A framework for power and sensitivity analyses for quantitative genetic studies of natural populations, and case studies in Soay sheep (Ovis aries)

Abstract Wild quantitative genetic studies have focused on a subset of traits (largely morphological and life history), with others, such as behaviors, receiving much less attention. This is because it is challenging to obtain sufficient data, particularly for behaviors involving interactions between individuals. Here, we explore an indirect approach for pilot investigations of the role of genetic differences in generating variation in parental care. Variation in parental genetic effects for offspring performance is expected to arise from among-parent genetic variation in parental care. Therefore, we used the animal model to predict maternal breeding values for lamb growth and used these predictions to select females for field observation, where maternal and lamb behaviors were recorded. Higher predicted maternal breeding value for lamb growth was associated with greater suckling success, but not with any other measures of suckling behavior. Though our work cannot explicitly estimate the genetic basis of the specific traits involved, it does provide a strategy for hypothesis generation and refinement that we hope could be used to justify data collection costs needed for confirmatory studies. Here, results suggest that behavioral genetic variation is involved in generating maternal genetic effects on lamb growth in Soay sheep. Though important caveats and cautions apply, our approach may extend the ability to initiate more genetic investigations of difficult-to-study behaviors and social interactions in natural populations.

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A rare MHC haplotype confers selective advantage in a free-living ruminant

10.1101/2020.03.25.008565 ◽

2020 ◽

Author(s):

Wei Huang ◽

Kara L Dicks ◽

Jarrod D Hadfield ◽

Susan E Johnston ◽

Keith T Ballingall ◽

...

Keyword(s):

Life Span ◽

Mhc Class Ii ◽

Balancing Selection ◽

Natural Populations ◽

Class Ii ◽

Ovis Aries ◽

Fluctuating Selection ◽

Soay Sheep ◽

Mhc Genes ◽

Mhc Class Ii Genes

AbstractThe major histocompatibility complex (MHC) is the most variable gene family known in vertebrates. Parasite-mediated selection (PMS) is believed to be the main force maintaining diversity at MHC genes, but it has proven hard to demonstrate the exact PMS regime that is acting in natural populations. Demonstrating contemporary selection on MHC alleles is not trivial, and previous work has been constrained by limited genetic tools, low sample sizes, short time scales and anticonservative statistical approaches. Here, we use a conservative statistical approach to examine associations between MHC genes and fitness components, using haplotypes of expressed MHC class II genes in a large sample of Soay sheep (Ovis aries) monitored over their lifetimes between 1989 and 2012. Of the eight MHC haplotypes (A-H) identified, we found that haplotype C was associated with decreased male breeding success, haplotype D was associated with increased female life span, and haplotype F was associated with decreased female life span. Consistent with the increased lifespan in females, haplotype D has increased in frequency throughout the study period. Our results suggest the existence of contemporary balancing selection on MHC class II genes in Soay sheep as might be expected under the hypotheses of rare allele advantage or fluctuating selection and do not support an effect of heterozygous advantage.

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The limits of normal approximation for adult height

European Journal of Human Genetics ◽

10.1038/s41431-021-00836-7 ◽

2021 ◽

Author(s):

Sergei A. Slavskii ◽

Ivan A. Kuznetsov ◽

Tatiana I. Shashkova ◽

Georgii A. Bazykin ◽

Tatiana I. Axenovich ◽

...

Keyword(s):

Complex Traits ◽

Adult Height ◽

Normal Approximation ◽

Classical Model ◽

Model Complexity ◽

Test Case ◽

Genetic Studies ◽

Quantitative Genetic ◽

Profound Influence ◽

Log Normal

AbstractAdult height inspired the first biometrical and quantitative genetic studies and is a test-case trait for understanding heritability. The studies of height led to formulation of the classical polygenic model, that has a profound influence on the way we view and analyse complex traits. An essential part of the classical model is an assumption of additivity of effects and normality of the distribution of the residuals. However, it may be expected that the normal approximation will become insufficient in bigger studies. Here, we demonstrate that when the height of hundreds of thousands of individuals is analysed, the model complexity needs to be increased to include non-additive interactions between sex, environment and genes. Alternatively, the use of log-normal approximation allowed us to still use the additive effects model. These findings are important for future genetic and methodologic studies that make use of adult height as an exemplar trait.

