spider: an R package for species identity and evolution

spider: Species identity and evolution is an R package developed by the Lincoln University molecular ecology lab group to do a range of analyses that various lab members wanted to run that were not yet implemented in R. In particular, the package provides functions for conducting sliding window analyses on DNA sequences, the calculation of identification efficacy of a library of reference DNA sequences, and the segregation of distance matrices into their inter- and intra-specific components.

The above are the main attractions, and the ones that we tend to write about when promoting it in places like the 4th International Barcode of Life Conference. There's a bunch of other neat utilities in there also though. A couple of the ones that I particularly enjoy are tiporder(), which returns the tip labels in the order in which they appear on the tree; paa() which conducts population aggregate analysis on a dataset; and rosenberg() which calculates Rosenberg's probability of monophyly for the nodes on a tree.

Spider is available on CRAN, and R-Forge, the latter providing opportunities to report bugs and to collaborate in the future development of the package should you desire to do so.

Vanuatu Caddisflies

A recently published paper by Kjell Johanson revises the caddisfly fauna of Vanuatu, descibing 12 new species and providing a key to the species currently known from the archipelago. It is an important contribution to the knowledge of the caddisfly fauna of the region, as most of the previous work done on the fauna of the region is several decades old.

A couple of things stood out to me in this paper. The first is that Orthotricha has not been recorded from any other oceanic Pacific islands. These are small (2-3 mm wing length) creatures, and it is likely that they just haven't been collected elsewhere in the Pacific. The second was their discovery that a female of Triplectides australis had a large number of larvae inside her abdomen. While I was hitherto unaware that ovoviviparity occurred in caddisflies, it turns out that this has been known since 1890, the first instance of it being confirmed by Prof. Wood-Mason in the following manner:

I threw the insect alive into a liqueur-glass of whiskey that happened to be ready at hand.

Adult caddisflies tend to be overlooked by the general public, usually being confused as small, fairly dull-looking moths. Their larvae are aquatic where they form an important part of the macro-invertebrate fauna of streams, and can be useful as indicators of water quality and stream health. Unfortunately, very little biological information is recorded in the paper, and larvae are not considered. In part this is due to Malaise and light traps providing the bulk of the material that was considered in the revision. Discovering and describing larvae and their habitats is a natural application of the taxonomic effort of this paper.

References

Johanson KA, Wells A, Malm T, Espeland M. 2011. The Trichoptera of Vanuatu. Deutsche Entomologische Zeitschrift 58(2): 279-320.

Wood-Mason J. 1890. On a viviparous caddis fly. Annals and Magazine of Natural History 6th series, 6: 139-141.

TVNZ streaming America's Cup races live

Good news for New Zealand sailing fans: TVNZ is now streaming the AC45 world series matches live. Check out the sailing news page of their website to be directed to the links. Replays can be accessed by clicking through their OnDemand links, but the price paid is having to endure a Microsoft ad before getting into the actual footage. Access to the full replays on YouTube is once again delayed for viewers from NZ, but hopefully will be available in a week or so.

Unfortunately, coverage of the San Diego races has been a bit of a debacle. A lack of communication regarding the course, time of live streams, and delays in the posting of full replays have left a fans with a sour taste in their mouths. I am personally annoyed that the full replays for Port Cities Challenge that kicks off the event are not available. Let us hope that the organisers are learning valuable lessons so they don't make these mistakes again.

Using Sweave with Beamer: A note on fonts

Recently, I've been preparing a poster using the LaTeX packages Beamer and beamerposter. The poster discusses a bunch of R stuff that I've been doing lately, so I successfully used Sweave to incorporate R code into the poster. However, I had some trouble with package names that I wanted to typeset as small caps. The package names looked the same as the rest of the text. A bit of sleuthing around revealed Sweave as the culprit. In the Sweave.sty package, on line 20, it calls the deprecated LaTeX package "ae", which for some reason doesn't recognise small caps. Changing the package to "lmodern" made small caps turn up correctly within the text.

Unfortunately, my problems had not yet been solved completely. I had mentioned the package names in the titles which were set in bold. I thus had created a fairly commonly encountered bugbear with LaTeX—the non-compatibility of bold and small caps in computer modern font. While there are workarounds for this (see this Stack Exchange and TeX FAQ for more details), unfortunately these solutions did not work with Beamer.

So, I set about finding a font that both looked alright, and would accomodate bold and small caps. I found that using helvetica would be fine, but had to be loaded after Sweave to work. As my Sweave block kept placing the \usepackage{Sweave} immedediately before \begin{document}, I resorted to calling helvetica in the Sweave file itself.

The relevant lines in of the Sweave.sty (lines 18-21) file. Before:

\ifthenelse{\boolean{Sweave@ae}}{%
\RequirePackage[T1]{fontenc}
\RequirePackage{ae}
}{}%

After:

\ifthenelse{\boolean{Sweave@ae}}{%
\RequirePackage[T1]{fontenc}
\RequirePackage[scaled]{helvet}
}{}%

Microscopy mounting media II

Today I found a brilliantly written, hugely informative, and well-illustrated guide to Safe Microscope Techniques for Amateurs, written by Walter Dioni. It is a series of four articles, originally published in Micscape, the magazine of the Microscopy UK organisation.

"Safe Microscope Techniques for Amateurs" discusses liquid media, solid media, mixed media and glycerin jellies. All techniques are explained clearly and several suggestions for equipment or readily available appropriate subsitutes are given. In summary, the series is an excellent introduction to microscope mounting techniques and gives some very useful tips for making good microscope mounts.

Old codes

The International Code of Zoological Nomenclature is the document that details the rules of how the scientific names of animals are managed. It's a complex document with a rich history, and it is necessary to consult previous editions for correct knowledge as to the reasoning behind some of the provisions of the code. Old editions tend to be fairly hard to come by, but thankfully the Biodiversity Heritage Library has them digitised and on the interweb for all to enjoy. Thus, it holds copies of the first (1961), second (1964), third (1985), and fourth (current, 1999) editions are all available. The current edition is also available from the official website as an indexed html version.

Jetsetting Dragonflies

Image: Muhammad Mahdi Karim

Not only not are dragonflies some of the best aeronauts of the insect world, some also have the greatest endurance. A couple of years ago, it was discovered that the globe skimmer dragonfly (Pantala flavescens) migrates from India to South East Africa via the Indian Ocean islands of the Maldives and the Seychelles, and back via East Africa. That's a grand total of around 18 000 km. That's a fair bit further than the 11 000 km I recently traveled from New Zealand to South Africa. It is considered that the round trip takes place over several generations, but it's still an amazing phenomenon.

For more information, there's news reports from Wildlife Extra and the Daily Mail; and a blog post from National Geographic. There's even a graphic on DeviantArt celebrating the journey. To hear it from the horse's mouth (so to speak) watch a video of Charles Anderson himself talking about his findings.