Indirect genetic effect model using feeding behaviour traits to define the degree of interaction between mates: an implementation in pigs growth rate

Supplement intake and liveweight (LW) data were collected daily and remotely by digital in-paddock technologies (electronic feeder (EF) and walk-over-weighing scale (WOW)) to study the effect of forage quantity and quality on the intake of a self-fed supplement (molasses-lick blocks (MLB)), LW, liveweight change (LWC), and feeding behaviour of grazing beef cattle. Fifty-two crossbred weaners were rotationally grazed or fed for 254 days on different forages: sudangrass (SG), autumn pastures (P), winter pastures with concentrate (P+C), oat crops (OC), lucerne hay (LH), and oaten hay (OH). Forage quantity and quality were measured on the day of entry (high feed availability) and exit (low feed availability) stages of grazing or hay delivery. The intake of MLB was 111% higher (p < 0.05) at low compared to high feed availability, and this was also reflected in the feeding behaviour of animals (e.g., greater feeding frequency and rate). Moreover, there was a large temporal variability of daily MLB intake (Coefficient of variation (CV) = 146.41%). Supplementing MLB improved LWC only with SG, P, or OH (p < 0.05). The behaviour of animals around MLB reflects changes in feed quantity and quality and could be used to enhance cattle grazing and nutritional management in real time.

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Differential Thermotolerance Adaptation between Species of Coccidioides

Journal of Fungi ◽

10.3390/jof6040366 ◽

2020 ◽

Vol 6 (4) ◽

pp. 366

Author(s):

Heather L. Mead ◽

Paris S. Hamm ◽

Isaac N. Shaffer ◽

Marcus de Melo Teixeira ◽

Christopher S. Wendel ◽

...

Keyword(s):

Growth Rate ◽

Linear Mixed Effect Model ◽

Phenotypic Difference ◽

Dimorphic Fungi ◽

Mixed Effect ◽

Valley Fever ◽

Solid Media ◽

Effect Model ◽

Molecular Phylogenetic ◽

Similar Growth

Coccidioidomycosis, or Valley fever, is caused by two species of dimorphic fungi. Based on molecular phylogenetic evidence, the genus Coccidioides contains two reciprocally monophyletic species: C. immitis and C. posadasii. However, phenotypic variation between species has not been deeply investigated. We therefore explored differences in growth rate under various conditions. A collection of 39 C. posadasii and 46 C. immitis isolates, representing the full geographical range of the two species, was screened for mycelial growth rate at 37 °C and 28 °C on solid media. The radial growth rate was measured for 16 days on yeast extract agar. A linear mixed effect model was used to compare the growth rate of C. posadasii and C. immitis at 37 °C and 28 °C, respectively. C. posadasii grew significantly faster at 37 °C, when compared to C. immitis; whereas both species had similar growth rates at 28 °C. These results indicate thermotolerance differs between these two species. As the ecological niche has not been well-described for Coccidioides spp., and disease variability between species has not been shown, the evolutionary pressure underlying the adaptation is unclear. However, this research reveals the first significant phenotypic difference between the two species that directly applies to ecological research.

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Prediction of genetic merit for growth rate in pigs using animal models with indirect genetic effects and genomic information

Genetics Selection Evolution ◽

10.1186/s12711-020-00578-y ◽

2020 ◽

Vol 52 (1) ◽

Cited By ~ 1

Author(s):

Bjarke G. Poulsen ◽

Birgitte Ask ◽

Hanne M. Nielsen ◽

Tage Ostersen ◽

Ole F. Christensen

Keyword(s):

