Island endemic genera and phenetics (that special issue)

(The following is the sixth part of a series of posts on an Annals of the Missouri Botanical Garden special issue on “Evolutionary Systematics and Paraphyly”. All posts in this series are tagged with “that special issue”.)

Following an introduction and the contributions of Lockhart et al., Hörandl, and George, the fifth full paper in the special issue is Stuessy et al.'s “Paraphyly and endemic genera of oceanic islands: Implications for conservation”.

The main argument is quickly summarised, and it has actually already been made before by the same author, only then in a considerably more concise manner (Hörandl & Stuessy, 2010). When new species arrive on oceanic islands via long distance dispersal, in the most extreme cases as a single seed or a single pregnant female, they may find themselves presented with many new possibilities. Some selection pressures from their original habitat may not exist on the island, and there may be unused niches ready for the taking. The new arrivals also undergo a severe genetic bottleneck, carrying only a small fraction of the genetic diversity of the mainland population in themselves.

This means that island colonisers often have the chance of undergoing spectacular adaptive radiations in a short time. Echium and Sonchus in the Canary Islands, fruit flies or the Silver Swords in Hawaii are just some examples. In the words of Stuessy et al.,

Because of the speed of the divergence, it might be that the island genera are genetically not so divergent from the continental relatives, but they are usually very divergent morphologically, hence their recognition at the generic level.

So because they looked superficially very distinctive after their adaptive radiation into new niches, island lineages were traditionally often treated as genera distinct from the mainland genera they evolved out of. With the advent of phylogenetic systematics, however, they are sunk into these mainland genera, so that these island lineages are not island-endemic genera any more; they are just the island's representatives of the widespread mainland genus.

So what? So, according to Stuessy et al., this:

these actions could have a substantial effect on world island conservation.

This is, as far as I can see, as explicit as the paper makes the argument for paraphyletic taxa, but it is still clear what this is about. The idea is undeniably that one should keep island endemic genera because they make a better sell for conservation politics than mere endemic species.

Huskisson Mangrove Boardwalk

After today, I can definitely recommend the Mangrove Boardwalk of Huskisson, New South Wales, to any botanically or ecologically interested visitors of the Jervis Bay area.

Both mangrove species of the Sydney area were present: the larger Avicennia marina (Avicenniaceae) with grey lower leaf sides and orange flowers, which is also shown in the above picture, and the smaller Aegiceras corniculatum (Myrsinaceae) with glabrous leaves and white flowers. Unfortunately, the former was only in bud and the latter was mostly just past flowering. As most readers will probably know, magroves are extremely salt tolerant shrubs or trees growing in coastal mud flats or estuaries.

A particular attraction of the mud flats, and especially to young children, are seven species of crabs. We believe we saw at least three of them, including the green one above which we saw on the decaying wreck of a little rowing boat. There were also various species of fish, but those were harder to photograph.

Less of an attraction, it has to be admitted, were these mosquitoes. They were rather large and could suck an astonishing amount of blood as we found when one was killed after her meal... Note to self: next time, bring mosquito repellent.

Anyway, definitely worth a visit. I had never before seen such a nice and accessible mangrove swamp.

Botany picture #188: Lobelia anceps

We are spending the holidays at the coast, where I ran into this little flower. Lobelia anceps (Lobeliaceae) occurs in wet seepages on the coast of eastern Australia.

An eighteen pages long perfect solution fallacy (that special issue on paraphyly)

(The following is the fifth part of a series of posts on an Annals of the Missouri Botanical Garden special issue on “Evolutionary Systematics and Paraphyly”. All posts in this series are tagged with “that special issue”.)

As I am looking at the next contribution to Annals of the Missouri Botanical Garden's special issue on how awesome it would be if only we would accept paraphyletic groups as they did in the 1950ies, it seems as if I should start with the following disclaimer.

I want it to be understood that I have the highest respect for the life works of everybody involved, and for their publications other than the one we are currently dealing with. I do not wish to offend, but merely to critically discuss the scientific merits of 'evolutionary' systematics versus phylogenetic systematics, and specifically whether the arguments presented by the former school of thought make any sense. It also needs to be understood that my opinions expressed here are my own and are not necessarily those of my employer, nor those of my line manager, of my colleagues, of my friends, of my relations or, for that matter, of my pot plants. The same applies to all my posts, of course.

With that out of the way: the contribution I will discuss today, The case against the transfer of Dryandra to Banksia (Proteaceae) is … not a terribly well written paper.

For background, several years ago it was found that both molecular and morphological data showed Western Australian Dryandra to be phylogenetically nested within more widespread Banksia. It is no exaggeration to say that a Dryandra is just a Banksia with a shorter inflorescence, and consequently most taxonomists and systematists decided to unite the two genera. However, the “loss” of Dryandra as a distinct genus has left many people profoundly unhappy. One of these people appears to be the author of the present contribution.

