Thursday, 30 September 2010

Featured insect: Oxymorostes riedeli (Coleoptera: Hybosoridae)

Oxymorostes riedeli Copyright Mario Toledo
It's been an interesting month, and what better way to finish it off than with an interesting beetle! I present Oxymorostes riedeli, a bizarre leaf-litter inhabiting beetle from West Papua described in 2009 by Alberto Ballerio. Not only does this beetle look wierd with its out-of-proportion pronotum being wider than its elytra, but it also has several cavities in its mouthparts and underside the function of which is currently unknown. Several other beetles, most notably the bark beetles, have similar cavities known as mycangia in which they store the spores of their food fungus. This is unlikely to be the case in this beetle though, as fungal spores have not been found in them. They did however have an "unknown substance of uncertain origin" inside them, for which there was "an unsuccessful attempt was made to analyze the substance". Just adds to the wierdness really.

Oxymorostes is placed in the subfamily Ceratocanthinae of the Hybosoridae, a worldwide though little known family similar to the scarab beetles. The Ceratocanthinae in general are pretty cool, with some very beautiful species in it such as this currently unknown Eusphaeropeltis species from Malaysia.

Eusphaeropeltis species


Ballerio A. 2009. Unusual morphology in a new genus and species of Ceratocanthinae from New Guinea (Coleoptera: Scarabaeoidea: Hybosoridae). The Coleopterists Bulletin 63(1):44-53

Ballerio A, Maruyama M. 2010. The Ceratocanthinae of Ulu Gombak: high species richness at a single site, with descriptions of three new species and an annotated checklist of the Ceratochanthinae of Western Malaysia and Sinagapore (Coleoptera, Scarabaeoidea, Hybsoridae). Zookeys 34:77-104

Grebennikov VV, Leschen RAB. 2010. External exoskeletal cavities in Coleoptera and their possible mycangial functions. Entomological Science 134:81-98

Wednesday, 22 September 2010

Microscope mounting media

Currently for work, I'm starting to explore and become familiar with the Springtails (Collembola). They are fascinating little creatures, but are a bit hard to identify with any degree of certainty without mounting them on a microscope slide.

There are a number of different techniques of mounting specimens on a microscope slide. None are the best for all situations though. For quick, temporary mounts, liquids such as Glycerol and Lactic acid can be suitable. For longer-lasting mounts, more complex mixtures usually involving various hazardous substances are used. The Smithsonian Copepod Page and a guide to insect collection curation both give an excellent overview of the longer-term options available for slide mounting specimens, as well as recipes for the various fluids and mixtures. Additionally, the Natural History Museum has a page giving a summary of the results of a mailing list discussion on the subject.

It seems though that the general consensus is that the resin Canada Balsam is THE medium for long-term (i.e. greater than 20 years) mounting of specimens. Despite concerns about requiring Xylene in its preparation, the long time required to make the slides, and concerns that its refractive index is sometimes too high for some specimens, it remains the time-tested solution for microscope mounting of specimens that need to go the distance. A paper describing its use is available in the New Zealand Entomologist.


Palma RL. 1978. Slide-mounting of lice: a detailed description of the Canada balsam technique. New Zealand Entomologist 6(4):432-436

Walker AK, Crosby TK. 1988. The preparation and curation of insects. DSIR Information Series 163. DSIR; Wellington.

Thursday, 9 September 2010

Image-stacking software for Linux

Back in the day, when I was still Windows-based, I was able to get some pretty decent focus-stacked ("automontage") photos of insects using the brilliant freeware programs DeepFocus and PrepareStack written by Stuart Ball. Unfortunately, I can't find the download anywhere, though his detailed manual is still available. While commercial applications are available, I have not yet found an open-source version that will suffice. Internet searches indicate that ImageMagick's "combine" might be suitable, when given a suitable stack of photos. Preparing that stack is a little trickier. There are suggestions that GIMP might be suitable, however as far as I can see, there are no published scripts or tutorials that make it easier beyond tedious manual adjustments. I will continue to look around and see if I can work out some sorta fix.

Wednesday, 8 September 2010

Canterbury Earthquakes part III

As more people keep following the GeoNet website, they are starting to notice the seismic activity in areas other than Christchurch. A few people I've talked to have expressed concern that the Saturday 7-pointer has sparked earthquakes around the country. This is incorrect, as earthquakes below magnitude 3 are extremely common and as can be seen in the plot below, they occur throughout the country.

A closer look at the magnitude of these earthquakes shows their temporal distribution is fairly uniform. What is interesting is that prior to the time of the big one there appears to be a lull in the frequency of lower-level earthquakes nation-wide. Is this at all significant? I don't know.

The magnitude follow a right-skewed normal distribution with a mean of 2.47 and a standard deviation of 0.617, while their depth follows an approximate Poisson distribution with a mean of 44 km.

Looking at the seismic activity within the Canterbury region, we see that earthquakes appear to have been fairly randomly distributed throughout the region until the 4 September quake. Only a single tremor was detected from the vicinity of the recently revealed fault, an insignificant 2.31 that occurred on the 21st of March. That there weren't more tremors closer to the time would seem to count against the hypothesis of big earthquakes being preceeded by smaller ones.

As before, data was gained from the Quake Search data download query provided by GNS, and the data, R code and a file giving the location of Canterbury towns is available for all.

