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:
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 ->
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<Aabb=aaBb<AaBb=AAbb=aaBB<AABb=AaBB<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
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).