Friday, 31 August 2012

PhD week 26: Half a year gone

Unidentified Irenimus species.

Well... six months ago I started my PhD. It's been a busy few months, writing my proposal, visiting to insect collections around the country, and going to Arizona to attend a workshop on weevil taxonomy. Happily, everything seems to be going to plan. I feel that I'm starting to have an idea as to what morphological characters I should be looking at in order to differentiate between species. I've got a feel for what the valid, previously described species look like. And I'm close to having most of my techniques sorted.

What will the next six months look like? I'll be doing field work over the next few months, focusing on the type localities of the previously described species. This will result in a large number of specimens which I'll be able to look at morphologically, as well as providing material for DNA sequencing. Work on both these aspects will hopefully continue progressing as well as they've begun, with the common species (at least) well characterised by the end of the year. I will have to start on an identification key to the species of Irenimus, though it will only be a rough draft at this stage of the game. I may also have a student help me with some behavioural/biological research that is related but secondary to the core questions of my PhD.

I won't need to be bored!

   McCulloch D. 2010. A History of Christianity: The First Three Thousand Years London: Penguin
   Psalms 105–107

David Winter—Code for Evolutionary Biology
OpenOffice community forum—File locked for editing
VII Southern Connection Congress
New Zealand Herald—Yachting: Only four challengers enter America's Cup

America's Cup World Series—San Fransisco 23–26 August 2012

Tuesday, 28 August 2012

PhD week 25: Databasing

Gratuitous image: Bizarre oriental brentid weevils. From left to right:
Arrenodes xiphias, Calodromus mellyi female, C. mellyi male, Ceocephalus forcipatus.
Modified from BioDivLibrary's Flickr Photostream.

The raw data for taxonomic research comes from specimens—parts of individual organisms preserved and held in collections as a perpetual record. In the case of entomological taxonomy, we tend to deal with whole organisms. This is not the case for everyone. It is not particularly convenient to preserve whole whales or trees, for example. Also, because insects are small, common and don't have vertebrae, large numbers can be collected and stored. This means that I am in the fortunate position of having many hundreds of specimens to look at, which will give me an appreciation of the variation that exists within and between species. The downside is that I have many hundreds of specimens to look at and manage.

A range of data can be obtained from these specimens, including geographic coordinates, details of morphological features and DNA sequences. To manage everything, I've given each specimen a unique number which serves as a data identifier. I have a spreadsheet into which I enter the geographic and morphological data for each specimen; and the DNA sequences are stored as a FASTA formatted file.

While some might argue that a relational database may be more suited for this sort of thing, I am content with the system at present. Because the focus is on specimens, as opposed to collecting events or other aspects involving multiple specimens, the spreadsheet is suitable. Having the unique specimen number also means that it should be fairly straightforward to migrate the data into a relational database if necessary.

Psalms 102–104

Public Domain Review
Inkscape books
A guide to Inkscape
Geometry and Postscript

Leo Tolstoy—War and Peace Book 2 LibriVox audiobook

Star Trek: Deep Space Nine Season 5

Monday, 20 August 2012

PhD week 24: Back home

Gratuitous image: New Zealand weevils. From left to right:
Stephanorhynchus crassus, Ancistropterus prasinus, Rhicnobelus rubicundus, Novitas nigricans.
Modified from images on BioDivLibrary's Flickr Photostream.

As enjoyable as my Arizona trip was, it's great to be home in every way with one exception. The weather. The past week in Canterbury has consisted of cold and foggy, overcast days with very little sunshine or clear skies, and the horrible Christchurch drizzle or 'chizzle' as we've begun to call it—light rain that's accompanied by a breeze that whips it into your face and cuts through your clothing—has never been too far away. A far cry from the hot, dry, sunny days that I had started getting used to in Arizona.

Thanks to the workshop and my visit to Auckland, I've been inspired to start doing more dissections, and to try and slide-mount whole specimens of disarticulated weevils. Thus, a lot of the week was spent organising laboratory space to do such things, and ordering appropriate tools for the job. It'll be a couple of weeks before I'm able to start actually doing making slide mounts or using my fancy new tools, but I'm looking forward to it.