Growth Rate ◽

Animal Model ◽

Genetic Effect ◽

Predictive Performance ◽

Genetic Effects ◽

Relationship Matrix ◽

Genomic Information ◽

Indirect Genetic Effects ◽

Group Members ◽

Direct Genetic Effect

Abstract Background Several studies have found that the growth rate of a pig is influenced by the genetics of the group members (indirect genetic effects). Accounting for these indirect genetic effects in a selection program may increase genetic progress for growth rate. However, indirect genetic effects are small and difficult to predict accurately. Genomic information may increase the ability to predict indirect genetic effects. Thus, the objective of this study was to test whether including indirect genetic effects in the animal model increases the predictive performance when genetic effects are predicted with genomic relationships. In total, 11,255 pigs were phenotyped for average daily gain between 30 and 94 kg, and 10,995 of these pigs were genotyped. Two relationship matrices were used: a numerator relationship matrix ($${\mathbf{A}}$$ A ) and a combined pedigree and genomic relationship matrix ($${\mathbf{H}}$$ H ); and two different animal models were used: an animal model with only direct genetic effects and an animal model with both direct and indirect genetic effects. The predictive performance of the models was defined as the Pearson correlation between corrected phenotypes and predicted genetic levels. The predicted genetic level of a pig was either its direct genetic effect or the sum of its direct genetic effect and the indirect genetic effects of its group members (total genetic effect). Results The highest predictive performance was achieved when total genetic effects were predicted with genomic information (21.2 vs. 14.7%). In general, the predictive performance was greater for total genetic effects than for direct genetic effects (0.1 to 0.5% greater; not statistically significant). Both types of genetic effects had greater predictive performance when they were predicted with $${\mathbf{H}}$$ H rather than $${\mathbf{A}}$$ A (5.9 to 6.3%). The difference between predictive performances of total genetic effects and direct genetic effects was smaller when $${\mathbf{H}}$$ H was used rather than $${\mathbf{A}}$$ A . Conclusions This study provides evidence that: (1) corrected phenotypes are better predicted with total genetic effects than with direct genetic effects only; (2) both direct genetic effects and indirect genetic effects are better predicted with $${\mathbf{H}}$$ H than $${\mathbf{A}}$$ A ; (3) using $${\mathbf{H}}$$ H rather than $${\mathbf{A}}$$ A primarily improves the predictive performance of direct genetic effects.

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Effect of social group size and initial live weight on feeder space requirement of growing pigs given food ad libitum

Animal Science ◽

10.1017/s1357729800052851 ◽

2002 ◽

Vol 75 (1) ◽

pp. 75-83 ◽

Cited By ~ 20

Author(s):

S.P. Turner ◽

M. Dahlgren ◽

D.S. Arey ◽

S.A. Edwards

Keyword(s):

Growth Rate ◽

Group Size ◽

Social Group ◽

Feeding Behaviour ◽

Interactive Effect ◽

Live Weight ◽

Growing Pigs ◽

Space Requirement ◽

Ad Libitum ◽

Feeder Space

AbstractFeeder space allowance should be sufficient to ensure adequate access to food for all group members, irrespective of competitive ability. However, the influence of social group size on minimum feeder space requirement of pigs given food ad libitum is poorly understood. Performance, aggression and feeding behaviour were assessed over a 6-week period from 29·3 (s.e. 0·19) kg live weight, using four replicates of a 2 ✕ 2 factorial design with two group sizes (20 v. 80) (small and large) and two feeder space allowances (32·5 v. 42·5 mm per pig) (low and high). Food intake was significantly lower in the low feeder space allowance treatments (1·44 v. 1·56 (s.e.d. 0·050) kg per pig per day, P < 0·05) and group mean growth rate was reduced in the later phase between 41 and 56 kg live weight. There was no main effect of group size or interactive effect between group size and feeder space allowance on performance. Mean skin lesion score and the frequency of aggression given or received at the feeders was unaffected by treatment. Heavy weight pigs showed similar feeding behaviour in each treatment, but light pigs visited the feeder more frequently in groups of 20 (23·1 v. 16·0 (s.e.d. 2·04) visits per pig per day, P < 0·05) and spent the greatest time feeding when at a low feeder space allowance (5461 v. 4397 (s.e.d. 288·8) s per pig per day, P < 0·05). To avoid a depression in growth rate, pigs >40 kg should be allocated a minimum feeder space allowance of 42·5 mm per pig. There was little indication of a need to specify differential feeder space allowances according to group size.

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Effects of number and siting of single-space feeders on performance and feeding behaviour of growing pigs

The Journal of Agricultural Science ◽

10.1017/s002185960006740x ◽

1994 ◽

Vol 122 (3) ◽

pp. 465-470 ◽

Cited By ~ 27

Author(s):

A. T. S. Morrow ◽

N. Walker

Keyword(s):

Growth Rate ◽

Feed Intake ◽

Feeding Behaviour ◽

Agricultural Research ◽

Block Design ◽

Growing Pigs ◽

Feed Conversion ◽

Randomized Block Design ◽

Ad Libitum ◽

Number Of Visits

SUMMARYTwo experiments of randomized block design were carried out at the Agricultural Research Institute of Northern Ireland in 1991/92 involving groups of 20 pigs fed ad libitum from single-space feeders with built-in water supply from 37 kg to slaughter at 91 kg liveweight.Treatments were replicated 16 and 6 times respectively in Experiments 1 and 2. In the first experiment, one feeder perpen was compared with two feeders per pen positioned side by side. Two feeders increased feed intake (P < 0·05) but had no significant effects on growth rate or feed conversion. With two feeders, the total time that feeders were occupied and the number of visits to feeders were both increased, while the number of enforced withdrawals from feeders and the amount of queuing were both decreased compared with the single feeder. In the second experiment, placing two feeders 2 m or more apart instead of side by side had no significant effects on feed intake or growth rate but improved feed conversion efficiency by 4%. This improvement was associated with fewer and longer visits to feeders but no difference in enforced withdrawals or queuing. In both experiments all treatments showed broadly similar patterns of diurnal feeding behaviour with two peaks of activity daily, a smaller peak pre-midday and a larger one in the afternoon. This pattern was influenced more by number of visits to feeders than by the mean duration of each visit. It is recommended that two single-space feeders are used in pens of 20 finishing pigs when non-pelleted diets are offered ad libitum and that feeders are sited some distance apart, not side by side.

