De-Extinction: Return of the Endlings?

This blog has looked at the extinction and extirpation of many species and admittedly, has been fairly pessimistic. However, it has yet to consider the growing phenomenon of 'de-extinction', perhaps there is room for a little optimism? Is this a realistic approach to conservation or is it a load of Jurassic Park wannabe nonsense? The idea based on using preserved or "ancient" DNA from several individuals of an extinct species and creating clones of each of them, we would be able to create a new and viable population of that species. There are cryo-zoos, such as the one in San Diego, which store frozen DNA of extinct species with the potential to form these clones. Much of the attention given to, and work within, de-extinction focuses on this cloning aspect, but other researchers have attempted to work through selectively back breeding a species from its genetically similar living descendants.

De-extinction efforts have already been made for many species that we have seen recent endlings of, such as the passenger pigeon, the Pyrenean ibex and the Tasmanian tiger, whereas some scientists are working on much older animals such as the woolly mammoth. However, 60,000 years is effectively the age limit for use of DNA, so dinosaurs won't be happening any time soon. The first de-extinction in history was the Pyrenean ibex, which was done in 2009 by creating a clone egg using the DNA of Celia, the (formerly) last ibex, which was taken shortly before she died in 2000. Unfortunately, the ibex was short lived and died within 10 minutes but scientists are planning to reattempt when cloning techniques have improved. This attempt, in itself, was an improvement on previous attempts in 2003 which had failed to produce an egg capable of surviving the full gestation period. Significant progress has also been made for the passenger pigeon, where DNA has been preserved in museum specimens. Unfortunately the DNA of these specimens is contaminated and fragmented due to the way they have been preserved and kept, as oppose to the ibex DNA which was stored in liquid nitrogen. However, it is still possible to reconstruct the genome by synthetic hybridisation of the DNA fragments with the genome of its closest living relative, the band tailed pigeon, which scientists are currently working on. This would then be used to create cells which contain passenger pigeon genes, which would then be injected into band-pigeon embryo with the goal to create a band pigeon which lays passenger pigeon eggs and acts a surrogate parent for it.

National Geographic cover of de-extinction issue; Source.

Since 2013, a team of scientists from South Korea and Russia have been working on the de-extinction of woolly mammoths.  There have been difficulties as although mammoths have been found well preserved, their DNA has not been intact enough to produce viable embryos for a clone based de-extinction. Alternatively, a second method has been investigated which involves the artificial insemination of elephant eggs with preserved woolly mammoth sperm. The elephant-mammoth hybrid offspring would be able to be cross-bred over several generations to produce near pure mammoths. Again, this has been unsuccessfully due to mammal sperm cells lose their potency after over 15 years in freezing. The major problem has been finding usable DNA, blood recovered from the 2013 carcass provides an apparently good chance of successful cloning - we will have to wait and see. Others are pursuing different routes to restoring the mammoth, Harvard geneticists are working on migrating components of the mammoth genome into the Asian elephant genome in order to create viable hybrids. Adrian Lister, a renowned mammoth expert, highlighted that there is a lack of suitable habitat remaining for any resurrected mammoths and that, as highly social animals, they would suffer from existing in very small numbers. However, a Pleistocene rewilding experiment known as 'Pleistocene Park' (not joking), could provide refuge for the mammoths and would also benefit from the grazing herd behaviours in recreation of steppe. Interestingly, Pleistocene Park also aims to prove that it was not climate change but over-hunting and other human interferences that lead to the disappearances of these grasslands and associated species during the Pleistocene. This could be a exciting new evidence in the debate surrounding the Pleistocene megafaunal extinctions.

Pleistocene Park in Siberia; Source.

