Andrew Pask Associate Professor and Reader
The University of Melbourne
"Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore"
https://www.nature.com/articles/s41559-017-0417-y
Andrew very Kindly answered questions from the worlds best Facebook thylacine page
https://www.facebook.com/groups/ThylacineDebate/
Q/Do they have a rear opening pouch ?
Pask-Yes – a few different marsupial species that burrow have this (wombat for eg.) – presumably so they don’t fill it up with dirt while they are digging.
Q/How did the role of climate (penultimate glacial cycle) accelerate” a decline in diversity ?
Pask-During times of climate and vegetation change populations have to move – food can become scarce and this leads to a decline in animal numbers. This decline in population size often leads to a loss of genetic diversity.
Q-What are the hurdles (and possible time frame) for a cloned thylacine to become a reality?
Pask-Firstly, we cannot clone without a living cell, so the de-extinction projects are creating genomes, rather than cloning a genome. For the mammoth project scientists are using an elephant cell line and adding the changes to make it look like a mammoth genome. A similar approach would be needed for the thylacine. The closest living relative is a numbat and they are anteaters. so not an ideal genome to begin with! Devil has a closer diet. There are a LOT of hurdles. Currently genome editing on the scale needed to make a thylacine-like devil genome is not possible – but there have been huge advances in this space. If it moves forward at the same pace as next-generation sequencing technologies… then it is feasible to think that in a decade (or 2) genome editing of this scale might be possible.
The next hurdles are all associated with what to do with that cell. Assisted reproductive technologies (ART) are well developed for placental mammals. Think IVF. This can be done in humans and mice and livestock – but this has not been achieved yet in marsupials. Making recombinant embryos (with different cell types) is also well developed in placental mammals but has not been done in marsupials. We also don’t know a huge amount about the early development of the marsupial embryo and when best to transfer a potential embryo back into the females reproductive tract. We would have to find a good surrogate mum – for both the size of the developing young and time of gestation and pouch exit – to host the embryo. None of these hurdles are trivial.
Q-A very few species have black striped hind quarters, the numbat and the african zebra duiker for instance. These species live in very different ecological niches. Why the similar coat paterns? What is the adaptive 'purpose' of the stripes? Does it have anything to suggest about thylacine ecology/behaviour?
Pask-This is a great question that has stumped scientists for years. The short answer is – we have no idea! Stripes were thought to aid in camouflage or being cryptic while stalking prey, but some good studies in to this phenomenon have never confirmed that stripes give any advantage on that front! So we don’t know! Probably different species have them for different reasons though.
Q-How limiting was the lack of genetic diversity? Was there specific markers for afflictions detected?
Pask-The paper we just published looked at the effective population size – estimating the number of breeding individuals – and we showed it went though a bottle neck, meaning that the numbers got very low. This goes hand-in-hand with a loss of genetic diversity (differences) in the genome. We also published a paper a few years back that did a survey of a lot of museum specimens and looked at a region of their mitochondrial DNA across a broad range of thylacines collected both before and during the bounty (when they were hunted). This confirmed a VERY low amount of genetic diversity in their DNA, even less than we currently see in the devil population which contracted the facial tumour and enables it to spread so readily. So based on a similar marsupial with a similar lack of diversity – this is our marker for population health.
Q-Where did the museum obtain it's sample?
Pask-The specimens comes from a full litter of four pouch young that were received with their mother (C5752) in 1909. All four pouch young were removed from the after their mother was killed in the wild.
Q-Firstly thank you very much Andrew for this, and obviously for your contribution to the subject. I'd like to ask something that has long confused me but which has been discussed in your paper, convergence. in the paper it says 'diet was a significant predictor of cranial shape', but as I understand it the diet as suggested by dentition of thylacines, would have been far less generalist than canids? One quick one, am I correct in understanding that your results suggest that the Thylacinidae are a sister group to the Dasyuridae, and is it the numbat or the devil that's most close to it. OK that was two. Thank you very much.
Pask-Thylacines represent a basal branch of the Dasuromorphs and the numbat is the next and closest branch to the thylacine. Ie. Its closest living relative.
The convergence of skull shape that we see, as measured by similarities in landmarks across the skulls, is driven by diet as large predatory mammals require similar features to allow similar bite forces, muscle attachment sites and other adaptations to deal with the mechanical loading of large prey. The thylacine shared a near identical dental formula (4.1.3.4 / 3.1.3.4) to other closely related taxa, including small insectivorous bandicoots (5.1.3.4 / 3.1.3.4 ), but dissimilar to the canids (3.1.4.3 / 3.1.4.2), however, the teeth have been adapted for carnivory ie have evolved long sharp canines for piercing and jagged molars for tearing flesh - similar to the kinds of tooth structures seen in canids (another example of convergence driven by diet).
