Monday, 30 August 2010

German Beetles

In addition to having a superb gallery of photos of a huge number of weevils (see one of my previous posts), Christoph Benisch and colleagues have been displaying a featured beetle every week. In addition to having a typical beauful photo of the chosen insect, it is accompanied by a short note on its biology, distribution and lifecycle. Many of the species are endangered and rarely found, while others are strange or unusual in other respects.

Biomolecular Graphics

A recently published article in PLoS Computational Biology is one by Cameron Mura and colleagues that discusses the great potential held by biomolecular graphics. It discusses the terminology, tools and how to go about teaching yourself the basics. While it is very biochemistry-focussed, the highlight of the paper "Box 2: Nine Simple Rules for Biomolecular Graphics" present some very useful hints to guide any scientific illustrator.


Mura C, McCrimmon CM, Vertrees J, Sawaya MR. (2010). An Introduction to Biomolecular Graphics. PLoS Computational Biology 6(8): e1000918. doi:10.1371/journal.pcbi.1000918

Tijdschrift voor Entomologie

Tijdschrift voor Entomologie is the Journal published by the Netherlands Entomological Society. The society has a bit of a heritage---it was founded in 1845, and has remained in action since. The Journal itself is has open access to PDFs of all papers published from 1998 until two years ago. Volumes published before 1923 are available at the Biodiversity Heritage Library.

This clearly illustrates what I think is a growing trend. Literature published since 2000 can generally be easily found online. The same goes for literature older than 1925---there's a good chance it's on BHL. However, it's actually fairly difficult to find the literature published in the period in between (i.e. 1925--2000). No doubt this will change as the sliding window of Copyright slowly moves over this time period. In addition, I think that some societies and publications are starting to fill this gap of their own goodwill, which is excellent also.

Friday, 27 August 2010

Speech recognition in Linux

Whenever I'm looking at specimens under the microscope and noticing differences, I find it very difficult to stop what I'm doing, look at a bit of paper, and write it down. I'd much prefer to talk about it while looking at the specimen.

The first solution is to record yourself while talking. Audacity is a free, open-source music editing program that is pretty decent. I don't know how useful hard-core sound engineers would find it, but it's not bad for the application that I'm wanting to use it for, namely, recording my voice while I waffle on about what a specimen looks like. I could then listen to the recording repeatedly and transcribe what I say. More efficiently though, I'd be keen for some sorta sound recognition software a la Dragon NaturallySpeaking. NaturallySpeaking is the biggest-selling voice recognition software, and by all accounts it's pretty good. It does require some coin though, so I'm looking for less expensive, preferably open-source programs.

Unfortunately, it doesn't seem like there's much out there. A wikipedia page is a good entry point to the problem. Apparently one of the biggest issues is the lack of a voice database to test algorithms on. To solve this issue, VoxForge has been set up to encourage people to upload recordings and to work on the problem. The Ubuntu Wiki also has a page giving a bit of a road map of what Ubuntu want to see done. It looks like it might be a good project to start working on.

Monday, 23 August 2010

Crosby Codes

Entomologists with any interest in the New Zealand fauna will no doubt have come across the two-letter codes affectionately known as "Crosby codes". These codes denote geographical regions in New Zealand and are used for the purposes of grouping and retrieving specimens. They are named after Trevor Crosby, the lead author of two papers in 1976 and 1998 where these codes were defined. The 1998 paper expanded the codes to include New Zealand's offshore islands, and includes written descriptions of the boundaries between each region.

The codes have proved to be very useful in the entomological context, and have also been used in many other fields where the distribution within New Zealand is important.


Crosby TK, Dugdale JS, Watt JC. 1976. Recording specimen localities in New Zeland: an arbitrary system of areas and codes defined. New Zealand Journal of Zoology 3:69 + map.

Crosby TK, Dugdale JS, Watt JC. 1998. Area codes for recording specimen localities in the New Zealand subregion. New Zealand Journal of Zoology.25:175-183

Friday, 20 August 2010

Phylogenetic trees online

The other day, an article was published in PLoS One describing a newly developed JavaScript library to visualise phylogenetic trees online: jsPhyloSVG. It's pretty nifty, and there's some pretty cool functionality that you can build into the trees. It's all based on the PhyloXML standard for describing phylogenetic trees and networks, but can display trees stored as other formats, in particular the common NEWICK format. The resulting files are viewable in any web browser, though Internet Explorer is dragging the chain a bit and does not yet support the full interactivity that other browsers are capable of.

It would be real cool to be able to export trees made and manipulated in R into PhyloXML format, and subsequent into PhyloSVG. Might be a fun project to work on when I've scraped some other things off my plate...


