Research

There are many different research projects that use The Lattice Project. This page explains these projects in more detail.

NOTE: If you use The Lattice Project for your work, please cite us by choosing from among the appropriate recent publications listed on our publications page.



Projects by Grid Service



GARLI

The Cummings Laboratory, the Leptree project, and others are using GARLI to infer evolutionary relationships based on DNA sequence data.

The Leptree project investigates evolutionary relationships within the insect order Lepidoptera (moths and butterflies), in particular of higher taxa, such as families, superfamilies and infraorders. This molecular "backbone phylogeny" is based on the analysis of up to 26 protein-coding nuclear genes (~19kb) for currently 123 taxa, but work on a matrix for 550 to 600 taxa is well underway. The chief method of analysis used in this study is a nucleotide model maximum likelihood search in GARLI. The most commonly applied model is the generalized time-reversible model with a gamma distribution of rates and a proportion of invariant sites (GTR+G+I). The Leptree project relies heavily on the computational resources provided by The Lattice Project, as the sheer number of heuristic searches is not feasible to run on an individual desktop machine. The bulk of these heuristic searches consist of bootstrap replicates (up to 2,000 per analysis), but in addition, due to the heuristic nature of the search, multiple searches (up to 500) are required for confidence in having found the maximum likelihood tree. For the Leptree project, many analyses of these types are carried out; e.g., for individual and combined genes, synonymous and non-synonymous data partitions, and with and without topological constraints for subsequent hypothesis testing.


The Sower lab is studying hagfish evolution. Hagfish, which lack both jaws and vertebrae, are considered the most primitive vertebrate known, living or extinct. They have long been the enigma of vertebrate evolution not only because of their evolutionary position, but also because of our lack of knowledge on fundamental processes. Key elements of the reproductive endocrine system in hagfish have yet to be elucidated. Here, the presence and identity of a functional glycoprotein hormone (GPH) have been elucidated from the brown hagfish Paramyxine atami. The hagfish GPH consists of two subunits, α and β, which are synthesized and colocalized in the same cells of the adenohypophysis. The cellular and transcriptional activities of hagfish GPHα and -β were significantly correlated with the developmental stages of the gonad. The purified native GPH induced the release of gonadal sex steroids in vitro. From our phylogenetic analysis, we propose that ancestral glycoprotein α-subunit 2 (GPA2) and β-subunit 5 (GPB5) gave rise to GPHα and GPHβ of the vertebrate glycoprotein hormone family, respectively. The identified hagfish GPHα and -β subunits appear to be the typical gnathostome GPHα and -β subunits based on the sequence and phylogenetic analyses. We hypothesize that the identity of a single functional GPH of the hagfish, hagfish GTH, provides critical evidence for the existence of a pituitary-gonadal system in the earliest divergent vertebrate that likely evolved from an ancestral, prevertebrate exclusively neuroendocrine mechanism by gradual emergence of a previously undescribed control level, the pituitary, which is not found in the Protochordates.


Miriam Reyna-Fabián aims to solve the intra- and inter-genus relationships of more than 15 species of rotifers, currently assigned to the family Brachionidae. Species of this family are free-living organisms and they compose part of the zooplankton in freshwater and marine systems. Variation in morphological characters has traditionally been used to differentiate species. However, the taxonomic positions of 3 species — Brachionus patulus, B. macracanthus and B. polyacanthus — have been controversial. A study based on scanning electron microscopy of the trophy (Segers et al., 1993) proposed erecting these 3 species to a new genus: Plationus.

The phylogenetic analyses of the family Brachionidae were carried out through the analysis of genes encoding cytochrome oxidase subunit 1 (Cox 1) and the domains (D2-D3) of the 28S rRNA. A total of 23 sequences, including 8 outgroups, were aligned. The phylogenies derived from this study were used to evaluate the validity of the new genus Plationus. Our analyses support the hypothesis that Plationus patulus and P. macracanthus compose a distinct clade from Brachionus and Platyias with high bootstrap values.

  • Reyna-Fabian ME, Laclette JP, Cummings MP, Garcia-Varela M. 2010. Validating the systematic position of Plationus Segers, Murugan & Dumont, 1993 (Rotifera: Brachionidae) using sequences of the large subunit of the nuclear ribosomal DNA and of cytochrome C oxidase. Hydrobiologia 644:361-370.


