FitTetra 2.0-improved genotype calling for tetraploids with multiple population and parental data support

BackgroundGenetic studies in tetraploids are lagging behind in comparison with studies of diploids as the complex genetics of tetraploids require much more elaborated computational methodologies. Recent advancements in development of molecular techniques and computational tools facilitate new methods for automated, high-throughput genotype calling in tetraploid species. We report on the upgrade of the widely-used fitTetra software aiming to improve its accuracy, which to date is hampered by technical artefacts in the data.ResultsOur upgrade of the fitTetra package is designed for a more accurate modelling of complex collections of samples. The package fits a mixture model where some parameters of the model are estimated separately for each sub-collection. When a full-sib family is analyzed, we use parental genotypes to predict the expected segregation in terms of allele dosages in the offspring. More accurate modelling and use of parental data increases the accuracy of dosage calling. We tested the package on data obtained with an Affymetrix Axiom 60k array and compared its performance with the original version and the recently published ClusterCall tool, showing that at least 20% more SNPs could be called with our updated.ConclusionOur updated software package shows clearly improved performance in genotype calling accuracy. Estimation of mixing proportions of the underlying dosage distributions is separated for full-sib families (where mixture proportions can be estimated from the parental dosages and inheritance model) and unstructured populations (where they are based on the assumption of Hardy-Weinberg equilibrium). Additionally, as the distributions of signal ratios of the dosage classes can be assumed to be the same for all populations, including parental data for some subpopulations helps to improve fitting other populations as well. The R package fitTetra 2.0 is freely available under the GNU Public License as Additional file with this article.</p

Dynamics of Intersexual Dominance and Adult Sex- Ratio in Wild Vervet Monkeys

Intersexual dominance relations are important for female mammals, because of their consequences for accessing food and for the degree of sexual control females experience from males. Female mammals are usually considered to rank below males in the dominance hierarchy, because of their typical physical inferiority. Yet, in some groups or species, females are nonetheless dominant over some males (partial female dominance). Intersexual dominance, therefore, also depends on traits other than sexual dimorphism, such as social support, social exchange, group adult sex-ratio, and the widespread self-reinforcing effects of winning and losing fights, the “winner-loser effect.” The importance of sex-ratio and the winner-loser effect remains poorly understood. A theoretical model, DomWorld, predicts that in groups with a higher proportion of males, females are dominant over more males when aggression is fierce (not mild). The model is based on a small number of general processes in mammals, such as grouping, aggression, the winner-loser effect, the initially greater fighting capacity of males than females, and sex ratio. We expect its predictions to be general and suggest they be examined in a great number of species and taxa. Here, we test these predictions in four groups of wild vervet monkeys (Chlorocebus pygerythrus) in Mawana game reserve in Africa, using 7 years of data. We confirm that a higher proportion of males in the group is associated with greater dominance of females over males; a result that remains when combining these data with those of two other sites (Amboseli and Samara). We additionally confirm that in groups with a higher fraction of males there is a relatively higher (a) proportion of fights of males with other males, and (b) proportion of fights won by females against males from the fights of females with any adults. We reject alternative hypotheses that more dominance of females over males could be attributed to females receiving more coalitions from males, or females receiving lowered male aggression in exchange for sexual access (the docile male hypothesis). We conclude that female dominance relative to males is dynamic and that future empirical studies of inter-sexual dominance will benefit by considering the adult sex-ratio of groups.</p

Efficacy of management and monitoring methods to prevent post-harvest losses caused by rodents

The presence of pest rodents around food production and storage sites is one of many underlying problems contributing to food contamination and loss, particularly influencing food and nutrition security in low-income countries. By reducing both pre- and post-harvest losses by rodents, millions of food-insecure people would benefit. As there are limited quantitative data on post-harvest rice losses due to rodents, our objectives were to assess stored rice losses in local households from eight rural communities and two rice milling factories in Bangladesh and to monitor the effect of different rodent control strategies to limit potential losses. Four treatments were applied in 2016 and 2017, (i) untreated control, (ii) use of domestic cats, (iii) use of rodenticides, (iv) use of snap-traps. In total, over a two-year period, 210 rodents were captured from inside people’s homes, with Rattus rattus trapped most often (n = 91), followed by Mus musculus (n = 75) and Bandicota bengalensis (n = 26). In the milling stations, 68 rodents were trapped, of which 21 were M. musculus, 19 R. rattus, 17 B. bengalensis, 8 Rattus exulans, and 3 Mus terricolor. In 2016, losses from standardised baskets of rice within households were between 13.6% and 16.7%. In 2017, the losses were lower, ranging from 0.6% to 2.2%. Daily rodent removal by trapping proved to be most effective to diminish stored produce loss. The effectiveness of domestic cats was limited