Smits SA, Ouverney CC. (2010). jsPhyloSVG: A Javascript library for visualizing interactive and vector-based phylogenetic trees on the web. PLoS ONE 5(8): e12267. doi:10.1371/journal.pone.0012267

Vanuatu Birds Website

Buff-bellied Monarch Neolalage banksiana
While reading the paper on white-eye blood parasites, I noticed a link to the VanBirds website. It is an incredible website, and an excellent resource for both casual bird watchers and serious ornithologists. It has photos of many of the bird species found in the archipelago. In addition, it has recordings of the calls of many of the species also. Most importantly though, the website collates records of birds throughout the archipelago and displays them on a map as shown by this map of the distribution of the Vanuatu endemic flycatcher, the buff-bellied monarch (Neolalage banksiana, pictured above). It appears to be well-maintained, being last updated on the 25th of May this year.

This website is very impressive and is a highly valuable resource for the ornithology of Vanuatu. It is all the more remarkable, as it appears to be very much a grass-roots type effort and claims to have had no external funding thus far. It would be awesome to see more sites like this spring up for the other Melanesian island groups.

Monday, 16 August 2010

Featured insect: Pantorhytes plutus (Coleoptera: Curculionidae)

The weevil genus Pantorhytes is a large genus placed in the tribe Pachyrhynchini in the subfamily Entiminae. It consists of over 74 species found primarily in New Guinea, but also being found in the Solomon Islands and Queensland. The species pictured here, P. plutus is found in the Bismarck Archipelago. A map showing the distribution of specimens in the Australian National Insect Collection (see here also) can be found here

Pantorhytes plutus and a number of other species in the genus have become major pests of cacao trees, particularly in PNG. All the species have fairly limited ranges, such that P. szentivanyi, P. albopunctulatus and P. healyi are pests in the Northern Province of PNG, P. torricellianus is a problem in the Sepik region, P. plutus through the Bismarcks, and P. biplagiatus through Bougainville and the Solomon Islands. The genus has had a surprisingly large amount of study done on their biology, including egg development, and control. A couple of studies have looked at their dispersal, including one study that used a radioactive isotope tracing technique, which provided theoretical insight into mathematical models of insect dispersal. A parasitic wasp, Pristocera rufa is known to parasitize P. szentivanyi, though not to such an extent as to be a reliable biological control agent.

They are such a threat, they have made it onto a page detailing the world's worst cocoa problems (though I cannot find any other evidence that Pantorhytes are in Tuvalu), and accordingly there's been a number of studies dealing to their control (such as this one and this one).Biopesticides, including Beauveria bassiana have also proved to be of use in their control. A photo of an infected beetle is shown above.

A circular detailing their control in the Solomon Islands recommends using ants as a form of biological control. Unfortunately, two of the species they recommend for this control are the yellow crazy ant (Anopolepis gracilipes) and the little fire ant (Wasmannia auropunctata). Both these species are highly invasive generalist predators and scavengers which have adverse effects on more than just Pantorhytes weevils in cacao plantations. Should they already be present in the area, their use as a control agent may be encouraged, but they should NOT be introduced anywhere for that purpose if they aren't already there.

Gressitt JL. 1966. The weevil genus Pantorhytes (Coleoptera) involving cacao pests and epizoic symbiosis with cryptogamic plants and microfauna. Pacific Insects 8(4):915-965.
Setliff GP. 2007. Annotated checklist of weevils from the Papuan region (Coleoptera: Curculionoidea). Zootaxa 1536. 296pp.
Stibick JNL. 1978. The genus Pantorhytes (Coleoptera: Curculionidae) Division A. I Addistions and changes to the common and major cacao species. Pacific Insects 18(3&4):115-136.

Sunday, 15 August 2010

Downloading DNA sequences into R

A while ago, a friend of mine needed to download a number of different DNA sequences from Genbank, the online repository for the vast majority of DNA sequences read from all organisms by labs all over the world. This is not a problem. The "ape" package in R has a nifty function, read.GenBank(), that downloads the sequences identified by the accession numbers given to the function into a DNAbin object. Thus, read.GenBank("AY883003") downloads the sequence AY8833003, the internal transcribed spacer 2 gene for Anthonomus grandis, the cotton boll weevil. read.GenBank() is able to read a vector of accession numbers, making easy to download a lot of sequences if you're willing to give it the time.

All well and good. Unfortunately, the base function returns only the accession number as the name of the sequence. My friend was downloading sequences of many different genes from several different species. Understandably, mere accession numbers are not particularly helpful in this situation, and more information is helpful for processing datasets such as this. Thankfully, a quick hack of the function ensured that species and gene region info could be downloaded with the sequences, solving the problem. It also extended the function's utility significantly and in my opinion is now much more useful for phylogenetics-type work.

