Lifemap: Exploring the Entire Tree of Life

International audienceThe Tree of Life (ToL) is meant to be a unique representation of the evolutionary relationships between all species on earth. Huge efforts are made to assemble such a large tree, helped by the decrease of sequencing costs and improved methods to reconstruct and combine phylogenies, but no tool exists today to explore the ToL in its entirety in a satisfying manner. By combining methods used in modern cartography, such as OpenStreetMap, with a new way of representing tree-like structures, I created Lifemap, a tool allowing the exploration of a complete representation of the ToL (between 800,000 and 2.2 million species depending on the data source) in a zoomable interface. A server version of Lifemap also allows users to visualize their own trees. This should help researchers in ecology and evolutionary biology in their everyday work, but may also permit the diffusion to a broader audience of our current knowledge of the evolutionary relationships linking all organisms

L'arbre du vivant: Etat des lieux et visualisation

National audienceL'arbre de la vie représente l'intégralité des liens évolutifs qui unissent les espèces de notre planète. Sa reconstruction fait l'objet de nombreuses études, aidées par l'essor des nouvelles techniques de séquençage à haut débit. Sa visualisation est un véritable défi. L'évolution des espèces depuis plus de 3,5 milliards d'années a conduit à la biodiversité actuelle, dont nous ne connaissons qu'une petite partie. Les liens de parenté, ou liens évolutifs, qui existent entre toutes ces espèces forment un arbre, nommé « arbre de la vie » (ou arbre du vivant), où chaque feuille représente une espèce et chaque noeud un ancêtre, à la manière des arbres généalogiques

Tanglegrams are misleading for visual evaluation of tree congruence

Evolutionary Biologists are often faced with the need to compare phylogenetic trees. One popular method consists in visualizing the trees face to face with links connecting matching taxa. These tanglegrams are optimized beforehand so that the number of lines crossing (the entanglement) is minimal. This representation is implicitly justified by the expectation that the level of entanglement is correlated with the level of similarity (or congruence) between the trees compared. Using simulations, we show that this correlation is actually very weak, which should preclude the use of such technique for getting insight into the level of congruence between trees

SONIFICATION OF PHYLOGENETIC TREES: LISTENING TO EVOLUTION

International audienceA phylogenetic tree is a visual representation of the evolutionary relationships linking organisms or species, analogous to a genealogy for members of a family. In phylogenetic trees, nodes represent ancestors, leaves represent species, and edges represent time or the amount of character or genetic change. The visualization and the comparison of such hierarchical structure can be very challenging, especially when the number of species is high. In this work, we suggest a new approach for getting insights into the main structural features of phylogenetic trees. We define simple rules for the sonification of a phylogeny and apply them to the simplified tree of Boroeutheria, a group of mammals comprising, among others, human, mouse, rabbit, whale and cat. This approach appears to be very promising for better apprehending tree structures

Zombi: A phylogenetic simulator of trees, genomes and sequences that accounts for dead lineages

International audienceHere we present Zombi, a tool to simulate the evolution of species, genomes and sequences in silico, that considers for the first time the evolution of genomes in extinct lineages. It also incorporates various features that have not to date been combined in a single simulator, such as the possibility of generating species trees with a pre-defined variation of speciation and extinction rates through time, simulating explicitly intergenic sequences of variable length and outputting gene tree - species tree reconciliations

Innovative multidimensional gait evaluation using IMU in multiple sclerosis: introducing the semiogram

