Seminar 4 2010 Question Page

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  LENScience Senior Biology Seminar Series 2010

Ancient Secrets in the Seaweed

Seminar 4 2010


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Ancient Secrets in the Seaweed Seminar Question Page

This is the place to post questions before the seminar, that will be answered in the seminar.  You can also add questions after the seminar is over.


Transcript of Questions and Answers from the seminar


1. Kieran - Logan Park
Are different parts of DNA more susceptible to mutation?

Dr. Crid Fraser

Yes. It’s relates to how often the DNA is being used. Mutations are more likely to be found in areas that don’t code for proteins. The parts of DNA that code for proteins are more important and therefore are more likely to be conserved – this means that mutations in these regions are likely to have a major impact on the organism e.g. death or failure to reproduce therefore the mutation isn’t passed on. What’s interesting in the variation that I found in the kelp, I found 117 variable sites over a 600 base pair region. Pretty much all of them were synonymous changes, that is they didn’t actually cause any changes in the protein produced by that part of DNA. So you can get variation that doesn’t affect the protein and that’s often what we’re looking for when we’re doing phylogenetic analysis.
Note from Michal – the chance of a mutation occurring is the same for all parts of DNA, what is different is whether or not that mutation gets passed on to offspring. This is more likely in non coding regions of the DNA.

2. Tom Norton – Nelson College and Cherry – Hillcrest High.
How scientists do chose the target genes to analyse when investigating the phylogeny of related organisms? / How are the haplotypes chosen in the genome?

Dr. Crid Fraser

A lot of it is chance; a lot depends on what you can get to amplify and what turns out to be informative. But you do set out with some ideas in mind e.g. certain gene regions that other studies have shown to be useful in related taxa. It also helps if these genes have been used in other taxa because there are probably primers available that you can use to get something from the DNA and then design better primers. You also need to decide if you are going to use mitochondrial or nuclear DNA (or in plants DNA from chloroplasts). As you know each type is inherited differently. Mitochondrial DNA (mtDNA) is inherited only from the mother (in most species). Nuclear DNA is inherited from both parents. mtDNA is often used for this sort of question because it has a relatively rapid mutation rate (compared to nuclear genes). In addition, it is generally easier to work with (as there are multiple copies per cell) and its mode of inheritance gives unambiguous trees.

3. Cherry – Hillcrest High School
Can you explain the difference between the top and bottom numbers on a phylogenetic tree?

Prof Hamish Spencer

The one at the top is called a Bayesian posterior probability. Its values range between 0 and 1. This number is calculated by a software programme. The programme looks at the phylogenetic tree it thinks is the best and records all the branches in that tree. It then changes that tree a little bit and asks ‘Is that a good tree given the data that I’ve got?’ In other words ‘Is that the kind of tree that can generate the type of data that I’ve got?’ If the answer is yes, then it keeps that tree. If the answer is no then it throws away the rearranged tree, goes back to the original and makes another small change. Again it asks ‘Is that a good tree?’ and if its yes it again keeps that tree. At the end of doing that lots and lots and lots of times the programme looks to see what proportion of the branches found in the huge collection of trees it kept from all its rearranging, are also found in the original tree that it thinks is the best. If nearly all of the good trees have a particular branch from the best tree then there’s good support from the data for that particular branch. The number is the proportion of time the software found good trees with that particular branch. It scales this proportion as a number between 0 and 1.
The likelihood or bootstrap values are quite different. `These are underneath the branches and range between 0 and 100. Bootstrapping is a very clever idea that involves re-sampling the data you have. The programme starts with all the data you originally collected – in this case the DNA sequences - and then takes a sample from it. The programme constructs a phylogenetic tree from the sample and looks to see which of the branches in the tree we think is the best are found in the tree that was constructed from the sample data. Then the programme does this again –takes another sample from the data we already have and looks to see which of the branches from the best tree are also in that tree from the sub-sample. These samples are called pseudo samples. The programme takes a lot of these pseudo samples and constructs a tree for each one. What it is looking for is how often branches found in the pseudo-sample trees are also in the tree you think is the best. The more there are the higher the bootstrap value and the more the data supports the branches that are in that best tree. The number shown is the percentage of times the branch in the best tree is found in the huge collection of pseudo-sample trees.
So while they are completely different ways of coming up with the numbers they use a similar idea of looking at a lot of trees – rearranged or pseudo-sample trees, respectively -- and asking what proportion of those trees contain the branch that you’re interested in.

