Is There a Place for This Species to Live if We Successfully Bring It Back?
If we know why the species we are considering for de-extinction went extinct in the first place, is it possible to correct whatever went wrong? In the case of the dodo, we would have to create a cat- and rat-free zone on Mauritius into which the unextinct dodos could be placed. If this is not possible, either because there is no habitat that could be set aside for these purposes or because it’s just too hard to keep out rats and cats, then the dodo is not an appropriate candidate for de-extinction.
The loss of suitable habitat—whether by deforestation, development, pollution, or the introduction of parasites and predators—seems to be the most common cause of extinctions that have been caused indirectly by humans (if we assume that humans only cause extinctions directly by overexploitation). Yet, more and more humans live on this planet every day, which means we take up more and more space and need more and more food, which translates into the increasingly rapid and destructive conversion of natural habitat into land for human use. A major challenge to any de-extinction effort will therefore be to secure suitable habitat for the unextinct species. Suitable habitat will have to (i) include appropriate prey or food to sustain the unextinct population; (ii) exclude predators or competitors (including invasive species) that would drive the species back into extinction, while at the same time leaving sufficient numbers of carnivores in the system so as not to destabilize the food web; (iii) be devoid of disease, parasites, or pollutants; (iv) imitate as much as possible the temperature and precipitation regimes of the native habitat of the species; and (v) be sufficiently large to support a self-sustaining population.
Interestingly, this whole process might be simpler for species that we drove to extinction directly through hunting, as their habitat may still exist. Of course, the survival of these species would rely on our not hunting them to death a second time. Like exotic species that are alive today, unextinct species would have to be protected from increasingly creative and dangerous poachers, using laws and statutes that are in many cases difficult to enforce.
How Will Introducing This Species Affect the Existing Ecosystem?
The extinction of a species changes the ecosystem in which it once lived. Over time, the ecosystem restabilizes, and the niche that was once filled by the extinct species is either filled by a different species or eliminated. The longer a species has been gone, the more likely it is that the ecosystem has adapted to its absence. So when the species is reintroduced, what effect will that reintroduction have on the species that live there today?
When passenger pigeons flocked in large numbers across eastern North America, the landscape was different than it is today. The deciduous forest was more widespread, American chestnut trees were plentiful, and people were not. Passenger pigeons were a dominant and destructive force in the eastern deciduous forest. They fed primarily on large seeds: oak acorns and the nuts of hickories, beeches, and chestnuts. Flocking in the billions, hungry passenger pigeons could destroy the entire seed crop of a forest stand in very little time. When they nested, as many as five hundred birds would nest in a single tree, and when they left the nests, they tended to leave behind dead trees covered in bird droppings. When they went extinct, this avian version of a non-stop EF5 tornado came to a screeching (squawking?) halt. Since that time, humans have converted much of the historic deciduous forest into towns, cities, and agricultural land. What would a flock of a billion passenger pigeons eat today? What effect would their de-extinction have on the remaining deciduous forest? On agriculture? On the bird species and other animal species that live there today, with which unextinct passenger pigeons would compete for access to food and nesting grounds?
It may be that some unextinct species would have minimal destabilizing effects on present-day ecosystems. Careful evaluation of the consequences of reintroduction is required, however, and not simply from the perspective of whether that particular species would survive after reintroduction. If a species’ de-extinction would lead to changes to the existing habitat that in turn would threaten living species, then that species is not a good candidate for de-extinction.
Finally, as disingenuous as it may seem at first, it would be remiss not to think about the effect that the de-extinction would have on human populations. Few East Coasters would be overjoyed at the site of a billion passenger pigeons darkening the sky just above their freshly manicured lawns and newly waxed SUVs, for example. But there are subtler aggravations that would probably make this particular de-extinction unpopular. If unextinct passenger pigeons were protected as endangered species, people who enjoy hunting pigeons for sport may find themselves facing new restrictions about when and where pigeons can be hunted, or even whether pigeons can be hunted at all, given the presumed difficulty of distinguishing the unextinct passenger pigeons from common pigeons that were once unprotected game. And a billion passenger pigeons would probably require quite a lot of protected habitat, which would have to be repurposed from somewhere.
