In the late 19th century the passenger pigeon, once the most abundant bird in North America, and possibly the world, went extinct. Three-to-five billion passenger pigeons once glided across the skies (a remarkably large number for any vertebrate) and so it raises the question: how could such a large population die off never to be seen again?
This is the question Drs. Beth Shapiro and Richard Green pondered. “Why didn’t little tiny populations of this bird survive in some refugial forest somewhere? Why did they just go from billions to none?” Shapiro posited.
Ecologists at University of California, Santa Cruz Paleogenomics Lab, Shapiro and Green used ancient DNA to try to answer these questions. Ancient DNA is defined as isolating DNA (the carrier of genetic information) from specimens that are dead more than 100 years or from biological samples that have not already been preserved specifically for DNA analyses. The field got its start in 1985 with the extraction and sequencing of DNA from a 150-year-old museum specimen – an extinct subspecies of the zebra. Since then, scientists have been able to reconstruct the complete genomes from several extinct species, such as Neanderthals and mammoths.
In the case of the passenger pigeon, Shapiro, Green and their colleagues, were able to generate an entire genome sequence by taking a tiny piece of toe pad from several birds preserved in museums. With this genetic information, they were able to compare genomes with its closest living relative, the band-tailed pigeon. Unlike its cousin, the band-tailed pigeon does not live in groups of billions. In fact, the present-day population is three orders of magnitude smaller than passenger pigeons, adding to the mystery of the passenger pigeon’s disappearance.
Theory predicts genetic diversity increases in proportion to the size of the population, but it turns out this was not the case for the passenger pigeon. Using ancient DNA, the research team discovered that passenger pigeons may have evolved traits that were adaptive when their population was large but that made it more difficult for them to survive when their population dwindled. Until this discovery, many assumed the cause of their death was from hunting. While hunting contributed to a significant decline in population, we now know the ultimate cause of their disappearance was low genetic diversity. As the birds shrank in number, they did not have the genetic diversity to adapt to the changing environment. The research was published as a cover story in Science.
Genomics is expanding our knowledge of evolution
Prior to the genomic revolution, our understanding of evolution relied primarily on the discovery and study of fossils. With advances in science, such as the Human Genome Project and the development of next-generation sequencing, scientists can now compare complete genome sequences between and within living species, leading to new discoveries. For example, in late 2017 Shapiro and Green discovered a new genus of horse using ancient DNA. And, in this 2016 video, they speak about ancient DNA and what is possible with this technology, using examples of DNA extracted from old bones.
“Now there is technology for answering mysteries about where we come from and how the other organisms that we share the world with got here and the way that they are,” said Green. “It’s a testament to the power of this approach that we can learn things about populations that lived and died in the past and are now extinct.”
With foundation support, Shapiro and Green are developing new techniques that will significantly expand ancient DNA use for research. The approaches will enhance our understanding of the evolutionary relationships between extinct and surviving species and give researchers new tools to ask novel and important evolutionary questions.
“Providing scientists, like Drs. Shapiro and Green, with the support and freedom to pursue new approaches is an important aspect of our funding,” said Gary Greenburg, Ph.D., program officer of the Moore Foundation’s Science Program. “New techniques can have a profound impact on the field by enhancing scientific knowledge through pathways previously unknown.”
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