Friday, 26 October 2012

PhD week 34: Meetings, meetings, meetings

1911 Solvay conference

It was a short week, thanks to Labour Day on Monday. While it was nice to have a day off, it did make the rest of the week rather hectic. The frentic pace was not helped by my plans to be in the field all of next week. The trickiest part of the week was sorting out meetings with a number of different people. Figuring out a time that suited without interfering with plans to get some actual work done was a difficult task. However, I think I (largely) managed to do it, and had the privilege of having good talks with people on a range of subjects including website design, collecting localities in Central Otago, the need for students to understand data management, what to get a student to do over summer, and how my PhD is going.They haven't been as significant as the conference pictured above (The 1st Solvay Conference), but they've each been helpful and enjoyable in their own way.

   Polkinghorne J. 1996. Beyond Science. The Wider Human Context.Cambridge University Press, Cambridge
   McCulloch D. 2010. A History of Christianity: The First Three Thousand Years London: Penguin
   Psalms 132–134

Natural History Museum—Beetle Blog
Papers Past—Tour of the Hon. W. J. Hall-Jones

Wednesday, 24 October 2012

PhD week 33: Going long

Diagram of the mitochondrial DNA genome of Drosophila yakuba
Diagram showing the arrangement of genes in the mitochondrial genome of Drosophila yakuba. This is the typical arrangement for insects.

Mitochondria are organelles in the cell that provide energy-carrying molecules that are used in other cell functions. They do this in a manner somewhat analogous to a hydroelectric power station by creating an electrochemical gradient across a membrane, then using this gradient to power a turbine that produces the molecules. It's a place where a lot of activity is happening, and it needs a repair crew immediately on hand to keep it running. For this reason, there is a small amount of DNA inside the mitochondrion that contains the vital proteins and RNA units that are required for optimal performance.

Because there are a lot of mitochondria in each cell, mitochondrial DNA tends to be easily amplified from a range of organisms, making mitochondrial genes the regions of choice for phylogenetic analyses. One gene in particular, cytochrome c oxidase subunit 1 (COI), has been earmarked as being the gene of choice for specimen identification or DNA barcoding as it is otherwise known. For both these reasons, I am keen to use this gene in my analyses of Irenimus relationships. However, I'm finding that this is more easily said than done. It seems that entimine weevils have a lot of variation in these genes, which makes them hard to amplify. One idea that I will be trying involves trying to amplify the 5000 base pair region between the 12S gene (which is often less variable between species) and COI. A schematic is shown above.

To assist in planning this endeavour, I am able to make use of the resources available on Genbank. Genbank is a repository for DNA sequence data collected by scientists around the world. One can use this data to get an idea of where might be good places to position PCR primers, which provide the starting points for amplification. Unfortunately, there are only two complete weevil mitochondrial genomes available on Genbank—For Naupactus xanthographus and an unidentified Sphenophorus species. In addition, there are partial genomes available for 26 other species. However, these partial genomes cover everything but the region that I'm wanting to use, so are rather uninformative for my purposes. It looks like my plan going forward is just going to have to involve going in blind.

   Mazur MA. 2012. First record of the tribe Eugnomini Lacordaire 1863 (Coleoptera: Curculionidae) from Fiji, with description of Pactola fiji sp. n.Zootaxa 3517: 63–70
   Psalms 130–131

Renaming files in Linux
Inkscape Manual—Patterns along paths
Wikipedia—The Planets
Half of all wetlands destroyed since 1900

Tuesday, 16 October 2012

PhD week 32: Steady as she goes

Royal spoonbill Platalea regia
Royal Spoonbill Platalea regia. From igor_nz's flickr photostream. License: CC: BY-NC-SA

The PhD journey involves boldly entering new and exciting territory, and discovering new techniques and methods of analysis. It also involves doing the same thing over and over again. This past week has involved more of the latter. Dissections, databasing and communication with colleagues—this week has had all three with abundance.

The above does not mean that the week was somewhat ho-hum. On the contrary, many of the dissections I made this week were on species and genera that I have little familiarity with, and it was great seeing the results and thinking about what it all means in the greater context.

