Genetic+Variation+and+Change


 * This standard has two parts to uncover:**
 * the factors that cause variation and the factors that cause changes in allele frequency?**

If all the genes were identical, all individuals in a population would be identical. Obviously, this is not how it is. In every species there is variation between individuals. Some genes come in different possible types, and the version that individuals inherits makes their phenotypes different (as well as the environment). These versions of the genes are called alleles of a gene. We have to think of a population as a big set of alleles, which is called a gene pool. The gene pool is all the possible alleles that any breeding individuals might get to breed with. The gene pool is the supply place for the alleles for the next generation.

This population of frogs all have a gene for their colour. Some of them have the alleles for green colour, some have the alleles for blue and some have the alleles for red. All the alleles are able to be passed on when this collection of individuals breed. How many of each allele are actually passed on will depend on a couple of things.

The proportion of them that are in the gene pool is called the frequency of the alleles. If the proportions of alleles change, the allele frequency has changed. In this simplified frog pool example at the moment, there are 12 green alleles, 2 blue alleles and one red allele (counting the colour dots in the gene pool). If the red ones die out for any reason, then the next generation will have maybe 13 green alleles and 3 blue alleles. The allele frequency has changed. This is what this topic is about. How do the gene pools of a population change? What scientists are actually measuring is how do the allele frequencies of the gene pool change.

This cute [|youtube clip is a simple] but snappy introduction, with a good explanation of alleles and how to count their frequency. Watch it now, its not long.

In class we created populations with cut out Tuatara pictures, we counted the number of alleles for the Tuatara, we added up the A alleles and the a alleles, and the Z alleles and the z alleles, and turned them into a percentage. Then we changed the situation for the population of Tuatara, and counted up the alleles every generation under new circumstances. For example we changed the population by splitting it into two groups separated by a river, by having a disease kill all but one type of tuatara, by moving tuatara from one population to another. People noticed that if you ended up with a small population then the effects of a change were really noticeable, when compared to a big population. These are all events that happen in the real world. In biological terms we **changed the frequency of the alleles** in the Tuatara population each generation. The techniques used to change the alleles were migration, by random chance (genetic drift) and by natural selection. Each of these ideas becomes a major topic for us developed in part two of this page (see below).

Part One What factors create genetic variation?

How does a gene pool get to have brand new alleles or new combinations of the alleles so that there is variation? If there was just one type of allele then there would be no change.

A gene is actually a chemical carried on a chromosome. There must have been an original chemical version, and any new versions must have arisen through a mutation. Once there were two versions, there were new combinations possible, and making new combinations of the versions of the genes happens through meiosis. So how is Variation created in a gene pool? There are two main ways - Mutation and Meiosis. (the description for Meiosis is further down this page)

=**Mutation**=


 * M**utation is a permanent change in the sequence or type of bases that make up the DNA for a gene. If the new sequence of bases creates a genotype that is successful the new allele may become established in the gene pool.

Say we go from a code like AAC GGT AGA CCG AAT GGT to AAC CCT AGA CCG AAT GGT,

This set of bases might make enough of a change to the protein it codes for to make blue eyes instead of black (simple example), if that happens in a sperm or egg and doesn't stop the resulting baby surviving to breed then the new blue coding DNA gets to be in the gene pool.

All new alleles must have originally been a result of a mutation. A mutation that occurs in a body cell will not be passed on in the gene pool. The only way the mutation can be passed on is if it is in a sex cell that is fertilized and makes a successful organism. Then the mutation is in the gene pool.

The cell called a sex cell is a gamete. The body cell is called a somatic cell. The difference between a gamete and a somatic cell is the sets of chromosomes. A gamete only has a half set of chromosomes, a somatic cell has a full set of chromosomes. Two gametes joining together creates a cell with a full set of chromosomes, thus a somatic cell. This somatic cell then goes on to form the whole body by mitotic cell divisions. Each cell should be an identical copy of the original first cell (which is called a zygote). Any mutations that occur in these genes will stay within this body. Unless..... the mutations occur in the special sex cells of this body. **Then** the new allele can be passed on. **Then** the allele will enter the gene pool.

