The North Sea bottom trawl fishery is a typical multispecies fishery. A single haul catches many different species, including plaice, sole, cod, turbot, red mullet, tub gurnard, and monk fish. These species tend to associate with other species instead of swimming together in schools, so it is almost impossible to catch one species without also catching a lot of others. Fisheries scientists like to call this a technical interaction between the species: they interact not through predation or competition, but through ending up in the same net.
If a bottom trawl fisher runs out of cod quota he can do three things: buy additional cod quota from other fishers, stop fishing, or keep on fishing but throw all cod that he catches back into the sea (which is what we call discarding of fish). So if this fisher is not allowed to discard his cod catch, and there is nobody who can sell him any cod quota, he is forced to stop fishing altogether. Cod is then called the 'choke species': the species that stops you from fishing when its quota runs out. If you were allowed to discard fish you would continue fishing as long as there is at least one species that can still be caught. As far as I know there is no term for this sort of species, but I kind of like the term slack species.
The EU is about to introduce a ban on discarding, and to set TAC (Total Allowable Catch) levels for a number of species whose catch has so far been unrestricted (for instance red mullet, brill, and sea bass). Unsurprisingly, fishers are adamantly opposed. To them 'more species under a TAC regime' means 'more potential choke species'. They prefer fisheries policy to regard a few major species only, and to accept the bycatch of all other species.
MSY is flawed in two ways...
I admit that my first reaction was something like "oh, so these guys just want the right to fish a species to extinction if it suits them". But on second thought they point towards two flaws in the principle of Maximum Sustainable Yield (MSY), which is currently the guiding principle in fisheries policy worldwide. MSY is the largest possible annual catch you can get sustainably. If a stock is never fished, it is at its maximum possible size, but you don't catch anything. If you fish a little every year, the stock will be a bit smaller, and you catch a little bit every year. Fish some more, and the stock will be somewhat smaller while your catches are larger. As you keep on intensifying your fishing, however, you reach a point where not only the stock declines but also your catch. The maximum catch you can have every year without depleting the stock is called MSY.
The first problem with MSY is that it is based solely on biological principles. Economists have long argued for Maximum Economic Yield to be the guiding principle: this is the annual catch that maximizes, in a sustainable manner, the total revenues minus the total costs from fishing. MEY means that you take into account not only biological growth, but also the costs of fishing and the price of the fish. In the simple text book models this actually means fishing a bit less than under MSY to take advantage of the fact that more abundant fish is easier, and hence cheaper, to catch.
Second, the principle of MSY does not only ignore costs and prices, but also technical interactions. If you took these into account, a policy that maximizes the sum of the MEY over all species would allow fishers to overfish some species, and to underfish others. Mind you: 'overfishing' does not necessarily mean depleting a fish stock. It simply means that fishing pressure is higher than the fishing pressure that would lead to MSY. So you can sustainably overfish a stock! It's just that in general you shouldn't do that, because it gives you less fish under higher costs than you would have under MSY. In a multispecies fishery, however, it may be more efficient to overfish some species because that would allow more catch of other species that are more valuable, more productive, or both.
Note that trading quota could relieve some of the pain, but not all. If cod quota are very low compared to other quota, cod will eventually become a choke species, trade or no trade.
...but what is the alternative?
Ideally TACs should be set taking technical interactions into account. Fisheries biologists are working on this problem, but I suspect that it remains a very complex issue. On the other hand, current TACs are certainly not realistic in multispecies fisheries, so any consideration of technical interactions would be welcome.
Then there is the issue of discarding: the EU can either allow fishers to discard unwanted catch, as has been the policy so far, or ban discards, as the EU is about to do. In theory, if discards are allowed, fishers can keep on fishing as long as there is a 'slack species'. It sounds horrible that fishers go on fishing, throwing over board everything they don't need, but be aware that not all discarded catch is dead or dying, although the survival rate can be very small. A discard ban will have the advantage that the researchers who do stock assessments have better catch data, because so far they had only very crude estimates of how much fish were discarded. This matters, because stock assessments lean heavily on landings data, which underestimates catch if part of the catch is discarded. On a longer term a discard ban may also give a strong incentive to develop more selective fishing technologies, although it is highly unlikely that bottom trawling will ever be 100% selective.
Additionally, perhaps the current system of catch quota could be complemented with the possibility to rent additional quota from the government for, say, the first few choke species. Under such a policy you would indeed catch a bit more of the choke species and a bit less of the slack species, because catching all species would become too expensive. The rental price would still give an incentive to fish more selectively, but the fishery would not be shut down completely as soon as the choke species quota run out. The problem, of course, is setting the right prices: they should reflect the value of the loss of future catches of the choke species, which depends not only on biological growth, but also on the price of the choke species, the costs of catching it, and the discount rate. A daunting task indeed.