In order to understand the effect of nuclear transfer technology on the physiology of lactation and milk fatty acid composition in dairy cattle (Holstein breed), the present study compares the milk yield and composition from bovine somatic cell cloned (n=5) and control animals (n=5) at 180 days in milk (DIM) maintained together under the same conditions. All cows were offered the same total mixed ration ad libitum. At 180 DIM, the cloned had a higher body weight (BW; P<0.01) compared with control animals, whereas comparable body condition score (BCS) was observed among the 2 groups. The cloned cows had a lower milk yield and milk protein and lactose yields (P<0.05) and had a tendency (P=0.08) for a lower milk fat yield. Conversely, no differences in milk fat, protein and lactose concentrations were observed in cloned compared with control animals. Similar milk fatty acid (FA) concentrations were observed in cloned and control cows except for two minor FA, cis-9 C10:1 and C17:0 (P<0.05) that were higher in the cloned. The milk fat cis-9 C14:1/C14:0, cis-9 C16:1/C16:0, cis-9 C18:1/C18:0, cis-9, trans-11 C18:2/trans-11 C18:1 concentrations ratios were not different in cloned and control. The milk medium-(C10–C16) and long-(∑C18) chain FA yields were lower (P<0.05) in cloned compared with control animals. The mRNA abundance of genes encoding for SCD1, SCD5, ACACA and FABP3 genes in mammary tissue was similar (P>0.05) in cloned and non-cloned animals. Conversely, cloned animals had a lower (P<0.05) mRNA abundance of LPL and a tendency (P<0.10) for lower mRNA abundance of FASN and CD36 genes compared with control. The absence of major differences of milk constituent concentrations, milk FA composition and of the SCD desaturation indices observed between cloned and conventional animals suggest a comparable nutritional quality of milk for these animals. The noticed differences in milk long chain-FA yields were consistent with modulation of mammary lipogenic pathway as suggested by lower mRNA abundance of LPL gene in cloned compared with control. Otherwise, differences in the partitioning of nutrients between the mammary gland and other tissues cannot be excluded as suggested by the higher BW and lower milk yield observed in cloned. Altogether, these observations may be attributed to different genetic background and/or to epigenetic modifications due to the nuclear transfer technology that may affect the growth and the physiological adaptation to lactation and impact the dairy performances. Further investigations are required to identify the mechanisms underlying these differences.

In order to understand the effect of nuclear transfer technology on the physiology of lactation and milk fatty acid composition in dairy cattle (Holstein breed), the present study compares the milk yield and composition from bovine somatic cell cloned (n=5) and control animals (n=5) at 180 days in milk (DIM) maintained together under the same conditions. All cows were offered the same total mixed ration ad libitum. At 180 DIM, the cloned had a higher body weight (BW; P<0.01) compared with control animals, whereas comparable body condition score (BCS) was observed among the 2 groups. The cloned cows had a lower milk yield and milk protein and lactose yields (P<0.05) and had a tendency (P=0.08) for a lower milk fat yield. Conversely, no differences in milk fat, protein and lactose concentrations were observed in cloned compared with control animals. Similar milk fatty acid (FA) concentrations were observed in cloned and control cows except for two minor FA, cis-9 C10:1 and C17:0 (P<0.05) that were higher in the cloned. The milk fat cis-9 C14:1/C14:0, cis-9 C16:1/C16:0, cis-9 C18:1/C18:0, cis-9, trans-11 C18:2/trans-11 C18:1 concentrations ratios were not different in cloned and control. The milk medium-(C10–C16) and long-(∑C18) chain FA yields were lower (P<0.05) in cloned compared with control animals. The mRNA abundance of genes encoding for SCD1, SCD5, ACACA and FABP3 genes in mammary tissue was similar (P>0.05) in cloned and non-cloned animals. Conversely, cloned animals had a lower (P<0.05) mRNA abundance of LPL and a tendency (P<0.10) for lower mRNA abundance of FASN and CD36 genes compared with control. The absence of major differences of milk constituent concentrations, milk FA composition and of the SCD desaturation indices observed between cloned and conventional animals suggest a comparable nutritional quality of milk for these animals. The noticed differences in milk long chain-FA yields were consistent with modulation of mammary lipogenic pathway as suggested by lower mRNA abundance of LPL gene in cloned compared with control. Otherwise, differences in the partitioning of nutrients between the mammary gland and other tissues cannot be excluded as suggested by the higher BW and lower milk yield observed in cloned. Altogether, these observations may be attributed to different genetic background and/or to epigenetic modifications due to the nuclear transfer technology that may affect the growth and the physiological adaptation to lactation and impact the dairy performances. Further investigations are required to identify the mechanisms underlying these differences.

