Featured insect: Polyrhanis dabraensis (Coleoptera: Cicindelidae)

Tiger beetles (family Cicindelidae) are active predators as adults, pursuing their prey by running and flying. The larvae are bizarre looking things, and catch their prey by sitting and waiting in holes in clay banks and the like (such as one I found in my youth in the Solomon Islands that had taken up residence in a spent WWII rifle cartridge)

Polyrhanis dabraensis is a beautiful tiger beetle from Western New Guinea that was recently described by Andrey Matalin and Fabio Cassola. The insect fauna of this region is fairly poorly known, but the tiger beetles are doing fairly well for themselves. A total of 64 species are known from the region, though undoubtedly more are yet to be discovered. A list of the known species is available on the Website of the Papua Insects Foundation, which also includes images for a select number of species.

Picture courtesy of the Korean Society of Applied Entomology, Taiwan Entomological Society and the Malaysian Plant Protection Society.

References

Matalin AV, Cassola F. 2012. A new species of the genus Polyrhanis Rivalier, 1963 (Coleoptera: Cicindelidae) from Papua (New Guinea, Indonesia). Journal of Asia-Pacific Entomology 15(1): 196-199.

Bishop Museum Occasional Papers

I thought that I had blogged here before regarding the availability of the Bishop Museum Occasional Papers; but it seems that I was mistaken. Suffice to say, the Bishop Museum is in the process of digitising the issues of BMOP and making them available online. It is actively occuring—today I was able to see a few articles that were unavailable previously. The Occasional Papers and pretty much everything published by the Bishop Museum form a immensely valuable body of knowledge for South Pacific biology; and it should be considered a first port-of-call for anyone keen on the fauna and flora of the region.

Moorean Insects on Flickr

The Moorea Biocode is an ambitious project that aims to DNA barcode every organism on the island of Moorea in French Polynesia.The project has an online database with records of the specimens collected thus far, many of which contain photographs (e.g. the weevil gallery). There's also a Flickr stream that have a number of nice photos, including the beautiful Cranopoeus pictured above, and a cool-looking Proterhinus.

Unfortunately, it's still a little to early to really see the benefits of the project. The DNA sequences are not yet available (as far as I can tell); and many of the photos above are unidentified, or worse, misidentified at the family level. The project has great potential, but we'll have to wait a little while longer before the above resources become really useful for South Pacific zoology.

Picture courtesy of the Moorea Biocode Flickr stream

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}
}{}%