Seminar 2 2011 Discussion Page

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LENScience Senior Biology Seminar Series 2011
Rethinking Polynesian Origins Challenge 2
Challenge 3



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South City High School - Student MB    16th April 2pm

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Rethinking Polynesian Origins - Discussion Page

Challenge Question 1 


The scientific team investigating the migration of the Pacific used both ancient and modern mitochondrial DNA (mtDNA) in their investigations. Discuss why mtDNA rather than nuclear DNA is used in research like this and the differences in information that can be obtained from ancient and modern mtDNA samples. 


Whakatane High - Gianni 14 April

mtDNA is used instead of nDNA because nuclear DNA changes as a result of both recombination during meiosis and mutations while mtDNA only changes as a result of mutations and is only passed down through females. This enables ancestral tracking because the mutation comes only from one parent. Therefor any variation in mtDNA within a species has occured over time through mutations (at an approx. constant rate).

mtDNA is also easy to work with because it has a much smaller genome  than nuclear DNA and does not contain any introns so it is easier to analyse and create phylogenetic tree.

Lisa Matisoo-Smith, Allan Wilson Centre, 5 May
Nice answer, but you need to make sure that you address the full question – you haven’t answered the section about ancient vs modern DNA! See below

Michal Denny, LENScience 6 May

Gianni, you have given us a very concise and biologically correct answer to the first part of the question. You have explained the key difference between mtDNA and nuclear DNA. To develop this answer further you need to link this difference to why mtDNA is more useful, for example explaining how mt DNA is more useful for ancestral tracking. 



Onehunga high School -Maryanne Funaki and Jaedan Prior-Gabolinscy 14 April 2011

One reason why mtDNA is used rather than nuclear DNA is because it is inherited through the maternal line only, therefore it does not recombine so it is fairly easy to trace back to its origin with the exception of mutations that would have changed it slightly through time and that gives a clear indication of differences in population. Also because mtDNA is present in a large number of copies in every single cell around 2000 to 3000 per cell, because there is such a large number, it means that if they decay you would still have a few copies of mtDNA over time, this compared with only 2 copies of nuclear DNA per cell, this means that there is a much bigger abundance in DNA once they start to break down. Very good, but you need to be explicit that this provides a distinct advantage for ancient DNA studies. Due to the higher mutation rate of mitochondrial dna compare with nuclear dna is because mtDNA is not proof read by the enzyme DNA polymarate, therefore it is much easier to study the rate of mutation over a period of time, this means that there a bigger mutations (more mutations – it is a number not a size issue) over a long period of time compared to nuclear dna.This can actually be a problem for studies between species that have been separated for a long time. Too much variation (particularly in “hot spots”) will confuse the evolutionary reconstruction. This is why mtDNA (especially the hypervariable region) is generally used to study variation within species – unless you are looking at a particularly conserved part of the mtDNA genome, such as COI which is used to study variation between species.
The study of ancient history is more complicated because of modern times and the ease of transport over long distances, this has lead to human migration becoming much more frequent, and so genotypes specific to one culture may have been lost or spread through a different culture because of ease of long distance travelling. Due to the flow of migration it has become very hard to verify the origin of the native inhabitants. Nucleic DNA becomes mixed much faster than mtDNA as mtDNA does have genetic influence from the father.

Michal Denny, LENScience 15 April

Hi Gianni, Maryanne and Jaedan. It's great to see the 3 of you taking the plunge and starting off the challenge questions. I'll comment in more depth on your answers later as will Lisa. But in the meantime there is one area that all of you need to look at again - that's the second part of the question - discuss the differences in information that can be obtained from both ancient and modern mtDNA samples, neither answer addresses this. Maryanne and Jaedan you also need to re-read your answer to fix a couple of mistakes - the name of the enzyme and also I suspect the word 'not" is missing from your last sentence :-)

Lisa Matisoo-Smith, Allan Wilson Centre 5 May -The green comments interspersed in the answer are from Lisa.



Sacred Heart College - Student Gerry T - 9.30a.m. 16 April

Nuclear DNA is a result of fusion between the maternal set of DNA in the ovum and the paternal set of DNA in the sperm during fertilization. Mitochondrial DNA, on the other hand, are small, circular DNA found in the organelle mitochondria. In research of migration paths and such, mitochondrial DNA is more suited than nuclear DNA to the task specifically because of the way in which they are passed on. Nuclear DNA will contain DNA from both parents, thus the offspring will have half of his genes from his parents, a quarter the next generation up and so forth. The change in DNA sequence due to recombination and crossing-over during meiosis to produce gametes will make it difficult to use to trace the origins of the individual. Mitochondrial DNA, however, are always inherited from the maternal line only because mitochondrial DNA do not recombine with any other DNA. In addition, all the mitochondria in the ovum and later the embryo are solely from the mother, as is all other cell material. Also, mitochondrial DNA undergoes a predictable rate of mutation that is caused by reactive oxygen species produced from cellular respiration, which occurs in close proximity to it. Thus, one can use mitochondrial DNA to trace one’s maternal lines, making it suitable for the task.

