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NCEA | Walkthrough GuideLevel 2BIOLOGY

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GENETIC VARIATION AND CHANGE

Introduction 3

Evolution and Gene Pools 4

Evolution 4Defining a Population 6Genes and Alleles: The Gene Pool 6

Sources of Variation 7

Sexual Reproduction 8Crossing Over 10Independent Assortment 11Summary 13Mutations 14

Monohybrid Inheritance 16

Dominance 16Genotype and Phenotype Ratios 17Co-dominance 18Incomplete Dominance 19Lethal Alleles 20Multiple Alleles 22

Dihybrid Inheritance 23

Punnett Squares 24Linked Genes 26Test Cross 28

Factors Causing Change in a Gene Pool 29

Genetic Diversity 30Natural Selection 31Genetic Drift 34Migration 35Founder Effect 36Bottleneck Effect 37Putting It All Together 39

Key Terms 40

Level 2 Biology | Genetic Variation and Change

Level 2 Biology - Genetic Variation and Change | © Inspiration Education Limited 2017. All rights reserved.3

INTRODUCTIONNo doubt you’ve heard the word ‘evolution’ being thrown about all over the place (Charles Darwin and humans evolving from apes and all that) but what is it actually all about? Well, in this topic we'll break all of those big concepts down to an idea you may already be familiar with - the humble gene.

This topic takes differences occuring on a DNA or cellular level, and looks at them from the level of a population. Instead of looking at how individuals can differ, we’re interested in how we can get different populations looking different to each other over time.

What will you learn in this walkthrough guide?

First, we’re going to start big, with the idea of evolution and “gene pools”. Gene pools tell us all about the alleles and genetic variation present in a population - and how they can change over time.

Next, we’ll explore where all the variation we see around us comes from – why do you look different from your family when you share such similar DNA?

Carrying on from the concepts you would have learnt last year in genetics, we’ll look at the relationship between different alleles. We'll be expanding on the dominant-recessive relationship you would have learnt about last year. We’ll then look at all these ideas in the context of dihybrid inheritance: two traits at a time.

Finally, we’ll look at the idea that changing allele frequencies are necessary for evolution to occur. There’s a few ways this can be done: mutations, genetic drift, migration, founder effect and bottleneck effect.

We’ll bring it all together at the end and summarise how small differences in DNA can result in macro changes to how populations look and act.

A word on exam strategy.

Genetics is generally a pretty jargon intensive topic; you need to know some pretty big words! The key is to push through that phase of “OMG, are they even speaking English?” and try and break down each word one-by-one.

Here at StudyTime, we’re pretty much GCs (good citizens), so to help you out, we’ve made this guide in plain English as much as we can. We’ve also included a glossary for some of the key terms that you’ll need to master for your exam.

4 Level 2 Biology - Genetic Variation and Change | © Inspiration Education Limited 2017. All rights reserved.


If learning key words first off scares you (or bores you), then focus on understanding the concepts the first time around, and then memorise the definitions so you can explain it the way the NCEA wants you to.

In fact, in this guide, we focus on helping you to understand the concepts first. We use examples and analogies to help you understand Biology in a way that is fun, and makes sense in the real world.

However, the language we use isn’t always something you can directly write in your exam! When this is the case, we offer a more scientific definition or explanation (in a handy blue box) underneath. These boxes are trickier to understand on your first read through, but contain language you are allowed to write in your exam. Look out for them to make sure you stay on target!

EVOLUTION AND GENE POOLSLet’s skip the pleasantries and get straight into it – I’m sure you’re dying to know what you need to cram for the exam:

Understand why biologists worship evolution and learn to appreciate its wondrous powers. Evolution is all about populations rather than the individual, so it might help to actually define what a population is. The gene pool: what is it and why it is so important to evolution

Evolution

In Level One, you were introduced to genetics. You learnt all about what is happening on the micro level inside cells, and how DNA is organised into genes - which dictate how an organism looks and acts.

In this standard, we’re not so interested in looking at what DNA is doing inside cells, or even in looking at individual organisms. Instead, we need to broaden our view of genetics to think about what is happening to whole populations of organisms. That’s right - we’re going big!

We’ll start our journey by coming to terms with this simple fact:


Level 2 Biology | Gene ExpressionLevel 2 Biology | Genetic Variation and Change

An individual organism cannot evolve

This is because evolution involves an actual change to DNA.

DNA is the genetic information locked away deep inside your cells. Because it is locked deeply away, it is very difficult to change.

Even when an individual gets used to new situations (like starting NCEA last year for example) they haven’t actually evolved. Just because you’ve done countless internals and externals by now, it doesn’t mean your genes have changed.

Even after new experiences, an individual’s alleles remain unchanged.

Evolution is the large scale change in the genetic make-up of populations over generations. It is due to gradual and cumulative changes in allele frequencies amongst the members of the population.

Therefore, evolution requires reproduction and new offspring to be created. While an individual’s alleles will remain unchanged throughout its life, the allele frequencies within a population will change over time.

Allele frequency refers to the relative number of each allele present within a population.

Population Change Over Time

Generation 1 Generation 2 Generation 3

STOP AND CHECK:

Turn your book over and see if you can remember:

The definition of evolution. Why an individual organism cannot evolve – hint: think of the definition.

Try to explain it in your own words.



Defining a Population

You are probably very familiar with the word ‘population’.

We talk about the populations of cities and countries all the time

When we talk about the population of people in New Zealand, we are referring to every human being who lives in New Zealand.

Similarly, we could talk about the population of sheep in New Zealand (which outnumbers the human population by 6 to 1 and therefore makes people from overseas laugh).

The biological definition of population is pretty much the same as the day-to-day use of the word

A biological population is a group of the same species that lives in the same area and breeds with each other.

STOP AND CHECK:


The definition of a population in biology.


Genes and Alleles: The Gene Pool

Just like in Level 1 Genetics and Level 2 Gene Expression, the words ‘gene’ and ‘allele’ are going to be very important in this topic. No doubt you’ve got the definitions on some flashcards from last year (although they may well have vanished into oblivion by now).

