PhD week 4: Publications and World Cups

Something exciting arrived in the university library this week. And no, it wasn't something geeky like a new book on weevils or phylogenetics. No, this was something other people could get excited about, and they sure did:

Yes indeed, that is the Web Ellis Trophy, the Rugby World Cup, of which New Zealand is currently the proud holder (not to crow about it though...).

There's a maxim in the academic world: "Publish or perish". Publication is essential for communicating the discoveries that you've made and the bit of the world that you've had a bit of insight into. There is also a lot of emphasis on using publications and the venues they're published in as a measure of your quality of the research you do and are carefully considered in hiring, firing, promoting and receiving grants. Publications are important.

They also take up a lot of time. Most of this week was spent dealing with various aspects of the publication process; from finishing and submitting a manuscript dealing some of my own research from before starting this PhD, to discussing our response to the reviews of a second manuscript on which I am a coauthor, to reviewing a third at the request of a publisher to give my opinion on how the paper may be improved before publication. There's a fourth manuscript that I need to have a look at for another journal that is lying on my desk, and which I won't get around to this week too.

While it occasionally feels like a waste of time, this process is what keeps science going. And with everybody doing their bit of the work, it gets spread fairly well. So, although this week was taken up with this aspect of doing science, I should be able to spend the next few weeks looking at some weevils, and doing some lab work which will get me going towards the next publication.

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Read:
Garonna AP, Dole SA, Saracino A, Mazzoleni S, Cristinzio G. 2012. First record of the black twig borer Xylosandrus compactus (Eichoff) (Coleoptera: Curculionidae, Scolytinae) from Europe. Zootaxa 3251: 64–68

Fletcher AC, Bourne PE. 2012. Ten Simple Rules for Starting a Company. PLoS Computational Biology 8(3): e1002439.

Wilkins JS. 2009. Defining Species. A Sourcebook from Antiquity to Today. New York: Peter Lang

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

Kirkpatrick R. 2009. Beyond the Wall of Time. Sydney: Voyager

Psalms 28–32

Listened:
National Geographic Music

Watched:
Dropkick Murphys—I'm Shipping Up to Boston

Star Trek: Deep Space Nine Season 1

PhD week 3: Francis Polkinghorne Pascoe

Taxonomy has had a long history, with the current system of naming organisms being proposed by Carolus Linnaeus in 1758. As you can imagine, the task of naming the world's biodiversity has engaged a large number of people throughout the past 250 years. As part of the process of identifying species and describing new ones, we come across the names of the people who have gone before and worked on the same creatures. Learning more about the lives of these people can serve practical ends, such as resolving when and where specimens may have originated from. Often though, it is simply very satisfying to learn more about the people who have been fascinated by the same subject, and makes one feel part of a story with a past and a future.

Portrait of Francis P Pascoe. Courtesy of the Royal Entomological Society via Zimmerman (1994).

Francis Polkinghorne Pascoe (1813–1893) was an English entomologist who was originally trained in the medical profession and served in the British Navy for a time, and travelled widely during this time. He returned to England and got married. It proved to be a tragically short marriage, and upon his wife's death in 1851 he devoted himself to natural history, focusing particularly on the taxonomy of beetles. He was fairly broad in this work, though he made particularly important contributions on the longhorn beetles and the weevils; and the fauna of Southeast Asia, Australia, New Zealand and the Pacific. He was made a fellow of the Royal Entomological Society, and was president of that prestigous organisation for a time.

He described a number of the genera of New Zealand weevils. Most importantly for me, he described Irenimus and its type species, Irenimus parilis. This species is important as it fixes the identity of the genus to those species that are similar to it. It will be an important addition to my collection.


References:
Zimmerman EC. 1993. Australian Weevils (Coleoptera: Curculionoidea). Volume III - Nanophyidae, Rhynchophoridae, Erirhinidae, Curculionidae: Amycterinae, Literature consulted. CSIRO, Australia

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Read:
Deans AR, Yoder MJ, Balhoff JP. 2012. Time to change how we describe biodiversity. Trends in Ecology and Evolution 27(2): 78-84

Wilkins JS. 2009. Defining Species. A Sourcebook from Antiquity to Today. Peter Lang, New York

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

Kirkpatrick R. 2008. Dark Heart. Sydney: Voyager

Psalms 22–27; 1 Corinthians 13

Websites:
Open DELTA project

Jon Chui—Pictoral guide to interpreting IR spectra

How to Interpret Near Infrared Spectra for a Variety of Applications

Stuff.co.nz—McMurdo Sound's toothfish population at risk

Stuff.co.nz—A helping hand for Hutton's shearwater

Tetepare: The last wild island

Listened:
Rvd Dr John Polkinghorne—An introduction to the science and religion dialogue (mp3 file)

