Deep phylogeographic splits add genetic differentiation that has nothing to do with today's landscape. Following Maier et al. (2022), the lineage effect of a pair is the time to the most recent common ancestor of the two sites' lineages, and zero when both belong to the same lineage. Adding it as a predictor lets a model account for that history.
Arguments
- from, to
Site IDs of each pair.
- lineages
A data.frame with site IDs in the first column and lineage names in the second.
- tmrca
A data.frame with two lineage columns and the time since they split in the third (any units; only relative values matter to the models). Pairs of lineages not listed get
NA.
Examples
ex <- corridor_example()
lin <- sf::st_drop_geometry(ex$sites)[, c("site", "lineage")]
lineage_cross(c("M01", "M01"), c("M02", "M30"), lin, ex$lineage_tmrca)
#> [1] 0 0