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Waking the Dead: Bringing Extinct Species Back to Life

TIME Video: Conservationists and scientists have a saying, “extinction is forever.” But soon biologists will clone long-gone animals in the hope to redefine that axiom to “DE-extinction is forever.” Stewart Brand and Ben Novak share their thoughts on de-extinction and Revive & Restore’s flagship project, The Great Passenger Pigeon Comeback.

The Great
Passenger Pigeon
Comeback

This is the first project to revive an extinct animal using its museum-specimen DNA. Once it succeeds, the techniques will be applicable to hundreds of other extinct species.

› Project goals
› Why passenger pigeons?
› Progress to date
› UC Santa Cruz Paleogenomics Lab partnership
› History of the passenger pigeon
› Population ecology

Project goals

The goal of The Great Passenger Pigeon Comeback is to bring the passenger pigeon all the way back using the genome of the band-tailed pigeon and state-of-the-art genomic technology.

Female passenger pigeon. Painting byTim Hough.

Female passenger pigeon. Painting by Tim Hough.

The genomes of the two birds will be compared in close detail, to determine which differences are most crucial. The data and analysis will begin with the process of converting viable band-tailed DNA into viable passenger pigeon DNA. Later stages in the project will involve newly developed and advancing techniques for CRISPR genome editing and germ line transfer to generate live passenger pigeons from the DNA.

Research for the Great Passenger Pigeon Comeback will encompass not only the stages of comparative genomics, bio-engineering, captive breeding, and then wild release, but also the topics of population genetics, paleo-ecology, dietary investigation, habitat assessment, experimental ecology, and finding a pathway for altering band-tailed pigeons to produce the optimal surrogate parent. These areas of research are proving to be important considerations for all candidates for de-extinction as well as endangered candidate species for genetic assistance.

Why passenger pigeons?
The passenger pigeon is a compelling choice for de-extinction. Humans hunted them to extinction from a population of billions until 1914 when none remained. The return of this iconic species by human hands would be a suitable and extraordinary twist in the story of the passenger pigeon. In developing how science approaches de-extinction, a series of criteria for a de-extinction candidate has emerged. According to this criteria, the passenger pigeon offers relative technical practicality for the scientific work of de-extinction. No single species offers an easily achievable, prime candidate for de-extinction, however the passenger pigeon is a model species poised at the optimal middle ground of ease and difficulty. It is a species that is not only feasible to successfully bring back, but also presents enough challenges to push the science forward and open up the possibility of de-extinction to many more species. An extinct mouse would be an easy win for de-extinction, but it does not challenge us to produce the methods necessary to revive birds or reptiles. The passenger pigeon is also a model species for thoroughly testing the process of de-extinction. There are sufficient specimens and enough recorded history to establish a great understanding of the species’ past. This allows us to plan its future in a knowledgeable and responsible manner and also offers an ideal opportunity to learn about extinction. This knowledge will be essential to understanding and helping other species that are critically endangered.

Progress to date
Updated 9/2/14

To fully understand the passenger pigeon genome we need to sequence genomes to a high degree of quality and then analyze the genetic diversity of many passenger pigeons to understand which mutations are variable and which mutations are fixed between the passenger pigeon and its relative the band-tailed pigeon. The passenger pigeon proves not to give up its secrets easily. To study the ecology of the species requires not only multiple specimens, but old specimens; nearly complete mitochondrial genomes from 3,800 year old passenger pigeons have been sequenced and assembled and are helping solve the species’ past. Even older remains are being pursued for work.  Our total data set includes mitochondrial and nuclear DNA from 40 specimens now.

Our passenger pigeon samples came from the collections of the Royal Ontario Museum, Field Museum of Natural History, Denver Museum of Science and Nature, and the Rochester Museum and Science Center. Their DNA has already proven to be quite good in quality and has moved our project closer to obtaining our goal of a full passenger pigeon genome. Our highest quality specimen, ROM 34.3.23.2, aka “Passenger Pigeon 1871,” was selected for full genome sequencing, which commenced October, 2013. Since then a second specimen, ROM 40360 has also been sequenced to high coverage for full genome assembly.