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Sex Differences in Feeding Behaviour at Feeding Station Scale in Soay Sheep (Ovis Aries)

Behaviour ◽

10.1163/1568539042360143 ◽

2004 ◽

Vol 141 (8) ◽

pp. 999-1020 ◽

Cited By ~ 7

Author(s):

◽

Keyword(s):

Feeding Behaviour ◽

Ovis Aries ◽

Intake Rate ◽

Same Sex ◽

Soay Sheep ◽

Food Items ◽

Feeding Station ◽

Foraging Decisions ◽

Mouth Size ◽

Mechanistic Response

AbstractHerbivorous ungulates live in a spatially heterogeneous environment making foraging decisions at a range of hierarchical scales, from bite size to landscape. We investigated the factors that control intake rate in Soay sheep (Ovis aries) when discrete items of food were sparsely distributed at the feeding station scale. Within the feeding station we varied the difficulty of accessing food, distance between items of food, difficulty of finding the food and complexity of the feeding station and recorded how intake rate responded in relation to body size, mouth size and the sex of the animal. Our findings demonstrated how increasing difficulty of accessing food, and increasing complexity of the feeding station negatively affected intake rate. The expected mechanistic response that smaller animals or animals with smaller mouth size were better at handling discrete small items of food, was overridden by individual and sexual differences in behaviour. We also considered that intake rate within a feeding station could be maximised by optimising the spatial pattern of offtake, and the results clearly indicated that both sexes tended to show clustered patterns of offtake. Animals of the same sex responded in a similar way to the difficulty in handling food items; males persevered more than females and consequently were less handicaped by having larger mouths. We discussed these results in relation to behavioural and body mass differences between the sexes and animals.

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A quantitative genetic study of starvation resistance at different geographic scales in natural populations of Drosophila melanogaster

Genetics Research ◽

10.1017/s0016672310000327 ◽

2010 ◽

Vol 92 (4) ◽

pp. 253-259 ◽

Cited By ~ 12

Author(s):

JULIETA GOENAGA ◽

JUAN JOSÉ FANARA ◽

ESTEBAN HASSON

Keyword(s):

Drosophila Melanogaster ◽

Genetic Correlations ◽

Natural Populations ◽

Food Shortage ◽

Population Variation ◽

Phenotypic Variance ◽

Starvation Resistance ◽

Natural Genetic Variation ◽

Quantitative Genetic ◽

Variation Explained

SummaryFood shortage is a stress factor that commonly affects organisms in nature. Resistance to food shortage or starvation resistance (SR) is a complex quantitative trait with direct implications on fitness. However, surveys of natural genetic variation in SR at different geographic scales are scarce. Here, we have measured variation in SR in sets of lines derived from nine natural populations of Drosophila melanogaster collected in western Argentina. Our study shows that within population variation explained a larger proportion of overall phenotypic variance (80%) than among populations (7·2%). We also noticed that an important fraction of variation was sex-specific. Overall females were more resistant to starvation than males; however, the magnitude of the sexual dimorphism (SD) in SR varied among lines and explained a significant fraction of phenotypic variance in all populations. Estimates of cross-sex genetic correlations suggest that the genetic architecture of SR is only partially shared between sexes in the populations examined, thus, facilitating further evolution of the SD.

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The genetic architecture of helminth-specific immune responses in a wild population of Soay sheep (Ovis aries)

PLoS Genetics ◽

10.1371/journal.pgen.1008461 ◽

2019 ◽

Vol 15 (11) ◽

pp. e1008461 ◽

Cited By ~ 7

Author(s):

Alexandra M. Sparks ◽

Kathryn Watt ◽

Rona Sinclair ◽

Jill G. Pilkington ◽

Josephine M. Pemberton ◽

...

Keyword(s):

Immune Responses ◽

Genetic Architecture ◽

Wild Population ◽

Ovis Aries ◽

Soay Sheep

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A quantitative genetic analysis of fitness and its components in Drosophila melanogaster

Genetics Research ◽

10.1017/s0016672300024526 ◽

1986 ◽

Vol 47 (1) ◽

pp. 59-70 ◽

Cited By ~ 50

Author(s):

Trudy F. C. Mackay

Keyword(s):

Drosophila Melanogaster ◽

Natural Populations ◽

Strongly Correlated ◽

Wild Type ◽

Relative Contribution ◽

Quantitative Characters ◽

Quantitative Genetic ◽

Bristle Number ◽

Metric Traits ◽

Average Fitness

SummaryForty-one third chromosomes extracted from a natural population of Drosophila melanogaster were assessed for net fitness and for the quantitative characters viability, net fertility, female productivity, male weight, abdominal bristle number, and sternopleural bristle number. Net homozygous and heterozygous fitness of the third chromosomes was estimated by competition against a marked balancer third chromosome. Average fitness of the homozygous lines relative to wild-type heterozygotes was 0·13, indicating substantial inbreeding depression for net fitness. All significant correlations of quantitative characters with fitness and with each other were high and positive. Homozygous fitness is strongly correlated with net fertility, viability, and female productivity, moderately associated with male weight, and not significantly associated with bristle traits. The combination of metric traits which best predicts homozygous fitness is the simple multiple of viability and female productivity. Heterozygous fitness is not correlated with homozygous fitness; furthermore, the relative contribution of metric traits to fitness in a heterozygous population is likely to be different from that deduced from homozygous lines. These observations are consistent with a model of genetic variation for fitness in natural populations caused by segregation of rare deleterious recessive alleles.