The sort of question that comes up is:

2014 Explain the process of gametic mutation including what it is, and where it occurs.___ Not all gametic mutations may enter the gene pool. Discuss why the allele for .... has not become established in the wild gene pool. In your discussion : describe what a gene pool is explain the process of natural selection explain how natural selection influences allele frequencies in a gene pool.

2012 Mutations can result in the formation of new alleles, but not all alleles enter the gene pool of a population.

Discuss this statement, considering the following points in your response: What is meant by the terms: mutation and gene pool Differences between somatic and gametic mutation The factors that determine whether an allele enters the gene pool.

Using the Assessment Schedule to help prepare your answers in this years exam is a good technique. The answer for this paper is as below. Assessment Schedule for 2012.

Gene pool is (all) the genes or alleles (held by the individuals) in a population. Mutation can be defined as a (permanent) change in the DNA. Somatic mutations occur in any cells of the body other than in the gametes Gametic mutations only occur in sex cells, eg, sperm / eggs (accept pollen).

Explanation of why these are different in terms of producing new alleles that can enter the gene pool include: A mutation which changes the DNA / base sequence might occur which creates a new allele. Somatic mutations are not passed on from one generation to the next / Somatic mutations only affect the individual organism in which the cells have mutated. Gametic mutations are (heritable) transferred to the next (& possibly subsequent) generations OR Gametic mutations are not limited to the individual in which the original mutation has occurred. Not all gametic mutations will enter the gene pool – e.g through redundancy of gametes ,which means that a lot of gametes are created and not all of them are fertilised so lots don't enter the gene pool, or through creating a lethal allele, which means that the mutation might create an allele that actually fails because it makes a genotype that causes death.

=**Meiosis**= which involves understanding how these events during meiosis make gametes unique - Crossover and Recombination, Independent Assortment and Segregation of alleles.

[|Mr Andersen takes a simple talk thr]ough the purpose of Meiosis, with some explanation of key words. It is 9 minutes, but you can stop and start him when it gets too complicated.


 * Introduction to Meiosis and Chromosomes.**

Meiosis is the cell division that creates sex cells or gametes. It creates the cells with a half set of chromosomes, not just any half though. The new cells have to have one of each of the pairs of chromosomes. Humans have 23 pairs of chromosomes, our sperm or eggs have 23, one of each pair.

The first step is to understand that chromosomes come in pairs, called HOMOLOGOUS pairs, (because they have the same locations for the genes on them).

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A set of chromosome pictures is called a karyotype. They can be used to diagnose people's health in a broad way. Go to the biology.arizona link to match chromosomes and diagnose three different patients. Click on the chromosomes matching homologous pair to work out which chromosome abnormality the patient has. I think it is really interesting. http://www.biology.arizona.edu/human_bio/activities/karyotyping/karyotyping.html

When gametes are formed it is important that the chromosomes are separated into the gametes correctly. Each of the disorders you identified in the activity are from incorrect meiosis.

The steps in Meiosis are very clear.

The first step involves the chromosomes doubling up (as in the picture above if you look really carefully), then they line up next to their homologous pair across the spindle, the spindle then pulls the homologous pairs apart and then does a second separation when it pulls the paired chromosomes apart. So two separations because of the doubled chromosome at the start.

Watch both of the animations of Meiosis ,I and II. Meiosis I splits the homologous pairs apart, and then Meiosis II splits the doubled chromosomes apart. At the end the gamete has half the number of chromosomes.

http://www.biology.arizona.edu/cell_bio/tutorials/meiosis/page3.html

Back in the day we had to learn the names and steps of Meiosis,now you don't need to memorise the names for assessments, but recognising the stages is relevant for understanding the processes and how variation happens, how the chromosomes are passed on and made to be different from the parent chromosomes as well,

We learned the word 'IPMAT' to remember the order of the stages (I =inter, P= Pro, M = Meta, A =Ana and T = Telo, the names of the phases)



This image comes from this website. http://www.ib.bioninja.com.au/higher-level/topic-10-genetics/101-meiosis.html. Notice how it starts with one cell with two pairs of chromosomes. It ends with four cells with two chromosomes,not paired. These are the gametes.

