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There are countless sources, both peer-reviewed and popular, explaining how overuse and misuse of antibiotics is breeding a new generation of antibiotic-resistant "superbugs" such as MRSA (Methicillin-resistant Staphylococcus aureus) and MDR-TB (multidrug-resistant Tuberculosis). Over in the animal kingdom, the opposite seems to be happening - species after species is becoming endangered and/or extinct as humans destroy or alter their habitat through increased hunting, farming, construction, etc.

Are there any non-human animals that have been found to have evolved resistance to human encroachment into or alteration of their habitat in a way analogous to how bacteria have evolved resistance to human attempts to get rid of them? For example, this could consist of:

  • an animal that has adapted stronger bones to better survive collisions with vehicles
  • an animal that has significantly increased its blood coagulation rate to survive gunshot wounds from hunters
  • an animal that has developed better vision to see in urban environments
  • an animal that has evolved a skin pigment change that enables them to not take as much damage when they are sprayed with agricultural pesticides

One answer that came to mind is domestic animals - the horse and dog in prehistory, the cat in ancient Egypt, etc. That seems too obvious on one hand, and on the other hand may not really be an answer, as there seems to be no indication that pre-domestic animals were endangered by humans in any meaningful way. Are there animals that have significantly adapted themselves to surviving as wild animals in human-influenced environments?

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    $\begingroup$ Welcome to Biology.SE! Is there any reason to exclude the numerous "pest" species (e.g.s: cockroaches, mice, rats) that often "share" our homes? $\endgroup$
    – tyersome
    Commented Jun 15, 2020 at 16:24
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    $\begingroup$ "Evolved" is rather tricky, but there are a number of species that live happily in places densely populated by humans: pigeons, the urban peregrine falcons that nest on skyscrapere & prey on them, urban coyotes, bears that feed on trash, even the occasional mountain lion that comes into town to visit the casinos: kcra.com/article/a-mountain-lion-in-a-casino-don-t-roulette-out/… $\endgroup$
    – jamesqf
    Commented Jun 15, 2020 at 16:39
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    $\begingroup$ By excluding cats, you're excluding what is possibly the clearest example. Cats don't fit the normal profile of domesticated animals -- you can't tame a cat the way you can tame a dog or a horse. One explanation for this is that cats weren't domesticated. Instead, they evolved to fit into an agrarian society. $\endgroup$
    – Mark
    Commented Jun 16, 2020 at 1:44
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    $\begingroup$ An example given in "Guns, Germs and Steel" is the simple observation that megafauna extinctions were near total anywhere humans first arrived as fully evolved homo sapiens, but significantly less extreme anywhere humans had been co-evolving with the local megafauna (in particular Africa, to a lesser extent across Eurasia). We can't say precisely what attributes and behaviors African/Eurasian megafauna evolved that American/Australian megafauna did not, but the historical evidence suggests that simply having time to co-evolve to deal with humans helped a lot. "Fear of humans" seems likely. $\endgroup$
    – ShadowRanger
    Commented Jun 17, 2020 at 1:50
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    $\begingroup$ There are some good examples of behavioural adaptations to urban environments listed here: independent.co.uk/news/science/… $\endgroup$
    – Riot
    Commented Jun 17, 2020 at 11:57

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Note: This is an answer to the last line of your question.

A classical example of animals adapting to the influence of humans on their environment is the adaption of the Peppered Moth.

Here is a brief summary:

The peppered moth was originally a mostly unpigmented animal (<1800). During the industrial revolution in the southern parts of the UK a lot of coal was burned. This led to soot blackening the countryside. Soon afterwards, a fully pigmented variety was first observed. Only a hundred years later, in 1895, this pigmented variety almost completely displaced the unpigmented variety.

It has been shown that the pigmentation is under strong selective pressure as birds hunt these moths. Since birds rely on their visual system to detect their prey, the variety that blends in with its environment (=camouflage) has a selective advantage over the variety that stands out.

As pointed out by Tim in the comments, since the 1970s there has been a rapid reversal with unpigmented animals being more abundant. As far as I understand, it is accepted that this reversal is due to a decrease in human induced air pollution leading to less sooty barks on trees which makes the unpigmented variety harder to prey upon.

Addendum: genetic basis of adaption

In a beautiful recent study, the causal mutation for the pigmented, or melanic, variety was identified: A ~9kb transposon insertion in the first intron of the gene cortex. The authors calculate that this mutation happened in the year 1819, a few years after the industrial revolution was in full swing. The interpretation is that due to sooty tree bark this mutation, causing pigmented moth, was under strong selection.