In order to understand the effect of nuclear transfer technology on the physiology of lactation and milk fatty acid composition in dairy cattle (Holstein breed), the present study compares the milk yield and composition from bovine somatic cell cloned (n=5) and control animals (n=5) at 180 days in milk (DIM) maintained together under the same conditions. All cows were offered the same total mixed ration ad libitum. At 180 DIM, the cloned had a higher body weight (BW; P<0.01) compared with control animals, whereas comparable body condition score (BCS) was observed among the 2 groups. The cloned cows had a lower milk yield and milk protein and lactose yields (P<0.05) and had a tendency (P=0.08) for a lower milk fat yield. Conversely, no differences in milk fat, protein and lactose concentrations were observed in cloned compared with control animals. Similar milk fatty acid (FA) concentrations were observed in cloned and control cows except for two minor FA, cis-9 C10:1 and C17:0 (P<0.05) that were higher in the cloned. The milk fat cis-9 C14:1/C14:0, cis-9 C16:1/C16:0, cis-9 C18:1/C18:0, cis-9, trans-11 C18:2/trans-11 C18:1 concentrations ratios were not different in cloned and control. The milk medium-(C10–C16) and long-(∑C18) chain FA yields were lower (P<0.05) in cloned compared with control animals. The mRNA abundance of genes encoding for SCD1, SCD5, ACACA and FABP3 genes in mammary tissue was similar (P>0.05) in cloned and non-cloned animals. Conversely, cloned animals had a lower (P<0.05) mRNA abundance of LPL and a tendency (P<0.10) for lower mRNA abundance of FASN and CD36 genes compared with control. The absence of major differences of milk constituent concentrations, milk FA composition and of the SCD desaturation indices observed between cloned and conventional animals suggest a comparable nutritional quality of milk for these animals. The noticed differences in milk long chain-FA yields were consistent with modulation of mammary lipogenic pathway as suggested by lower mRNA abundance of LPL gene in cloned compared with control. Otherwise, differences in the partitioning of nutrients between the mammary gland and other tissues cannot be excluded as suggested by the higher BW and lower milk yield observed in cloned. Altogether, these observations may be attributed to different genetic background and/or to epigenetic modifications due to the nuclear transfer technology that may affect the growth and the physiological adaptation to lactation and impact the dairy performances. Further investigations are required to identify the mechanisms underlying these differences.

As a consequence of climate change, forage crops in Belgium are increasingly subjected to late spring water deficits, threatening the autonomy of cropping systems. The goal of this study was to compare the yield performances of forage crops under water deficit conditions, and identify the underlying drought tolerance mechanisms. For this purpose, quantitative and qualitative yield traits along with several gas exchange-related physiological traits were measured in the field on 8 genotypes belonging to 4 different species under both well-watered and water deficit conditions. In addition, whole plant transpiration response curves to water deficit conditions were examined under greenhouse and growth chamber conditions. The investigation showed yield genetic variability under drought, which was not linked to field-based instantaneous measurements. In contrast, whole plant transpiration sensitivity to increasing vapor pressure deficit (VPD) was correlated with the yield performances. This multi-environmental study highlights the importance of the crop sensitivity to VPD as a major player in the yield variability. | À cause du réchauffement climatique, les cultures fourragères en Belgique sont soumises à des déficits hydriques de fin de printemps plus importants, menaçant l’autonomie fourragère des exploitations agricoles. Le but de cette étude était de comparer les rendements de différentes espèces et variétés fourragères en situation de déficit hydrique imposé et d’identifier les mécanismes de tolérance à la sécheresse sous-jacents. Les rendements qualitatif et quantitatif ainsi que plusieurs paramètres d’échanges gazeux ont été mesurés sur 8 génotypes appartenant à 4 espèces en conditions hydrique limitante et bien irriguée. De plus, la réponse de la transpiration de la plante entière à des conditions de déficit hydrique a été évaluée en serre et chambre de culture. Notre étude a révélé l’existence d’une variabilité génétique des rendements en situation de sécheresse, celle-ci n’étant pas corrélée avec les paramètres instantanés mesurés au champ. Au contraire, la sensibilité de la transpiration de la plante entière au déficit en pression de vapeur (VPD) était fortement corrélée avec les rendements. Cette étude multi-environnementale souligne l’importance des réponses des cultures au VPD dans l’établissement de ces performances.

