Institute Des Science Of Levolution Of Montpellier Ise M

Sainte-Foy-lès-Lyon, France

Institute Des Science Of Levolution Of Montpellier Ise M

Sainte-Foy-lès-Lyon, France
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Matsieva J.,University of California at Davis | Kelk S.,Maastricht University | Scornavacca C.,Fred Hutchinson Cancer Research Center | Whidden C.,Institute Des Science Of Levolution Of Montpellier Ise M | Gusfield D.,University of California at Davis
IEEE/ACM Transactions on Computational Biology and Bioinformatics | Year: 2017

Evolutionary data has been traditionally modeled via phylogenetic trees; however, branching alone cannot model conflicting phylogenetic signals, so networks are used instead. Ancestral recombination graphs (ARGs) are used to model the evolution of incompatible sets of SNP data, allowing each site to mutate only once. The model often aims to minimize the number of recombinations. Similarly, incompatible cluster data can be represented by a reticulation network that minimizes reticulation events. The ARG literature has traditionally been disjoint from the reticulation network literature. By building on results from the reticulation network literature, we resolve an open question of interest to the ARG community. We explicitly prove that the History Bound, a lower bound on the number of recombinations in an ARG for a binary matrix, which was previously only defined procedurally, is equal to the minimum number of reticulation nodes in a network for the corresponding cluster data. To facilitate the proof, we give an algorithm that constructs this network using intermediate values from the procedural History Bound definition. We then develop a top-down algorithm for computing the History Bound, which has the same worst-case runtime as the known dynamic program, and show that it is likely to run faster in typical cases. © 2017 IEEE.

Dupont-Prinet A.,Montpellier University | Dupont-Prinet A.,Institute Des Science Of Levolution Of Montpellier Ise M | Chatain B.,French Research Institute for Exploitation of the Sea | Grima L.,French Research Institute for Exploitation of the Sea | And 5 more authors.
Journal of Experimental Biology | Year: 2010

The specific growth rate (SGR) of a cohort of 2000 tagged juvenile European sea bass was measured in a common tank, during two sequential cycles comprising three-weeks feed deprivation followed by three-weeks ad libitum re-feeding. After correction for initial size at age as fork length, there was a direct correlation between negative SGR (rate of mass loss) during feed deprivation and positive SGR (rate of compensatory growth) during re-feeding (Spearman rank correlation R=0.388, P=0.000002 Following a period of rearing under standard culture conditions, individuals representing 'high growth' phenotypes (GP) and 'high tolerance of feed deprivation' phenotypes (DP) were selected from either end of the SGR spectrum. Static and swimming respirometry could not demonstrate lower routine or standard metabolic rate in DP to account for greater tolerance of feed deprivation. Increased rates of compensatory growth in GP were not linked to greater maximum metabolic rate, aerobic metabolic scope or maximum cardiac performance than DP. When fed a standard ration, however, GP completed the specific dynamic action (SDA) response significantly faster than DP. Therefore, higher growth rate in GP was linked to greater capacity to process food. There was no difference in SDA coefficient, an indicator of energetic efficiency. The results indicate that individual variation in growth rate in sea bass reflects, in part, a trade-off against tolerance of food deprivation. The two phenotypes represented the opposing ends of a spectrum. The GP aims to exploit available resources and grow as rapidly as possible but at a cost of physiological and/or behavioural attributes, which lead to increased energy dissipation when food is not available. An opposing strategy, exemplified by DP, is less 'boom and bust', with a lower physiological capacity to exploit resources but which is less costly to sustain during periods of food deprivation. © 2010. Published by The Company of Biologists Ltd.

McKenzie D.J.,UMR5119 | Vergnet A.,French Research Institute for Exploitation of the Sea | Chatain B.,French Research Institute for Exploitation of the Sea | Vandeputte M.,French Research Institute for Exploitation of the Sea | And 4 more authors.
Journal of Experimental Biology | Year: 2014

Although food deprivation is a major ecological pressure in fishes, there is wide individual variation in tolerance of fasting, whose mechanistic bases are poorly understood. Two thousand individually tagged juvenile European sea bass were submitted to two 'fasting/feeding' cycles each comprising 3 weeks of food deprivation followed by 3 weeks of ad libitum feeding at 25°C. Rates of mass loss during the two fasting periods were averaged for each individual to calculate a population mean. Extreme fasting tolerant (FT) and sensitive (FS) phenotypes were identified that were at least one and a half standard deviations, on opposing sides, from this mean. Respirometry was used to investigate two main hypotheses: (1) tolerance of food deprivation reflects lower mass-corrected routine metabolic rate (RMR) in FT phenotypes when fasting, and (2) tolerance reflects differences in substrate utilisation; FT phenotypes use relatively less proteins as metabolic fuels during fasting, measured as their ammonia quotient (AQ), the simultaneous ratio of ammonia excretion to RMR. There was no difference in mean RMR between FT and FS over 7 days fasting, being 6.70±0.24 mmol h-1 fish-1 (mean ± s.e.m., N=18) versus 6.76±0.22 mmol h-1 fish-1 (N=17), respectively, when corrected to a body mass of 130 g. For any given RMR, however, the FT lost mass at a significantly lower rate than FS, overall 7-day average being 0.72±0.05 versus 0.90±0.05 g day-1 fish-1, respectively (P<0.01, ttest). At 20 h after receiving a ration equivalent to 2% body mass as food pellets, ammonia excretion and simultaneous RMR were elevated and similar in FT and FS, with AQs of 0.105±0.009 and 0.089±0.007, respectively. At the end of the period of fasting, ammonia excretion and RMR had fallen in both phenotypes, but AQ was significantly lower in FT than FS, being 0.038±0.004 versus 0.061±0.005, respectively (P<0.001, t-test). There was a direct linear relationship between individual fasted AQ and rate of mass loss, with FT and FS individuals distributed at opposing lower and upper extremities, respectively. Thus the difference between the phenotypes in their tolerance of food deprivation did not depend upon their routine energy use when fasting. Rather, it depended upon their relative use of tissue proteins as metabolic fuels when fasting, which was significantly lower in FT phenotypes. © 2014. Published by The Company of Biologists Ltd.

Anselmetti Y.,Institute Des Science Of Levolution Of Montpellier Ise M | Anselmetti Y.,CNRS Biometry and Evolutionary Biology Laboratory | Berry V.,Montpellier University | Chauve C.,Simon Fraser University | And 5 more authors.
BMC Genomics | Year: 2015

We exploit the methodological similarity between ancestral genome reconstruction and extant genome scaffolding. We present a method, called ARt-DeCo that constructs neighborhood relationships between genes or contigs, in both ancestral and extant genomes, in a phylogenetic context. It is able to handle dozens of complete genomes, including genes with complex histories, by using gene phylogenies reconciled with a species tree, that is, annotated with speciation, duplication and loss events. Reconstructed ancestral or extant synteny comes with a support computed from an exhaustive exploration of the solution space. We compare our method with a previously published one that follows the same goal on a small number of genomes with universal unicopy genes. Then we test it on the whole Ensembl database, by proposing partial ancestral genome structures, as well as a more complete scaffolding for many partially assembled genomes on 69 eukaryote species. We carefully analyze a couple of extant adjacencies proposed by our method, and show that they are indeed real links in the extant genomes, that were missing in the current assembly. On a reduced data set of 39 eutherian mammals, we estimate the precision and sensitivity of ARt-DeCo by simulating a fragmentation in some well assembled genomes, and measure how many adjacencies are recovered. We find a very high precision, while the sensitivity depends on the quality of the data and on the proximity of closely related genomes. © 2015 Anselmetti et al.

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