The birds have also been granted pardon on a number of notable occasions. Jimi Hendrix reputedly set free a pair on Carnaby Street in London in the late 1960s, which some say helped create the now huge London parakeet population. And by releasing forty parakeets in 1974 “because Brussels could use some more color,” the owner of a Belgian zoo single-handedly founded the country’s entire population, now numbering some 30,000 birds—more than 4,000 of which sleep every night on the appropriately named De Neck Street in Brussels. This may have been a bit more green, red, orange, yellow, and blue than zoo director Guy Florizoone (note the name) had intended.
Like the house crow, the ring-necked parakeet is another example of a tropical bird that, seemingly effortlessly, has set itself up as an enterprising urban bird in northern Europe. The birds benefit from the urban heat islands and the fact that there is food to be had in cities in winter (they particularly like to monopolize the strings of peanuts that people put out for smaller songbirds). It also helps that the species’ native range includes the foothills of the Himalayas, so it may already have been pre-adapted to cold spells. Thanks to all these factors, the squawking flocks of fast-flying parakeets are now a familiar sight to most European urbanites. In Paris, I see them squabbling over access to tree hollows in Versailles, and zipping in noisy groups across the evening sky high above Boulevard Montparnasse, on their way to their favorite communal sleeping trees in Parc Montsouris. They fly around in the Jardin des Plantes and among the tall plane trees of Jardin de Luxembourg. Ariane le Gros, a biologist with the Muséum National d’Histoire Naturelle, says: “You find them in more and more parks of Paris, as the population expands really fast.”
Le Gros is one of the biologists who have begun studying how the gene pools of urban species are structured, using an approach known as “phylogeography.” Phylogeography began in the 1980s as a way to tell the evolutionary history of natural populations of animals and plants. It usually involves looking at a large number of “markers,” variable bits in the DNA of a species, for a lot of specimens from different parts of a species’ area of distribution. Phylogeographers can then use such rich information on the genetic make-up of a species to trace back its history. They can calculate what has been the mostly likely colonization route. Or they can see if a population has perhaps been reduced in size at some point in the past, and, if so, how long ago. For example, even if nobody had ever found a single human fossil, phylogeographic analysis of DNA of people living today would still tell us that we evolved in Africa, the routes by which we colonized the rest of the planet, which mountains and deserts blocked our progress, and roughly how many colonists had been involved at each migratory step. It would tell us how long ago each of these steps was taken. It would also tell us, for example, that the gene pool of northern Europe is well mixed, thanks to its long history of travel and trade and intermarriage between people from different parts of the continent. The interior of New Guinea, on the other hand, would show a gene pool much more fragmented by the impassability of the mountainous, thickly forested country. Phylogeography, in other words, is a way to peek into a species’ past via its present-day genes.
In recent years, phylogeographers have begun plying their trade on urban species. By looking at the DNA of urban flora and fauna, they are able to answer many crucial questions that cannot be answered in any other way. What Ariane Le Gros wanted to know was, for example, where do the parakeets of Paris come from? And also: do they form a single well-mixed population or are they split into separate tribes? To get answers to those questions, she caught about 100 parakeets in private gardens close to the Parc de Sausset in the north of Paris and near Parc de Sceaux in the south of the city. Le Gros took DNA samples from blood and the roots of plucked breast feathers and used these to get eighteen “markers” on the birds’ chromosomes and carry out a phylogeographic study.
To her surprise, her analysis told her that the south-Paris and north-Paris parakeets are as different from one another as they are from those in other European cities, which leads her to conclude that the Paris parakeets come from at least two different stocks. This means that parakeets were released or escaped at least twice in Paris or—less likely, thinks Le Gros—that one or both of them have flown in from elsewhere (the parakeets from northern Paris, for example, are quite similar to those that inhabit Marseille, whereas those from southern Paris are genetically unique within Europe). Either way, what is clear is that they did not mix much since they settled in their respective quarters of the city. This may seem surprising, given that they are fast-flying birds that, it appears, could easily traverse the twelve miles in between.