This link goes to a video that clearly shows the paired homologous chromosomes, https://www.youtube.com/watch?v=vA8aMpHwYh0&index=10&list=RDiCL6d0OwKt8, yes there is a lot to watch but you need to spend a lot of time on this process.

http://www.biomanbio.com/GamesandLabs/Genegames/snurfle_meiosis_and_genetics.html This is a quiz, and you need to know about the cell stages, if you don't know them just click your way through each quiz, you will get told the answers as you go!! No barriers to learning here.

http://highered.mcgraw-hill.com/sites/9834092339/student_view0/chapter30/stages_of_meiosis.html Do this one once you know some of the terms.

Just making four gametes isn't going to make a lot of variation. It is the steps that are really really important for making unique gametes. This is how most variation in individuals comes about. (It would be a shame to have to wait for mutations to make us look different from our brother or sister).

There are two steps which make a lot of variation in the gametes' chromosomes. Crossover and recombination, when the homologous chromosomes double and line up they can link up with their matched chromosome, the alleles are at the same locus on the chromosome so they can be swapped on to the matched chromatid. The term for this is synapsis. AND Independent Assortment means that each pair of homologous chromosomes (which have doubled so there are four homologous chromosomes) ends up being put into one of the 4 gamete cells in quite a different order from the next homologous chromosomes.

Segregation of Alleles means each gamete gets one of the pair of alleles an adult cell has. (If your gamete had both alleles, when it combined at fertilisation the number of alleles at that gene locus would be more than 2). This way when the gametes combine they restore the number of alleles to normal, and it is possible for a combination of the alleles, different from the one each parent had, to be passed on.

I know. What was that!

watch Mr Andersen, and Crash Course Biology. All 3 will take about 30 minutes so get something to eat while you watch. (Turn off that music device you have plugged in to your ear)

Mr Andersen - https://www.youtube.com/watch?v=16enC385R0w Crash Course Biology - Meiosis https://www.youtube.com/watch?v=qCLmR9-YY7o A student video, best meiosis video ever? https://www.youtube.com/watch?v=35ncSrJOwME

And yet another good version of an explanation of meiosis, which links to why this process is so important to the variation in populations, (why do gametes matter to make any set of siblings have variation between them). https://www.youtube.com/watch?v=rqPMp0U0HOA So do we have a handle on the steps of Meiosis and how it makes gametes that are not straight copies of the adult cell? email me at debbiem@opotikicol.school.nz to tell me if you got it or not.

Predicting the genes that will come out in the next generation.

 * Monohybrid Crosses**


 * We can predict what the gametes will possibly pass on by using punnett squares to recreate the possibilities of crosses between certain individuals.**

Use the alleles of each parent to predict the gametes they have. Then cross the gametes on a table to work out the possible new combinations.

Parent RR * rr

gametes R or R and r or r
 * =  ||= R ||= R ||
 * = r ||= Rr ||= Rr ||
 * = r ||= Rr ||= Rr ||

There is a 100 % chance of having Rr genotype and whatever the R allele makes happen.

but in the next generation Rr * Rr there is more variation. parents Rr * Rr

gametes R or r and R or r Now there is 1/4 chance of having RR, a 2/4 chance of having Rr,and a 1/4 chance of having rr but a 3/4 chance of showing the R phenotype,and a 1/4 chance of showing the recessive phenotype. (because 3 have at least one R which is dominant and you only need one to make that type).
 * || R || r ||
 * R || RR || Rr ||
 * r || Rr || rr ||

There are many many examples of these ratios to practice. This first worksheet is a fun one. The second one is too but it doesn't have Sponge Bob.

Now use the same principle to calculate the prediction for inheriting the alleles from two different genes.
 * Dihybrid Crosses**

One gene has to have two alleles, and so does the other, so we are talking about four alleles now.

parents RR WW * rr ww

gametes RW or rw

The offspring will all be Rr Ww

But if we cross the next generation RrWw * RrWw

we now get 4 different gametes for each RW, Rw, rW, rw

These are the random combinations made by the independent assortment of chromosomes during Metaphase in meiosis. We can't tell which gamete is going to fertilise the other gamete so we have to work out a punnett square and the ratios for each type possible.

