Wednesday, 24 March 2010

Conservation Biology papers with a Pacific focus

The most recent (April 2010) issue of Conservation Biology has a number of papers which focus on the fauna, flora and environment of the South Pacific.

The issue starts off with an editorial by David Melick on economic schemes to negate carbon emissions. In particular he deals with the scheme to compensate landowners for NOT cutting down forests on their land (REDD) and the way this has played out thus far in the Papua New Guinea scene. He ends with this very pertinent statement:

... REDD will come to nothing if the system is not supported by the people who own and live in the forests. If the process is not rushed (it may take years, not months) and the PNG government is willing to accept international scrutiny and advice, forest governance and communitybenefits for the rural poor may finally be improved significantly...

Highly relevant for all who work in the South Pacific, particularly those of us with a western, productivity-based mindset. As the Mainland cheese ads say---Good things take time.

William Laurance and others discuss the impact of Oil Palm cultivation and some of the issues and opportunities surrounding it. In particular, they discuss the Roundtable on Sustainable Palm Oil (RSPO) a nonprofit organisation that hopes to promote and market sustainably grown palm oil. Unfortunately, its track record appears to be fairly poor. The seeming blind eye the organisation has taken toward the destruction caused by growing oil palm in peat swamps is singled out as being a major failing of the RSPO. however Laurance et al. refuse to be pessimistic about the situation and make some recommendations, most of which involve fairly major restructuring of the RSPO and developments in its monitoring and enforcement policies. However, the real problem in the situation is the lack of market demand for sustainably grown palm oil, meaning that the RSPO has little clout.

Alison Boyer revisits the very high extinction rate of Pacific Island birds, this time investigating what ecological traits seem to have an influence on extinction rate. She concludes that differences in endemism, body size and diet influence the potential for extinction and gives a list of bird species that may be worthy of a higher threat category than currently given.

Shankar Aswani and Armagan Sabetian look at the impact that urbanisation has had on the parrotfish population around Gizo and Munda, in the Western Province of the Solomon Islands. Not surprisingly, they found that over the period 2004--2005 parrotfish numbers decreased around Gizo. However, they did find that some customary management systems were effectively preserving larger and greater numbers of parrotfish. The most effective systems were those that prevented all fishing in certain areas.

Mayeul Dalleau and team looked at shallow marine habitats around Wallis Island and used digital imagery and habitat maps as surrogates for biodiversity in the proposal of marine protected areas. While they promote this method as being an effective and efficient of surveying large areas, they do recognise that it is very desirable to do some actual field work to complement the habitat data, particularly in regions such as the Red Sea which has a very different environment from the oceanic Pacific islands.

It's a good issue. Well worth a read, certainly if any of the above issues pique your interest.


Aswani S, Sabetian A. 2010. Implications of Urbanization for Artisanal Parrotfish Fisheries in the Western Solomon Islands. Conservation Biology 24(2): 520-530

Boyer AG. 2010. Consistent Ecological Selectivity through Time in Pacific Island Avian Extinctions Conservation Biology 24(2): 511-519

Dalleau M, Andréfouët S, Wabnitz CCC, Payri C, Wantiez L, Pichon M, Friedman K, Vigliola L, Benzoni F. 2010. Use of Habitats as Surrogates of Biodiversity for Efficient Coral Reef Conservation Planning in Pacific Ocean Islands. Conservation Biology 24(2): 541-552

Laurance WF, Koh LP, Butler R, Sodhi NS, Bradshaw CJA, Neidel JD, Consunji H, Vega JM. 2010. Improving the Performance of the Roundtable on Sustainable Palm Oil for Nature Conservation. Conservation Biology 24(2): p 377-381

Melick, D. 2010. Credibility of REDD and Experiences from Papua New Guinea. Conservation Biology 24(2): 359-361

Wednesday, 17 March 2010

Interrupting R processes in Ubuntu

It's funny how things happen. Yesterday I was working away on a project in R and the unenjoyable happens---the process hangs for longer than desired. I operate R in the standard GNOME terminal in Ubuntu and the only way I knew was to close the entire application getting rid of all objects at the same time. Not cool. Thirty minutes or more of fruitless searching gave no indication as to a better way of doing things and I was really wishing the ESC key worked as it does in Windows.