A first draft of the band-tailed pigeon genome has been assembled from sequencing the DNA of “Sally,” the band-tailed pigeon (seen on KQED Quest Documentary “Reawakening Extinct Species“). Sequencing was completed at the UCSC paleognomics laboratory. Genes are being analyzed between the band-tailed pigeon and the passenger pigeon with this first draft, and refined drafts will complete the picture as work moves forward.

Next Steps: Bioinformatics

Nearly a century after the last passenger pigeon died in 1914, the team of scientists working on the Great Passenger Pigeon Comeback is on the verge of assembling – arranging to create a representation of the original chromosomes – a “first draft” of the genome of this species.

Dr. André Soares, UCSC Paleogenomics Lab, is leading the computational analysis and assembly of the new passenger pigeon data. The focus of the team’s work is now on finalizing the assembly of the passenger pigeon genome using the rock pigeon and band-tailed pigeon draft genomes as references. The team is confident that all essential DNA regions will assemble successfully, paving the way for the de-extinction of the passenger pigeon.

We have developed and are analyzing ecological studies using our genomes to give insight into the passenger pigeon’s historical populations and how they interacted with the environment. These findings will be used to create a passenger pigeon recovery plan for future reintroduction to the wild, which includes ultimately identifying and selecting wild release sites, calculating target population size, and predicting ecological impact and management needs.

A 15-year Project in the Making

Our major goal: to bring the Passenger Pigeon all the way back. The work necessary to achieve this goal includes comparing the assembled passenger pigeon genome to the genome of its closest living relative, the band-tailed pigeon, to reveal the DNA regions that make these two species different (2013-2016). This information will allow the team to replace segments of the band-tailed pigeon genome with the essential passenger pigeon sequences (planned to begin 2015). The resulting passenger pigeon genome will be transferred into germ cells of band-tailed pigeons, using techniques still in development, to generate live passenger pigeons (target date 2022). The live birds will be bred in captivity and eventually returned to the wild (soft release to the wild target date 2027). Every step of the way, the genetic variability of the passenger pigeon will be prioritized, incorporating diversity from multiple specimens spanning nearly 4,000 years of ecological history across Northeastern North America, to make sure the end result is a diverse and viable population.

UCSC Paleogenomics Lab partnership
Revive & Restore is partnering with University of California Santa Cruz’s state-of-the-art Paleogenomics Lab for the Great Passenger Pigeon Comeback.

At the Lab, researchers are incorporating experimental and computational approaches to a wide range of evolutionary and ecological questions— mostly involving the application of genomic techniques— to better understand how species and populations such as the passenger pigeon evolve through time. Evolutionary biologist Dr. Beth Shapiro, an expert in ancient DNA laboratory techniques and paleogenomics, jointly leads the Lab with Dr. Richard “Ed” Green, a bioinformatician and expert in modern and ancient genome assembly and analysis. Dr. Shapiro, whose work focuses on how populations of organisms respond to climate and habitat change over time, has been working in collaboration with Dr. Green for several years to assemble passenger pigeon DNA. Additionally, Dr. Green has already developed tools for the eventual assembly of the full passenger pigeon genome. Revive & Restore’s research consultant Ben Novak has contributed vital input on the research, design and planning of the Great Passenger Pigeon Comeback since he joined the Lab as a visiting researcher in early 2013. Lab researcher, Dr. André Elias Rodrigues Soares is leading the computational analysis of new passenger pigeon data, focusing on the population genetics and demography of the species.

