Wednesday, January 30, 2013

Botany picture #28: Menyanthes trifoliata

For comparison, Menyanthes trifoliata, another aquatic Menyanthaceae with strikingly ciliate flowers. I took this picture in 2008 in Hamburg's Planten un Blomen.

Using Australian and German computers at the same time

At work, I unsurprisingly use an Australian desktop PC. When traveling, I carry with me a cheap Australian netbook. At home, however, I still have a clunky old German laptop (now with broken monitor hinge, hooray) that I bought at the beginning of my second postdoc. It can sometimes be trying to move between the first two and the last of these.

One fairly obvious problem is the different arrangement of some letters. To those who do not know, Y and Z are switched around, and I don't have the foggiest idea why. This results in many a Skype chat message, e-mail or even manuscript draft containing words like "sorrz", "mz" or similar. Luckily, my brain seems to have cerebellum routines for both arrangements so that it usually does not take more than three or so mistypings to start getting it right again.

A bit more problematic is that virtually everything but the numbers and remaining letters is also rearranged between the two countries. Be it slash or backslash, brackets or hyphen, plus or colon, everything is in a different place on my home laptop than at work. Again, why? Pure sadism?

Even worse: several characters familiar to the user of German keyboards are quite simply missing on Australian ones. Of course I don't expect Ä, Ö or Ü on an Anglo-Saxon machine*. But why is the degree symbol ° also missing? Surely Australians have often reason to write about degrees Celsius, latitudes or longitudes? (Yes, I know that MS Word has a key combination for that, but Word is not the alpha and the omega of software. This, for example, I am typing directly into the browser.)

Still, all that would be tolerable if not for the synergistic meeting of two other problems. First, Germans write 1,5 and 1.492 where Anglo-Saxons write 1.5 and 1,492. Again, please don't ask me why, it is not my fault. Second, MS Excel automatically interprets nearly every number that it does not easily understand as a date, and every date that it misunderstands as a number. Without asking. And of course you cannot get the original data back when it does that.

And that is what "inspired" me to write this rant. (Sorry.) Yesterday evening I entered some specimen data into an Excel sheet at home, including some dates of collection, and today I open it at work and find a quarter of the dates have miraculously turned into numbers around 34,000. At least I noticed that immediately; two years ago I was working on a sheet with more than 100,000 lines and only noticed that thousands of geographic coordinates had been turned into nonsensical dates after I had already sunk a few days into the next steps of my work pipeline, all of which I consequently had to repeat.

If you ever transfer your spreadsheets onto a foreign computer, beware.


*) Although it could be mentioned that the German keyboard generously provides keys for diacritical marks like Á despite their irrelevance for written German. Perhaps we are such good friends with the French...

Botany picture #27: Nymphoides montana

Further to last week's post from Kosciuszko National Park where I embarrassingly first called it a water lily, see here a closeup of Nymphoides montana (Menyanthaceae). Although its floating leaves and submersed growth represent an obvious case of parallel evolution with the true water lilies (Nymphaeaceae), it has very different flowers. Where water lilies have many free floral organs, the Menyanthaceae are typical Asterids with their 5-merous flowers and fused petals.

They are a small plant family of global distribution which is often characterized by beautifully ciliate corollas and a preference for wet habitats. Members of the genus Nymphoides in particular are apparently popular ornamentals.

Tuesday, January 29, 2013

Botany picture #26: Ranunculus lyallii

And as another example, this time from the southern hemisphere, the very spectacular Ranunculus lyallii. I took this picture at Arthur's Pass, New Zealand, in 2010. The occasion was the conference field trip of the annual meeting of the Australasian Systematic Botany Society.

Monday, January 28, 2013

Ranunculus, part 5: Criteria for "evolutionary" classification

This is part of a series on a paper by Hörandl & Emadzade (subsequently H&E) suggesting an "evolutionary", i.e. pre-cladistic, classification of Ranunculus. See the previous installments here: part 1, part 2, part 3, part 4.

In the last paragraph of the materials and methods section we find what I consider the most crucial element of this case study in "evolutionary" systematics, its criteria for classification. Phylogenetic systematics has one simple criterion for accepting a suggested supraspecific taxon as valid: monophyly. That means a taxon can be accepted as valid if and only if it includes all descendent species of one common ancestral species, and not only some of them. What I would need to see to take "evolutionary" systematics seriously is an alternative criterion that is just as testable, objective and universal. Why do I stress these three properties so much?

