The Ultimate Guide to Whole Genome Resequencing: Basic and Advanced Facts (II)

Random Genetic Drift: A machine error occurs when a gamete is sampled from a certain generation of gene bank to form the next generation of individuals. This machine error causes a change in the frequency of a gene to be called a random drift or inheritance of the gene Drifting. In other words, when using random sampling to establish a small group, the phenomenon of random fluctuations in gene frequency due to sampling errors.

Ancestor Effect or Founder Effect: The effect of a few individuals whose gene frequency determines the gene frequency in their offspring is an extreme genetic drift.

Migration Pressure (also called Gene Flow): For some reason, a part of the group with a certain gene frequency moves into another group with a different gene frequency, and crosses to settle, which will cause the gene frequency of the moved group to change.

Effective Population Size (Ne): Refers to the ideal population size with the same gene frequency variance or the same heterozygosity decay rate with the actual population, which reflects the size of the population average inbreeding coefficient increment and the average homozygosity of the genes in the population genetic structure.

Neutral theory: It is believed that most mutations at the molecular level are neutral or near-neutral, and natural selection has no effect on them. These mutations are preserved or tend to disappear by random drift from generation to generation, thereby forming evolution at the molecular level changes or intra-species variation.

Mutation Pressure: Under certain conditions, the mutation rate of a group can be significantly increased, resulting in mutation pressure, which increases the frequency of a certain gene.

Selection Pressure: Affected by certain environmental conditions, certain mutant types are affected by selection, which reduces the frequency of mutant genes.

Selection: The phenomenon of population genetics where the proportion of individuals of a certain genotype changes during the generation of a group of genes under the intervention of humans and nature (Zhang Yuan 2001; Ma Yunlong 2015).

Positive Selection or Directional Selection: Positive selection is the most common form of selection. When a new favorable mutation occurs in the population, the fitness of the corresponding position will be transformed into the other extreme from one extreme. In this process of adaptive evolution, selection is a potential driving force that favors the directional evolution of mutation sites.

Negative Selection or Purifying Selection: when a certain phenotypic trait in a population no longer adapts to the current environment or breeding needs, the allele frequency associated with the trait will be reduced or be eliminated. Usually the phenotypic traits associated with this type of allele are detrimental to the survival and reproduction of the population in the current environment.

Balance Selection: Some alleles are homozygous only in a small number of individuals in normal hybrid populations, and are lower in fitness than heterozygotes, and then will appear to be beneficial for the development of multiple alleles on many sites. Therefore, balanced selection can maintain genetic diversity in the population rather than selecting only the most favorable genotype. (That is, due to hyperdominance and other effects, the potential action sites of certain traits in the population always maintain a high genetic polymorphism and corresponding high heterozygosity in the selected action line, which may be related to heterosis in livestock breeding).

Parallel Selection: Corresponding to balanced selection, between different subgroups of the same species group, due to accidental or other subjective factors, the potential genetic loci affecting certain traits are selected in the same direction. It is called parallel selection. (For example: the choice of milk production in different cow breeds).

Divergent Selection: The selection effect causes potential genetic loci that affect certain traits to evolve in different directions in different subgroups (for example: long-winged and residual wings of Drosophila).

Selective Sweep: Under the theory of neutral evolution, a new mutation often takes a long time to reach a higher frequency in the population, and the degree of linkage disequilibrium around these mutations will depend on the recombination rate. The effect of this time is almost completely attenuated by degradation. Therefore, the vast majority of sites on the genome that are not subject to selection will always be in a random drift state, and the linkage disequilibrium formed between each other is easy to decay, and the haplotype length is relatively short. However, under the effect of selection, the population favorable allele frequency will reach a higher value in a shorter period of time, and the effect of recombination will be hedged to a certain extent without causing substantial degradation of long-range haplotypes. At the same time, the linkage disequilibrium under selection will cause the gene frequency of the neutral site near the selection site to increase and form a long-range haplotype homozygote. In population genetics, this phenomenon of reduced polymorphism of some chromosome segments caused by selection is called selective clearance.

Hitchhiking Effect: The neutral sites around the selection site benefit from the rapid increase in gene frequency due to the selection effect, which is commonly known as the "hitchhiking" effect.

Selection Signature: The selective sweeping and "free-riding" effects belong to the same population genetic phenomenon expressed from different angles, and they are both obvious features left by the selection effect on the genome. This feature is called the selection signal.

To be continued in Part III…