Tuesday, 16 December 2008

Search function for Taxonomic database

I just uploaded the search function for the Butterfly Taxonomic Database:


The search field can take up to three arguments of butterfly names (no matter whether you enter genus or species names), and the script will look for genus and species names that will match your query.

For example a search for the species Euptychia enyo will output this taxon but also all other Euptychia and even Corades enyo:

Still have to get rid of the duplicates like the second Euptychia enyo at the bottom of the returned results.

Saturday, 13 December 2008

Taxonomic database

In order to keep track of the ever changing butterfly names, we are working on a "Taxonomic database" for butterfly names.


We are generating LSIDs for each butterfly name, including basic info such as the original combination of names from primary literature, list of synonyms and/or homonyms if they exits, type localities, some collection localities and a map when suitable.

We are working on generating RDF files for keeping this info readable for computers as well.

So far we have made available a checklist function for reporting species names according to Biogeographic region and family-level classification. We are on the works to finish up the search function.

Wednesday, 9 April 2008

Genomic outpost serve the phylogenomic pioneers: designing novel nuclear markers for genomic DNA extractions of Lepidoptera

This paper just came out:

PDF Wahlberg, N. & C. Wheat. 2008. Genomic outpost serve the phylogenomic pioneers: designing novel nuclear markers for genomic DNA extractions of Lepidoptera. Systematic Biology, 57(2): 231-242. doi:10.1080/10635150802033006

List of vouchers.

Niklas Wahlberg and Chris Wheat describe a cool way to "easily" find new genes for phylogenetic inference. The authors wonder how many genes are necessary for getting a robust phylogeny. Maybe the more, the merrier, but for butterflies at least, they say that between 3 and 5 genes should be okay —for most of the nodes. If you want to be sure about relationships of ambiguous taxa, get 11 genes then.

From the abstract:
Increasing the number of characters used in phylogenetic studies is the next crucial step towards generating robust and stable phylogenetic hypotheses—i.e., strongly supported and consistent across reconstruction method. Here we describe a genomic approach to finding new protein-coding genes for systematics in nonmodel taxa, which can be PCR amplified from standard, slightly degraded genomic DNA extracts. We test this approach on Lepidoptera, searching the draft genomic sequence of the silk moth Bombyx mori, for exons >500 bp in length, removing annotated gene families, and compared remaining exons with butterfly EST databases to identify conserved regions for primer design. These primers were tested on a set of 65 taxa primarily in the butterfly family Nymphalidae. We were able to identify and amplify six previously unused gene regions (Arginine Kinase, GAPDH, IDH, MDH, RpS2, and RpS5) and two rarely used gene regions (CAD and DDC) that when added to the three traditional gene regions (COI, EF-1α and wingless) gave a data set of 8114 bp. Phylogenetic robustness and stability increased with increasing numbers of genes. Smaller taxanomic subsets were also robust when using the full gene data set. The full 11-gene data set was robust and stable across reconstruction methods, recovering the major lineages and strongly supporting relationships within them. Our methods and insights should be applicable to taxonomic groups having a single genomic reference species and several EST databases from taxa that diverged less than 100 million years ago.

Wednesday, 26 March 2008

Global climate change is good for butterflies

larva of Satyrinae butterfly on grass hostplant
Sort of off-topic, though.

Our paper: Peña & Wahlberg (2008) Prehistorical climate change increased diversification of a group of butterflies. Biology Letters; is coming out today (probably, at least online). However, it already got a short note on London's Telegraph (here).
Here is the doi link: 10.1098/rsbl.2008.0062
and here links to the PDFs: http://nymphalidae.utu.fi/publi.htm

From the abstract:
Satyrinae butterflies (Lepidoptera: Nymphalidae) and grasses (Poaceae) are very diverse and distributed worldwide. Most Satyrinae use grasses as hostplants, but the temporal scale of this tight association has been unknown. Here we present a phylogenetic study of Satyrinae butterflies and related groups, based on 5.1 kilobases from six gene regions and 238 morphological characters for all major lineages in the “satyrine clade”. Estimates of divergence times calibrated using a fossil from Late Oligocene indicate that the species rich tribe Satyrini diversified to its current 2,200 species simultaneously with the expansion and radiation of grasses during the dramatic cooling and drying up of the Earth in the Oligocene. We suggest that the adaptive radiation of grass feeders in Satyrini was facilitated by the ubiquitousness of grasses since 25 Mya, which was triggered by a change in global climate.

Monday, 10 March 2008

Butterfly references database

Some time ago I created a very simple reference database, my Butterfly references database. My idea is to have it for toying around with web services as a way to harvest data from the internet relevant to Nymphalidae butterflies.

As Rod Page has been blogging about, it would be really useful to have a way of linking species names (butterflies in our case) to their original descriptions.

This would speed up taxonomic work since lack of access to primary literature is one of the issues that is crippling taxonomic practice around the globe. This is particularly true in countries where access to primary literature is unthinkable... and coincidentally those countries are the ones that host most of the world's biodiversity! Because I am from Peru, I have been there... 've done that.

So, my new toy, the Butterfly references database only has a few bibliographic references for testing purposes. However it has a web service already. It is able to provide data of bibliographic references in XML format. Thus, now our voucher database will ask the reference database whether it holds references containing a particular species' voucher that any human user might be looking at at the voucher's page. Currently this is done using the RESTful protocol.

For example if you are looking for the butterfly Morpho aurora, you might stumble upon one of our pages for specimens of that species:

If you look a the center bottom you will see a "Relevant literature" field containing a full reference of paper by Patrick Blandin (2006). No bibliographic references data is contained in the voucher database, all that info is being queried and processed from the reference database "on the fly" and "on demand" according to user's input.

Unfortunately most of the hardcore taxonomic literature is old and published in obscure journals. So most likely there will be no "Digital object identifier" (DOI) or PDF files on the web for most of the references. I am currently trying to gather more info for each reference and put it available on the reference database which already points to some DOIs and web addresses of sites hosting PDF files.

Friday, 7 March 2008

RSS feed for NSG butterfly voucher database

I put up a RSS feed for the Voucher database. It will report the last entries that we upload or update in the database. If you want to subscribe just point your RSS reader software to the opening page: http://nymphalidae.utu.fi/db.php

The RSS feed contains the Genus and Species names of the particular specimen, including a thumbnail of the voucher picture if it exists and links to the voucher's page.

Sunday, 24 February 2008

First post

Hi there,

My name is Carlos Peña and I am involved in developing the NSG's voucher specimen database. This web application is what we, the NSG group, use to handle data for our research on the Systematics of the butterfly family Nymphalidae.

Thus, this blog is intended to record the efforts in making the voucher database and other databases (hopefully!) able handle biological data on Nymphalidae butterflies such as information of collection specimens, geographic distributions, molecular sequences, taxonomic literature and nomenclature of names.

Let's see how it goes!