Monday, March 28, 2016

The Australian Native Bee Book

We went for a walk at the Australian National Botanic Gardens on the weekend, and I saw Tim Heard's The Australian Native Bee Book at the Botanical Bookshop.

I have always loved hymenopterans, and especially the eusocial ones (bees, wasps, ants). As the focus of the book is on eusocial stingless bees, I pretty much had to buy it. You see, during my field trips to South America years ago I frequently ran into the genus Trigona and its relatives. Here the nest entrance of a colony in a hotel courtyard in eastern Bolivia:

They are much smaller than honeybees and, as the name implies, do not have a sting. I knew that they are traditionally kept for honey in Central America, but because each hive produces only a fraction of the honey produced by a honeybee hive that practice is sadly dying out. Unfortunately, I never learned much more about their biology and diversity.

The Australian Native Bee Book focuses on keeping Australian stingless bee hives for honey, propolis, pollination services, and simply for conservation and education. Everything relevant is covered, from hive building across colony division to pests and parasites.

I will not attempt to keep any myself - we don't have the space, and these bees do not actually occur in the colder climate of Canberra - but one gets just as much out of the book on the biology, behaviour and diversity of these insects. It is really and truly one of those "everything you ever wanted to know but didn't know where to look up" scenarios. Their nesting, life cycle, global biogeography, taxonomic history, foraging strategy, and much more are described.

At the same time the style shows that rarely achieved combination of using clear explanations, superb images, and unpretentious language that will make sense even to a complete layperson (as I am with regard to bee-keeping) without being dumbed down or misrepresenting anything (which I can judge for some other topics like systematics or biogeography). To cite just the part on why the native stingless bees are not all called Trigona any more, something that is obviously close to one of the main topics of this blog:
Rasmussen's phylogeny also shows that the remainder of the Australian stingless bees called Trigona (and their Asian relatives) are not related to American Trigona. The first Trigona named was a South American species, so that group got to keep the name according to the rules of naming animals. This meant that the Australian/Asian bees needed a new name. (...) Nobody likes it when plant and animal names change, but there are clear reasons for, and advantages to, making these changes. It does not make sense to call all these species Trigona when they are not closely related. It clouds our thinking about patterns. 
Beautifully put, and very succinctly explained.

I would definitely recommend this book to those who loves bees, and especially the eusocial ones.

Sunday, March 27, 2016

Species tree method update: ASTRAL

I have just updated and restructured my long reference blog post on species tree methods. The occasion is that I have tried out ASTRAL for the first time today, so I decided to add it to the list.


The only inputs are a text file with all the gene trees in Newick format and, if there are multiple alleles per species, an allele assignation table. In that case, also make sure to download the "multiple individuals" version here instead of the master version. The program needs Java and is run through the command line.

ASTRAL is fast and very flexible, and the results I got are meaningful although without branch lengths, limiting the downstream use cases. It is available for all three major operating systems and worked seamlessly on my Linux computer.

Downsides are the aforementioned command line operation, at least for people who are unfamiliar with that, and in my eyes the feeling that the developers are uncomfortable with and may not trust their current multiple individuals version ("The code for handling multiple individuals is in its infancy and might not work well yet").

Apart from adding ASTRAL and iGTP, I reorganised the long blog post to be a list of software tools in contrast to a list of methods. I hope it will continue to be useful to people searching the internet for an overview and comparison of species tree methods.

Saturday, March 26, 2016

Discordant paraphylies executed

Strangely, editors of systematics journals do not appear to tire of opinion pieces rehashing the discussion about paraphyletic taxa that had already been laid to rest in the 1970s. The newest example of such a publication showing up in my alerts is Seifert et al. 2016 in the journal Insectes Sociaux, who  take issue with suggested taxonomic changes in ants.

As usual I would like to tease apart the argumentation, examine it for its merits, and consider if there is anything new in it that constitutes a good reason to accept paraphyletic taxa. But first, the title of the piece, which is (sorry to say) one of the most unwieldy titles I have ever seen on a scientific publication:
Banning paraphylies and executing Linnaean taxonomy is discordant and reduces the evolutionary and semantic information content of biological nomenclature
If I may attempt to rephrase a bit, I think the authors mean the following:
Banning paraphyletic taxa is incompatible with Linnaean taxonomy and reduces the evolutionary and semantic information content of biological nomenclature
...although that is still too long, and it is not clear what is meant with evolutionary and semantic in this context. At any rate, this already suggests what the two main arguments in favour of paraphyly might be. Both of them are not exactly new and have repeatedly been dealt with at length, but of course the hope is that the present paper acknowledges the cladist responses and provides additional counter-arguments instead of ignoring them.

Sunday, March 20, 2016

Conan the Cimmerian

I have made it a habit over the last few years to collect what one might want to call fantasy/science fiction pulp literature classics, either at the local charity book fair or, sometimes, by buying collections outright from online book sellers. Examples include Edgar Rice Burroughs' Barsoom and Venus series and, recently, Robert E. Howard's original Conan stories and the second book of Alan Burt Akers' Dray Prescot series.

Honestly I do not buy these books because I expect to be overwhelmed by their literary quality. I buy them because they are classics; they have influenced generations of fantasy and SF authors, movies and memes, and consequently I would like to get a feel for them. I also do hope that they are entertaining, and here I am actually quite flexible.