Gene: A sequence of bases (in DNA) that codes for a particular trait (e.g. hair colour).

Allele: An alternative form of a gene (e.g. blonde hair, brown hair, black hair).

Within a population, different individuals have different combinations of alleles

These combinations depend on what they inherited from their parents.

Imagine that we could somehow write down a list of every single gene in every person



in New Zealand and count up how many of each type of allele is present in the population. We haven’t actually done this, but the concept is really useful.

Biologists have a name for the total set of alleles that are present within a population: the gene pool. The alleles present in the gene pool are all of the alleles that could possibly be passed onto the next generation.

A gene pool describes the number and nature of all of the alleles available in an interbreeding population.

Gene Pool

bb b

b

bb

b

BB

B

STOP AND CHECK:


The difference between a gene and an allele. The definition of a gene pool.

Try explain it in your own words.

Quick Questions

What is the link between gene pools, or allele frequencies, and evolution?

SOURCES OF VARIATIONThe gene pools of some populations have very little variation

This is the case if most individuals in the population have exactly the same alleles.

However, other populations have lots of variety in their gene pools

This is because they have more alternative forms of their genes – more alleles.

Just look at the human population. Every individual is different (apart from identical twins), because they have different combinations of alleles.

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Saeran Maniparathy



So, our gene pool has quite a lot of variation. This external is all about the processes that help make this variation happen.

So, where does genetic variation come from?

What happens in sexual reproduction that makes sure that everybody is unique? • We’ll need to cover: crossing-over and independent assortment – two

important processes in meiosis.

Time to revisit mutations: what are their effects on the DNA and how do they increase genetic diversity?

Sexual Reproduction

Remember the differences between asexual and sexual reproduction? While asexual reproduction involves one parent passing all of their DNA on to the next generation, sexual reproduction involves two separate parents - each with their own set of DNA.

This means that offspring from sexual reproduction contain a combination of alleles from each parent. This combination is entirely due to chance, and differs in every child - even ones from the same parents.

Therefore, sexual reproduction creates genetic variation by shuffling alleles into new combinations

Sexual reproduction involves one gamete (sex cell) from each of two individuals combining to form a new individual. The new individual is therefore not identical to either parent.

In humans, these gametes are the sperm and the egg.

Each gamete contains half a set of chromosomes, so that when the gametes come together, a cell with full set of chromosomes is made. We call a cell with a full set of chromosomes diploid.

This new cell is the first cell of a new individual.

+

Asexual Reproduction:

Sexual Reproduction:



Gametes are made by a process called meiosis

This is different to mitosis, which you may have learned about before.

In mitosis, a cell divides to create two identical copies of itself. Essentially, it clones itself.

However, in meiosis, a cell divides to create four cells which are different from each other and from the original cell. Each of the four cells is a gamete and so only has half a set of chromosomes. We call a cell with half a set of chromosomes haploid.

Let’s go through the process of meiosis

There are three steps that you need to know really well, because they shuffle allele combinations around to create variation, just like shuffling a pack of cards.

Look out for:

1. Crossing over 2. Independent assortment 3. Segregation

Before meiosis occurs, the DNA in the cell replicates

This is so that there are two identical copies of every chromosome. The two copies are called sister chromatids and after they are copied, they stick around each other, bound together by a special cellular ‘glue’.

A chromatid is one copy of replicated DNA. It is usually found attached to its identical 'sister chromatid', until it is separated during meiosis or mitosis.

The copies of the chromosomes then line up along the centre of the cell

Cell after DNAReplication

Copies of chromosomes lined up



When this happens, crossing over also occurs between the chromosomes.

Before we get too deep, let’s pause here and have a closer look at crossing over in the next section.

STOP AND CHECK:


The purpose of meiosis and why it is important in sexual reproduction. What needs to happen before Meiosis can occur.


Crossing Over

So, we’ve paused meiosis with our replicated sister chromatids lined up in the centre of the cell. Before we go any further in our journey, let’s make a couple of things clear.

In a normal human cell, there are 23 pairs of chromosomes

Each pair has one chromosome inherited from the mother (maternal) and one chromosome inherited from the father (paternal).

These chromosomes are called homologous because they have the same series of genes on them, but may have different alleles coding for each gene (that’s why your Mum looks different to your Dad).

Homologous chromosomes carry the same genes at the same locations.

When the cell replicates its DNA, it copies the maternal chromosome and the paternal chromosome in each pair

This means that there are two identical copies of every maternal chromosome and two copies of every paternal chromosome. The identical copies (the sister chromatids) stick together.

As we said before, the chromosomes line up along the centre of the cell at the start of meiosis. The two copies of the maternal chromosome line up side-by-side with the two copies of the paternal chromosome.

Crossing over is the swapping of sections of DNA between homologous chromosomes.



In other words, the two copies of the maternal chromosome swap some sections of DNA with the two copies of the paternal chromosome. This jumbles up the alleles, so that the chromosomes end up with different combinations of alleles to what they had before.

As a result, the sister chromatids are no longer identical, because they now have different combinations of maternal and paternal alleles.

Crossing over is one of the steps of meiosis that creates variation.

After crossing over, the homologous chromosomes are pulled to opposite poles of the cell.

STOP AND CHECK:


What happens during crossing over. Which chromosomes cross over? How crossing over increases the genetic variation.


Independent Assortment

Now, let’s talk about independent assortment.

When the chromosomes line up along the centre of the cell, they do so randomly

So, at the first chromosomal location, the maternal chromosome (made up of two sister chromatids) may line up on the left of the centre and the paternal chromosome (made up of two sister chromatids) may lean towards the right. Meanwhile, at the second location, they may be the other way around.



Independent assortment refers to the fact that, the way each pair of maternal and paternal chromosomes orients itself does not have an effect on how the next pair arranges. This creates a large amount of possibilities regarding the inheritance of maternal and paternal DNA.

When the homologous chromosomes are pulled to opposite poles of the cell, all of the chromosomes on the left move to the left (and vice versa). Therefore, it is down to chance how many paternal chromosomes go to one end and how many go to the other end.

