Seminar 2 2011 Question Page

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  LENScience Senior Biology Seminar Series 2011

Rethinking Polynesian Origins

Seminar 2, 2011

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SouthCity High School: Student BC - 25th April 2pm

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Rethinking Polynesian Origins Seminar Question Page

This is the place to post questions before the seminar, that you would like answered in the seminar.  We will post answers to all the questions asked on the wiki, during the seminar and in the LiveChat here. You can also add questions after the seminar is over.

Palmerston North Girls' High School: Student SP - 3rd April 11.59am

Hi. I was wondering the rate at which DNA breaks down after an organism's death, and therefore how it is possible to extract intact DNA which is thousands of years old?

Professor Lisa Matisoo-Smith, Allan Wilson Centre, Live 7th April

The main factor that affects the breakdown of DNA and therefore how old the remains can be to successfully extract DNA from, are environmental conditions - the conditions the bones were kept in. Neanderthal DNA which is between 30 000 and 40 000 years old, has been successfully extracted from remains found mostly in cave sites in Northern Europe. The constant cool temperatures, and dry conditions are probably the reason why these remains have been relatively well preserved. The hot and wet conditions in the Pacific are the worst possible conditions for DNA preservation so we have a hard time getting DNA out of material that's only a few thousand years old.

Also, what are the key differences between the Lapita people and today's modern-day humans? Are we simply more evolved or an entirely different species? If both types of people still existed, would inter-breeding be possible? Thank you. :-)

Professor Lisa Matisoo-Smith, Allan Wilson Centre, 13th April

There are no differences at all between the Lapita people and people living in those regions of the Pacific today. With few exceptions (perhaps the small population of Homo floresiensis living until 13,000 BP in Flores) all people living for the last 30,000 years belong to the same species – Homo sapiens, and could interbreed. If a “Lapita” person was sitting next to you in class today, you wouldn’t spot them as being any different from the population of New Zealand in general! Keep in mind that the Lapita people are only removed from you by about 120 generations – or 3,000 years.

Epsom Girls Grammar School: Student EC - 31st March 10.35am

I was wondering how is Ancient DNA extracted and preserved? Also, how do researchers find out how old an extract of ancient DNA is?

Professor Lisa Matisoo-Smith, Allan Wilson Centre, Live 7th April

As soon as an organism dies the DNA starts to break down and won’t be repaired. This process is also affected by the environment in which the organism died and the bones are left in. The DNA can be preserved in cells found inside the cortical bone (the outer tissue of bone). But from the time of death the tissue and cells are being attacked by environmental factors. We find the best preserved DNA in teeth because the enamel is very strong and will protect the DNA. We can also get DNA from other bones but it is generally damaged and mixed with DNA from the environment such as the bacteria which have got into the bone

DNA is extracted by grinding the bone or tissue, bursting the cells and extracting the total genomic DNA (generally we get it to bind to silica beads and then wash away all of the cell debris). We then have to amplify the particular bit of the DNA we are interested in - for example the mitochondrial DNA – using the Polymerase Chain Reaction (PCR).

When we extract the DNA, we extract all the DNA that is there – not just from the organism that we’re interested in but all of the other organisms that have invaded that bone. The big problems for researchers have been dealing with all the other DNA that’s contaminated the sample and also the damage done to the DNA. This is one of the big advantages to the new Next Generation Sequencing technologies (for more on these and how sequencing technology has changed click here >>>  ). In the past we used PCR and primers to amplify the specific base sequences we were interested in. But because of damage the DNA gets broken into small pieces and changes to the bases can occur. That was a real problem with the Neanderthal DNA; it was in such small fragments that most of it couldn’t be amplified using traditional approaches (PCR and Sanger sequencing). But the new Next Generation Sequencing can amplify tiny fragments of DNA and you can amplify all of the DNA. The new technology also means we can get more than just mtDNA from ancient DNA samples. Because there are lots more mitochondria in each cell, there’s more chance that mtDNA will be preserved. But the new techniques mean we can now get nuclear DNA as well as mtDNA.

To find out how old the DNA is we look at the archaeological context the fossil remains were found in or we can radiocarbon date the bones.

I am also interested in participating in the National Genographic project. How would I take part in this if I was interested in finding out more about the ancestry of my family?

