Prospects for Building the Tree of Life from Large Sequence Databases

We assess the phylogenetic potential of ~300,000 protein sequences sampled from Swiss-Prot and GenBank. Although only a small subset of these data was potentially phylogenetically informative, this subset retained a substantial fraction of the original taxonomic diversity. Sampling biases in the dat...

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Bibliographic Details
Published in:Science (American Association for the Advancement of Science) 2004-11, Vol.306 (5699), p.1172-1174
Main Authors: Driskell, Amy C., Ané, Cécile, Burleigh, J. Gordon, McMahon, Michelle M., O'Meara, Brian C., Sanderson, Michael J.
Format: Article
Language:English
Subjects:
Algorithms
Animals
Anopheles - classification
Anopheles - genetics
Biodiversity
Biological and medical sciences
Biological Evolution
Classification
Computational Biology
Data sampling
Databases, Nucleic Acid
Databases, Protein
Datasets
Diverse techniques
Evolutionary biology
Fundamental and applied biological sciences. Psychology
Genetics
Genomics
Groves
Inferences
Molecular and cellular biology
Multigene Family
Numbers
Phylogenetics
Phylogeny
Plant Proteins - genetics
Plants - classification
Plants - genetics
Sampling
Spodoptera - classification
Spodoptera - genetics
Taxa
Taxonomy
Topology
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Summary:We assess the phylogenetic potential of ~300,000 protein sequences sampled from Swiss-Prot and GenBank. Although only a small subset of these data was potentially phylogenetically informative, this subset retained a substantial fraction of the original taxonomic diversity. Sampling biases in the databases necessitate building phylogenetic data sets that have large numbers of missing entries. However, an analysis of two "supermatrices" suggests that even data sets with as much as 92% missing data can provide insights into broad sections of the tree of life.
ISSN:0036-8075
1095-9203
DOI:10.1126/science.1102036