The survival of many species in particular areas depends on their ability to move across the territory. When a road cuts through a place, animals like squirrels, snakes, insects, etc are put into immense danger. In the article I read, it talked about how many snake species in the western ghats in India are being threatened because they get killed regularly by vehicles while crossing roads. Poor things can't even be seen by the incoming cars and trucks, and you can't really blame them for being so short that they can't see the fast incoming vehicles in time to dodge them.
Maybe making small drains / tunnels below the roads at various points could help. Just a simple pipe that's put across the road, before laying it on. And the ground around those places could be leveled in such a way as to channel the critters to the pipes. Such channels below the road are probably used at places for handling rainwater flowing downhill. But we probably need to enlarge them to accommodate the animals as well.
Maybe some another idea... but whatever the case, we need to do something to let nature cross roads in peace and in one piece if we're going about laying roads all over the place.
A sad example of not taking care of such things can be seen on the villages divided by the Delhi-Gurgaon NH-12 expressway - the people who made the roads didn't bother constructing any under or over bridges across this multi-lane high speed non-stop expressway. At many places, the nearest signals or bridges were several kms away. Doesn't make sense to walk 5 kms this way or that just to cross a road, right? It's shocking to know that hundreds of villagers were killed while trying to cross this expressway over the course of a year before the government woke up and begun constructing foot overbridges. The insensitivity of the in-a-hurry-commuters using the expressway was demonstrated when they'd opinionate that why should they slow down for crossers, and that it's the crossers' fault. It's really upsetting to know that people can have the capability to think only halfway through an argument. They didn't think about what the villagers would do if they couldn't cross at all. If even people can be so much harmed by the big roads that cut through their lands, think of the animals.