Olivier Martin

A congruence index for testing topological similarity between trees

MOTIVATIONnPhylogenetic trees are omnipresent in evolutionary biology and the comparison of trees plays a central role there. Tree congruence statistics are based on the null hypothesis that two given trees are not more congruent (topologically similar) than expected by chance. Usually, one searches for the most parsimonious evolutionary scenario relating two trees and then one tests the null hypothesis by generating a high number of random trees and comparing these to the one between the observed trees. However, this approach requires a lot of computational work (human and machine) and the results depend on the evolutionary assumptions made.nnnRESULTSnWe propose an index, I(cong), for testing the topological congruence between trees with any number of leaves, based on maximum agreement subtrees (MAST). This index is straightforward, simple to use, does not rely on parametrizing the likelihood of evolutionary events, and provides an associated confidence level.nnnAVAILABILITYnA web site has been created that allows rapid and easy online computation of this index and of the associated P-value at http://www.ese.u-psud.fr/bases/upresa/pages/devienne/index.html

Genome-Wide Crossover Distribution in Arabidopsis thaliana Meiosis Reveals Sex-Specific Patterns along Chromosomes

In most species, crossovers (COs) are essential for the accurate segregation of homologous chromosomes at the first meiotic division. Their number and location are tightly regulated. Here, we report a detailed, genome-wide characterization of the rate and localization of COs in Arabidopsis thaliana, in male and female meiosis. We observed dramatic differences between male and female meiosis which included: (i) genetic map length; 575 cM versus 332 cM respectively; (ii) CO distribution patterns: male CO rates were very high at both ends of each chromosome, whereas female CO rates were very low; (iii) correlations between CO rates and various chromosome features: female CO rates correlated strongly and negatively with GC content and gene density but positively with transposable elements (TEs) density, whereas male CO rates correlated positively with the CpG ratio. However, except for CpG, the correlations could be explained by the unequal repartition of these sequences along the Arabidopsis chromosome. For both male and female meiosis, the number of COs per chromosome correlates with chromosome size expressed either in base pairs or as synaptonemal complex length. Finally, we show that interference modulates the CO distribution both in male and female meiosis.

A teleonomic model describing performance (body, milk and intake) during growth and over repeated reproductive cycles throughout the lifespan of dairy cattle. 1. Trajectories of life function priorities and genetic scaling

The prediction of the control of nutrient partitioning, particularly energy, is a major issue in modelling dairy cattle performance. The proportions of energy channelled to physiological functions (growth, maintenance, gestation and lactation) change as the animal ages and reproduces, and according to its genotype and nutritional environment. This is the first of two papers describing a teleonomic model of individual performance during growth and over repeated reproductive cycles throughout the lifespan of dairy cattle. The conceptual framework is based on the coupling of a regulating sub-model providing teleonomic drives to govern the work of an operating sub-model scaled with genetic parameters. The regulating sub-model describes the dynamic partitioning of a mammal females priority between life functions targeted to growth (G), ageing (A), balance of body reserves (R) and nutrient supply of the unborn (U), newborn (N) and suckling (S) calf. The so-called GARUNS dynamic pattern defines a trajectory of relative priorities, goal directed towards the survival of the individual for the continuation of the specie. The operating sub-model describes changes in body weight (BW) and composition, foetal growth, milk yield and composition and food intake in dairy cows throughout their lifespan, that is, during growth, over successive reproductive cycles and through ageing. This dynamic pattern of performance defines a reference trajectory of a cow under normal husbandry conditions and feed regimen. Genetic parameters are incorporated in the model to scale individual performance and simulate differences within and between breeds. The model was calibrated for dairy cows with literature data. The model was evaluated by comparison with simulations of previously published empirical equations of BW, body condition score, milk yield and composition and feed intake. This evaluation showed that the model adequately simulates these production variables throughout the lifespan, and across a range of dairy cattle genotypes.