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Individual selection leads to collective efficiency through coordination

10.1101/422287 ◽

2018 ◽

Author(s):

Arthur Bernard ◽

Nicolas Bredeche ◽

Jean-Baptiste André

Keyword(s):

Social Interactions ◽

Genetic Effect ◽

Evolutionary Robotics ◽

Genetic Mutation ◽

Single Mutation ◽

Individual Selection ◽

Alternative Strategies ◽

Evolutionary Trap ◽

Evolutionary Consequence ◽

Indirect Genetic Effect

Social interactions involving coordination between individuals are subject to an “evolutionary trap.” Once a suboptimal strategy has evolved, mutants playing an alternative strategy are counterselected because they fail to coordinate with the majority. This creates a detrimental situation from which evolution cannot escape, preventing the evolution of efficient collective behaviours. Here, we study this problem using the framework of evolutionary robotics. We first confirm the existence of an evolutionary trap in a simple setting. We then, however, reveal that evolution can solve this problem in a more realistic setting where individuals need to coordinate with one another. In this setting, robots evolve an ability to adapt plastically their behaviour to one another, as this improves the efficiency of their interaction. This ability has an unintended evolutionary consequence: a genetic mutation affecting one individual’s behaviour also indirectly alters their partner’s behaviour because the two individuals influence one another. As a consequence of this indirect genetic effect, pairs of partners can virtually change strategy together with a single mutation, and the evolutionary barrier between alternative strategies disappears. This finding reveals a general principle that could play a role in nature to smoothen the transition to efficient collective behaviours in all games with multiple equilibriums.

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The Price equation as a bridge between animal breeding and evolutionary biology

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2019.0360 ◽

2020 ◽

Vol 375 (1797) ◽

pp. 20190360 ◽

Cited By ~ 2

Author(s):

P. Bijma

Keyword(s):

Evolutionary Biology ◽

Genetic Effect ◽

Price Equation ◽

Response To Selection ◽

Theme Issue ◽

Heritable Variation ◽

Indirect Genetic Effect ◽

Trait Distribution ◽

The Social ◽

Genetic Standard Deviation

The genetic response to selection is central to both evolutionary biology and animal and plant breeding. While Price's theorem (PT) is well-known in evolutionary biology, most breeders are unaware of it. Rather than using PT, breeders express response to selection as the product of the intensity of selection ( i ), the accuracy of selection ( ρ ) and the additive genetic standard deviation ( σ A ); R = iρσ A . In contrast to the univariate ‘breeder's equation’, this expression holds for multivariate selection on Gaussian traits. Here, I relate R = iρσ A to PT, and present a generalized version, R = i w ρ A , w σ A , valid irrespective of the trait distribution. Next, I consider genotype–environment covariance in relation to the breeder's equation and PT, showing that the breeder's equation may remain valid depending on whether the genotype–environment covariance works across generations. Finally, I consider the response to selection in the prevalence of an endemic infectious disease, as an example of an emergent trait. The result shows that disease prevalence has much greater heritable variation than currently believed. The example also illustrates that the indirect genetic effect approach moves elements of response to selection from the second to the first term of PT, so that changes acting via the social environment come within the reach of quantitative genetics. This article is part of the theme issue ‘Fifty years of the Price equation’.

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PSI-17 Genetic analysis of weaning weight in Hungarian Simmental cattle

Journal of Animal Science ◽

10.1093/jas/skab235.503 ◽

2021 ◽

Vol 99 (Supplement_3) ◽

pp. 274-275

Author(s):

Afees Ajasa ◽

Barnabás Vágó ◽

Imre Füller ◽

István Komlósi ◽

János Posta

Keyword(s):

