If two individuals have a certain phenotype, does that mean they must have the same genotype?

"Phenotype" simply refers to an observable trait. "Pheno" simply means "observe" and comes from the same root as the word "phenomenon". And so it's an observable type of an organism, and it can refer to anything from a common trait, such as height or hair color, to presence or absence of a disease. Frequently, phenotypes are related and used--the term is used--to relate a difference in DNA sequence among individuals with a difference in trait, be it height or hair color, or disease, or what have you. But it's important to remember that phenotypes are equally, or even sometimes more greatly influenced by environmental effects than genetic effects. So a phenotype can be directly related to a genotype, but not necessarily. There's usually not a one-to-one correlation between a genotype and a phenotype. There are almost always environmental influences, such as what one eats, how much one exercises, how much one smokes, etc. All of those are environmental influences which will affect the phenotype as well.

PHENOTYPE AND GENOTYPE

Definitions: phenotype is the constellation of observable traits; genotype is the genetic endowment of the individual. Phenotype = genotype + development (in a given environment). To consider these in the context of evolutionary biology, we want to know how these two are related. In a narrow "genetic" sense, the genotype defines the phenotype. But how, in and evolutionary sense, does the phenotype "determine" the genotype? Selection acts on phenotypes because differential reproduction and survivorship depend on phenotype. If the phenotype affecting reproduction or survivorship is genetically based, then selection can winnow out genotypes indirectly by winnowing out phenotypes.

How do we get from genotype to phenotype? Central dogma: DNA via transcription to RNA via translation to protein; proteins can act to alter the patterns and timing of gene expression which can lead to cytodifferentiation where cells take on different states; cell communication can lead to pattern formation and morphogenesis and eventually we have an adult!

Genotype is also used to refer to the pair of alleles present at a single locus. With alleles 'A' and 'a' there are three possible genotypes AA, Aa and aa. With three alleles 1, 2, 3 there are six possible genotypes: 11, 12, 13, 22, 23, 33. First we must appreciate that genes do not act in isolation. The genome in which a genotype is found can affect the expression of that genotype, and the environment can affect the phenotype.

Not all pairs of alleles will have the same phenotype: dominance when AA = Aa in phenotype, A is dominant, a is recessive. An allele can be dominant over one allele but recessive to another allele. Model of dominance from enzyme activity: no copies produce no phenotype, one copy produces x amount of product and two copies produces 2x then the alleles are additive and there is no dominance (intermediate inheritance). If one copy of the allele produces as much product (or has as high a rate of flux) as a homozygote then there is dominance. There are cases where the heterozygote is greater in phenotypic value than either homozygote: called overdominance

Single genes do not always work as simply as indicated by a dominance and recessive relationship. Other genes can affect the phenotypic expression of a given gene. One example is epistasis ("standing on") where one locus can mask the expression of another. Classic example is a synthetic pathway of a pigment. Mutations at loci controlling the early steps in the pathway (gene 1) can be epistatic on the expression of genes later in the pathway (gene 3) by failing to produce pigment precursors (e.g. albinos) A-> gene 1 -> B -> gene 2 -> C gene 3 -> Pigment

Genes can also be pleitropic when they affect more than one trait. The single base pair mutation that lead to sickle cell anemia is a classic example. The altered hemoglobin sequence is not the only effect: lower oxygen affinity=anemia; clogged capillaries=circulatory problems; in heterozygote state=malarial resistance. Mutations in cartilage are another example since cartilage makes up many different structures the effects of the mutation are evident in many different phenotypic characters.

Polygenic inheritance can be explained by additive effects of many loci: if each "capital" allele contributes one increment to the phenotype. With one locus and additive effects we have three phenotypic classes: AA, Aa and aa. With two loci and two alleles in a strictly additive model (i.e., no epistasis or other modifying effects) we can have five phenotypic classes aabb and the intermediate phenotypic values can be produced in more ways, so should be more frequent. The more loci affecting the trait, the greater number of phenotypic classes.

PATTERNS OF VARIATION

Evolution by Natural Selection rests on the following principles:

1. there is variation in natural populations

2. the variation is heritable; has a genetic basis

3. more offspring are produced than will survive each generation: struggle for existence

4. if heritable variation affects survival/reproduction, there will be differential reproduction=selection

Without genetic variation there will be no evolution. Thus, characterizing the genetic variation in natural populations is fundamental to the study of evolution. (see The Genetic Basis of Evolutionary Change by Lewontin , 1974)

What kinds of variation are there? Discrete polymorphisms (e.g., Biston betularia) easily noticed, but not frequent or representative of the variation in natural populations (eye color in humans also quasi discrete). Continuously varying traits can be described by the mean x = (Xi)/n and variance V = 1/nS(Xi-x)2. Examples: the carrots in the Burpee Catologue; human height. Continuously varying traits will have both a genetic and environmental components.

How much genetic variation is there? Historical debate: Classical school held that there was very little genetic variation, most individuals were homozygous for a "wild-type" allele. Rare heterozygous loci due to recurrent mutation; natural selection purges populations of their "load" of mutations. Balance school held that many loci will be heterozygous in natural populations and heterozygotes maintained by "balancing selection" (heterozygote advantage). Selection thus plays a role in maintaining variation.

How do we measure variation? To show that there is a genetic basis to a continuously varying character one can study 1) resemblance among relatives: look at the offspring of individuals from parents in different parts of the distribution; can estimate heritability (more later). 2) artificial selection: pigeons and dogs show that there is variation present; does not tell how much variation

Protein electrophoresis: phenotype = gene product of specific locus (loci). Took off in mid 60's (Lewontin and Hubby, 1966; Harris, 1966); still used. Grind up organism in buffer, apply homogenate to gel (starch, acrylamide), apply electric field, proteins migrate in gel according to charge, stain gel with histochemical stain for enzyme activity, bands reveal variation. Do this for many loci and can estimate: proportion of loci polymorphic per population (10-60%, depending on organism); proportion of loci heterozygous per individual (3-20% depending on organism). The technique provides a minimum estimate because different amino acid sequences may migrate at the same rate in the gel.

DNA variation. Measure the genetic material directly; sequencing is the most precise but the most laborious; restriction enzyme analysis faster but has less information. These techniques have revealed that there is even more genetic variation that what was revealed by protein electrophoresis. Hence the debate between the Classical and Balance schools of genetic variation has evolved into a debate about the forces maintaining genetic variation: the Neutralist-Selectionist controversy (or debate). Some loci are neutral; others under selection (more in lecture on Molecular Evolution). The debate is not over.

How is variation apportioned within and among populations? Hierarchy in patterns of variation: are populations either melanistic or normal; or do populations contain some of both; if so what are the frequencies in different populations? Is the variation within or among populations?

Spatial Patterns of Variation

Geographical isolates: discontinuous or disjunct distribution. Is there differentiation?Are there continuous distributions, clinal variation, abrupt discontinuities ("step" cline).