PhyloTree Build 17: the human mitochondrial DNA phylogeny

The 5,435 haplogroups of PhyloTree Build 17 (van Oven 2015) as distributed by Haplogrep 3 (release 17.2 of phylotree-rsrs-17), one row per haplogroup, rooted at mtMRCA. Use phylotreeKey() to turn the tree, or part of it, into an identification key, and phylotree17_mutations for the mutations one per row.

Usage

phylotree17

Format

A data frame with 5,435 rows and 5 columns:

haplogroup: Haplogroup name.
parent: Name of the parent haplogroup (NA for mtMRCA).
depth: Number of branches from mtMRCA.
n_subclades: Number of direct subclades.
mutations: Space-separated mutations of the branch leading to this haplogroup, as written by Haplogrep.

Source

Haplogrep 3 tree phylotree-rsrs-17, release 17.2, commit 0e79ddf1b78f7a1b81fb5d607bc31a6ddea7b18b, src/tree.xml (https://github.com/genepi/phylotree-rsrs-17), MIT license. The conversion and a script that checks these data against GitHub are in data-raw/phylotree17/ in the package sources.

Details

Rows are in the order of Haplogrep's tree.xml, which is preorder (each haplogroup directly before its subclades). Names and mutations are Haplogrep's, verbatim: names such as H2a+152 16311 or K1b1+(16093) label branches that PhyloTree leaves unnamed, and two names (M4’’67, M4’’67+16311!) contain the Unicode character U+2019. Haplogrep's trailing space on one name is trimmed.

Mutations are in RSRS orientation: each is the state on the branch leading to the haplogroup. 16362C is a substitution (position and derived base), 263G! a back-mutation (it reverts the latest change at that position; !! marks a second reversion), 315.1C or 5899.XC an insertion (X: unspecified length) and 249d a deletion. Unlike some other copies (e.g. MToolBox's), PhyloTree's unstable mutations, which PhyloTree prints in parentheses, are included; the parentheses are not recorded.

References

van Oven M (2015). PhyloTree Build 17: Growing the human mitochondrial DNA tree. Forensic Science International: Genetics Supplement Series 5, e392-e394. doi:10.1016/j.fsigss.2015.09.155

Schönherr S, Weissensteiner H, Kronenberg F, Forer L (2023). Haplogrep 3 - an interactive haplogroup classification and analysis platform. Nucleic Acids Research 51, W263-W268. doi:10.1093/nar/gkad284

Examples

head(phylotree17)
#>    haplogroup      parent depth n_subclades
#> 1      mtMRCA        <NA>     0           2
#> 2          L0      mtMRCA     1           2
#> 3 L0a'b'f'g'k          L0     2           2
#> 4   L0a'b'f'g L0a'b'f'g'k     3           2
#> 5     L0a'b'g   L0a'b'f'g     4           2
#> 6       L0a'g     L0a'b'g     5           2
#>                                                       mutations
#> 1                                                              
#> 2 263A 1048T 3516A 5442C 6185C 9042T 9347G 10589A 12007A 12720G
#> 3                                       189G 4586C 9818T 16172C
#> 4          73A 185A 195T 263G! 2245G 5603T 11641G 15136T 15431A
#> 5                         93G 95C 236C 8428T 8566G 9755A 16148T
#> 6                                                 11176A 16188G
phylotree17[phylotree17$parent %in% "H2a2a", ]
#>      haplogroup parent depth n_subclades   mutations
#> 3007     H2a2a1  H2a2a    16           8        263A
#> 3016     H2a2a2  H2a2a    16           0 152T! 6716G