Notes for Understanding Evolution - Chapter 3

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General guide on these review questions here

Chapter 3: HeritableVariation


a) Explain Mendel's observations in terms of the modern terminology of genes and alternative alleles.
b) Understand the primary consequence of meiosis.
c) Read through the notes below and summarize how the basic relationship between genotypes and phenotypes can be understood in terms of: i) simple dominance vs. incomplete dominance vs. codominant expression pattern at a given gene locus; ii) the potential for a trait to be determined by multiple gene loci.
d) Read through the notes below and summarize how sex linkage can alter the more normal distribution of genotypes and phenotypes expected with autosomal linkage.
e) Understand the cause and consequences of linkage and crossing over.


Featured Scientist: Gregor Mendel

source of image

Links: 1 - 2 - 3 - 4

I. Mendel's Principle of Segregation

RQ3.1: Give an example of the expected consequence of Mendel's principle of segregation.

RQ3.2: Explain, in words, what it means that an allele is recessive.

II. Application of Mendelian Principles

RQ3.3: How likely is it that two heterozygous individuals together produce four offspring that are all homozygous recessive?

III. Chromosomal Basis of Heredity

RQ3.4: Describe what a human karyotype looks like.

IV. Mitosis and Meiosis

RQ3.5: What is the primary consequence of meiosis in diploid organisms?

V. Mendel and the Chromosomal Theory of Heredity

RQ3.6: Describe how Walter Sutton extended Mendel's conclusions about heridity.

VI. Mendel's Principle of Independent Assortment

RQ3.7: Describe the expected proportion of offspring from one parent heterozygous for two loci (e.g., NnGg, where N and G are each the dominant of two alleles for different gene loci on different autosomal chromosomes) crossed with another parent who has the genotype NNGg.

VII. Three or More Gene Pairs

RQ3.8:What is the probability that a given offspring from parents with the genotypes AABbCC x AaBbCc will have the genotype AaBBCc?

VIII. Significance of Genetic Recombination

RQ3.9: What is the chance of recovering an individual that is homozygous dominant for all of five independently assorting heterozygous pairs involved in a cross? (AaBbCcDdEe x AaBbCcDdEe) (Challenge: What is the general exponential form of the answer to the same question except with 22 independently assorting heterozygous pairs?)

IX. Linkage and Crossing Over

RQ3.10: Why does linkage between loci tend to decrease the amount of variability among offspring compared to the case where loci are unlinked?

RQ3.11: How is the concept of crossing over related to linkage?

Notes for Lecture 2/11/03 Prof. Eernisse, CSUF Biol. 404

Genetics - the science of inheritance

How are things inherited?

Can't separate genetic studies from the facts of sexual reproduction

Think of an egg or sperm as an information carrier

Put two gametes, one egg and one sperm, together, you get a zygote

A zygote grows up into an adult and makes its own gametes

Think of an organism as a collection of characteristics or traits

Some traits are observable, like hair or eye color

Others are cellular or biochemical traits, like blood type or the possession of certain kinds of digestive enzymes

Behavioral traits can even be inherited, for example, a bird song.

Some birds can sing the characteristic song for their species without ever hearing it before.

Some traits can be extremely variable, for example, skin color

Other traits, such as whether or not you have hemoglobin molecules show no variation, at least in surviving animals. If you don't have it you die at an early embryonic stage.

What determines whether you will have, say, black hair

biochemical: If you have an enzyme specific for the production of black pigment; no pigment, no hair color.

genetic: Enzymes are proteins; information on DNA molecules codes for the particular proteins. DNA is in the chromosomes.The info needed to produce the enzymes is in the chromosomes.