Effect of concentrate percentage on ruminal pH and time-budget in dairy goats

The aim of this study was to compare rumen pH and time-budget in eight mid-lactation goats receiving two diets in a cross-over design (low-concentrate diet (L): 30% and high-concentrate diet (H): 60% concentrate). Feeding H increased daily intake (4.3 ± 0.08% v. 4.7 ± 0.08% of body weight for L and H, respectively) and daily milk production (3.01 ± 0.130 v. 3.50 ± 0.130 kg/day of 3.5% fat-corrected milk for L and H, respectively). It decreased milk fat and inverted the fat-to-protein ratio (1.07 ± 0.054 v. 0.94 ± 0.054 for L and H, respectively). As suggested by the percentage of time spent with rumen pH below 6.0 (23.4 ± 6.60% v. 39.9 ± 5.88% for L and H, respectively), H was more acidogenic than L. When offered H instead of L, goats spent less time eating (298 ± 17.5 v. 265 ± 17.5 min for L and H, respectively) and ruminating (521 ± 21.0 v. 421 ± 21.0 min for L and H, respectively) but more time resting (352 ± 27.1 v. 459 ± 21.1 min for L and H, respectively) over a 24-h period. They also tended to spend more time drinking (20 ± 2.9 v. 25 ± 2.9 min for L and H, respectively; P = 0.08) when offered H rather than L. These differences in activities were mainly observed during the first hours following feeding. When offered H, goats adapted their feeding behaviour around the feedings, which allowed them to limit the physiological disturbances potentially inducible by H and to increase milk production, without experiencing too much acidosis.

CODA (crossover distribution analyzer): quantitative characterization of crossover position patterns along chromosomes

BackgroundDuring meiosis, homologous chromosomes exchange segments via the formation of crossovers. This phenomenon is highly regulated; in particular, crossovers are distributed heterogeneously along the physical map and rarely arise in close proximity, a property referred to as interference. Crossover positions form patterns that give clues about how crossovers are formed. In several organisms including yeast, tomato, Arabidopsis, and mouse, it is believed that crossovers form via at least two pathways, one interfering, the other not.ResultsWe have developed a software package - CODA, for CrossOver Distribution Analyzer - which allows one to quantitatively characterize crossover patterns by fitting interference models to experimental data. Two families of interfering models are provided: the gamma model and the beam-film model. The user can specify single or two-pathways modeling, and the software package infers the models parameters and their confidence intervals. CODA can handle data produced from measurements on bivalents or gametes, in the form of continuous crossover positions or marker genotyping. We illustrate the possibilities on data from Wheat, corn and mouse.ConclusionsCODA extends the kind of crossover data that could be analyzed so far to include gametic data (rather than only bivalents/tetrads) when using two-pathways modeling. It will also enable users to perform analyses based on the beam-film model. CODA implements that models complex physics and mathematics, and uses a summary statistic to overcomes the lack of a computable likelihood which has hampered its use till now.

Simple representation of physiological regulations in a model of lactating female: application to the dairy goat

A dynamic model of the lactating dairy goat, combining a minimum of mechanistic representations of homeorhetic regulations and a long-term approach, was developed. It describes (i) the main changes in body weight, dry-matter intake, milk production and composition of a dairy goat; (ii) the succession of pregnancy and lactation throughout the productive life; and (iii) the major changes in dynamics induced by the female profile (production potential and body weight at maturity). The model adopts a pull approach including a systematic expression of the production potential and not representing any feed limitation. It involves three sub-systems. The reproductive events sub-system drives the dynamics through time with three major events: service, kidding and drying off. It also accounts for the effect of production potential (kg of milk at the peak of lactation) and lactation number (potential reached at the fourth lactation). The regulating sub-system represents the homeorhetic mechanisms during pregnancy and lactation with two sets of theoretical hormones, one representing gestation and the other lactation. The operating sub-system describes the main physiological flows and the energetic requirements linked to these functions through a compartmental structure. Simulations were run in order to test (i) the behaviour of the model at the scale of the productive life for an average profile of female (60 kg at maturity and 4 kg of milk at peak); (ii) the sensitivity of the simulated dynamics (mainly milk production and body reserves) to the production potential and body weight at maturity; (iii) external validation with comparison of model outputs to data from the experimental flock of Grignon and data from the French milk record organization (French organism in charge of animal recording for dairy farmers). The results at the scale of one productive life show the model simulates a relevant set of dynamics. The sensitivity analysis suggests that the model fairly well simulates the link between a females ability to produce and mobilise reserves. Finally, external validation confirms the models ability to simulate a relevant set of physiological dynamics while pointing out some limits of the model (simulation of milk fat and protein content dynamics, for example). The results illustrate the relevance of the model in simulating biological dynamics and confirm the possibility of including minimum representations of homeorhetic regulations with a simple structure. This simplicity gives an opportunity to integrate this basic element in a herd simulator and test interactions between females regulations and management rules.