4. Emily – Auckland Girls' Grammar School
Can the rate of mutation change and what would cause a change to the molecular clock?

Prof Hamish Spencer

Yes the rate of mutation can change. You might have noticed on the phylogram that the branches were different lengths, that all of the species around at the present time didn’t have the same total length of branch leading to them. This is because there is some variation along different branches of a tree in the rate at which their molecular clock is ticking. So there can be changes. The original molecular clock assumed that the rate of change was constant in all the branches of the tree all the time. But now modern mathematical techniques can adjust for differences in the mutation rate.

5. Gracie - Otago Girls
How much variation in the DNA does there have to be for something to be classified as a different species?

Dr Crid Fraser

This is a difficult question to answer. There is no one definite answer; there’s not a specific number that defines how different a clade or a lineage would have to be for you to say it’s a different species. You need to look at other aspects as well, for example morphology – how a plant or animal looks. You might, for example, find that all individuals of a certain colour are quite genetically different to those of a different colour. In the kelp that I was looking at, I got differences in the mitochondrial DNA of around 4-5% between some of the lineages. That would normally be enough for us to start thinking that these are probably different species, but without additional information (such as morphological and ecological data) it is difficult to be sure. Another good test is whether they can interbreed and produce viable offspring, but for kelp this is quite tricky as you don’t have the years it would take to breed kelp to reproducing age in the lab. So in the end we use a combination of genetic data and other factors to draw our conclusions – this is why taxonomy (the science of putting names – eg species names - on organisms) is constantly being revised as more information (eg genetic information) comes in.

6. Jenny – Unlimited Paenga Tawhiti

This species of Kelp is unique because it floats by a honeycomb like structure which is unique. It prevents the kelp from being damaged by strong waves. Is this further evidence that the kelp is more likely to be by dispersed by currents (because it survives for a longer time)?

Dr Crid Fraser

Certainly the toughness and buoyancy of the kelp is helping it to survive for a long time, which will help it to get around the ocean. Another thing about kelp that will help it to disperse is that, unlike plants, kelp doesn’t have roots - it doesn’t need to be attached to the earth to grow. It absorbs nutrients from the water and gets energy from sunlight. So really kelp drifting at sea is just as likely to survive as kelp attached to the rocks (although there are fewer nutrients out in the open ocean). Whether other species of seaweed are as good as dispersing depends partially on their buoyancy and strength. Seaweeds that are less strong and buoyant are likely to sink or get torn apart by the waves. But Durvillaea antartica is a very large plant and a major component of the habitat of the intertidal zone so you can often have other seaweeds species growing on the kelp - if D. antartica can raft across the ocean then it could probably take other seaweed species with it.

7. Amber – Wellington Girls
Why did you choose to study bull kelp for your PhD? What made it so interesting?

Dr Crid Fraser
I never really thought about seaweed until I came to NZ. I was looking for a topic for my PhD as I’d finished my undergraduate degree and was doing my honours in Australia at the Australian Museum - at the time I was working on worms. But I was looking for several things when I was thinking about a PhD. I was looking for a good supervisor or supervisors – people I could talk to easily and who would be there to answer my questions. I had spoken to students who were working with some supervisors that I was interested in and they’d said “don’t work with them, they never have time to answer your questions”. So for a PhD the supervisor is really important, whether you can get along with them and whether they will be there to help you. I was also really keen to get to Antarctica or the sub-antarctic islands. So that was something I was looking for – a project that would take me to some of these places.
The other factor, which may sound surprising, is that I was keen to get out of Sydney - it’s too big and noisy, whereas Dunedin is perfect, nice and quiet and relaxed. So all these factors come into consideration when looking for a project.
Actually when I started on this project I wasn’t planning to work on the seaweed, I was working on the animals which live in the holdfasts of the seaweed. But bit by bit, as I worked on the project I started to get some really exciting results from the seaweed even though initially I’d just been playing with it in the lab as an extra. The results were so exciting that in the end bull-kelp consumed my PhD!