A typical (diploid) organism has pairs of chromosomes; for each pair, one that came from the sperm and one that came from the egg.

trait - characteristic common to all members of a species

variations (or states) - forms that a trait may take


trait of pea plant = height
variations (characters) = tall or short

gene - sequence of DNA on a chromosome pair that codes for production of a trait

alleles - alternate forms of gene

gene pair - symbolized as pair of letters, such as 'AA'

alternate alleles - 'A' or 'a'

homozygous pair of alleles - both the same, as in 'AA' or 'aa'

heterozygous pair of alleles - both different, as in 'Aa'

A variation is dominant when produced by a single allele, no matter what the partner allele is.

'AA' or 'Aa' both produce the same variation.

A variation is recessive if it can be produced only by a homozygous pair of alleles ('aa' ).

Phenotype - term that describes trait and its variation

Example: tall pea plants

Genotype - term for the paired alleles that produce a phenotype

Simple dominant

Phenotypic variation 1: dominant variation produced by two genotypes (AA or Aa)

Phenotypic variation 2: recessive variation produced by one genotype (aa)


Tall peas (TT or Tt)
Short peas (tt)

Outline of following notes:

1) Inheritance pattern problems (basic relationship between genotypes and phenotypes)

simple dominance vs. incomplete dominance

trait determined by multiple alleles

2) Modifier problems

For a given inheritance pattern, how do modifiers alter the distribution of genotypes and phenotypes?

Examples of modifiers:

autosomal linkage (certain alleles for two or more genes are always on
the same or opposing chromosomes)

sex linkage (e.g., humans: alleles found on the "X" or sex-determining chromosomes)

1) Inheritance patterns

A. Simple dominant

Phenotypic variation 1: dominant variation produced by two genotypes (AA or Aa)

Phenotypic variation 2: recessive variation produced by one genotype (aa)


Tall peas (TT or Tt)
Short peas (tt)

Simple Dominant Inheritance Pattern Cross Rules

Remember: AA or Aa genotypes produce one variation aa genotype produces another variation

One variation x Same variation

A. AA x AA = AA
B. AA x Aa = AA + Aa
C. aa x aa = aa

D. Aa x Aa = AA + Aa + aa

One variation x Other variation

E. AA x aa = Aa

F. Aa x aa = Aa + aa Note that A, B, and C all yield one variation, so that it would be hard to know which genotypes were crossed.

Cross D is especially powerful. We know that we have crossed two heterozygotes.

If we make lots of crosses, we should get approximately a 3:1 ratio for D.

Can you see why? This is where a Punnett square comes in handy.

Cross E and F are both crosses of different variations and both yield different results.

Mendel's pea examples are all examples of simple dominant inheritance.

B. Another kind of inheritance is "Incomplete Dominance" where a heterozygote
has a phenotype intermediate between each homozygote phenotype. (See below for an
example of the similar but not equivalent "codominance" expression pattern.)

Example of incomplete dominance:

Morning Glory flower color

Genotype RR has a red phenotype
Genotype WW has a white phenotype
A heterozygote resulting from a RR x WW cross (RW) has a pink phenotype

Some would use "rr" instead of "WW" but we would be talking about
the same thing. I think that using "W" instead of "r" for the "white"
allele type emphasizes that neither "R" or "W" is dominant.

As we did for the case of simple dominance, here are the incomplete
dominance pattern cross rules:

Remember: RR,RW, and WW all produce different variations

      One variation        x           Same variation

G.       RR             x                RR      = RR
H.       WW            x               WW      = WW
I.        RW            x               RW      = RR + RW + WW

      One variation        x           Other variation

J.         RR            x               WW      = RW
K.        RR            x               RW      = RR + RW

L.       WW            x               RW      = WW + RW

Notice that you could determine the genotypes crossed depending on
the results observed. For this reason, incomplete dominance is even
simpler than simple dominance. There is a one-to-one correspondence
between genotypes and phenotypes.

C. Another type of inheritance pattern is multiple alleles.

An example is human blood types (ABO blood typing)

four variations: A, B, AB, or O

three alleles determine blood type, I(A), I(B), and i
(or A, B, and O, where A and B are dominant to O)

AA = variation 1
BB = variation 2
OO = variation 3
AB = variation 4 (example of codominance*)
AO = variation 1 (simple dominance)
BO = variation 2 (simple dominance)

The multiple alleles case is just a mixture of the previous two cases.

