The genetic history of Mayotte and Madagascar cattle breeds mirrors the complex pattern of human exchanges in Western Indian Ocean.

Despite their central economic and cultural role, the origin of cattle populations living in Indian Ocean islands still remains poorly documented. Here, we unravel the demographic and adaptive histories of the extant Zebus from the Mayotte and Madagascar islands using high-density SNP genotyping data. We found that these populations are very closely related and both display a predominant indicine ancestry. They diverged in the 16th century at the arrival of European people who transformed the trade network in the area. Their common ancestral cattle population originates from an admixture between an admixed African zebu population and an Indian zebu that occurred around the 12th century at the time of the earliest contacts between human African populations of the Swahili corridor and Austronesian people from Southeast Asia in Comoros and Madagascar. A steep increase in the estimated population sizes from the beginning of the 16th to the 17th century coincides with the expansion of the cattle trade. By carrying out genome scans for recent selection in the two cattle populations from Mayotte and Madagascar, we identified sets of candidate genes involved in biological functions (cancer, skin structure, and UV-protection, nervous system and behavior, organ development, metabolism, and immune response) broadly representative of the physiological adaptation to tropical conditions. Overall, the origin of the cattle populations from Western Indian Ocean islands mirrors the complex history of human migrations and trade in this area.

A novel robust PLS regression method inspired from boosting principles: RoBoost-PLSR.

The calibration of Partial Least Square regression (PLSR) models can be disturbed by outlying samples in the data. In these cases the models can be unstable and their predictive potential can be depreciated. To address this problem, some robust versions of the PLSR Algorithm were proposed. These algorithms rely on the downweighting of these outliers during calibration. To this end, it is necessary to estimate an inconsistency measurement between the samples and the model. However, this estimation is not trivial in high dimensions. This paper proposes a novel robust PLSR algorithm inspired from the principles of boosting: RoBoost-PLSR. This method consists of realising a series of one latent variable weighted PLSR. RoBoost-PLSR is compared with the PLSR algorithm calibrated with and without outliers and also with Partial Robust M-regression (PRM), a reference robust method. This evaluation is conducted on the basis of three simulated datasets and a real dataset. Finally Roboost-PLSR proves to be resilient to the tested outliers, and can achieve the performances of the reference PLSR calibrated without any outlier.

Ex-ante assessment of different vaccination-based control schedules against the peste des petits ruminants virus in sub-Saharan Africa.

BACKGROUND: Peste des petits ruminants (PPR) is a highly contagious and widespread viral infection of small ruminants (goats and sheep), causing heavy economic losses in many developing countries. Therefore, its progressive control and global eradication by 2030 was defined as a priority by international organizations addressing animal health. The control phase of the global strategy is based on mass vaccination of small ruminant populations in endemic regions or countries. It is estimated that a 70% post-vaccination immunity rate (PVIR) is needed in a given epidemiological unit to prevent PPR virus spread. However, implementing mass vaccination is difficult and costly in smallholder farming systems with scattered livestock and limited facilities. Regarding this, controlling PPR is a special challenge in sub-Saharan Africa. In this study, we focused on this region to assess the effect of several variables of PVIR in two contrasted smallholder farming systems. METHODS: Using a seasonal matrix population model of PVIR, we estimated its decay in goats reared in sub-humid areas, and sheep reared in semi-arid areas, over a 4-year vaccination program. Assuming immunologically naive and PPR-free epidemiological unit, we assessed the ability of different vaccination scenarios to reach the 70% PVIR throughout the program. The tested scenarios differed in i) their overall schedule, ii) their delivery month and iii) their vaccination coverage. RESULTS: In sheep reared in semi-arid areas, the vaccination month did affect the PVIR decay though it did not in goats in humid regions. In both cases, our study highlighted i) the importance of targeting the whole eligible population at least during the two first years of the vaccination program and ii) the importance of reaching a vaccination coverage as high as 80% of this population. This study confirmed the relevance of the vaccination schedules recommended by international organizations.

Modelling the Dynamics of Post-Vaccination Immunity Rate in a Population of Sahelian Sheep after a Vaccination Campaign against Peste des Petits Ruminants Virus.

