The Great Comeback: Bringing a Species Back from Extinction
What if extinction could be undone? The disappearance of the once-numerous passenger pigeon inspired one budding young geneticist to right a great ornithological wrong.
Eleven years ago, as an eighth grader from a school in Alexander, North Dakota, with fewer than 100 students, I won best project for my division of the State Science Fair. This victory would go on to decide the course of my life. I won with a project that was completely intellectual and had no experimental portion of any kind: It concerned the possibility of someday “cloning the dodo bird,” that iconic poster bird of extinction.
At that science fair, a judge from the North Dakota Pigeon Association told me that the dodo bird was in the pigeon family. This fact nestled in my brain and grew. I had little conscious idea of what this inkling of passion would soon become.
A short time later, I was in a bookstore looking through a text on the history of conservation efforts by the National Audubon Society, a book I implored my parents to purchase for me. Thumbing through page after page, I came to a photograph. It was a pigeon. Like the dodo bird, it was an extinct pigeon, but in shape it looked much more like the doves that flew over my prairie home and the pigeons that strut the streets of every city.
It was the most beautiful bird I’d ever seen. I needed that photograph. This beautiful, bygone species is known as the passenger pigeon, and to the overcompensating Linnaean Latin science lovers it is Ectopistes migratorius. It was once the most numerous bird in the world, but this species succumbed to our activities. The last one died on September 1, 1914, her body found in her aviary at 1 p.m. The passenger pigeon was gone from the skies. I’ve made it my life’s work to bring it back.
Finding the Materials to Do The Impossible
I soon learned that I was too late to be the first one doing passenger pigeon research. In the next year and a half, two papers would be published by two different labs studying passenger pigeon DNA. With these other groups conducting research, it proved to be difficult to get passenger pigeon samples. I shifted work to a new species and tried as hard as I could to figure out how to get my hand into passenger pigeon research.
I sent sample requests around the world for tissue to work with, hoping I could “sneak” it in amongst my current work until I got money for the expensive pieces of the process. I reworked the angle of the project and delved into harder-to-find records: the archaeological specimens of the bird. Then, in February 2011, I went to Chicago’s Field Museum to sample mastodon fossils for my master’s thesis project. I asked to visit the ornithology collection.
Much to my surprise, Dave Willard, now the emeritus curator of birds at the museum, had seen my proposal for tissue many weeks earlier. In that moment, he was obliged to cut tiny spots of flesh from the feet of three passenger pigeon males shot near Troy, New York, 152 years ago. It was my first chance to ever hold the bird I love, and to see them so closely in hand was a culminating moment—one that, sadly, I feel more intensely now, looking back at the photographs of a smiling 24-year-old holding FMNH 47396.
Nine months later, I extracted the DNA and prepared it for sequencing, a process involving four very laborious days of work. Now I needed the money to obtain the precious DNA code locked in what was now a tiny tube of clear liquid—almost a ghost of the once-living pigeon that flew over the trees of New York.
My work has come a great distance since that tiny tube of clear liquid passed hands from mine into the lab tech at the sequencing facility. Just three weeks later, what was returned to me were digital files containing the As, Ts, Cs, and Gs of deciphered DNA fragments. In a sample like this, DNA might not come directly from the specimen; it can come from bacteria and tiny fungal spores growing on the specimen’s tissues during the century that it sat in a museum collection’s drawer. DNA from the curators—and eventually, even from myself—works its way into the tiny crevices of texture in the tissue.
Two hundred thirty million DNA sequences resulted from the first run of my three passenger pigeons. Just over 250 million DNA sequences resulted from the second run. All of this DNA was held in between the thin glass walls of what to anyone would seem like a microscope slide; this is actually a flow cell for DNA sequencing, split into thin canals within the glass for DNA molecules to bind and replicate and be scanned throughout a process of repetitive binding reactions.
Fragments of old dead DNA live out their final blasts of reanimated life in the reactions of our research, to become stagnant again in that flow cell for the rest of time—if anyone bothers to keep the cell. Mine is framed next to my passenger pigeon feathers.
Of my nearly 500 million DNA sequences, about 50% of it is bacteria. A small fraction is human. And a small fraction is unknown in origin—a problem we won’t solve until we manage to sequence the DNA of every life-form on Earth.
I know that there may be actually 40% passenger pigeon DNA in my data. Some of the unknown bits are pigeon DNA that doesn’t map to a previously published pigeon genome, that of the rock pigeon, because it is too different. Our DNA work with the band-tailed pigeon shows us that it is a much closer code reference to the passenger pigeon, proving to be its closest living relative. And thanks to that, as well, we now know that to rebuild a passenger pigeon we need to use the genome and tissues, as well as the potential parenting, of the band-tailed pigeon, Patagioenas fasciata.