The resulting function is read.GB(). It currently reads the "ORGANISM", "DEFINITION", and "ACCESSION" fields of Genbank files which record the information regarding species identity, gene region and accession number respectively. These are stored in the resulting DNAbin object as an attribute, and can be returned in the following manner:

attr(a, "species")
attr(a, "gene")
attr(a, "accession_num")

The current default names for the sequences are returned in a standard format: accession number|scientific name.

Full credit goes to Emmanuel Paradis who wrote the original function, and who wrote it in such a way that it was fairly painless to extend it in the manner above.

Saturday, 14 August 2010

Pacific Disaster Network

The Pacific Disaster Network is a website devoted to the monitoring of natural disasters within the region and the dissemination of publications, reports and conference proceedings relevant to regional humanitarian efforts.

Its stated aim is to be:

the largest and most comprehensive information resource for Disaster Risk Management for the Pacific Island Countries.
The portal will provide a valuable resource to all Disaster Risk Management partners working in the Pacific region including government agencies, regional bodies, non-government organisations and international agencies.

The website displays alerts of natural disasters, has a LOT of publications and reports of relevant to natural disasters, public health and agricultural issues. It is a fairly exhaustive site, but unfortunately one that is fairly unintuitive to use(for me at least..) at first glance. Exploring it further reveals more of its power and utility. The homepage leads with a satellite map from Google and a box giving the latest alerts, giving the promise that the location of these alerts will be visualised. Unfortunately this is not the case; a pity for people like me who like to be able to see where events are occuring on a map.

The website is a collaboration between the South Pacific Applied Geosciences Commission (SOPAC), the United Nations Development Programme (UNDP), the International Red Cross and the UN Office for the Coordination of Humanitarian Affairs (OCHA).

Monday, 9 August 2010

Zookeys and Cybertaxonomy

Taxonomy is changing... Rather, the way that taxonomy is done is undergoing large shifts from the traditional way thanks to the advent of the internet. A recent Zookeys special issue published a couple of forum papers showing how data presented online in Scratchpads can be nigh-on automatically converted into a publishable document in Zookeys.

While my previous comments on Scratchpads were less than complementary, this application of them is pretty cool. Whether or not it will completely streamline the process of publication more than the usual is another question, but it will be interesting to see.

Tonga Science Network

In a collaboration between the University of Canterbury and the Tongan Ministry of Education, a new website has been launched: the Tonga Science Network. This website aims to promote and help disseminate science that is relevant to Tonga's environment and economy. Researchers are invited to register on the website and contribute content to smooth the flow of knowledge back to those who need to use it. Another cool feature is the "connections" that shows who has worked with who, and encourages the formation of new collaborations.

All in all, it's a neat initiative and hopefully will resolve one of the major issues I see with science in the Pacific, namely that most research is done by foreigners. This in turn means that relatively little of the results (despite the best intentions of most researchers) is returned to interested parties within the country, other than by laborious and ongoing literature searches. As with all community-type initiatives, it will only be as good as those who use it. It's made a good start though, and here's hoping that will continue.

Wednesday, 4 August 2010

NZ Scholarships for Pacific Island Students

Good news for those Pacific Island students wanting to study in New Zealand. John Key has just announced that the number of scholarships available to Pacific Islanders will increase from 100 to 200 next year. These include full scholarships as well as a deal where students will be given a student loan that will be written off if they return to their country of origin. The scholarships will be administered by NZAID. Those currently offered can be seen on their scholarships page.

Read the article in the New Zealand Herald here.

Tuesday, 3 August 2010

Houseflies of New Caledonia and Vanuatu

Musca domestica
Over the past couple of months, Marcia Couri and colleagues have published two monographs on the Muscidae of New Caledonia and Vanuatu. These two papers describe six new species with nine other species recorded from the region for the first time. The world-wide house fly Musca domestica (pictured here) is newly recorded from a number of islands throughout Vanuatu.

These papers are important additions to our knowledge of Melanesian flies. They give keys and diagnoses for the genera and species found in each archipelago, and give comments on the wider distribution of the flies found. Unfortunately, there are few illustrations, limited to line drawings of taxonomically important structures of the newly described species. While this may limit their utility to users who don't already have some familiarity with the group, these paper effectively summarize the housefly fauna of the region and provide a good basis for the further study of this important group.

Couri MS, Pont AC, Daugeron C. 2010. The Muscidae (Diptera) of Vanuatu. Zootaxa 2556: 1–39
Couri MS, Pont AC, Daugeron C. 2010. The Muscidae (Diptera) of New Caledonia. Zootaxa 2503: 1–61