Leptree P.I. Jerry Regier and six colleagues, including Leptree postdoc Andreas Zwick, have published a phylogenomic analysis in Nature which strongly resolves long-controversial deep nodes in the phylogeny of Arthropoda, the largest phylum of Metazoa. The work stems from the NSF Biocomplexity Program project entitled
"Higher-Level Arthropod Phylogenomics," with which Leptree has interacted closely.

The data set consists of 62 single-copy nuclear protein-coding genes (41 kb of aligned sequence) from 75 species representing every major arthropod lineage plus outgroups.
A subset of 21 of the most rapidly-evolving of these genes is being used in the Leptree molecular study of Lepidoptera phylogeny.

Leptree PI Michael Cummings and colleagues are currently leading an NSF-sponsored project entitled "Grid, Public and GPU Computing for the Tree of Life," which seeks to expand the computing power available to phylogeneticists by combining Grid and GPU (graphics processing unit) computing. The Project Summary for this work is reprinted below.

In a modern desktop computer, the GPU can do many scientific calculations faster than the central processing unit (CPU).
In particular, the GPU's massively parallel architecture is uniquely suited to the calculations performed in phylogenetic inference under the maximum likelihood criterion. Cummings and his colleagues are among the first to exploit the power of the GPU for phylogenetics.

The University of Maryland was recently named a Center of Excellence in GPU computing by, and received a major hardware gift from, NVIDIA Corporation, a leading GPU manufacturer. Cummings' work on GPU phylogenetic computing is one of the featured applications in the UMD news release about this award.

From the UMD story:

"NVIDIA, a world leader in visual computing technology, has named the University of Maryland a CUDA Center of Excellence in recognition of the university's quality and diversity of supercomputing research and Maryland's leading work integrating CUDA-enabled graphics processing units (GPUs) into computer science education and multidisciplinary research. The prestigious and highly competitive award includes three years of project funding from NVIDIA and the gift of a high-performance supercomputer GPU cluster.

"CUDA is NVIDIA's computing architecture that enables its GPUs to be programmed using industry standard programming languages. This allows the massive parallel processing power of GPUs to be applied to a broad range of computing applications beyond graphics....

"[One] user will be Michael Cummings, associate professor of biology and a scientist in the university's Center for Bioinformatics and Computational Biology. Cummings will be applying the technology to evolutionary studies. "GPUs provide an excellent opportunity to speed up the intensive numerical calculations associated with inferring the evolutionary relationships of organisms in the tree of life," he said."

Project Summary for"Grid, Public and GPU Computing for the Tree of Life"

This proposal seeks to accelerate ATOL (Assembling the Tree of Life) research, and phylogenetic research more broadly, by creating tools that expand the computing power freely available to all phylogeneticists. The central idea is to combine Grid and GPU (graphics processing unit) computing to take better advantage of a diversity of computing resources, particularly existing desktop processingcapacity available through public-computing. The main product will be a Grid system, customized for phylogenetic tree search and accessed through a user-friendly web interface, that links thousands of individual computers world-wide. The likelihood-based tree search program GARLI (Genetic Algorithm for Rapid Likelihood Inference), will serve as the initial model application during development. The new system is intended to allow analyses that far transcend what one can do on a single desktop computer or moderate-sized cluster. For example, it should become possible to carry out extensive bootstrap analyses in little more time than is now required for a single tree search. The project will also exploit a second under-utilized resource inside desktop computers, namely the graphics processing unit (GPU), which can do many scientific calculations faster than the central processing unit (CPU). A free, open-source library (C/C++) for maximum likelihood calculations using parallel CPU/GPU processing will be developed. GARLI versions will be developed that take advantage of major GPU platforms. Subsequent development will extend to other likelihood-intensive methods (e.g., Bayesian analysis). Five participating ATOL projects will help test the new tools, and publish a collaborative evaluation of the performance of the new system across the diverse phylogenetic problems they represent.

The taxon information pages (accessible thorough: http://www.leptree.net/taxon_info ) now have a new system for indicating authorship. Authorship is more prominently labelled at the top of the "view all" page for each taxon, and the citation reference at the bottom of every page now includes authorship for each particular taxon page. This makes authorship of these pages clearer, and provides all the information users need to cite a LepTree taxon page in one easy-to-find location.

The initials results of the Leptree molecular project have now been published in BMC Evolutionary Biology. The paper is available
here. The abstract is reprinted below.

Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study

Jerome C Regier, Andreas Zwick, Michael P Cummings, Akito Y Kawahara, Soowon Cho, Susan Weller, Amanda Roe, Joaquin Baixeras, John W Brown, Cynthia Parr, Donald R Davis, Marc Epstein, Winifred Hallwachs, Axel Hausmann, Daniel H Janzen, Ian J Kitching, M Alma Solis, Shen-Horn Yen, Adam L Bazinet and Charles Mitter

BMC Evolutionary Biology 2009, 9:280doi:10.1186/1471-2148-9-280
Published: 2 December 2009

Abstract (provisional)

Background

In the mega-diverse insect order Lepidoptera (butterflies and moths; 165,000 described species), deeper relationships are little understood within the clade Ditrysia, to which 98% of the species belong. To begin addressing this problem, we tested the ability of five protein-coding nuclear genes (6.7 kb total), and character subsets therein, to resolve relationships among 123 species representing 27 (of 33) superfamilies and 55 (of 100) families of Ditrysia under maximum likelihood analysis.

Results

Our trees show broad concordance with previous morphological hypotheses of ditrysian phylogeny, although most relationships among superfamilies are weakly supported. There are also notable surprises, such as a consistently closer relationship of Pyraloidea than of butterflies to most Macrolepidoptera. Monophyly is significantly rejected by one or more character sets for the putative clades Macrolepidoptera as currently defined (P < 0.05) and Macrolepidoptera excluding Noctuoidea and Bombycoidea sensu lato (P [less than or equal to] 0.005), and nearly so for the superfamily Drepanoidea as currently defined (P < 0.08). Superfamilies are typically recovered or nearly so, but usually without strong support. Relationships within superfamilies and families, however, are often robustly resolved. We provide some of the first strong molecular evidence on deeper splits within Pyraloidea, Tortricoidea, Geometroidea, Noctuoidea and others. Separate analyses of mostly synonymous versus non-synonymous character sets revealed notable differences (though not strong conflict), including a marked influence of compositional heterogeneity on apparent signal in the third codon position (nt3). As available model partitioning methods cannot correct for this variation, we assessed overall phylogeny resolution through separate examination of trees from each character set. Exploration of "tree space" with GARLI, using grid computing, showed that hundreds of searches are typically needed to find the best-feasible phylogeny estimate for these data.

Conclusions

Our results (a) corroborate the broad outlines of the current working phylogenetic hypothesis for Ditrysia, (b) demonstrate that some prominent features of that hypothesis, including the position of the butterflies, need revision, and (c) resolve the majority of family and subfamily relationships within superfamilies as thus far sampled. Much further gene and taxon sampling will be needed, however, to strongly resolve individual deeper nodes.

Annotated review and discussion of phylogenetically important characters for families and subfamilies of Gelechioidea (Insecta: Lepidoptera).
Sibyl Rae Bucheli, 2009. Zootaxa 2261: 1-22.

Abstract: Gelechioidea is a large, diverse superfamily of microlepidoptera that is difficult to characterize due to its species richness. The main working taxonomic unit for Gelechioidea seems to be the subfamily level, although many researchers use the taxonomy of family and subfamily interchangeably. Some researchers believe the superfamily should be split into several superfamilies to better diagnose lineages. Only recently have there been attempts at comprehensive treatments that aim to address world fauna of the entire superfamily rather than focusing on a few local families. This work reviews the revisional history of Gelechioidea, focusing on major taxonomic publications. It also addresses character state delineation and terminology for many taxa in some cases establishing equivalence across authors for the first time. Finally, it reviews major trends in phylogenetics and classification of the megadiverse lineage Gelechioidea.

We recently made it possible for authors to illustrate taxon template entries with photos or anatomical drawings, and to link to other sources of information. Adding links and images to taxon pages is not hard, and our new online directions will guide you through the process. You can find the directions here.

Jennifer Zaspel won the Entomological Society of America Foundation's Snodgrass Memorial award for outstanding research on her dissertation entitled "Systematics, biology, and behavior of fruit-piercing and blood-feeding moths in the subfamily calpinae (Lepidoptera: Noctuidae)". She will be presented with a certificate and cash award at the December 2009 ESA meeting in Indianapolis.
Congratulations Jen!

Molecular Biology and Genetics of Lepidoptera

Amanda D. Roe, Susan J. Weller, Joaquin Baixeras, John Brown, Michael P. Cummings, Donald R. Davis, Akito Y. Kawahara, Cynthia S. Parr, Jerome C. Regier, Daniel Rubinoff, Thomas J. Simonsen, Niklas Wahlberg, Andreas Zwick

This is a book chapter on the Evolutionary Framework for Lepidoptera Model Systems. pp. 1-24 In Goldsmith, M. & F. Marec (eds.), Genetics and Molecular Biology of Lepidoptera. CRC Press, Boca Raton.

Figure 1.1 from Roe et al. 2009. Representatives of superfamilies containing model systems.

This poster, written for the June Lepidopterists' Society and Association for Tropical Lepidoptera annual meeting, Chetumal, Quintana Roo, Mexico (meeting rescheduled for September 23rd-26th), gives the latest on our group's progress. Take a look!
http://www.leptree.net/system/files/LepTreeposterMay2009.jpg