More on trying to use SNAPP

Further to my notes on the BEAST template SNAPP from a few days ago, here is a little issue that people who happen upon this blog via entering SNAPP into a search engine might be interested in:

Check the 'totalcount' values in your XML files before starting the BEAST run.

You would think that if you entered a SNP dataset with the three character states 0, 1 and 2* into BEAUTi, it would recognise three character states and write totalcount="3" into the XML file, wouldn't you?

Well, I thought so too, but apparently it will, at least as version 2.1.3 on my machines, randomly pick either a 2 or a 4. No idea why. Nor do I have any idea how BEAST interprets the 0, 1, 2 states when it only expects two states. What I do know is that you can correct the XML file manually - simply do a search and replace of totalcount="(whatever the wrong number is)" with totalcount="3" -, and that my analyses are even slower now that I have corrected BEAUTi's mistakes. But at least this explains why I got nonsensical results in some cases. Yippee.

Footnote

*) Homozygous for the major allele, heterozygous, and homozygous for the minor allele, respectively.

Back to Richard Zander's Framework: about a book review

Richard Zander, the author of the Framework for Post-Phylogenetic Systematics (which I reviewed for a society newsletter, see also my blog posts here, here, here, here and here) is outraged by what he calls a “particularly nasty” review of his book by Andrew Brower in the journal Cladistics. Of course his book was never going to be received well by this bastion of the school of systematics he is most aggressively opposed to, but he complains that the review “lacks understanding and collegial dignity”.

He submitted a supposedly “light-hearted” response to Cladistics but was turned down; and although they may exist somewhere I cannot remember ever having seen a rebuttal to any book review in any journal before, so that does not surprise me. His reply can therefore be found in Phytoneuron, a journal that I had never heard of before. It seems to be an online-only, one man operation, whose review process is described as follows (accessed 17 December 2014):

Submissions will be promptly reviewed for content and style by the editor, based on his own knowledge and expertise. If deemed appropriate or necessary by the editor, or if requested by the author, review by other botanical peers will be sought.

Zander's reply consists mostly of a complaint about Brower's “disparagements” and two arguments by analogy; the latter I found so bizarre that I felt motivated to write this post. First, however, the tone.

Trying to use SNAPP

I really should rewrite my post on species tree methods one of these days. But at the moment I do not have the energy, and so I will simply write a few words on my experience with SNAPP.

Anybody who happens upon my species tree methods post will see that despite being more of a parsimony guy myself I have a lot of praise for BEAST. It is fast (for a Bayesian method) and very user-friendly. "Normal" BEAST is for standard gene tree phylogenetics, *BEAST or starBEAST is the add-on for species tree analyses based on multiple independent genes, and the still fairly novel SNAPP is the add-on for species tree analyses based on Single Nucleotide Polymorphism (SNP) data.

With genomic sequencing, SNPs are only going to become more important for the study of closely related organisms. If you have species that are very recently derived, any individual gene sequence is probably going to be extremely similar between them. This means that the approach of inferring species trees from the reconciliation of multiple gene trees is unlikely to work: instead of gene trees you are likely to get gene "combs", simply unresolved relationships.

There will still be thousands of little individual mutations differentiating your study specimens, but they will be distributed all across their genomes. This is why they are called SNPs: Single Nucleotide Polymorphisms each surrounded by conserved sequence regions.

The idea of SNAPP is now to use the SNPs from multiple samples per species directly to infer the species phylogeny, without any intermediate steps like alignments or gene trees. For this, it uses the coalescent model and the usual Bayesian Marcov Chain Monte Carlo approach. This sounds very attractive, especially after the good experiences with BEAST, and also very rigorous.

Unfortunately, so far my attempts at using SNAPP have been rather frustrating. There are three main issues:

• SNAPP appears to be rather capricious as to whether it will run at all or whether it will fall over. The only machine on which I can get it to run consistently is our family computer, a Linux machine. On the Windows machine at work it is also very consistent in that it always error messages and crashes.
• BEAST in general is known to have a problem with missing data although it can at least be tricked into accepting an allele missing for a species. Still, the same problem applies to SNAPP; a colleague had to throw out most of the data and samples he had to get missing data below ca. 5% before he could do an analysis. In my dataset that is just not possible, I'd be left with too few SNPs.
• Finally, SNAPP is really. Really. Really. Slow. A hundred SNPs, no problem, I can run a decent analysis over a day. Five hundred SNPs? Forget it. Our high performance computing cluster at work did 1,000 generations over a few hours, and I need it to do at least ten million generations; do the math. At home I just tried a dataset reduced to 200 SNPs, and it seems as if it will finish in three months. All that sounds like First World Problems, but the thing is, the whole point of genome-wide SNPs is that you have thousands of them. A SNAPP analysis of my whole dataset is just not going to happen, even if I did not have the missing data issue on top of it.

I will see what I can do, but at the moment this new piece of software seems to be a realistic option only for rather small datasets, on the lines of the Amplified Fragment Length Polymorphisms I generated for my Ph.D. more than a decade ago...