Friday, 27 July 2012

PhD week 21: Farewells

Danio from India
Not-so-gratuitous picture: cyprinid fishes in the genus Danio from India. Courtesy of the Biodiversity Heritage Library. Licence: CC: BY-SA-NC.

It is a sad fact of the academic life that one has to be a mercenary to one extent or another. Jobs tend to be few and far between, particularly when one becomes extremely specialised in a particular field. This requires that if you're wanting to work as a scientist, you need to be willing to move to where the jobs are.

This week we farewelled two people who had done their PhDs here at Lincoln and who are starting postdoctorate positions in two very different parts of the world. One is heading to the Czech republic to study weeds, while the other is heading to Manaus in Brazil to study fish. Both have been good people to have around, and they will be missed.

Of course, one of the benefits of this diaspora is that one ends up knowing people in all sorts of places. Brazil and the Czech republic have just become that much higher on our list of places to visit sometime.

   Morin A, Urban J, Sliz P. 2012. A quick guide to software licensing for the scientist-programmer. PLoS Computational Biology 8(7): e1002598
   Pratchett T. 2011. Snuff London: Corgi
   Psalms 86–89

E-utilities Quick Start
Bug report on Clementine interfacing with iPods
Psychological Statistics—The aesthetics of error bars

Leo Tolstoy—War and Peace Book 1 LibriVox audiobook
Per Landgren—Natural History: from Aristotle to Linnaeus - Influences on the Early Modern Relation between the Bible and Science
William Carrol—Creation and Contemporary Science: The Legacy of Thomas Aquinas

Star Trek: Deep Space Nine Season 5

Wednesday, 25 July 2012

Systematics of South Pacific sap beetles

Carpophilus maculatus, Carpophilus cheesmani and Carpophilus oculatus
The species of Carpophilus of particular interest: dorsal habitus above, male parameres below.

Two and a half years ago, I completed my MSc looking at the sap beetles in the genus Carpophilus. In particular, I looked at the C. oculatus species complex from the South Pacific. The species was first described in 1864, before it settled into obscurity. It was only mentioned a few times in the literature until 1993, when Ron Dobson published the results of a study where he looked at a large series of the species. He described three subspecies, two of which were widespread and sympatric, while the third was confined to Vanuatu. Another species, C. maculatus is rather similar in appearance, to the extent that questions were being raised as to the validity of the taxon complex.

My task was to look at this group using molecular methods. In particular, I used three genes to investigate the relationships between these four taxa, and any other species of Carpophilus I could get my grubby hands on. I found that C. maculatus is indeed a distinct species from C. oculatus, and also found sufficient evidence to warrant raising the subspecies from Vanuatu to a full species. The other two subspecies, while being somewhat distinct, did not form entirely separate groups, which suggests that something interesting has happened in the genetic history of these taxa. It was a successful and enjoyable project, and I am proud to say that I completed my MSc with first class honours.

So far, so good. However, the currency of modern academia is peer-reviewed publications. The preparation of manuscripts is an arduous process, and over the past two years the one describing the aforementioned research has been languishing on various people's desks (mine, mainly). In the past month though, it been brought into the light of day and has been published in Molecular Phylogenetics and Evolution. Check it out! If you don't have access to it, feel free to email the author.

Brown SDJ, Armstrong KF, Cruickshank RH. 2012. Molecular phylogenetics of a South Pacific sap beetle species complex (Carpophilus spp., Coleoptera: Nitidulidae). Molecular Phylogenetics and Evolution, 64(3), 428–440

Tuesday, 24 July 2012

PhD week 20: Auckland

Auckland War Memorial Museum
Landcare Research Auckland
The Auckland War Memorial Museum (top) and Landcare Research (bottom)

I spent the past week in Auckland visiting two of the major insect collections in New Zealand, namely the New Zealand Arthropod Collection (affectionately known as NZAC) housed by Landcare Research, and the Auckland Museum. Both these collections are nationally important, and a visit to these insitutions is vitally important for anyone studying the insects of New Zealand in any depth. I spent five happy days immersing myself in getting a better understanding of the genera of NZ's broad-nosed weevils and going through the unsorted Irenimus in the collections. A bigger job than it sounds! I returned to Christchurch with just short of 1000 specimens to look at over the next few years. That should keep me occupied for a decent amount of time. My time up there coincided with the arrival of Steve Davis, a fellow weevil-man who is visiting NZAC for a time. It was great meeting him, and discussing methods, characters and aspects of the New Zealand weevil fauna.

