GOGOT: a method for the identification of differentially expressed fragments from cDNA-AFLP data

<p>Abstract</p> <p>Background</p> <p>One-dimensional (1-D) electrophoretic data obtained using the cDNA-AFLP method have attracted great interest for the identification of differentially expressed transcript-derived fragments (TDFs). However, high-throughput analysis of the cDNA-AFLP data is currently limited by the need for labor-intensive visual evaluation of multiple electropherograms. We would like to have high-throughput ways of identifying such TDFs.</p> <p>Results</p> <p>We describe a method, GOGOT, which automatically detects the differentially expressed TDFs in a set of time-course electropherograms. Analysis by GOGOT is conducted as follows: correction of fragment lengths of TDFs, alignment of identical TDFs across different electropherograms, normalization of peak heights, and identification of differentially expressed TDFs using a special statistic. The output of the analysis is a highly reduced list of differentially expressed TDFs. Visual evaluation confirmed that the peak alignment was performed perfectly for the TDFs by virtue of the correction of peak fragment lengths before alignment in step 1. The validity of the automated ranking of TDFs by the special statistic was confirmed by the visual evaluation of a third party.</p> <p>Conclusion</p> <p>GOGOT is useful for the automated detection of differentially expressed TDFs from cDNA-AFLP temporal electrophoretic data. The current algorithm may be applied to other electrophoretic data and temporal microarray data.</p

A European reference collection of rose varieties : final report

An integrated pilot database was constructed containing administrative, morphological and molecular data as well as pictures of each variety. In spite of some encountered difficulties, it was demonstrated that two laboratories can produce substantially equivalent data and that the molecular data produced is useful as a tool for managing reference collections, prescreening and quality assuranc

Patterns and process during the diversification of the cichlid fishes in Lake Malawi, Africa

The 500-1000 cichlid species endemic to Lake Malawi constitute one of the most rapid and extensive radiations of vertebrates ever discovered. The objective of this dissertation was to test the assumptions and predictions of several recently published models of cichlid speciation. First, a novel assay of female choice was used to evaluate the role of visual cues during conspecific recognition. The results of this experiment demonstrate that females are able to identify conspecific mates using only visual cues. Second, the assumptions of a recent model of speciation via intrasexual selection were tested by comparing aggressive behavior during territorial contests among five closely related cichlid species from Lake Malawi. I found that interactions between conspicuously heteromorphic males tend to be less aggressive than between those of homomorphic males. Third, I used transect data to evaluate the intrinsic and extrinsic factors that have affected the dispersal of 17 closely related cichlid species introduced to Thumbi West Island in Lake Malawi. A quarter of a century after their initial introduction, I found that the translocated cichlid community around Thumbi West Island is still in a state of flux, as many species continue to spread around the island. Next, I evaluated the patterns of divergence predicted by three competing speciation models that differ in the temporal action of natural and sexual selection by using AFLP to reconstruct the evolutionary relationships among 20 species of the ubiquitous rock dwelling subgenus Pseudotropheus tropheops. I found that cladogenesis is associated with numerous unambiguous changes in male color states. A geometric morphometric analysis of the lower jaw of these taxa revealed that the repeated differentiation of jaw morphology is associated with species habitat preference. Finally, I used AFLP data to reconstruct the evolution of species within three genera of sand dwelling cichlids that construct elaborate male display platforms. I found that sister taxa with distinct bower morphologies, and that exist in discrete leks separated by only 1-2m of depth, are divergent in both sexually selected and ecological traits. These phylogenies suggest that the forces of sexual and ecological selection have been intertwined during the speciation of these groups

Characterizing the phylogenetic distribution of cryptic species in the Rhodophyta using novel gene sequence analysis and molecular morphometrics

The Rhodophyta (red algae) are an ancient crown group of the Eukarya (ca. 1400-1500 million years), comprised of 5000 - 6000 species. Gametophytes of taxa excluding the speciose Class Florideophyceae are typically of very simple unicellular, filamentous or foliose morphologies. These simple morphologies are often homoplasious (resulting from convergent or parallel evolution) and can be indistinguishable among distinct taxa, leading to cryptic species. As a result, historical morphology-based taxonomy is often not congruent with evolutionary history. Intraspecific genetic variation is not yet characterized for non-Florideophyceae taxa. Here the intraspecific genetic variation was characterized for a locally endemic, morphologically distinct bangiophyte red alga, Bangia maxima Gardner using inter simple sequence repeat (ISSR) patterns from 91 individual filaments across seven local populations. A high degree of genetic variation was observed over very small distances (< 25 cm) and very little genetic exchange was observed between populations. It is possible that B. maxima is a true endemic species and its population dynamics may differ from other Bangia species. Metrics of sequence-based identification rely on genetic divergence among isolates to distinguish taxonomic units independent of morphology. Such metrics are especially useful for morphologically simple or cryptic species. The mitochondrial cytochrome oxidase c subunit 1 gene has been proposed for the Florideophyceae. An evaluation of this gene as a metric for non-Florideophyceae taxa was undertaken and limited utility was demonstrated in most lineages of Rhodophyta due to poor or inconsistent amplification and conflicts with nuclear and plastid phylogenies. Patterns of genetic divergence among taxa are used to infer evolutionary relationships. The nuclear ribosomal small subunit (nSSU rRNA) is the taxonomically broadest pool of gene sequence data for the Rhodophyta. The use of stochastic models of nucleotide evolution is the most common approach to inferring phylogenies using this gene, ignoring much of its evolutionary information as different characters that contribute to secondary structure (e.g. paired nucleotides) are treated independently. The incorporation of structural information leads to more biologically realistic evolutionary models increasing phylogenetic resolution. Parametric models incorporating structural information were used here to more fully resolve phylogenies for all known Rhodophyta lineages. Novel phylogenetic topologies were observed and well supported for each Class within the Rhodophyta resulting in a number of formally proposed or suggested taxonomic revisions. These include phylogenetic resolution of Rhodophyta Classes, support for the introduction of 11 genera within the Bangiales and support for various taxonomic revisions within the Florideophyceae previously proposed but not yet fully adopted. As structure evolves more slowly than its constituent sequence, secondary structure elements can further resolve evolutionary relationships, especially in lineages as old as the Rhodophyta. A novel encoding of secondary structure elements and subsequent multivariate analysis was performed for all known Rhodophyta nSSU rRNA gene sequences, reinforcing phylogenetic results. Computer programs developed for these analyses are publicly available. The analyses presented here significantly advanced understanding of the evolutionary distribution of cryptic species within the Rhodophyta. Furthermore, useful methods for the characterization of such species are presented, as is a demonstration of the utility of biologically realistic sequence models parameterizing nSSU rRNA structure in resolving ambiguous phylogenetic relationships. Most importantly, this work also represents a significant improvement toward taxonomy congruent with evolutionary history for the Rhodophyta