Saturday, January 26, 2013

Botany picture #25: Ranunculus lanuginosus

With all the talk about Ranunculus, botany pictures from that genus seem appropriate. Here one of my favorites from the northern hemisphere, R. lanuginosus (Ranunculaceae). It is one of the largest species in Germany and, as the Latin name indicates, quite hairy.

Thursday, January 24, 2013

Field work in Kosciuszko NP (2)

As announced, another post from Kosciuszko National Park, although less opulent this time. Today we ascended Mt Stillwell and visited another locality in Perisher Valley.

 Perisher Valley as seen from the peak of Mt Stillwell.

Wednesday, January 23, 2013

Field work in Kosciuszko NP

This week a student and I are conducting field work in Kosciuszko National Park. We are searching for native daisies, especially billy buttons (genus Craspedia). This is the alpine area of New South Wales and really not the kind of landscape a European would first associate with Australia.

Some of the major peaks, with Mt Kosciuszko, the highest mountain of Australia, in the left half of the picture and the Snowy River in the right half. The mountain and consequently the national park are named after Tadeusz Kosciuszko, a national hero of Poland, Lithuania, Belarus and the USA (!) who, as one may guess, lived a very turbulent life. Read more about him here if interested.

Douglas Adams' Hitchhiker's Guide novels

It has been many years since I last read the Hitchhiker's Guide to the Galaxy series of novels, and I remember enjoying them very much then. However, recently I picked them up again, I am now in the fourth book, and it occurs to me that they are actually not all that well written*. Don't get me wrong - Douglas Adams could write beautiful and witty prose, he presented a huge number of hilarious ideas, and he had a great talent for the absurd. The problem is simply that a huge number of hilarious ideas gives you a great stand-up comedy routine but not necessarily a great novel. In other words, what irks me is the story-telling aspect of the books.

Tuesday, January 22, 2013

Botany picture #24: Todea barbara

Todea barbara is the third and last Osmundaceae in this small series of botany pictures. Like several other members of its family, this species can get very large and is thus known as the King Fern. It occurs in South Africa, Australia and New Zealand. These particular pictures were taken in the Botanic Gardens of Sydney in 2011.
As can be seen here, this species does not have morphologically specialized fertile pinnae like the two last Osmundaceae.

Monday, January 21, 2013

Ranunculus, part 4: Inferring reticulate evolution

This is part of a series on a paper by Hörandl & Emadzade (subsequently H&E) suggesting an "evolutionary", i.e. pre-cladistic, classification of Ranunculus. See the previous installments here: part 1, part 2, part 3.

Going through the introduction took quite long, but that is to be expected as it mentions many of the concepts that are controversial. Some of that will come up again in the discussion, but then it should hopefully not take as long again. What I still want to get out of the paper is essentially whether H&E have found the elusive universal, objective and testable criterion for the circumscription of supraspecific taxa that can replace the criterion of monophyly.

Saturday, January 19, 2013

Botany picture #23: Osmunda claytoniana

Osmunda claytoniana (Osmundaceae), Canada, 2012. In contrast to the European species from the last picture, the fertile pinnae are in the middle part of the fronds. This arrangement looks if anything even weirder.

Friday, January 18, 2013

Peer reviewers from hell

Before a manuscript is accepted by a scientific journal, it has to undergo peer review. The editor of the journal sends it out to competent colleagues who suggest either acceptance as is, minor revision (language, presentation), major revision (re-analyze, major rewrite, etc.) or outright rejection. In turn, the reviewers' own manuscripts are likewise reviewed pro bono by other colleagues. In my area the authors generally do not know who their reviewers were, the idea being that nobody should have to fear offending somebody, especially very influential colleagues, by reviewing their papers negatively. On the other hand, the reviewers generally know the name of the authors, which is a possible source of positive or negative bias on their part.

The ideal is, of course, that we should all be objective, fair to each other, and provide constructive criticism within a reasonable time. That ideal is not always achieved. Personally, I think I was overall pretty lucky so far, but between my own less positive experiences and additional tales told by friends and colleagues, I have enough material for a list of how not to do it. I present to you Peer Reviewers From Hell.

Wednesday, January 16, 2013

Botany picture #22: Osmunda regalis

Osmunda regalis (Osmundaceae), Botanic Garden of the University of Halle, Germany, 2008. The Osmundaceae are a small but very interesting family of ferns. They are an old group and possibly the sister clade to all other leptosporangiate ferns. The family was apparently more abundant in the Mesozoic than today as documented by a fairly good fossil record.