8. Jenny – Unlimited Paenga Tawhiti

Some currents are warm or cool and rise and fall- they also reverse in El Niño/La Nina events. Would these variables have a significant effect on the dispersal patterns of the kelp?

The temperature of currents will definitely have an effect on the kelp, but not so much on where it disperses to as how well it can survive. There are studies that show that drifting kelp from cold climates becomes less reproductively viable at warmer temperatures. This is especially true of Durvillaea antarctica, which thrives in the really cold areas of the sub antartic and around NZ. You don’t find it in the warm waters of the tropics. So if a current like the Humbolt current along Chile takes it up towards the tropics it probably won’t survive and won’t be able to colonise that region.

In terms of El nino and La nina events - they occur over a period of several years so they could help occasionally reach places it wouldn’t otherwise reach. But in the long term what we’re looking at with these phylogeographic studies are processes that drive patterns of genetic variation over thousands of years - so El nino and La nina are unlikely to have an effect on the bigger scale.

9. Theodore - Sacred Heart (Auckland)  and Gemma - Waiuku College
Does the habitat to which the kelp is typically found in ultimately have any affect to whether the kelp is buoyant or not?
Is there kelp in Antarctica because the diagram didn’t show any?

This particular species of bull kelp doesn't occur in Antartica, probably because of ice scour. It does occur on the sub antartic islands where ice only occasionally reaches. For example South Georgia is partially glaciated, and where those glaciers break off, causing chunks of ice to float into the ocean, bull kelp cannot grow. But there are pockets of South Georgia that are protected from ice scour and in those pockets Durvillaea antarctica grows quite happily. So it seems that the limits of Durvillaea are determined by the limit of ice and obviously Antartica is strongly affected by ice.

I think that habitat can affect buoyancy but there’s not a lot of research that has looked into this yet. There have been a number of solid-bladed species (or non-buoyant species) of Durvillaea described from the sub-antartic islands, southern Chile and the Patagonian fjords, which when we’ve looked at them, have turned out to be genetically identical to buoyant Durvillaea antarctica. I think maybe what’s driving this is that around these sub-antartic islands, the water is a lot clearer that around NZ or the coast of Chile. Maybe when the water is that clear, the kelp can occupy deeper waters so non buoyant individuals are able to establish. Normally they need to be buoyant to keep them up the top of the water where they can absorb sunlight. In NZ if Durvillaea antarctica wasn’t buoyant it would down in the murky water, and would not get enough light to survive.



Questions from the seminar that weren't answered at the end

Nelson College. Tom Norton:Student. 2:30 p.m. 9th June 2010

Are there any other studies on other species, which reinforce or contradict the conclusions Ceridwen has drawn from her research?

Michal Denny 14th June 2010

For the answer to this question go to the Challenge 1 discussion page, where another student has asked a similar question http://lens.auckland.ac.nz/index.php/Seminar_4_2010_Discussion_Page



Unlimited Paenga Tawhiti. Student. Jenny Loader. 8pm; 9 June

I can see from the charts given that the Kelp is very likely to have been spread by currents. The 'red' subspecies can be traced from NZ (where it probably survived the last ice age) right around Antarctica. The same is true for some Chilean species which have probably dispersed via the ACC and then the South Pacific Peru current. This current flows to the equator which may explain why some Chilean species are not represented in the rest of the Sub-antarctic region.

Could this evidence be further proven by analysing the smaller differences between gene pools in the same subspecies? - the most varied one would theoretically be the population around the Macquarie Islands- having travelled almost all the way back to NZ

Dr Crid Fraser - 15 June 2010

Yes - even though we found exactly the same mitochondrial DNA haplotype at almost all the sub-antarctic islands (this is how we know these populations are all probably recently derived from a single source), the populations could possibly show genetic differences in other markers. For example, there are bits of DNA called 'microsatellites' - these are repeating fragments of short sequences, eg AGAGAGAGAGAGAGAGAGAG. When this sort of sequence is being copied, sometimes mistakes are made - in a way, the copier gets lost in all the repeating AGs and adds one or two extra, or drops some, so individuals end up with AG repeating sequences of different lengths. This is a good way to study small differences within and among populations - I think if we tried this in kelp, we might find that some of the sub-antarctic populations are genetically distinct from others. This would be cool, because then we could fish rafts out of the sea and be able to pinpoint which island they came from!