BACKGROUND: Peste des petits ruminants (PPR) is an acute infectious viral disease affecting domestic small ruminants (sheep and goats) and some wild ruminant species in Africa, the Middle East and Asia. A global PPR control strategy based on mass vaccination-in regions where PPR is endemic-was recently designed and launched by international organizations. Sahelian Africa is one of the most challenging endemic regions for PPR control. Indeed, strong seasonal and annual variations in mating, mortality and offtake rates result in a complex population dynamics which might in turn alter the population post-vaccination immunity rate (PIR), and thus be important to consider for the implementation of vaccination campaigns. METHODS: In a context of preventive vaccination in epidemiological units without PPR virus transmission, we developed a predictive, dynamic model based on a seasonal matrix population model to simulate PIR dynamics. This model was mostly calibrated with demographic and epidemiological parameters estimated from a long-term follow-up survey of small ruminant herds. We used it to simulate the PIR dynamics following a single PPR vaccination campaign in a Sahelian sheep population, and to assess the effects of (i) changes in offtake rate related to the Tabaski (a Muslim feast following the lunar calendar), and (ii) the date of implementation of the vaccination campaigns. RESULTS: The persistence of PIR was not influenced by the Tabaski date. Decreasing the vaccination coverage from 100 to 80% had limited effects on PIR. However, lower vaccination coverage did not provide sufficient immunity rates (PIR < 70%). As a trade-off between model predictions and other considerations like animal physiological status, and suitability for livestock farmers, we would suggest to implement vaccination campaigns in September-October. This model is a first step towards better decision support for animal health authorities. It might be adapted to other species, livestock farming systems or diseases.

Performance evaluation of two serological tests for contagious bovine pleuropneumonia (CBPP) detection in an enzootic area using a Bayesian framework.

A Bayesian approach, allowing for conditional dependence between two tests was used to estimate without gold standard the sensitivities of complement fixation test (CFT) and competitive enzyme-linked immunosorbent assay test (cELISA) and the serological prevalence of CBPP in a cattle population of the Central Delta of the Niger River in Mali, where CBPP is enzootic and the true prevalence and animals serological state were unknown. A significant difference (P = 0.99) was observed between the sensitivities of the two tests, estimated at 73.7% (95% probability interval [PI], 63.4-82.7) for cELISA and 42.3% (95% PI, 33.3-53.7) for CFT. Individual-level serological prevalence in the study population was estimated at 14.1% (95% PI, 10.8-16.9). Our results indicate that in enzootic areas, cELISA performs better in terms of sensitivity than CFT. However, negative conditional sensitivity dependence between the two tests was detected, implying that to achieve maximum sensitivity, the two tests should be applied in parallel.

Demographic dynamics and off-take of cattle herds in southern Mali.

The herds of 95 families were monitored for 1 year in eight villages in the cotton-growing region of southern Mali. In 2006-2007, reproduction performances were average, with 0.54 calvings/year per cow, and mortality was low. Herd numerical productivity is not very high, less than 0.13/year, because of the high proportion of males kept for animal draught. Depending on the herd size, the behaviour of the families differs, in terms of off-take and in-take of animals. Families that only have one or two draught animals seek to increase their animal draught capacity, with a negative net off-take (-0.13/year). Families with two to three cows have a very low net off-take (0.02/year), with culling of adult animals compensated by purchase. They therefore capitalised this year, with an annual herd growth of 8%. Families with a very large herd (20 to 50 cows) take off more of their stock, with a net off-take of 0.08/year (very few animal purchases) and make a stock growth of 5%. And finally, families with an average-sized herd (6 to 19 cows) take off the whole of the year's production, with a net off-take of 0.11/year and a nil stock growth rate. The use of a demographic model made it possible to measure the sensitivity of the productivity rate to the different demographic parameters.

Assessment of age at first parturition by accounting censored data: the example of small ruminants in agropastoral herds in Senegal.