History of the passenger pigeon
The first written record of passenger pigeons occurs in a ship captain’s journal in the year 1534 and recounts “an infinite number of wood pigeons.” Throughout the formation of the early British colonies into the United States, the flocks of passenger pigeons were observed to number in the billions. Several ornithologists have tried to calculate the size of flocks that were recorded to take days to fly over a town. It’s suggested that some flocks were a mile wide and 300 miles long, dense enough to block out the sun. During the 1800s poultry farms and ranches hadn’t established sufficiently to feed the growing population of immigrants to the United States. A trip to the marketplace was filled with the meat of all types of wild game. The pigeon’s giant flocks became an easy source of abundant food. The invention of the telegraph allowed food companies to track the passenger pigeon’s movements and “head them off” with hired trappers and shooters. The completion of the railroad between Chicago and New York City changed the industry from harvesting for local markets to shipping to more profitable city markets, and so the harvest of passenger pigeons boomed. During the 1870s millions upon millions of birds were consumed for food. Their feathers made bed mattresses and pillows. Live birds were caught and shipped by the thousands for trap-shooting tournaments. There were certainly at least one billion passenger pigeons alive in 1878, but by 1890 only tens could be spotted anywhere. The last wild birds were shot between 1900 and 1902. This was a shock to the people of that time who believed their numbers would never be diminished. Unfortunately, no one ever put effort into raising the birds in captivity. At the time, pigeon fanciers were more interested in flashy domestic breeds and exotic species from Southeast Asia. Passenger pigeons were thought to be readily available from the wild, so breeding deemed unnecessary. One captive flock was alive when the last birds in the wild disappeared. The flock was highly inbred and the individuals were already quite old. They died off without producing successful offspring over the next few years, until a female living at the Cincinnati Ohio Zoo, named Martha was the last of the species. On September 1, 1914 Martha died. The passenger pigeon became extinct.

Ben Novak studying Martha, the last passenger pigeon in the world (left). She died on September 1, 1914, at the Cincinnati Zoo. She was preserved in ice and sent to the Smithsonian Institution in Washington DC, where she is occasionally displayed with a male (on right). Note the red eye, iridescent neck feathers, red feet, and (in the male) peach-colored breast and blueish back. Photo credit Ryan Phelan.

Ben Novak studying Martha, the last passenger pigeon in the world (left). She died on September 1, 1914, at the Cincinnati Zoo. She was preserved in ice and sent to the Smithsonian Institution in Washington DC, where she is occasionally displayed with a male (on right). Note the red eye, iridescent neck feathers, red feet, and (in the male) peach-colored breast and blueish back.
Photo credit Ryan Phelan.

Population ecology
Using the fossil record of the passenger pigeon and ancient pollen grains we now know that passenger pigeons lived and thrived throughout the past 250,000 years – adapting to major climate changes from ice ages to dry hot climates. Gut contents of passenger pigeons that were collected in the 1800s did not survive, but were documented to contain tree mast — the majority of which is comprised of oak acorns. Based on how living pigeon species interact with good food sources, we can hypothesize that the passenger pigeon was dependent on deciduous forests. Its primary food source were the acorns of diverse oak species, and the abundance of acorns may have been a limiting factor in population size. The passenger pigeon’s mega flocks impacted acorn and nut crops each year, each mega flock acting as a “seed-predator” that shaped the diversity of tree types throughout the forest. This relationship caused cycling disturbances of the kind that generate biodiversity turnover, and thus over time the passenger pigeon sustained high biodiversity in forest ecosystems. There are several theories as to how the passenger pigeon reached such large numbers. Some believe that the species was abundant for hundreds of thousands of years, while others have postulated that the species “exploded” in population much more recently, perhaps due to the end of the last ice age or a relationship with Amerindian hunter/gatherers and agricultural communities that developed even more recently. Our population genetics work aims to fill in the details of these many hypotheses that historical data and research cannot fully answer.

Reflections on
Martha’s Centennial

 

The passenger pigeon was once the world’s most plentiful bird. September 1 is the centenary of the bird’s extinction. Martha, the last pigeon of the species, died at the Cincinnati Zoo and now can be viewed at the Smithsonian Institution in Washington DC. 

By Ben Novak

September 1, 2014

There is no limit to the alluring curiosities of living things, and no end to the mysteries of those gone.