Tuesday, 7 September 2010

Canterbury Earthquakes part II

Since posting last night, there's been several more aftershocks, including several big ones. The total now stands (at 7:00pm) at 304 aftershocks, 70 greater than 4 on the Richter scale, 29 greater than 4.5, and 10 greater than 5. A couple of the fives happened last night, waking us up, and causing more damage to several buildings around town.

This evening's installment is a map of the region of Canterbury where the earthquakes have been centred, showing the epicentre of all aftershocks and their magnitudes. It appears that while smaller tremours have been centred fairly widely, the larger magnitude earthquakes have been centred more around the epicentre of the initial 7.1 quake. As before, I've made the the data and R code available.

The region around the epicentre of the initial quake has been surveyed by GNS scientists. They've got some pretty awesome aerial photos showing the location of the fault on their webpage detailing their work.

Vanishing taxonomists

A recent article published in the Canadian newspaper "The Globe and Mail" titled "The case of the vanishing taxonomists" is another article that again is lamenting the demise of taxonomists and highlighting the fact that more are dying than are being trained. Those of us who follow these things will learn nothing particularly new, as it has been repeated many times before.

The morphological taxonomist, engrossed in a single group and identifying its members by visual inspection, is increasingly an emeritus professor or someone near retirement. Younger scientists are drawn to molecular taxonomy, where powerful new techniques in the study of DNA have revealed interspecies connections never before suspected.

It's a little frustrating reading these sorts of articles, particularly as a young scientist who does want to be a taxonomist and get paid for doing so. Although the paragraph above makes it sound as if there's noone wanting to follow in their footsteps, in my experience I have come across a number of postgraduate science students who would love to get into taxonomy. The problem is that there is very little money in it, and that jobs with significant components of taxonomic research are few and far between. The "taxonomic impediment" could easily be solved if there were dedicated funding rounds for the employment of early-career taxonomists.

Monday, 6 September 2010

Less than negative?

An interesting thing that I found while doing the analysis for my previous post on the Canterbury earthquakes, was the difficulty of constraining figures less than a negative number. For example:

a<-seq(1, 10, 1)
b<-a[a>3 & a<7]
c<-seq(-1, -10, -1)
d<-c[c<-3 & c>-7]

> a
[1] 1 2 3 4 5 6 7 8 9 10
> b
[1] 4 5 6
> c
> d
[1] -1 -2 -3 -4 -5 -6

The boolean operator for selecting a range less than a negative number ends up being the same as the assignment operator. To get around this I simply define the function neg()

neg<-function(x) -x
c<-seq(-1, -10, -1)
d<-c[c<neg(3) & c>neg(7)]

> c
[1] -1 -2 -3 -4 -5 -6 -7 -8 -9 -10
> d
[1] -4 -5 -6

Canterbury Earthquake

4:35 am on Saturday morning, I was woken up by a 7.1 magnitude earthquake, the epicentre being approximately 30 km west of where I live in Christchurch, New Zealand. The earthquake was one of the largest that New Zealand has experienced, and has been the most destructive one since the earthquake that struck Napier in 1931. Thankfully, the suburbs around the area that I live in suffered minimal damage, with most roads and houses essentially unscathed.

While the initial earthquake was fairly scary, it has been the aftershocks that have been the most unnerving. By this time we're starting to get fairly used to them, but they are still keeping all of us on edge. There's been a number, and now that I have access to the internet, I made it my mission to find out how many there's been thus far. The New Zealand Herald newspaper has published an online article showing the locations of all the aftershocks, but a bit scant on other details.

The New Zealand research institute Geological and Nuclear Sciences (GNS) is the primary monitor of New Zealand's earthquakes and makes all their data available online. In particular their Quake Search tool allows you to download CSV, KML and other files of any earthquakes that satisfy any given criteria. The GeoNet website in general is an excellent source of all sorts of information with regard to natural hazards in the New Zealand region.

I downloaded the data for the past week and started pulling out a bunch of trends. The two that I'll post here for now are the following:

Until 6 Sep 2010 19:03 NZST there has been 257 aftershocks, ranging between 2.4 and 5.4 on the Richter scale. Of these, there have been 64 with magnitudes above 4; 24 above 4.5; and 7 above 5. The average has been 3.6.

The comparison between the earthquakes recorded prior to and following the earthquake is remarkable. The four days prior to the earthquake there were no earthquakes originating within the Canterbury region (defined as being between 42--44 degrees S and 171--173 degrees E). Since Saturday morning, the region has been shaking like nothing else.

A line plot only of the Canterbury earthquakes does show that the aftershocks are lessening in frequency and intensity. Further playing around with the data and the plot might show this more effectively though.

A plot comparing the magnitude of each quake with its depth is quite interesting. The vast majority of the Canterbury earthquakes are fairly shallow (<20 km). Once again, further analysis will show if this is a significant thing or not, but it does explain why they've been so easily felt.

Feel free to look at the R code and the CSV file I used for the plots above.

Wednesday, 1 September 2010

apply functions in R

Getting to know the "apply"s in R is extremely handy for using the language efficiently and effectively. Unfortunately, the help files tend to be rather information-dense and are fairly overwhelming for newcomers. A recent blog post by Neil Saunders provides a thorough overview and tutorial of the apply family, illustrated by simple and reproducible examples. I suspect I will refer to it frequently from here on in.