These problems of course extend beyond passenger pigeons. If new and different categories of protected species emerge, regulations enacted to prevent their (re)extinction may make previously accessible wilderness off-limits to recreation, much to the chagrin of hunters, campers, hikers, and so on. Farmers are unlikely to support de-extinction of species like the Carolina parakeet, which was driven to extinction precisely because it was an agricultural pest. And ranchers already unhappy about the idea of wolf reintroduction will hardly embrace the idea of saber-toothed cats roaming freely in proximity to their livestock, looking for an evening meal.
Other species are less objectionable on the grounds of how much they might annoy their human neighbors. The mammoth, for example, may be one of the least potentially annoying species on the list of candidate species for de-extinction. The most appropriate habitat for the mammoth is, after all, the Arctic, where human populations are sufficiently small and isolated that the mammoth is not likely to get in their way.
Indeed, Dr. Sergey Zimov, the director of the Northeast Science Station of the Russian Academy of Science in Cherskii, Russia, is intent on recreating the habitat of the mammoth so that it has somewhere to live once its de-extinction is successful. His Pleistocene Park is a nature reserve on the Kolyma River, south of the science station in Cherskii, in northeastern Siberia. Pleistocene Park is in the most northerly part of the habitat that was once the mammoth steppe—the rich tundra grassland that supported mammoths and other grazing herbivores during the Pleistocene ice ages (plate 2). Zimov has already introduced horses from the Urals, bison from eastern Europe, and four different species of deer into Pleistocene Park, and these populations are healthy and self-sustaining. Recently, Zimov decided to expand his operation and establish a second Pleistocene Park in a more southerly location, where the less harsh climate is more amenable to supporting large numbers of herbivores. This second park, which he calls Southern Pleistocene Park, is located in the Tula region, approximately 250 kilometers south of Moscow. Over time, Zimov plans to introduce bison, auroch, horses, wolves, and large cats into Southern Pleistocene Park, which—unlike the Pleistocene Park in northeastern Siberia—is easily accessible by car from Moscow. Both of these locations would likely provide appropriate mammoth habitat, re-creating communities that existed more than ten thousand years ago that should be able to persist without bothering or being bothered by humans.
Will It Be Possible to Learn the Genome Sequence?
With this question, we transition from the big picture to the finer grains of de-extinction. In other words, we now ask whether de-extinction is technically possible, or whether it will become so in the foreseeable future. Each of these topics will be covered in detail in the next chapters and so are touched on only briefly below.
The first technical step in de-extinction is to learn the genome sequence of the extinct species. Well, not just the genome sequence. Really, we want to know what the key genetic differences are between the exti
nct species and any closely related living species. I’ll explain what that means in more detail later, but for now let’s simply ask: “Can we sequence all of the nucleotides in the genome of this extinct species and then piece those nucleotides together to learn what the sequence of that genome is?”
First, some vocabulary. Genomes are big places, but the molecules that make up genomes are tiny (figure 5). Genomes are made up of chromosomes, which in turn are made up of long strands of nucleotides—the building blocks of DNA. Nucleotides each contain a nitrogen base, a five-carbon sugar, and a phosphate group. DNA genomes contain four different nucleotides, each with a different nitrogen base: adenine (A), guanine (G), cytosine (C), and thymine (T). Nucleotides are strung together along a sugar phosphate backbone to make up nucleic acids like deoxyribonucleic acid, or DNA. Genomic DNA is double-stranded, which means that when it is in a stable state, the nucleotide on one strand is bound to a complementary nucleotide on the other strand. A nucleotide that is paired to its complementary nucleotide is called a base-pair. Genome sizes are usually reported in base-pairs, which will be half the number of nucleotides.