Blindside—With Shivering Hearts We Wait

Watched:
Alaskan Audubon Society—Godwit Migration

Dispersal of crickets to New Caledonia

An eneopterine cricket in the genus Cardiodactylus. Photo courtesy of Guido Bohne

New Caledonia is one of the largest islands in the Pacific, being exceeded only by New Guinea, New Britain, and the main islands of New Zealand. Like New Zealand, the composition of the biota, which includes several relict groups such as the Amborella shrub and the Kagu (Rhynochetus jubatus), has lead many to believe that the island is a fragment of Gondwana, with a long biological history. Also like New Zealand, this story has been questioned in recent years by geological evidence that the island underwent submergence at various points in its history, and that the biota is a result of long-distance dispersal. Cue a classic dispersal-vicariance stoush that is a trademark of biogeographic discussion.

In the dispersal corner is Romain Nattier and coauthors, who present evidence of a "recent" arrival in New Caledonia of the eneopterine crickets. This subfamily of crickets have a wide range throughout several islands of the Pacific, South-East Asia and South America. Their analysis of four genes show that the New Caledonian eneopterine crickets are most closely related to species on other Melanesian islands, and that they've likely been in New Caledonia for "only" 5–16 million years. They then use this evidence to indicate argue against an ancient presence of New Caledonia.

I've got no quarrel with their conclusions regarding this group of crickets. The evidence for a recent arrival of these guys seems pretty clear. However, I do wonder why the authors chose this group of insects to test their hypothesis. The distribution of the non-New Caledonian species suggests that this group is fairly vagile. Their presence in archipelagoes such as Vanuatu, a young island group by most people's standards, hints at their dispersal ability. Much more convincing with regard to their New Caledonia drowning hypothesis would be one of the groups that is less likely to move around as much. Of course, with this criteria, the taxon of choice would be likely to be one of the relict species—which by definition are species poor and with few close relatives—leading to a biased outcome.

I was surprised that none of the Australian representatives were closely related to the New Caledonian crickets. An Australia–New Caledonia link is a fairly common pattern in New Caledonian biogeography, but it hasn't held up in this instance. I was also surprised by the sister-taxon relationship between a genus in Fiji and Samoa, and a couple of genera in Central and South America. Those sorts of relationships seem fairly strange, but not too much stock can be placed on it without knowing more details about the group, and the sampling regime used in the study.

As always, this is not the last word on the subject of the origin of New Caledonia and its biota. It isn't even the definitive on the evolution of this group of crickets. This is one piece of the puzzle that is New Caledonia's biota, and one that will illuminate further research on the natural history of the island, as well as being a valuable addition to the literature of eneopterine crickets.


References:
Nattier R, Robillard T, Desutter-Grandcolas L, Couloux A, Grandcolas P. 2011. Older than New Caledonia emergence? A molecular phylogenetic study of the eneopterine crickets (Orthoptera: Grylloidea). Journal of Biogeography 38: 2195–2209

PhD week 2: Weevil larvae

Unidentified broad-nosed weevil larva

This week, in addition to continuing to prepare my proposal (focusing primarily on comparative phylogenetic methods), I was able to spend a little bit of time looking at specimens of weevil larvae. Weevil larvae are legless grubs with few features that obviously distinguish different groups from each other. However, on closer (and patient!) inspection, there are a number of subtle features that enable the identification of many larvae to generic level. One of the questions I will be looking at is: can the larvae of different Irenimus species be differentiated from each other?

The key to any taxonomic work is familiarity—familiarity with both the organisms being studied, and with the methods used in the process. I haven't tried to identify larvae before, so this was my chance to get to grips with the process and characters involved. I was able to find a few larval specimens that I had lying around, and so I tried my hand at dissecting them and getting my eye in regarding larval morphology.

Conveniently enough, my introduction to weevil larvae went well. The process of dissection was straightforward, and I was able to navigate my way around the keys available fairly happily. Unfortunately, I was unable to properly identify the specimen shown above, but that's not too surprising given that only a small proportion of New Zealand's weevil larvae have been described. I also haven't yet got myself a microscope slide mounting procedure that I'm really happy with, so I haven't progressed on to that aspect of the work yet.