I’ve joined forces with a sweep of other interested scientists to fully assemble the genome of the passenger pigeon and explore its natural history in a way that historical accounts have never afforded before.
The Great Comeback
The Great Comeback stands as one of the first de-extinction projects in the world. It will be the first project in history to bring an extinct bird back to life and set the precedent and protocol for this work in the future, from well-known birds to the ancient and mysterious.
Imagine bringing back to life such legends as the dodo bird, once believed to be a mere Lewis Carroll fantasy; or the vibrant Carolina parakeet that brought streaks of green to New England winters; or the “penguin of the north,” the great auk. Birds such as these have inspired art and instilled a sense of beauty that has defined cultures throughout history. To build a future that includes them would be a powerful achievement, not just for science, but for humanity as a whole.
Among these icons, the passenger pigeon stands out as potentially the most significant for ecology, research, breeding, and re-wilding prospects. How this work is formed is thus vitally important to the future of de-extinction.
The Great Comeback project’s five phases are as follows.
Phase 1: Sequencing the genome and analyzing the genome. Goal: identifying the areas of the band-tailed pigeon genome to be modified and understanding passenger pigeon population biology and paleo-ecology.
Phase 2: Cell research. Goal: producing cells that can be used to engineer a living passenger pigeon genome.
Phase 3: Genome creation. Goal: synthesizing passenger pigeon DNA regions identified as significant in phase 1 and integrating these into band-tailed pigeon cells isolated in phase 2. Alter original cell line into multiple cell lines by inserting genetic diversity from phase 1 specimens.
Phase 4: Captive breeding. Goal: using altered cells from phase 3 to create rock pigeon/passenger pigeon breeding chimeras. These chimeras are used to breed pure passenger pigeons. Pure passenger pigeons produce a captive flock for sustainable population growth.
Phase 5: Re-wilding. Goal: producing a naturally migrating and ecologically functional wild population of passenger pigeons.
In the Beginning… Producing Technology
The first big step of this project is producing cell cultures. Currently, this is a hot topic in avian biotech, as it is impossible to clone a bird in the way that mammals are cloned. Multiple pathways are being explored, so pursuing a variety of routes is necessary for our work.
The main two cell types we are interested in are induced pluripotent stem cells (iPSCs) and primordial germ cells (PGCs). Ultimately, some type of germ cell, sperm, or PGC needs to be transmitted through a host parent to breed with passenger pigeons. The ideal host will be what in genetics is called a chimera, an organism derived from at least two distinct cell populations. In this case, one cell population would come from band-tailed pigeons and the other from passenger pigeons through techniques described below.
Culturing PGCs directly to hold our passenger pigeon genome is the most efficient predicted route, but potentially the most difficult. Stem cells can provide multiple pathways for transmission of traits, as they may be able to be programmed into germ cells and even bypass that cell stage to produce sperm or egg cells. Stem cells can be worked with in the lab for many cell generations, which is necessary for the genome engineering we’ll need to do.
In short: Phase 2 focuses on developing the cell technologies to create a passenger pigeon breeding line. These cell technologies can be perfected in captive flocks of band-tailed pigeons and rock pigeons. The facilities for these birds can very well be the same facilities in which passenger pigeons will be bred and raised, and thus form an overlap between our phase 4 and phase 2 partners.
Phase 3 takes the cells from phase 2 and the genetic understanding from phase 1 and creates a living passenger pigeon genome.
This technology is being pioneered right now. We have already begun genome-sequencing work in a collaborative partnership with paleogenomics investigators Beth Shapiro and Ed Green of the University of California, Santa Cruz, and peripheral collaborators at the Smithsonian Institution who are interested in analyzing the species ecology. Sal Alvarez, a private bird breeder, has provided the necessary band-tailed pigeon embryos for cell culturing, and is lending his experience in developing a care plan for captive breeding of the new passenger pigeon. Advanced Cell Technology Inc., under the supervision of Robert Lanza, has joined the project for producing and experimenting with iPSCs. The lab of George Church, professor of genetics at Harvard Medical School, will be handling the genome creation and engineering.
The ability to synthesize sequences of passenger pigeon code into real DNA molecules has been improving each year from its inception in 2003. And as the synthesis of DNA increases in capability, it is simultaneously dropping in price.
Synthesized passenger pigeon DNA code will be “written” into the genome of the band-tailed pigeon, swapping out the band-tailed pigeon DNA code for the equivalently positioned passenger pigeon code in the chromosomes.