Figure 5. The structure of DNA. DNA is made up of four chemical building blocks called nucleotide bases: adenine (A), cytosine (C), guanine (G), and thymine (T). DNA exists in a winding, two-stranded “double helix” structure, which is formed because the nucleotide bases pair up with each other, creating a ladder-like structure and connecting the two strands. The order of the nucleotide bases, which is also known as the DNA sequence, contains the information necessary to build and maintain an organism.
Genomes vary considerably in the number of base-pairs they contain and in the number of chromosomes among which these base-pairs are distributed. The human genome comprises around 3.2 billion base-pairs, which are found on 23 chromosomes. The loblolly pine genome comprises 22.2 billion base-pairs but only 12 chromosomes. The common carp genome contains 1.7 billion base-pairs distributed among 100 chromosomes. The huge variation in plant and animal genomes is linked neither to the complexity of the organism nor to the number of genes that are encoded by those genomes.
Chromosomes are too long to sequence all at once using existing sequencing technologies. When scientists sequence DNA, they therefore begin by shearing the chromosomes into smaller fragments. These fragments are double-stranded, so their length is also reported as a number of base-pairs. Depending on the sequencing technology to be used, these fragments will vary from fewer than 100 base-pairs long to several thousand base-pairs long. After the DNA has been sheared and sequenced, the fragments are reassembled into chromosomes. To summarize the process of sequencing a genome: First, cut it up. Then, put it back together again.
Now that some of the jargon has been demystified, let’s outline the steps of sequencing and assembling the genome of an extinct species. First, we collect remains from the species that we plan to bring back to life—bones, teeth, skin, hair, whatever we can find. Then, we extract and collect as much DNA as we can from those remains. Next, we sequence the DNA. Finally, we take that DNA and carefully assemble the tiny pieces together to make bigger and bigger pieces, and eventually chromosomes.
If you were paying attention, you’ll have noted that we skipped the step in which we shear the DNA into smaller fragments. When working with ancient DNA, we don’t need this step. The DNA comes pre-sheared. In fact, over-sheared is a better way to refer to it. Over-shearing is bad: the shorter a fragment of DNA is, the harder it is to figure out where it goes in the genome.
There is more. These short DNA fragments are also in pretty bad shape. Thanks to chemicals and other biomolecules in the environment, individual nucleotides can become broken or damaged in a way that changes their molecular structure. Molecules with altered structures are read incorrectly during the sequencing process, resulting in mistakes in the genome sequence. The rate of DNA decay is slower in some environments (for example, in the Arctic, where the mammoth lived) than in others (for example, in the tropics, where the dodo lived). This means that species whose native ranges did not include regions of the world where remains are likely to be preserved are probably not ideal for de-extinction.
Finally, we have to deal with what we call contamination. Contamination in the broadest sense refers to any DNA that is co-extracted from the bone or other tissue that does not come from the organism whose genome we are trying to sequence. It might be DNA from microorganisms that colonized the bone after it was buried in the ground, or from plants whose roots grew around the bone while it was in the ground. It might also be DNA that was introduced into the bone as it was being excavated or handled in the lab. A bone might contain an enormous amount of preserved DNA only a very tiny fraction of which is of interest to us.
Professor Svante Pääbo leads a research group at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, and he and his research group have recently sequenced and assembled the Neandertal genome. His group is very interested in understanding what it means to be human. One way to approach this question is to compare the human genome with closely related genomes of great apes and ask what genetic changes have happened within our genome sequence since we diverged from our common ancestor with other great apes. Our closest living relative is the chimpanzee. The human and chimpanzee genomes are around 98–99 percent identical, which means that what distinguishes us from chimpanzees probably has to do with the other 2 percent. But 2 percent of a 3.2 billion base-pair genome is still a lot of DNA to sort through. Neandertals are much more closely related to humans than are chimpanzees. By sequencing the Neandertal genome, Pääbo is able to focus more narrowly on those genetic changes that are unique to our species.