It’s the same with the maternal chromosomes.

This creates variation, because it mixes the maternal and paternal chromosomes into new combinations:

Possibility 1 Possibility 2

Once the cell has been split down the middle, creating non-identical cells:

1. The chromosomes in each of these two cells line up along the middle of the cell again.

2. The two sister chromatids from each chromosome are pulled to opposite ends of the cell, creating a second split, and resulting in four daughter cells.

This is segregation

The sister chromatids split up, so each of the four cells gets only one allele for each trait.

Segregation refers to way maternal and paternal chromatids are randomly split into each daughter cell. Due to crossing over, sister chromatids are not identical. Therefore, the segregation of the sister chromatids means that it is down to chance which gamete gets which alleles.

Meiosis



Finally, the cell divides, creating four unique cells with half the normal set of chromosomes.

Why is it important to understand all of this?

Well, crossing over, independent assortment and segregation mean that each of the four gametes have a different combination of alleles. So, the parent is not just passing on an exact copy of their chromosomes to their offspring.

In sexual reproduction, two gametes fuse together, one from each parent. Because of meiosis, all of the gametes each parent makes have different combinations of alleles and it is random which two gametes happen to come together to make a new individual.

As a result, no matter how many offspring two individuals have, every single one will be different, because of the variation introduced by meiosis.

STOP AND CHECK:


The steps of meiosis from crossing over onwards. What happens during independent assortment in meiosis. How independent assortment increases the genetic variation in the offspring.


Summary

That’s a lot of information to take in, so here’s a summary:

Meiosis: Cell division to create four unique gametes, each with half a set of chromosomes.



Homologous chromosomes: Pairs of maternal and paternal chromosomes (same chromosomes, but different alleles).

Sister chromatids: Identical copies of chromosomes made by DNA replication.

Crossing over: Sections of DNA are swapped between homologous chromosomes. This results in the chromosomes having new combinations of alleles variation.

Independent assortment: When homologous chromosomes line up at the centre of the cell, they do so independently of all of the other pairs. This means that it is random which combination of chromosomes ends up in which cell variation.

Segregation: The chromatids that the parent has are split up randomly, so that each gamete ends up a single allele for each trait. Which alleles it ends up with are down to chance variation.

Figuring out what’s going on in meiosis can be hard to get your head around. Try drawing out a cell with the maternal chromosomes in one colour and the paternal chromosomes in another colour. Now line the pairs up along the middle of the cell. Make sure you understand the difference between the homologous chromosomes and the sister chromatids on your diagram. See whether you can draw pictures showing crossing over, independent assortment and segregation.

Mutations

Mutation is the only process that can create new alleles.

That’s right. Even though we just told you all about the sources of variation in meiosis, it is important to remember that processes such as crossing over, independent assortment and segregation only shuffle around the alleles - they don’t create new ones! Mutations actually create new alleles. This is because:

Mutations are changes in the base sequence of DNA.

This can result in the wrong protein being made from the DNA instructions. If the wrong protein is made, it can often lead to disease, and cause harm - but sometimes, mutations can be beneficial.

Before we get too ahead of ourselves though, let’s have a think back to level one and remember the difference between gametic and somatic cells.

Sex cells are gametic cells, non-sex cells are somatic cells

Mutations can either be somatic, occurring in somatic/body cells, or gametic, occurring in gametic/sex cells.



Mutations in somatic cells aren’t passed onto the next generations, but mutations in gametic cells are

When a mutation occurs in a somatic cell it will only affect cells in that area. This means that they only affect the individual in which the mutation occurred and can’t be passed on. A somatic cell is never used to pass DNA onto a baby, so therefore, any changes to their DNA do not end up in the offspring and are not inherited.

Gametic mutations occur in the cells that are about to become the gametes: the egg or the sperm. Because the gametes are involved in reproduction and create the offspring, gametic mutations will be passed down to the offspring.

Since the offspring begin as a single cell, ALL cells of the offspring will have the same genetics. Therefore, gametic mutations will be present in every single somatic cell in the offspring as well.

Therefore, if an individual has a mutation occurring on a gametic cell, and the individual with the mutation is able to reproduce, then a new allele has been added to the gene pool.

This adds variation to the gene pool, because there are more alleles that could potentially be passed on.

If the individual is unable to reproduce, or the mutation occurs on a somatic cell, then there is no way that the new allele can be passed on, so we don’t include it in the gene pool.

STOP AND CHECK:


The definition of a mutation. How mutations affect the gene pool of a population.

Quick Questions

How are new alleles produced in the gene pool? Why is it basically impossible for two siblings to have the exact same DNA? What is the difference between how mutations and meiosis increase the genetic

diversity in a population? What is the source of genetic diversity in populations which reproduce asexually

through mitosis?

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MONOHYBRID INHERITANCEBack in Level 1 Genetics, you learned how to use Punnett Squares. Punnett Squares help us to see the probability of different combinations of alleles being inherited when two parents have offspring. In Level 2, you’ll use those same principles and apply them to different forms of allele relationships.

Here's what we'll be doing in the next section:

Revisiting the dominant-recessive relationship between alleles. Crunching those numbers and getting some genotype and phenotype ratios out of the Punnett Squares. Introducing co-dominance and incomplete dominance. When we said that one allele is dominant and one is recessive, it’s not that we lied, it’s just that we didn’t mention the whole truth… Lethal alleles: why they aren’t fun and why they make calculating genotype and phenotype ratios that extra bit annoying. Multiple alleles: just when you thought you had a handle on two alleles and their relationships, let’s throw in some more alleles for particular traits.

Dominance

Let’s throw it back to level one science with an example to make sure you understand the concept of dominance:

A classic example to understand dominance is eye colour

The allele for brown eyes is dominant, meaning that it will always be expressed in the phenotype if it is present.

The allele for blue eyes is recessive, meaning that it will only be expressed if there is no dominant allele to mask it.

Knowing this, we can assign each allele its own letter:

We give the dominant brown eye allele a capital letter (B) and the recessive blue eye allele a lower-case letter (b).