The Neel lab is studying phylogenetic relationships among North American members of the genus Agalinis Raf. These species represent a taxonomically challenging group and there have been extensive historical revisions at the species, section, and subsection levels of classification. The genus contains many rare species, including the federally listed endangered species Agalinis acuta. In addition to evaluating the degree to which historical classifications at the section and subsection levels are supported by molecular data sampled from 79 individuals representing 29 Agalinis species, we assessed the monophyly of 27 species by sampling multiple individuals representing different populations of those species. Twenty-one of these species are of conservation concern in at least some part of their range.


Silvana Marten-Rodriguez aims to understand the role of pollinators in the evolution of floral traits and breeding systems in the Antillean tribe Gesnerieae by combining phylogenetic approaches with ecological studies. The tribe Gesnerieae encompasses species specialized for hummingbird or bat pollination as well as some generalized species pollinated by bats, hummingbirds and insects. Preliminary phylogenies suggest various independent pollination system transitions as well as the evolution of reproductive assurance mechanisms (i.e. autonomous self-pollination). Low frequencies of hummingbird visitation and high pollen limitation in specialized hummingbird pollinated species might be responsible for these transitions.


Arthropod relationships:


Leaf mining moths and relatives:


The 1400 species of hawkmoths (Lepidoptera: Sphingidae) comprise one of most conspicuous and well- studied groups of insects, and provide model systems for diverse biological disciplines. However, a robust phylogenetic framework for the family is currently lacking. Morphology is unable to confidently determine relationships among most groups. As a major step toward understanding relationships of this model group, we have undertaken the first large-scale molecular phylogenetic analysis of hawkmoths representing all subfamilies, tribes and subtribes.



Structure

Julie B. Hebert is examining population structure of a leafmining fly, Phytomyza glabricola, on its two host plants, Ilex coriacea and I. glabra. Results from Structure indicate significant host-associated differentiation in the flies, but also show signs of current migration and gene flow. She is also using Structure to examine potential hybridization between the two Ilex species.



HMMPfam

The Edwards Laboratory is using the HMMPfam service to compute Pfam assignments for all bacterial, plasmid, and virus protein sequences from Swiss-Prot, TrEMBL, GenBank, RefSeq, and TIGR's CMR, plus an inclusive set of all plausible Glimmer predictions from RefSeq bacterial genomes. These protein sequences, and their Pfam assignments, are used in the Rapid Microorganism Identification Database.The HMMPfam service is also being used as a model for "data-heavy" bioinformatics applications on The Lattice Project grid infrastructure, a collaboration between the Cummings and Edwards laboratories.

  • N.J. Edwards and F. Pineda. Poster at ASMS (2006). Rapid Microorganism Identification Database, 2006.



Complab

Dr. Catherine Dibble's Computational Laboratories Group uses agent-based simulation models to study the geographic spread of Avian Influenza across the United States in order to quantify the relative pandemic risk of US cities and determine optimal intervention strategies. The grid service being used is Complab.

  • Catherine Dibble, Stephen Wendel, and Kristofor Carle (University of Maryland). Simulating Pandemic Influenza Risks of U.S. Cities. In Proceedings of the 2007 Winter Simulation Conference, 2007.



gsi

The Cummings Laboratory is using gsi to assess the performance of the statistic in a variety of situations.

  • Cummings, M. P., M. C. Neel and K. L. Shaw. 2008. A genealogical approach to quantifying lineage divergence. Evolution 62:2411-2422.



MARXAN

Maile Neel and Joanna Grand are using Marxan to quantify the effects of poor and incomplete data on the ability to capture biological diversity in nature reserves.

  • Grand, J., M. P. Cummings, A. G. Rebelo, T. H. Ricketts, and M. C. Neel. 2007. Biased data reduce efficiency and effectiveness of conservation reserve networks.
    Ecology Letters 10:364-374.



CNS

The Laboratory of David Fushman runs protein:protein docking algorithms on Lattice. When driven by experimentally derived constraints, these will help in modeling the structures of large multi-subunit proteins, and the interactions of such proteins with various ligands. CNS is the featured grid service in this project.

  • Varadan, R., Assfalg, M., Raasi, S., Pickart, C. & Fushman, D. Structural Determinants for Selective Recognition of a Lys48-Linked Polyubiquitin Chain by a UBA Domain. Mol Cell 18, 687-98 (2005).



MDIV and IM

Floyd Reed and Holly Mortensen from the Laboratory of Sarah Tishkoff have run a number of MDIV and IM simulations through The Lattice Project. These are studies in molecular population genetics that seek to use DNA sequence polymorphism to estimate the times of divergence and migration rates among ethnically diverse human populations in Africa.