England was given an uncomfortable reminder last week of the impact of its swelling number of inhabitants. Over the past two millennia, hundreds of its native plants and animals have been rendered extinct because the human population has risen from about one million to more than 51 million.

Victims have ranged from the great auk and the lynx to the humble blue stag beetle and Davall's sedge. More to the point, 480 of the 492 species made extinct since Roman times have disappeared in the past two centuries. Rates of eradication are rising, a trend that bodes badly for the future of the countryside, a report states.

Produced by Natural England, the government agency responsible for the countryside, "Lost Life: England's Lost and Threatened Species" focuses only on wildlife on English soil, although it has broad lessons for all of Britain. We live on "a fortress built by Nature for herself", Shakespeare claimed. If so, she is now paying a heavy price for its construction, as the study makes clear.

According to the report, a total of 24% of butterfly species and 22% of amphibians have been wiped out in England, along with individual types of wildlife such as Mitten's beardless moss; York groundsel, a weed only discovered in the 1970s; and Ivell's sea anemone, which was last seen in a lagoon near Chichester. Add to this the wolf, the wildcat and other large mammals and the level of devastation of our wildlife becomes chillingly apparent.

Indeed, the situation is far worse than the one outlined in the study, its lead author Dr Tom Tew, chief scientist of Nature England, admitted last week. The agency was as conservative and careful as it could in compiling the report, he told the Observer. "We wanted to avoid accusations of being alarmist." As a result, "Lost Life" underestimates, by a fair amount, the numbers of extinctions of animals and plants in England that have taken place in recent years. "There are many more species that we think we have lost, but we have not included them because they are not officially extinct." Examples include the golden eagle and the sturgeon. Both are occasionally seen in England but no longer breed here. In addition, the banded mining bee, the brilliant moon beetle and the lichen, Opegrapha paraxanthodes, have also been posted missing, presumed extinct.

The report highlights a number of culprits, though it is emphatic about the worst offender: habitat loss. The great inroads made into the English countryside by farmers and builders has had a devastating effect on our wildlife, destroying food sources, shelter and homes for hundreds of species.

"Urban spread is one cause of habitat loss, of course, but farming has had the greatest impact by far," added Dr Tew. "We have ploughed over the landscape, ripped up woods and drained our wetlands – and rare mosses, damselflies and corncrakes have disappeared as a result." Intriguingly, analysis shows extinctions occurred in two main waves, both based on farming revolutions.

Dr Tew explained: "The first wave of extinctions occurred when the Victorians' post-industrial revolution started to take effect on land management. We started using steam tractors and devices like that. In addition, there were large numbers of men still employed as gamekeepers." The impact in use of this machinery and intensive landkeeping was a peak of extinctions between 1900 and 1910, a time when wildlife like the agile and moor frogs as well as the orache moth disappeared.

Then, after 1945, there was a major push to ensure food security, with the use of chemical fertilisers and pesticides increasing. Again this triggered a peak in extinctions that included those of plants like the purple spurge and insects like the Norfolk damselfly.

"Other factors are involved, of course – such as pollution and invasion by non-native species," said Dr Tew. "However, habitat loss remains the worst offender, although trends are beginning to shift. Climate change is beginning to have an effect, and by the middle of the century I am sure it will be accounting for the vast majority of future extinctions of English wildlife."