Add sex-determination traits (Tree of Sex)

Joins sexual-system and sex-determination traits to a taxify() result by looking up accepted_name. Covers plants, vertebrates and invertebrates; some traits are group-specific (selfing for plants, environmental sex determination for vertebrates, haplodiploidy for invertebrates).

Usage

add_tree_of_sex(x, cols = NULL, verbose = TRUE)

Arguments

x

A data.frame returned by taxify().

cols

Which columns to attach: NULL (default) the curated set, "all" every column the source carries, or a character vector of names. See enrichment_cols.

verbose

Logical. Default TRUE.

Value

The same data.frame with additional columns:

tos_taxon_group

Source group (plants/vertebrates/invertebrates).

tos_sexual_system

Sexual system (vocabulary differs by group).

tos_karyotype

Sex-chromosome system (XY/ZW/XO/homomorphic/...).

tos_genotypic

Heterogamety (male/female heterogametic/GSD/...).

tos_molecular_basis

Molecular basis (Y dominant/W dominant/dosage).

tos_selfing

Selfing (plants; self compatible/incompatible).

tos_environmental_sd

Environmental sex determination (vertebrates; TSD/...).

tos_haplodiploidy

Haplodiploidy (invertebrates).

Details

Source: Tree of Sex (Tree of Sex Consortium 2014, Scientific Data, CC0). Coverage: ~37.5k species across plants, vertebrates and invertebrates.

References

The Tree of Sex Consortium (2014) Tree of Sex: a database of sexual systems. Scientific Data 1:140015. doi:10.1038/sdata.2014.15

Examples

if (FALSE) { # \dontrun{
taxify("Silene latifolia", backbone = "gbif") |>
  add_tree_of_sex()
} # }