Ancient DNA is any DNA extracted from the tissues of ancient specimens not preserved for DNA extraction. Modern DNA is DNA extracted from live specimens and preserved for the purpose of research. Modern mtDNA proves to be a useful tool to find similarities between different populations of organisms, especially origins, by looking at the similarities and differences, thus enabling us to trace evolution and migration patterns. However, mitochondrial DNA is only capable of telling us whether different populations have the same origins, but it does not tell us when the separation occurred. This is where ancient mitochondrial DNA comes in. The date of introduction of new genetic material can be estimated provided the age of the remains is known. With this, researchers can accurately estimate when the two populations separated.

Lisa Matisoo-Smith, Allan Wilson Centre 5 May
Nice answer! Strictly speaking, though, mtDNA can tell us about when populations diverged – as was done in the original mtDNA studies of Cann, Stoneking and Wilson. It is done by applying a molecular clock. But for relatively recent events – such as the settlement of Polynesia, the time frame is too short to apply a molecular clock (the whole of Polynesian prehistory is within the error ranges!). This is where ancient DNA analyses of dated (radiocarbon dated) archaeological samples CAN provide the information regarding the dates of arrivals or divergences.

Michal Denny, LENScience 6 May

I agree, a very nice answer. I like the way you've started by clearly and concisely explaining the difference between mtDNA and nuclear DNA and then linked this to the context of the question. You've used a similar structure for the second part of the question, which is also good. Well done.



GerryT: Thanks for the comments. Just a few questions though. In terms of the application of the molecular clock hypothesis, what is the range that a certain event must fall into to be considered as a 'recent event'? Also, different organisms have different rate of molecular change, right? If this is true, why is it so and is the only way to determine this through observation, comparison and extrapolation? Or is there something else to it as well?

Lisa Matisoo-Smith, Allan Wilson Centre 12 May

Very good question. The answer is that there is no one single answer – the age range for molecular clock estimates vary according to the part of the genome you are studying, how much sequence data you have and which of a range of evolutionary models you might apply. But generally for mtDNA data, the error ranges are in the +/- a few thousand years. And since we are looking at the settlement of Remote Oceania happening in the last 3000 years, the error ranges mean that molecular dates don’t really help in the debates about timing of human arrival. So it is a bit of a ballpark figure, but I would say that events that have happened in the last 10,000 years are problematic for molecular dating.

There is a debate about different rates in different organisms and the application of a molecular clock in general. What is essential though is that, when doing molecular clock estimates, you use some “known” date to calibrate your clock – allowing you to compare and measure the genetic distance that accumulated between two species over a known period of time. Sarich and Wilson used the separation of Old World and New World Monkeys to calibrate their first clock of hominid evolution. For human mtDNA, some suggest that the archaeological evidence of human arrival in Australia & New Guinea (Sahul) at 50,000 years ago is the best calibration point. The ape human split of 6 MYA is also used to calibrate human DNA mutation rates.
Have a look at: http://www.nature.com/scitable/topicpage/the-molecular-clock-and-estimating-species-divergence-41971 for a good discussion

Cheers,
Lisa



Sacred Heart College - Student David Broderick -12:02 p.m. 4/25/2011

mtDNA is DNA which is found in the mitochondria of the cell while nuclear DNA is found in the nucleus of the cell. There is less mtDNA (no, it is actually the opposite) than Nuclear DNA in an organism and mtDNA is inherited only from the mother as opposed to having a set of DNA from both parents as is the case in nuclear DNA. mtDNA is preferable for research projects studying origin as it has a predictable rate of mutation and is inherited only through the mother. Therefore this means that mutations in the mtDNA will always be passed from the mother to the offspring. This has applications in this research as because the mutation will always be passed on the researchers can use samples from different populations of kiore on the different islands and compare the mutations found in the mtDNA to work out how related the two different populations are. While this will not tell them when the migrations occurred as there is no way of knowing when the mutation occurred. However by working out how related the two species are one can determine whether or not the formation of the two populations occurred at the same time. In this type of research both ancient and modern mtDNA is used. Ancient DNA samples are samples of DNA taken from the preserved tissue, bones of dead organisms. Modern DNA samples are samples which are taken from modern day organisms. There are likely to be differences in these two mtDNA samples as while any mutations will be passed on new mutations will have occurred in the population. These differences are useful to the investigation as if a mutation has occurred in the modern DNA which is also found in ancient DNA of another population we can determine that at some point these populations had geneflow. This could indicate that the population with the mutation in its ancient DNA was settled by the population with it only in their modern DNA, Sorry, again, you seem to have this turned around. If the ancient sample in one population had the particular mutation it is more likely that that was the source population. A modern population cannot be ancestral to something that lived before it! although there could also be other answers such as trade, warfare or communication between the two islands. There is also the challenge of the fact that the DNA taken from the ancient samples can be deteriorated as it breaks down. This challenge is significant in the research done by the team in the pacific as the climatic conditions are ideal for the DNA to break down as opposed to being preserved to the quality needed for research.