BackgroundQuantifying gait using inertial measurement units has gained increasing interest in recent years. Highly degraded gaits, especially in neurological impaired patients, challenge gait detection algorithms and require specific segmentation and analysis tools. Thus, the outcomes of these devices must be rigorously tested for both robustness and relevancy in order to recommend their routine use. In this study, we propose a multidimensional score to quantify and visualize gait, which can be used in neurological routine follow-up. We assessed the reliability and clinical coherence of this method in a group of severely disabled patients with progressive multiple sclerosis (pMS), who display highly degraded gait patterns, as well as in an age-matched healthy subjects (HS) group.MethodsTwenty-two participants with pMS and nineteen HS were included in this 18-month longitudinal follow-up study. During the follow-up period, all participants completed a 10-meter walk test with a U-turn and back, twice at M0, M6, M12, and M18. Average speed and seven clinical criteria (sturdiness, springiness, steadiness, stability, smoothness, synchronization, and symmetry) were evaluated using 17 gait parameters selected from the literature. The variation of these parameters from HS values was combined to generate a multidimensional visual tool, referred to as a semiogram.ResultsFor both cohorts, all criteria showed moderate to very high test–retest reliability for intra-session measurements. Inter-session quantification was also moderate to highly reliable for all criteria except smoothness, which was not reliable for HS participants. All partial scores, except for the stability score, differed between the two populations. All partial scores were correlated with an objective but not subjective quantification of gait severity in the pMS population. A deficit in the pyramidal tract was associated with altered scores in all criteria, whereas deficits in cerebellar, sensitive, bulbar, and cognitive deficits were associated with decreased scores in only a subset of gait criteria.ConclusionsThe proposed multidimensional gait quantification represents an innovative approach to monitoring gait disorders. It provides a reliable and informative biomarker for assessing the severity of gait impairments in individuals with pMS. Additionally, it holds the potential for discriminating between various underlying causes of gait alterations in pMS

Balance Impairment in Radiation Induced Leukoencephalopathy Patients Is Coupled With Altered Visual Attention in Natural Tasks

Background: Recent studies have shown that alterations in executive function and attention lead to balance control disturbances. One way of exploring the allocation of attention is to record eye movements. Most experimental data come from a free viewing of static scenes but additional information can be leveraged by recording eye movements during natural tasks. Here, we aimed to provide evidence of a correlation between impaired visual alteration in natural tasks and postural control in patients suffering from Radiation-Induced Leukoencephalopathy (RIL).Methods: The study subjects were nine healthy controls and 10 patients who were diagnosed with RIL at an early stage, with isolated dysexecutive syndrome without clinically detectable gait or posture impairment. We performed a balance evaluation and eye movement recording during an ecological task (reading a recipe while cooking). We calculated a postural score and oculomotor parameters already proposed in the literature. We performed a variable selection using an out-of-bag random permutation and a random forest regression algorithm to find: (i) if visual parameters can predict postural deficit and, (ii) which are the most important of them in this prediction. Results were validated using the leave-one-out cross-validation procedure.Results: Postural scores indeed were found significantly lower in patients with RIL than in healthy controls. Visual parameters were found able to predict the postural score of RIL patients with normalized root mean square error (RMSE) of 0.16. The present analysis showed that horizontal and vertical eye movements, as well as the average duration of the saccades and fixations influenced significantly the prediction of the postural score in RIL patients. While two patients with very low MATTIS-Attention sub score showed the lowest postural scores, no statistically significant relationship was found between the two outcomes.Conclusion: These results highlight the significant relationship between the severity of balance deficits and the visual characteristics in RIL patients. It seems that increased balance impairment is coupled with a reduced focusing capacity in ecological tasks. Balance and eye movement recordings during a natural task could be a useful aspect of multidimensional scoring of the dysexecutive syndrome

Coexistence of two sympatric cryptic bat species in French Guiana: insights from genetic, acoustic and ecological data

International audienceBackground: The distinction between lineages of neotropical bats from the Pteronotus parnellii species complex has been previously made according to mitochondrial DNA, and especially morphology and acoustics, in order to separate them into two species. In these studies, either sample sizes were too low when genetic and acoustic or morphological data were gathered on the same individuals, or genetic and other data were collected on different individuals. In this study, we intensively sampled bats in 4 caves and combined all approaches in order to analyse genetic, morphologic, and acoustic divergence between these lineages that live in the same caves in French Guiana