Checking emails this morning though, and I discover an exchange on R-help that goes through exactly what I needed to know... From these emails then I have discovered that:
  • Pressing Ctrl+C should work in the terminal.
  • If that doesn't work, open another terminal console and type
    ps aux | grep R

    kill -s INT PID
  • The first line allows you to discover the PID number of your particular R instance, which is then used in the second line.
  • In the second line above, INT may be replaced by HUP in some cases.
  • The above methods set up an alert-thing to tell the program to stop. When the computations are done externally of R, it can't be executed before the external codes checks back with R. If the external code doesn't do this regularly or at all, killing the entire program is the only way out. If none of the above work, this is probably what has happened and it may be a good idea to let the package author know about the problem...
Thanks to all involved in this exchange: Adam Kramer, Duncan Murdoch, Simon Urbanek, Matthew Keller and Ted Harding

J. O. Westwood medal for insect taxonomy

In 2006, the Royal Entomological Society established a prestigious award aiming to encourage insect taxonomy particularly revisionary work resulting in definitive monographs---the J. O. Westwood Medal for excellence in insect taxonomy. The award is given biennially and nominations for the 2012 medal are currently being accepted for papers published between 1 April 2009 and 31 March 2011.

The award honours John Obadiah Westwood (1805-1893), who was an influential British entomologist who was instrumental in establishing the Royal Entomological Society and was an original proponent of the use of type species for genera.

Since its establishment, the medal has been given out twice. Marianne Horak was the first recipient in 2008 for her work on Australian tortricid moths. This year's recipient is Art Borkent for his 2008 work on world fauna of the frog-biting midges (Corethrellidae), published in Zootaxa. Both recipients received glowing reports from the assessment panel including such phrases as "A monumental work ... absolutely exemplary" and "A true model for the taxonomic/systematic treatment of a taxon." Unfortunately, due to the nature of monographs, these tomes are big and expensive to publish which makes it difficult for those of us who want to learn from these masters to get hold of a copy of these papers and model our own work on them.

Congratulations to Art Borkent and, more belatedly, Marianne Horak for their superb achievements. While taxonomy may not be in most enviable of situations and despite the moaning of we taxonomists, publications and awards such as these demonstrate that it's not dead yet...

Borkent A. 2008. The frog-biting midges of the world (Corethrellidae: Diptera). Zootaxa 1804:1--456

Horak M. 2006.
The Olethreutine moths of Australia (Lepidoptera: Tortricidae). Monographs on Australian Lepidoptera Series 10:1--528, CSIRO publishing.

Wednesday, 10 March 2010

Featured insect: Platytenes occultus (Coleoptera: Curculionidae)

Last year, Gregory Setliff (of New Guinea weevil checklist fame) and Peter Larson described Platytenes occultus, a handsome, widespread and common weevil found throughout the Solomon Islands including Bougainville. Until this time, this species has been mistaken for Platytenes varius; until now the only known member of the genus. Platytenes varius is much more widespread, being found from Sulawesi, to New Britain and the Cape York Peninsula. These weevils are part of the subfamily Cryptorhynchinae which are found throughout the world. Most species localised in distribution and so the wide range of both Platytenes species is remarkable.

Both species of Platytenes are frequently found in association with the betel nut palm (Areca catechu) which is grown throughout the Solomon Islands, New Guinea and the Molluccan islands for its fruits which are chewed with pepper leaves and lime powder as a stimulant. This suggests that the wide range of these species may be due to human-mediated movement through the historic trade of betel nuts and palms within the region.

In keeping with typical cryptorhynchine development, the Platytenes species have been reared from wood. As yet, there are no records of specimens being reared from betel palm; rather they've been reared from Ficus and Nauclea species.

