Re: Cladistic notation

[Mike Taylor <mike@indexdata.com>]

> Date: Mon, 7 Jul 2003 18:24:41 -0500
> From: "Charles Roustan" <charlesroustan@softhome.net>
>
> David Marjanovic wrote in some message not long ago:
> 
> +--allzero outgroup
> |--*Caudipteryx* (forgot to mention: composite of all species)
> |--this grouping was not supported without reweighting:
> |    |--Scansoriopterygidae
> |    |--*Archaeopteryx*
> |    |--basal Troodontidae
> |    `--+--*Microraptor* (forgot to mention: composite of both species)
> |       `--+--*Rahonavis*
> |          `--*Shenzhouraptor*
> `--+--*Sapeornis* (always here when the above grouping is present)
>    `--+--*Yandangornis*
>       `--+--*Confuciusornis*
>          `--+--*Jibeinia*
>             `--+--+--*Yanornis*
>                |  |--*Yixianornis*
>                |  |--*Vorona*
>                |  `--+--*Patagopteryx*
>                |     `--all 8 other Euornithes
> {lots of snipping}
> 
> This too, I can understand and if I was asked to turn this into a
> regular text-book-style cladogram I could do it [...]

Yes.  The algorithm is actually _very_ simple.  Just pick up your
computer screen (it's easier if you have a laptop) and turn it 135
degrees anticlockwise, so that the top-right corner of the screen
points downwards.  _Et voila!_, you have a nice, book-style branching
tree.

Others have answered parts of the rest of your question, but I'll try
to summarise:

> [...] although I would ask myself the reason for all the asterisks
> [...]

As others have said, they indicate italics, which are conventionally
used to show a valid, formally established scientific genus or species
name.  (Some people also like to use italics for higher-level taxon
names, but that's not common yet and may never be.)

[For that reason, I very much dislike TMK's suggestion of using an
asterisk to indicate "incertae sedis" (uncertain position) -- we're
all too trained to pretty much ignore asterisks in proximity with
taxon names.  Better just spell it out.]

> [...] I've seen that some of you add ?

If you see a cladogram like

        Alphasauria
        |?Betasaurus
        | Gammasaurus
        ...

The question-mark before "Betasaurus" means that it _maybe_, or even
probably, belongs under Alphasauria, but that we can't say for sure --
perhaps because the remains are too framentary to analyse
satisfactorily.  (Then again, we can't really say _anything_ for
_sure_ :-)  So you could say that the question mark indicates a higher
than usual level of uncertainty.)

> [...] and {} [...]

It depends how you've seen these used.  As you'll have already read in
the FAQ, if you see a cladogram like this:

        Alphasauria = { Gammasaurus + Deltaraptor }
        |?Betasaurus
        | Gammasaurus
        ...

then that means the taxon Alphasauria is defined as the smallest clade
that includes both Gammasaurus and Deltaraptor -- that is, the most
recent common ancestor (MRCA) of those taxa, together with all its
descendents.

> [...] and _ [...]

Again, as others have said, underscores are sometimes used to indicate
formal names.  For the same reasons as Colin McHenry, I prefer
underscores to asterisks, but both are used.

> and some of you even talk about sets and subsets [...]

I'm not sure what this refers to.

> [...] and place things between quotation marks.

Quotes are sometimes used to indicate a genus that was wrongly
supposed to contain a particular species.  For example, the name:
        "Megalosaurus" nasicornis
refers to the species _nasicornis_ which was originally (but we now
think wrongly) assigned to the genus _Megalosaurus_.  (It's now known
as _Ceratosaurus_ nasicornis.)  You tend to see this most often with
old genus names, which got all sorts of stuff referred into them.

> I've thought about it and I've come to different conclusions, I'm
> sure in one of them I've gotten it right, but I think you all use
> different "add-ons" in your cladograms, is it a matter of choice?
> is there more than one way to make an ASCII cladogram?

No, it's pretty much standardised with the exception that italics for
formal names are various (A) left unadorned, (B) indicated with
asterisks or (C) indicated with underscores.

 _/|_    _______________________________________________________________
/o ) \/  Mike Taylor  <mike@indexdata.com>  http://www.miketaylor.org.uk
)_v__/\  Orthogonality uber alles!

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