Reef fish phylogeny and connectivity

A paper on the intraspecific phylogeny of the damsel fish Pomacentrus moluccensis was published the other day by Joshua Drew and Paul Barber as a short communication in Molecular Phylogenetics and Evolution. This paper is well worth reading as it demonstrates that specimens from Fiji form a monophyletic sister group to those from further west. Vanuatu species are also monophyletic, while those from the Solomons to Sumatra form a third, most derived clade.

What makes this interesting is that this runs counter to the traditionally accepted mode of dispersal in the Pacific, where the area around New Guinea and Indonesia act as a source area for the remainder of the Pacific.

As the authors point out, this story is based only on mitochondrial DNA sequences, and as such only tell a partial story of P. moluccensis' history. More data may change the story somewhat, but the results published here are intruiging and will hopefully stimulate further investigation.

References:

Drew, J., and Barber P. H. (2009) Sequential cladogenesis of the reef fish Pomacentrus moluccensis (Pomacentridae) supports the peripheral origin of marine biodiversity in the Indo-Australian archipelago. Molecular Phylogenetics and Evolution. 53(1): 335-339.

Picture stolen from the Encyclopedia of Life (http://eol.org/pages/212092)

Ubuntu, Vista and partitions

In the weekend someone decided that they should have my computer instead of me. This reminded me of GK Chesterton's famous quote

Thieves respect property. They merely wish the property to become their property that they may more perfectly respect it.

Or possibly make a quick buck. I'm keeping an eye on Trademe...

However, every cloud has a silver lining, and this one is that I'm able to justify buying a new computer. It also allows me to fulfill my desire to try out Linux, and so I've done it in the form of dual-booting my new laptop with the pre-loaded Vista, with the latest and greatest Ubuntu 9.04. Lots of teething issues of course, but it's been pretty good over the past 12 hours or so...

The key one though is partitioning. I want to have a main, large, data partition that would be accessible by both Vista and Linux. I am currently using Gparted to accomplish this, and have found this tutorial rather helpful.

I've found that defragging the hard drive might be the way to go to get Vista's portion of the hard drive down. Alternatively, I might use get rid of Ubuntu for a little while and make the partitions initially using Gparted.

A couple of hours later:
After talking to colleagues, it seems that the best thing to do might be to mount the Windows hard drive to Ubuntu, as described here and here. And though I thought that Ubuntu came with ntsf read/write ability as a default, this suggests otherwise.

And a few more, possibly useful, links:
Partitioning using Gparter
The ntfs-config package

That's the journey thus far! For the record, I'm installing Ubuntu 9.04, and I'm using a Toshiba satellite L300 preloaded with Vista....

Biological graphics and illustration

Illustration is a key part of biological communication, and is particularly important in taxonomic descriptions where subtle differences in shape can be the best definition of a species. Body elongate, gradually and almost uninterruptedly narrowed towards the front anyone?

For this reason, I've recently been playing around with graphics a bit and have been learning about the different formats and their strengths and weaknesses. In particular, I'm starting to get rather excited about using vector graphics for the line illustrations that are so useful for species descriptions. The biggest obstacle that I can see is drawing from the specimen in question into the computer program. I'm not sure how the best way of going about this is. Unfortunately, there does not appear to be widespread awareness of the benefits of vector graphics, and there are no tutorials that I've found on biological illustration using vector graphics.

There is however this very good introduction to modifying photographs for publication in the brilliant Zootaxa.

If you're wondering, I use GIMP for modifying bitmaps, and Inkscape for vector graphics.

Proc. Roy. Soc. special issue on the Solomons

While searching for a paper on insect distribution on the Solomon Islands, I came across the 1969 special issue of the Proceedings of the Royal Society A on aspects of the biology and geology of what was then known as the British Solomon Islands Protectorate. It's an eclectic mix - articles include details on the soil, vegetation, fungi, Collembola, molluscs and shoreline ecology of the islands.

Unfortunately though, the articles aren't available for the general public - articles are only available with a subscription, or if you want to fork out some hard-earned cash to see the article. The latter option may or may not be too bad, but they don't make it easy to find out exactly what it'll cost you to see each article. Experience with previous journals would suggest it could be rather excessive - I've seen some which try and charge $25-30 USD for a 10-page article... Not my idea of a bargain.

It's great this issue is online. It is rather unadvertised and unknown (at least... I've never come across it before...), but it is a shame that it's not freely available. Oh well.....

Japanese Weevil database

As some might have guessed from reading other articles on the blog, I have a rather soft spot for the Curculionoidea. Weevils with their snouts and their amazing variety of shapes and sizes are incredibly cool. Funnily enough though, they remain comparatively neglected by biologists. It's good to see that the excellent Japanese curculiologists Katsura Morimoto and Hiroaki Kojima are adressing this problem with the Japanese Weevil Database. All the navigation is in Japanese, but it's pretty easy to find your way around even if your knowledge of Japanese leaves a lot to be desired. I'm mainly impressed by the scope of the site and the pretty pictures...

Morphometrics

I have recently been getting more interested in morphometric analysis, in particular shape and colour analysis. Turns out that they teach a course on this stuff at Imperial College and the Natural History Museum in London. Not only that, but they put all their teaching material online. It's good stuff. Good stuff that is if you like seeing lots of mathematical formulas and multivariate statistics....

Update: I've just come across this site which is maintained by James Rohlf, one of the big names in morphometrics. Rather useful!

Beetle pictures from Southeast Asia

While researching for an upcoming talk, I found the following webpage:

Southeast Asian Beetles

It's pretty cool. It's got very good pictures of over 2000 specimens from 71 different families of weevils. It's also got a very cool and useful interactive locality map which allows you to quickly find specimens from areas of interest. It's based on the Drupal website system, which I personally find rather clunky, but it is free, open source and reasonably easy to develop in.

This site is also another example of the importance of taxonomy, and how much needs to be done in biodiversity-rich regions like Southeast Asia. Comparatively few of the beetles featured have been identified to species level, no doubt due to a combination of there being no relevant specialists and there being a large amount of work to describing new species and revising previous species hypotheses.