Not quite, says Le Gros. Even though the birds could fly up to nine miles in a day, they don’t really like to cross built-up areas, because, unlike many other urban birds, they cannot live without trees. They need them for roosting at night, since their feet are not made for perching on rocky ledges like pigeons. And they need them for their nests, because, even in the city, they insist on breeding in tree hollows. In a thoroughly stony city like Paris, where even famous parks like Place des Vosges or the Tuileries consist of little more than swathes of sandy path with a few rows of dusty trees, and hardly qualify as green spaces, suitable habitat is hard to come by. The many miles of treeless cityscape that separate the parks of Paris where the parakeets do feel at home, are probably sufficient to keep the city’s populations from genetically blending.
And that’s just birds. Think of more ground-bound city animals, and the phenomenon of fragmentation gets even more acute. Bobcats (Lynx rufus), for example. These smallest of the world’s four species of lynx occur throughout most of North America. They are about twice the size of a domestic cat, and although they were, and still are, hunted intensively for sport and for their soft and attractively patterned fur, they have survived quite successfully and in recent years have been making a bit of a comeback. More and more bobcats are beginning to set themselves up in suburbia, where they sometimes get chased up trees by domestic dogs. They even dare to penetrate the inner city now and then, although their favorite habitat is forest edge with plenty of rabbits and rodents.
In Southern California, wildlife biologist Laurel Serieys did a phylogeographic study of the bobcats within Los Angeles and the region north and northwest of it. This vast area is a patchwork of city sprawl, agriculture, vegetated hills, and residential estates. And roads. Lots and lots of roads. The 56-by-31-mile area that Serieys studied is cut into four quarters by two of the US’s busiest freeways: Route 101, running east–west, and Interstate 405, running north–south. Between them, these ten-lane highways, the scenes of many a Hollywood car chase, support some 700,000 vehicles per day, throwing off secondary and tertiary roads all over the place. But while they connect the human populations, these arteries of traffic, Serieys found, are very efficient at disconnecting the bobcats from one another.
Using an arsenal of animal-friendly capturing devices (padded foothold traps, cage traps, and box traps), supplemented with occasionally encountered roadkill, she and her colleagues were able to obtain DNA samples from nearly 400 bobcats prowling the area. The cats’ genetics clearly betrayed how the roads carve up their habitat. Bobcats in the section east of the I-405 and south of Route 101, on the northern edge of Los Angeles (Beverly Hills, Hollywood, and around the Hollywood Bowl) formed one tribe, genetically very different from the ones north of Route 101, living in the planned community of Thousand Oaks, until 1969 home of Jungleland, where they filmed Tarzan. The Thousand Oaks bobcats again have different DNA from those south of Route 101, but west of the I-405, in the non-urban Santa Monica Mountains.
While bobcats cannot cross freeways, they easily traverse smaller roads. Hence, the genetic structure of their population is determined only by really big highways. But tinier mammals, like mice, are impeded even by lesser streets. In New York, zoologist Jason Munshi-South of Fordham University has made a name for himself by mapping the exact phylogeographic structure of the city’s wil
d mice.
When I first met Munshi-South, back in 2005, he was a lean tropical forest ecologist doing his doctorate on small jungle mammals from the same university in Malaysian Borneo where I was working. Now, when I meet him again over Skype in 2017, I see a transformed man. He has exchanged his jungle gear for a shirt and pullover, his tropical sleekness for urban ring-bearded solidity, and chats with me from behind a reliable oak desk in his Fordham office. But the rodentology paraphernalia on the wall behind him betray that he is still very much a field zoologist. Except that the “field” is now no longer the tropical rainforest, but New York City’s parks.
“It was originally a side project,” he says of his first forays into studying the white-footed mouse (Peromyscus leucopus), back in 2007. “I met some people at a meeting who gave a presentation on citizen science and small mammals in New York City, and that’s how I became interested. So I rounded up some undergraduates and started trapping that first summer.”
