The Great Passenger Pigeon Comeback has set ambitious goals to hatch the first generation of new Passenger Pigeons before 2025 and begin trial wild releases in the following 15 years. Below is our interactive roadmap revealing our timelines of past work and future work necessary to achieve these goals including our current status of each project phase.
With the help of several partners, a series of significant milestones have been achieved for the Great Passenger Pigeon Comeback, Revive & Restore’s longest running project. Passenger Pigeon de-extinction has fueled global dialogue on developing de-extinction as a conservation tool; our program has been used as a case study by independent researchers in many publications. The partnerships and insights gained through our flagship project’s progress has set the stage for rapid developments for Heath Hen de-extinction and discussions for building other avian projects.
October 2018 Project Update
Work on Phase 2 has officially begun, and project lead Ben Novak has begun breeding his flock of Cas9 germline chimeras – birds capable of making genome engineering in pigeons more efficient. This research will pave the way for the genetic rescue of all wild birds. Keep reading for a full update on the growing flock and for recent coverage in the Wall Street Journal.
Meet the Scientists Bringing Extinct Species Back from the Dead
Wall Street Journal
“The last known passenger pigeon—a bird named Martha—died in captivity at a Cincinnati zoo in 1914. Her demise sparked the passing of modern conservation laws to protect other endangered species in the U.S.” Now, more than 100 years later, the Passenger Pigeon is again advancing conservation.
Although the de-extinction of the Passenger Pigeon will likely take decades, de-extinction research is already generating foundational science that could transform bird conservation. Furthermore, Passenger Pigeon de-extinction offers a new opportunity to achieve long-term conservation goals for woodland forests in the eastern United States.
In fall 2017, project lead Ben Novak began the first experiments to genetically engineer pigeons, using domestic rock pigeons as a model to begin testing the feasibility of editing genomes of living birds for the extinct Passenger Pigeon’s traits. Over the past year, Novak has breed a flock of rock pigeons that are capable of making genome engineering in pigeons far more efficient.
“The pigeons are outwardly unremarkable. Thirteen birds, ages two weeks to three months, occupy a coop at an animal research facility west of Melbourne, Australia. They’re descendants of the common rock pigeon, recognizable denizens of city squares and park benches—with one small but crucial distinction,” writes the Journal. “These are the first pigeons in history with reproductive systems that contain the Cas9 gene, an essential component of the Crispr gene-editing tool. The squabs of this flock will be born with the Cas9 gene in every one of their cells, allowing scientists to edit their offspring with DNA from the extinct passenger pigeon. Those birds, if everything goes to plan, will be the first live animals edited with traits from a species that no longer exists.”
The Flock
Project Phases
Learn about our Phase 1, Phase 2, and Phase 3 highlights and current status below:
Phase 1 – Since 2012, through our collaborative partnership with the UCSC Paleogenomics Lab, we have:
- Sequenced DNA from 37 Passenger Pigeons, including 2 whole genomes;
- Sequenced, assembled, and publicly released a high quality reference genome for the Band-tailed Pigeon;
- Made valuable scientific discoveries of the species’ evolution and population genomics.
Not only have we discovered that the Passenger Pigeon was a well adapted, resilient, and ancient bird, we have identified some of the first genes that may help revive the species.
In 2017, we welcome aboard a new project partner to sequence and research more genomes for Passenger Pigeon de-extinction, the Center for Genome Architecture at Rice University’s Baylor College of Medicine.
Phase 2 – In fall 2017, project lead Ben Novak began the first experiments to genetically engineer pigeons, using Domestic Rock Pigeons as a model to begin testing the feasibility of editing genomes of living birds for the extinct Passenger Pigeon’s traits.
Our next Phase 2 goal is to raise money to begin developing germ-line transmission, the most efficient reproductive technique for creating genome-edited birds, for pigeons. With adequate support, our project partner Crystal Bioscience, a world leader in avian biotechnologies, may begin initial experiments with Domestic Rock Pigeons. Success with Rock Pigeons will lay the foundation needed to work with Band-tailed Pigeons.
Phase 3 – Novak’s master’s thesis analyzed the ecological niche of the Passenger Pigeon. His research, completed in summer 2016, determined that the Passenger Pigeon was the ecosystem engineer of eastern North American forests. New ecological studies important for Passenger Pigeon restoration are underway.
Our Partners at the Bronx Zoo recently completed research of Band-tailed Pigeon captive breeding, examining optimal care conditions and studying the development of chicks to adulthood. This is invaluable data for Passenger Pigeon captive breeding work.
In July 2017, project collaborator Holland Shaw began raising Revive & Restore’s small Band-tailed Pigeon flock at his home in Massachusetts, the first step in growing our flock to raise future revived Passenger Pigeons.