*Codominance is very similar to incomplete dominance but not equivalent. In codominance expression, each allele expresses its phenotype, similar to the expression seen in the homozygote of each alternative allele. In incomplete dominance expression there is a blending of these two phenotypes to produce a third phenotype which differs from either, as in red x white = pink.

D. Polygenic trait is one determined my multiple gene pairs, acting together.
There are generally a large number of variations possible.

An example is fingerprint patterns in humans

2) Modifiers

A. X-linkage (humans)

22 of our chromosome pairs are autosomes

1 pair are the sex chromosomes

Sex chromosomes are different from autosomes because they are unmatched.
In humans, an X chromosome is much larger than the Y chromosome.

Sex chromosomes determine the sex of a progeny:

A human female is XX
A human male is XY

A human male as one X chromosome from mom, but dad contributes a Y chromosome.

A human female got an X chromosome from mom and another X chromosome from dad.

Sex chromosomes also have genes that produce other various traits.

A female has inheritance patterns that follow the previous rules, depending
on whether combinations of alleles follow simple dominant or incomplete
dominance patterns.

A male may only have a single allele, because the corresponding allele from
the Y chromosome is absent. If so, he is "hemizygous" for that trait.

Red-green color blindness is an example of a sex-linked trait.

C is dominant to c

Genotype                  Phenotype

X(C)X(C)              Non-colorblind female
X(C)X(c)              Non-colorblind female
X(c)X(c)              Colorblind female
X(C)Y                 Non-colorblind male
X(c)Y                 Colorblind male

Notice that a colorblind male can blame his mom.
If his mom is not colorblind, then she is heterozygous.
If his mom is colorblind, then her father was as well.
Was her mom?

B) Another kind of linkage occurs when separate genes are on the same chromosome.

The following example is from Punnett's research on sweet peas (Yes, the same Reginald Crundall Punnett for whom the Punnett Square is named)

Punnett (and William Bateson, another earlier proponent of Mendelism) worked with "Painted Lady" and "Duke of Westminster" varieties of sweet peas.

                  Trait 1 (color)     Trait 2 (Standard)
Painted Lady:        red (b)             erect (E)
Duke of Westminster: purple (B)          hooded (e)

Punnett Square (Punnett called this a "chessboard" square; it was renamed in his honor in 1950's)

F(1)     Eb

eB      EeBb

could also be written:

F(1)      Eb
eB        eB

F(2) cross of EeBb hybrids

          EB     Eb    eB     eb

          EB     Eb    eB     eb
EB        EB     EB    EB     EB

          EB     Eb    eB     eb
Eb        Eb     Eb    Eb     Eb

          EB     Eb    eB     eb
eB        eB     eB    eB     eB

          EB     Eb    eB     eb
eb        eb     eb    eb     eb

With some thought, you should be able to predict that (if there were
no linkage) the F(2) offspring should produce the following:

9:3:3:1 ratio of Erect Purple:Erect Red:Hooded Purple:Hooded Red

Instead, Punnett observed:

         Eb     eB

         Eb     eB
Eb       Eb     Eb

         Eb     eB
eB       eB     eB

1:2:1 ratio of Erect Red:Erect Purple:Hooded Purple

The explanation is that these two traits are linked.
That means that they are NOT independently assorting during meiosis 1

In this case, the two traits are always on opposite chromosomes:
they are said to be "in repulsion"

In other cases, they might always be on the same chromosome:
they would be "in coupling"

Two other concepts that you should be aware of:

Pleiotropy - a single allele has more than one distinguishable effect (e.g., same allele gives Siamese cats their distinctive coloration and their characteristic crossed eyes)

Epistasis - one gene allele influences the expression of another (e.g., albino mice)

