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Updated: Jun 13, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
The Data are Insufficient to Confidently Root the SARS-CoV-2 Phylogenetic Tree
1Fred Hutchinson Cancer Center, Howard Hughes Medical Institute, Seattle, WA 98103, USA.
Abstract:
Several years ago, I published a paper that described the discrepancy between outgroup and date-based methods for rooting the SARS-CoV-2 phylogenetic tree, and proposed the discrepancy could arise from biases among the available early viral sequences. Here, I explain why the root remains uncertain, including via an interactive narrative at https://nextstrain.org/groups/jbloomlab/narratives/SARS2-rooting/early-SARS2-trees-v1 that enables the reader to examine the underlying data and understand discrepancies that lead different methods to reach different inferences about the root. I also demonstrate clear evidence of bias among the earliest available sequences, and explain why the root of the SARS-CoV-2 tree cannot be conclusively resolved with the current data.
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