Age at first parturition (AFP) is an important reproductive trait when evaluating the herd productivity in tropical small-holder farming systems, particularly for small ruminants with high demographic turnover and commercial utilization. The article reports the AFP probability distributions calculated on goats and sheep herds monitored for more than 10 years in three low-input livestock farming systems located from northern to southern Senegal (Louga, Kaymor, and Kolda) and representing different agroecological conditions and animal phenotypes. The AFP distributions were estimated with the Kaplan-Meier (KM) survival analysis accounting for censoring (females lost to follow-up before their first parturition). When measured by the KM estimator of the AFP median, the precocity for both species was almost 4 months later in Louga than in Kaymor and Kolda. In Louga, the precocity was 1.6 months later for sheep than for goats and 2.9 months in Kaymor and Kolda. These estimates were higher than those obtained with the common and crude approach that removes censored data before calculation (relative bias ranged from -12% to -22% for the AFP mean depending on species and site) and those already published in previous studies on the same data sets. In on-farm small ruminant studies focusing on reproductive traits such as AFP distributions, we recommend using survival models (e.g., the KM method) to avoid potential biases due to data censoring.

A metapopulation model for the spread and persistence of contagious bovine pleuropneumonia (CBPP) in African sedentary mixed crop-livestock systems.

Contagious bovine pleuropneumonia (CBPP) is endemic in several developing countries. Our objective is to evaluate the regional CBPP spread and persistence in a mixed crop-livestock system in Africa. A stochastic compartmental model in metapopulation is used, in which between-herd animal movements and the within-herd infection dynamics are explicitly represented. Hundred herds of varying size are modelled, each sending animals to n other herds (network degree). Animals are susceptible, latent, infectious, chronic carrier or resistant. The role of chronic carriers in CBPP spread being still debated, several chronic periods and infectiousness are tested. A sensitivity analysis is performed to evaluate the influence on model outputs of these parameters and of pathogen virulence, between-herd movement rate, network degree, and calves recruitment. Model outputs are the probability that individual- and group-level reproductive numbers R(0) and R(*) are above one, the metapopulation infection duration, the probability of CBPP endemicity (when CBPP persists over 5 years), and the epidemic size in infected herds and infected animals. The most influential parameters are related to chronic carriers (infectiousness and chronic period), pathogen virulence, and recruitment rate. When assuming no CBPP re-introduction in the region, endemicity is only probable if chronic carriers are assumed infectious for at least 1 year and to shed the pathogen in not too low an amount. It becomes highly probable when assuming high pathogen virulence and high recruitment rate.

Evaluation of 12-month interval methods for estimating animal-times at risk in a traditional African livestock farming system.

Demographic parameters are useful for assessing productivity and dynamics of tropical livestock populations. Common parameters are the annual instantaneous hazard rates, which can be estimated by m/T (where m represents the number of the considered demographic events occurred during the year and T the cumulated animal-time at risk). Different approaches are encountered in the literature for computing T from on-farm survey data. One crude approach ("the 12-month interval approach") only uses estimations of herds' sizes at beginning and end of the year and aggregated counts of demographic events over the year. I evaluated the potential biases in using four 12-month interval methods (M1-M4) to estimate T. Biases were evaluated by comparing the 12-month estimates to gold-standard values of T. Data came from long-term herd monitoring on cattle and small ruminants in extensive agro-pastoral systems. Animal-times at risks were correctly estimated in average by methods M1, M2 and M4 (average relative biases

Time-delay dynamics for contagious bovine pleuropneumonia.

Modelling of contagious disease usually employs compartmental SEIR-like models where the waiting times in respective compartments are exponentially distributed. In this paper, we are interested in investigating how the distributions of sojourn times in infective compartments affect the dynamics and persistence of the contagious bovine pleuropneumonia, a chronic respiratory disease of cattle. Two kinds of extreme distributions of the sojourn times are considered: a Dirac delta-function and truncated Gaussian function leading to a model with (non-constant) delay and the classical exponential distribution that stands for a model without delay. Expressions of the basic reproductive numbers are derived and dynamical behaviours are discussed for the three models. It is found that the spreading of disease exhibits wave-like oscillations for the time-delay dynamics. In contrast, the disease appears to last longer when the spreading is described by the classical dynamics without delay. Subsequently, the time-delay dynamics turns out to be more appropriate for the description of an experimental epidemic of CBPP.

Within-herd spread of contagious bovine pleuropneumonia in Ethiopian highlands.

