Canada is a long way from the South Pacific I know. I know also that their insects are very, very different from those in this part of the world which I know and love. But they have done a lot of excellent work on their own insects and now they've decided to open the floodgates and let all and sundry benefit from their work.
On a page that begins: "The Entomological Society of Canada (ESC) has obtained copyright permission from Her Majesty the Queen in the Right of Canada" they have put online in PDF form over 30 years of publications including the extremely valuable "Manual of Nearctic Diptera" volumes 1 to 3, and publications on the weevils and bark beetles of that fair northern country.
I'm looking forward to reaping the benefits...
Sunday, 23 May 2010
Thursday, 20 May 2010
South American Weevils
.jpg)
This, the next website on the weevils of the world, is the extremely indepth website of Juan Enrique Barriga-Tuñón on the beetles of South America. As is expected, this is an extremely ambitious project and the fact that it has such a range of photos from several orders and numerous countries speaks of the passion of its creator.
The photos are of varying quality from well-focussed, well-coloured dorsal and lateral images that would no doubt be invaluable for identification (such as the Acrotomopus obtusus pictured here); to dark, poorly-focussed images that are of little value for identification purposes.
Several pages include short species accounts that include specimen labels and reference lists. The species from Argentina in particular frequently have these species pages devoted to them. The site is in Spanish, however there no block of spanish prose and the navigation is straight-forward enought that I (who is not known for my grasp of spanish) was able to get around easily.
Having a cursory scroll through many of the species listson the site, it strikes me that these countries don't seem to have too many genera, but that many of these genera have a huge number of species in them. Naupactus and Listronotus are a couple of the cases in point in the Argentina list above. Whether this is evidence of some hyper-radiations in the evolution of these things, or merely that these particular genera have had more taxonomic work done on them than the others I don't have the familiarity with the region and the fauna to tell.
Thursday, 13 May 2010
European weevil photos
Surfing the internet just now I stumbled across the website of Attila Podlussány, a Hungarian amateur entomologist with a particular interest for weevils.To the left is a photo of the beautiful Stephanocleonus nigrosuturatus. This photo, and a whole lot more, are featured in the extensive photo gallery. That link directs one to the Curculionidae gallery, however most of the other curculionoid families have galleries of their own also.
An excellent resource for people interested in European weevils, and for people who like looking at nice photos of cool animals in general.
Wednesday, 28 April 2010
Transitions in R redux
Previously, I shared with the world a function to create a pairwise matrix of the number of transitions and transversions between two DNA sequences. Klaus Schliep kindly pointed out the possibility of a bug in the function and offered a faster, more accurate version. Thanks Klaus!
The previous version of the function considered the difference between an unknown base (coded as N) and a T as a transition. The new version does not detect this difference.
titv<-function(dat){
mat<-as.matrix(dat)
res<-matrix(NA, ncol=dim(mat)[1], nrow=dim(mat)[1], dimnames=list(x=names(dat), y=names(dat)))
for(i in 1:(dim(mat)[1] - 1)){
for(j in (i+1):dim(mat)[1]){
vec<-as.numeric(mat[i,])+as.numeric(mat[j,])-8
res[j,i]<-sum(!is.na(match(vec,c(200,56))))#Transitions
res[i,j]<-sum(!is.na(match(vec,c(152,168,88,104))))#Transversions
}
}
res
}
The previous version of the function considered the difference between an unknown base (coded as N) and a T as a transition. The new version does not detect this difference.
Wednesday, 24 March 2010
Conservation Biology papers with a Pacific focus
The most recent (April 2010) issue of Conservation Biology has a number of papers which focus on the fauna, flora and environment of the South Pacific.
The issue starts off with an editorial by David Melick on economic schemes to negate carbon emissions. In particular he deals with the scheme to compensate landowners for NOT cutting down forests on their land (REDD) and the way this has played out thus far in the Papua New Guinea scene. He ends with this very pertinent statement:
Highly relevant for all who work in the South Pacific, particularly those of us with a western, productivity-based mindset. As the Mainland cheese ads say---Good things take time.
