Why did the Passenger Pigeon go extinct?

Even though passenger pigeons were killed by human hunters, it is still not clear how a species can go from being a billion to nothing in fifty years. Are genetics able to provide us with any useful clues about this?

The extinction of the passenger bird is one of the most remarkable extinctions. It was a human achievement that has been unmatched in recorded history. Because humans are so obsessed with killing and large-scale habitat destruction, this iconic bird’s population plummeted from billions down to zero within fifty years. How could they be so quickly declining? They didn’t kill every one of them, surely? Why shouldn’t mind-bogglingly large and widespread populations help a species survive? Why can’t some pigeons live in remote locations?

The mystery of continues

Researchers published a 2014 study to find out how such a large bird species could be extinct. This is especially important considering that many scientists believe that passenger pigeons are the most populous bird species ever. The 2014 study showed that, despite their large population, passenger pigeons have much less genetic diversity than was expected. According to the study’s authors, passenger pigeons weren’t always abundant ( ref; more).

According to researchers, the numbers of passenger pigeons had either increased dramatically in recent years (similarly to the current human population explosion) or they fluctuated naturally by at least a thousand times over short periods. This pattern can be seen in many outbreak species such as the Australian plague locusts, Chortoicetes terminifera and lemmings Lemmus. The 2014 study’s authors concluded that the passenger bird was an “outbreak” species and that periodic population crashes caused genetic bottlenecks, which reduced the expected level of genetic diversity. The authors also suggested that the passenger pigeon’s natural decline was already underway before European colonists and immigrants pushed it over the edge to extinction.

A new study ( ref ) challenges this conclusion. The authors of this study sequenced and analyzed four passenger pigeon genomes as well as 41 mitochondrial genomes taken from individuals across this bird’s vast range. They found that the diversity of the passenger pigeon gene was very low in comparison to their overall population.

However, when researchers looked at the whole genome, they discovered that there was a wide range of genetic diversity. Some regions had low levels of diversity while others had high levels. This was not expected. Researchers reasoned that if passenger pigeon population fluctuated by a thousandfold over long periods of time, then genetic variation in all regions should also be affected.

They also discovered that the genetic diversity of the mitochondrial genome was not consistent with the genomic data. The passenger pigeon’s mitochondrial genome showed that their population was stable over the past 20,000 year period. This includes dramatic changes in the climate, like the end of the last North American ice age. It is exactly when you would expect to see population fluctuations.

More curious

The Ectopistes Migratorius was a handsome, medium-sized passenger pigeon that lived in large, communal colonies across the eastern United States. This species, which is sleek and slim, was designed for speed and could wander over great distances (Figure 1, A).

The genome of the passenger pigeon captured its peregrinating lifestyle (Figure 1B).

As I said, it was widely accepted that the population of passenger pigeons experienced large periodic fluctuations which, in turn reduced their overall genetic diversity to levels that were not expected. Natural selection could also be responsible for the unusually high level of genetic diversity. Natural selection could also be responsible for the unusually high level of genetic diversity. This phenomenon, where one gene has an effect on the fate of others in its genetic neighborhood, is called the “hitchhiking effect” ( ref).

Researchers compared the genetic diversity of the passenger bird to that of the band-tailed pigeon Patagioenas fasciata.

These two species are close relatives and are very similar in their ecology. However, there is one major difference that was particularly important for this study. The population of the band-tailed bird is smaller than the passenger pigeons’, and has always been.

“The only thing that is different between them is their population size,” stated Beth Shapiro, a senior co-author of this study and molecular biologist. She is also a professor at the University of California Santa Cruz.

Professor Shapiro and her coworkers took tiny tissue samples from the toes of passenger pigeon specimens taken across the eastern United States (Figure 1, A), for this purpose. These are now held in several museum collections. The research team was able to extract the nuclear and mitochondrial genomes of individual passenger pigeons using these tissue samples. The genetic markers of the passenger pigeon were compared to those of the banded pigeon.

Professor Shapiro and her collaborators discovered that certain portions of the passenger-pigeon genome contained high genetic diversity. This indicates that they lived in large populations for a long time (Figure 2).

However, other areas of the passenger pigeon genome showed a lower level of genetic diversity than expected (Figure 2), despite them being “neutral mutations”. While neutral mutations are not beneficial or harmful, they can be used as raw material for natural selection as the birds adapt to changing environments. The authors concluded that passenger pigeon’s genome had a strong natural selection “hitch-hiking effect”.