   Fitzhugh K . 2006. The philosophical basis of character coding for the inference of phylogenetic hypotheses. Zoologica Scripta 261–286
   Vanin SA, Guerra TJ. 2012. A remarkable new species of flesh-fly mimicking weevil (Coleoptera: Curculionidae: Conoderinae) from Southeastern Brazil. Zootaxa 3413: 55–63
   Vanin SA, BenĂ¡ DC, Albertoni FF. 2012. Description of immature stages of Phelypera shuppeli (Boheman, 1834) with comments on natural history (Coleoptera: Curculionidae: Hyperinae). Zootaxa 3423: 45–60
   Psalms 100–101

Smithsonian guide to North American Mammals
Wikipedia—List of mammals of North America
Page ranges in awk
The Atavism—Measuring population differentiation in R

Wednesday, 15 August 2012

A method for subsetting FASTA files

I got back my first sequences for various Irenimus specimens this past week, and have created nice, clean contigs from the forward and reverse sequences. I've done this using FinchTV and Seaview, saving the results as a FASTA file with all of forward, reverse and consensus sequences for each specimen. Saving the data in this format has the benefit of being suitable for tracking through version control software, which means that every change I make to the file can be recalled. I'm only using one file for creating the contigs, but I'm using three gene regions, which will then need to be aligned with each other in the future. Thus, I need to have a method for subsetting my master document into smaller files with only those sequences from the same gene regions.

To do this, I have come up with a convention for naming the sequences I wish to use down the line:

From here, all sequences from a certain gene region can be retrieved using a little piece of awk magic. For example, all sequences from the 28S ribosomal RNA region (i.e. those starting with the line >28S|....) can be obtained by running the following code in the terminal:
awk '/>/{p=0};/>28S/{p=1} p' raw_sequences > 28S.fasta
A big thanks to for pointing out how this might be achieved.

Tuesday, 14 August 2012

PhD week 23: Arizona continued

Fijian baridine weevil
An unidentified baridine weevil from Fiji

I returned to Chirstchurch yesterday morning, after two very pleasant weeks in Arizona. One of the things that really struck me during my trip was how globalised the world is. Particularly pertinent examples include: Australian and New Zealand plants being the first things I saw when I arrived in Los Angeles; the apples we had for our lunches at the research station were from New Zealand, and looking at Fijian weevil specimens at Arizona State University.

A few of the other things that I learned in Arizona were:

  • Tell a good story with your research. Encourage people to want to become more interested in the group by revealing interesting biology, morphology, distributions etc.
  • Characters useful for identification may not be good for revealing relationships and vice versa
  • Get some good dissecting gear. I'll be doing a lot, so I shouldn't mess around with cheap alternatives when I have the option of buying better stuff. Fine Science Tools has been recommended to me as being a supplier of quality dissecting equipment.
  • Squirrels can be a lot bigger than I had realised

Overall, my time in the States was very enjoyable. I saw some amazing plants, animals and landscapes; and it was great hanging out with others who were enthusiastic and knowledgeable about beetles and the world in general. I have returned inspired and with new ideas and methods to try out. It was well worth the trip.

   Pine-Coffin RS (translator). 1961. The confessions of Saint Augustine Middlesex: Penguin
   Psalms 90–99

Hangman in R
Manu—Birds of Polynesia

Leo Tolstoy—War and Peace Book 2 LibriVox audiobook
Coldplay—Mylo Xyloto

The Hunger Games
The Billy T James Show

Sunday, 5 August 2012

PhD week 22: Arizona

Cave Creek Canyon, Arizona
The entrance to Cave Creek Canyon, Chiricahua Mountains, Arizona, USA.

Getting formal training in weevil systematics is rather rare. To date, most of my knowledge of weevils has been self-taught, or gleaned through discussions with other weevil people. So it happened, that when I heard that a workshop on weevil taxonomy was going to be held this month, I signed up like a shot.

Thus, I now find myself in southeastern Arizona, halfway through a week of learning about the weevil diversity of North America in the company of over 20 other keen people. These people include some of the most respected names in weevil taxonomy, the course being tutored by Bob Anderson, Nico Franz, Gregory Setliff, Anthony Cognato and Charles O'Brien. The workshop has involved a formal talks and demonstrations, field collections, and plenty of specimen identification and informal discussions about weevil biology, morphology and relationships.

The workshop is being held at the American Museum of Natural History's Southwestern Research Station, situated in the Chiricahua Mountains of Arizona. The station is surrounded by oak/juniper woodland, and all sorts of amazing plants and animals are abundant within close proximity of the station. Thus far, I have seen squirrels, rattlesnakes, deer, bombardier beetles, tarantulas, solifuges, woodpeckers, and hummingbirds, all without trying too hard.

   Pine-Coffin RS (translator). 1961. The confessions of Saint Augustine Middlesex: Penguin
   Pratchett T. 2011. Snuff London: Corgi
   Psalms 90–95

Rise Against—Endgame
Sufjan Stevens—The Age of Adz

Star Trek: Deep Space Nine Season 5