fact that a majority of reconciliation software pick up a random optimal solution that is returned to the end-user. However, the alternative solutions should not be ignored since they tell different stories that parsimony considers as viable as the output solution. In this paper, we describe a polynomial space and time algorithm to build a minimum reconciliation graph -- a graph that summarizes the set of all most parsimonious reconciliations. Amongst numerous applications, it is shown how this graph allows counting the number of non-equivalent most parsimonious reconciliations

Inferring gene duplications, transfers and losses can be done in a discrete framework

UMR AGAP : équipe GE2popInternational audienceIn the field of phylogenetics, the evolutionary history of a set of organisms is commonly depicted by a species tree – whose internal nodes represent speciation events – while the evolutionary history of a gene family is depicted by a gene tree – whose internal nodes can also represent macro-evolutionary events such as gene duplications and transfers. As speciation events are only part of the events shaping a gene history, the topology of a gene tree can show incongruences with that of the corresponding species tree. These incongruences can be used to infer the macro-evolutionary events undergone by the gene family. This is done by embedding the gene tree inside the species tree and hence providing a reconciliation of those trees. In the past decade, several parsimony-based methods have been developed to infer such reconciliations, accounting for gene duplications (D), transfers (T) and losses (L). The main contribution of this paper is to formally prove an important assumption implicitly made by previous works on these reconciliations, namely that solving the (maximum) parsimony DTL reconciliation problem in the discrete framework is equivalent to finding a most parsimonious DTL scenario in the continuous framework. In the process, we also prove several intermediate results that are useful on their own and constitute a theoretical toolbox that will likely facilitate future theoretical contributions in the field

Inferring evolutionary trees with strong combinatorial evidence

We consider the problem of inferring the evolutionary tree of a set of n species. We propose a quartet reconstruction method which specifically produces trees whose edges have strong combinatorial evidence. Let Q be a set of resolved quartets defined on the studied species, the method computes the unique maximum subset Q* of Q which is equivalent to a tree and outputs the corresponding tree as an estimate of the species' phylogeny. We use a characterization of the subset Q* due to (Bandelt86) to provide an O(n4) incremental algorithm for this variant of the NP-hard quartet consistency problem. Moreover, when chosing the resolution of the quartets by the Four-Point Method (FPM) and considering the Cavender-Farris model of evolution, we show that the convergence rate of the Q* method is at worst polynomial when the maximum evolutive distance between two species is bounded. We complete these theoretical results by an experimental study on real and simulated data sets. The results show that (i) as expected, the strong combinatorial constraints it imposes on each edge leads the Q* method to propose very few incorrect edges; (ii) more surprisingly, the method infers trees with a relatively high degree of resolution

Maximum agreement and compatible supertrees

AbstractGiven a set of leaf-labelled trees with identical leaf sets, the MAST problem, respectively MCT problem, consists of finding a largest subset of leaves such that all input trees restricted to these leaves are isomorphic, respectively compatible. In this paper, we propose extensions of these problems to the context of supertree inference, where input trees have non-identical leaf sets. This situation is of particular interest in phylogenetics. The resulting problems are called SMAST and SMCT.A sufficient condition is given that identifies cases where these problems can be solved by resorting to MAST and MCT as subproblems. This condition is met, for instance, when only two input trees are considered. Then we give algorithms for SMAST and SMCT that benefit from the link with the subtree problems. These algorithms run in time linear to the time needed to solve MAST, respectively MCT, on an instance of the same or smaller size.It is shown that arbitrary instances of SMAST and SMCT can be turned in polynomial time into instances composed of trees with a bounded number of leaves.SMAST is shown to be W[2]-hard when the considered parameter is the number of input leaves that have to be removed to obtain the agreement of the input trees. A similar result holds for SMCT. Moreover, the corresponding optimization problems, that is the complements of SMAST and SMCT, cannot be approximated in polynomial time within any constant factor, unless P=NP. These results also hold when the input trees have a bounded number of leaves.The presented results apply to both collections of rooted and unrooted trees

PhySIC_IST: cleaning source trees to infer more informative supertrees

Background: Supertree methods combine phylogenies with overlapping sets of taxa into a larger one. Topological conflicts frequently arise among source trees for methodological or biological reasons, such as long branch attraction, lateral gene transfers, gene duplication/loss or deep gene coalescence. When topological conflicts occur among source trees, liberal methods infer supertrees containing the most frequent alternative, while veto methods infer supertrees not contradicting any source tree, i.e. discard all conflicting resolutions. When the source trees host a significant number of topological conflicts or have a small taxon overlap, supertree methods of both kinds can propose poorly resolved, hence uninformative, supertrees. Results: To overcome this problem, we propose to infer non-plenary supertrees, i.e. supertrees that do not necessarily contain all the taxa present in the source trees, discarding those whose position greatly differs among source trees or for which insufficient information is provided. We detail a variant of the PhySIC veto method called PhySIC IST that can infer non-plenary supertrees. PhySIC IST aims at inferring supertrees that satisfy the same appealing theoretical properties as with PhySIC, while being as informative as possible under this constraint. The informativeness of a supertree is estimated using a variation of the CIC (Cladistic Information Content) criterion, that takes into account both the presence of multifurcations and the absence of some taxa