Remember from level one that the genotype of an organism describes the alleles that it has, and the phenotype calculates the physical result of the genotype.



Using these definitions, and our knowledge of dominance, we can identify genotypes from phenotypes:

A brown-eyed individual might be homozygous dominant (BB) or heterozygous (Bb).

A blue-eyed individual can only be homozygous recessive (bb).

STOP AND CHECK:


The 3 main genotypes. Which phenotype – dominant or recessive – will each genotype produce?

The difference between a dominant and recessive allele. The conventions used for representing a dominant and recessive allele.


Genotype and Phenotype Ratios

When two individuals reproduce, we can represent the gametes involved using a punnett square. We can use this punnett square to calculate genotype and phenotype ratio, and answer questions such as:

If two heterozygous individuals mate, what will be the phenotypes of their offspring?

B

BB

Bb

B

b

b

Bb

bb

From the completed Punnett Square, we can see that when two individuals who are heterozygous for eye colour have children, there is a 75% probability that the phenotype of the offspring will be brown eyes (BB or Bb) and a 25% probability that the phenotype of the offspring will be blue-eyed (bb).

The genotypic ratio is 1 BB : 2 Bb : 1 bb.

The phenotypic ratio is 3 brown eyes : 1 blue eyes.



Remember that Punnett Squares only show probabilities, not what will definitely happen

Hopefully that was all revision for you. In Level 2, we look at what happens when we don’t have the nice dominant-recessive relationship that you are used to… No, don’t groan! Surely you must be bored of Level 1 punnet squares by now. Things are about to get far more interesting.

STOP AND CHECK:

What are the possible genotypes, phenotypes and their ratios for a cross between:

A homozygous dominant brown-eyed (BB) individual and a heterozygous brown-eyed (Bb) individual, where blue eye colour is a recessive trait.

Two heterozygous brown-haired (Hh) individuals, where blonde hair is a recessive trait.

Why do the true genotype and phenotype ratios not always match the predicted ratios using punnet squares?

Co-dominance

If you think you’ve got dominance all figured out, it’s time to think again. In fact:

In some situations, both possible alleles are dominant and both are expressed in the phenotype

Co-dominance refers to a situation where two alleles are equally dominant, so the physical expression of each allele can be seen in the individual.

A great example of this in humans is in the case of blood types.

People with blood type A are homozygous AA. People with blood type B are homozygous BB. In a heterozygous AB individual, both A and B are co-dominant, so both the A proteins and the B proteins are expressed in the person’s blood.

This means that there are three possible genotypes: AA, BB and AB as well as three possible phenotypes: blood types A, B and AB.

Compare this to the dominant-recessive eye colour example

In that relationship, there are still three possible genotypes: BB, bb and Bb, but only two possible phenotypes: brown or blue eyes.



So, if two people with blood type AB have children, for each child there is a 50% chance that they will have blood type AB, a 25% chance that they will have blood type AA and a 25% chance that they will have blood type BB.

Confirming this with a punnett square, we would get:

A

AA

AB

A

B

B

AB

BB

Genotypic ratio: 1 AA : 2 AB : 1 BB.

Phenotypic ratio: 1 A : 2 AB : 1 B.

In the animal kingdom, co-dominance can present itself in more visible ways, such as speckled fur when both fur colours are expressed.

STOP AND CHECK:


What is the difference between the two alleles in a full dominant-recessive relationship versus the two alleles in a co-dominant relationship?


Incomplete Dominance

In co-dominance, both alleles are dominant and so both are expressed.

But in incomplete dominance, neither allele is completely dominant

In a heterozygote, where both alleles are present, the result is a blending of the two phenotypes to create a new, distinct phenotype.

Incomplete dominance refers to the inability for any allele to mask another allele. This results in a blended phenotype.

For example, snapdragon flowers have two alleles for their petal colour

One allele (F) codes for a red colour phenotype while the other (f) codes for a white



colour phenotype. In a heterozygote snapdragon (Ff), the red and white phenotypes blend to create a pink colour phenotype.

If a red snapdragon is mated with a white snapdragon, then all of the offspring will always be pink (heterozygous).

F

Ff

Ff

f

F

F

Ff

Ff

If two pink snapdragons mate, then for each of the offspring they produce, there is a 25% chance of being red, a 50% chance of being pink and a 25% chance of being white.

F

FF

Ff

F

f

f

Ff

ff

Genotypic ratio: 1 FF : 2 Ff : 1 ff

Phenotypic ratio:

STOP AND CHECK:


What is the difference between the two alleles in a full dominant-recessive relationship versus the two alleles in an incomplete dominant-recessive relationship?


Lethal Alleles

This sounds like dangerous territory - and it is. These alleles are well named.



Some alleles are deadly when they are in particular genotypes, but not when they are in other genotypes

Lethal alleles are alleles which cause death when they are in their homozygous form, but allow carriers of the heterozygous genotype to survive.

An example of this phenomenon is sickle cell anaemia in humans

Red blood cells carry oxygen around the body. An essential part of red blood cells is haemoglobin.

The dominant haemoglobin allele (H) codes for normal haemoglobin, but there is a recessive allele (h) that codes for sickle-shaped haemoglobin. Sickle-shaped haemoglobin cannot carry oxygen properly, so it is a big problem.

People who are homozygous dominant (HH) have completely normal haemoglobin. People who are heterozygous (Hh) have some sickle-shaped haemoglobin, but enough normal haemoglobin to be able to survive. However, people who are homozygous recessive (hh) cannot survive, because they cannot get oxygen around their bodies.

So, if two heterozygous people (who are able to survive, but have a disease called sickle-cell anaemia) have children, the phenotypic ratio is different than might be expected.

H

HH

Hf

H

h

h

Hh

hh

Phenotypic ratio: 1 normal haemoglobin : 2 sickle-cell anaemia.

Any combination of sperm and egg that results in an hh genotype will not survive, so there is no third phenotype.



STOP AND CHECK:


The definition of a lethal allele. What happens to the genotype and phenotype ratios when there is a lethal allele.


