Matthew B. Hamilton - Population Genetics

Species	Mating system		Method	References
Humans
Homo sapiens	outcrossed	0.0001–0.046	pedigree	Jorde (1997)
Snail
Bulinus truncates	selfed & outcrossed	0.6–1.0	microsatellites	Viard et al. (1997)
Domestic dogs
Breeds combined	outcrossed	0.33	allozyme	Christensen et al. (1985)
German Shepard	outcrossed	0.10
Mongrels	outcrossed	0.06
Plants
Arabidopsis thaliana	Selfed	0.99	allozyme	Abbott et al. (1989)
Pinus ponderosa	outcrossed	−0.37	allozyme	Brown (1979)

Determining the genotypes of individuals at enzymatic protein loci is a rapid technique to estimate genotype frequencies in populations. Protein analysis was the primary molecular genotyping technique for several decades before DNA‐based techniques became widely available. Alleles at loci that code for proteins with enzymatic function can be ascertained in a multi‐step process. First, fresh tissue samples are ground up under conditions that preserve the function of proteins. Next, these protein extracts are loaded onto starch gels and exposed to an electric field. The electrical current results in electrophoresis where proteins are separated based on their ratio of molecular charge to molecular weight. Once electrophoresis is complete, the gel is then “stained” to visualize specific enzymes. The primary biochemical products of protein enzymes are not themselves visible. However, a series of biochemical reactions in a process called enzymatic coupling can be used to eventually produce a visible product (often nitro blue tetrazolium or NBT) at the site where the enzyme is active (see Figure 2.11). If different DNA sequences at a protein enzyme locus result in different amino acid sequences that differ in net charge, then multiple alleles will appear in the gel after staining. The term allozyme (also known as isozyme) is used to describe the multiple allelic staining variants at a single protein locus. Allozyme electrophoresis and staining detects only a subset of genetic variation at protein coding loci. Amino acid changes that are charge neutral and nucleotide changes that are synonymous (do not alter the amino acid sequence) cannot be detected by allozyme electrophoresis methods. Refer to Manchenko (2003) for a technical introduction and detailed methods of allozyme detection.

Figure 2.11 An allozyme gel stained to show alleles at the phosphoglucomutase or PGM locus in striped bass and white bass. The right‐most three individuals are homozygous for the faster migrating allele (FF genotype), while the left‐most four individuals are homozygous for the slower migrating allele (SS genotype). No double‐banded heterozygotes (FS genotype) are visible on this gel. The + and – indicate the anode and cathode, respectively, ends of the gel. Wells where the individual samples were loaded into the gel can be seen at the bottom of the picture. Gel picture kindly provided by J. Epifanio.

(2.12)

where k is the number of alleles at the locus, the p i 2and 2 p i p jterms represent the expected homozygote genotype frequencies with random mating based on allele frequencies, and indicates summation of the frequencies of the k homozygous genotypes. Under random mating, . This quantity was called the gene diversityby Nei (1973) to distinguish it from the heterozygosity when there is non‐random mating within populations and to recognize that it is a quantity that can be applied to polyploids (see Meirmans et al. 2018). The expected heterozygosity can be adjusted for small samples by multiplying H eby 2 N /(2 N − 1) where N is the total number of genotypes (Nei and Roychoudhury 1974), a correction that makes little difference unless N is about 50 or fewer individuals. In a similar manner, the observed heterozygosity ( H o) is the sum of the frequencies of all heterozygotes observed in a sample of genotypes:

(2.13)

where the observed frequency of each heterozygous genotype H iis summed over the h = k ( k − 1)/2 heterozygous genotypes possible with k alleles. Both H eand H ocan be averaged over multiple loci to obtain mean heterozygosity estimates for two or more loci. Heterozygosity provides one of the basic measures of genetic variation, or more formally genetic polymorphism, in population genetics.

The fixation index as a measure of deviation from expected levels of heterozygosity is a critical concept that will appear in several places later in this text. The fixation index plays a conceptual role in understanding the effects of population size on heterozygosity ( Chapter 3) and also serves as an estimator of the impact of population structure on the distribution of genetic variation ( Chapter 4).

Mating among relatives alters genotype frequencies but not allele frequencies.

Mating among relatives and the probability that two alleles are identical by descent.

The coancestry coefficient and autozygosity.

Phenotypic consequences of mating among relatives.

Inbreeding depression and its possible causes.

The many meanings of inbreeding.

The previous section of this chapter showed how non‐random mating can increase or decrease the frequency of heterozygote genotypes compared to the frequency that is expected with random mating. The last section also introduced the fixation index as well as ways to quantify heterozygosity in a population. This section will build on that foundation to show two concepts: (i) the consequences of non‐random mating on allele and genotype frequencies in a population and (ii) the probability that two alleles are identical by descent. The focus will be on positive genotypic assortative mating (like genotypes mate) or inbreeding since this will eventually be helpful to understand genotype frequencies in small populations. The end of this section will consider some of the consequences of inbreeding and the evolution of autogamy.