Observation of a non-adiabatic geometric phase for elastic waves

We report the experimental observation of a geometric phase for elastic waves in a waveguide with helical shape. The setup reproduces the experiment by Tomita and Chiao [A. Tomita, R.Y. Chiao, Phys. Rev. Lett. 57 (1986) 937-940, 2471] that showed first evidence of a Berry phase, a geometric phase for adiabatic time evolution, in optics. Experimental evidence of a non-adiabatic geometric phase has been reported in quantum mechanics. We have performed an experiment to observe the polarization transport of classical elastic waves. In a waveguide, these waves are polarized and dispersive. Whereas the wavelength is of the same order of magnitude as the helix's radius, no frequency dependent correction is necessary to account for the theoretical prediction. This shows that in this regime, the geometric phase results directly from geometry and not from a correction to an adiabatic phase.Comment: 13 figure

Genetic structure and evolution of the Leishmania genus in Africa and Eurasia: what does MLSA tell us

Leishmaniasis is a complex parasitic disease from a taxonomic, clinical and epidemiological point of view. The role of genetic exchanges has been questioned for over twenty years and their recent experimental demonstration along with the identification of interspecific hybrids in natura has revived this debate. After arguing that genetic exchanges were exceptional and did not contribute to Leishmania evolution, it is currently proposed that interspecific exchanges could be a major driving force for rapid adaptation to new reservoirs and vectors, expansion into new parasitic cycles and adaptation to new life conditions. To assess the existence of gene flows between species during evolution we used MLSA-based (MultiLocus Sequence Analysis) approach to analyze 222 Leishmania strains from Africa and Eurasia to accurately represent the genetic diversity of this genus. We observed a remarkable congruence of the phylogenetic signal and identified seven genetic clusters that include mainly independent lineages which are accumulating divergences without any sign of recent interspecific recombination. From a taxonomic point of view, the strong genetic structuration of the different species does not question the current classification, except for species that cause visceral forms of leishmaniasis (L. donovani, L. infantum and L. archibaldi). Although these taxa cause specific clinical forms of the disease and are maintained through different parasitic cycles, they are not clearly distinct and form a continuum, in line with the concept of species complex already suggested for this group thirty years ago. These results should have practical consequences concerning the molecular identification of parasites and the subsequent therapeutic management of the disease

Un algorithme de parcimonie efficace pour la réconciliation d'arbres de gènes/espèces avec pertes, duplications et transferts

National audienceTree reconciliation is anapproach that explains the discrepancies between two evolutionary trees by a number of events such as speciations, duplications, transfers and losses. It has important applications in ecology, biogeography and genomics, for instance to decipher relationships between homologous sequences. (Results) We provide a fast and exact reconciliation algorithm according to a parsimony criterion that considers duplication, transfer and loss events. We also present experimental results that give first insights on the conditions under which parsimony is able to accurately infer evolutionary scenarios involving such events. Over all, parsimony performs well under realistic cases, as well as for relatively high duplication and transfer rates. As expected, transfers are in general less accurately recovered than duplications. Availability: www.lirmm.fr/phylariane

Characteristics of patients with haematological and breast cancer (1996–2009) who died of heart failure-related causes after cancer therapy

Aims: To describe the characteristics and time to death of patients with breast or haematological cancer who died of heart failure (HF) after cancer therapy. Patients with an index admission for HF who died of HF-related causes (IAHF) and those with no index admission for HF who died of HF-related causes (NIAHF) were compared. Methods and results: We performed a linked data analysis of cancer registry, death registry, and hospital administration records (n = 15 987). Index HF admission must have occurred after cancer diagnosis. Of the 4894 patients who were deceased (30.6% of cohort), 734 died of HF-related causes (50.1% female) of which 279 (38.0%) had at least one IAHF (41.9% female) post-cancer diagnosis. Median age was 71 years [interquartile range (IQR) 62–78] for IAHF and 66 years (IQR 56–74) for NIAHF. There were fewer chemotherapy separations for IAHF patients (median = 4, IQR 2–9) compared with NIAHF patients (median = 6, IQR 2–12). Of the IAHF patients, 71% had died within 1 year of the index HF admission. There was no significant difference in HF-related mortality in IAHF patients compared with NIAHF (HR, 1.10, 95% CI, 0.94–1.29, P = 0.225). Conclusions: The profile of IAHF patients who died of HF-related causes after cancer treatment matched the current profile of HF in the general population (over half were aged ≥70 years). However, NIAHF were younger (62% were aged ≤69 years), female patients with breast cancer that died of HF-related causes before hospital admission for HF-related causes—a group that may have been undiagnosed or undertreated until death