Contrary to the poetic nature of “righting past wrongs” that some attribute to the de-extinction of passenger pigeons, I view the de-extinction of the passenger pigeon as a project seeded in our present and future; it is a pivotal exercise in thought stressing the recognition that we are the drivers of change on this planet and that we have the cognitive ability to take responsibility for the direction of that change. If anything can be said of the past, it is that had we been conscious of this long ago, Martha would not have been the last of her kind. Visitors to the Cincinnati Zoo would not enter a memorialized tomb of a species, but perhaps view the elegant beauty of North America’s greatest species, once unmatched in number by any other living thing.

I do not often think of Martha. Martha died in an undignified manner, in a cage. But this indignant view is only placed upon her by the afterthought of the casual dismissal of her kind’s disappearance. The grand flocks of passenger pigeons, such blue meteors streaking through the sky, did not die in a cage. Martha’s legacy of conservation is not to be found in that tomb at the zoo; it is in the beating heart of every buffalo, pronghorn, egret, alligator, whooping crane, and condor. It is in every species that lives today thanks to the conservation movement that gained traction from her death. A movement that now seems at the height of its vitality. Conservation is at a turning point for both the proponents and opponents to the value of biodiversity on this singular planet. A turning point that the de-extinction of the passenger pigeon can sway towards the value of life, just as the extinction of the passenger pigeon did so powerfully a century ago.

The de-extinction of the passenger pigeon is about the pigeon’s place in the forests of tomorrow. To know how to proceed we must explore the past. My thoughts in the pursuit of de-extinction are to the great flocks of passenger pigeons and how they shaped the forests. My imagination bends to the blue backed miniature dinosaurs rustling through the forest floor for fallen acorns and beechnuts. Martha never had the chance to truly know what she was. She was never among the great flocks of passenger pigeons. She never flew hundreds of miles in a day, streaking through branches at 60 mph “passing like a thought” as John James Audubon once so perfectly wrote. None of this belittles her worth to history or her intrinsic value as a living being, it merely gives perspective which I believe many do not consider. I am often asked about Martha in relation to de-extinction, and I am always at a loss for the right form of reverie, since I do not see an individual passenger pigeon – I see a species.

An individual identity though is what catalyzed such a presence to the conservation community. For the first undeniable time extinction had a face; extinction had a name. Today the dodo bird is an icon of extinction and the mammoth a giant of de-extinction prospects, but during the 19th century there were people that believed the dodo bird was a myth and that mammoths would be discovered still alive in the unexplored reaches of America. Extinction, even for these emblems of the notion, was as debated as climate change is today. When the giant flocks disappeared, the title of “endling” fell to Martha. And with her passing a revolution occurred. Extinction was real. It was humankind’s fault. And it wasn’t an isolated incident. Bison were practically gone, turkey endangered, and beaver on the brink of extirpation. Many animals we see as common today were shadows at the turn of the 20th century. Imagine if we can develop protocols to take advantage of the best of technology and build on the most efficient proven practices so that species on the edge of extinction today are recovered a century from now. The passenger pigeon’s unique advantages and challenges for de-extinction can make that future a reality.

The realm of study that builds de-extinction may very well recapitulate the elegance of the bird; the regal rusty-peach breast and wind-cutting tail can be engineered. A new passenger pigeon may cause an internal debate in the on-looker, but when the piercing red iris meets the on-looker’s gaze, in a moment of deep connection, it will remove all doubt, as if to say “I am the passenger pigeon reborn.”

The spirit of this animal will be as vibrant as Martha. Unlike Martha, this new bird’s story doesn’t have to end in a cage. With a generation behind it, these new birds can grace the forests again and enrich the dancing cycles of the trees; they will enrich our souls if we open our hearts to them. The renaissance of their newfound proliferation will change the world, the way Martha has already. We ultimately write the story. Martha’s story is a call to action still, a century after her death. Her story is far from over.

Learn more about the extinction of the passenger pigeon: 

A Feathered River Across the Sky: The Passenger Pigeon’s Flight to Extinction by Joel Greenberg. 

From Billions to None: The Passenger Pigeon’s Flight to Extinction, a documentary which will be shown widely on PBS stations. 

The Royal Ontario Museum events and collections.


