Fossil calibration points used for dating Fern Tree of Life (FTOL)
con_fossils.Rdcon_fossils was used for the consensus tree; ml_fossils was used for the
ML tree.
Format
A tibble (data frame) with 54 rows and 12 columns.
- n_fos
Unique ID number for fossil
- minimum_age
Minimum age to apply to fossil constraint
- node_calibrated
Node calibrated by fossil constraint. Combination of 'affinities' and 'affinities_group'
- fossil_taxon
Taxonomic name of fossil (without author)
- affinities_group
Type of group the fossil belongs to (crown or stem)
- affinities
Narrowest clade the fossil belongs to; the clade whose date is constrained by the fossil
- monophyly
Are the affinities monophyletic? 'Yes', 'No', or 'Monotypic'
- number_tips
Number of tips in the clade constrained by the fossil
- mrca
Node number of MRCA for the clade constrained by the fossil
- stem_mrca
Node number of the parent node of the MRCA for the clade constrained by the fossil
- tip_1
Name of one taxon that defines the clade constrained by the fossil
- tip_2
Name of another taxon that defines the clade constrained by the fossil
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 54 rows and 12 columns.
Details
The fossils in con_fossils and ml_fossils are generally the same, but the
node each calibrates may differ between the trees because of differences in
topology. Also, in some cases, a given fossil may only be applied to the ML
or consensus tree (not both) because the topology of the tree makes that
fossil redundant with another fossil.
The node corresponding to the fossil constraint is defined as the most recent common ancestor (MRCA, column 'mrca') of two tips columns ('tip_1' and 'tip_2') for crown affinities, or its parent node (column 'stem_mrca') for stem affinities. The two tips are identified automatically for monophyletic clades, or by hand for non-monophyletic clades. 'mrca' is not defined for monotypic groups (only 'stem_mrca').
Does not include the constraint on the root of the tree.
For further details on methods used for molecular dating, see Nitta et al. 2022.