In addition to spending time doing work, I was also able to enjoy spending time with family, viewing the Wildlife Photographer of the Year Exhibition at Auckland Museum, going to a hardcore show featuring Terror and Antagonist A.D., dancing tango at Cafe Limon, and having dinner at Father Ted's Irish Bar with Steve. A good balance, methinks.

   Pratchett T. 2011. Snuff. London: Corgi
   Psalms 81–85

Tuesday, 17 July 2012

PhD week 19: Dissections

Image of Rhabdoscelus obscurus male genitalia, from Sharp and Muir (1912). Courtesy of the Biodiversity Heritage Library. Licence: CC: BY-SA-NC.

As part of the process of undergoing a taxonomic revision of an insect group, it is important to consider the internal anatomy of the organisms in question. In particular, characteristics of the male genitalia are especially useful for differentiating between species, and for ascertaining relationships between species. For an example of how differences in genitalia can be more obvious than external characters, check out the beautiful leaf beetles Spilopyra sterlingi and S. sumptuosa (compare figures 5 vs 6 and 82 vs 84).

One of the pioneers who investigated insect genitalia in a taxonomic context was David Sharp, who in conjunction with his son-in-law Frederick Muir, published a nearly 200 page monograph that spanned the breadth of beetle diversity. It took several decades for the technique to take hold, but these days, if you have a look at any of the insect taxonomy papers in Zootaxa or Zookeys, it is likely that you will find that these characters have been used in that research. The problem with the technique is that is holds no relevance to readers who are not familiar with the taxon, but for those who are these drawings are frequently the most useful part of the paper.

The process of insect dissection is fairly straightforward—soften the insect, remove the abdomen, open it up to reveal the structures of interest, and then tease them out. Doing it on a creature that is around 3 mm can be a bit challenging. Like everything, the process is fairly intimidating at first but as one becomes more comfortable and skillful at the technique, it quickly becomes a simple routine that is done rapidly and easily. Of course, once the data is collected, it then has to be interpreted! However, that is a story for another time.

Reid CAM, Beatson M. 2010. Revision of the Australo-Papuan genus Spilopyra Baly (Coleoptera: Chrysomelidae: Spilopyrinae). Zootaxa 2692: 1–32
Sharp D, Muir F. 1912. The comparative anatomy of the male genital tube in Coleoptera. Transactions of the Entomological Society of London (3) 477–642

   McCulloch D. 2010. A History of Christianity: The First Three Thousand Years London: Penguin
   Psalms 77–80

Fitting models to discrete characters
Wikipedia—Vernier scale
Wikipedia—Gloria Patri
Systematics and Biogeography— the blog of David Williams and Malte Ebach

Star Trek: Deep Space Nine Season 4

Friday, 6 July 2012

PhD week 18: Sickness and admin stuff

Paussine beetles
Gratuitous picture: illustrations of paussine beetles from the
Biodiversity Heritage Library Flickr Photostream. License: CC: BY-SA-NC

The start of this week was disrupted by both me and my wife being somewhat ill. Thus, Monday and Tuesday was spent at home, convalescing over multiple hot drinks, keeping warm, generally trying to keep each other's spirits up, and watching far too much trashy TV. Started coming back into work on Wednesday, but didn't really manage to get much momentum, instead spending time doing various administration-type things. I did manage to spend some time in the collection this afternoon, which was useful for clarifying some ideas about morphological characters, but in terms of hard-core research, unfortunately that's been it for this week.

   McCulloch D. 2010. A History of Christianity: The First Three Thousand Years London: Penguin
   Psalms 73–76

CERN press release regarding the Higg's boson
Rule of St Benedict
Wikipedia—Andrei Rublev, Iconographer
Commentary on Rublev's Icon of the Trinity

A Game of Thrones audiobook read by Roy Dotrice

PhD comics—The Higgs Boson explained
Evolution according to Prometheus
Planet Dinosaur
Star Trek: Deep Space Nine Season 4