Tuesday, 13 December 2011

spider: an R package for species identity and evolution

spider: Species identity and evolution is an R package developed by the Lincoln University molecular ecology lab group to do a range of analyses that various lab members wanted to run that were not yet implemented in R. In particular, the package provides functions for conducting sliding window analyses on DNA sequences, the calculation of identification efficacy of a library of reference DNA sequences, and the segregation of distance matrices into their inter- and intra-specific components.

The above are the main attractions, and the ones that we tend to write about when promoting it in places like the 4th International Barcode of Life Conference. There's a bunch of other neat utilities in there also though. A couple of the ones that I particularly enjoy are tiporder(), which returns the tip labels in the order in which they appear on the tree; paa() which conducts population aggregate analysis on a dataset; and rosenberg() which calculates Rosenberg's probability of monophyly for the nodes on a tree.

Spider is available on CRAN, and R-Forge, the latter providing opportunities to report bugs and to collaborate in the future development of the package should you desire to do so.

Vanuatu Caddisflies

A recently published paper by Kjell Johanson revises the caddisfly fauna of Vanuatu, descibing 12 new species and providing a key to the species currently known from the archipelago. It is an important contribution to the knowledge of the caddisfly fauna of the region, as most of the previous work done on the fauna of the region is several decades old.

A couple of things stood out to me in this paper. The first is that Orthotricha has not been recorded from any other oceanic Pacific islands. These are small (2-3 mm wing length) creatures, and it is likely that they just haven't been collected elsewhere in the Pacific. The second was their discovery that a female of Triplectides australis had a large number of larvae inside her abdomen. While I was hitherto unaware that ovoviviparity occurred in caddisflies, it turns out that this has been known since 1890, the first instance of it being confirmed by Prof. Wood-Mason in the following manner:
I threw the insect alive into a liqueur-glass of whiskey that happened to be ready at hand.

Adult caddisflies tend to be overlooked by the general public, usually being confused as small, fairly dull-looking moths. Their larvae are aquatic where they form an important part of the macro-invertebrate fauna of streams, and can be useful as indicators of water quality and stream health. Unfortunately, very little biological information is recorded in the paper, and larvae are not considered. In part this is due to Malaise and light traps providing the bulk of the material that was considered in the revision. Discovering and describing larvae and their habitats is a natural application of the taxonomic effort of this paper.


Johanson KA, Wells A, Malm T, Espeland M. 2011. The Trichoptera of Vanuatu. Deutsche Entomologische Zeitschrift 58(2): 279-320.

Wood-Mason J. 1890. On a viviparous caddis fly. Annals and Magazine of Natural History 6th series, 6: 139-141.