The authors claim that this is due to the abundance of passenger pigeons and their incredible mobility. This allowed for beneficial mutations to spread quickly across the population, while detrimental mutations were wiped out just as quickly. The “hitchhiking effect” model describes how strong natural selection affected the diversity of nearby genes that were neither beneficial or detrimental.

Mass murder is impossible

It is obvious, in retrospect, that the passenger pigeon was unable to tolerate much hunting, and certainly not the kind of constant, intense slaughter that European colonists and immigrants subjected them to.

Professor Shapiro stated, “Our mass killing of them over the course a decade was just too quick for evolution to keep pace.”

Professor Shapiro explained in an email, “Our study showed that passenger pigeons are strikingly well-adapted to living in large numbers.” Natural selection is extremely efficient in large populations. This means that even if the environment changed slowly, such as it did after the last Ice Age, they would still be able adapt to the changes.

The 1800s saw a sudden shift in passenger pigeon ecology due to hunting.

Professor Shapiro stated in an email that “we killed millions of passenger-pigeons within the span of only a few passengers pigeon generation.” “Passenger pigeons had no time to adjust to this new environment. They didn’t die because there was not much diversity… they died because they suddenly found themselves in an environment very different to the one they were used to. This environment was still being overexploited and they now lack an efficient way to adapt to this change.

What can we learn from this terrible extinction? This study and the 2014 study do not provide genetic insight into how the passenger-pigeon disappeared so rapidly. None of the published research has been able to predict the number of passenger pigeons that would be killed before the population collapses into insignificance, forever. What was the line?

Conservation can be difficult work. Conservation biologists generally assume that large populations correspond to high genetic diversity. This, presumably, acts like a buffer against extinction. The passenger pigeon is a strong warning sign that this assumption may not be true.

Professor Shapiro agreed that there is more to a population’s survival than its size. She noted that conservation efforts must be taken long before the species’ population drops below what we consider a critical level.

Professor Shapiro stated that “we think now of restoring [endangered] species by creating patches of protected habitat.” “But, we don’t know if their evolution throughout their history means they aren’t fit to live in small numbers.”

It is likely that the passenger pigeon was incapable of surviving in small relict communities. They were able to survive in large numbers, which was probably their best survival strategy. No predator could possibly kill them all. This strategy can be seen in some animals and insects, as well as in some vertebrate species. The fate of the Atlantic cod, Gadus Morhua, was remarkably similar to that of the passenger Pigeon. These fish were once abundant along Newfoundland’s Grand Banks. However, their numbers plummeted due to overfishing in the 1990s. Despite the fact that the Grand Banks cod population has been largely eliminated from fishing since more than 15 years ago ( ref), the fishery is declining and will likely disappear in 20 years.

Genetics is only one part of the story. Historical reports indicate that passenger pigeons are behaviorally adapted for living in large groups.

Gemma Murray (UCSC evolutionary biologist) was the lead author. These behaviors might be able to work well when your population is large and dense. These behaviors didn’t work when hunting had a large impact on their population and their numbers plummeted in the 19th Century.

Professor Shapiro’s data and those of her colleagues show that passenger pigeons lacked the genetic resources to adapt to small communities. This may have been due to a decrease in genetic diversity. This was due to widespread and systematic abuse by humans.

Professor Shapiro noted that “The passenger pigeon extinction could have been avoided.” It was all our fault. This amazing animal was over-hunted, over-exploited and it’s our fault. We should be more careful today.


Gemma G. R. Murray and Andre E. R. Soares were also present. Natural selection shaped the rise and fall of passenger pigeon genomic diversity, Science, 358:951-954 | doi:10.1126/science.aao0960

Also known as

Pei-Jen L. Shanera and Robert M. Zink were the authors. Drastic population fluctuations explain the rapid extinction of the passenger pigeon, Proceedings of the National Academy of Sciences, 111(29):10636-10641 | doi:10.1073/pnas.1401526111

The Passenger Pigeon Extinction: It’s Complex

John Maynard Smith (1974) and John Haigh (1974). The hitch-hiking effect of a favourable gene, Genetic Research, 23(1):23-35 | doi:10.1017/S0016672300014634

Why did the Passenger Pigeon go extinct? | @GrrlScientist

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