Motivation Outline Near intron positions are reliable phylogenetic markers: An application to holometabolous insects Veiko Krauss, Christian Thümmler, Franziska Georgi, Jörg Lehmann, Peter F. Stadler and Carina Eisenhardt Bioinformatics Group, Department of Computer Science, University of Leipzig Bled, Slovenia, Feb 18 2008 J. Lehmann NIPs are reliable phylogenetic markers 1/29 What are introns? Phylogeny? from: Charles Darwin, “On the Origin of Species” (1859) Short introduction to phylogenetics/cladistics A novel marker class: Near-intron-positions Application to holometabolic insect orders Discussion and Outlook Outline 1 Short introduction to phylogenetics/cladistics 2 A novel marker class: Near-intron-positions 3 Application to holometabolic insect orders 4 Discussion and Outlook J. Lehmann NIPs are reliable phylogenetic markers 4/29 Short introduction to phylogenetics/cladistics A novel marker class: Near-intron-positions Application to holometabolic insect orders Discussion and Outlook Definitions Genome-level characters Outline 1 Short introduction to phylogenetics/cladistics 2 A novel marker class: Near-intron-positions 3 Application to holometabolic insect orders 4 Discussion and Outlook J. Lehmann NIPs are reliable phylogenetic markers 5/29 Short introduction to phylogenetics/cladistics A novel marker class: Near-intron-positions Application to holometabolic insect orders Discussion and Outlook Definitions Genome-level characters Molecular phylogenetics & cladistics hierarchical classification of species based on evolutionary ancestry using molecular data input data: set of species, characteristics, and corresp. character states for each species final result: cladogram inferring of phylogenies: parsimony, maximum likelihood, bayesian approaches J. Lehmann NIPs are reliable phylogenetic markers 6/29 Short introduction to phylogenetics/cladistics A novel marker class: Near-intron-positions Application to holometabolic insect orders Discussion and Outlook Definitions Genome-level characters Some definitions (cladistics) plesiomorph: character states defined to have been present before the lca of a species group; ancestral (“original”) synapomorph: character states that were present only in the lca; common derived; (“changed”) homoplasy: character shared by multiple species not due to common ancestry → is to be avoided in cladistic analysis J. Lehmann NIPs are reliable phylogenetic markers 7/29 Short introduction to phylogenetics/cladistics A novel marker class: Near-intron-positions Application to holometabolic insect orders Discussion and Outlook Definitions Genome-level characters Some definitions (cladistics) plesiomorph: character states defined to have been present before the lca of a species group; ancestral (“original”) synapomorph: character states that were present only in the lca; common derived; (“changed”) homoplasy: character shared by multiple species not due to common ancestry → is to be avoided in cladistic analysis J. Lehmann NIPs are reliable phylogenetic markers 7/29 Short introduction to phylogenetics/cladistics A novel marker class: Near-intron-positions Application to holometabolic insect orders Discussion and Outlook Definitions Genome-level characters Some definitions (cladistics) plesiomorph: character states defined to have been present before the lca of a species group; ancestral (“original”) synapomorph: character states that were present only in the lca; common derived; (“changed”) homoplasy: character shared by multiple species not due to common ancestry → is to be avoided in cladistic analysis J. Lehmann NIPs are reliable phylogenetic markers 7/29 Short introduction to phylogenetics/cladistics A novel marker class: Near-intron-positions Application to holometabolic insect orders Discussion and Outlook Definitions Genome-level characters Problems with molecular sequence comparisons Evolutionary (eukaryotic) tree still remains partly unresolved: only few