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    $\begingroup$ This is a famous example of observed evolution. The early research had a couple of hiccups, but plenty of other research has verified it. +1 $\endgroup$
    – J.G.
    Commented Jun 16, 2020 at 19:24
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    $\begingroup$ This is a famous example of natural selection. One should take care about equating that with evolution, which includes genetic mutation as an essential component. As far as I am aware, the peppered moth case has not been shown to have involved introduction of new or variant genes, but rather just environmental factors favoring a previously rare phenotype. $\endgroup$
    – John Bollinger
    Commented Jun 17, 2020 at 21:35
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    $\begingroup$ @JohnBollinger, the authors of this recent paper (nature.com/articles/nature17951) find that a transposable element in the 'cortex' gene is causal for the pigmented moth variety. They calculate that the insertion happened around 1819 when the industrial revolution was well underway. I don't want to overload the answer - do you think it would make sense adding to the answer as an addendum? $\endgroup$
    – dtadres
    Commented Jun 17, 2020 at 22:05
  • $\begingroup$ That's (obviously) news to me, @dtadres. In any case, I was primarily responding to your first comment, not directly to the answer, which presently does a smooth job of avoiding the question of how to label the phenomenon it describes. I think it's doubtful that the OP cares much about the distinction, so I think the answer is fine as it is, but if you want to add an addendum referring to the paper then I don't think it would be overbearing. $\endgroup$
    – John Bollinger
    Commented Jun 17, 2020 at 22:20
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Many insects (as well as some other animals) have documented resistance to pesticides.

For example, the German cockroach (Blattella germanica) can be resistant to multiple insecticides1. In addition, some populations of this cockroach are now repelled by glucose, which leads to them avoiding traps2.

References:

1: Fardisi, M., Gondhalekar, A. D., Ashbrook, A. R., & Scharf, M. E. (2019). Rapid evolutionary responses to insecticide resistance management interventions by the German cockroach (Blattella germanica L.). Scientific reports, 9(1), 8292.

2: Wada-Katsumata, A., Silverman, J., & Schal, C. (2013). Changes in taste neurons support the emergence of an adaptive behavior in cockroaches. Science, 340(6135), 972-975.

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Bighorn sheep are developing smaller horns and elephants are becoming tuskless in Africa:

The horns of some bighorn sheep are getting smaller, because hunters are picking off the most impressive rams before they reach their breeding peak

Elephant poaching, for example, is thought to have led to an increase in the number of tuskless animals in Africa.

Source

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    $\begingroup$ Though it's an interesting question whether these statistical adaptations represent survival benefit for the populations. $\endgroup$
    – jlawler
    Commented Jun 16, 2020 at 18:42
  • $\begingroup$ Rattlesnakes in the southwest US are learning to stay quiet around humans so they don't get shot. $\endgroup$
    – Lee Daniel Crocker
    Commented Jun 18, 2020 at 18:53
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Nightingales have adapted to city noises by singing louder. Given that one function of singing is finding a mate there must indeed be a high, direct selection pressure to make oneself heard. Other birds have adapted in a similar fashion, e.g. by singing in a higher pitch, or at different times.

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Not so much physical changes, but changes in behavior caused by human activity has numerous examples.
Foxes, pigeons, sea-gulls adapt very well to city life. Some species nowadays have larger numbers in cities than in the country side.
Polar bears are another good example. Disappearing sea-ice and increased human activity in the Artic has turned many polar bears into pre-dominantly garbage scavengers in stead of hunters/carrion-eaters.

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    $\begingroup$ Is the polar bear adaptation really due to evolution? Have there really been enough generations to allow this to happen? I suspect they're just naturally flexible enough that they've been able to alter their behavior. Kind of like how human society has suddenly adapted to Coronavirus. $\endgroup$
    – Barmar
    Commented Jun 16, 2020 at 15:11
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    $\begingroup$ @Barmar That’s the question isn’t it. Polar bears are opportunistic scavengers, but in what degree this is evolution? It’s probably too recent to say for sure. Another thing about polar bears: they are moving South and come in ranges where regular brown bears live. Hybrids are becoming ever more common. These hybrids are apparently fertile with polar and brown bears leading to the question if polar bears are actually a separate species or just a local color variant of the brown bear. Biologists can’t agree on that one. $\endgroup$
    – Tonny
    Commented Jun 16, 2020 at 16:32

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