William Laurance and others discuss the impact of Oil Palm cultivation and some of the issues and opportunities surrounding it. In particular, they discuss the Roundtable on Sustainable Palm Oil (RSPO) a nonprofit organisation that hopes to promote and market sustainably grown palm oil. Unfortunately, its track record appears to be fairly poor. The seeming blind eye the organisation has taken toward the destruction caused by growing oil palm in peat swamps is singled out as being a major failing of the RSPO. however Laurance et al. refuse to be pessimistic about the situation and make some recommendations, most of which involve fairly major restructuring of the RSPO and developments in its monitoring and enforcement policies. However, the real problem in the situation is the lack of market demand for sustainably grown palm oil, meaning that the RSPO has little clout.
Alison Boyer revisits the very high extinction rate of Pacific Island birds, this time investigating what ecological traits seem to have an influence on extinction rate. She concludes that differences in endemism, body size and diet influence the potential for extinction and gives a list of bird species that may be worthy of a higher threat category than currently given.
Shankar Aswani and Armagan Sabetian look at the impact that urbanisation has had on the parrotfish population around Gizo and Munda, in the Western Province of the Solomon Islands. Not surprisingly, they found that over the period 2004--2005 parrotfish numbers decreased around Gizo. However, they did find that some customary management systems were effectively preserving larger and greater numbers of parrotfish. The most effective systems were those that prevented all fishing in certain areas.
Mayeul Dalleau and team looked at shallow marine habitats around Wallis Island and used digital imagery and habitat maps as surrogates for biodiversity in the proposal of marine protected areas. While they promote this method as being an effective and efficient of surveying large areas, they do recognise that it is very desirable to do some actual field work to complement the habitat data, particularly in regions such as the Red Sea which has a very different environment from the oceanic Pacific islands.
It's a good issue. Well worth a read, certainly if any of the above issues pique your interest.
References:
The issue starts off with an editorial by David Melick on economic schemes to negate carbon emissions. In particular he deals with the scheme to compensate landowners for NOT cutting down forests on their land (REDD) and the way this has played out thus far in the Papua New Guinea scene. He ends with this very pertinent statement:
... REDD will come to nothing if the system is not supported by the people who own and live in the forests. If the process is not rushed (it may take years, not months) and the PNG government is willing to accept international scrutiny and advice, forest governance and communitybenefits for the rural poor may finally be improved significantly...
Highly relevant for all who work in the South Pacific, particularly those of us with a western, productivity-based mindset. As the Mainland cheese ads say---Good things take time.
William Laurance and others discuss the impact of Oil Palm cultivation and some of the issues and opportunities surrounding it. In particular, they discuss the Roundtable on Sustainable Palm Oil (RSPO) a nonprofit organisation that hopes to promote and market sustainably grown palm oil. Unfortunately, its track record appears to be fairly poor. The seeming blind eye the organisation has taken toward the destruction caused by growing oil palm in peat swamps is singled out as being a major failing of the RSPO. however Laurance et al. refuse to be pessimistic about the situation and make some recommendations, most of which involve fairly major restructuring of the RSPO and developments in its monitoring and enforcement policies. However, the real problem in the situation is the lack of market demand for sustainably grown palm oil, meaning that the RSPO has little clout.
Alison Boyer revisits the very high extinction rate of Pacific Island birds, this time investigating what ecological traits seem to have an influence on extinction rate. She concludes that differences in endemism, body size and diet influence the potential for extinction and gives a list of bird species that may be worthy of a higher threat category than currently given.
Shankar Aswani and Armagan Sabetian look at the impact that urbanisation has had on the parrotfish population around Gizo and Munda, in the Western Province of the Solomon Islands. Not surprisingly, they found that over the period 2004--2005 parrotfish numbers decreased around Gizo. However, they did find that some customary management systems were effectively preserving larger and greater numbers of parrotfish. The most effective systems were those that prevented all fishing in certain areas.
Mayeul Dalleau and team looked at shallow marine habitats around Wallis Island and used digital imagery and habitat maps as surrogates for biodiversity in the proposal of marine protected areas. While they promote this method as being an effective and efficient of surveying large areas, they do recognise that it is very desirable to do some actual field work to complement the habitat data, particularly in regions such as the Red Sea which has a very different environment from the oceanic Pacific islands.
It's a good issue. Well worth a read, certainly if any of the above issues pique your interest.