synapomorphies among higher taxa in monophyletic groups many cases of homoplasy (character convergence/reversion) J. Lehmann NIPs are reliable phylogenetic markers 8/29 Short introduction to phylogenetics/cladistics A novel marker class: Near-intron-positions Application to holometabolic insect orders Discussion and Outlook Definitions Genome-level characters Genome-level characters Higher-order features (genome-level characters) esp. to supplement molecular studies (to be weighted w.r.t. morphological/DNA data) character distributions allow evaluation of different (ordinal) tree hypotheses by counting synapomorphies Some examples mitochondrial gene arrangements retrotransposon markers (transposon insertion analysis, e.g. for mammalian introns) intron markers (variation in spliceosomal intron positions) J. Lehmann NIPs are reliable phylogenetic markers 9/29 Short introduction to phylogenetics/cladistics A novel marker class: Near-intron-positions Application to holometabolic insect orders Discussion and Outlook Definitions Genome-level characters Genome-level characters Higher-order features (genome-level characters) esp. to supplement molecular studies (to be weighted w.r.t. morphological/DNA data) character distributions allow evaluation of different (ordinal) tree hypotheses by counting synapomorphies Some examples mitochondrial gene arrangements retrotransposon markers (transposon insertion analysis, e.g. for mammalian introns) intron markers (variation in spliceosomal intron positions) J. Lehmann NIPs are reliable phylogenetic markers 9/29 Short introduction to phylogenetics/cladistics A novel marker class: Near-intron-positions Application to holometabolic insect orders Discussion and Outlook Outline 1 Short introduction to phylogenetics/cladistics 2 A novel marker class: Near-intron-positions 3 Application to holometabolic insect orders 4 Discussion and Outlook J. Lehmann NIPs are reliable phylogenetic markers 10/29 Short introduction to phylogenetics/cladistics A novel marker class: Near-intron-positions Application to holometabolic insect orders Discussion and Outlook NIP character - synapomorphic distribution J. Lehmann NIPs are reliable phylogenetic markers 11/29 Short introduction to phylogenetics/cladistics A novel marker class: Near-intron-positions Application to holometabolic insect orders Discussion and Outlook Holometabolous insect phylogenies NIP analysis Results Outline 1 Short introduction to phylogenetics/cladistics 2 A novel marker class: Near-intron-positions 3 Application to holometabolic insect orders 4 Discussion and Outlook J. Lehmann NIPs are reliable phylogenetic markers 12/29 Short introduction to phylogenetics/cladistics A novel marker class: Near-intron-positions Application to holometabolic insect orders Discussion and Outlook Holometabolous insect phylogenies NIP analysis Results Holometabolous insects (Endopterygota) Main characteristics complete metamorphosis (holometabolism) insects with distinctive larval, pupal, and adult stages major orders: Coleoptera (beetles, e.g. Tribolium) Diptera (flies, e.g. Drosophila) Hymenoptera (ants, bees, sawflies, wasps; e.g. Apis) Lepidoptera (butterflies, moths; e.g. Bombyx) J. Lehmann NIPs are reliable phylogenetic markers 13/29 Short introduction to phylogenetics/cladistics A novel marker class: Near-intron-positions Application to holometabolic insect orders Discussion and Outlook Holometabolous insect phylogenies NIP analysis Results Holometabolous insects (Endopterygota) Main characteristics complete metamorphosis (holometabolism) insects with distinctive larval, pupal, and adult stages major orders: Coleoptera (beetles, e.g. Tribolium) Diptera (flies, e.g. Drosophila) Hymenoptera (ants, bees, sawflies, wasps; e.g. Apis) Lepidoptera (butterflies, moths; e.g. Bombyx) J. Lehmann NIPs are reliable phylogenetic markers 13/29 Relatedness of major groups widely accepted hypothesis: NIP-based analysis supports: (Coleoptera (Hymenoptera (Diptera+Lepidoptera))) (Hymenoptera (Coleoptera (Diptera+Lepidoptera))) Short introduction to phylogenetics/cladistics A novel marker class: Near-intron-positions Application to holometabolic insect orders Discussion and Outlook Holometabolous insect phylogenies NIP analysis Results Dataset compilation J. Lehmann NIPs are reliable phylogenetic markers 15/29 Example alignment and cladogram A Aedes Anopheles Drosophila Bombyx Tribolium Nasonia Apis Acyrthosiphon Pediculus Daphnia Schistostoma Strongylocentrotus Ciona Gallus Danio Nematostella AA Consensus 331-0 335-0 339-0 = TACAACCAA------------------------ATGGACTCCGGA------------------------GAGGATGCGCAG------------------------GAGGAATTC TACAATCAG------------------------ATGGATTCGGGC------------------------GAGGACGCGCAG------------------------GAAGAGTTC TACAATCAG------------------------ATGGACAGCGGC------------------------GAGGATGCCCAA------------------------GAGGAGTTC TACAACCAA------------------------ATGGAATGTGGT------------------------GAAGATGCTCAGgtgattaa//ttatattttttcagGAGGAATTC TACAACCAA------------------------ATCGACAGCGGC------------------------GAAGACGCCCAGgtccgctt//aatcatttttacagGAAGAGTTC TACAATCAGgtacatag//aggcttattttcagATTGAATCAGGA------------------------GAAGATGCTCAA------------------------GAGGAATTT TACAATCAGgtacaata//aggcttctttccagATAGAATCAGGA------------------------GAAGATGCACAT------------------------GAAGAATTT TATAATCAGgtaaagtc//ttgaatttctttagATTGATGCCGGT------------------------GACGATATTAAG------------------------GAAGAATTT TATAATCAA------------------------ATCGATTCAGGA------------------------GAGGATGCACAA------------------------GAGGAATTT TACAATCAAgtaatttt//tatgcaattgatagATTGATTCTGGA------------------------GAAGACGCACAA------------------------GAAGAGTTT TATAATCGC------------------------AGTGATGATGTAgtaagtag//tacctaccttatagGAGGATATTTTA------------------------GAGGAATCA TACAATCAA------------------------CAGGATCTG---gtaagttt//ttctgtccccgtagGAAGAGGCCCAG------------------------GAAGAGTTT TATAATGAC------------------------ATGGAGTCGGTGgtaagttc//tatataaattgcagGAAGACGCACAA------------------------GAGGAGTTT TACAATCAG------------------------ATGGATTCCACTgtaagtct//gatttcctttacagGAAGATGCGCAG------------------------GAGGAATTT TACAACCAG------------------------CTTGATCAG---gtatcttg//tacatctttggcagGAGGAAGCCCAA------------------------GAGGAGTCA TACAACCAG------------------------ATGGACTCTGGGgtaagggt//ctttctatgaacagGAGGATGCACAG------------------------GAAGAGTTT Y N Q M/I D S G E D A Q E E F B Nema tostella Danio Gallus Ciona Strongylo Schisto centrotus stoma Daph nia Pedi culus Acyrtho siphon Apis Naso nia Tribolium Bombyx Droso phila Ano pheles Aedes Short introduction to phylogenetics/cladistics A novel marker class: Near-intron-positions Application to holometabolic insect orders Discussion and Outlook Holometabolous insect phylogenies NIP analysis Results Automated re-analysis Computational steps extraction of CDS for all obtained ortholog sets (118) multiple alignment of CDS (codon alignment) for each set naming of intron positions w.r.t. Apis protein NIP extraction: partial codon alignments Result: all 135 NIPs in agreement with manual analysis J. Lehmann NIPs are reliable phylogenetic markers 17/29 Example of a partial alignment (gi66516304) Short introduction to phylogenetics/cladistics A novel marker class: Near-intron-positions Application to holometabolic insect orders Discussion and Outlook Holometabolous insect phylogenies NIP analysis Results NIP character - synapomorphic distribution J. Lehmann NIPs are reliable phylogenetic markers 19/29 Apomorphic introns mapped onto the tree Short introduction to phylogenetics/cladistics A novel marker class: Near-intron-positions Application to holometabolic insect orders Discussion and Outlook Holometabolous insect phylogenies NIP analysis Results NIP distribution results J. Lehmann NIPs are reliable phylogenetic markers 21/29 Short introduction to phylogenetics/cladistics A novel marker class: Near-intron-positions