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I have been using alcohol for about 30 years (for storing Diptera) and offer a few comments.
Firstly, change the alcohol a week or two after collecting the specimen as the original fluid will become diluted. After that, its probably OK.
I always use screw capped plastic vials (don't like Eppendorf's as the caps can pop off). These vials are sold by various manufacturers in different sizes as cryopreservation tubes and are highly inert and stable. Adding glycerol at 5% will minimize risks if it drys out.
Keep specimens in the dark and preferably cool/cold and colour losses are reduced.
If you want to subsequently pin the specimen, hold it in ethyl acetate until the ethanol has exchanged and then dry it out on filter paper (you will find that oily flies like therevids loose their fat and become much better than if you pinned them immediately).
Normal 'india' ink seems to be stable for at least 30 years with no sign of deterioration but make sure the ink is absolutely dry before you put the label in the tube. I have noticed no deterioation with computer-printed labels over about 10 years and suspect that they are OK too.
A problem with wet preserved material is that dusting is hard to see . However it is usually possible with a bit of experience and changing the lighting and background carefully. I find that alcohol preserves morphology (apart from dusting) much better than does dry-mounting but colour can be a problem. Experience with a particular key usually solves this problem but not always, especially as wet material tends to fade.
One usuful tip; if your flies have important features that are hidden when the specimen shrivels on drying (eg. legs that close up hiding setae, genitalia that shrink and distort etc). Collect then into Gaults solution or similar (even dilute salt solution will do):- all the legs straighten out and everscible structures expand; you can then wah them with water before putting them in alcohol which will 'fix' the structures in their expanded state:- if you do this you may find yourself performing far fewer genutalia dissections!
Lastly; if you are in the business of describing species, please state if its a dry or wet specimen that is being described. e.g its common to find a black thorax with yellow dusting and the thorax could equally be described as black or yellow if described from dry (so many keys fall into this error and even famous dipterists do!). Wet material is more likely to be described as having a black thorax with yellow dusting and hence would be more accurate..........

One question I do have:- what to do with genitalia once they have become separated:- if they are put back with the specimen they might get lost but it would be dreadful practice to put them in another tube from the original specimen.
I'd appreciate any thoughts on this

hope it helps
cheers
Adrian