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In computer science and operations research, a genetic algorithm (GA) is a metaheuristic inspired by the process of natural selection that belongs to the larger class of evolutionary algorithms (EA). Genetic algorithms are commonly used to generate high-quality solutions to optimization and search problems by relying on biologically inspired operators such as mutation, crossover and selection.
Heritability is a statistic used in the fields of breeding and genetics that estimates the degree of variation in a phenotypic trait in a population that is due to genetic variation between individuals in that population. It measures how much of the variation of a trait can be attributed to variation of genetic factors, as opposed to variation of environmental factors. The concept of heritability can be expressed in the form of the following question: "What is the proportion of the variation in a given trait within a population that is not explained by the environment or random chance?"
Selective breeding is the process by which humans use animal breeding and plant breeding to selectively develop particular phenotypic traits (characteristics) by choosing which typically animal or plant males and females will sexually reproduce and have offspring together. Domesticated animals are known as breeds, normally bred by a professional breeder, while domesticated plants are known as varieties, cultigens, cultivars, or breeds. Two purebred animals of different breeds produce a crossbreed, and crossbred plants are called hybrids. Flowers, vegetables and fruit-trees may be bred by amateurs and commercial or non-commercial professionals: major crops are usually the provenance of the professionals.
Dog breeding is the practice of mating selected dogs with the intention of maintaining or producing specific qualities and characteristics. When dogs reproduce without such human intervention, their offspring's characteristics are determined by natural selection, while "dog breeding" refers specifically to the artificial selection of dogs, in which dogs are intentionally bred by their owners. Breeding relies on the science of genetics, hence a breeder who is knowledgeable on canine genetics, health, and the intended purpose of the dogs attempts to breed suitable dogs.
Purebreds, also called purebreeds, are "cultivated varieties" (cultivars) of an animal species achieved through the process of selective breeding.
Tree breeding is the application of genetic, reproductive biology and economics principles to the genetic improvement and management of forest trees. In contrast to the selective breeding of livestock, arable crops, and horticultural flowers over the last few centuries, the breeding of trees, with the exception of fruit trees, is a relatively recent occurrence.
A mating pool is a concept used in evolutionary computation, which refers to a family of algorithms used to solve optimization and search problems.
Plant breeders use different methods depending on the mode of reproduction of crops, which include:
In biology, culling is the process of segregating organisms from a group according to desired or undesired characteristics. In animal breeding, it is the process of removing or segregating animals from a breeding stock based on specific trait. This is done to exaggerate desirable characteristics, or to remove undesirable characteristics by altering the genetic diversity of the population. For livestock and wildlife, culling often refers to the act of killing removed animals based on their individual characteristics, such as their sex or species membership, or as a means of preventing infectious disease transmission.
Animal breeding is a branch of animal science that addresses the evaluation of the genetic value of livestock. Selecting for breeding animals with superior EBV in growth rate, egg, meat, milk, or wool production, or with other desirable traits has revolutionized livestock production throughout the entire world. The scientific theory of animal breeding incorporates population genetics, quantitative genetics, statistics, and recently molecular genetics and is based on the pioneering work of Sewall Wright, Jay Lush, and Charles Henderson.
Life history theory is an analytical framework designed to study the diversity of life history strategies used by different organisms throughout the world, as well as the causes and results of the variation in their life cycles. It is a theory of biological evolution that seeks to explain aspects of organisms' anatomy and behavior by reference to the way that their life histories—including their reproductive development and behaviors, post-reproductive behaviors, and lifespan —have been shaped by natural selection. A life history strategy is the "age- and stage-specific patterns" and timing of events that make up an organism's life, such as birth, weaning, maturation, death, etc. These events, notably juvenile development, age of sexual maturity, first reproduction, number of offspring and level of parental investment, senescence and death, depend on the physical and ecological environment of the organism.
In mathematical or statistical modeling a threshold model is any model where a threshold value, or set of threshold values, is used to distinguish ranges of values where the behaviour predicted by the model varies in some important way. A particularly important instance arises in toxicology, where the model for the effect of a drug may be that there is zero effect for a dose below a critical or threshold value, while an effect of some significance exists above that value. Certain types of regression model may include threshold effects.
In multivariate quantitative genetics, a genetic correlation is the proportion of variance that two traits share due to genetic causes, the correlation between the genetic influences on a trait and the genetic influences on a different trait estimating the degree of pleiotropy or causal overlap. A genetic correlation of 0 implies that the genetic effects on one trait are independent of the other, while a correlation of 1 implies that all of the genetic influences on the two traits are identical. The bivariate genetic correlation can be generalized to inferring genetic latent variable factors across > 2 traits using factor analysis. Genetic correlation models were introduced into behavioral genetics in the 1970s–1980s.