For the other part of your question: I think that kelp populations are very quickly established, and that once they are there it is hard for new genetic variants to break in. Imagine the coast of the South Island, New Zealand. Almost every available bit of rock is covered by kelp! Now imagine that a raft of bull-kelp drifts up to New Zealand from the sub-antarctic. If it is winter, the bull-kelp might be reproductively active, and if it is a female plant it would be releasing lots of eggs. But all the local, attached plants would also be releasing eggs and sperm! So the ocean near the shore would be a thick soup of millions and millions of kelp eggs and sperm (think about this next time you're surfing in the foam, hehe). The number of eggs released by a rare, rafted immigrant kelp would be tiny compared to all the eggs and sperm released by locals. Let's say there had been a storm a few weeks earlier, and a rock had rolled over, making one square metre of fresh rock available for new kelp to settle on. What are the chances that the eggs from the raft would get to settle on that rock? It is much more likely that the area would be settled by a new kelp of local origin. So, I think that once a population of kelp is established, new genetic variants have a lot of trouble getting in. In contrast, imagine the sub-antarctic islands just after the sea-ice receded after the LGM. Each island would have had beautiful, clean rocky shores - for any raft washing up on these shores, there would have been lots of opportunity for eggs and sperm to settle. This is why we see so little genetic variation in the sub-antarctic. Over time, mutations should lead to small changes in these populations - which explains why there is genetic diversity around the NZ sub-antarctic and and NZ mainland and Chile. You also asked if the 'red' kelp might survive better at colder temperatures. This is a good point, but I don't think it is likely - for one thing, even though the 'red' lineage was genetically distinct, almost all the differences in the DNA between this lineage and other lineages were synonymous (they would not cause any change in the protein produced). For another thing, the New Zealand sub-antarctic islands are much more genetically diverse than most of the sub-antarctic, and the water temperatures there are just as cold.


Theodore – Sacred Heart

Is this an example of the founder effect?
Prof Hamish Spencer - 15 June 2010

Yes. Indeed, it is an apparent example of multiple founder events. One (or more) for each island recolonized.


Ajay – Mt Roskill Grammar

How would you go about making or designing a primer to use in PCR?

Dr Crid Fraser - 15 June 2010

It is difficult to make a primer when we know NOTHING about the target bit of DNA - but usually we know something, or we have primers that work on related taxa. For example, if I was working on a crustacean (eg a prawn), I could look at sequences of DNA that other people have found for other crustaceans (eg crabs) and then try them out on the prawns. They probably wouldn't work very well, but with some luck and some effort, I might be able to get one or two sequences back. Once I have some sequences for my target species, I can design primers based on them. Primers need to be short (eg about 20 base pairs long). I would try to put a forward and reverse primer as far apart as possible at either end of the sequence. There are some characteristics of a short sequence that make a 'good' primer - eg the primers should not tend to bind to each other, or to fold over and bind on themselves, etc. - there is software that can tell you how well the new primers are likely to behave. A good starting place for designing primers is GenBank (http://www.ncbi.nlm.nih.gov/genbank/). This is an international database of DNA sequences - every time a paper is published that uses genetic data, the sequences have to be put into this or a similar database, so that anyone can see them. If I was starting work on a species had not been worked on before, I would look at GenBank to get sequences of closely related species, and I could design primers to try based on these sequences. So why design new primers if you need old ones to start with? Well, primers that are designed specially for one species or group of species can work much better and eliminate the risk of some errors. For example, I have just started working on a microscopic seaweed that is a parasite of bull-kelp. Because it grows through the bull-kelp tissue, when I extract its DNA it is hard to separate it from the kelp itself. But I have managed to design specific primers that will ONLY work on the parasite - that way I can be sure I am amplifying the right thing in the PCR, without worrying that I accidentally got the kelp instead.

Another approach has just become available with 'next generation' sequencing techniques. There are new technologies that let us sequence lots of DNA from an organism without necessarily knowing much about its DNA to begin with (although these sorts of technologies are often not very specific - they give back lots of bits of DNA sequence, but we generally don't choose which bits we get).



