Another journal cover

I am told that it never rains but it pours. Meteorologically this seems unlikely, but in other systems it may be true. Recently, I noted that in the past couple of months both Trends in Genetics and Transactions on Computational Biology and Bioinformatics have featured phylogenetic networks on their front covers, highlighting articles in their respective issues.

Now. I can note that Volume 190 Number 1 of Molecular and Biochemical Parasitology also illustrates a phylogenetic network. Hopefully, the widespread nature of these three journals reflects an increasing recognition of the importance of networks in phylogenetics.

The illustration is from the paper by Eva Tydén, Annie Engström, David Morrison and Johan Höglund: Sequencing of the β-tubulin genes in the ascarid nematodes Parascaris equorum and Ascaridia galli, on pages 38-43.

Trends in Genetics: The Future of Phylogenetic Networks

A couple of weeks ago I reported on those journal covers that I know illustrate phylogenetic networks. I am happy to report that networks have now also made it onto the cover of Volume 29 Issue 8 of Trends in Genetics. The cover illustration combines the traditional tree metaphor for phylogenetics with the new metaphor of a network.

The cover story is the review article by Eric Bapteste, Leo van Iersel, Axel Janke, Scot Kelchner, Steven Kelk, James McInerney, David Morrison, Luay Nakhleh, Mike Steel, Leen Stougie and James Whitfield: Networks: expanding evolutionary thinking, on pages 439-441.

The article is one of the tangible outcomes of the workshop last October, at the Lorentz Center in The Netherlands: The Future of Phylogenetic Networks. The workshop participants agreed that we should be active in promoting the use of networks for evolutionary analyses, and this article, written by a group of biologists and computational biologists, seeks to do just that.

There will be further outcomes of the workshop, including follow-up meetings at the same venue.

Networks and journal covers

If you've ever looked at the cover illustrations of phylogenetics journals, either biological or computational, you will have noticed that there are quite a few phylogenetic trees. Sometimes these trees show ancestral polymorphism, but mostly they are uncomplicated dichotomous structures. There are also often various types of biological networks on these covers, such as gene networks and ecological networks. However, there are almost never phylogenetic networks, irrespective of the journal contents.

So, it is with pleasure that we note that Volume 10 Issue 1 of the IEEE/ACM Transactions on Computational Biology and Bioinformatics illustrates not one but two phylogenetic networks.

The illustration is from the paper by Stefan Grunewald, Andreas Spillner, Sarah Bastkowski, Anja Bogershausen and Vincent Moulton: SuperQ: computing supernetworks from quartets, on pages 151-160.

These are unrooted data-display networks, of course. If we look for evolutionary networks, instead, then we need to go to Volume 23 Issue 5 of Trends in Ecology and Evolution (May 2008). Actually, it is difficult to believe that this was ever intended to be an evolutionary network, because the phylogenetic relationships shown are rather bizarre.

Destroying the Tree of Life?

In my previous blog post (Resistance to network thinking) I noted that a phylogenetic network is a generalization of a phylogenetic tree because "a network simplifies to a tree if there are no incompatible phylogenetic signals". Given this, to me it has often seemed somewhat odd that so many of the people who are interested in generalizing the Tree of Life into a Network of Life use metaphors suggesting that the tree first needs to be destroyed.

This approach was popularized by Ford Doolittle, who entitled his 2000 Scientific American [282(2): 90–95] article "Uprooting the Tree of Life", although this particular metaphor had previously been used by, for example, Elizabeth Pennisi [Science 284: 1305-1307].

This approach reached its apogee with the ridiculous cover of New Scientist in January 2009. The cover accompanied an article by Graham Lawton now mildly entitled: "Why Darwin was wrong about the Tree of Life" [201(2692): 34-39], although the editor (Roger Highfield) originally called it "Axing Darwin's tree".

As was noted at the time, this cover was "a misdirected and entirely inappropriate piece of sensationalism", which did no one any good (least of all the editor). A subsequent Letter to the Editor [by Dennett, Coyne, Dawkins and Myers] noted: "Nothing in the article showed that the concept of the Tree of Life is unsound; only that it is more complicated than was realised before the advent of molecular genetics."

So, it seems likely that the tree needs to be neither axed nor uprooted, nor "trashed" [Laura Franklin-Hall], nor even "politely buried" [Michael Rose]. In many cases all that is is needed is some osculations between the branches. Indeed, most of the scientific discussion is about how many osculations there are, and how we can best detect where they are, rather than about destroying the tree itself. A network is more general than a tree, rather than being a fundamentally different structure. Nevertheless, some people, such as Michael Syvanen, have been quoted as saying: "We've just annihilated the Tree of Life", when referring to their new network.

Book covers

Here is something for you to ponder. Of the three book covers that I know about that illustrate phylogenetic networks, the two by computational scientists have stylized "trees" with straight edges, such as one sees in graphs, while the one from a biologist has curved branches, such as one sees in nature. Who says that you can't judge a book by its cover?