A work does not have to be politically correct, I can take it as a product of its time as long as the author is not, well, repulsively reactionary even for their own time. It does not have to be superbly imaginative if the story is gripping, and it does not have to have a superb story if it is at least imaginative in its setting.

Edgar Rice Burroughs, for example, is rather predictable and formulaic:

10 Hero falls in love with princess
20 Princess gets abducted by villain or monsters
30 Hero battles against overwhelming odds to save his love
40 Just as the hero has rescued his love ... goto 20

But the stories are still fun to read because he is very inventive with the biology, politics, technology, culture and sociology of the Martians and Venusians, and apart from the recurrent damsel in distress theme his stories are actually quite okay even from a contemporary political perspective.

His Mars (Barsoom), for example, has green, red, yellow, white and black races. The really evil ones are the greens, blacks... and the whites. And when their evil leaders are defeated... even they can reform, under the leadership of one of their own race. Shocker - the black Martians do not actually need a white master to be civilised! And the kind of 'good' Martians we are supposed to identify with are the red ones... which are the product of interbreeding between whites, blacks and yellows. Clearly Burroughs was not a race essentialist or particularly concerned with racial purity. What is more, he did produce a later Barsoom novel with a fighting, self-confident heroine, defying his readers' expectations.

So now let's talk Conan, because that was the last series I read through, in the sense of buying a two volume collection of all the stories written by Howard himself, meaning not including any of the, shall we say, extended universe stories added by later authors.

Thursday, March 17, 2016

Botany picture #226: Conyza sumatrensis presumably

From a little trip to Cotter Avenue (not really an avenue but a playground and bathing site on Cotter River) last weekend:

These plants are rather too large to be Conyza bonariensis, so although the pappus does not entirely convince me as "golden" I will tentatively call them C. sumatrensis. Apart from general size and pappus colour (white to pink in C. bonariensis) the two species are rather similar.

Both are weeds introduced to Australia from the Americas, and they are rather common, widespread, and flower most of the year.

Saturday, March 12, 2016

Unnecessarily arcane botanical terminology

Sometimes the personal libraries of retired colleagues who want to downsize, or other left-over old books, are made presented in the corridor of our herbarium so that staff can pick what they still find useful. I have in this way acquired a number of valuable books, especially old Australian or New Zealand floras.

Recently I have in the same way picked up a book with great (unintentional) entertainment value. It is Taxonomic Terminology of the Higher Plants by H. I. Featherly in a 1973 reprint of the 1959 edition, published by Hafner Press. In case it isn't immediately clear, it is mostly a glossary of botanical terminology. To illustrate what is so funny about it, let's open the book randomly on pages 62 and 63 and look at a few selected entries just from this double page. Blue text is from the book, black font are my comments.

Friday, March 4, 2016

I have no idea why anybody uses LaTex

When I was in what would here be called high school, in the early 1990ies, I already had a mathematics teacher who was evangelising for LaTex in the classroom. I never bothered looking into it more deeply, as writing scientific papers in MS Word or LibreOffice worked quite well. But I kind of thought it would have its advantages, otherwise it would not have its niche.

In the last few weeks now I had to deal with a manuscript that was written in LaTex, i.e. I had to integrate the text into a larger Word document and I later had to peer review it. There are many things in life that I do not understand, often with regard to why people believe certain things or behave in certain ways. I can now add to the sum of my ignorance my complete lack of understanding why anybody would want to use LaTex.

Let's ignore for the moment that treating a text document with some bolding and some italics as a programming project already seems needlessly complicated. Yes, it would be easier to mark something and press ctrl-i than to put command tags around the phrase, and a text that is not interrupted by tags is also easier to proof-read, but fine, not the point now.

Point is, a few weeks ago I tried to get the text of this LaTex document into a larger Word document, together with other text elements. The author was unable to export it into Word for me, and another colleague agreed that it wasn't possible. Great. So while, for example, LibreOffice can easily export into a gazillion other formats, a user of LaTex apparently has to rely on all their collaboration partners also having LaTex installed. That seems somewhat inconvenient. I ultimately found a trial version of a Word add-on that allowed me to convert (at the cost of some major formatting disasters), and I sincerely hope I never have reason to buy the full version.

Now I had to review a later version of the same manuscript, and because I had to make lots of minor suggestions I very much wanted to use tracked changes instead of having to laboriously add individual comments to a PDF version. When I was told that LaTex has track changes functionality, I reasoned that using LaTex would also be the best for the authors, as in that way they would be able to easily open the annotated version they would receive from me, and the formatting would be untouched. And who knows, maybe it is a good idea to have LaTex installed anyway, in case another such manuscript comes past my desk in the future.

So let's look into getting LaTex for my Windows computer at work... aha, they recommend proTeXt. Let's see... "You can download the self-extracting protext.exe file from CTAN; it is well over 1GB."

AHAHAHAHAHA... no. They have got to be kidding, right?

What is the argument here? 'We are even clunkier and less efficiently programmed and less user-friendly than Word, but on the plus side...' Well, what? Easier to write mathematical formulas, perhaps? Is that it?

I will stay with LibreOffice and Zotero for the moment, thank you very much.