Insights into the Influence of Priors in Posterior Mapping of Discrete Morphological Characters: A Case Study in Annonaceae

Background - Posterior mapping is an increasingly popular hierarchical Bayesian based method used to infer character histories and reconstruct ancestral states at nodes of molecular phylogenies, notably of morphological characters. As for all Bayesian analyses specification of prior values is an integrative and important part of the analysis. He we provide an example of how alternative prior choices can seriously influence results and mislead interpretations. Methods/Principal Findings - For two contrasting discrete morphological characters, namely a slow and a fast evolving character found in the plant family Annonaceae, we specified a total of eight different prior distributions per character. We investigated how these prior settings affected important summary statistics. Our analyses showed that the different prior distributions had marked effects on the results in terms of average number of character state changes. These differences arise because priors play a crucial role in determining which areas of parameter space the values of the simulation will be drawn from, independent of the data at hand. However, priors seemed to fit the data better if they would result in a more even sampling of parameter space (normal posterior distribution), in which case alternative standard deviation values had little effect on the results. The most probable character history for each character was affected differently by the prior. For the slower evolving character, the same character history always had the highest posterior probability independent of the priors used. In contrast, the faster evolving character showed different most probable character histories depending on the prior. These differences could be related to the level of homoplasy exhibited by each character. Conclusions - Although our analyses were restricted to two morphological characters within a single family, our results underline the importance of carefully choosing prior values for posterior mapping. Prior specification will be of crucial importance when interpreting the results in a meaningful way. It is hard to suggest a statistically sound method for prior specification without more detailed studies. Meanwhile, we propose that the data could be used to estimate the prior value of the gamma distribution placed on the transformation rate in posterior mappin

Female emancipation in a male dominant, sexually dimorphic primate under natural conditions

In most group-living animals, a dominance hierarchy reduces the costs of competition for limited resources. Dominance ranks may reflect prior attributes, such as body size, related to fighting ability or reflect the history of self-reinforcing effects of winning and losing a conflict (the winner-loser effect), or both. As to prior attributes, in sexually dimorphic species, where males are larger than females, males are assumed to be dominant over females. As to the winner-loser effect, the computational model DomWorld has shown that despite the female’s lower initial fighting ability, females achieve some degree of dominance of females over males. In the model, this degree of female dominance increases with the proportion of males in a group. This increase was supposed to emerge from the higher fraction of fights of males among themselves. These correlations were confirmed in despotic macaques, vervet monkeys, and in humans. Here, we first investigate this hypothesis in DomWorld and next in long-term data of 9,300 observation hours on six wild groups of robust capuchin monkeys (Sapajus libidinosus; S. nigritus, and S. xanthosternos) in three Brazilian sites. We test whether both the proportion of males and degree of female dominance over males are indeed associated with a higher relative frequency of aggression among males and a higher relative frequency of aggression of females to males. We confirm these correlations in DomWorld. Next, we confirm in empirical data of capuchin monkeys that with the proportion of males in the group there is indeed an increase in female dominance over males, and in the relative frequency of both male-male aggression and aggression of females to males and that the female dominance index is significantly positively associated with male male aggression. Our results reveal that adult sex ratio influences the power relation between the sexes beyond predictions from socioecological models.</p

Comparing gradual debonding strategies after prolonged cow-calf contact: Stress responses, performance, and health of dairy cow and calf

We assessed effects of two-step debonding strategies in calf rearing systems with different types of prolonged cow-calf contact (CCC) on stress responses, health and performance of dairy cows and calves. Forty-eight Holstein Friesian cow-calf pairs had either: 1) full contact including suckling, where contact was reduced before weaning via fence-line separation at day 49 (FC-FS) (n = 10); 2) full contact, where contact was reduced at day 56 by fitting calves with a nose-flap (FC-NF) (n = 10); 3) partial contact (calves were housed in a pen adjacent to the cow area allowing physical contact on initiative of the dam but no suckling), where contact was reduced before weaning by moving the calf box from the wall to prevent physical contact at day 49 (PC-BW) (n = 6); 4) partial contact, where contact was reduced the week after weaning by moving the calf box away from the wall at day 63 (PC-AW) (n = 12); 5) no contact (calves were removed from dam directly after birth and housed in a calf barn), calves were weaned at day 56 (NC) (n = 10). Between weeks 7–10, we assessed physiological stress parameters, weight gain, and the health status of calves, plus general activity patterns based on accelerometer sensor data of cow-calf pairs before, during and after the debonding interventions. Additionally, calves were subjected to four consecutive behavioural tests (i.e. open field, novel object, voluntary human approach and involuntary human approach test) prior to permanent separation at day 70 and their behavioural responses were assessed via video recordings to assess fearfulness. Machine-harvested milk yields of cows were evaluated during weeks 6–12. Data were analyzed with (generalized) linear mixed models. Throughout the debonding period, FC-NF calves had an impaired growth rate (P = 0.02). In weeks 6–9, FC-FS and FC-NF cows had lower machine-harvested milk yields than PC-BW, PC-AW, and NC cows (P ≤ 0.01). We found no differences in responsiveness of calves to behavioural tests, except that NC calves exhibited more solitary play events compared to PC and FC calves in the novel object test (P = 0.002). Overall, our results imply that calves with partial CCC showed low stress responses to debonding, whereas abrupt weaning with a nose-flap during full contact seemed most stressful. Machine-harvested milk yield of FC cows seemed to recover once calves were weaned. More research into strategies to improve the process of debonding is warranted