For more detail of the milestones accomplished to date and our future steps for Passenger Pigeon de-extinction, scroll over the icons on the project roadmap below showing the timelines of different research elements of the programs three phases.
Timeline: Passenger Pigeon De-Extinction
The passenger pigeon project is the founding project of Revive & Restore. February 8th, 2012 a meeting was held at Harvard University to discuss the feasibility of initiating passenger pigeon de-extinction. The meeting kicked off bringing together a team of advisors, collaborators, partners and initial project designs.
Passenger pigeon de-extinction was publicly announced at TEDxDeExtinction, outlining an early vision of the long term project to restore the role of passenger pigeons to eastern North American forests. This announcement rode on the heels of a recently formed partnership with the UCSC Paleogenomics laboratory to complete phase 1 of passenger pigeon de-extinction: genome research.
September 1st, 2014 marked the centennial of the Passenger Pigeon’s extinction. Revive & Restore’s The Great Passenger Pigeon Comeback teamed up with the multi-institutional social awareness outreach program Project Passenger Pigeon throughout the year sharing results of our early genetics and ecological studies to strengthen the message of the Passenger Pigeon’s “cautionary tale” to motivate conservation of living species. Our de-extinction work is featured in Project Passenger Pigeon’s book “A Feathered River Across the Sky” and documentary “From Billions to None”.
The Great Passenger Pigeon Comeback program served as a model for discussing the process, considerations, and obstacles necessary to overcome for the de-extinction of the Great Auk, at a meeting hosted by Lord Viscount Matthew Ridley at the Centre for Life, New Castle Upon Tyne, England.
The first publication resulting from Revive & Restore’s partnership with the UCSC Paleogenomics Lab reveals the origins of the Passenger Pigeon lineage for the first time. The Passenger Pigeons evolution split from its living relatives ~12 million years ago. The paper includes the first full mitochondrial DNA sequences of twelve pigeon and dove species ever published, five of which belong to other extinct species, notably the iconic Dodo bird. In August 2016 Ben Novak traveled to the island nation of Mauritius to discuss how Passenger Pigeon de-extinction is making it possible to consider reviving the Dodo bird.
Revive & Restore gathered researchers from both Passenger Pigeon and Heath Hen de-extinction efforts and several new partners for a 1 day meeting hosted at the California Academy of Sciences, marking the first bird focused meeting since Revive & Restore’s formation in 2012. Our de-extinction programs were used as a basis to discuss the future of genetic rescue biotechnologies and applications for endangered birds while outlining roadmaps for the programs’ next steps.
Project Lead Ben J. Novak begins working with Revive & Restore. Preliminary analyses of DNA quality begins on 3 passenger pigeon specimens collected from the Field Museum of Natural History (FMNH), Chicago. Tissues from the FMNH birds were handled at the McMaster Ancient DNA Centre. Data from the FMNH birds was processed and analyzed by Ben Novak, Steven Salzberg and Daniela Puiu of Johns Hopkins University, and Zev Kronenberg and Mark Yandell of the University of Utah. These early analyses provided the data needed to design a full passenger pigeon genome project.
After analyzing DNA quality from over 40 passenger pigeon specimens from the Royal Ontario Museum, the highest quality specimens were selected for full genome sequencing, which began October 8th, 2013 at the University of California of San Francisco. Sequences were mapped to the published rock pigeon genome to begin studying the species until the band-tailed pigeon genome was available.
DNA from four passenger pigeons, including “Passenger Pigeon 1876“, have been mapped to the complete band-tailed pigeon reference genome, filling in 20-100 million base pairs of missing sequence for each sample that could not be mapped using the rock pigeon genome. The final passenger pigeon genomes total nearly 960 million base pairs of the total 1.1 billion base pair genome.
Analysis of Passenger Pigeon population genomics is completed and the findings released in prepublished format on Cold Spring Harbor Laboratory’s biorxiv preprint server. Our analyses reveal a robust species, resilient to environmental changes and adapted to its social lifestyle. With the aid of the band-tailed pigeon’s completed transcriptome, the UCSC Paleogenomics Lab researchers identified several genes that may be involved in the unique social adaptations of Passenger Pigeons in contrast to the territorial breeding nature of Band-tailed Pigeons.
Tissue samples from a band-tailed pigeon specimen obtained from the American Museum of Natural History (AMNH), New York City, were processed at George Church’s Harvard Lab. The data was sequenced at the Farnecombe Metagenomics Facility, McMaster University, Hamilton Ontario. A first draft assembly of the band-tailed pigeon genome was constructed by a team at the Beijing Genomics Institute under researcher Guojie Zhang. The DNA, from archival tissue, was not of sufficient quality to produce an adequate reference genome. Fresh tissue was needed to move forward.
