TY  - JOUR
A1  - Hill, Natascha
A1  - Leow, Alexander
A1  - Bleidorn, Christoph
A1  - Groth, Detlef
A1  - Tiedemann, Ralph
A1  - Selbig, Joachim
A1  - Hartmann, Stefanie
T1  - Analysis of phylogenetic signal in protostomial intron patterns using Mutual Information
JF  - Theory in biosciences
N2  - Many deep evolutionary divergences still remain unresolved, such as those among major taxa of the Lophotrochozoa. As alternative phylogenetic markers, the intron-exon structure of eukaryotic genomes and the patterns of absence and presence of spliceosomal introns appear to be promising. However, given the potential homoplasy of intron presence, the phylogenetic analysis of this data using standard evolutionary approaches has remained a challenge. Here, we used Mutual Information (MI) to estimate the phylogeny of Protostomia using gene structure data, and we compared these results with those obtained with Dollo Parsimony. Using full genome sequences from nine Metazoa, we identified 447 groups of orthologous sequences with 21,732 introns in 4,870 unique intron positions. We determined the shared absence and presence of introns in the corresponding sequence alignments and have made this data available in "IntronBase", a web-accessible and downloadable SQLite database. Our results obtained using Dollo Parsimony are obviously misled through systematic errors that arise from multiple intron loss events, but extensive filtering of data improved the quality of the estimated phylogenies. Mutual Information, in contrast, performs better with larger datasets, but at the same time it requires a complete data set, which is difficult to obtain for orthologs from a large number of taxa. Nevertheless, Mutual Information-based distances proved to be useful in analyzing this kind of data, also because the estimation of MI-based distances is independent of evolutionary models and therefore no pre-definitions of ancestral and derived character states are necessary.
KW  - Mutual Information
KW  - Evolution
KW  - Gene structure
Y1  - 2013
U6  - https://doi.org/10.1007/s12064-012-0173-0
SN  - 1431-7613
VL  - 132
IS  - 2
SP  - 93
EP  - 104
PB  - Springer
CY  - New York
ER  - 
TY  - JOUR
A1  - Steinert, Bastian
A1  - Cassou, Damien
A1  - Hirschfeld, Robert
T1  - CoExist overcoming aversion to change preserving immediate access to source code and run-time information of previous development states
JF  - ACM SIGPLAN notices
N2  - Programmers make many changes to the program to eventually find a good solution for a given task. In this course of change, every intermediate development state can of value, when, for example, a promising ideas suddenly turn out inappropriate or the interplay of objects turns out more complex than initially expected before making changes. Programmers would benefit from tool support that provides immediate access to source code and run-time of previous development states of interest. We present IDE extensions, implemented for Squeak/Smalltalk, to preserve, retrieve, and work with this information. With such tool support, programmers can work without worries because they can rely on tools that help them with whatever their explorations will reveal. They no longer have to follow certain best practices only to avoid undesired consequences of changing code.
KW  - Design
KW  - Experimentation
KW  - Human Factors
KW  - Continuous Testing
KW  - Continuous Versioning
KW  - Debugging
KW  - Evolution
KW  - Explore-first Programming
KW  - Fault Localization
KW  - Prototyping
Y1  - 2013
U6  - https://doi.org/10.1145/2480360.2384591
SN  - 0362-1340
VL  - 48
IS  - 2
SP  - 107
EP  - 117
PB  - Association for Computing Machinery
CY  - New York
ER  -