Effect of Type of Cow-Calf Contact on Health, Blood Parameters, and Performance of Dairy Cows and Calves

Prolonged cow-calf contact (CCC) could potentially improve dairy calf welfare. However, it is currently unknown how different types of CCC affect animals' biological functions. We evaluated health and performance parameters of dairy calves and their dams, where calves: (i) had no contact with their dam (NC), in which the calf was removed from the dam directly after birth (n = 10); (ii) were allowed to have partial contact (PC) with their dam, in which the calf was housed in a calf pen adjacent to the cow area allowing physical contact on the initiative of the dam but no suckling (n = 18); (iii) were allowed to have full contact (FC) with their dam, including suckling, in which calves were housed together with their dams in a free-stall barn (n = 20). Throughout the first 7 weeks postpartum, data were collected on the health status, fecal microbiota, hematological profile, immune and hormonal parameters, and growth rates of calves, and on the health status, metabolic responses, and performance of dams. Overall, FC calves had more health issues (P = 0.02) and a tendency for higher antibiotic usage (P = 0.07) than NC calves. Additionally, FC calves showed elevated levels of erythrocytes, hematocrit, hemoglobin, and leukocytes on day 49 compared to NC calves (P < 0.001). Calf fecal microbiota changed over time, and we found preliminary evidence that fecal microbiota is affected by the type of CCC, as reflected by differences in relative abundances of taxa including Lactobacillus in FC calves compared to NC and PC calves except on days 7 and 66. The FC calves had a greater average daily gain in body weight than NC and PC calves (P = 0.002). Cow health was not affected by the type of CCC, although in the first 7 weeks of lactation FC cows had a lower machine-gained milk yield accompanied by a lower fat percentage than NC and PC cows (P < 0.001). These results indicate that full contact posed a challenge for calf health, presumably because the housing conditions of FC calves in this experimental context were suboptimal. Secondly, ad libitum suckling leads to higher weight gains and negatively affected milk fat content besides machine-gained yields. More research into strategies to improve cow-calf housing and management in CCC systems is warranted

Effect of Type of Cow-Calf Contact on Health, Blood Parameters, and Performance of Dairy Cows and Calves

Prolonged cow-calf contact (CCC) could potentially improve dairy calf welfare. However, it is currently unknown how different types of CCC affect animals' biological functions. We evaluated health and performance parameters of dairy calves and their dams, where calves: (i) had no contact with their dam (NC), in which the calf was removed from the dam directly after birth (n = 10); (ii) were allowed to have partial contact (PC) with their dam, in which the calf was housed in a calf pen adjacent to the cow area allowing physical contact on the initiative of the dam but no suckling (n = 18); (iii) were allowed to have full contact (FC) with their dam, including suckling, in which calves were housed together with their dams in a free-stall barn (n = 20). Throughout the first 7 weeks postpartum, data were collected on the health status, fecal microbiota, hematological profile, immune and hormonal parameters, and growth rates of calves, and on the health status, metabolic responses, and performance of dams. Overall, FC calves had more health issues (P = 0.02) and a tendency for higher antibiotic usage (P = 0.07) than NC calves. Additionally, FC calves showed elevated levels of erythrocytes, hematocrit, hemoglobin, and leukocytes on day 49 compared to NC calves (P < 0.001). Calf fecal microbiota changed over time, and we found preliminary evidence that fecal microbiota is affected by the type of CCC, as reflected by differences in relative abundances of taxa including Lactobacillus in FC calves compared to NC and PC calves except on days 7 and 66. The FC calves had a greater average daily gain in body weight than NC and PC calves (P = 0.002). Cow health was not affected by the type of CCC, although in the first 7 weeks of lactation FC cows had a lower machine-gained milk yield accompanied by a lower fat percentage than NC and PC cows (P < 0.001). These results indicate that full contact posed a challenge for calf health, presumably because the housing conditions of FC calves in this experimental context were suboptimal. Secondly, ad libitum suckling leads to higher weight gains and negatively affected milk fat content besides machine-gained yields. More research into strategies to improve cow-calf housing and management in CCC systems is warranted