Many species are very large and robust compared to other ferns, and their large fronds often have specialized pinnae carrying the sporangia; in most other leptosporangiate ferns, the sporangia are found either on otherwise normal pinnae or an entire frond is turned into a specialized sporophyll. In the case of this European species, the apex of the frond carries the sporangia and is visibly different from the lower pinnae. The next botany picture will show a species with a different arrangement.

Tuesday, January 15, 2013

Ranunculus, part 3: Morphological versus molecular data

This is part of a series on a paper by Hörandl & Emadzade (subsequently H&E) suggesting an "evolutionary", i.e. pre-cladistic, classification of Ranunculus. See the previous installments here: part 1, part 2.

Continuing with the introduction, the second paragraph starts as follows:
Evolutionary classification further attempts to integrate information on structure and function into the taxonomic concept (Stuessy, 1987; Mayr and Bock, 2002; Hörandl, 2007, 2010; Stuessy and König, 2008).
As a counterpoint, I strongly suggest to read Hennig (1975). Dealing with the same claim then advanced by Ernst Mayr, he demonstrated handily that trying to accommodate two very different criteria of classification in the same system will only result in confusion. In the end, the system is completely useless because you cannot even consistently read one of the two stories - common descent or phenological similarity - out of it.

The remainder of the second paragraph introduces the issue of morphological characters. After stating that morphological data contains phylogenetically useful information, the authors raise the problem of homoplasy arising from parallel evolution or reversal. One could mention here that DNA characters, with only four different character states at each position, and considering that at least coding regions will also be under selective pressure, are not entirely free from the same problems either, but okay.

Staying with the topic of morphological data, H&E examine the different ways in which it is used.

Sunday, January 13, 2013

Morning stroll through the ANBG

I should really do a separate post on the Australian National Botanic Gardens soon, and perhaps also on a few other botanic gardens I have seen over the past few years. Today, however, just a few pictures from when we visited the ANBG this morning:

Friday, January 11, 2013

Botany picture #21: Hieracium aurantiacum

Hieracium aurantiacum (Asteraceae) from Germany, 2012. The orange hawkweed is my favorite species in its large but mostly yellow-flowered genus although unfortunately it is also a badly invasive weed. If you visit the Alpine areas of Australia, you will frequently encounter signs advising tourists to report any sighting of this plant as its aggressive spread could endanger the local flora.

Where they are at home and harmless, the species is however very attractive with its combination of orange flowers and dark capitular bracts. It spreads vegetatively with stolons and makes a good ground cover in sunny, not too wet gardens in temperate areas. In fact, one of the reasons I like it so much is that we had in our garden when I was a teenager.

If you are botanically interested yourself, it is probably no news to you that what most novices would call the flowers of the daisy family, are actually heads consisting of many tiny flowers or "florets". In these photographs, and especially in the second one, it is clearly visible that each of the tongue-shaped pseudo-petals has five teeth, which are really the five lobes of a strongly zygomorphic corolla. One can also see in most of them that they are associated with their own bifid style, although the anther tube around the latter is not so obvious.

The daisy family is very large, and it is divided into numerous subfamilies and tribes based on sometimes rather technical characters. The one the hawkweeds, lettuce and dandelion belong to, tribe Cichorieae, is, however, easily recognized by possessing milky sap and only five-toothed highly zygomorphic florets. Other tribes generally have a combination of zygomorphic ray florets and actinomorphic disc florets (sunflower) or only the latter (thistles). The hawkweeds are one of the taxonomically most complex genera of plants because of their many apomictic microspecies, with opinions on the species number ranging from a few hundred to many thousand. Personally, I find the species concept underlying the latter number ludicrous, but that is a topic for another time.

Thursday, January 10, 2013

Graphical illustration of some important concepts and terms

The following is about phylogenetic systematics and its detractors again. Please disregard if the topic does not interest you.

Some concepts and terms are often misunderstood, confused or conflated, and it seems useful to illustrate them in a concise way for later reference.

Wednesday, January 9, 2013

Botany picture #20: Viscum minimum

Viscum minimum (Santalaceae) at the Botanic Garden of Zurich, 2010. Like its larger sisters, this tiny mistletoe is a hemiparasite, drawing nutrients and water from a host plant but doing its own photosynthesis. In this case, probably only very little. The host is a succulent Euphorbia.