References:
Wednesday, 17 March 2010
Interrupting R processes in Ubuntu
It's funny how things happen. Yesterday I was working away on a project in R and the unenjoyable happens---the process hangs for longer than desired. I operate R in the standard GNOME terminal in Ubuntu and the only way I knew was to close the entire application getting rid of all objects at the same time. Not cool. Thirty minutes or more of fruitless searching gave no indication as to a better way of doing things and I was really wishing the ESC key worked as it does in Windows.
Checking emails this morning though, and I discover an exchange on R-help that goes through exactly what I needed to know... From these emails then I have discovered that:
Checking emails this morning though, and I discover an exchange on R-help that goes through exactly what I needed to know... From these emails then I have discovered that:
- Pressing Ctrl+C should work in the terminal.
- If that doesn't work, open another terminal console and type
ps aux | grep R
kill -s INT PID The first line allows you to discover the PID number of your particular R instance, which is then used in the second line. - In the second line above, INT may be replaced by HUP in some cases.
- The above methods set up an alert-thing to tell the program to stop. When the computations are done externally of R, it can't be executed before the external codes checks back with R. If the external code doesn't do this regularly or at all, killing the entire program is the only way out. If none of the above work, this is probably what has happened and it may be a good idea to let the package author know about the problem...
J. O. Westwood medal for insect taxonomy
In 2006, the Royal Entomological Society established a prestigious award aiming to encourage insect taxonomy particularly revisionary work resulting in definitive monographs---the J. O. Westwood Medal for excellence in insect taxonomy. The award is given biennially and nominations for the 2012 medal are currently being accepted for papers published between 1 April 2009 and 31 March 2011.
The award honours John Obadiah Westwood (1805-1893), who was an influential British entomologist who was instrumental in establishing the Royal Entomological Society and was an original proponent of the use of type species for genera.
Since its establishment, the medal has been given out twice. Marianne Horak was the first recipient in 2008 for her work on Australian tortricid moths. This year's recipient is Art Borkent for his 2008 work on world fauna of the frog-biting midges (Corethrellidae), published in Zootaxa. Both recipients received glowing reports from the assessment panel including such phrases as "A monumental work ... absolutely exemplary" and "A true model for the taxonomic/systematic treatment of a taxon." Unfortunately, due to the nature of monographs, these tomes are big and expensive to publish which makes it difficult for those of us who want to learn from these masters to get hold of a copy of these papers and model our own work on them.
Congratulations to Art Borkent and, more belatedly, Marianne Horak for their superb achievements. While taxonomy may not be in most enviable of situations and despite the moaning of we taxonomists, publications and awards such as these demonstrate that it's not dead yet...
References:
Borkent A. 2008. The frog-biting midges of the world (Corethrellidae: Diptera). Zootaxa 1804:1--456
Horak M. 2006. The Olethreutine moths of Australia (Lepidoptera: Tortricidae). Monographs on Australian Lepidoptera Series 10:1--528, CSIRO publishing.
The award honours John Obadiah Westwood (1805-1893), who was an influential British entomologist who was instrumental in establishing the Royal Entomological Society and was an original proponent of the use of type species for genera.
Since its establishment, the medal has been given out twice. Marianne Horak was the first recipient in 2008 for her work on Australian tortricid moths. This year's recipient is Art Borkent for his 2008 work on world fauna of the frog-biting midges (Corethrellidae), published in Zootaxa. Both recipients received glowing reports from the assessment panel including such phrases as "A monumental work ... absolutely exemplary" and "A true model for the taxonomic/systematic treatment of a taxon." Unfortunately, due to the nature of monographs, these tomes are big and expensive to publish which makes it difficult for those of us who want to learn from these masters to get hold of a copy of these papers and model our own work on them.
Congratulations to Art Borkent and, more belatedly, Marianne Horak for their superb achievements. While taxonomy may not be in most enviable of situations and despite the moaning of we taxonomists, publications and awards such as these demonstrate that it's not dead yet...
References:
Borkent A. 2008. The frog-biting midges of the world (Corethrellidae: Diptera). Zootaxa 1804:1--456
Horak M. 2006. The Olethreutine moths of Australia (Lepidoptera: Tortricidae). Monographs on Australian Lepidoptera Series 10:1--528, CSIRO publishing.
Subscribe to:
Posts (Atom)