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donovan-h-parks / PhyloRank

Assign taxonomic ranks based on evolutionary divergence.
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Why the interval for each taxonomic rank is median RED ± 0.1 ? #15

Closed 326reborn closed 3 years ago

326reborn commented 3 years ago

Hello, When I caculate the RED for each taxa, I find that taxonomic ranks were set as median RED ± 0.1 in the PhyloRank and your paper. I wonder why it's 0.1 ranther than other cutoff?

Thanks Yu Zhang

donovan-h-parks commented 3 years ago

Hi. There is no deep justification for the cutoff being +/-0.1. A relatively broad range was selected to reflect RED being an approximation of time of divergence, the desired to retain the current placement of the majority of taxa, and the desire to have taxa on well-supported nodes.

326reborn commented 3 years ago

Thank you for such a quick reply! So it means we should adjust this cutoff according to the feature of taxa we interested in like ciliates. Can I understand as this?

donovan-h-parks commented 3 years ago

It can certainly be adjusted with the goal of picking an interval that allows the majority of existing taxa to be retained while providing a reasonable level of normalization across the tree. This is ultimately a tradeoff. On the one hand, retaining existing names is important as they are widely recognized and changing them hampers scientific communication. On the other hand, the goal of RED is to provide a quantitative criteria for defining ranks which normalizes taxa such that all taxa at the same rank arose at (roughly) same time in the past.