Professor Lisa Matisoo-Smith, Allan Wilson Centre, 13th April

Have a look at the Genographic web page (click here >>>) – all of the information is there about requesting a kit to sample and have your DNA tested. Women can only obtain their mtDNA information; Men can obtain either mtDNA or Y chromosome lineages, or both – if they want to pay for two kits. It costs about $100 US dollars for each test.

Epsom Girls Grammar School: Student JT, 5th April 17:50pm

Are there any differences between the modern humans who lived in the time of the Neanderthals and interbred with them, and modern humans of the present time?

Professor Lisa Matisoo-Smith, Allan Wilson Centre, Live 7th April

It depends on what you mean by differences, but what we see in terms of the DNA, certainly mtDNA, between modern and ancient populaitons of Homo sapiens is that the variation is within the normal range of variations. So we are all members of the same species. However, as more nuclear DNA sequencing is done from samples from ancient Homo sapiens it will be interesting to see if there are differences associated with more recent population events such as the Plague which caused a major population crash so we may see some differences in frequency.

Hutt Valley High School: Student JC, 7th April

Humans have trillions of cells most with mitochondria in them, how variable are the mtDNA sequences between the cells of an individual human?

Professor Lisa Matisoo-Smith, Allan Wilson Centre, 13th April

Generally the DNA in all of our cells is identical (nuclear and mtDNA) – but occasionally there is a situation where there are more than one mtDNA sequences in an individual cell or in different cells – this is known as heteroplasmy, and it is relatively rare. This can be caused by a mutation occurring in one of the mtDNA of an oocyte but the mutation has not yet reached fixation in the entire mitochondrial genome of the oocyte. Thus the child inherits two different mtDNA sequences – which continue to reproduce themselves. Eventually over a few generations, one of the mtDNA types generally will become the dominant type and therefore the single mtDNA type that is passed on. In a sense we are watching evolution in action when we see this happen.
If the mother has a heteroplasmy in her mtDNA, her children could experience one of several possible outcomes:

1. The child has a heteroplasmy at the same position. The child could inherited some mitochondria with the ancestral genome and some with the descendant genome, so the child would have some of each in his or her cells. The proportion of ancestral to descendant genome can vary in each generation and in each child.
2. The child has only the descendant genome. Only mitochondria with the mutation were passed on to the child. If the child is female, then her children will also inherit only descendant genome.
3. The child has only the ancestral genome. Only mitochondria without the mutation were passed on to the child. If the child is female, then her children will also inherit only the ancestral genome.
Good question!

Rotorua Boys' High School Student (Live question 7th April)

Are parasites suitable for commensal studies and has anyone studied this before?

Professor Lisa Matisoo-Smith, Allan Wilson Centre, Live 7th April

Yes we have had people using parasites for example Helicobacter pylori which is the bacterial parasite that causes stomach ulcers. We actually see very population specific strains of this parasite. Researchers are also looking at other parasites and seeing if they could be applied to the commensal approach.

Question from the LiveChat (numerous students 7th April)

There has been a lot of discussion on the LiveChat of the impact of disease exposure on the survival of species as they migrated from Africa and beyond. Can you explain the relationship between exposure to new diseases and migration patterns?

Professor Lisa Matisoo-Smith, Allan Wilson Centre, Live 7th April

This is an interesting question. If a population is constantly being exposed to new diseases then the population will eventually develop resistance to that disease. But it is a evolutionary race between the host and the disease causing organism. European populations developed resistance to many diseases over a long period of time, whereas other populations not in that same environment were not exposed to those diseases and therefore didn't develop a resistance. So when Europeans arrived in the Pacific they were carrying disease organisms that had little impact on their own health, but when introduced to a population that had no resistance it had a significant impact on the new population. This was a major problem wherever Old World populations came into contact with New World populations such as in the Pacific and the Americas.

But in some cases migrations into new environments reduced the pathogen and parasite load of certain populations. We think for example the movement of people across the Bering Strait (between North East Asia and the Americas) is thought to have reduced the pathogen load. 

Auckland Grammar School: Boris Yow (Live question 7th April)

Is there any correlation between an increase in brain capacity and the secondary migrations into Polynesia for example to allow for the greater navigational skills?

