Voseq, web database for molecular phylogenetics

• Are you working in molecular phylogenetics? Do you and your lab produce lots of DNA sequences. 
• Are you tired of trying to find your sequences among several text files and Excel sheets? 
• Do you wish there was a easy-to-use database to keep track of sequences and their associated voucher specimens? 
• Did you ever wished there was a system to create molecular datasets for analysis in PAUP or MrBayes by just a few clicks of a mouse? 

If the answers are "yes", then VoSeq might be for you. VoSeq is a voucher and DNA sequence web application database aimed for people working in molecular phylogenetics.

Main features of VoSeq:

• Keep track of your sequences and associated voucher specimens. 
• You upload your data to VoSeq and the back-end relational database will allow you to easily search, fetch, update, etc your DNA sequences or voucher data. 
• With a few clicks, you can create ready-to-run datasets in NEXUS, Phylip, TNT formats, as well as FASTA files for submission to GenBank. 
• Use the BLAST capabilities to find similar sequences among those you have, or BLAST against GenBank. 
• Automated integration with public web services such as Flickr (for posting your voucher photos) and Yahoo Maps (for plotting voucher localities). 
• You can install it in your computer for private use, or set it up in a shared server for collaborative work via the internet. 
• and more. 

The publication describing VoSeq came out recently:

Peña, C. & Malm, T. (2012). VoSeq: a Voucher and DNA Sequence Web Application PLOS ONE, 7 (6) DOI: 10.1371/journal.pone.0039071

• You can check out a test installation of VoSeq with sample data here: http://www.nymphalidae.net/VoSeq/
• The full documentation is here: http://nymphalidae.utu.fi/cpena/VoSeq_docu.html 
• Download from here: https://github.com/carlosp420/VoSeq 
• VoSeq is actively being developed and if you have questions or need help using it. Let us know! 

Carlos Peña: mycalesis@gmail.com 
Tobias Malm: tobemalm@gmail.com

Relaciones evolutivas de las mariposas monarca y sus parientes

Image by Gustavo (lu7frb) via Flickr

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

New butterfly from Colombia

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

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

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

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.