   Polkinghorne J. 1996. Beyond Science. The Wider Human Context.Cambridge University Press, Cambridge
   McCulloch D. 2010. A History of Christianity: The First Three Thousand Years London: Penguin
   Teilhard de Chardin P. 1955. The Phenomenon of Man London: Fountain
   The Qur'an Surat 5: Al-Maaida via Zekr
   Psalms 127–129

Boops Boops—Self publishing "failed" thesis chapters on Figshare
Ask Ubuntu: Convert PDF to image

Monday, 8 October 2012

PhD week 31: Sorting

A bench of Irenimus. A portion of the specimens available to me.

One of the tricky parts of taxonomic research is to go from a mass of unsorted specimens to a nicely curated collection of putative species. When confronted by a collection of well over 1000 specimens, this task can be somewhat intimidating.

André Larochelle and Marie-Claude Larivière in their Fauna of New Zealand volume to the ground beetle tribe Harpalini present a helpful outline of the process they took in revising the group. In summary, it goes as follows:

  1. Borrow as many specimens as possible.
  2. Label the borrowed specimens with their collection of origin.
  3. Roughly group similar-looking specimens.
  4. Within these groups, subdivide further by geography
  5. Dissect a number of specimens from each of these geographic/morphological groups.
  6. Identify putative species and make drawings of dissection results.
  7. Make correlations between the results of the dissections and the external morphology.
  8. Photograph specimens.
  9. Describe the taxa
  10. Compare putative species with the type specimens of previously described species.
  11. Construct identification key
This list gives a handy guide to the way ahead. When broken down into jobs described above, the effort becomes somewhat less herculean.

Larochelle A, Larivière M-C. 2005. Harpalini (Insecta: Coleoptera: Carabidae: Harpalinae). Fauna of New Zealand 53: 1–160

   Polkinghorne J. 1996. Beyond Science. The Wider Human Context.Cambridge University Press, Cambridge
   Borg MJ. 2001. Reading the Bible Again for the First Time. HarperOne, New York.
   McCulloch D. 2010. A History of Christianity: The First Three Thousand Years London: Penguin
   Teilhard de Chardin P. 1955. The Phenomenon of Man London: Fountain
   Psalms 123–127

Ubuntu Community Help Forum—Webcams

Star Trek: Deep Space Nine Season 6

SPIDER makes the top 10 barcoding publications of 2012

In the recent Barcode Bulletin published by iBoL, our humble paper announcing the R package spider: Species identity and evolution made second on their list of the top 10 publications of 2012. Not bad for a side project!

Spider is available for download from CRAN, and R-Forge. Be sure to check out the spider website as well for a tutorial on the use of the package.

Brown SDJ, Collins RA, Boyer S, Lefort M-C, Malumbres-Olarte J, Vink CJ, Cruickshank RH. 2012. Spider: An R package for the analysis of species identity and evolution, with particular reference to DNA barcoding.Molecular Ecology Resources 12: 562–565.

Tuesday, 2 October 2012

PhD week 30: Epitimetes lutosus

Epitimetes lutosus Pascoe (Coleoptera: Curculionidae: Entiminae)

The best things always happen serendipitously. Over the past week I got asked to identify some weevils that had turned up in some pitfall traps set by one of the research institutes on the Canterbury Plains. They were Epitimetes lutosus Pascoe, a weevil that was described from Christchurch and by all accounts is endemic to the plains. It is represented in national insect collections by less than 30 species, and its larvae and biology are unknown.

A jar full of Epitimetes lutosus

I was pretty excited by this find and asked for more, if they managed to get some. I got a call a few days later saying they got some others, and if I could come and pick them up. I arrived to find the container pictured above—literally hundreds of specimens from a single agricultural field. Plenty enough for pinning, dissecting, extracting DNA, and generally essentially anything else one would require specimens for!

   Borg MJ. 2001. Reading the Bible Again for the First Time. HarperOne, New York.
   McCulloch D. 2010. A History of Christianity: The First Three Thousand Years London: Penguin
   Psalms 119–122

Huffington Post—Reef fishes of the East Indies Book release
XKCD—Click and Drag

Project 86—Wait for the Siren