Contagious bovine pleuropneumonia (CBPP) is a major threat for cattle health and production in Africa. This disease is caused by the small-colony type of Mycoplasma mycoides subspecies mycoides (MmmSC). Transmission occurs from direct and repeated contacts between sick and healthy animals. Veterinary services recently reported a resurgence of CBPP in the province of West Wellega, in the Ethiopian highlands. A research program was set up to estimate the epidemiological parameters of the within-herd infection spread. A follow-up survey was implemented in 71 sampled herds of the Boji district (West Wellega province). Fifteen herds were classified as newly infected and used in a serological- and clinical-incidence study. The overall 16-month cumulative sero-incidence risk was 34%. Clinical cases were recorded for 39% of the seropositive cattle; case-fatality risk was 13%. There was no evidence of benefit on infection spread of CBPP-control measures used locally by farmers (isolation or antibiotic treatments of sick animals). This might be related to a lack of power in the statistical analyses or to a quality problem for the medications used (and more generally, for health-care delivery in the Boji district).

A mathematical model of the effects of chronic carriers on the within-herd spread of contagious bovine pleuropneumonia in an African mixed crop-livestock system.

Contagious bovine pleuropneumonia (CBPP) is a respiratory disease of cattle; CBPP is caused by Mycoplasma mycoides subsp. mycoides small colony. CBPP is a major cause for concern for African countries (because of mortality, animal-production losses and cost of control). The clinical form of the disease is the more infectious (contagion occurs essentially through coughing). However, chronic lung lesions with viable mycoplasmas can persist in recovering cattle. Animals presenting these lesions might have a time-delimitated infectious phase. Such carriers are suspected to generate field outbreaks (although this hypothesis remains debated). We investigated the potential quantitative effects of these chronic carriers on the within-herd CBPP spread. Data were collected during a longitudinal field herd survey in a mixed crop-livestock system in the Ethiopian highlands. Two stochastic Markov-chain models' outputs (seroconversion dynamics, basic reproduction ratio R0, cumulative clinical incidence and risk of herd infection) were compared given different hypotheses on the carrier infectiousness. The late seroconversions observed in the field data were fitted correctly only for the highest carrier infectiousness we considered (mean chronic duration of 1 year and carriers 50-times less infectious than clinical cases). Although sensitivities (in terms of disease impact in the herd) were in general negligible when the carrier infectiousness was low (e.g. when carriers were assumed to be 1000-times less infectious than clinical cases), they rapidly became important when the infectiousness increased.

Use of Akaike information criteria for model selection and inference. An application to assess prevention of gastrointestinal parasitism and respiratory mortality of Guinean goats in Kolda, Senegal.

A field experiment was carried out in Kolda (southern Senegal) from July 1986 to July 1988. Its goals were to: (1) describe the patterns of mortality of female Guinean goats by age, season and year; (2) assess preventive measures against respiratory diseases and gastrointestinal parasitism in reducing mortality; and (3) estimate the overall impact of these measures on survival to 1 year of age. Preventive measures for respiratory disease included vaccination against peste des petits ruminants (PPR) and pneumonic pasteurellosis (Pasteurella multocida types A and D). Control of gastrointestinal parasites was by deworming does with morantel (7.5mg kg(-1), three times during the rainy season). The effects of vaccines and deworming were tested in a randomised factorial field experiment with villages being the experimental units. A total of 19 villages, 113 goat herds and 1,458 goats were included in the study. Generalised linear models of survival for five cohorts of goats (defined by five different birth seasons) used a binomial assumption for the response distribution and a complementary log-log link. Explanatory variables included age, season, year, vaccination, deworming and their interactions. A complex a priori model was built on the basis of previous epidemiological knowledge; a purposely selected set of simpler models was compared to this full model by the Akaike information criterion (AIC) and derived statistics. Inference on 1-year survival and treatment effects accounted for model-selection uncertainty. It was carried out with a bootstrap procedure and used information from the whole set of selected models. Large variations in mortality by year and season were observed but no regular seasonal pattern was apparent. Mortality probabilities of kids in dewormed groups decreased quickly after birth, but remained elevated up to 9 months of age in the non-dewormed groups. Deworming lowered the risk of mortality. Vaccination alone was not protective (except during an observed outbreak of PPR).