Work in Progress

New Passenger Pigeon Genomes

By Beth Shapiro, PhD
Associate Professor, Ecology and Evolutionary Biology
Co-Principal Investigator of the Paleogenomics Lab, University of California Santa Cruz

June 19, 2014

As you may know, a different group (not us — Ouch!) has published a paper in PNAS on June 16 (see abstract and link) in which they use genome sequence data from several preserved passenger pigeons to infer long-term demographic trends in the bird.

It is important to the de-extinction effort because it shows (as our data do) that passenger pigeon populations fluctuated in size through time, as resource availability changed. This means that we probably won’t need to bring back billions of birds in order for their populations to be sustainable, as long as we can keep ourselves from killing them.

The paper maps passenger pigeon genetic data to a published genome from the Rock dove, Columba livia, and uses these data to infer changes in their population size through time. They also do a very nice reconstruction of what niche space would have been available to these birds during the Holocene.

In addition to sequencing a few more passenger pigeon genomes (which will be useful to evaluate how genetically diverse they were), we are assembling and annotating the genome of the band-tailed pigeon. Because the band-tailed pigeon is the most closely related living pigeon to the passenger pigeon, we can use these data to figure out what genetic changes are unique to the passenger pigeon. This will be key to resurrecting passenger pigeon traits in living birds.



Project Update:
The Great Passenger Pigeon Comeback

February 27, 02014

The year 02013 was a productive time for our flagship project: The Great Passsenger Pigeon Comeback. Outreach for 02013 included presentations at TEDxDeExtinction, the Mississippi Flyway Council meeting, the American Ornithologists’ Union annual meeting, the Association of Zoos and Aquariums annual conference, and various education and public presentations engaging diverse audiences from elementary and high school students to researchers, scientists and administrators of academia, zoos, the United States Fish and Wildlife Service, and project enthusiasts of all walks of life. In the lab, under the leadership of Ben Novak (Revive & Restore) and Dr. Beth Shapiro (UC Santa Cruz Paleogenomics Lab) several major milestones for the project have been completed.

Progress continues into 02014 with bioinformatics and ecological research. Upcoming conferences and meetings concerning avian biotech are forming the initiation of project designs for the cellular and genomic editing that will produce living passenger pigeons from the genome studies currently in development.

Next Steps: Bioinformatics

Nearly a century after the last passenger pigeon died in 1914, the team of scientists working on the Great Passenger Pigeon Comeback is on the verge of assembling – arranging to create a representation of the original chromosomes – a “first draft” of the genome of this species.

Read More

Dr. André Soares, UCSC Paleogenomics Lab, is leading the computational analysis and assembly of the new passenger pigeon data. The focus of the team’s work is now on finalizing the assembly of the passenger pigeon genome using the rock pigeon and band-tailed pigeon genomes as references. The rock pigeon genome has already been serving as a reference and as soon as the band-tailed pigeon genome is assembled it will fill gaps and produce a higher quality mapping. The team is confident that all essential DNA regions will assemble successfully, paving the way for the de-extinction of the passenger pigeon.

We will be developing ecological studies in order to give insight into the passenger pigeon’s historical populations and how they interacted with the environment. These findings will be used to create a passenger pigeon recovery plan, which includes ultimately identifying and selecting wild release sites, calculating target population size, and predicting ecological impact and management needs.

A 15-year Project in the Making

Our major goal: to bring the Passenger Pigeon all the way back. The work necessary to achieve this goal includes comparing the assembled passenger pigeon genome to the genome of its closest living relative, the band-tailed pigeon, to reveal the DNA regions that make these two species different. This information will allow the team to replace segments of the band-tailed pigeon genome with the essential passenger pigeon sequences. The resulting passenger pigeon genome will be transferred into germ cells of band-tailed pigeons, using techniques still in development, to generate live passenger pigeons. The live birds will be bred in captivity and eventually returned to the wild. Every step of the way, the genetic variability of the passenger pigeon will be prioritized, incorporating diversity from multiple specimens spanning 250 years of ecological history across Northeastern North America, to make sure the end result is a diverse and viable population.