As a consequence of climate change, forage crops in Belgium are increasingly subjected to late spring water deficits, threatening the autonomy of cropping systems. The goal of this study was to compare the yield performances of forage crops under water deficit conditions, and identify the underlying drought tolerance mechanisms. For this purpose, quantitative and qualitative yield traits along with several gas exchange-related physiological traits were measured in the field on 8 genotypes belonging to 4 different species under both well-watered and water deficit conditions. In addition, whole plant transpiration response curves to water deficit conditions were examined under greenhouse and growth chamber conditions. The investigation showed yield genetic variability under drought, which was not linked to field-based instantaneous measurements. In contrast, whole plant transpiration sensitivity to increasing vapor pressure deficit (VPD) was correlated with the yield performances. This multi-environmental study highlights the importance of the crop sensitivity to VPD as a major player in the yield variability. | À cause du réchauffement climatique, les cultures fourragères en Belgique sont soumises à des déficits hydriques de fin de printemps plus importants, menaçant l’autonomie fourragère des exploitations agricoles. Le but de cette étude était de comparer les rendements de différentes espèces et variétés fourragères en situation de déficit hydrique imposé et d’identifier les mécanismes de tolérance à la sécheresse sous-jacents. Les rendements qualitatif et quantitatif ainsi que plusieurs paramètres d’échanges gazeux ont été mesurés sur 8 génotypes appartenant à 4 espèces en conditions hydrique limitante et bien irriguée. De plus, la réponse de la transpiration de la plante entière à des conditions de déficit hydrique a été évaluée en serre et chambre de culture. Notre étude a révélé l’existence d’une variabilité génétique des rendements en situation de sécheresse, celle-ci n’étant pas corrélée avec les paramètres instantanés mesurés au champ. Au contraire, la sensibilité de la transpiration de la plante entière au déficit en pression de vapeur (VPD) était fortement corrélée avec les rendements. Cette étude multi-environnementale souligne l’importance des réponses des cultures au VPD dans l’établissement de ces performances.

Forage species to associate in multispecies grasslands, in order to both productivity, perenniality and quality for farmers, are better known in the various conditions of soils and climate of French territory, based on regional experiences obtained by experiments fields. For the suckling cattle breeding area of north Massif Central and for cutting, the presence of adapted species as cocksfoot, lucerne and red clover is more important than number of species or seeds quantity. | Les espèces fourragères à associer dans des prairies multi-espèces apportant à la fois productivité, pérennité et qualité aux éleveurs, se précisent dans les conditions variées de milieux du territoire français, grâce à l’expertise régionale acquise au travers d’essais. Pour la zone d’élevage allaitant du nord du Massif Central et pour la fauche, la présence d’espèces adaptées comme le dactyle, la luzerne et le trèfle violet, apparaît prépondérante au nombre d’espèces ou à la dose de semis.

Forage species to associate in multispecies grasslands, in order to both productivity, perenniality and quality for farmers, are better known in the various conditions of soils and climate of French territory, based on regional experiences obtained by experiments fields. For the suckling cattle breeding area of north Massif Central and for cutting, the presence of adapted species as cocksfoot, lucerne and red clover is more important than number of species or seeds quantity. | Les espèces fourragères à associer dans des prairies multi-espèces apportant à la fois productivité, pérennité et qualité aux éleveurs, se précisent dans les conditions variées de milieux du territoire français, grâce à l’expertise régionale acquise au travers d’essais. Pour la zone d’élevage allaitant du nord du Massif Central et pour la fauche, la présence d’espèces adaptées comme le dactyle, la luzerne et le trèfle violet, apparaît prépondérante au nombre d’espèces ou à la dose de semis.