Multiple Alleles

That title might cause another groan. Until now, we’ve only ever talked about traits that have just two possible alleles. This means that we’ve only had to deal with three possible genotypes at a time. But now we are going to have to break the news that…

…some traits actually have multiple different possible alleles

A multiple allele system refers to a gene which has more than two possible alelles.

But don’t fret. An individual will only ever have two of these alleles at a time (one from mum and one from dad), so it’s not as bad as it sounds.

We’ve already mentioned blood types in the section about co-dominance. There, we talked about blood types A, B and AB, but you might have been thinking, hang on, my blood type is O! Yes, O is the third allele for blood type.

So, if an individual can have any two alleles for blood type, what are the possible combinations?

The homozygous genotypes: AA, BB and OO or the heterozygous genotypes: AB, AO and BO. So just by adding in one extra allele, we’ve suddenly got six possible genotypes to deal with!

Examiners love to use this example, because there’s so much going on. A and B are dominant over O, but A and B are co-dominant with each other. To summarise, these are all the combinations we can get for blood type! Notice that whilst A and B are always expressed, O is only expressed in the homozygous recessive genotype.

AA – Blood type A. AB – Blood type AB.BB – Blood type B. AO – Blood type A.OO – Blood type O. BO – Blood type B.



Imagine how complicated it gets when there are more than 3 possible alleles! The trick is to take your time with these questions, and use all of the information given to you in the exam. If you understand the concepts of dominance, you’ll always have enough information to work out the answer!

STOP AND CHECK:


What is meant by the term, “multiple alleles”.


Quick Questions

Imagine there are two alleles: one allele for red hair colour and one allele for white colour. What phenotypes would you expect when the relationship between the two alleles is:

• Complete dominant• Incomplete dominant• Co-dominant

Achondroplasia, which causes dwarfism, is due to a mutated gene (F). With two copies of this defective allele (FF), the results are fatal. Heterozygotes (Ff) end up with achondroplasia and recessive homozygotes (ff) are unaffected by any condition. What is the genotype and phenotype ratio in the offspring after a cross between two heterozygotes?

DIHYBRID INHERITANCENow that you’ve got monohybrid inheritance figured out, why not tackle the next challenge with dihybrid inheritance? Rather than just looking at one trait, we’re looking at two traits at the same time!

In this section, we’re going to help you:

Understand how to draw a punnett square for dihybrid inheritance. Rather than the easy-peasy 2x2 table, try tackle a 4x4 punnett square. Learn about linked genes and the genotype/phenotype ratios that occur as a result.

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Punnett Squares

Up until now, we’ve been looking at monohybrid inheritance. This means we’ve been using punnett squares to figure out the probability of offspring having particular phenotypes for just one trait, like eye colour.

But what if we want to know the probability of offspring having brown eyes and blond hair?

Then we need to look at two traits at once.

That might sound horrifyingly complicated, but don’t worry! You’ll be making big Punnett squares that look really complicated, but actually work in exactly the same way as the ones you’re used to.

Dihybrid inheritance refers to the simultaneous inheritance of alleles for two different genes. Punnett squares which show dihybrid inheritance explore how likely alleles for different genes are to be inherited together.

Let’s say that we’ve got some pea plant seeds in front of us

One of their traits is their shape. There is a dominant allele for round seeds (R) and a recessive allele for wrinkled seeds (r).

One of their other traits is their colour. There is a dominant allele for yellow seeds (Y) and a recessive allele for green seeds (y).

If we pick up a round, yellow seed, its genotype could be RRYY, or RrYY, or RrYy, because R and Y are dominant. If we pick up a wrinkled, green seed, its genotype has to be rryy, because r and y are recessive.

So how do we draw a Punnett square for when two heterozygous pea plants (RrYy) are bred together (crossed)?

Remember that when we draw a normal punnett square, we think about the possible gametes that each parent might make.

If we’re looking at an individual who is heterozygous for eye colour (Bb), then we know that the two alleles will be segregated into different gametes during meiosis. So, some of the individual’s gametes will have the B allele and some will have the b allele.

The same thing happens with this dihybrid situation. The R and r alleles will be



segregated and the Y and y alleles will be segregated. So, each gamete will have one allele for seed shape (R or r) and one allele for seed colour (Y or y). The possible gametes are: RY, Ry, rY and ry.

We can put these into a Punnet square just like we usually do – except the Punnet square will be much bigger!

RYRy

rY

ry

RY Ry rY ry

Now we can go through and fill the other boxes in, to find out the possible genotypes of the offspring. Just do it exactly like you normally do.

Here’s a tip to make it look professional: write the R’s first and then the Y’s. Also, write any capital R’s before the little r’s and any capital Y’s before the little y’s.

RY RRYYRRYy

RrYY

RrYy

RRYy

RRyy

RrYy

Rryy

RrYY

RrYy

rrYY

rrYy

RrYy

Rryy

rrYy

rryy

Ry

rY

ry

RY Ry rY ry

Now let’s figure out the phenotypic ratio

Using a highlighter can be really useful here.

Let’s colour code all genotypes leading to a round, yellow phenotype in colour. The genotypes leading to a round, green phenotype can be in colour. All genotypes leading to a wrinkled, yellow phenotype can be colour and all genotypes leading to a wrinkled, green phenotype can be colour. (Yes, those last two colours aren’t very logical, but you’re only going to have so many highlighter colours, right?!) Now to put that highlighting plan into action…

RY RRYYRRYy

RYY

RrYy

RRYy

RRyy

RrYy

Rryy

RrYY

RrYy

rrYY

rrYy

RrYy

Rryy

rrYy

rryy

Ry

rY

ry

RY Ry rY ry



Brilliant, now we can write out the expected phenotypic ratio of the offspring:

9 round, yellow seeds : 3 round, green seeds : 3 wrinkled, yellow seeds : 1 wrinkled, green seed.

The poor old homozygous recessive genotype (rryy) doesn’t get much of a look in.

But remember, the Punnett square only shows the probabilities

So, it would be possible (just unlikely) for the two RrYy parents to produce offspring all with wrinkled, green seeds.

