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I've been trying to put a phylogeny tree into a scientific paper. This tree includes ~220 species, which is too too large for one page for journal articles (Letter or A4 size). But in my paper it is crucial to show the whole tree on which the among-species distribution of a characteristic is indicated. I have looked up some journal issues but so far haven't found any similarly large phylogeny in one article. How do people usually treat this kind of situation in scientific papers? Could anybody tell me how to do it, or show me examples? Thank you so much.

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Which journal and article type are you thinking of? I'd probably suggest it would have to be a supplement if it's too large for a page - is it also possible to simplify the graphic you are trying to display, perhaps by grouping? –  GriffinEvo Dec 26 '13 at 7:54
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Have you tried contactating the editors about this problem? Usually they are helpful. –  Chris Dec 26 '13 at 11:14

3 Answers 3

up vote 2 down vote accepted

Also, don't forget that you can deposit your full tree in treebase. So you can show the collapsed tree in the paper, and give a link to the full tree somewhere in the text.

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The simplest way of course is to add it to the supplementary materials. However, 220 species are not that many, you should be able to fit that into a page. You have not shown us your tree so it is kind of hard to give specific advice but I am guessing that you have a linear rather than circular tree. If you convert it to a circular tree you should be able to fit it on a single page.

Here are a few random examples of large circular trees I found on the internet:

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If you update your question to show us the actual tree I might be able to give you more specific advice. For example, you could split the tree into smaller ones, each showing a specific order or class or whatever resolution you are working on. There are various tricks you can try but they all depend on the details.

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A circular tree is basically the only way to fit a large number of species onto a single page. Obviously, there is a tradeoff between being able to read each of the species names and the number of species you have in your tree. If the big pattern is important, rather than individual names, then you should be fine. Just make the species names as small as they need to be to fit. You can also include an arbitrarily large PDF of your tree with legible names as a supplement. –  kmm Dec 26 '13 at 16:37

It is not always essential to show a big tree. My opinion might be biased but it seems to me that huge figures with illegible labels are just a gimmick to make the reader feel that it is a great analysis (another case is that of networks).

First of all it is important to decide what is that you really want to convey from your figure. For example if your comparing some species with different clades then you can show the last common ancestor instead of showing all members of the clade.

As far as 220 species are concerned it will be tough to fit all of them stacked. But if you split them into two stacks it would be possible to fit with all labels legible (Paper=A4, Fontsize=6pt).

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Agreed about people just wanting to make it look fancy - I often see people making figures (using R they have been to me for help with coding) and once they've put a lot of effort in to a figure they realize it doesn't really show the point but have become to attached to it because it was so hard to make. Wish more would think, before starting to make the figure, about what they want their figure to show - would save a lot of time and hassle! –  GriffinEvo Dec 27 '13 at 12:26
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LOL @GriffinEvo "become too attached to it because it was so hard to make".. This can become a PhD comics strip :) –  WYSIWYG Dec 27 '13 at 13:22

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