Sunday, 27 November 2016

Cook Islands Insect Expedition: Funding Granted!

Satellite image of Rarotonga, Cook Islands. Image via Wikimedia Commons. Licence: Public Domain.

As the tagline of this blog suggests, I have a profound interest in the biota and people of the South Pacific. I was fortunate to spend an influential part of my childhood in the Solomon Islands, then managed to work on beetles across the South Pacific for my MSc research. Since I've moved on to studying weevils, I've been very keen to contribute to a greater knowledge of the weevil fauna of the Pacific; but until now I haven't had the financial support, nor a topic that is simultaneously ambitious enough to be useful but also achievable.

The Cook Islands caught my eye about a year or so ago, when I realised that the weevil fauna of the group was essentially unknown. What little was published usually didn't get beyond a mention of "Rarotonga" or "Cook Islands" in the Distribution section of a species account in papers that had a different geographic focus. The superb Cook Islands Biodiversity Database lists 35 species of weevil from the Islands, which included several undescribed species and unidentified taxa. Further investigation of the literature revealed that it wasn't just the weevils that were barely known from the Cooks—few collecting expeditions have been undertaken, and not many insect taxa have published data available.

Holotype of Ptilopodius aitutakii Beaver and Maddison. One of two weevils described from the Cook Islands. Image courtesy of Auckland Museum. Licence: CC: BY.

This lack of knowledge surprised me, given the Cook Islands' strategic location in the South Pacific. Being approximately halfway between Samoa and Tahiti, it's in a key position to test hypotheses of the cause of the eastward attenuation of species richness and diversity that is such a feature of the biogeography of the South Pacific. Much has also been made of the fact that several taxa find their eastward limit around Samoa and Tonga, without having data from Niue or the Cook Islands to ascertain if this eastward limit is truly the case or not. A comprehensive work on the weevils of the Cook Islands would be able to confirm or refute some of these ideas of distribution of species in the South Pacific.

The small size of the islands made them attractive too. Rarotonga, the largest and highest of the group, is still only 62 km2 in area and 650 m at its highest point. Not too much time (in theory at least!) would be required to make comprehensive collection in the available habitats.

The combination of the geographic location of the Cook Islands, and their small size lets me predict that weevil fauna will be fairly small and depauparate. I'm expecting that the total number of species will be around 200 or so. This is also beneficial, as it gives me hope that I may be able to write up the results of any collecting done in a timely and efficient manner. Additionally, although I expect a lot of the species to be endemic to the Cooks, the genera they represent are likely to be widely distributed, which would result in this work giving me a good foundation for further, future work on the weevils of other Pacific archipelagos

So there were the Cook Islands: small enough to collect everywhere in the space of a few weeks, an unknown fauna with a low number of species that could be written up in a short period of time and opportunity for first-hand experience with Pacific weevil taxa. In my opinion at least, this potential project held a lot of promise.

I am honoured that the board of the New Zealand Winston Churchill Memorial Trust considered it to have a lot of merit also. The trust funds overseas travel that bring New Zealanders into contact with other cultures, learn from their experiences and contribute to the community through their research and knowledge. Over 850 fellowships have been granted since the establishment of the Trust in 1965 and includes artists, educators, economists, academics and musicians. It's an impressive list of highly talented people and it's very humbling to be included among them.

The Trust has offered funding to cover two months in the Cook Islands, collecting weevils and other insects on Rarotonga, Atiu, Mangaia and Mitiaro. I expect it to be a great adventure, and one that I hope will prove productive and useful. I plan to go in March 2017, and intend to post semi-regular updates on aspects of the preparation for the trip, the expedition as it happens, and the aftermath of specimen sorting, preparation and identification. I very grateful that the Winston Churchill Memorial Trust has provided support for this expedition, and I'm excited about being able to make a significant contribution to our knowledge of the insects of the Cook Islands.

Thursday, 12 February 2015

Stereo microscope stage for insects made out of LEGO®

The IMps. Photo courtesy of Dupont et al via ZooKeys. Licence: CC: BY.

I loved LEGO® as a child. It's been a long, long time since I last played with it, but I think I've just found a project that will encourage me back into it. A group of entomologists at the Natural History Museum have developed some designs to create microscope stages (dubbed IMps) with two axes of movement out of LEGO pieces, and have released them to the world in a paper published in Zookeys. These microscope stages allow fine movement of specimens under the microscope, allowing one to precisely manoeuvre the specimen in order to see or photograph particular structures. The designs published by Dupont et al are an elegant, portable and cheap solution; with the added benefit of playing with LEGO.

References:
Dupont S, Price B, Blagoderov V. 2015. IMp: The customizable LEGO® Pinned Insect Manipulator. ZooKeys 481: 131–138.

Sunday, 16 June 2013

PhD week 67: 15 Month Report

Diplacodes trivialis—Today's picture of the day on Wikimedia Commons. Licence: CC: BY-SA.

One of the more critical pieces of administration that Lincoln University requires of PhD students is that at around 15 months after starting their studies, the student gives a presentation to a select group of academics, including the student's supervisory team. This presentation explains what progress has been made to that point, what problems had been encountered, and what the plan is from that point onward. It's a process that is designed to identify problems fairly early in the piece and to revise the scope of the study where everyone has a bit more of a realistic view than in the proposal stage.

This past week, I had mine. I didn't find it particularly arduous, and the general consensus was that I was doing fairly well. A couple of concerns were raised, mainly around timing of certain aspects of my research, and encouraging that I clarify the exact questions in one of my objectives. I found it encouraging, looking back over the past 15 months, and comparing what I said I would do with what I've actually done. Happily enough, I wasn't too unrealistic in most of my proposals, but there are a few aspects which I haven't done to the extent that I would've liked. The timing of the report was a little annoying, as it took time away from other things that I would've liked to have done, but overall I found the process to be a valuable one.


