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