- beg-evodevo@psb.ugent.be - maillist.psb.ugent.be

[Beg-evodevo] Gene Family Evolution across 12 Drosophila Genomes
by Klaas Vandepoele 02 Dec '07

02 Dec '07

*Gene Family Evolution across 12 /Drosophila/ Genomes* Matthew W. Hahn, Mira V. Han, and Sang-Gook Han

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[Beg-evodevo] PubMed :: Evolutionary consequences of a large duplication event in Trypanosoma brucei: Chromosomes 4 and 8 are partial duplicons
by Klaas Vandepoele 29 Nov '07

29 Nov '07

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[Beg-evodevo] About :: Consequences of genome duplication (Semon & Wolfe)
by Klaas Vandepoele 22 Nov '07

22 Nov '07

2 quotes from this excellent review: "but RGL (reciprocal gene loss) has not yet been documented on a whole-genome scale in plants. In view of the numerous WGDs that have occurred during angiosperm evolution, the inevitable RGLs that can be inferred to have happened afterwards must be considered as prime suspects for agents of plant speciation. Hard evidence implicating RGLs as a cause of speciation is, however, still lacking in both plants and fishes, in contrast to /Drosophila." /"The plant kingdom is the uncontested big kahuna of polyploidization, but simpler non-plant systems still offer many lessons that can help us understand the waves of successive WGDs that have washed over angiosperm evolution." In conclusion: - some interesting objectives for future research can be distilled from this paper (Seb captures some of these nicely in his IWT project!). Concerning RGL, the Scannell/Wolfe papers in Nature/GR are pioneering. - we should be cautious about providing all our plant comparative genomics data to the community (i.e. we /first /should try to extract the nice biological stories before releasing the data). Or in other words: Ken has already proven to be extremely aware & fast ;-) best, Klaas PS. Sorry for cross-posting -- ================================================================== Klaas Vandepoele, PhD Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium E-mail: Klaas.Vandepoele(a)psb.ugent.be Website: http://bioinformatics.psb.ugent.be/ ==================================================================

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[Beg-evodevo] Evolutionary developmental biology and genomics. [Nat Rev Genet. 2007] - PubMed Result
by Yves Van de Peer 18 Nov '07

18 Nov '07

http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&dopt=AbstractPlus&db=… -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.ugent.be http://bioinformatics.psb.ugent.be/

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[Beg-evodevo] Consequences of genome duplication. [Curr Opin Genet Dev. 2007] - PubMed Result
by Yves Van de Peer 18 Nov '07

18 Nov '07

http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&dopt=AbstractPlus&db=… -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.ugent.be http://bioinformatics.psb.ugent.be/

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[Beg-evodevo] PLoS Genetics - Gene Family Evolution across 12 Drosophila Genomes
by Klaas Vandepoele 12 Nov '07

12 Nov '07

http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10.1371…

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[Beg-evodevo] ScienceDirect - Trends in Genetics : A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages
by Cindy Martens 10 Nov '07

10 Nov '07

*A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages* * Tomislav Domazet-Los(o, Josip Brajkovic' and Diethard Tautz* Macroevolutionary trends traditionally are studied by fossil analysis, comparative morphology or evo-devo approaches. With the availability of genome sequences and associated data from an increasing diversity of taxa, it is now possible to add an additional level of analysis: genomic phylostratigraphy. As an example of this approach, we use a phylogenetic framework and embryo expression data from /Drosophila/ to show that grouping genes by their phylogenetic origin can uncover footprints of important adaptive events in evolution. -- ================================================================== Cindy Martens VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM Tel: +32 (0)9 331 38 22 Fax: +32 (0)9 331 38 09 E-mail: cindy.martens(a)psb.ugent.be Website: http://bioinformatics.psb.ugent.be/ ==================================================================

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[Beg-evodevo] Comparative genome analysis across a kingdom of eukaryotic organisms: Specialization and diversification in the Fungi -- Cornell et al., 10.1101/gr.6531807 -- Genome Research
by Cindy Martens 05 Nov '07

05 Nov '07

http://www.genome.org/cgi/reprint/gr.6531807v1 -- ================================================================== Cindy Martens VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM Tel: +32 (0)9 331 38 22 Fax: +32 (0)9 331 38 09 E-mail: cindy.martens(a)psb.ugent.be Website: http://bioinformatics.psb.ugent.be/ ==================================================================

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[Beg-evodevo] gene duplication in mammals
by Stefanie De Bodt 29 Oct '07

29 Oct '07

The Pattern of Evolution of Smaller-Scale Gene Duplicates in Mammalian Genomes is More Consistent with Neo- than Subfunctionalisation -- ================================================================== Stefanie De Bodt, PhD VIB Department of Plant Systems Biology, UGent Bioinformatics and Evolutionary Genomics Technologiepark 927 B-9052 Gent Belgium Tel: 32 (0)9 3313692 Website: http://bioinformatics.psb.ugent.be ==================================================================

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[Beg-evodevo] Reconcilation with non-binary species trees :: NOTUNG update
by Klaas Vandepoele 29 Oct '07

29 Oct '07

http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&dopt=AbstractPlus&db=… Apparently the only shortcoming of NOTUNG (ie cannot handle multifurcated trees when preforming tree reconciliation) is now partially resolved: they now can handle such species trees, but apparently still require binary gene trees... Klaas *1: *Comput Syst Bioinformatics Conf. <javascript:AL_get(this, 'jour', 'Comput Syst Bioinformatics Conf.');> 2007;6:441-52.[image: Click here to read]<http://www.ncbi.nlm.nih.gov/entrez/utils/fref.fcgi?PrId=5265&itool=Abstract…> Links <javascript:PopUpMenu2_Set(Menu17951846);> Reconcilation with non-binary species trees.*Vernot B*<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=PubMed&Cmd=Search&Term=%22Verno…>, *Stolzer M*<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=PubMed&Cmd=Search&Term=%22Stolz…>, *Goldman A*<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=PubMed&Cmd=Search&Term=%22Goldm…>, *Durand D*<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=PubMed&Cmd=Search&Term=%22Duran…> . Departments of Biological Sciences and Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA. durand(a)cs.cmu.edu. Reconciliation is the process of resolving disagreement between gene and species trees, by invoking gene duplications and losses to explain topological incongruence. The resulting inferred duplication histories are a valuable source of information for a broad range of biological applications, including ortholog identification, estimating gene duplication times, and rooting and correcting gene trees. Reconciliation for binary trees is a tractable and well studied problem. However, a striking proportion of species trees are non-binary. For example, 64% of branch points in the NCBI taxonomy have three or more children. When applied to non-binary species trees, current algorithms overestimate the number of duplications because they cannot distinguish between duplication and deep coalescence. We present the first formal algorithm for reconciling binary gene trees with non-binary species trees under a duplication-loss parsimony model. Using a space efficient mapping from gene to species tree, our algorithm infers the minimum number of duplications and losses in O(|V(G)| . (k(S) + h(S))) time, where V(G) is the number of nodes in the gene tree, h(S) is the height of the species tree and k(S) is the width of its largest multifurcation. We also present a dynamic programming algorithm for a combined loss model, in which losses in sibling species may be represented as a single loss in the common ancestor. Our algorithms have been implemented in NOTUNG, a robust, production quality tree-fitting program, which provides a graphical user interface for exploratory analysis and also supports automated, high-throughput analysis of large data sets.

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