DNA sequencing at the UCSC Paleogenomics Lab began for a new band-tailed pigeon reference genome, using a blood sample supplied by Sal Alvarez of Exotic Wings International. The startup company Dovetail Genomics partnered with us to work on the genome of this bird, named “Sally” after her caretaker.
The band-tailed pigeon reference genome is completed by Dovetail Genomics. The genome is just over 1 billion base pairs in size and of high quality. This genome was constructed using short DNA sequences from a female band-tailed pigeon named Sally, alive and well today. Gaps from hard to assemble genome regions were bridged using a special long range DNA sequence (the specialty of Dovetail Genomics) that was obtained from a cell culture grown from one of Sally’s offspring. This cell culture was generated by Advanced Cell Technology, Inc. (now Ocata Therapeutics). The DNA from the AMNH band-tailed pigeon has now been mapped to this reference genome, providing two band-tailed pigeon genomes for analysis.
The protein-coding transcriptome of the Band-tailed Pigeon is finished, identifying 19,528 protein coding genes. Future work is needed to identify non-protein coding elements in the transcriptome, which will be important for de-extinction. Non-coding transcriptome elements include gene regulators – the on/off and volume knobs for expressing traits.
The Great Passenger Pigeon comeback is partnering with the Center for Genome Architecture, Baylor College of Medicine, Rice University to assemble the genomes of the South American Band-tailed Pigeons housed at the Bronx Zoo and additional Passenger Pigeon specimens. Comparing multiple subspecies of Band-tailed Pigeon to a larger set of Passenger Pigeon genomes will help narrow down which mutations are truly unique to Passenger Pigeons as a whole species.
Phase 1.3 has started, comparing the genomes of four passenger pigeons and two band-tailed pigeons to identify the mutations that separate the two species. A first pass of the genomes has shown that the species are ~3% different, based on preliminary identification of nearly 25 million mutations. The next step will be to categorize which of these mutations affect genes and which mutations do not. For that the transcriptome of the band-tailed pigeon needs to be completed.
The Band-tailed Pigeon reference genome and all data for Band-tailed Pigeons and Passenger Pigeons have been deposited to the National Center for Biotechnology’s publicly accessible genbank database. Any researcher or individual in the world can now begin comparing the genomes of these two species and contribute insights to Passenger Pigeon de-extinction. Our own preliminary analysis shows ~62,000 mutations that generate differences in ~12,800 protein-coding genes. Among these mutations are some of the unique adaptations key to the Passenger Pigeon’s ecological function.
Revive & Restore contracted Crystal Bioscience to develop the protocols for primordial germ cell isolation in pigeon species. Crystal Bioscience is a leader in working with avian primordial germ cell isolation and culturing – a necessary process for de-extinction with any bird species. Using rock pigeons, Crystal Bioscience identified the optimal embryonic developmental stage to isolate germ-cells. This work serves as a precursor to working with Band-tailed Pigeons in the future.
In order to move forward with developing a viable cell culture for genome editing we need to raise $60,000 for every 6 months or research until we have success. We can start by developing cell cultures for Domestic Rock Pigeons, which are readily available for research. There is a good likelyhood we could have success in the first 6 months. Once we can culture primordial germ cells and optimize germ-line transmission for Domestic Rock Pigeons, we can transfer those techniques to the Band-tailed Pigeon. To proceed with such work we need a well managed flock of Band-tailed Pigeons. Project collaborators Holland Shaw and John Bender have volunteered to help expand our small flock of Band-tailed Pigeons to the numbers needed for a successful de-extinction program. To do so we need to equip them with a breeding facility capable of housing birds for our project. John Bender has designed a facility that can be build for $20,000. You can help set this work in motion by donating to The Great Passenger Pigeon Comeback.
Project leader, Ben Novak, is starting a 3 year program to test genome editing in Domestic Rock Pigeons as a model for Passenger Pigeon de-extinction. Ben Novak’s proposal for working with Rock Pigeons is taking advantage of current approaches that can be conducted without cultured primordial germ cells. While the genome editing capabilities without cultured primordial germ-cells is limited and a slower process, the optimization of methods for handling embryos and caring for engineered birds will be instrumental to an efficient de-extinction program as well as genetic rescue of other birds with similar parenting behaviors to pigeons. The main goal of the work is establish proof of concept for altering the traits of living pigeons using the template of an extinct species. This work represents the first genome editing experiments of the Great Passenger Pigeon Comeback.
Once cell cultures, breeding facilities, and genome editing ground work is in place we can begin editing the band-tailed pigeon genome into the new passenger pigeon genome, using the library of information developed in Phase 1. Advancements in CRISPR/Cas9 genome editing in model species are paving the way for our work. Every year the system becomes more efficient, capable of editing larger regions of the genome and performing higher numbers of simultaneous genome edits. It’s difficult to predict how long creating a passenger pigeon will take, but we aim to produce the new passenger pigeon genome in 3 years or less.