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Read:
May BM. 1993. Larvae of Curculionoidea (Insecta: Coleoptera): a systematic overview. Fauna of New Zealand 28: 1–226

Paradis E. 2006. Analysis of Phylogenetics and Evolution using R. 1st Edition. Use R! New York: Springer

Solodovnikov AY. 2007. Larval chaetotaxy of Coleoptera (Insecta) as a tool for evolutionary research and systematics: less confusion, more clarity. Journal of Zoological Systematics and Evolutionary Research 45(2): 120-127

Freckleton RP. 2009. The seven deadly sins of comparative analysis. Journal of Evolutionary Biology 22: 1367–1375

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

Kirkpatrick R. 2007. Path of Revenge. Sydney: Voyager

Psalms 18–21; Hosea 4

Websites:
Wikipedia—Thomas Burnet

Wikipedia—Charles Peirce

Coleoptera Poloniae—Database of Polish Beetles (includes photos)

Listened:
Madball—Legacy

Followed:
Cricket: New Zealand vs South Africa 2nd test match

Phylogeny of Pacific pigeons

Orange dove Ptilinopus victor. Picture courtesy of aviceda on Flickr

In the avifauna of the Pacific, pigeons rule. Considering the region as a whole, pigeons are one of the most widespread and speciose groups of birds in the area. In particular, the imperial pigeons (Genus Ducula) and the fruit doves (Genus Ptilinopus) are especially widespread, being found from South-east Asia to French Polynesia, and with most major islands having at least one endemic species. Despite this diversity however, South Pacific pigeons have tended to not be included in analyses of pigeon evolution as a whole.

To rectify this, Gillian Gibb and David Penny present a phylogeny estimated from a number of mitochondrial genes that includes 9 species of imperial pigeon, and 13 species of fruit dove (including the orange dove Ptilinopus victor shown above), along with representatives of a number of other pigeon genera. Australasia and Oceania have the bulk of the representation in this analysis—of the 25 genera represented, only 10 have no species in the region.

They found that the imperial pigeons are monophyletic (that is, they form a natural grouping) and are rather distinct from the remainder of the pigeons sampled. The fruit doves on the other hand are prevented from forming a natural clade by the presence of the cloven-feathered dove (Drepanoptila holosericea) of New Caledonia, and the blue dove (Alectroenas madagascariensis) of (you guessed it...) Madagascar. When you look at pictures of these two, it's not surprising that they might be fairly close to Ptilinopus. What is surprising though, is that these two species are resolved as being sister taxa, despite being so geographically distant from each other. This puzzle obviously requires rather more investigation.

References:
Gibb GC, Penny D. (2010). Two aspects along the continuum of pigeon evolution: A South-Pacific radiation and the relationships of pigeons within Neoaves. Molecular Phylogenetics and Evolution 56: 698–706

Interactive function for distances in plots

The following R function returns the distance between two points located on a plot. The distance returned is in the same units as that of the plot.

interDist <- function(x){
    aa <- locator(2)
    dx <- aa$x[2] - aa$x[1]
    dy <- aa$y[2] - aa$y[1]
    sqrt(sum(c(dx^2, dy^2)))
}

PhD Week 1: Irenimus and subalpine plateaux

The Denniston Plateau

The first weekend of my PhD was spent on the Denniston Plateau on the West Coast, doing nothing to do with my studies. I was there to participate in a BioBlitz organised by Forest and Bird to raise awareness about the plateau at the same time as finding more about the biota of the area. I focussed on weevils, as is my want, and had a very enjoyable couple of days in one of New Zealand's lesser-known environments. Probably the highlight for me was finding a couple of specimens of Icmalius abnormis a weevil which I haven't collected before and which is in a group on which I'm doing a little work on the side.

Icmalius abnormis

It was back to reality on Monday, and the week was spent doing work on my proposal. This is a document that outlines the intended course that the next three years of my life will take, and goes into some detail as to how exactly I will do what I intend to do. As you can imagine, the document will be rather lengthy, but the overall aim of my project is as follows.

Unidentified species of Irenimus

My PhD will involve looking revising the taxonomy of the New Zealand grassland weevil genus Irenimus. There are approximately 50 species in the genus, but their identification is very difficult, relying primarily upon descriptions written around 100 years ago. The larvae feed on plant roots, while adults feed on vegetation and pollen. Some species can be found in modified pasture, reaching pest levels in some situations. In addition, they are frequently found to be non-target hosts of parasitic wasps introduced to control other pest weevil species. There are a number of interesting ecological questions, such as their degree of host-plant specificity (especially larval host-specificity), what adults and larvae are feeding on in modified pasture, and what sort of parasitoids attack them. However, all of these questions rely on being able to identify the weevils with confidence and accuracy. This is the aspect that I will be focussing on over the next three years. I expect that it will be challenging, but I also expect that it will be enjoyable and am looking forward to seeing where this project will take me, how it develops, and how our knowledge of these creatures will increase.