In the end, a cell culture will exist that harbors the passenger pigeon genome. From this first cell culture, genetic diversity can be integrated, deciphered from the byproduct population genetic studies of this project. Immunity, or disease-fighting, genes, are one such type of gene in which multiple alleles in the population generate a healthy flock and keep inbreeding low. With multiple genetic cell lines, we can create a diverse population from the start of breeding, greatly increasing the efficiency of producing a viable species.
The Hatching of a New Era
These newly made passenger pigeon cells usher in the onset of phase 4. The production of a parent generation to host the passenger pigeon DNA depends upon the types of cells used to create the passenger pigeon genome. The type of parent created then sets the pace for captive breeding. Using PGCs—whether cultured purely or programmed from stem cells—will generate a chimera capable of breeding passenger pigeon chicks immediately.
A second method that will yield passenger pigeons is to produce sperm from stem cells and use this sperm to inseminate band-tailed pigeons, creating hybrids (half band-tailed pigeon, half passenger pigeon). Artificial insemination is used extensively in modern poultry, with a high rate of success. By introducing the passenger pigeon sperm again to the first hybrid generation, we decrease the number of alleles descended from band-tailed pigeon. Repeating this step again and again will produce passenger pigeons with less than 1% band-tailed pigeon genes within five generations. From there, it can be almost completely bred out, similar to the concept of back breeding.
The preparation and construction of phases 4 and 5 can begin. The needed facilities must factor in the requirements to raise passenger pigeons that behave naturally—a significant challenge for a species that will be born without its own parents, but not dissimilar to captive breeding projects that separate young from parents. Surrogate pigeon parents can be cosmetically dyed to resemble passenger pigeon coloration and fool chicks into seeing passenger pigeon parents.
The life cycle of the passenger pigeon must be simulated from day one. The surrogate parents must be bred and trained several generations in advance to eat the same diet as the passenger pigeon. Weaning of the young at the precise time is important, as passenger pigeon development relies on the juveniles’ social cohort, rather than on parental guidance.
Breeding facilities must replicate the forest environment where the passenger pigeons bred and lived in order to facilitate this social cohort formation. This will also force the birds to develop natural tendencies, such as foraging for food in the undergrowth rather than relying on provided food dishes.
Zoo exhibits over the past century have emphasized habitat simulations, so, with the right team, much of this process is quite simple. These breeding facilities can be built at the same time that phase 1 and phase 2 are proceeding. The facilities should accommodate both rock pigeons and band-tailed pigeons for use as surrogate parents.
The Challenges of Rerelease
Releasing the species to the wild once a sustainable captive flock is produced represents the greatest challenge to the work, both biologically and politically. The regulatory issues for releasing these birds could be quite complicated, for instance. And communicating effectively about the science behind the project and its goals will be a challenge. One can anticipate alarms about any attempt to resurrect the dead (extinct).
As for the biological challenges, a “soft-release approach” has shown to have the highest rate of success with bird species. This requires outdoor aviaries for raising birds, which exposes the birds to the habitat in a protected manner that allows them to acclimate. The passenger pigeon is a nomadic migrating species and needs to move from one area to another throughout the year: This will require multiple outdoor facilities in different zones.
Here’s the good news. In finding their way across a new terrain, passenger pigeons may be able to rely on help from a relative. Homing pigeons can facilitate migration from one site to another, replicating exactly the historical way that passenger pigeon juveniles joined adult flocks. By using this cycle for several generations—moving from one site to another at random—it will be possible to train the slowly re-wilding population to move nomadically and not rely on any one site annually. Passenger pigeons in their historical abundance were too immensely dense in numbers to use the same spot more than a few seasons at a time, due to the available resources. Thus, the pigeons would cycle through different roosting and nesting sites over time, allowing regeneration.
The first step here is to build up the population within the aviaries. This will also allow us to recreate the high-density social structure of the pigeons. Even at a small population size, the pigeons need to collectively learn the behaviors of the mega-flocks they once were. As the population grows, they will be more densely packed into these aviaries.
When the birds begin to fly from one site to the next in enormous numbers, and when the first generations ferry the next, we can take away the surrogate parents and surrogate flocks and take down the aviaries. The passenger pigeon will then rediscover the forests of its former habitat. At that point, we will have success: the de-extinction of the passenger pigeon.
About the Author
Ben J. Novak has studied ecology and evolution at Montana State University, specializing in paleontology, ecology, and genetics. His Great Comeback project is a Revive and Restore initiative under the Long Now Foundation, longnow.org/revive/projects/.
Portions of this essay were adapted with permission from the Web site passengerpigeon.org/flights.html.
Readers who are interested in joining the passenger pigeon de-extinction campaign are encouraged to visit the Great Comeback page on Facebook.
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