Plusieurs espèces légumières sont des plantes grimpantes, soit par des vrilles comme le pois ou les Cucurbitacées (melon, concombre, courge, pastèque…), soit grâce à une tige volubile comme le haricot ou, parmi les espèces tropicales, l’igname et plusieurs espèces de Vigna. Les formes sauvages de ces espèces sont à longue tige grimpante mais, à la suite de la domestication, au cours de la diversification, des mutants ont été sélectionnés. Ils sont caractérisés par des entre-nœuds plus courts, la perte de la volubilité de la tige et éventuellement la disparition des vrilles.

Plusieurs espèces légumières sont des plantes grimpantes, soit par des vrilles comme le pois ou les Cucurbitacées (melon, concombre, courge, pastèque…), soit grâce à une tige volubile comme le haricot ou, parmi les espèces tropicales, l’igname et plusieurs espèces de Vigna. Les formes sauvages de ces espèces sont à longue tige grimpante mais, à la suite de la domestication, au cours de la diversification, des mutants ont été sélectionnés. Ils sont caractérisés par des entre-nœuds plus courts, la perte de la volubilité de la tige et éventuellement la disparition des vrilles.

Key messageBud burst disruption, carbon depletion and tree dieback in spring were experimentally linked to N shortage the previous autumn. Dieback occurred despite tree N concentrations were compatible with plant survival: their N stores being blocked in the roots and woody axes.ContextTree dieback is generally linked to hydraulic failure or carbon (C) starvation but seldom to poor nitrogen (N)resources.AimWe provide here an experimental evidence linking autumn N shortage, C depletion and tree dieback in spring.MethodsYoung peach trees were either N deprived or fertilised in autumn, and then fed in excess in spring. Springsupplies were 15 N-labelled. The effects of the deprivation on tree development, N uptake and C status were then assessed by coupling in situ measurements of shoot development with organ biochemical and isotopic determinations.ResultsAll deprived trees died within 3 months after burst. Bud burst was severely disrupted, and vegetative growth limited to the expansion of a few leaves. The dead trees absorbed between 39 and 117mg 15N in spring, and their roots and axes contained 758 mg more nitrogen than the fertilised trees, suggesting that they did not mobilise their N reserves in spring.They also had lower non-structural carbohydrate concentrations (<3.9 % DW) than the fertilised trees (>15.4 % DW), which were below the threshold accepted for plant survival.ConclusionTwo possible causes of total non-structural carbon (or TNC) depletion are discussed: insufficient storage due to advanced leaf senescence or increase in the C costs regarding winter embolism recovery

Key messageBud burst disruption, carbon depletion and tree dieback in spring were experimentally linked to N shortage the previous autumn. Dieback occurred despite tree N concentrations were compatible with plant survival: their N stores being blocked in the roots and woody axes.ContextTree dieback is generally linked to hydraulic failure or carbon (C) starvation but seldom to poor nitrogen (N)resources.AimWe provide here an experimental evidence linking autumn N shortage, C depletion and tree dieback in spring.MethodsYoung peach trees were either N deprived or fertilised in autumn, and then fed in excess in spring. Springsupplies were 15 N-labelled. The effects of the deprivation on tree development, N uptake and C status were then assessed by coupling in situ measurements of shoot development with organ biochemical and isotopic determinations.ResultsAll deprived trees died within 3 months after burst. Bud burst was severely disrupted, and vegetative growth limited to the expansion of a few leaves. The dead trees absorbed between 39 and 117mg 15N in spring, and their roots and axes contained 758 mg more nitrogen than the fertilised trees, suggesting that they did not mobilise their N reserves in spring.They also had lower non-structural carbohydrate concentrations (<3.9 % DW) than the fertilised trees (>15.4 % DW), which were below the threshold accepted for plant survival.ConclusionTwo possible causes of total non-structural carbon (or TNC) depletion are discussed: insufficient storage due to advanced leaf senescence or increase in the C costs regarding winter embolism recovery

