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Subtree power analysis finds optimal species for comparative genomics

Jon D. McAuliffe·Michael I. Jordan·Lior Pachter
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Abstract

Sequence comparison across multiple organisms aids in the detection of regions under selection. However, resource limitations require a prioritization of genomes to be sequenced. This prioritization should be grounded in two considerations: the lineal scope encompassing the biological phenomena of interest, and the optimal species within that scope for detecting functional elements. We introduce a statistical framework for optimal species subset selection, based on maximizing power to detect conserved sites. In a study of vertebrate species, we show that the optimal species subset is not in general the most evolutionarily diverged subset. Our results suggest that marsupials are prime sequencing candidates.

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Jon D. McAuliffe, Michael I. Jordan, Lior Pachter. 2004-12-06. Subtree power analysis finds optimal species for comparative genomics. https://arxiv.org/abs/q-bio/0412012

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