http://www.idlewords.com/2010/03/scott_and_scurvy.htm
So when the Admiralty began to replace lemon juice with an ineffective substitute in 1860, it took a long time for anyone to notice. In that year, naval authorities switched procurement from Mediterranean lemons to West Indian limes. The motives for this were mainly colonial - it was better to buy from British plantations than to continue importing lemons from Europe. Confusion in naming didn't help matters. Both "lemon" and "lime" were in use as a collective term for citrus, and though European lemons and sour limes are quite different fruits, their Latin names (citrus medica, var. limonica and citrus medica, var. acida) suggested that they were as closely related as green and red apples. Moreover, as there was a widespread belief that the antiscorbutic properties of lemons were due to their acidity, it made sense that the more acidic Caribbean limes would be even better at fighting the disease.
In this, the Navy was deceived. Tests on animals would later show that fresh lime juice has a quarter of the scurvy-fighting power of fresh lemon juice. And the lime juice being served to sailors was not fresh, but had spent long periods of time in settling tanks open to the air, and had been pumped through copper tubing. A 1918 animal experiment using representative samples of lime juice from the navy and merchant marine showed that the 'preventative' often lacked any antiscorbutic power at all.