The white-footed mouse (big beady black eyes, a grayish-brown coat with strikingly white belly and feet), Munshi-South reminds us, “is not the mouse you find running around your apartment. This is a native species, been here long before humans.” A few hundred years ago, in the time that Eric Sanderson re-creates in the Mannahatta Project of Chapter 1, the whole New York area would have been covered in forest and meadows, with white-footed mice everywhere. They would have formed one continuous population, a well-mixed gene pool with DNA flowing freely through it, as is still the case today in non-urban areas on North America’s east coast. In early twenty-first-century New York City, what remains of the mice and their original habitat are populations marooned in isolated patches that have stayed green and we now call parks. Central Park in Manhattan and Prospect Park in Brooklyn are the largest, but the native mice also live in small ones like Willow Lake in Queens.
Although they are imprisoned in these parks (they will only travel under cover of vegetation and most parks are not connected by anything that’s green), the mice are doing quite well there, especially in the smallest parks, which are too small to support predators like owls or foxes. “There also aren’t as many competitors,” says Munshi-South. “Particularly things like deer … They really decimate the understory in a lot of places where they’ve become abundant, and that reduces the resource base for white-footed mice considerably. But in the city, I mean, they don’t really have many competitors.”
As a result, the New York City parks are well stocked with white-footed mice, and have been so since these parks became isolated by urban development around the end of the nineteenth century. As Munshi-South and his students found after they trapped hundreds of mice in birdseed-baited cage traps in fourteen of the city’s parks, those 120 years or so have been enough for the mice in each park to evolve their own park-specific DNA. For every mouse they caught, they snipped off the last one centimeter of the tail before releasing the animal. This does not harm the mouse much, and it gave the researchers enough tissue to run their genetic tests. Those tests showed that the mouse population in virtually each park, even ones right next to each other, had its own genetic signature. This is something that in the wild is normally only found across much larger areas, like entire states. “Someone could give us a mouse, not tell us where it was from, and we could determine what park it came from. That’s how different they’ve become,” he says.
What the white-footed mice in New York City parks show, just like the bobcats around Los Angeles and the parakeets in Paris, is that urban environments are often so patchy that the gene pools of urban wildlife get split into a multitude of tiny slivers. This is not surprising, in a world with 22 million miles of paved road, where for one-fifth of the land surface the road density is so great that no roadless areas of smaller than a half square mile remain. Usually, it’s those long, linear barriers like paved roads, but also railways and walkways, the traffic they carry or the buildings along them that bisect these gene pools, keeping animals or plants and their genes from crossing freely.
Sometimes, it’s this infrastructure itself that is a species’ habitat, like in the case of the London Underground mosquitoes of the preface, where each tube line has its own mosquito population. Or the cellar spiders (Pholcus phalangioides) that Martin Schäfer of the University of Bonn studied in buildings in five European cities. He discovered that the spiders living in different rooms within one building jointly form a single gene pool, but that each building is a separate gene pool: the spiders move chambers, but rarely move house.
The received wisdom among biologists is that such gene-pool fragmentation is bad for a species’ chances of survival. The idea is that in these small, isolated populations, there’s a lot of inbreeding: mating is among relatives and if that relative happens to carry a genetic defect, chances are that you carry it too, and so will your joint offspring. Also, genetic variation disappears because of chance events: if a genetic variant is carried by 5 percent of the animals in a population, then in a big population, 5 percent may still mean hundreds of animals. Not likely that those will all expire without leaving offspring. But in a small population of a few dozen animals, the handful that carry this gene might, by some chance misfortune, all fail to breed one year, and take this rare gene with them to their graves. Such a tendency for the genes of a small population to become ever more uniform is called “genetic drift.” Drift and inbreeding deteriorate the “genetic health” of a population. Genetic diseases may gain a holdfast, and the loss of variability may mean that the population cannot adapt if conditions change.