Comparing gradual debonding strategies after prolonged cow-calf contact: Stress responses, performance, and health of dairy cow and calf

We assessed effects of two-step debonding strategies in calf rearing systems with different types of prolonged cow-calf contact (CCC) on stress responses, health and performance of dairy cows and calves. Forty-eight Holstein Friesian cow-calf pairs had either: 1) full contact including suckling, where contact was reduced before weaning via fence-line separation at day 49 (FC-FS) (n = 10); 2) full contact, where contact was reduced at day 56 by fitting calves with a nose-flap (FC-NF) (n = 10); 3) partial contact (calves were housed in a pen adjacent to the cow area allowing physical contact on initiative of the dam but no suckling), where contact was reduced before weaning by moving the calf box from the wall to prevent physical contact at day 49 (PC-BW) (n = 6); 4) partial contact, where contact was reduced the week after weaning by moving the calf box away from the wall at day 63 (PC-AW) (n = 12); 5) no contact (calves were removed from dam directly after birth and housed in a calf barn), calves were weaned at day 56 (NC) (n = 10). Between weeks 7-10, we assessed physiological stress parameters, weight gain, and the health status of calves, plus general activity patterns based on accelerometer sensor data of cow-calf pairs before, during and after the debonding interventions. Additionally, calves were subjected to four consecutive behavioural tests (i.e. open field, novel object, voluntary human approach and involuntary human approach test) prior to permanent separation at day 70 and their behavioural responses were assessed via video recordings to assess fearfulness. Machine-harvested milk yields of cows were evaluated during weeks 6-12. Data were analyzed with (generalized) linear mixed models. Throughout the debonding period, FCNF calves had an impaired growth rate (P = 0.02). In weeks 6-9, FC-FS and FC-NF cows had lower machineharvested milk yields than PC-BW, PC-AW, and NC cows (P <= 0.01). We found no differences in responsiveness of calves to behavioural tests, except that NC calves exhibited more solitary play events compared to PC and FC calves in the novel object test (P = 0.002). Overall, our results imply that calves with partial CCC showed low stress responses to debonding, whereas abrupt weaning with a nose-flap during full contact seemed most stressful. Machine-harvested milk yield of FC cows seemed to recover once calves were weaned. More research into strategies to improve the process of debonding is warranted

Sensitivity of labile carbon fractions to tillage and organic matter management and their potential as comprehensive soil quality indicators across pedoclimatic conditions in Europe

Soil quality is defined as the capacity of the soil to perform multiple functions, and can be assessed by measuring soil chemical, physical and biological parameters. Among soil parameters, labile organic carbon is considered to have a primary role in many soil functions related to productivity and environmental resilience. Our study aimed at assessing the suitability of different labile carbon fractions, namely dissolved organic carbon (DOC), hydrophilic DOC (Hy-DOC), permanganate oxidizable carbon (POXC, also referred to as Active Carbon), hot water extractable carbon (HWEC) and particulate organic matter carbon (POMC) as soil quality indicators in agricultural systems. To do so, we tested their sensitivity to two agricultural management factors (tillage and organic matter input) in 10 European long-term field experiments (LTEs), and we assessed the correlation of the different labile carbon fractions with physical, chemical and biological soil quality indicators linked to soil functions. We found that reduced tillage and high organic matter input increase concentrations of labile carbon fractions in soil compared to conventional tillage and low organic matter addition, respectively. POXC and POMC were the most sensitive fractions to both tillage and fertilization across the 10 European LTEs. In addition, POXC was the labile carbon fraction most positively correlated with soil chemical (total organic carbon, total nitrogen, and cation exchange capacity), physical (water stable aggregates, water holding capacity, bulk density) and biological soil quality indicators (microbial biomass carbon and nitrogen, and soil respiration). We conclude that POXC represents a labile carbon fraction sensitive to soil management and that is the most informative about total soil organic matter, nutrients, soil structure, and microbial pools and activity, parameters commonly used as indicators of various soil functions, such as C sequestration, nutrient cycling, soil structure formation and soil as a habitat for biodiversity. Moreover, POXC measurement is relatively cheap, fast and easy. Therefore, we suggest measuring POXC as the labile carbon fraction in soil quality assessment schemes in addition to other valuable soil quality indicators.</p