As mentioned earlier, selective back-breeding from the closest living relatives of animals is another option for potential de-extinctions. This is being done for aurochs in Europe, based on genetic material taken from bone and teeth fragements. The last European aurochs were lost in 1627 after a long history of over-hunting and exploitation, but their descendants (most modern cattle breeds) are abundant throughout Europe. The genetic material provides a goal, so that cattle can be bred to try and reach as close to the original aurochs as possible, both phenotypically and genotypically. Early attempts resulted in the created of a new breed, Heck cattle, which are at best vague-lookalikes. Currently there are two projects, the TaurOs Project and the Uruz Project, which are competing to resurrect a true, or atleast very close to, aurochs within the next 20 years. Earlier this year, it was proposed that there could be the potential to bring back Lonesome George, or at least a genetically very similar species, by a breeding programme rather than cloning. Even if the animals themselves are clones, captive breeding, which has proved successful in many conservation efforts, will be a major part of de-extinction.

So, whilst it seems that de-extinction is scientifically possible, the bigger question is rather, should we actually be doing this? Proponents of de-extinction such as Stewart Brand would argue that we have the ability and the moral obligation to repair the damage we have done, so there is no excuse not to. Others such as Adrian Lister would say that efforts and resources should be focused on conserving currently endangered extant species. The lack of suitable habitat is also a concern for many species. I feel that whilst there is certainly value and appeal in resurrecting species and "righting our wrongs", it must be done carefully and must not detract the need for conservation efforts to currently endangered species. This is not an alternative to conservation. This is an unfortunate second best to not having lost the species in the first place.

The Mystery (or not) of the Megafauna

Between 50,000 - 10,000 years ago over 90 genera and many hundreds of species of megafauna went extinct in what have become known as the Late Quaternary Megafaunal extinctions. Megafauna, or for our purposes large mammals weighing over 44 kg, lived around the globe on all continents except Antarctica but today they persist only in Africa. The causes for this dramatic decline in species over a relatively short window of time is a contentious topic which has two polar ends: humans and climate. Some papers argue that humans were the overriding factor through a variety of impacts such as hunting and habitat destruction, whilst others maintain that climate change was the real killer.

Some of the Quaternary Megafauna; Source.

The megafauna were more vulnerable to extinction than other animals, which is in part why they suffered such extreme losses, whether they be from humans or climate. In general, animals of a large size are more vulnerable to extinctions due to larger ranges and lower population densities. Johnson argued, however, that is was not size but a slow life history (slow reproductive rates and few young) that made the megafauna more susceptible to extinctions. Due to the fact that they have long lives (and therefore later sexual maturity) and relatively few young, they are more vulnerable to sudden changes in climate and habitat because it takes longer for generations to pass and therefore longer for the species to adapt to these changes. This supports climate causes over human, as hunting hypotheses focus on body-size. Johnson also found that those alpine, arboreal and nocturnal species with lower reproductive rates experienced less extinctions, likely due to their reduced exposure to humans but there is no clear link to climate.

Barnosky et al. conducted a review of the evidence from a variety of fields. They found that in some areas, such as Eurasia and North America there was strong evidence that humans contributed to the extinctions but also that pronounced climate change had a significant role. In Australia, humans were almost exclusively responsible for the loss of 21 genera whilst there was scarce evidence for the influence of climate. In other areas of the world, South America and Africa, there was not sufficient evidence to make a judgement on the causes of the extinctions, despite the fact that South America experienced the greatest species loss of any continent. In Africa, there is a very low number of genera lost in comparison to other continents. Why? This is yet another unanswered question but we think it is due to coevolution of humans alongside the megafauna.

Assessment of causes of extinction on each continent; Source.

There are various hypotheses for human caused extinctions, but I will briefly discuss the most common ideas. 

1. Blitzkrieg

Whilst this is now considered somewhat outdated by most scientists, one of the first ideas about the loss of megafauna was that humans had hunted them to extinction at such a rapid rate that their populations did not have a chance to recover. First proposed by Martin, the hypothesis assumes that as the animals had not encountered humans before, they would naively not be afraid of them and therefore easily hunted. Martin sought to provide explanation for the fact that there were so few archaeological sites containing extinct megafaunal remains, as the hypothesis put the extinctions within the space of 500-1000 years so interactions between humans and extinct species would have been brief. There are, however, a number of issues with this hypothesis. There is a severe lack of archaeological sites where large mammals are associated with stone tools and Barnosky et al state that when the entire breadth of climatic and archaeological evidence is considered, that blitzkrieg scenarios can be firmly rejected in western Europe, Siberia, Alaska, and probably Australia and central North America. Additionally, Wroe et al. among others argued that prey naivete would not have been sufficient for blitzkreig, as this is really not how animals work - prey quickly learn to flee from new predators. Whilst we know that hunting and predation by humans did have an impact on populations, and of certain species in particular, we know fairly certainly that it was not a blitzkrieg.

