In the best traditions of a murder mystery, the finger of blame has been pointed in several directions. Were the dolphins pursued to their untimely deaths by a killer whale? Did they do themselves in by taking a wrong turn when they were chasing fish? Or - and this has become the favourite theory - was it the Royal Navy who dunnit?

What we know so far is that on Monday more than 70 common dolphins got into difficulties near Falmouth and 26 of them died, having stranded themselves in shallow waters on the Cornish coast. Given their image as friendly and intelligent creatures, the deceased mammals have needed no spin-doctor to ramp up public outrage at this tragedy. We want to know what happened, and this is no job for a sleepy local policeman or even a sharp-eyed old lady. In this case the sleuths are the great and the good of the conservation world, who have duly rallied to collect and examine the evidence and solve the mystery. Step forward Sarah Dolman, science officer of the Whale and Dolphin Conservation Society.

“It's quite straightforward,” she says. “Mass strandings of common dolphins are unusual. These animals were stranded on two river systems 15km [9.3 miles] apart. There was a third group of animals milling around inside Falmouth harbour. They are an offshore species so you wouldn't expect that. They are sociable animals so you would expect them to be together. The fact that they had separated out is unusual.

“The post mortems were undertaken on Monday afternoon and on Tuesday, and they showed that the animals were healthy and had no food in their stomachs, so they hadn't been feeding before they were stranded. From that we know that they weren't following fish.”

Could they have been fleeing from a predator? Again, Dolman says that if this were the case they would not have spread into three groups up to 15km apart. “It looks like they were frightened,” she says.

Cue scary music. By what or whom? By yesterday morning the media had nailed the Royal Navy with the claim that it had been carrying out live firing exercises hours before the dolphins died. Case closed, it seemed. But the twists and turns were beginning. Not true, said the Ministry of Defence. “The last naval gunnery took place three days before, 60 miles away,” it asserted in a statement.

But Dolman is undeterred and points out that, however insistent the MoD is that it wasn't responsible, its statements have not been entirely consistent. “Originally we were told that there were no activities happening offshore. It appears now that there were a number of activities in the days leading up to the stranding. We are calling for a full, thorough and public investigation. We have lots of pieces of information.”

The knowledge that the dolphins were healthy when they died rules out the possibility of disease. But the key pieces of intelligence come from scientific studies that suggest a link between stranded sea mammals and military sonar. Paul Jepson, of the Institute of Zoology, who carried out this week's post-mortem examinations, has published research suggesting that sonar could induce a condition in mammals that is similar to the decompression sickness suffered by human divers.

“New UK and Spanish findings provided the first evidence of a decompression sickness-like disease in marine mammals,” he writes. “The proximity of this, and several earlier beaked whale mass strandings in the Canary Islands, to naval exercises using active sonar suggest that acoustic exposure may be a causal or precipitating factor in the pathogenesis of this gas embolic condition.”

This theory has also been supported by scientists at Woods Hole Oceanic Institution in Massachusetts, who found evidence of decompression sickness in the bones of sperm whales. In 2004 their study concluded that the risk of such damage could be increased by anything that disrupted the slow ascent of the mammals to the surface. Acoustic signals from a submarine were thought to be one potential cause of disruption - and since the 1930s navies have been pinging sound pulses into the ocean and listening for the echoes to detect other vessels and mines. When an enemy is at close range, vessels also use mid-frequency sonar to gather more definitive information. When a ship hunting for mines, or a survey vessel, needs a highresolution picture of the seabed, higher, shorter-range frequencies are used.

Dolman comments on the link between stranded sea mammals and sonar: “It's not conclusive but in most of these examples we have increased use of mid-frequency naval sonar. Beached whales don't do very well, and other species seem to be susceptible as well. You can imagine that if there was a noise moving along the seabed, these animals would have no choice but to come in close to shore. These marine species are difficult to study, we don't know much about them or the threats they face. This really is a new area of study.