Professor Lisa Matisoo-Smith, Allan Wilson Centre, Live 7th April

What is very interesting about this is that Neanderthal had a bigger brain capacity than modern Homo sapiens, but ultimately became extinct. But in terms of the migrations through the Pacific there is no evidence of greater cranial capacity. We're talking about populations of Homo sapiens only within the last few thousand years so we are a single species with no significant variation in cranial capacity other than that due to general variation in body size.

Sacred Heart College: David B (Questions from the LiveChat 7th April).
When working out evolutionary relationships to create a phylogenetic tree, how do you calculate when a mutation happened?

Professor Lisa Matisoo-Smith, Allan Wilson Centre, Live 7th April

There have been many studies that have shown that mutations occur at a predictable rate and these can be used to estimate when a mutation first appeared. What we're also doing now is using dated fossil remains to test the assumptions that underpin these calculations. We have to generally use some well accepted date to calibrate the “clock” or rate of change of the particular part of the genome we are studying. Commonly we use the date of the human/ape split (5-7 MYA) to calibrate the rates when we are looking at variation between human populations. We determine the topology or general shape of the tree first – seeing how closely related the various sequences are – this gives us the relative relationships. We then have to determine the root of the tree to indicate the oldest or most divergent lineages. A chimpanzee sequence was used to root the human mtDNA tree, because we know that we shared a common ancestor with the other great apes long ago – so it is used as the “outgroup” which determines where the root of the tree will be.

For more about about how molecular clocks are used to estimate species divergence click here>>>

Were there any hominins apart from Homo sapiens that got over the water gap (Wallacea)?

Professor Lisa Matisoo-Smith, Allan Wilson Centre, 13th April

Homofloresiensis got out to Flores, which would have involved crossing major water barriers. But there is no evidence of H. floresiensis in Australia or New Guinea, so it didn’t appear to make it all the way to Sahul.

Is there a difference between the Polynesian pig and the European one?

Professor Lisa Matisoo-Smith, Allan Wilson Centre, 13th April

Nope – they belong to the same species – but there are a few unique mtDNA mutations that occurred in the earliest pigs that were brought out to the Pacific and we do still find those mutations in some of the pigs living on Pacific Islands today. Many other lineages however have also been introduced since European breeds have been traded and brought into the region.

Makoura College: Tessa (Question from the LiveChat 7th April).
In the diagram showing gene flow between the different populations of Homo, who were the Han population?

Professor Lisa Matisoo-Smith, Allan Wilson Centre, Live 7th April

The Han are a Chinese population.

Do scientists have mtDNA info on the Moriori compared to the Māori populations?

Professor Lisa Matisoo-Smith, Allan Wilson Centre, 13th April 

No, not yet as far as I am aware. Samples have been collected from Māori from both the north and south Islands, but I do not know if any sampling has been undertaken specifically from individuals of Moriori descent.

Are there any unusual gene markers that show up in Pacific populations indicating any genetic contributions from South America?

Professor Lisa Matisoo-Smith, Allan Wilson Centre, 13th April

So far there is no ancient DNA evidence of South American genes in the Pacific. There has been historic admixture as many Pacific peoples were forcefully taken for labour in South America during the historic period and some returned with South American partners. Rapa Nui (Easter Island) which is now considered to be part of Chile, has the highest levels of admixture (between Pacific and South American populations) but it appears that this is all relatively recent (not pre-Columbian). We do know, however, that since the kumara was present in the Pacific prior to the arrival of Europeans, that there was some contact between the two groups – the name itself is derived from the American Indian (Bolivan) word ‘Kumar’ – so there had to have been contact that included some face to face discussion – in other words, the kumara couldn’t have floated over to the Pacific islands. We think that it was most likely that the Pacific peoples – who were some of the greatest sailors and navigators in the world, were the most likely ones who made the contact by sailing across to the Americas and back, and not the other way around.

Hillcrest High School students (Question from the LiveChat 7th April).

Martin: I was under the impression that a set of seven substantially different Mitochondrial Eves had been traced rather than just one. Can you shed some light on this or am I missing something obvious?