Tuesday, January 8, 2013

Ranunculus, part 2: The state of the art from the perspective of "evolutionary" systematists

This is part of a series on a paper by Hörandl & Emadzade (subsequently H&E) suggesting an "evolutionary", i.e. pre-cladistic, classification of Ranunculus. See the previous part here.

Let us start right at the beginning of the paper, with the introduction. This is where the state of the art is described, and so obviously we will find here the authors' view of the supposed shortcomings of phylogenetic systematics and how their own approach, evolutionary systematics, can supposedly rectify the situation.
Biological classification has been revolutionized by phylogenetic principles, and nowadays there is a broad consensus that shared ancestry is a primary criterion for grouping concepts.
Of course there is also a virtual consensus that shared ancestry should be the only criterion for grouping species into higher order taxa.

Sunday, January 6, 2013

Family trip to Kosciuszko National Park

To escape from the annual meeting of people who puzzlingly consider the inhalation of burnout fumes to be not only a legitimate form of entertainment but the greatest that has ever been devised, we made a trip to the northern part of Kosciuszko National Park over the weekend.

Canberra is currently experiencing temperatures in the 35-40°C range, and we also hoped that it would be cooler in the mountains. It was, but not as much as one would wish for. Photos below the fold.

Saturday, January 5, 2013

Botany picture #19: Eriophorum angustifolium

Eriophorum angustifolium (Cyperaceae) in Eastern Germany, 2008. I am generally not very fond of the sedge family but make an exception for this genus with its distinctive infructescences.

Friday, January 4, 2013

"Evolutionary" classification of Ranunculus, part 1

One of my hobbies, if that term is permitted, is to try and understand the stance of those who call themselves "evolutionary" systematists (ES) - the minority of taxonomists and systematists who desperately try to turn the wheel of progress back by a few decades and return to the time before formally accepted supraspecific taxa had to be circumscribed to be monophyletic. Especially at the end of 2010 and the beginning of 2011, I tried to find out if I had overlooked any decent arguments and if they were perhaps right in their assertion that the insistence on monophyly does not make sense.

After digging through dozens of publications and opinion pieces, some of them more intellectually coherent than others, I have concluded that most ES don't understand phylogenetic systematics (in particular the difference between tokogeny and phylogeny and that only species relationships matter), some of them don't even understand how parsimony analyses work, and all their arguments are built on fallacies or false premises except perhaps one, and that one is built on the assumption that we want to classify demonstrably ancestral species in a Linnean framework, which is virtually never the case. What is more, all their arguments have repeatedly been shown to be wrong or unfounded but they simply soldier on regardless; there is probably no point trying to convince many of them any more if it has not worked so far.

However, not for nothing did I start by saying that it is one of my interests. I remain curious if any of them comes up with something novel and intriguing, and in particular if they can make any new suggestions for what may be their fundamental methodological problem: the complete lack of a universal, objective and testable criterion for segregating paraphyletic residues from monophyletic groups nested within them.

Thursday, January 3, 2013

Botany picture #18: Sempervivum tectorum

Sempervivum tectorum (Crassulaceae), a succulent that I had on my own balcony in 2005. Although one generally keeps them for the leaf rosettes, the flowers are pretty too. Over the years, I built up quite a nice collection of succulents and Lamiaceae but had to give everything away when I moved to Australia due to quarantine restrictions.

Wednesday, January 2, 2013

Simplistic molecular phylogenetics and incomplete lineage sorting

By now, a whole generation of botanists has been trained with molecular techniques. While the 1980ies and early 1990ies were the heyday of morphology-based cladistic analyses, most phylogenetic studies today are conducted with DNA sequence data.

However, many higher level relationships in plants are by now well understood. Not all, of course - the exact phylogenetic relationships of the major groups of seed plants, for example, are still problematic, especially with regard to the closest relatives of the flowering plants. But we now have a fairly good understanding of the phylogeny of the flowering plants, and can be confident that most major plant families have either been confirmed to be monophyletic (daisies, orchids, grasses, etc.) or else recircumscribed to make them so (mint family, heath family, etc.). Consequently, attention is increasingly turning to lower taxonomic levels, to infer relationships in groups of closely related species. This is important both to further improve our classification and as a prerequisite for studies in evolutionary biology, biogeography, and other areas.

In the light of this shift in focus, it is especially troubling to realize that a surprising number of colleagues has a very simplistic view of how to use molecular data for phylogenetics - a view that is fairly unproblematic at higher taxonomic levels but fatal at the lower ones. Lemme explain.