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Read:
Marra M. 2008. Quaternary fossil beetles from New Zealand. New Zealand Entomologist 31:5–16

Stephens PA, Buskirk SW, Martinez del Rio C. 2007. Inference in ecology and evolution. Trends in Ecology and Evolution 22(4):192–197

Wild AL, Maddison DR. 2008. Evaluating nuclear protein-coding genes for phylogenetic utility in beetles. Molecular Phylogenetics and Evolution 48:877–891

The Atavism—Sunday spinelessness: How could I forget Phronima?

Carl Boettiger: Theoretical Ecology and Evolution—Is your phylogeny informative?

Scherer K. 2012. What good is religion anyway?. The Listener 3747

Psalms 13–17; Daniel 1

Followed:
Cricket: New Zealand vs South Africa 1st test match

Listened:
Gotan Project—Tango 3.0

Comback Kids—Turn it Around

Trigonopterus diversity in New Guinea

The weevil genus Trigonopterus is found in the islands of Indonesia, eastwards to Fiji and Samoa. There are around 90 described species, but thanks to the work of Alexander Riedel, the true diversity of the genus is becoming apparent. One of the latest works of Riedel and coauthors was published earlier this year in PLoS ONE, and describes how a DNA barcoding approach is helping to make sense of the group.

In this study, over 1000 specimens were collected from five broad regions of New Guinea. Initial sorting suggested that there were 270 species represented in this group with each area possessing an average of 41 species. After sorting, these specimens had their COI gene sequenced and analysed using a number of different methods. These analyses slightly increased the total number of species to 279, due to the presence of very similar-looking species being present in the sample.

The authors argue that when facing sorting through groups of greater than 50 species, it becomes inefficient to circumscribe them using traditional means. In these situations, DNA barcoding approaches can make the task more tractable and form a solid base for ongoing taxonomic research. In addition, they recommend that Trigonopterus form a key group for use in biodiversity assessment surveys within Melanesia.

This study shows how much there is to learn about the biota of Melanesia. Unfortunately though, the are resources available for researchers interested are relatively scarce. Additionally, most of the research done is by researchers based in places such as Europe and the States, with involvement by Pacific Islanders generally being limited to providing technical assistance. This paper is a case in point. While a 'man blo niu guinea' is a coauthor, he was not involved in the experimental design or in the writing of the paper; both valuable skills for success in science. Locally based scientists in the Pacific will continue to struggle until more funding becomes available from their governments, and they take opportunity to be involved in all parts of the scientific process from design to publication.

References:
Tanzler R, Sagata K, Surbakti S, Balke M, Riedel A (2012) DNA barcoding for community ecology—How to tackle a hyperdiverse, mostly undescribed Melanesian fauna. PLoS ONE 7(1): e28832.

USP online book store

Over the years, the University of the South Pacific has published a number of important books on the natural history, politics and cultures of the South Pacific. Most of these books can be purchased at their online book store. Prices are in US dollars and are pretty reasonable. Unfortunately, the kicker is postage, which adds on around $10 per book ordered. However, this isn't surprising considering the location of Fiji. Despite that, the book store remains an important outlet for all sorts of interesting reading on the Pacific.

2nd Fiji Conservation Science Forum

I had the privilege of attending the 1st Fiji Conservation Science Forum in 2009, and greatly enjoyed the quality of the talks and science presented, and the enthusiasm of the attendees. Unfortunately, I was unable to get along to the 2nd meeting, held 14–16 September 2011, but I gather that it likewise was an informative and exciting meeting. The abstracts are available at the Wildlife Conservation Society website, and show the breadth of territory covered by the forum.

The Fiji Conservation Science Forums are an excellent initiative that have and will continue to inspire science in the South Pacific. I wish the organisers all the best in their preparations for a third forum in the next couple of years.

PhD Week 0: Beginnings

Today was officially the first day of my PhD. As such, it was mainly spent completing one or two bureaucratic tasks, and contemplating how to implement systems such as regular computer backups. With the Denniston Plateau BioBlitz happening this weekend, it meant that a fair amount of the day was also spent preparing for that.

While checking my emails, I was pleasantly surprised to discover a paper by Nico Franz in the latest issue of the Zoological Journal of the Linnean Society. The paper, looking at a group of weevils primarily found in the Caribbean, goes into some depth regarding useful morphological features for estimating the evolution of these creatures. It will be a useful paper to consider as I look at my weevils over the coming weeks and months.

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Read:
Franz NM. 2012. Phylogenetic reassessment of the Exophthalmus genus complex (Curculionidae: Entiminae: Eustylini, Geonemini). Zoological Journal of the Linnean Society 164: 510–557

Wilkins JS. 2009. Defining Species. A Sourcebook from Antiquity to Today. Peter Lang, New York

1 Corinthians 1:18–25; 8:1–3


Listened:
Becoming the Archetype—Dichotomy