Any one of these combinations is possible. The probability of each of the possible phenotypes is 9: 3: 3: 1. ( state what they look like here though) and genotype ratio of 1:2:1:2:4:2:1:2:1. They should both add up to16.
 * * || RW || Rw || rW || rw ||
 * RW || RR WW || RR Ww || Rr WW || Rr Ww ||
 * Rw || RR Ww || RR ww || Rr Ww || Rr Ww ||
 * rW || Rr WW || RR Ww ||= rr WW || rr Ww ||
 * rw || Rr Ww || Rr ww || rr Ww || rr ww ||

Another common cross is RrWw * rrww

The genotype ratio is 1 rrWw : 1 rrww: 1 rrWw : 1 rrww
 * * || RW || Rw || rW || rw ||
 * rw || RrWw || Rrww || rrWw || rrww ||

and the phenotype ratio is also1:1:1:1 depending on what the alleles stand for.

The practice doesn't change. keep the letters for each trait together, i.e RR WW not RWRW, and put the dominant letters first,RrWw, not rRwW This link will take you through the whole thing again from the beginning, but with an american lady, media type="custom" key="26894382"

And as always the exam questions are really useful practice.

The 2014 exam used pumpkins genes as an example, if W is White Skin and w is Yellow Skin, and D is disk shape while d is sphere shape, you can workout the very simple cross in the word document. The question after the punnett square was to describe the phenotype ratio for the cross.



There are some trickier examples, Incomplete Dominance, Co-Dominance, Multiple Alleles and Lethal Genes.

Links [|here to Amoeba Sisters video's on YouTube, they go over each type in a simple way.]

Each Punnett square is a prediction. Real Life examples are used in Pedigree Crosses, showing inheritance of a trait in a family tree.


 * Analysing Pedigree Cross problems** - how to attack the family tree. It is mostly trial and error- workout every possible case, I try to start with the offspring that is different from both the parents, that tells you that the parents are heterozygous eh. This Biology teacher cared so much that he put a movie on youtube!! using A not eh,(joke). Remember that sex-linked genes are on the X and the Y chromosomes, and autosomal genes are on the other chromosomes, the difference is whether you write an XA, Xa, or Ya or YA, or AA or Aa or aa to explain the genotype. eh?

No watch the movie, he does it pretty well.

https://www.youtube.com/watch?v=HbIHjsn5cHo

Some classic Pedigree Cross situations Huntington's Chorea- if you inherit a dominant allele you will develop this disorder. Therefore you want to be homozygous recessive to not get this disease. Another dominant allele that causes a rare disorder is achondroplasia, a skeletal disorder causing dwarfism.

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Cystic Fibrosis and Tay Sachs Disease - carried by a recessive allele,so in order to have this disorder you need to inherit two recessive alleles. Both parents must be carriers and have a normal phenotype. They have a 1/4 chance of having a baby with the disorder every time they have babies. other children may be carriers of the recessive allele and will possibly pass it on to their children.

Two disorders, Haemophilia or red-green colour blindness - these disorders are carried as recessive alleles on the X chromosome. Females need to inherit two recessive alleles to show the disorder, but males only need to inherit one recessive allele. They must inherit a Y chromosome from their father,and that chromosome has no allele for this gene on it. Unaffected (but carrier) mothers pass the disorder on to their sons. Mothers are the carrier, there are no carrier fathers. Affected fathers pass it on to their daughters.



The allele that causes haemophilia was used to help solve the mystery of the murder of the Russian royal family, during WWI. Check out the application of genetic knowledge at the DNAi site, using Recovering the Romanov's case study http://www.dnai.org/d/

The Pedigree Cross shows the relationship between individuals. It is possible to predict the possible offspring from any genotype for a parent, this website has a clear step by step guide to using punnett squares to predict the likely offspring. http://www2.edc.org/weblabs/Punnett/Punnettsquares.html

http://www.biotopics.co.uk/genes/pedigr.html explains what the pedigree crosses look like.