2.Sitzkrieg 

The wittily named Sitzkrieg hypothesis refers to the slower, sometimes indirect impacts humans would have had on megafaunal populations other than directly hunting them. This includes habitat loss and fragmentation, use of fire, and the introduction of foreign species and diseases. This has proven difficult to quantify as, for example, we cannot pinpoint whether charcoal comes from human or natural fire events and it is also difficult to know the extent of habitat loss. We have seen in island communities that 'sitzkrieg' style events have caused extinctions through multiple effects and synergy with hunting. For example, black rats as a human introduced species have caused extirpations in island communities, but this has not been replicated on mainland. Some suggest a hyper-disease hypothesis in which extinction is a result of hyper-virulent diseases to which the native species have no resistance. Again, there is a lack of evidence to support this - we do not actually know of any such extremely lethal cross species pathogens, for example. In their review, Koch and Barnosky find that none of the indirect sitzkrieg models make strong predictions regarding the megafaunal extinctions. Of all, the factors, habitat alteration seems the most likely culprit but it is unlikely any sitzkrieg parameters were dominant causes of the extinctions.

Hyper-disease, plausible or silly?; Source.

As for environmental hypotheses, climate change is the prevailing theory but there are also some other weird ideas out there.

1. Climate change

Throughout the last 50kyrs, there has been a lot of fluctuation between warm and cold events in the climate, known as Dansgaard–Oeschger (D-O) events (rapid warming events) and Heinrich events (cold events).  These events are likely to have caused abrupt shifts in temperature and precipitation which would destabilise habitats and species ranges. In a recent paper, Cooper et al identified that many extinctions seem to coincide with D-O events, shown in the graph below. Additionally, Gill et al found that Sporormiella (a dung fungus associated with large herbivores) declines in correlation with D-O events and overall gradually throughout the period, contrary to the aforementioned blitzkrieg ideas. The other trend we see is a gradual warming from the last glacial maximum (26.5kya) to the Holocene (11 kya), after which temperatures remain relatively stable. This warming would have caused major ecological changes, in particular the reduction of tundra biome and taiga forests reaching further north. Some species, such as mammoths, were not adapted to these warmer, wetter forests and would have suffered from a decreased range and were likely unable to keep up with a shifting habitat due to their large size and slow reproductive cycles.

Light grey bars represent interstadial warming events and have a marked association with extinctions; Source

2. A comet?

The Younger Dryas impact hypothesis suggests that a barrage of meteorites hit the ice sheet in North America and created instability and caused the onset of the Younger Dryas. However, this is widely discredited as we have evidence (such as Gill's sporormiella) that tells us the megafaunal extinctions were not clustered around or after 12.9kya when the impact occurred. The event itself is disputed due to lack of typical bolide indicators found in sediments from that time. So, not really anything to write home about, but just letting you know what's out there. ;)

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In summary, as shown in the original graph by Barnosky et al, the evidence points towards a mix of human impacts with a background of climatic events as the drivers of megafaunal extinctions across the Northern Hemisphere Whilst the jury is still out for most of the Southern Hemisphere, Australian extinctions appear to be very closely related to human impacts, with little climatic correlation. We have a good understanding of what happened to many of these genera, as shown by the number of green circles representing 'robust evidence' in Barnosky's graph, but there is still room for improvement, particularly for understanding what happened in South America and Africa. It would be interesting to hear your opinions on all this, particularly if you disagree with anything I've said! As always, questions and debate and welcomed in the comments section.