The fantastic news is, whenever you have to find the phenotypic ratio for a cross between two heterozygous parents, the phenotypic ratio will always be 9:3:3:1.

Definitely make sure to do the Punnett square anyway, but you can check that it gives you this ratio. Of course, combining homozygous parents will give you different answers - but we don’t have to worry about them too much.

Try doing a Punnet square for a cross between a RrYy individual and a rryy individual and you’ll see that the Punnett square doesn’t need to be quite so big.

STOP AND CHECK:

Determine the genotype and phenotype ratios for the following crosses involving seed shape and seed colour:

RRYY x RrYy RrYy x RRyy Rryy x rrYy rryy x RRYY

Linked Genes

Remember our old friend, crossing over? When the maternal and paternal homologous chromosomes line up during meiosis, sections of DNA get swapped between the homologous chromosomes. This means that the maternal chromosome ends up with some of the alleles that were originally on the paternal chromosome, and vice versa.



Imagine the seed shape and seed colour genes exist on the same chromosome

Seed Shape

Seed Colour

In an RrYy individual, one chromosome has the R allele and the Y allele and the other individual has the r allele and the y allele.

In the Punnett square, we wrote that one gamete has chromosome RY and one has chromosome ry – that makes sense.

But we also wrote that one has chromosome Ry and another has chromosome rY. How is this possible? Because of crossing over, alleles can be been switched around! Crossing over creates variation, which is why we need that enormous Punnett square!

But some genes are linked.

We don’t mean that they’re physically tied together, but they are so close together on a chromosome that if one of them is switched to the homologous chromosome in crossing over, it’s likely that the other one will go too. This means that they are unlikely to be separated by crossing over.

Linked genes are genes which are highly likely to cross over together during meiosis.

In the RrYy pea plant example discussed above, if the alleles couldn’t be separated by crossing over, then the only possible gametes would be RY or ry. This is because the R and Y alleles and the r and y alleles are so close together that they are unable to separate from each other when crossing over happens. Ry and rY are therefore no longer possible combinations. This would shrink the Punnett square by quite a lot:

RY

RRYY

RrYy

RY

ry

ry

RrYy

rryy

As you can see, the number of possible genotypes that the offspring could have has decreased from 16 to just 4.



In other words, the variation created by meiosis has just reduced dramatically

In an exam question, that’s what the marker will be looking for: the decreased amount of variation that is possible when genes are linked.

STOP AND CHECK:


What it is meant by the term, “linked genes” – in other words, how are some genes linked?

What is the effect of linked genes on the possible genotypes in the offspring?


Test Cross

Test crosses can be done in relation to monohybrid and dihybrid inheritance.

They are used to determine what the genotype of an individual with the dominant trait is

That’s because an individual with the dominant phenotype can either be homozygous dominant or heterozygous.

It is often important to know the genotype, especially when selectively breeding animals or plants. When you want a particular trait, you only want to breed homozygotes, which are commonly called pure-breeds. This is because, if they’re homozygous dominant, they will only pass on the dominant allele - and if they’re homozygous recessive, they will only pass on the recessive allele.

Test crosses are done by “testing” the individual with the dominant phenotype with an individual with the recessive phenotype (as they must be homozygous recessive).

There are essentially two outcomes:

1. If any of the offspring show the recessive phenotype the individual must be heterozygous in order to pass on a recessive allele.

• Remember, an offspring gets 1 allele from its father and 1 allele from its mother. An offspring with the recessive phenotype must be homozygous recessive, thus receiving a recessive allele from its father and a recessive allele from its mother.



2. If none of the offspring show the recessive phenotype is it likely that the individual is homozygous dominant.

Notice how for the second option we said it is “likely”?

We can never say that an individual is homozygous dominant with 100% certainty (unless the DNA is actually sequenced).

This is because fertilisation is random and it is possible for a heterozygous individual to never end up passing on their recessive allele creating the impression they are homozygous dominant.

To increase the likelihood of an organism being homozygous dominant in a test cross, there needs to be a very large number of offspring produced, all of which need to have the dominant phenotype.

STOP AND CHECK:


How and why a test cross is carried out. Why there is never 100% certainty that an organism is homozygous dominant in a test cross. How can the likelihood be increased?


Quick Questions

Using your own example, how could a test cross be used to work out whether an organism is pure breeding for a trait?

Think back to the dihybrid inheritance of seed colour and seed shape. How can someone determine if they have a plant which is pure-breeding for both round seeds and yellow seeds?

FACTORS CAUSING CHANGE IN A GENE POOLSo, you now know about the two processes that create variation in a gene pool: mutation and meiosis (crossing over, independent assortment and segregation). You also know how to predict variation using punnett squares, and how monohybrid and

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dihybrid inheritance work.

That’s brilliant, but we can’t stop there! There are other factors at work too.

Every gene pool has particular allele frequencies

What on earth do we mean by allele frequencies? It is how common each allele is in the population.

Mutations change the allele frequencies of gene pools by actually adding in new alleles.

But we also need to look at the other factors that change the frequencies of alleles: natural selection, genetic drift and migration.

By the end of this section you should:

Be able to explain the process of natural selection (“survival of the fittest”) and why nature can be cruel to some animals. Understand how genetic drift uses random chance to change the allele frequencies. Know how migration mixes and tosses up the allele frequencies in a gene pool.Understand the two processes: Bottleneck and Founder effect. What’s happening and what will be the effect on the gene pool?

Genetic Diversity

We’re going to start off this section by making something very clear. Although the topics in this section can take a lot of energy to understand - and they certainly involve a lot of energy for the population to go through, they are very, very important!

Genetic diversity describes the differences in a population. The more genetically diverse it is, the greater amount of different alleles there are present, and the more differences it has within it.

