When full DNA sequences opened the way to comparing many different genes in different organisms, the comparisons proved confounding. Rather than clarifying the tree that seeks to show how life evolved, they often produced new trees that differ from the traditional tree and conflict with each other as well. Now some microbiologists, pointing to evidence that microbes have swapped genes wantonly over evolutionary history, say that many of these genes are an unreliable guide to evolutionary history and the old tree is still basically sound. But others think it9s time to uproot the old tree and are proposing candidates for new trees based on specific features of the genome and cell structure. And still others worry that gene swapping has turned the tree of life into a tangled briar whose lineages will be next to impossible to discern.
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Elizabeth Pennisi (1999) studied this question.