Professor Lisa Matisoo-Smith, Allan Wilson Centre, Live 7th April

It's not that you're missing something obvious - this shows the power of the popular press. The Seven Daughters of Eve is a book written about the various mitochondrial lineages that we see primarily in European populations. The seven lineages are all part of the post Out of Africa migration - the L3 lineage we referred to earlier. But they all share a common maternal ancestor - Mitochondrial Eve. There are multiple mitochondrial lineages that can be traced back to a single mitochondrial lineage that existed in Africa around 100 000 to 150 000 years ago.

Vincent: Is there any evidence linking skin colour and climate - especially in the Pacific - thinking of the wide range of skin tones and latitudes in the Pacific islands. If not climate - any other links?

Professor Lisa Matisoo-Smith, Allan Wilson Centre, 13th April

That is a good question and an explanation of skin colour variation would require a major discussion – maybe a future LENS seminar??? Much work has been done on the evolution of skin colour variation (check out this excellent lecture by Nina Jablonski - Click here>>> )

But in terms of much of the Pacific (Remote Oceania), people have not been in the environment long enough for major changes to take place (only 3000 years). But, the fact that we have the highest rates of skin cancer in the world in NZ and Australia, does indicate that people with little melanin (light skinned) are not ideally suited to the high UV we have in this region of the world. Darker skin provides protection from UV radiation. We do, however, need a certain amount of UV in order to produce Vitamin D – without it we end up having rickets and other diseases caused by lack of calcification of the bones. Unfortunately, we are seeing the rates of these diseases increase today with darker skinned people (or even not so dark skinned people who cover themselves e.g. in burka or even in sunscreen or just staying inside all of the time) living in low UV regions.

Chris: If the final migration into Polynesia only happened 2000 years ago and it originated from an area more around Taiwan rather than further Oceania might it have been influenced or affected by the Chinese civilisation present at that time? I believe the Han dynasty at that time had far-reaching influence and had navigational technology such as the compass. I've heard that dingos in Australia were introduced by Chinese sailors.

Professor Lisa Matisoo-Smith, Allan Wilson Centre, 13th April

Dingoes have been in Australia for at least 3,500 years (which means that we have archaeological remains dating to that time), but they may have arrived earlier. They can be traced through their mtDNA back to Asian village dogs, and they were probably introduced through trade and migration routes that we know existed between Island Southeast Asia and Australia/New Guinea. Several items (obsidian, jade, animals etc) have been traded through the region for thousands of years.

Jason: Why is it that only the tips of the Y chromosome are changed (recombined) and what are the processes that cause these changes?

Professor Lisa Matisoo-Smith, Allan Wilson Centre, 13th April

Recombination is a natural process that occurs between homologous chromosomes during meiosis. The pseudo-autosomal parts of the Y may recombine with portions of the X chromosome but most of it does not because the X and the Y are not homologous chromosomes.

Kelston Boys: Iefata (Question from the LiveChat 7th April).

Did the Moriori have a similar language as the Polynesians?

Professor Lisa Matisoo-Smith, Allan Wilson Centre, 13th April

Yes – the Moriori language is very closely related to Māori (some even suggest it is a dialect of Māori) and both are very closely related to other Polynesian languages in particular those of East Polynesia. New Zealand Māori, Cook Island Māori and Tahitian are all pretty much mutually intelligible and belong to a subgroup of Polynesian languages called Tahitic.

Are the different races of Pacific people formed out of mutation?

Professor Lisa Matisoo-Smith, Allan Wilson Centre, 13th April

There is only ONE race of people in the world. The different characteristics of the peoples of the Pacific today are the result of different population histories and interactions as well as adaptations to local conditions (such as malaria). Many of the people who live in Near Oceania (New Guinea and the Solomon Islands) can trace their ancestry back to the peoples who arrived there over 30,000 years ago. The peoples of Remote Oceania, including Polynesia, have mixed ancestry including these ancient populations of Near Oceania and more recent arrivals, probably coming more recently (in the last few thousand years) from Island Southeast Asia.

Is there evidence of diseases when Homo erectus was alive?

Professor Lisa Matisoo-Smith, Allan Wilson Centre, 13th April

We do see that Homo erectus suffered from many of the same diseases – for example bone infections that Homo sapiens do, but we will only ever know about the diseases that affect the bones – that is all that remains of Homo erectus.

Onehunga High School students  (Questions from the LiveChat 7th April).

Andrew: Can a huge contribution of genes from one individual be detected in Polynesia?