This potential problem is why conservationists are always going on about corridors and connecting populations of endangered animals. It is probably why many species eventually cannot sustain themselves in the subdivided environment that cities constitute. But while they are still hanging on, the randomness of drift and inbreeding causes each isolated population to be dealt a different mix of genes. This is how the signal of genetic fragmentation can be picked up by scanning the genomes of bobcats, parakeets, white-footed mice, and any other species whose gene pool is no longer happily sloshing around.
According to Munshi-South, not all species with fragmented gene pools succumb. “There’s these other species, especially the ones we don’t think about, the ones that are just there … that I find really interesting.” His white-footed mice are one of these survivors. Despite being so subdivided that each city park has its own genetic signature, the mice seem not to be suffering from the ill effects of inbreeding or genetic drift. If anything, they appear to be thriving. “I think species that can achieve relatively high population densities in a number of places in the city will generally do okay.”
The reason that the mouse population in each park has a distinct genetic make-up, says Munshi-South, is probably not only because of inbreeding and drift, but because of what he calls local adaptation. Each park has its own isolated band of white-footed mice. And since the mice are not going anywhere, nothing stands in the way of them evolving to suit the local conditions precisely.
To study this exciting possibility in more detail, Munshi-South and his student Stephen Harris undertook an innovative genetic project. They caught mice in several New York City parks, and also in some rural sites outside the city. The aim of this new study was not to just look at a few random markers in the genome, but to study a large number of actual genes active in the rodents’ organs. Sadly, to do so, these mice had to sacrifice more than just a snippet of their tails, for urban science. The researchers killed each captured mouse, removed liver, brains, and gonads, and extracted all the so-called messenger-RNA from these organs. Messenger-RNA (or, “mRNA”) is what a gene is copied into before the cell uses its code to produce a protein. So, the pool of mRNA extracted from an organism tells you which genes are actively being used in the body, and what their exact DNA-codes are.
Then, from this huge pool of genetic information, they picked out all the genes that were more different across parks than expected by chance, sinc
e those were the ones that apparently had evolved in different directions in different parks. In Central Park, for example, the mice had a distinctly aberrant AKR7 gene. This gene takes care of neutralizing aflatoxin, a toxic and cancer-promoting substance produced by a fungus that often grows on mouldy nuts and seeds. For some reason (perhaps discarded snacks?), the Central Park mice seem to be more exposed to this. Another gene that had evolved in a striking manner in Central Park was FADS1, which plays a role in dealing with high-fat diets—again a tell-tale sign that these white-footed mice had evolved to manage typical Central Park food stuff. Other genes were noticeably different in other parks, and most were either diet-related, or had to do with exposure to pollution. There were also various immune-related genes, which makes sense, says Munshi-South: “Very easy to spread disease when you’re in a small population.”
Cut to the Hollywood bobcats. There, one chunk of the population subdivided by freeways also seems to have been able to evolve their immune system. Between 2002 and 2005, the bobcats in the city of Thousand Oaks, cut off from the rest of the population by Route 101, suffered from an epidemic of mange, a debilitating skin disease caused by parasitic mites. Research by the National Parks Service showed that the illness mostly struck bobcats that had already been weakened by exposure to rat poisons, which are being used liberally in households and by exterminators. The poisoned rodents were eaten by the bobcats, weakening the bobcats’ immune systems, which made them susceptible to mange. This disease can be fatal in the long run, and it was fatal to so many bobcats that it created a few years of very strong natural selection, with annual survival rates falling from nearly 80 percent to only around 20 percent. This caused the immune system to evolve so quickly that the signal could even be picked up in the genetic data collected by Laurel Serieys. She found that the bobcats captured before the mange epidemic had a very different set of so-called MHC and TLR genes than after the epidemic. These genes produce proteins that recognize disease-causing micro-organisms, such as the mites themselves or the bacteria that enter the skin after it has been breached by the tunneling mites. Apparently, only bobcats with just the right combination of immune genes survived the onslaught and made it through the bottleneck, changing the genetic make-up of this section of bobcat territory for good.
Darwin Comes to Town Page 10