A flock of South American Band-tailed Pigeons were rescued from illegal wildlife trade and brought to the Bronx Zoo, where collaborator David Oehler initiated a research program to gain knowledge for Passenger Pigeon de-extinction by studying the care needs and development of Band-tailed Pigeon offspring.
Project collaborator Paul Marini conducted a pilot study of band-tailed pigeon breeding cycles. This data is crucial to knowing how many breeding band-tailed pigeons will be needed for producing germ-line chimeras to breed new passenger pigeons. This data also adds to the ongoing work at the Bronx Zoo building the foundation of understanding adequate care to both band-tailed pigeons and passenger pigeons in captivity.
Our two breeding pairs of Band-tailed Pigeons, including “Sally”, arrived at their new home in New England under the care of project collaborator Holland Shaw. This is the first step in conditioning Band-tailed Pigeons to live in Passenger Pigeon environments and to begin expanding our flock for further research purposes.
Once we have raised $20,000 for our custom breeding facility, project collaborator John Bender will begin a series of experiments as he expands our Band-tailed Pigeon flock. The crucial experiments to be carried out include: 1) testing surrogate parenting, also known as cross-fostering, of Band-tailed Pigeon hatchlings by Domestic Rock Pigeons; 2) conditioning Domestic Rock Pigeons to breed and raise young in Passenger PIgeon like colonies in trees; and 3) acclimating newly raised Band-tailed Pigeons to the same diet as historic Passenger Pigeons. These experiments are vital to establishing the protocols and resources for raising the first generation of de-extinct Passenger Pigeons.
Captive breeding the new generation of passenger pigeons will be accomplished with surrogate parents to boost numbers. Our goal is breed a flock large enough to hatch at least 100 spare offspring each year that can move to soft release facilities. This stage will require several breeding facilities and many pigeon-care experts – some of which have already pledged to assist this work when it begins.
Soft release facilities are used by many bird recovery programs – they have been key to the successful recovery of the Mauritius pink pigeon. Our project will follow this precedent, by using large aviaries surrounding woodland habitats so that the birds are contained for our study but exposed to weather and wild conditions. In these facilities we can release other animals to study how the new passenger pigeons interact. The pigeons will begin breeding and raising offspring in these facilities. When these birds appear adapted to their habitat we will begin free release to the wild.
When the new passenger pigeons are released to the wild they will be monitored and studied as they explore the forests of eastern North America. Over the years the wild population will be supplemented by soft release reared birds until the flocks are sustaining and growing – a flock of 10,000 birds will meet this goal. The true end goal will be reached when a flock is large enough to re-establish disturbance/regeneration cycles for future productive forests rich in diversity.
Project leader Ben Novak begins researching the historical ecology of the Passenger pigeon, starting with population genetics studying the paleoecology of eastern N. American forests. A thorough understanding of the species’ ecology will be necessary for successful restoration to the wild. Thinking forward to de-extinction goals, collaborator Holland Shaw is conducting extensive trials testing the breaking point of tree limbs so that we can understand the population density that once generated beneficial canopy disturbances – a population density we will need to achieve again to produce the ecological benefits we hypothesize will be gained from Passenger Pigeon de-extinction.
Studies of the Passenger Pigeons dietary ecology begin using living pigeons as models to understand the limitations and impacts of the PAssenger Pigeons feeding and potential seed dispersal on the forest plants it once consumed – food chain relationships which de-extinct Passenger PIgeons will resume someday. This data will be important to predict the impacts of Passenger Pigeons on not only the plants they eat, but the animals they will compete with for food.
Ben Novak completes his masters thesis, synthesizing the results of population genetics, dietary ecology, and forest paleoecology. The recent trends in population size were gained using complete mitochondrial genome sequences of of 41 passenger pigeons (three of which date to 4,000 years old). When comparing the population history of the PAssenger Pigeon to changes in forests it becomes clear that not only was the Passenger Pigeon a superbly adaptable species, but it was the major ecosystem engineer of eastern N. American forests – this discovery reveals the true value of returning Passenger Pigeon flocks to eastern N.American forests, the details of are summarized here.
Work continues on the paleoecology of the Passenger Pigeon to re-evaluate historic hypotheses of the species’ biology. With a new team of collaborators we are underway conducting spatial analyses of Passenger Pigeon observation records with various habitat factors to further clarify the ecological niche space of the species. In addition we are analyzing ratios of juvenile to adult Passenger Pigeon specimens to re-evaluate the long held belief that as Passenger Pigeons became rare they were unable to breed successfully with the scientists that recently published a challenging hypothesis based on egg collection records from the final years of the Passenger Pigeon’s extinction.