A population with low genetic diversity (or variation) is less likely to survive a sudden change in environment, while a population with high genetic diversity (or variation) is much more likely to survive. Remember, nature couldn’t care less about the individuals; it’s about the population as a whole. To understand this, let’s use an example:

Imagine a zombie outbreak occurs across the globe. If there was no genetic variation across all humans, either everybody will be immune or everybody will be non-immune to the zombie virus. If there is no immunity, then everybody becomes a zombie and eventually dies: the human race ceases to exist. Thankfully, the human race has lots



and lots of genetic variation, which means that there is a good chance that some people would be immune to the zombie virus. As long as these people are fast enough and not too tasty to zombies, then the human race will be able to continue existing.

No variation:

Variation:

Natural Selection

Charles Darwin was the first person to come up with the idea that populations evolve by natural selection. He’s pretty famous (everyone can picture the old man with the big white beard – don’t get confused with Santa though).

So, you might have heard of natural selection before, but do you know what it actually is? Let’s go through it.

We’ve already said that populations have variation

Hopefully you were paying attention when we went through mutations and sexual reproduction!

If there is variation in a population in a particular environment, some alleles might give individuals an advantage, so that they have more chance of surviving and reproducing compared to an individual without that allele.

We say that an advantageous allele increases the fitness of the individual

We don’t mean fitness in the usual, exercise-related sense though. In biology, the definition of fitness is: the ability of an individual to survive and reproduce.

Individuals with an advantageous allele are likely to produce more offspring, thereby passing on that advantageous allele to the next generation. On the other hand, the individuals with the less advantageous allele are likely to produce less offspring and so that allele is less likely to get passed on.



This goes on generation after generation:

dark green is favoured

light green less likely to survive

+ reproduce

more dark greenless light green

Natural selectionselect for dark green

phenotype

Variation

future selection

What happens to the allele frequencies of advantageous and disadvantageous alleles?

As a result, the advantageous allele increases in frequency in the gene pool (because it keeps getting passed on), while the other allele decreases in frequency (because it is less likely to get passed on). That’s pretty logical, right?

GG and Gg =

G

g

gg =

gg

ggGG

GG

GG GG

GG

GG

GGGg

gg

gg

G frequency = = 28

G

g

14

g frequency = = 6834

G frequency = = 4812

g frequency = = 4812

G = = 1 88

g = = 0 08

We say that the advantageous allele has been ‘selected for’.

Because of natural selection, populations become better suited to their environments over time.

Natural selection refers to the tendency of individuals with more environmentally favourable alleles to survive. This makes them more likely to pass their alleles on to the next generation - resulting in a greater frequency of these alleles in the gene pool.



Natural selection is easier to picture with an example

Imagine that a species of caterpillar has some light green individuals and some dark green individuals.

The caterpillars eat the leaves of a few different types of trees.

A disease strikes one species of tree: the one with light green leaves.

All of those trees die, but the trees with dark green leaves survive

Now the dark green caterpillars have an advantage over the light green caterpillars, because they are camouflaged against the leaves and so are less likely to be eaten by predators.

However, the light green individuals stand out against the dark green leaves, so they are more likely to be spotted and eaten.

As a result, more of the dark green caterpillars than the light green caterpillars survive and reproduce, passing the allele for dark green colouring onto their offspring. Over generations, the dark green allele increases in frequency in the gene pool and the light green allele decreases in frequency. Eventually, every individual might end up with the dark green allele (it might become fixed).

As a result, the caterpillar species are now better suited to their environment – they have evolved through the mechanism of natural selection.

This can be illustrated using the same diagram we showed earlier:

dark green is favored

light green less likely to survive

+ reproduce

more dark greenless light green

Natural selectionselect for dark green

phenotype

This population is better suited to their enviroment

Variation

future selection

STOP AND CHECK:


What is meant by the term, “fitness” in biology. How natural selection acts on a population: why is it sometimes referred to as “survival of the fittest”.




Genetic Drift

Genetic drift also results in some alleles increasing in frequency in gene pools, while other alleles decrease in frequency

In natural selection, these changes in frequency happen for a reason: the advantageous alleles increase in frequency and the less or disadvantageous alleles decrease in frequency. People tend to understand natural selection, because it makes a lot of sense.

Genetic drift can be harder to come to terms with, because it is the change in allele frequencies due to chance.

Starting “population”

Draw50 : 50 6 : 4

2nd“generation”

Draw60 : 40 7 : 3

3rd“generation”

Draw70 : 30 4 : 6

4th“generation”

40 : 60

So, what kind of chance events cause genetic drift?

Have a look back at the section on meiosis. There we saw that crossing over, independent assortment and segregation result in every gamete having a different combination of alleles.

When a sperm and an egg meet, it is completely random which combinations of alleles happen to be in that particular sperm and that particular egg. That means that it is also random which of the parents’ alleles get passed onto the offspring and which don’t.

Millions of these chance events can result in the allele frequencies of the gene pool changing between generations, for no reason at all.

Genetic drift refers to the changes in allele frequency within a gene pool between generations, which are completely due to chance.



STOP AND CHECK:


The process of genetic drift and how it changes the make-up of the gene pool. What determines the effect that genetic drift has on the population.


Migration

Migration is the movement of individuals from one population to another.

The word immigration is probably very familiar to you.

You hear it used to describe people moving into one country from another country. If you are the person moving out of a country to another country, then you are emigrating. Both immigration and emigration are just types of migration: moving from one population to another.

Can you work out how migration changes the allele frequencies of populations?

When individuals move into a population, their alleles are added to the population’s gene pool. The allele frequencies in the other population might be different, so it might be that the new immigrants all have a particular allele which is rare in the population they have arrived in. So, when their alleles are added to the gene pool of their new population, the allele frequencies change.

Similarly, when individuals leave a population, they take their alleles with them, out of the gene pool. If most of the individuals that leave have a particular allele, then their migration results in a change in the allele frequencies of the population left behind.

emigration

Population I Population II

immigration

aaaa

aa

aa

AA AAAA

AA

AaAa



In the example above, the white-coloured bird leaves Population I, taking with it 2 ‘a’ alleles, and joins Population II. Before migration, Population II had no recessive (‘a’) alleles.

STOP AND CHECK:


What migration is: what’s the difference between immigration and emigration? The effect that migration has on the gene pool of a population.