Our landmark analyses did not consider tooth type or shape. Skulls are used for lots of things other than just eating/obtaining prey, so there may be other behavioural, physiological and mechanical aspects behind their convergence in skull shape. (answered by Axel Newton and Christy Hipsley who did the skull morphometrics)
Q-What the realistic percentage chance of a cloned thylacine taking its first breath in the next 20 years?
Pask-That’s difficult to answer. See list of hurdles to a previous question above. I do think we will see some de-extinction projects get close within that time frame – like the mammoth – there is a huge effort on that front. My research is not aimed at de-extinction, but I will follow the advances with a great deal of interest!
Q-Do we have knowledge about the relative genetic diversity of museum specimens? If so does it show a lack of diversity across samples?
Pask-Yes. We did deep sampling and they concur with VERY low genetic diversity estimates – see above. This diversity was limited both before and during them being hunted to extinction. (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0035433)
Q-In the unlikely event that thylacines were re-discovered in the wild would cloning help supplement, from a genetic point of view what would be a population in crisis?
Pask-The whole process is MUCH easier if there were a living animal discovered. Yes the species would still be in very bad genetic shape, but under proper management even species with just a few animals left – like the cheetah can survive.
Q-Are there avenues of funding readily available to undertake your work - if so what is the major source of the funding?
Pask-The thylacine has never been funded by either of the major grant schemes (ARC or NHMRC) who fund the majority of Australian science. Most of my basic marsupial biology research has been funded by the ARC. The thylacine work was funded from university funds that I was awarded over the years. It has been a real labour of love project for me. I am fascinated by the thylacine and what we can learn from this unique species!
Q-Is work on bringing back other extinct species a help to your work - i.e., general advancements in technology and knowledge that can be applied to your work?
Pask-Definitely. De-extinction is not the goal of my research on the thylacine. But I will watch the de-extinction literature closely. There are big teams of outstanding researchers working on ways to facilitate the process of de-extinction and they have made some amazing progress. As you can see from my response above – even with the tech to make a thylacine-like cell – we still have a lot of hurdles before we could bring one back…
Q-What is the ultimate goal? Is it to learn more about DNA, genetics, cloning, or is it to return the animal from extinction?
Pask-My lab studies evolution and development – Evo-Devo. We have the complete genomes now of 1000s of species, but we still don’t understand a lot about how the genome functions. My main interest with the thylacine is because it is an extreme example of convergence with the dogs. This enables us to ask a simple question. When two species evolve to look nearly identical, do you also see the same changes in their DNA to get to that body form. Then we can ask, where are those changes in the genome? Together this information can tell us how evolution actually works at the DNA level. This has lots of implications for understanding the function of our own genome and defining regions of the genome important in development and disease.
Q-Why are you personally motivated to undertake this work?
Pask-I have always been fascinated by the thylacine (like many of you!). I did some work over a decade ago showing that we could get viable thylacine DNA from the museum specimens and resurrect its function in transgenic mice. However, at this time it was not possible to sequence the genome from such a fragmented sample (broken up bits of DNA). But the DNA sequencing tech changed so much in the past decade that this became easily achievable. Doing this project I not only got to persue one of my main research objectives looking at evo-devo of the genome, but also got to learn so much more about the biology of the thylacine. This is something we will continue to uncover with our work moving forward.
Q-Why choose the thylacine?
Pask-Because it is the BEST example of convergence that we know of in the mammals. See above.
Q-Original work on cloning the thylacine was launched with much fan fare as 'the end of extinction' did the media attention and the subsequent stalling of that project help or hinder your work? Was any of the work undertaken by the previous research useable?
Pask-Nothing was ever published from the study you mentioned so there was no useable data for us. When the first attempt was launched, genome sequencing was still in its infancy and such an undertaking would have cost hundreds of millions. The only affect on our work from this is that people assume we are also working on de-extinction which is still a long ways off for the thylacine.
Q-The palynological reference for the penultimate glacial cycle was from southeastern South Australian and western Victorian region.
Was it hard to extrapolate from those two regions to the rest of Australia ?
Pask-These events affect temperature on a global scale and so the effects of the cycle would have altered vegetation and habitats across the continent. Still, these are only correlates that we have drawn that coincide with the population drop.