Amber – Wellington Girls

Although there have been cyclic patterns of ice ages and temperature changes do you believe that humans have also contributed to climate change?

Dr Crid Fraser and Prof Hamish Spencer - 15 June 2010

HAMISH: Yes. The scientific evidence, from multiple sources, is overwhelming.
CRID: Absolutely. There is a huge amount of evidence to show that humans are having a major impact on climate change. Of course, the Earth has gone through natural cycles of climate change in the past, and will continue to do so in the future, but it is very clear that human activities are speeding up the rate of global warming (what's particularly worrying about this is that plants and animals might not have time to adapt or migrate to better climates - many will be driven to extinction). Climate change is now happening faster than we think it ever has before. Because we know (for sure) that some of our activities (eg burning fossil fuels) are changing the state of the atmosphere (see 'greenhouse effect'), and because we can see that climate change is speeding up as we increase these activities, we know we are changing the Earth's climate by our activities. Please read this letter signed by many of the world's most significant scientists (this was recently published in one of the most reputable scientific journals in the world) - it clarifies many of the issues: http://www.haowomen.info/cgi/reprint/sci;328/5979/689.pdf
Okay, so I know you are thinking "well, so what? If humans are influencing [note - I don't say CAUSING - the climate change we're seeing now is a combination of natural fluctuations AND human-induced changes] climate change, what does it matter, since the Earth has gone through cycles of climate change before?"

Well, think about it this way. Every major climate change in Earth's history has led to major changes in the distributions of plants and animals. Many that are unable to move or adapt go extinct. We can be pretty sure that, if we keep speeding up climate change, many plants and animals will disappear forever. This is not just important from the point of view of 'once lost, never regained' - yes it will be very, very sad if many taxa go extinct - but from an anthropocentric (human-centred) point of view, our own survival as a species could be compromised. Loss of biodiversity will lead to all sorts of changes we just can't predict (hypothetically - imagine there's a soil fungus that is really important for growing sugar cane, and climate change means the beetle that carries the fungus dies out, so the fungus doesn't spread - no more sugar cane! Yes, I'm making this example up, but the point is that every ecosystem is complex, and losing parts of an ecosystem can lead to drastic changes elsewhere). Also, sea level changes will force huge changes in where we can live - many major cities are on the coast.
I don't want these sorts of changes to happen - I like our world as it is. All it takes is a bit of awareness. We're a smart species, and we can design technologies to mitigate our impacts on climate change. The reasons we aren't really doing it yet are: 1) it's expensive, so governments prefer not to do it - but remember that most governments are only looking a few years ahead, until the next election, and 2) we're lazy - it's easier to drive a car to work and tell yourself 'I don't believe in climate change' than to walk or catch the bus. I'm not saying you need to go and live in a bark hut and not use electricity - just think about how you can make some differences at home, and lobby governments to make bigger changes that will really matter.



Additional Questions Post Seminar

Nelson College. Ellery Daines: Student 10/6/10

Was research done to prove that there was in fact any kelp on these sub-antarctic islands before the LGM?

Dr Crid Fraser - 11 June 2010

That's a good point - we are making a big assumption in saying that the sub-antarctic islands have been 'recolonised' by bull-kelp (Durvillaea antarctica) since the LGM. Okay, we have good evidence that those populations are pretty new, but how do we know bull-kelp was actually there before the LGM? In fact - we don't! We can't be sure. However, I feel reasonably confident in making the assumption that it WAS there before the last ice age. The buoyant characteristic of this bull-kelp is almost certainly not new - there are 'old' populations in both New Zealand and Chile (we can infer that from the high genetic diversity in these regions), so it looks like the species has been able to float across oceans for some time. If the kelp was able to travel (for example) from New Zealand to Chile long ago, why wouldn't it also have reached the sub-antarctic islands? This species is now found all over the rocky shores of pretty much all sub-antarctic islands that are beyond the reach of sea ice, and I can't see any good reason to think it never reached these places before the current interglacial period. However, I can only assume that it was - seaweeds like this hardly ever leave fossils, so we can't be sure. Your questions highlights the fact that in science we can never prove anything - all we can do is gather as much evidence as possible and make informed conclusions based on the results. One of the great and exciting things about science is that, as new evidence comes out, we often have to throw old hypotheses away and change our ideas.