Founder Effect

Imagine in a large population there is a small group of individuals who are sick of the way things are run and decide to gap it. Realistically, the small group might leave due to competition, they might get lost or left behind, or a freak accident separates them from the larger population.

Either way, they leave, set up their own camp, and make up their own population. This is known as the founder effect – think of the small group finding their own territory and making a separate population.

There are two things that can happen when the small group break off:

1. The small population has a similar gene pool to the original larger population.2. The small population has a different gene pool to the original larger population.

Chances are, the second option is most likely to occur

That’s because the small population is just a small sample of the original population. It’s likely that the ratio of alleles will be different.

Mother population New population

Founder Effect



In fact, there is a chance that certain alleles that were in the original population aren’t present in the new ‘founding’ group. On top of this, the group that left may have contained all of the members from the original population with a certain allele - meaning that their departure eliminated an allele from the original population.

Not only is it likely that the small population has a different gene pool, it is likely that it has reduced genetic diversity compared to the original population.

The 'founder effect' refers to the differences in gene pools between an original population, and a new populaiton created by its former members.

If we think back, we know that genetic drift has a larger effect on smaller populations, so new populations created through the ’founder effect’ are most susceptible to genetic drift.

STOP AND CHECK:


What happens during the Founder Effect. Why the gene pool of the founding population (the small group) is likely to be different to the larger population.


Bottleneck Effect

Picture a bottle:

It starts of large at the bottom and then suddenly there is a narrowing at the top.

In the Bottleneck Effect, we start with a large population, and suddenly it gets smaller

This could be due to a sudden change in climate, disease, loss of habitat, or maybe even HUMAN INTERACTION *shocked gasp*.



When a population greatly reduces in size, the small remaining population is often left with reduced genetic diversity

There is at least a different make-up of the gene pool, as the small populations makes up just a small sample.

Originalpopulation

Bottleneckingevent

Survivingpopulation

Often alleles may be lost from the population as well.

At this point, the same effects occur as with the Founder Effect: the population is more prone to genetic drift. Inbreeding is also likely, which decreases genetic diversity of the offspring.

The 'bottleneck effect' refers to the change in gene pool after an event causes a large population loss. Due to the population loss, there will be less alleles present, which can rapidly and randomly alter relative allele frequencies.

STOP AND CHECK:


What happens to the size of the population during the Bottleneck Effect – what might cause this change?

The effects the Bottleneck Effect has on the genetic diversity. Why genetic drift has a greater effect on the population after Bottleneck Effect occurs.

Try explain it in your own words.



Putting It All Together

Mutations and meiosis create variation in the gene pools of populations. Natural selection, genetic drift and migration act on the variation. Founder and Bottleneck Effect are specific events that may occur to a population and dramatically alter the genetic diversity.

This causes changes in the allele frequencies in the gene pool: evolution!

Quick Questions

Discuss the possible mechanisms by which evolution of a population may occur. Remember, define what evolution is.

Natural selection and migration are both able to alter the gene pool of a population. But what are the differences between these processes?

Natural selection and genetic drift are both able to alter the gene pool of a population. But what are the differences between these processes?

Compare Bottleneck and Founder Effect – what is the difference between these processes, and what similarities do they share?

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KEY TERMSTo help you out, we’ve collected a list of the key words you need to know and put them into a glossary for you.

Allele: An alternative form of a gene (e.g. blue eyes or brown eyes).

Allele frequencies: The commonness of each allele in a gene pool.

Co-dominance: Both alleles are dominant and both are expressed if present (e.g. AB blood type).

Crossing over: Sections of DNA are swapped between homologous chromosomes. This results in the chromosomes having new combinations of alleles.

Diploid: A diploid cell has a full set of chromosomes.

Dominant allele: An allele which will always be expressed in the phenotype if it is present because it will mask any recessive alleles.

Evolution: The change in the genetic make-up of populations over time.

Fitness: The ability of an individual to survive and reproduce.

Gamete: A haploid sex cell.

Gene: A sequence of bases (in DNA) that codes for a particular trait.

Gene pool: All of the alleles which are present in a population and which could possibly be passed onto the next generation.

Genetic drift: Changes in the allele frequencies of a population due to chance.



Genotypic ratio: A ratio showing the probability of the offspring of a particular cross having each possible genotype.

Haploid: A haploid cell has half a set of chromosomes.

Heterozygous: An individual that has two different alleles for a trait.

Homologous chromosomes: Pairs of maternal and paternal chromosomes.

Homozygous: An individual that has two identical alleles for a trait.

Incomplete dominance: Neither allele is completely dominant, so when both alleles are present, the two phenotypes blend to create a new, distinct phenotype.

Independent assortment: When homologous chromosomes line up at the centre of the cell, they do so independently of all of the other pairs. This means that it is random which combination of chromosomes ends up in which cell.

Linked genes: Genes which are so close together on a chromosome that if one of them is switched to the homologous chromosome in crossing over, it’s likely that the other one will go too.

Meiosis: Cell division to create four haploid gametes, which are different from each other and from the original cell.

Migration: The movement of individuals (and therefore of alleles) from one population to another.

Multiple alleles: Some traits have more than two possible alleles (but a single individual will only ever have two of the possible alleles).

Mutation: A change in the base sequence of DNA.



Natural selection: Individuals with more advantageous traits are more likely to survive and reproduce and so advantageous alleles increase in the population over generations. As a result, the population becomes better suited to its environment over time.

Phenotypic ratio: A ratio showing the probability of the offspring of a particular cross having each possible phenotype.

Population: A group of the same species that lives in the same area and breeds with each other.

Recessive allele: An allele which will only be expressed if there is no dominant allele to mask it.

Segregation: The chromatids that the parent has are split up randomly, so that each gamete ends up a single allele for each trait. Which alleles it ends up with are down to chance.

Sexual reproduction: Reproduction in which one gamete (sex cell) from each of two individuals combine to form a new individual.

Sister chromatids: Two identical copies of a chromosome, created by DNA replication. The sister chromatids are stuck together by a cellular ‘glue’.

biology level 2...level 2 iolog geneti variation and change if learning key words first off scares...

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