NSG's databases blog

Relaciones evolutivas de las mariposas monarca y sus parientes

noreply@blogger.com (cpena) — Fri, 26 Mar 2010 16:35:00 +0000

El colega Andrew Bower y amigos acaban de ver publicada su investigación en la filogenia y evolución de las mariposas monarca y parientes que están clasificadas en la subtribu Danaini.

Ellos han utilizado secuencias de ADN, datos morfológicos de adultos e inmaduros de estas mariposas para tratar de reconstruir la evolucion de este grupo de mariposas.

Este trabajo provee de una sólida hipótesis de la evolución de grupo, conviertiéndose en una guía de la clasificación de estas mariposas.

Los autores han estudiado mariposas de Australia, África, Indonesia, Islas Grand Caimán, Argentina, Tailandia, USA, Republica Dominicana, Brasil y una especie de Perú: la especie Danaus plexippus de Tingo María.

Brower, A.V., Wahlberg, N., Ogawa, J.R., Boppré, M. & Vane-Wright, R.I. (2010) Phylogenetic relationships among genera of danaine butterflies (Lepidoptera: Nymphalidae) as implied by morphology and DNA sequences. Systematics and Biodiversity, 8, 75-89. doi:10.1080/14772001003626814

Moving to Flickr

noreply@blogger.com (cpena) — Fri, 10 Apr 2009 12:22:00 +0000

Image via CrunchBase

All the voucher pictures in our NSG database take up to 2.5GB in hard disk space, which is quite a lot for 3300 pictures only.

This is indeed a problem if we decide to move the database into a private, commercial server because buying 2.5 GB of space can be quite expensive.

Then Flickr might be able to help. By having a PRO account, users are allowed to upload unlimited number of photos and even retaining the original sizes of high resolution photos, for only 25 USD per year. Quite a bargain indeed.

Since moving more than 3000 pictures can be tiresome, I used used Flickr's API interface and grabbed an API key.

Then I found the PHP class libraries of Phlickr very useful as a layer on top of Flickr's API.

I used Phlickr to harvest information from the NSG database and included it as Title, description and Tags of the photos to be uploaded to Flickr.

Almost everything worked as a charm. However, I found that Phlickr got problems in getting the image URL, by constructing the link using the wrong id of the photo. I had to fix it by hacking the Photo.php class -> function buildImgUrl()

The database then will link to the photo on Flickr:

Now people can comment on every picture and point out whenever we misidentify the vouchers. The possibility of adding notes on top of the photo might of some use.

NSG's photostream in Flickr: http://www.flickr.com/photos/nsg_db/

Started using Twitter

noreply@blogger.com (cpena) — Tue, 31 Mar 2009 21:31:00 +0000

Image via CrunchBase

I always wanted to have a cross-database plugin that would list some "recent news" of new vouchers and records uploaded to our voucher and reference databases. I tried to do it myself some years ago but it was too complicated to achieve.

But, it seems that Twitter might do the job.

from Wikipedia:

Twitter is a social networking and micro-blogging service that enables its users to send and read other users' updates known as tweets. Tweets are text-based posts of up to 140 characters in length.

So now every time I update the databases a script will create a tweet including a shortened url address to the respective voucher and record pages.

Since the tweets have to be up to 140 characters in length, I have to shorten the URLs. For this, I found the TinyURL service, but it was sluggish a couple of times so I switched over to Is.gd which has a very simple API.

And this is my twitter address http://twitter.com/carlosp420

Here a video explaining in a better way what Twitter might be all about: "The ultimate tool for exhibitionism"

New butterfly from Colombia

noreply@blogger.com (cpena) — Fri, 27 Feb 2009 08:47:00 +0000

Blanca Huertas and colleagues (Huertas, Ríos & Le Crom, 2009) describe a new Satyrinae butterfly in the genus Splendeuptychia from the Colombian Andes:

Splendeuptychia ackeryi Huertas, Ríos & Le Crom, 2009

This is the original citation:

Huertas, Blanca; Ríos, Cristóbal; Le Crom, Jean F. (2009) A new species of Splendeuptychia from the Magdalena Valley in Colombia (Lepidoptera: Nymphalidae: Satyrinae). Zootaxa 2014: 51–58.

see the paper here.

It seems this butterfly was found due to having particular mustache.

from ScienceDaily

from taxon_db

Search function for Taxonomic database

noreply@blogger.com (cpena) — Tue, 16 Dec 2008 17:49:00 +0000

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

http://www.nymphalidae.net/taxon_db/search.php

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.

Taxonomic database

noreply@blogger.com (cpena) — Sat, 13 Dec 2008 19:30:00 +0000

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

Here:
http://www.nymphalidae.net/taxon_db/

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.

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

noreply@blogger.com (cpena) — Wed, 09 Apr 2008 14:22:00 +0000

This paper just came out:

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.

Global climate change is good for butterflies

noreply@blogger.com (cpena) — Wed, 26 Mar 2008 09:41:00 +0000

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.

Butterfly references database

noreply@blogger.com (cpena) — Mon, 10 Mar 2008 11:16:00 +0000

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.

RSS feed for NSG butterfly voucher database

noreply@blogger.com (cpena) — Thu, 06 Mar 2008 22:35:00 +0000

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.

First post

noreply@blogger.com (cpena) — Sun, 24 Feb 2008 11:46:00 +0000

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!