This paper is a well-described, thorough description of a very attractive weevil and one which may have some economic impact due to its (as yet improperly determined) association with betel nut palms. Gregory Setliff has already produced an essential checklist for anyone interested in weevils of the region, and this paper further confirms that he's someone to watch with great interest in anticipation of more great work such as this.

Setliff GP, Larson PA. 2009. The Indo-Australian weevil genus Platytenes Pascoe, 1870 (Coleoptera: Curculionidae: Cryptorhynchinae). Insecta Mundi 00-79: 1-14.

Monday, 8 March 2010

LaTeX insect labels

No, not labels made out of the sap of Hevea brasiliensis, but labels typeset using the LaTeX typesetting language---a very versatile and powerful language that typesets rather nice looking documents. I wrote my thesis using it and found the experience to be very enjoyable and rewarding.

Up until now, I've printed labels for pinned insect specimens using a Word template. This has been adequate, however I find there are two really annoying aspects of this method. The first is that you've got to try and count how many carriage returns you enter to centre a single-lined habitat label, and if you get it wrong it messes up the rest of the document. The other is making duplicate labels, the only way which I know how being to copy the label data and "Ctrl-V" it as many times as required, once again ensuring there's neither too much or not enough space between labels.

So, with the thesis out of the way, I've turned my attention to creating a LaTeX template to create insect labels from an A4 sheet of paper. It is available here: labels.tex. Hopefully it is relatively straightforward to work out when you read the file and comments contained therein. The size of the labels is based on those in the classic New Zealand guide to insect curation (Walker and Crosby, 1988). I just found out that this very useful reference is freely available online here. Thanks Landcare Research!

The guts of the file is as follows:

To get a really small font suitable for insect labels, the following commands are made:

\def\supertiny{\font\supertinyfont = cmss10 at 3.75pt \relax \supertinyfont}

\def\supertinyitalic{\font\supertinyfont = cmssi10 at 3.75pt \relax \supertinyfont}

\supertiny is declared after \begin{document} to make the text of the entire document miniscule. Unfortunately, \emph doesn't work correctly when you've modified the size in this way, so \supertinyitalic is created and turned into a function \scinm which converts text (usually scientific names) into italics.

Next up is creating an environment to make duplicate labels:

\loop\ifnum \value{speclabel@} < \value{speclabel@@}
The above code is modified from that available in etiketka.cls in the shipunov package. Each set of labels (both locality and habitat labels) are prefaced with \begin{speclabel}[5] where 5 in this case indicates that the contents of the environment should be duplicated five times.

Finally, we want to have each label of a consistent height. I achieved this by employing the tabularx package. However, the vagaries of the tabularx package made it easier to program it using two environments rather than working out how to make a single one do it all:



{& \makebox{\usebox{\BoxB}}

This is a bit clunky, but it works. Reasonably well at least. BoxB creates a table of fixed width that contains a strut which fixes the height of the label. Currently this is 8 mm. When hablabel is nested within lab_height the contents of hablabel is put into a cell in a table the height of which is defined by BoxB. When the contents of hablabel takes up less height than BoxB, the result is a whole bunch of nicely spaced labels. When it takes up more height, things are pushed around a little, but it doesn't break labels.

Here's an example of a fully typeset label:

Nina Valley Track\\
Lewis Pass\\
1 Jan 2009\\
SDJ Brown\\

{\scinm{Weinmannia}} leaves close to road.

You can see the end results here.

I'm not much of a LaTeX programmer and undoubtedly there are more elegant, powerful and useful methods of programming the above. However, this provides for my needs adequately enough. Hopefully others might find it of use also.

While trying to figure how to do all this, a search on Google for "latex insect labels" gave this humble site as the first on the list. I figure that the least I can do is actually make sure that it delivers on its promise...

labels.tex is now available on gitHub. The PDF showing the results can be downloaded from Dropbox.

Walker AK, Crosby TK. 1988. The preparation and curation of insects. DSIR Information Series 163. DSIR; Wellington.