show longnow.org menu

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

As you may know, a different group (not us — Ouch!) has published a paper in PNAS on June 16 (see abstract and link below) 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.


Excerpt from: Proceedings of the National Academy of Sciences of the United States of America

Drastic population fluctuations explain the rapid extinction of the passenger pigeon

Chih-Ming Hunga,1, Pei-Jen L. Shanera,1, Robert M. Zinkb, Wei-Chung Liuc, Te-Chin Chud, Wen-San Huange,f,2, and Shou-Hsien Lia,2

Abstract
To assess the role of human disturbances in species’ extinction requires an understanding of the species population history before human impact. The passenger pigeon was once the most abundant bird in the world, with a population size estimated at 3–5 billion in the 1800s; its abrupt extinction in 1914 raises the question of how such an abundant bird could have been driven to extinction in mere decades. Although human exploitation is often blamed, the role of natural population dynamics in the passenger pigeon’s extinction remains unexplored. Applying high-throughput sequencing technologies to obtain sequences from most of the genome, we calculated that the passenger pigeon’s effective population size throughout the last million years was persistently about 1/10,000 of the 1800’s estimated number of individuals, a ratio 1,000-times lower than typically found. This result suggests that the passenger pigeon was not always super abundant but experienced dramatic population fluctuations, resembling those of an “outbreak” species. Ecological niche models supported inference of drastic changes in the extent of its breeding range over the last glacial–interglacial cycle. An estimate of acorn-based carrying capacity during the past 21,000 y showed great year-to-year variations. Based on our results, we hypothesize that ecological conditions that dramatically reduced population size under natural conditions could have interacted with human exploitation in causing the passenger pigeon’s rapid demise. Our study illustrates that even species as abundant as the passenger pigeon can be vulnerable to human threats if they are subject to dramatic population fluctuations, and provides a new perspective on the greatest human-caused extinction in recorded history.

Significance
The number of passenger pigeons went from billions to zero in mere decades, in contrast to conventional wisdom that enormous population size provides a buffer against extinction. Our understanding of the passenger pigeon’s extinction, however, has been limited by a lack of knowledge of its long-term population history. Here we use both genomic and ecological analyses to show that the passenger pigeon was not always super abundant, but experienced dramatic population fluctuations, which could increase its vulnerability to human exploitation. Our study demonstrates that high-throughput–based ancient DNA analyses combined with ecological niche modeling can provide evidence allowing us to assess factors that led to the surprisingly rapid demise of the passenger pigeon.


Blog of
Revive & Restore