Application to holometabolic insect orders Discussion and Outlook Holometabolous insect phylogenies NIP analysis Results Sources of homoplasy in NIP characters ancient small exons (differential loss of bordering introns) intron loss and gain in parallel J. Lehmann NIPs are reliable phylogenetic markers 22/29 Short introduction to phylogenetics/cladistics A novel marker class: Near-intron-positions Application to holometabolic insect orders Discussion and Outlook Ongoing work Proposed research Summary Outline 1 Short introduction to phylogenetics/cladistics 2 A novel marker class: Near-intron-positions 3 Application to holometabolic insect orders 4 Discussion and Outlook J. Lehmann NIPs are reliable phylogenetic markers 23/29 Short introduction to phylogenetics/cladistics A novel marker class: Near-intron-positions Application to holometabolic insect orders Discussion and Outlook Ongoing work Proposed research Summary Outlook Ongoing work Extension of automated analysis to include identification of orthologous sequences for metazoan species (tblastn on assembly data) gene structure annotation (CDS, intron positions) NIP extraction (incl. codon alignment+intron naming) extraction of intron (pair) matrices for phylogenetic analyses J. Lehmann NIPs are reliable phylogenetic markers 24/29 Short introduction to phylogenetics/cladistics A novel marker class: Near-intron-positions Application to holometabolic insect orders Discussion and Outlook Ongoing work Proposed research Summary Outlook - Proposed research Further NIP-based hypothesis evaluations: other large orders of the Holometabola contradicting hypotheses of Ecdysozoa and Coelomata (nematods, chordates, arthropods) branching pattern of arthropods J. Lehmann NIPs are reliable phylogenetic markers 25/29 Short introduction to phylogenetics/cladistics A novel marker class: Near-intron-positions Application to holometabolic insect orders Discussion and Outlook Ongoing work Proposed research Summary Outlook - Proposed research Additional analysis possibilities from intron orthology data (beyond NIP data): classical sequence-based phylogeny reconstruction reconstruction of intron structure based phylogenies mining of unknown structured non-coding RNAs in the pool of orthologous introns J. Lehmann NIPs are reliable phylogenetic markers 26/29 Short introduction to phylogenetics/cladistics A novel marker class: Near-intron-positions Application to holometabolic insect orders Discussion and Outlook Ongoing work Proposed research Summary Summary NIP study demonstrates support for a more basal position of the hymenopterans w.r.t. the beetles within the tree of holometabolous insects potential general usability of NIPs as novel phylogenetic marker in metazoans/eukaryotes J. Lehmann NIPs are reliable phylogenetic markers 27/29 Short introduction to phylogenetics/cladistics A novel marker class: Near-intron-positions Application to holometabolic insect orders Discussion and Outlook Ongoing work Proposed research Summary Evidence for the alternative hypothesis J. Lehmann NIPs are reliable phylogenetic markers 28/29 Short introduction to phylogenetics/cladistics A novel marker class: Near-intron-positions Application to holometabolic insect orders Discussion and Outlook Ongoing work Proposed research Summary Acknowledgements Many thanks to all the authors Veiko Krauss, Peter F. Stadler, Carina Eisenhardt, Franziska Georgi, Christian Thümmler Thank YOU! J. Lehmann NIPs are reliable phylogenetic markers 29/29 Short introduction to phylogenetics/cladistics A novel marker class: Near-intron-positions Application to holometabolic insect orders Discussion and Outlook Ongoing work Proposed research Summary Acknowledgements Many thanks to all the authors Veiko Krauss, Peter F. Stadler, Carina Eisenhardt, Franziska Georgi, Christian Thümmler Thank YOU! J. Lehmann NIPs are reliable phylogenetic markers 29/29
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