Lisa Matisoo-Smith, Allan Wilson Centre 5 May - The green comments interspersed in the answer are also from Lisa.

Good for you for picking up on the issue of the challenge presented by deterorating DNA. But if you extend it slightly you can point out that this makes mtDNA preferable for ancinet DNA research because of higher copy number – it is more likely to be preserved in ancient samples. Nuclear DNA is difficult to obtain from ancient remains – particularly prior to the development of next generation sequencing technologies!



Onslow College - Jennifer Randle 5.44pm 5/5/11

Tracing human origins has been something which people have been interested in for hundreds of years. We like to understand where we come from, and knowing where your ancestors and the ancestors of all humans came from is an important part of that. Recently, our ability to trace human and other organism’s origins has become exponentially better. This is due to new technology allowing us access to DNA as a genetically more precise means of tracing heritage. Two kinds of DNA are used in this origins research by biologists. Nuclear DNA, found in the nucleus of cells which make up an organism as well as the more recently discovered Mitochondrial DNA (mtDNA) which is found in cell organelles called Mitochondria. Both sets of DNA are widely used in research, but mtDNA has particular use in these origin studies due to differences in it structure, location and the information which can be gained from it. By understanding the differences between Nuclear DNA and mtDNA we can understand the best ways to take advantage of their potential to unlock genetic secrets never before understood.
DNA stands for Deoxyribonucleic acid. It is a long molecule consisting of two long polymers made up of units called nucleotides, with backbones made up of sugar and phosphate groups joined by ester bonds. DNA is what carries the genetic instructions used in the development and functioning of all organisms. It is often compared to a set of blueprints, or a recipe for an organism. The information for an organism is carried in segments of DNA called genes. Nuclear DNA is in the form of a double helix, and is found in the nucleus of eukaryotic organisms (complex cells with nucleus). Typically nuclear DNA codes for more of the genome (all hereditary information) of an organism than any other kind of DNA. Nuclear DNA is passed on sexually and your DNA is a combination of your father’s and your mother’s DNA. Mitochondrial DNA is in the form of a circle, and is found inside eukaryotic cells in organelles called mitochondria. Mitochondria are responsible for changing glucose molecules from food into ATP (Adenine Triphosphate) for the cell to use as energy for cell processes. Mitochondrial DNA typically codes for less of the genome than Nuclear DNA but it also has fewer genes; for humans 37 in mtDNA compared to 23,000 in Nuclear DNA. Mitochondrial DNA is maternally inherited, meaning it is only passed down from the mother (in very few instances in nature mtDNA is inherited from the father e.g. Honeybees).
DNA is used for many purposes. It is used in forensics for identifying individuals from hair, saliva or skin left at crime scenes e.g. from a perpetrator. It is used in Bioinformatics, which is the manipulation, searching and data mining of all biological information. Nuclear DNA is also very useful in Anthropological studies for studying heritage, which is why it is vital for comprehensive studies of migration. Because DNA collect mutations over time and these mutations are inherited, it contains historical information. Geneticists can compare this information and use them to deduce the evolutionary history of different organisms (phylogeny). Most commonly the type of DNA used to do this is mtDNA. There are several reasons for this, due to the advantages mtDNA has over Nuclear DNA. Firstly, there is much more of it. Cells can contain hundreds of copies of an organism’s mtDNA, because there can be many mitochondria in a cell, all carrying 4 or more copies of the DNA, whereas there is only one copy of the nuclear DNA in each cell. This significantly increases the chances of obtaining a usable sample for testing. MtDNA is also more useful as it is only inherited maternally and does not change from mother to child other than through mutation. The mutation rate for mitochondria is also predictable, making it possible for geneticists to construct estimates of relationships between individuals based on their mtDNA. Neither of these things is true for nuclear DNA, as it is inherited for both parents and is recombined from two different sets of DNA. The mutation rate for nuclear DNA is also much less predictable. MtDNA also has a population size approximately one quarter that of nuclear markers meaning it takes for less effort to obtain historical information from it.
However, there are also problems with using mtDNA for studying migration patterns based on ancestral evidence. Firstly, because it is not specific to one individual, it must be used in combination with other evidence for use in identification. Secondly, modern DNA does not show timing, only different origins. For migration patterns to be established, timing must be incorporated into the findings. Another issue is that although mtDNA is generally much more predictable, if there is an unusual occurrence in the history of an organism, such as a bottleneck in the population, the mtDNA information can confound simple interpretations of sequencing. But although these issues are present with use of mtDNA, the advantages still make it preferable for use in studies of migration patterns to nuclear DNA.