• KEY MESSAGE : Bud burst disruption, carbon depletion and tree dieback in spring were experimentally linked to N shortage the previous autumn. Dieback occurred despite tree N concentrations were compatible with plant survival: their N stores being blocked in the roots and woody axes. • CONTEXT : Tree dieback is generally linked to hydraulic failure or carbon (C) starvation but seldom to poor nitrogen (N) resources. • AIM : We provide here an experimental evidence linking autumn N shortage, C depletion and tree dieback in spring. • METHODS : Young peach trees were either N deprived or fertilised in autumn, and then fed in excess in spring. Spring supplies were ¹⁵N-labelled. The effects of the deprivation on tree development, N uptake and C status were then assessed by coupling in situ measurements of shoot development with organ biochemical and isotopic determinations. • RESULTS : All deprived trees died within 3 months after burst. Bud burst was severely disrupted, and vegetative growth limited to the expansion of a few leaves. The dead trees absorbed between 39 and 117 mg ¹⁵N in spring, and their roots and axes contained 758 mg more nitrogen than the fertilised trees, suggesting that they did not mobilise their N reserves in spring. They also had lower non-structural carbohydrate concentrations (<3.9 % DW) than the fertilised trees (>15.4 % DW), which were below the threshold accepted for plant survival. • CONCLUSION : Two possible causes of total non-structural carbon (or TNC) depletion are discussed: insufficient storage due to advanced leaf senescence or increase in the C costs regarding winter embolism recovery.

Meat supply chains have to face 3 major global stakes for their sustainable development: health (animal and human), equity and environment. Rising demand for meat and livestock sector development have serious consequences in terms of natural resources depletion, animal health, public health, structure of production and access to markets. In the same time, amenities of livestock production should be strengthen and better acknowledged in policies. We suggest 5 principles that will allow the sector to successfully improve its sustainability: efficiency in using natural resources, conservation of resources, protection of rural livelihoods, resilience of communities and ecosystems and governance of private and public initiatives.

Meat supply chains have to face 3 major global stakes for their sustainable development: health (animal and human), equity and environment. Rising demand for meat and livestock sector development have serious consequences in terms of natural resources depletion, animal health, public health, structure of production and access to markets. In the same time, amenities of livestock production should be strengthen and better acknowledged in policies. We suggest 5 principles that will allow the sector to successfully improve its sustainability: efficiency in using natural resources, conservation of resources, protection of rural livelihoods, resilience of communities and ecosystems and governance of private and public initiatives.

Projected climate change and increased pressure for adopting more sustainable agricultural practices calls for new approaches in breeding forage crops for the future. In the cool temperate regions of Europe they may benefit from a warmer and prolonged growing season, even though new stresses may emerge during autumn and winter, whereas further south risk of drought will increase. In addition, forage crops have to be able to use both nutrients and water more efficiently in the future in order to maximize production per unit area. Examples are given how perennial forage crops can be adapted to the projected envi-ronmental conditions in Europe through breeding. In the Nordic region the focus is on identifying traits that are important for high yields under changed overwin-tering conditions, as well as management practices. In maritime, oceanic Europe the focus is on forage grass and legume root systems for ecosystem service, nutri-ent and water use, and the advantages and potential for Festulolium, including its role in ruminant nutrition. In temperate and southern Europe, the aim is to develop varieties able to survive long drought periods and to recover rapidly following autumn rains, as well as improving adapted legume species to reduce the use of synthetic fertilizers, the environmental impacts of ruminant production systems and their dependency on external protein-rich feeds. Forage production systems, commonly found in areas less suited to grain production, can contribute significantly to future food security if the adaptation of forage crops to the future environmental challenges is successful.