Overview of progesterone profiles in dairy cows

The aim of this study was to gain a better understanding of the variability in shape and features of all progesterone profiles during estrus cycles in cows and to create templates for cycle shapes and features as a base for further research. Milk progesterone data from 1418 estrus cycles, coming from 1009 lactations, was obtained from the Danish Cattle Research Centre in Foulum, Denmark. Milk samples were analyzed daily using a Ridgeway ELISA-kit. Estrus cycles with less than 10 data points or shorter than 4xa0days were discarded, after which 1006 cycles remained in the analysis. A median kernel of three data points was used to smooth the progesterone time series. The time between start of progesterone rise and end of progesterone decline was identified by fitting a simple model consisting of base length and a quadratic curve to progesterone data, and this luteal-like phase (LLP) was used for further analysis. The data set of 1006 LLPs was divided into five quantiles based on length. Within quantiles, a cluster analysis was performed on the basis of shape distance. Height, upward and downward slope, and progesterone level on Day 5 were compared between quantiles. Also, the ratio of typical versus atypical shapes was described, using a reference curve on the basis of data in Q1-Q4. The main results of this article were that (1) most of the progesterone profiles showed a typical profile, including the ones that exceeded the optimum cycle length of 24xa0days; (2) cycles in Q2 and Q3 had steeper slopes and higher peak progesterone levels than cycles in Q1 and Q4 but, when normalized, had a similar shape. Results were used to define differences between quantiles that can be used as templates. Compared to Q1, LLPs in Q2 had a shape that is 1.068 times steeper and 1.048 times higher. Luteal-like phases in Q3 were 1.053 times steeper and 1.018 times higher. Luteal-like phases in Q4 were 0.977 times steeper and 0.973 times higher than LLPs in Q1. This article adds to our knowledge about the variability of progesterone profiles and their shape differences. The profile clustering procedure described in this article can be used as a means to classify progesterone profiles without recourse to an a priori set of rules, which arbitrarily segment the natural variability in these profiles. Using data-derived profile shapes may allow a more accurate assessment of the effects of, e.g., nutritional management or breeding system on progesterone profiles.

In response to comment on ‘A congruence index for testing topological similarity between trees’

In response to comment on ‘A congruence index for testing topological similarity between trees’ Damien M. de Vienne1,∗, Tatiana Giraud1 and Olivier C. Martin2,3 1Univ Paris-Sud, Laboratoire de Recherche en Informatique, UMR8623, Orsay F-91405; CNRS, Orsay F-91405, 2Univ Paris-Sud, UMR8626, LPTMS, Orsay F-91405; CNRS, Orsay F-91405 and 3Univ Paris-Sud, UMR8120, Laboratoire de Genetique Vegetale du Moulon, Gif-sur-Yvette F-91190, France

Turning a cow into a goat with a teleonomic model of lifetime performance

Predicting nutrient partitioning throughout lifespan is a major issue in modelling dairy female performance. A general framework has been proposed for dairy cattle. The key concept of this framework is to consider lifetime performance as a trajectory, goal directed towards reproductive success, genetically scaled and potentially altered by environment. The framework is based on two sub-models, namely a regulating model describing a time base pattern of priority for physiological functions and an operating sub-model driving energy partitioning. The objective of this work is to assess the suitability of the model to represent dairy goat lifetime performance. Eight parameters were modified to ‘turn a cow into a goat’: two parameters were related to foetal growth, three parameters were related to reproductive events timing, two parameters related to the scaling of body weight at maturity and milk potential and a parameter related to labile body mass mobilization. Individual records of the INRA experimental herd were used to assess the model suitability to simulate dairy goat performance. The result shows that the simulated body weight and milk production dynamics over three lactations were globally consistent with the data. Hence, adapting eight parameters from the dairy cow model was sufficient to simulate the performance of a dairy goat. This work opens perspective for the development of a generic animal model.