发展国际生物基因库倡议书.pptVIP

GenBank Huge amounts of data, easily accessible Rate of growth of phylogenetic knowledge Why have a phylogeny database? Archive data and trees (repeat old analyses with new tools) Synthesize new data sets and trees (supermatrices and supertrees) Big scale questions (tree shape, bias in tree building methods, stability of trees over time) Hypothesis testing : find all phylogenies for taxa with members in Gondwana -- do they show similar area cladograms, amounts of sequence divergence, etc. Who knows…(we won’t know until we try) Obstacles in the way Ontologies (consistent names for organisms, genes, and other kinds of data) How to store and query trees (what kind of queries do we want?) Summarising information in trees (supertrees) and matrices (supermatrices) Visualising very big trees Peruvian Diving-petrel(or, what’s in a name?) ITIS Pelecanoides garnotii NCBI Pelecanoides garnoti TreeBASE Pelecanoides garnoti AF076073 TreeBASE Names Projecthttp://darwin.zoology.gla.ac.uk/~rpage/TreeBASE/ Aim is to map every name in TreeBASE onto a valid taxonomic name (i.e., a name in a database, or in the literature) Use exact-, substring-, and approximate string matching (+ BLAST) So far 26819 out of 35084 names mapped There are known knowns, things we know that we know There are known unknowns, things we now know we don’t know But there are also unknown unknowns, things we do not know we dont know Why taxonomy matters Searching on “Aves” in TreeBASEfinds 4 studies with birds… Study #1: Gauthier, J., A.G. Kluge, and T. Rowe. 1988. Amniote phylogeny and the importance of fossils. Study #2: Harshman, J., C. J. Huddleston, J. P. Bollback, T. J. Parsons, and M. J. Braun. 2003 inpress. True and False Gavials: A Nuclear Gene Phylogeny of Crocodylia. Hedges, S. B., K. D. Moberg, and L. R. Maxson.1990. Tetrapod phylogeny inferred from 18s and 28s ribosomal RNA sequences and a review of the evidence for amniote relationships. van Dijk, M. A. M., E. Paradis, F.