Population Genetics. Matthew B. Hamilton

(a pair of alleles that make a diploid genotype) segregate independently into gametes so that in a large number of gametes half carry one allele and the other half carry the other allele.

Individual pea plants obviously have more than a single phenotype, and Mendel followed the inheritance of other characters in addition to seed coat color. In one example of his crossing experiments, Mendel tracked the simultaneous inheritance of both seed coat color and seed surface condition (either wrinkled [“angular”] or smooth). He constructed an initial cross among pure‐breeding lines identical to what he had done when tracking seed color inheritance, except now there were two phenotypes (Figure 2.4). The F2 progeny appeared in the phenotypic ratio of 9 round/yellow : 3 round/green : 3 wrinkled/yellow : 1 wrinkled/green.

      How did Mendel go from this F2 phenotypic ratio to the second law? He ignored the wrinkled/smooth phenotype and just considered the yellow/green seed color phenotype in self‐pollination crosses of F2 plants just like those for the first law. In the F2 progeny, 12/16 or three‐quarters had a yellow seed coat and 4/16 or one‐quarter had a green seed coat, or a 3 yellow : 1 green phenotypic ratio. Again using self‐pollination of F2 plants like those in Figure 2.3, he showed that the yellow phenotypes were (1/3 × ¾) one‐quarter pure and (2/3 × ¾) one‐half impure yellow. Thus, the segregation ratio for seed color was 1 : 2 : 1 and the wrinkled/smooth phenotype did not alter this result. Mendel obtained an identical result when considering instead only the wrinkled/smooth phenotype and ignoring the seed color phenotype.

Mendel concluded that a phenotypic segregation ratio of 9 : 3 : 3 : 1 is the same as combining two independent 3 : 1 segregation ratios of two phenotypes since (3 : 1) × (3 : 1) = 9 : 3 : 3 : 1. Similarly, the multiplication of two (1 : 2 : 1) phenotypic ratios will predict the two phenotype ratios (1 : 2 : 1) × (1 : 2 : 1) = 1 : 2 : 1 : 2 : 4 : 2 : 1 : 2 : 1. We now recognize that dominance in the first two phenotype ratios masks the ability to distinguish some of the homozygous and heterozygous genotypes, whereas the ratio in the second case would result if there was no dominance. You can confirm these conclusions by working out a Punnett square for the F2 progeny in the two‐locus case.

Figure 2.4 Mendel's crosses to examine the segregation ratios of two phenotypes, seed coat color (yellow or green) and seed coat surface (smooth or wrinkled), in pea plants. The stippled pattern indicates wrinkled seeds, while the solid color indicates smooth seeds. The F2 individuals exhibited a phenotypic ratio of 9 round‐yellow: 3 round‐green: 3 wrinkled‐yellow: 1 wrinkled‐green.

      Mendel’s second “law”: Predicts independent assortment of multiple loci: during gamete formation, the segregation of alleles of one locus is independent of the segregation of alleles of another locus.

      Mendel performed similar breeding experiments with numerous other pea phenotypes and obtained similar results. Mendel described his work with peas and other plants in lectures and published it in 1866 in the Proceedings of the Natural Science Society of Brünn in German where it went unnoticed for nearly 35 years. However, Mendel's results were eventually recognized, and his paper was translated into several languages. Mendel's rediscovered the hypothesis of particulate inheritance was also bolstered by evidence from microscopic observations of chromosomes during cell division that led Walter Sutton to propose in 1902 that chromosomes are the physical basis of heredity, supported by results obtained independently by Theodor Boveri at around the same time (see Crow and Crow 2002).

      Much of the currently used terminology was coined as the field of particulate genetics initially developed. Therefore, many of the critical terms in genetics have remained in use for long periods of time. However, the meanings and connotations of these terms have often changed as our understanding of genetics has also changed.

      Unfortunately, this has led to a situation where words can sometimes mislead. A common example is equating gene and allele. For example, it is commonplace for news media to report scientific breakthroughs where a “gene” has been identified as causing a particular phenotype, often a debilitating disease. Very often what is meant in these cases is that a genotype or an allele with the phenotypic effect has been identified. Both unaffected and affected individuals all possess the gene, but they differ in their alleles and therefore in their genotype. If individuals of the same species really differed in their gene content (or loci they possessed), that would provide evidence of additions or deletions to genomes. For an interesting discussion of how terminology in genetics has changed – and some of the misunderstandings this can cause, see Judson (2001).

Gene: A unit of particulate inheritance; in contemporary usage, it usually means an exon or series of exons, or a DNA sequence that codes for an RNA or protein.

      Locus (plural loci, pronounced “low‐sigh”): Literally “place” or location in the genome; in contemporary usage, it is the most general reference to any sequence or genomic region, including non‐coding regions.

      Allele: A variant or alternative form of the DNA sequence at a given locus.

      Genotype: The set of alleles possessed by an individual at one locus; the genetic composition of an individual at one locus or many loci.

      Phenotype: The morphological, biochemical, physiological, and behavioral attributes of an individual; synonymous with character and trait.

      Dominant: Where the expressed phenotype of one allele takes precedence over the expressed phenotype of another allele. The allele associated with the expressed phenotype is said to be dominant. Dominance is seen on a continuous scale that includes “complete” dominance (one allele completely masks the phenotype of another allele so that the phenotype of a heterozygote is identical to a homozygote for the dominant allele) and “partial” or “incomplete” dominance (masking effect is incomplete so that the phenotype of a heterozygote is intermediate to both homozygotes) and includes over‐ and under‐dominance (phenotype is outside the range of phenotypes seen in the homozygous genotypes). The lack of dominance (heterozygote is exactly intermediate to the phenotypes of both homozygotes) is when the effects of alleles are additive, a situation sometimes termed “codominance” or “semi‐dominance.”

      Recessive: The expressed phenotype of one allele is masked by the expressed phenotype of another allele. The allele associated with the concealed phenotype is said to be recessive.

      

2.2 Hardy–Weinberg expected genotype frequencies

       Hardy–Weinberg and its assumptions.

       Each assumption is a population genetic process.

       Hardy–Weinberg is a null model.

       Hardy–Weinberg in haplo‐diploid systems.

      Mendel's “laws” could be called the original expectations in population genetics. With the concept of particulate genetics established, it was possible to make a wide array of predictions about genotype and allele frequencies as well as the frequency of phenotypes with a one‐locus basis. Still, progress and insight into particulate genetics were gradual. Until 1914, it was generally believed that rare (infrequent) alleles would disappear from populations over time. Godfrey H. Hardy (1908) and Wilhelm Weinberg (1908) worked independently to show that the laws of Mendelian heredity