Professor Lisa Matisoo-Smith, Allan Wilson Centre, 13th April

No – we do not have any evidence that suggest that any one individual had a major genetic contribution to Polynesian populations. Some researchers however think that they might be able to track the movement of Genghis Kahn in his raids across Eurasia through looking at the distribution of what they think is his Y chromosome type! See: Zerjal, et el.; Xue, Y; Bertorelle, G; Wells, RS; Bao, W; Zhu, S; Qamar, R; Ayub, Q et al. (2003). "The Genetic Legacy of the Mongols". The American Journal of Human Genetics 72 (3): 717–721. Click here to read this paper >>>.

Maryanne: In the seminar it was said that Polynesian animals differ from the European ones of which they have descended - why is this so? What could have caused this?

Professor Lisa Matisoo-Smith, Allan Wilson Centre, 13th April

I think you may have misunderstood. With the exception of the kiore rat (Rattus exulans) the Polynesian animals are NOT different from the European breeds. Rattus exulans is however a different species than the rats introduced by Europeans (Rattus rattus and Rattus norvegicus). All three of these Rattus species are originally from Asia and they were carried by / with humans around the world.

Maryanne: How do we know that carbon dating is correct and accurate to the time period?

Professor Lisa Matisoo-Smith, Allan Wilson Centre, 13th April

There are many debates and discussions about the accuracy of radio carbon dating – and we know that different types of samples can be problematic or need corrections. But we do understand the chemistry pretty well to be able to recognise these problems and correct for them. Generally, we try to obtain multiple radio carbon dates from archaeological sites and on different types of material (e.g. bone, shell, wood) to make sure that they give reasonably reliable results. We also make sure that the dates make sense in terms of the context - like the samples obtained from the deepest layers should be the oldest.

Maryanne: Niueans are said to be made up of populations from Tonga and the Cook Islands do you think it would be possible for Niueans to resolve which populations they come from?

Professor Lisa Matisoo-Smith, Allan Wilson Centre, Live 7th April

Interesting question.What we have to remember here is that when we talk about populations we're not talking about biologically discrete identifiable groups. All the Pacific peoples share the same genes - there are not specific markers for say Tongans or Cook Islanders. What we know from mtDNA studies that have been done so far is that the mtDNA variation we see in New Zealand is a subset of what we see in East Polynesia, which is a subset of what we see in West Polynesia, which is a subset of the variation we see in other Pacific populations.

Erica: When working out evolutionary relationships to create a phylogenetic tree, how do you know they are related?

Professor Lisa Matisoo-Smith, Allan Wilson Centre, Live 7th April

We compare the DNA sequences and look at the similarities and differences we see in the DNA. The more similar the DNA sequences are between two organisms, the more recently they shared a common ancestor, and the more closely related they are compared with sequences that show more variation.

Onslow College: Jennifer (Questions from the LiveChat 7th April).
Given that Māori are so closely related to each other can you please explain why they find it hard to get compatible transplant tissues?

Professor Lisa Matisoo-Smith, Allan Wilson Centre, Live 7th April

This isn't my field of research but I think one of the problems with finding Māori and Polynesian organ donors is to do with the histocompatibility variation that we see in Pacific populations compared to European or Asian populations, it's just a different combination.

Kumara arrived in New Zealand before Spaniards began moving around Polynesia. Is this evidence for contact of Polynesians with South American indigenous culture? Are there any studies which have been done on commensal plant migration?

Professor Lisa Matisoo-Smith, Allan Wilson Centre, 13th April

Excellent question - Yes! The presence of the kumara is indeed evidence of contact – and a post-doc, Andrew Clarke, who is working in our labs here in Dunedin is looking at genetic variation in kumara and other commensal plants (for example the bottle gourd). You can check out his web site that has links to popular articles about his research (Click here>>>). Plant genetics are much more complicated than human or animal genetics though – and the remains rarely are recovered from the archaeological record, so we have to consider the possibility of recent admixture.

We have also identified the prehistoric introduction of chickens from Polynesia to the Americas (using ancient mtDNA studies) and have published this in the Proceedings of the National Academy of Science (PNAS) – ‘Google’ Alice Storey and Pacific chicken DNA to read about it!A link to the PNAS paper can be found in the seminar resources section of the seminar webpage. Click here>>>