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Epidemiology of nematode infections of Soay sheep (Ovis aries L.) on St Kilda

Parasitology ◽

10.1017/s0031182000074667 ◽

1992 ◽

Vol 105 (3) ◽

pp. 481-492 ◽

Cited By ~ 69

Author(s):

F. M. D. Gulland ◽

M. Fox

Keyword(s):

Population Density ◽

Infection Intensity ◽

Host Population ◽

Ovis Aries ◽

Sheep Population ◽

Soay Sheep ◽

Infective Larvae ◽

Population Crash ◽

Faecal Egg Counts ◽

Bad Weather

SUMMARYThe epidemiology of nematode infections of Soay sheep on the island of St Kilda over a period of 2 years (August 1988–August 1990) spanning a host population crash is described. Infective larvae (L3) levels on pasture were high (2422±365 L3/kg D.M. grass in midsummer 1988) when host population density was high, decreasing after the sheep population declined by 70% in early 1989 (601 ±14 L3/kg D.M. in midsummer 1989). The availability of infective larvae to sheep increased during the winter of 1988–1989, probably as a result of concentration of existing larvae on grass as vegetation was destroyed by bad weather and overgrazing. Increased availability of pre-parasitic stages was accompanied by a marked increased in faecal egg counts from sheep of all ages and both sexes. Prevalence and intensity of infection (faecal egg counts) were higher in males than females throughout the 2-year study (χ2 = 208.3, P < 0.005 and F1.2000 = 304, P < 0.001 respectively), except during the lambing periods, and decreased with age in both sexes. Changes in prevalence and intensity of strongyle infections were associated with changes in host population density. Prevalence and intensity of Dictyocaulus filaria larvae in faeces increased during the host population crash. Infection intensity decreased with age (F1.203 = 44.02, P < 0.001) and was higher in males than females (F1.203 = 13.45, P < 0.001).

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Quantitative genetic studies in the mouse (Mus Musculus L.)

Journal of Genetics ◽

10.1007/bf02984162 ◽

1971 ◽

Vol 60 (3) ◽

pp. 207-213 ◽

Cited By ~ 1

Author(s):

H. V. Dadlani ◽

S. S. Prabhu

Keyword(s):

Mus Musculus ◽

Genetic Studies ◽

Quantitative Genetic

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Application of Image Analysis in Studies of Quantitative Disease Resistance, Exemplified Using Common Bacterial Blight–Common Bean Pathosystem

Phytopathology ◽

10.1094/phyto-06-11-0175 ◽

2012 ◽

Vol 102 (4) ◽

pp. 434-442 ◽

Cited By ~ 17

Author(s):

Weilong Xie ◽

Kangfu Yu ◽

K. Peter Pauls ◽

Alireza Navabi

Keyword(s):

Image Analysis ◽

Common Bean ◽

Disease Severity ◽

Bacterial Blight ◽

Visual Assessment ◽

Common Bacterial Blight ◽

Genetic Studies ◽

Visual Scale ◽

Quantitative Genetic ◽

Visual Assessments

The effectiveness of image analysis (IA) compared with an ordinal visual scale, for quantitative measurement of disease severity, its application in quantitative genetic studies, and its effect on the estimates of genetic parameters were investigated. Studies were performed using eight backcross-derived families of common bean (Phaseolus vulgaris) (n = 172) segregating for the molecular marker SU91, known to be associated with a quantitative trait locus (QTL) for resistance to common bacterial blight (CBB), caused by Xanthomonas campestris pv. phaseoli and X. fuscans subsp. fuscans. Even though both IA and visual assessments were highly repeatable, IA was more sensitive in detecting quantitative differences between bean genotypes. The CBB phenotypic difference between the two SU91 genotypic groups was consistently more than fivefold for IA assessments but generally only two- to threefold for visual assessments. Results suggest that the visual assessment results in overestimation of the effect of QTL in genetic studies. This may have been caused by lack of additivity and uneven intervals of the visual scale. Although visual assessment of disease severity is a useful tool for general selection in breeding programs, assessments using IA may be more suitable for phenotypic evaluations in quantitative genetic studies involving CBB resistance as well as other foliar diseases.

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