Variance Components ◽

Random Effect ◽

Random Effect Model ◽

Genetic Effect ◽

Genetic Effects ◽

Covariance Model ◽

Genetic Covariance ◽

Weaning Weight ◽

Effect Model ◽

Maternal Heritability

Abstract The aim of the study was to partition the total phenotypic variation in the weaning weight of Hungarian Simmental calves into their various causal components. The data used was provided by the Association of Hungarian Simmental Breeders. The dataset comprised of the weaning weight records of 44,278 calves (sire = 879, dam = 14,811) born from 1975 to 2020. A total of six models were fitted to the weaning weight data. Herd, birth year, calving order and sex were included as fixed effects in the models. Model 1 had direct genetic effect as the only random effect. Model 2 had a permanent maternal environment as an additional random effect. Model 3 had both direct and maternal genetic effects, with their covariance is being zero. Model 4 was similar to Model 3 but with non-zero direct-maternal genetic covariance. Model 5 had direct, maternal genetic and permanent environmental effects and a zero direct-maternal genetic covariance. Model 6 was similar to model 5 but the direct-maternal genetic effect was assumed to be correlated. Variance components and genetic parameters were estimated using restricted maximum likelihood method with the Wombat software. The best fit model was determined using the Log likelihood ratio test. Inclusion of direct maternal genetic covariance increased the variance components estimates dramatically which resulted in a corresponding increase in the direct and maternal heritability estimates. The best fitted model (Model 4) had direct and maternal genetic effects as the only random effects with a non-zero direct-maternal genetic covariance. The direct heritability, maternal heritability and direct-maternal genetic correlation estimate of the best model was 0.57, 0.16 and -0.78, respectively. Our result suggests the problem of (co)sampling variation in the partitioning of additive genetic effect into direct and maternal components.

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Heritable spouse effects increase evolutionary potential of human reproductive timing

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2017.2763 ◽

2018 ◽

Vol 285 (1876) ◽

pp. 20172763

Author(s):

Simon R. Evans ◽

Dominique Waldvogel ◽

Nina Vasiljevic ◽

Erik Postma

Keyword(s):

Life Histories ◽

Genetic Effect ◽

Age At First Birth ◽

Reproductive Timing ◽

Evolutionary Potential ◽

Heritable Variation ◽

Indirect Genetic Effect ◽

Component Traits ◽

Human Reproductive ◽

Female Specific

Sexual reproduction is inherently interactive, especially in animal species such as humans that exhibit extended pair bonding. Yet we have little knowledge of the role of male characteristics and their evolutionary impact on reproductive behavioural phenotypes, to the extent that biologists typically consider component traits (e.g. reproductive timing) as female-specific. Based on extensive genealogical data detailing the life histories of 6435 human mothers born across four centuries of modern history, we use an animal modelling approach to estimate the indirect genetic effect of men on the reproductive phenotype of their partners. These analyses show that a woman's reproductive timing (age at first birth) is influenced by her partner's genotype. This indirect genetic effect is positively correlated with the direct genetic effect expressed in women, such that total heritable variance in this trait is doubled when heritable partner effects are considered. Our study thus suggests that much of the heritable variation in women's reproductive timing is mediated via partner effects, and that the evolutionary potential of this trait is far greater than previously appreciated.

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Estimates of (co)variance components and genetic parameters for growth traits in Suffolk lambs

Ciência Rural ◽

10.1590/s0103-84782013001200016 ◽

2013 ◽

Vol 43 (12) ◽

pp. 2215-2220 ◽

Cited By ~ 6

Author(s):

Priscilla Regina Tamioso ◽

Jaime Luiz Alberti Filho ◽

Laila Talarico Dias ◽

Rodrigo de Almeida Teixeira

Keyword(s):

Maternal Effects ◽

Variance Components ◽

Genetic Parameters ◽

Growth Traits ◽

Genetic Effect ◽

Additive Genetic Effect ◽

Ratio Test ◽

Effect Model ◽

Estimate Heritability ◽

Heritability Estimates

The study aimed to estimate the components of (co)variance and heritability for weights at birth (BW), weaning (WW) and 180 days of age (W180), as well as the average daily gains from birth to weaning (ADG1), birth to 180 days of age (ADG2) and weaning to 180 days of age (ADG3) in Suffolk sheep. Thus, three different single-trait animal models were fitted, considering the direct additive genetic effect (Model 1), the direct additive genetic and maternal permanent environmental effects (Model 2), and in Model 3, in addition to those in Model 2, the maternal additive genetic effect was included. After comparing models through the likelihood ratio test (LRT), model 3 was chosen as the most appropriate to estimate heritability for BW, WW and ADG1. Model 2 was considered as the best to estimate the coefficient of heritability for W180 and ADG2, and model 1 for ADG3. Direct heritability estimates were inflated when maternal effects were ignored. According to the most suitable models, the heritability estimates for BW, WW, W180, ADG1, ADG2 and ADG3 were 0.06, 0.08, 0.09, 0.07, 0.08 and 0.07, respectively, indicating low possibility of genetic gain through individual selection. The results show the importance of including maternal effects in the models to properly estimate genetic parameters even at post-weaning ages.

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