=The **factors that cause changes in allele frequency** is the other part to this Achievement Standard.=

Go back to the Gene Pool idea, how can events cause changes in the ratio of alleles found in gene pools between generations? Think about the gene pool situation. You have a group of alleles. If you bring in a new individual or send away an individual their alleles enter or leave the gene pool. Another scenario is one lot of alleles are really really successful so they breed a lot and this increases their proportion in the gene pool. A third scenario is that a chunk of the gene pool gets isolated, no one can tell which chunk and which alleles are in it. Those alleles form their own new gene pool. That's basically it,with flash names for each scenario.

What would you call it when a person moves from one country to another? Starts with M. its the same idea,

Migration.
Migration brings in or takes out the alleles of the individual arriving. Think about how wild animals often force young males to leave the family group to find appropriate mates. This increases the diversity of the gene pool. You can see in the picture below that a new individual brings in extra alleles, which changes the percentage of the brown allele straight away.

This link goes to a page that has an animation that [|models how an allele frequency] in a gene pool can be changed, don't worry about reading the whole article, just follow the animation.

When an animal moves into a new group to breed it changes the alleles of two groups, the group it emigrated out of, and the group it immigrated into. This increases the diversity in the new population and decreases the diversity in the old population.

I have tried to find examples to illustrate this, I was thinking about Prides of Lions, and how they enforce male cubs leaving their family to find a mate in a new family, so that their alleles will be different. The younger males spend a few years in no mans land growing bigger and stronger, until they are able to take over a pride. The dominant male gets to have cubs for just a few years until a new male comes that is bigger and stronger than them.

In New Zealand our insects could be influenced by migrating individuals being blown over from Australia.

Natural Selection
This process is the main mechanism by which populations evolve to suit their environment. The information on this topic is prepared in the page Evolution Patterns and Processes.

Return to this page to do some past questions and case studies.

Natural Selection reduces the variability in a gene pool. The pressures are on to be the best phenotype,so other phenotypes generally are selected against. Other phenotypes would only be useful if the environment changes,and then you will need the variations in the gene pool!

Genetic Drift
This process explains why sometimes there is no reason which individuals survive to breed, just random luck.

In a small population an individual.might not breed. There just aren't enough others to breed with.Their alleles are therefore not passed on to the next generation. Random luck.

Other times a large population might suddenly be reduced to a small population by a catastrophic event, the group that survives is just lucky, not better than any other group. Their alleles are the only ones left in the gene pool. Read about the New Zealand Black robin population rescue. This type of genetic drift is called a Population Bottleneck.

The other possibility is that a small break away group can become isolated from the main gene pool. The individuals in this group are only able to breed with each other, therefore their alleles are the beginning of a new gene pool, the founding group, so it is a Founder Effect. If a mutation happens to be in the alleles of that founding group, that allele is likely to become more common in a few generations.

Black Robin Case Study. http://en.wikipedia.org/wiki/Black_robin https://nzconservation.wordpress.com/tag/bottleneck-effect/ http://blackrobin.info/index.php?option=com_content&view=article&id=76:why-go-to-rangatira-island-for-13-weeks&catid=1&Itemid=3

The Gene for rim laying discussed in the wikipedia notes was in the 2014 exam. Wish we'd read this before then.

A lot of New Zealand species have been reduced to small populations vulnerable to genetic drift.

Cheetah Case study http://cheetah.org/about-the-cheetah/genetic-diversity/ http://evolution.berkeley.edu/evolibrary/news/070701_cheetah

Founder Effect Case Study http://evolution.berkeley.edu/evosite/evo101/IIID3Bottlenecks.shtml A human example http://www.pbs.org/wgbh/evolution/library/06/3/l_063_03.html

Sample question: The Black Robin The Chatham Island Robin (also called the black robin) was first discovered in the 1870’s. They are distinctly different from the robins found on the mainland because of their feather colour. The different feather colour from the mainland species may be a result of the founder effect. 1. What is the founder effect?

The Chatham Islands have probably never been connected to the mainland. 2. Explain why the subspeciation of the Chatham Island black robin is an example of the founder effect.

3 Discuss why genetic drift is likely to affect the Black Robin population.