Check out Online Mendelian Inheritance in [Humans]

Also see Terms to Know for Mendelian Genetics

Study Problems (not required to turn in):

    Links to Other Study Problems: 1 - 2 - 3

1) How many expected F(1) phenotypes will there be and what ratio will they be in?

a) a gene pair with alternate alleles, "B" and "b", with simple dominance, cross a BB male with a bb female

b) a gene pair with alternate alleles, "R" and "W", with incomplete dominance, cross a "RR" individual with a "WW" individual

2) Concerning multiple allele and polygenic inheritance, what is the difference between each of these and the simpler systems that are discussed above (such as Mendel's peas)?

3) For crosses for autosomal loci (i.e., not on sex chromosomes), what would be the F(2) result of

BbRrWw x bbrrww = ?:

a) with no linkage (all three genes on different chromosomes)
b) with complete linkage (all three genes on the same chromosome).

4) What does it mean for a trait to be or not to be "sex-linked"? How will cross results differ, depending on the sex of a progeny?

More notes I might get to:


Early ideas about reproduction

1) Aristotle (400 B.C.): male contributed "spirit" and female contributed "matter"
2) Mechanical Philosophy (17th century): Nature viewed like an intricate clock created by God
3) Preformation (18th century): Perfect homonucleus inhabited egg, inside that was another, etc. (think Russian dolls)

Preformation was viewed as the unfolding of preexisting structure

Eve had the encapsulated human history within her ovaries (the ovists)

Male Variation (spermaticists): same but homonucleus inside sperm

Complexity cannot arise from formless raw material

There must be "something" in the egg that regulates development

Preformationists thought that "something" was preformed parts

Now we know that it is encoded instructions in DNA

4) Epigeneticists (18th century opponents of preformationists):

Argued that visual appearance of development must be respected as the literal truth

Developing egg adds and changes structures, it does not "unfold"

Asked ovists why males existed at all

Asked spermaticists why thousands of sperm per ejaculation were needed

Concluded that both males and females contributed to offspring

5) Blending inheritance (19th century): hereditary material was blended

Rejection of preformation, but no satisfactory alternative

Animal and plant breeding was extensive, showed that both parents were important

6) Mendel (1866) and de Vries (1900): showed experimentally that blending of hereditary materials did not occur

Mendel did extensive experiments with the garden pea, Pisum, but the significance of his publications was not realized in his lifetime

Mendel's First Law: The Law of Segregation

Mendel identified two alternative forms for several traits

He crossed purebred lines (monohybrid crosses) to yield hybrids

Mendel concluded that each trait studied had a pair of factors

If the two factors were the same, they were called homozygous

If different, they were called heterozygous

One alternative form of a trait was the dominant trait

The other alterntive was the recessive trait

F(1) hybrids received "hereditary" factors from each of the parents but dominant trait masked the recessive trait, leading to a 3:1 observed ratio

F(2) generation revealed that the pea plants with the dominant trait were one third homozygous and two thirds heterozygous

The Punnett Square is used to simplify calculation of ratios Mendel's Second Law: Law of Independent Assortment

Mendel did experiments looking at two traits in the same cross (dihybrid crosses)

This revealed that the factors responsible for two (or more) traits are inherited independently

This can be understood once the process of meiosis is understood

These notes are modified from the following sources:

Collins, Angelo, and James H. Stewart. 1989. The knowledge structure of Mendelian genetics. Amer. Biol. Teacher 51(3): 143-149.

Davis, Lawrence C. 1993. Origin of the Punnett Square. Amer. Biol. Teacher 55(4): 209-212.

Huckabee, Colleen J. 1989. Influences on Mendel. Amer. Biol. Teacher 51(2): 84-88.

Other recommended lecture notes on Mendelian Genetics: 1 - 2


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This page created 8/16/01 © D.J. Eernisse, Last Modified 2/8/03, Links Last Completely Checked 1/30/03