Websites:
American Hardcore: A Tribal History

Saturday, 8 June 2013

PhD week 66: LaTeX fonts

As part of my research, I will be making labels that indicate the type status of a number of weevil specimens. To create these, I have adapted my previous method of creating specimen labels in LaTeX to include a coloured background. The result of this is that I need to make the font on the labels bigger and bolder.

Unfortunately, because of the idiosyncratic way that I had established my fonts in the document, this ended up being not as trivial as checking out the TeX font catalogue. Instead I wanted to get an idea of what fonts were available on my system, and set about trying to create a font sampler of my very own.

While it wasn't difficult to get a list of the fonts on my computer (using the advice given at StackExchange), it became somewhat more tricky to get an idea of what they looked like. Attempting to compile a test document revealed two errors: The first was that some fonts could not be loaded:

"Font xxxx not loadable: Bad metric (TFM) file"
In addition, some that passed the first test, threw a second error when compiled by themselves:
"mktexpk: don't know how to create bitmap font for xxxx"

A quick email to the texhax mailing list quickly elicited some useful responses, including a very useful code fragment that gets around the first error. The second one was a little harder to overcome. Updating my map file (as suggested by another StackExchange post) didn't seem to do the trick, and messing around in the man pages of mktexpk and related programs didn't suggest any possibilities to one as unfamiliar with the programs as I am.

The breakthrough came when I had the realisation that I could extract the names of the fonts directly from the map file itself. Using this in conjunction with the code fragment mentioned above, I was able to get a document that compiled correctly when broken into three parts of c. 3000 fonts to get around size and space limitations.

I did encounter the error

"pdfTeX error: (file xxxxx.pfb): cannot open Type 1 font file for reading"
which I solved by manually removing the offending lines from the .tex document. There (thankfully!) weren't many of these, so this was not a particularly arduous step. If you try and replicate this though, you have been warned! If you figure out how to get around this, please let me know.

I used R (via Sweave) to extract the names of the fonts from the map file and to create the tex file. Undoubtedly other languages could do the same thing, but I chose to stick with what I'm familiar with. The file is available from gitHub


Websites:
PILN Soundbites
FAO report: Edible insects. Future prospects for food and feed security
Where to buy tango music
RSPB
NHBS: Relentless Evolution by John Thompson

Sunday, 2 June 2013

PhD week 65: DMHF

Male (left) and female (right) weevil parts mounted in DMHF.

The internal morphology of insects is a veritable gold mine of interesting characters. Obviously, in order to find investigate these characters it is necessary to dissect specimens. Unfortunately, this results in disarticulated beetle bits that one needs to store somehow in order to look at them again in the future.

The classic method of storing dissected materials is in very small vials that can be kept on the pin that holds the remainder of the specimen. This can be useful, but is a bit fiddly to remove the pieces from the vial when one needs to look at them again. In addition, it's become difficult to buy smaller glass vials, and I'm not a fan of the polyurethane vials that are readily available.

An alternative method that I've been exploring this past week is using the mounting medium DMHF. This mountant is soluble in water and dries crystal clear. The method that I've been using is to put a drop of DMHF on a card, immediately place the parts into the medium, add sufficient DMHF to cover the parts entirely, and leave for a couple of days to set. The card is then pinned below the specimen, and the parts are both protected and readily viewable (see picture above). I haven't tried it yet, but I understand that removing the parts is as simple as placing the card in a small dish of water and waiting a few minutes for the DMHF to dissolve.

A frustrating part of working with DMHF is that it forms a skin soon after exposure to air (c. 30 seconds). This skin can make it a little tricky to manoeuver pieces after placing them into the medium. After a little bit of experience though, one can usually get pieces in without needing to do too much messing around with them after the fact. I've had a positive first experince with the stuff, and am intending to carry on using it for the time being at least.


Websites:
Logic Matters
NetKnots—Tautline Hitch
Arctic Terns breeding in Netherlands migrate via Australia
LaTeX Stack Exchange: What fonts are installed on my box?

Listened:
Norma Jean—Disconnecktie: The Faithful Vampire

Watched:
Star Trek (Original Series) Season One

Saturday, 25 May 2013

PhD week 64: Canterbury Museum

Canterbury Museum. Image courtesy of acroamatic via Flickr. License: CC: BY-SA-NC.

One of the things that I love about doing what I do is going to insect collections I haven't been to before, and discovering what cool things they have in them. Last week I visited the Canterbury Museum to look through their weevil collection to see what specimens of Irenimus they had. In the process I was able to identify a number of previously unidentified specimens, as well as correcting a couple of errors that had been made previously. There's not many jobs that can make a priceless national treasure even more valuable. and I'm lucky enough to have one that does!


Websites:
Vatican Radio—Culture of Encounter is the Foundation of Peace

Watched:
Star Trek (Original Series) Season One

Monday, 20 May 2013

PhD week 63: Geographic data extraction

A natural part of the taxonomic process is the collection of distribution data. These can be useful for figuring out species limits, and for determining geographical areas where some interesting biology may be found. They can also be used with other geographic data to get an idea of the spatial patterns of species diversity, or for inferring the environmental preferences of a species—the subject of a field called environmental niche modelling or species distribution modelling.

Some of the different data that can be used include climatic information such as that available from WorldClim, geological data (e.g. GNS' QMAP), or composite datasets such as the Land Environments of New Zealand (LENZ) dataset.

A nice little summary as to how one can do this sort of stuff in R is given on the The Molecular Ecologist blog.


Websites:
Zegrahm Expeditions review of journey to Melanesia

Watched:
Star Trek (Original Series) Season One

Twelve weeks of Star Trek:
Star Trek Into Darkness