Projected climate change and increased pressure for adopting more sustainable agricultural practices calls for new approaches in breeding forage crops for the future. In the cool temperate regions of Europe they may benefit from a warmer and prolonged growing season, even though new stresses may emerge during autumn and winter, whereas further south risk of drought will increase. In addition, forage crops have to be able to use both nutrients and water more efficiently in the future in order to maximize production per unit area. Examples are given how perennial forage crops can be adapted to the projected envi-ronmental conditions in Europe through breeding. In the Nordic region the focus is on identifying traits that are important for high yields under changed overwin-tering conditions, as well as management practices. In maritime, oceanic Europe the focus is on forage grass and legume root systems for ecosystem service, nutri-ent and water use, and the advantages and potential for Festulolium, including its role in ruminant nutrition. In temperate and southern Europe, the aim is to develop varieties able to survive long drought periods and to recover rapidly following autumn rains, as well as improving adapted legume species to reduce the use of synthetic fertilizers, the environmental impacts of ruminant production systems and their dependency on external protein-rich feeds. Forage production systems, commonly found in areas less suited to grain production, can contribute significantly to future food security if the adaptation of forage crops to the future environmental challenges is successful.

The objective of this work was to study nutritional strategies for decreasing methane production by ruminants fed tropical diets, combining in vitro and in vivo methods. The in vitro approach was used to evaluate the dose effect of condensed tannins (CT) contained in leaves of Gliricidia sepium, Leucaena leucocephala, and Manihot esculenta (39, 75, and 92 g CT/kg DM, respectively) on methane production and ruminal fermentation characteristics. Tannin-rich plants (TRP) were incubated for 24 h alone or mixed with a natural grassland hay based on Dichanthium spp. (control plant), so that proportions of TRP were 0, 0.25, 0.5, 0.75, and 1.0. Methane production, VFA concentration, and fermented OM decreased with increased proportions of TRP. Numerical differences on methane production and VFA concentration among TRP sources may be due to differences in their CT content, with greater effects for L. leucocephala and M. esculenta than for G. sepium. Independently of TRP, the response to increasing doses of CT was linear for methane production but quadratic for VFA concentration. As a result, at moderate tannin dose, methane decreased more than VFA. The in vivo trial was conducted to investigate the effect of TRP on different ruminal microbial populations. To this end, 8 rumen-cannulated sheep from 2 breeds (Texel and Blackbelly) were used in two 4 x 4 Latin square designs. Diets were fed ad libitum and were composed of the same feeds used for the in vitro trial: control plant alone or combined with pellets made from TRP leaves at 44% of the diet DM. Compared to TRP, concentration of Ruminococcus flavefaciens was greater for the control diet and concentration of Ruminococcus albus was least for the control diet. The methanogen population was greater for Texel than for Blackbelly. By contrast, TRP-containing diets did not affect protozoa or Fibrobacter succinogenes numbers. Hence, TRP showed potential for mitigating methane production by ruminants. These findings suggest that TRP fed as pellets could be used to decrease methane production.

The objective of this work was to study nutritional strategies for decreasing methane production by ruminants fed tropical diets, combining in vitro and in vivo methods. The in vitro approach was used to evaluate the dose effect of condensed tannins (CT) contained in leaves of Gliricidia sepium, Leucaena leucocephala, and Manihot esculenta (39, 75, and 92 g CT/kg DM, respectively) on methane production and ruminal fermentation characteristics. Tannin-rich plants (TRP) were incubated for 24 h alone or mixed with a natural grassland hay based on Dichanthium spp. (control plant), so that proportions of TRP were 0, 0.25, 0.5, 0.75, and 1.0. Methane production, VFA concentration, and fermented OM decreased with increased proportions of TRP. Numerical differences on methane production and VFA concentration among TRP sources may be due to differences in their CT content, with greater effects for L. leucocephala and M. esculenta than for G. sepium. Independently of TRP, the response to increasing doses of CT was linear for methane production but quadratic for VFA concentration. As a result, at moderate tannin dose, methane decreased more than VFA. The in vivo trial was conducted to investigate the effect of TRP on different ruminal microbial populations. To this end, 8 rumen-cannulated sheep from 2 breeds (Texel and Blackbelly) were used in two 4 x 4 Latin square designs. Diets were fed ad libitum and were composed of the same feeds used for the in vitro trial: control plant alone or combined with pellets made from TRP leaves at 44% of the diet DM. Compared to TRP, concentration of Ruminococcus flavefaciens was greater for the control diet and concentration of Ruminococcus albus was least for the control diet. The methanogen population was greater for Texel than for Blackbelly. By contrast, TRP-containing diets did not affect protozoa or Fibrobacter succinogenes numbers. Hence, TRP showed potential for mitigating methane production by ruminants. These findings suggest that TRP fed as pellets could be used to decrease methane production.

