Wednesday, September 10, 2014

Multi-access keys, especially of the Lucid type

Long time no blog - I am somehow not finding the energy at the moment as often as I would like to. I would like to discuss a paper I recently found but before I can do that we need to lay some groundwork.

Previously I have discussed traditional dichotomous identification keys. They are the most familiar tool used for the identification of organisms, but there are less popular alternatives. Tabular keys are one option, and I have seen one a few years ago in a revision of the Bolivian species of a plant genus. It looked more or less like this:

Leaves <2 cm: P. vulgaris, P. aurantia, P. sericea
Leaves 2-5 cm: P. intermedia, P. reptans
Leaves >5 cm long: P. longifolia, P. boliviana, P. andina
Leaves glabrous: P. vulgaris, P. aurantia, P. andina
Leaves woolly: P. intermedia, P. reptans, P. longifolia
Leaves pilose: P. sericea, P. boliviana

Using a key like this is perhaps less intuitive and potentially a bit more confusing, but it can work quite well for relatively low species numbers. In the above case, for example, you would know immediately that you were dealing with P. andina if your sample had glabrous leaves longer than 5 cm because that species is the only one with that specific combination of characters. On the other hand, if you had very small glabrous leaves on your specimen it could still be either P. vulgaris or P. aurantia, so you should look for additional characters further down the list.

But as mentioned, this quickly becomes unrealistic for larger numbers of taxa; you wouldn't want to navigate such a table if every line listed more than twenty species possessing that particular character. Luckily, these days we have computers to help us with managing the data, and this is why tabular keys are becoming more popular.

The way this works in practice is that the taxonomist who wants to build a key produces a character-by-species table which the end user will not have to deal with. Instead, the end user is confronted with a software tool that allows them to enter whatever characters they can easily see, and each time they enter one the program throws out all the species that do not match the new information. The identification process ends when the possible species have been narrowed down to one or, more realistically a small number that the user may then check individually to see if one of them looks like the specimen they have on hand.

Perhaps the most popular software tool for building and displaying digital multi-access keys is Lucid, which, however, is not open source. Example identification keys for various groups can be found on their key server. The one that I am most familiar with is the Wattle Key to the Australian species of Acacia (Fabaceae). The screenshots below are accordingly taken from the Wattle Key, merely to demonstrate how Lucid Keys work:

There are four windows. The upper left one shows characters, the upper right one shows all the species, in this case 1274. The lower two windows are empty at the beginning. Now if we enter a few characters...

...we see that the characters that have been used appear in the lower left window. On the right, excluded species have moved to the lower right window while the ones that are still matching the available information are still in the upper right one. Our goal is to get their number down as far as possible.

The trick here is obviously to know which characters are more likely to be useful. In the present case, I pretended to have a bipinnate Acacia in front of me simply because I know that there are relatively few of them. Eh voila, as we see my two character selections already excluded all but 50 species.

This looks pretty straightforward, but of course if you don't know the plant group that well you won't know which characters might be important. In that regard a dichotomous key is more helpful because here the specialist who wrote it will have selected the most important characters for the first few questions of the key (if they are competent, that is). On the other hand, if you don't have the characters on your specimen that the first two questions of a dichotomous key ask for, for example because they are fruit characters but your specimen was still only in flower, then you are better served with a multi-access key.

When I next post about identification keys, some more of the pros and cons of both approaches will become obvious.

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