The first complete Neandertal genome that Pääbo’s team published was a combination of DNA data that was sequenced from three different Neandertal bones. Each bone contained less than 5 percent Neandertal DNA, with the remaining 95 percent or more comprising mostly environmental DNA—soil microbes and their pathogens, plants, and the like. Of the Neandertal DNA sequences that were recovered from these bones, the average fragment length was forty-seven base-pairs. The human genome contains 3.2 billion base-pairs, so this is a bit like having a puzzle that can only be solved by correctly assembling 68 million puzzle pieces. Of course, thanks to damage and contamination, what they actually had was far more pieces than they needed, some of which were from the same puzzle but cut in a different way and some of which actually belonged to a different puzzle.
To help them to assemble the Neandertal genome, Pääbo’s team used the human genome, which was already sequenced and assembled, as a guide. To extend the puzzle analogy, if the forty-seven base-pair fragments of Neandertal DNA were the puzzle pieces, the human genome was the picture on the box top. Only that picture (because it was of a human and not a Neandertal) was not exactly the same as what the puzzle would look like when it was finished. Not identical, but close—maybe the picture was a different color, or maybe part of it was covered by a text box stating “contains very small parts.”
Assembling the Neandertal genome was not an easy task. However, it was much easier than assembling many other paleogenomes will be. First, the human genome is the best-resolved genome of any species to date, so the picture on the puzzle box top was nearly complete. The number and diversity of sequenced genomes is growing, but most species genomes are still only partially sequenced and assembled. Second, humans and Neandertals have a common ancestor within the last million years, probably closer to half a million years ago. This means that there hasn’t been much time for a huge number of differences to evolve between humans and Neandertals. The picture on the box top pretty closely reflected what the final puzzle would look like.
Not so for many species. In fact, the more evolutionary time that has passed between the divergence between the extinct species and the living species that would be used as a reference, the harder assembling the genome will be. At some point, the picture on the box goes from a slightly discolored version of the en
d product to something that you rescued from your dog’s mouth and then tried to piece together using your imagination and some sticky tape, to something that a herd of mammoths trampled while escaping a pride of cave lions. In the rain.
If there are no remains that contain recoverable DNA, then the species is not a candidate for de-extinction. If there are remains with recoverable DNA, but the species has no close relatives, assembling the genome from that DNA will be challenging—maybe very challenging. Critically, however, it is not impossible to assemble at least large chunks of the genome, even when the DNA that is preserved is in terrible condition.
Is There a Way to Transform the Genome Sequence into a Living Organism?
If we’ve made it to the step in which we’re considering how to create a living organism, we presumably have been able to generate a genome sequence (or a partial genome sequence), even if it might have been tough to do so. Now we have to transform that string of letters into a living thing. How?
There is no clear path from genome to living thing that can be followed for every organism. Some genomes, such as those sequenced from bacterial or viral organisms, are likely to require very little push to start behaving like they are alive. Other genomes are nowhere near becoming a living thing.
Two paths are generally considered when contemplating de-extinction. The first is to do what most people are referring to when they talk about cloning. To clone Dolly the sheep in 1996, scientists at the Roslin Institute, which is part of the University of Edinburgh in Scotland, removed a small piece of mammary tissue that contained living cells from an adult ewe and used the DNA in these cells to create an identical copy of the adult ewe. This process is called somatic cell nuclear transfer, or, more simply, nuclear transfer. I’ll explain how it works later, but for now it is sufficient to know that this is not likely to be the process used to bring many extinct species back to life. Cloning by nuclear transfer, unfortunately, requires intact cells. Unless tissue was taken from a living individual prior to the species’ extinction, nuclear transfer will not work. If we’re dealing with a species whose genome we have had to sequence and assemble, then we need a different approach.
How to Clone a Mammoth Page 5