Behavioural genetics, also referred to as behaviour genetics, is a field of scientific research that uses genetic methods to investigate the nature and origins of individual differences in behaviour. While the name "behavioural genetics" connotes a focus on genetic influences, the field broadly investigates genetic and environmental influences, using research designs that allow removal of the confounding of genes and environment. Behavioural genetics was founded as a scientific discipline by Francis Galton in the late 19th century, only to be discredited through association with eugenics movements before and during World War II. In the latter half of the 20th century, the field saw renewed prominence with research on inheritance of behaviour and mental illness in humans, as well as research on genetically informative model organisms through selective breeding and crosses. In the late 20th and early 21st centuries, technological advances in molecular genetics made it possible to measure and modify the genome directly. This led to major advances in model organism research and in human studies, leading to new scientific discoveries.
Plant breeding is the science of changing the traits of plants in order to produce desired characteristics. It has been used to improve the quality of nutrition in products for humans and animals. The goals of plant breeding are to produce crop varieties that boast unique and superior traits for a variety of agricultural applications. The most frequently addressed traits are those related to biotic and abiotic stress tolerance, grain or biomass yield, end-use quality characteristics such as taste or the concentrations of specific biological molecules and ease of processing . Plant breeding can be accomplished through many different techniques ranging from simply selecting plants with desirable characteristics for propagation, to methods that make use of knowledge of genetics and chromosomes, to more complex molecular techniques. Genes in a plant are what determine what type of qualitative or quantitative traits it will have. Plant breeders strive to create a specific outcome of plants and potentially new plant varieties, and in the course of doing so, narrow down the genetic diversity of that variety to a specific few biotypes.
The "missing heritability" problem is the fact that single genetic variations cannot account for much of the heritability of diseases, behaviors, and other phenotypes. This is a problem that has significant implications for medicine, since a person's susceptibility to disease may depend more on 'the combined effect of all the genes in the background than on the disease genes in the foreground', or the role of genes may have been severely overestimated.
Michael Edward "Mike" Goddard is a professorial fellow in animal genetics at the University of Melbourne, Australia.
Genome-wide complex trait analysis (GCTA) Genome-based restricted maximum likelihood (GREML) is a statistical method for variance component estimation in genetics which quantifies the total narrow-sense (additive) contribution to a trait's heritability of a particular subset of genetic variants. This is done by directly quantifying the chance genetic similarity of unrelated individuals and comparing it to their measured similarity on a trait; if two unrelated individuals are relatively similar genetically and also have similar trait measurements, then the measured genetics are likely to causally influence that trait, and the correlation can to some degree tell how much. This can be illustrated by plotting the squared pairwise trait differences between individuals against their estimated degree of relatedness. The GCTA framework can be applied in a variety of settings. For example, it can be used to examine changes in heritability over aging and development. It can also be extended to analyse bivariate genetic correlations between traits. There is an ongoing debate about whether GCTA generates reliable or stable estimates of heritability when used on current SNP data. The method is based on the outdated and false dichotomy of genes versus the environment. It also suffers from serious methodological weaknesses, such as susceptibility to population stratification.
In genetics, a polygenic score (PGS), also called a polygenic risk score (PRS), genetic risk score, or genome-wide score, is a number that summarises the estimated effect of many genetic variants on an individual's phenotype, typically calculated as a weighted sum of trait-associated alleles. It reflects an individual's estimated genetic predisposition for a given trait and can be used as a predictor for that trait. In other words, it gives an estimate of how likely an individual is to have a given trait only based on genetics, without taking environmental factors into account. Polygenic scores are widely used in animal breeding and plant breeding due to their efficacy in improving livestock breeding and crops. In humans, polygenic scores are typically generated from genome-wide association study (GWAS) data.
Rohan L. Fernando is a Sri Lankan American geneticist who is a professor of quantitative genetics in the Department of Animal Science at Iowa State University (ISU), US. Fernando's efforts have focused primarily on theory and methods for use of genetic markers in breeding, theory and methods for genetic evaluations of crossbred animals, methodology related to the estimation of genetic parameters and the prediction of genetic merit in populations undergoing selection and non-random mating, Bayesian methodology for analysis of unbalanced mixed model data, optimization of breeding programs, and use of computer simulation to study dynamics of genetic system.
References
- ↑ Crow & Kimura 1979, "Efficiency of truncation selection"
- ↑ H Muhlenbein, D Schlierkamp-Voosen (1993). "Predictive Models for the Breeder Genetic Algorithm". Evolutionary Computation. doi:10.1162/evco.1993.1.1.25. S2CID 16085506.
- "Chapter 14: Short-term Changes in the Mean: 2. Truncation and Threshold Selection"
- Crow 2010, "On epistasis: why it is unimportant in polygenic directional selection"
- Visscher et al. 2008, "Heritability in the genomics era - concepts and misconceptions"
- Visscher 2016, "Human Complex Trait Genetics in the 21st Century"
- Weight & Harpending 2016, "Some Uses of Models of Quantitative Genetic Selection in Social Science"
- Frost & Harpending 2015, "Western Europe, state formation, and genetic pacification"
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