“Now we know that there was MoD activity in the area, that needs to be investigated. At this stage it's too early to say definitely that it was noise, but it's high on the list of possibilities.”

Dolman is referring to reports from conservation organisations which maintain that a military vessel was using short-range sonar about 14 miles offshore when the dolphins died. The MoD has confirmed that there was activity in the area, but continued to claim in a statement yesterday that: “The Royal Navy has investigated the reports associated with this incident and believes it is extremely unlikely that any Royal Navy activity resulted in the unfortunate stranding of the dolphins.

“The only sonar transmissions were undertaken at least 12 nautical miles off the coastline using low-power, short- range equipment. No Royal Navy vessel in the South West had been using low-frequency sonar. It has also been confirmed that a submarine had been on exercise in the area recently, but its sonar was not transmitting.

“There has been no evidence of any of our vessels' sonar ever playing a part in beaching incidents like this. The Royal Navy takes its environmental responsibilities very seriously and always carries out environmental assessments before putting energy in the water.”

So the Royal Navy insists that it is innocent. “These are the facts,” says a spokesman. “There was passive listening, but that doesn't emit a ping that bounces through the water - it just listens. There was no low-frequency sonar.” What about mid-frequency sonar, I ask. The spokesman doesn't know about that, he concedes, but promises to investigate. What the MoD statement confirms is that the vessel had been using high-frequency sonar: “The survey vessel had been undertaking low-power, high-frequency, short-range sonar transmissions of existing in-service equipment, and had been using echo sounders, again operating at high frequencies, as used by many vessels throughout the world to detect the depth of water beneath their hull.” The spokesman wriggles. “Fishing vessels use sonar to track fish and it's a busy shipping area,” he suggests.

Ah, that old tactic. If you want to move the attention away from you, finger someone else. But what we do know is that mass strandings of sea mammals are becoming more common. Is this because of better reporting, or because of the use of sonar around the world?

The subject is a sensitive one. It is no coincidence that in 2005 Nato, conscious that it has a responsibility in this area, published a damage limitation report on marine mammals and active sonar, noting that the media had linked active sonar to mass whale deaths in North Carolina and to dolphin deaths in the Florida Keys. It was recommended that a working group should be set up. Navies worldwide are keen to keep their hands clean on this one, but they know that it is an issue they cannot ignore.

Open verdict: great animal mysteries

Lemmings

The myth of lemming suicide arose because of sudden, severe falls in the rodent's population. Scientists have long been puzzled by the four-year cycle: some blamed changes in food supply and habitat, but almost everyone else put it down to mass suicide. Now scientists say it is caused by a rise in predator populations, although some speculate that lemmings sometimes kill each other.

Bats

Thousands of bats are often found dead at the bottom of wind turbines, oddly unblemished, as if they had not hit anything before falling. One theory is that these are migrant bats that turn off their navigational systems because they are not searching for insects or food, and turn off their echo-location to conserve their energy resources, although this does not explain why they are unscathed.

Whales

Whales and dolphins found stranded on beaches or in shallow water near coasts have always generated suicide theories and mythical explanations. Some say the leader of a school can panic in shallow water, causing a mass change in direction. Others suggest that very old whales don't take account of changes in land mass in their navigational systems.

Noah's Ark

Was there a flood? The Encylopedia of Life identifies 1.8 million species, so how could the Ark have stayed afloat? “Impossible,” says encyclopedia director James Edwards. But Professor David Menton, of the Creation Museum in Kentucky, says Noah had to take only about 16,000 creatures, “and we can leave out organisms known to survive flooding, such as insects and worms”.

Elephants

Scientists still don't fully understand the innate compasses that aid animal migration. Many once thought that some animals had a “sixth sense”. Now some attribute seasonal and emergency migration to a sensitivity to the Earth's magnetic field. Elephants seem especially sensitive: before the 2003 Asian tsunami, dozens of elephants trumpeted and fled for higher ground, even breaking their chains to do so. How they can “predict” natural disasters remains a mystery.

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