Migratory studies require the use of both modern mtDNA, as well as ancient mtDNA. This is because each type of mtDNA comes with its own advantages and disadvantages when it comes to the retrieval and use of information from genome sequencing. From modern mtDNA, evidence can be obtained which can determine the relatedness of different populations of an organism. By comparing the mtDNA sequences, biologists can compare mutations between the populations, and work out how different they are, and what those differences are. However, modern mtDNA sequences show no timing for historical information, making it impossible to be the only type of mtDNA used for mapping migration. Working with modern mtDNA is relatively easy, as the cells are not damaged or degraded; therefore the mtDNA inside the cells is also unharmed. When the mtDNA is not damaged, it is easier to sequence it, meaning that the information from the mtDNA can be obtained in its entirety; making is much easier to work with. There is also a huge number of sources of modern mtDNA as mitochondria are present in almost all body cells, and for modern mtDNA samples, the skin, organs, and other parts of the body which decompose relatively quickly after death are still usable as sources for samples.
Ancient DNA can be loosely described as DNA obtained from any biological samples which have not been preserved for future DNA analyses. Ancient mtDNA is necessary for use in phylogenic studies because it is able to give the sense of the timing of events shown in modern mtDNA, although obtaining usable mtDNA is an issue. This is because ancient mtDNA has to be taken from organisms which have been dead for long enough for the cells, and the mtDNA in them to be degraded and damaged. Sequencing damaged or degraded mtDNA is very difficult and the results can be missing important pieces of information. Secondly, as the organism decomposes and more of the mtDNA becomes degraded beyond use, the amount of mtDNA available for testing decreases to the point where it is difficult to extract enough for a usable sample to sequence. Another problem which must be taken into account is the fact that DNA undergoes post-mortem mutations. The number of post-mortem mutations increases with time, so the older your sample is, the more different the results achieved from sequencing it will be to what the sequence originally was when the organism was alive. There are parts of the DNA which are more susceptible to these mutations than others, so these mutations can sometimes bypass statistical filters used to remove them. It has been suggested that the upper limit of DNA survival is 1 million years in place like the ice caps where it can be frozen and be extremely well preserved. In tropical areas this limit will be much lower, also dependent on the type of organism the DNA is being taken from. Scientists have however; been able to recover DNA from remains up to 5,000 years old in humans, and up to 17,000 years old in other species.
Research into migration patterns of species, such as that of the migration patterns of humans into the pacific, has been greatly enhanced in recent years by the addition of DNA evidence and history. Now that the technology is available, researchers can more accurately identify the origins of organisms and the way different populations interacted with each other. MtDNA is more useful in this research due to the ease of its recovery and its predictability, despite other issues with timing, which scientist work around by combining other data with the sequences to build up an accurate picture of events. The modern mtDNA used in these studies is much easier to work with than ancient mtDNA, but without the use of ancient mtDNA, the sense of timing necessary for an accurate picture of events is difficult to work out. As more knowledge and better technology becomes available to scientists, techniques and quality of information will increase. We will only continue to get a better picture of our past.
Jennifer Randle
Onslow College
Wellington

Michal Denny, LENScience 6 May

Jennifer, thank-you for your very thorough answer. You have obviously spent a lot of time doing back ground reading before constructing your answer. I have one suggestion for you though. Once you have written your first detailed answer to a question like this, go through your answer and ask yourself if everything you have written is relevant to the question? To help you decide what is relevant look closely at the question and identify the key words that help you to focus your answer. In this question I'd highlight the following words:

- mt and nuclear DNA

- ancient and modern DNA

- migration in the Pacific and use these as a guide as to what to leave in your answer and what to remove.

But apart from this your answer is a very clear and logical discussion where you have integrated your biological understanding into a coherent response. These are the skills that Scholarship is looking for so well done!.