Background: Given a gene and a species tree, reconciliation methods attempt to retrieve the macro-evolutionary events that best explain the discrepancies between the two tree topologies. The DTL parsimonious approach searches for a most parsimonious reconciliation between a gene tree and a (dated) species tree, considering four possible macro-evolutionary events (speciation, duplication, transfer, and loss) with specific costs. Unfortunately, many events are erroneously predicted due to errors in the input trees, inappropriate input cost values or because of the existence of several equally parsimonious scenarios. It is thus crucial to provide a measure of the reliability for predicted events. It has been recently proposed that the reliability of an event can be estimated via its frequency in the set of most parsimonious reconciliations obtained using a variety of reasonable input cost vectors. To compute such a support, a straightforward but time-consuming approach is to generate the costs slightly departing from the original ones, independently compute the set of all most parsimonious reconciliations for each vector, and combine these sets a posteriori. Another proposed approach uses Pareto-optimality to partition cost values into regions which induce reconciliations with the same number of DTL events. The support of an event is then defined as its frequency in the set of regions. However, often, the number of regions is not large enough to provide reliable supports. Results: We present here a method to compute efficiently event supports via a polynomial-sized graph, which can represent all reconciliations for several different costs. Moreover, two methods are proposed to take into account alternative input costs: either explicitly providing an input cost range or allowing a tolerance for the over cost of a reconciliation. Our methods are faster than the region based method, substantially faster than the sampling-costs approach, and have a higher event-prediction accuracy on simulated data. Conclusions: We propose a new approach to improve the accuracy of event supports for parsimonious reconciliation methods to account for uncertainty in the input costs. Furthermore, because of their speed, our methods can be used on large gene families. Our algorithms are implemented in the ecceTERA program, freely available from http://mbb.univ-montp2.fr/MBB/.

Background: Given a gene and a species tree, reconciliation methods attempt to retrieve the macro-evolutionary events that best explain the discrepancies between the two tree topologies. The DTL parsimonious approach searches for a most parsimonious reconciliation between a gene tree and a (dated) species tree, considering four possible macro-evolutionary events (speciation, duplication, transfer, and loss) with specific costs. Unfortunately, many events are erroneously predicted due to errors in the input trees, inappropriate input cost values or because of the existence of several equally parsimonious scenarios. It is thus crucial to provide a measure of the reliability for predicted events. It has been recently proposed that the reliability of an event can be estimated via its frequency in the set of most parsimonious reconciliations obtained using a variety of reasonable input cost vectors. To compute such a support, a straightforward but time-consuming approach is to generate the costs slightly departing from the original ones, independently compute the set of all most parsimonious reconciliations for each vector, and combine these sets a posteriori. Another proposed approach uses Pareto-optimality to partition cost values into regions which induce reconciliations with the same number of DTL events. The support of an event is then defined as its frequency in the set of regions. However, often, the number of regions is not large enough to provide reliable supports. Results: We present here a method to compute efficiently event supports via a polynomial-sized graph, which can represent all reconciliations for several different costs. Moreover, two methods are proposed to take into account alternative input costs: either explicitly providing an input cost range or allowing a tolerance for the over cost of a reconciliation. Our methods are faster than the region based method, substantially faster than the sampling-costs approach, and have a higher event-prediction accuracy on simulated data. Conclusions: We propose a new approach to improve the accuracy of event supports for parsimonious reconciliation methods to account for uncertainty in the input costs. Furthermore, because of their speed, our methods can be used on large gene families. Our algorithms are implemented in the ecceTERA program, freely available from http://mbb.univ-montp2.fr/MBB/.