Extract biogeographic range data mapped on a phylogeny at a given time in the past

Extracts the most likely ranges found along branches at a specific time in the past (i.e. the focal_time). Optionally, the function can update the mapped phylogeny (densityMaps) such as branches overlapping the focal_time are shorten to the focal_time, and the range mapping for the cut off branches are removed by updating the $tree$maps and $tree$mapped.edge elements.

Usage

extract_most_likely_ranges_from_densityMaps_for_focal_time(
  densityMaps,
  ace = NULL,
  tip_data = NULL,
  focal_time,
  update_densityMaps = FALSE,
  keep_tip_labels = TRUE
)

Arguments

densityMaps

List of objects of class "densityMap", typically generated with prepare_trait_data(), that contains a phylogenetic tree and associated posterior probability of being in a given range along branches. Each object (i.e., densityMap) corresponds to a range. The phylogenetic tree must be rooted and fully resolved/dichotomous, but it does not need to be ultrametric (it can includes fossils).

ace

(Optional) Numerical matrix that record the posterior probabilities of ancestral ranges at internal nodes, obtained with prepare_trait_data() as output in the $ace slot. Rows are internal nodes_ID. Columns are ranges. Values are posterior probabilities of each range per node. Needed to provide accurate estimates of ancestral ranges.

tip_data

(Optional) Named character string vector of tip ranges. Names are nodes_ID of the internal nodes. Needed to provide accurate tip values.

focal_time

Integer. The time, in terms of time distance from the present, at which the tree and mapping must be cut. It must be smaller than the root age of the phylogeny.

update_densityMaps

Logical. Specify whether the mapped phylogeny (densityMaps) provided as input should be updated for visualization and returned among the outputs. Default is FALSE. The update consists in cutting off branches and mapping that are younger than the focal_time.

keep_tip_labels

Logical. Specify whether terminal branches with a single descendant tip must retained their initial tip.label on the updated densityMaps. Default is TRUE. Used only if update_map = TRUE.

Value

By default, the function returns a list with three elements.

• $trait_data A named character string vector with ML ranges found along branches overlapping the focal_time. Names are the tip.label/tipward node ID.

• $focal_time Integer. The time, in terms of time distance from the present, at which the trait data were extracted.

• $trait_data_type Character string. Define the type of trait data as "biogeographic". Used in downstream analyses to select appropriate statistical processing.

If update_densityMaps = TRUE, the output is a list with four elements: $trait_data, $focal_time, $trait_data_type, and $densityMaps.

• $densityMaps A list of objects of class "densityMap" that contains the updated densityMap of each range/range, with branches and mapping that are younger than the focal_time cut off. The function also adds multiple useful sub-elements to the $densityMaps$tree elements.

  • $root_age Integer. Stores the age of the root of the tree.

  • $nodes_ID_df Data.frame with two columns. Provides the conversion from the new_node_ID to the initial_node_ID. Each row is a node.

  • $initial_nodes_ID Vector of character strings. Provides the initial ID of internal nodes. Used to plot internal node IDs as labels with ape::nodelabels().

  • $edges_ID_df Data.frame with two columns. Provides the conversion from the new_edge_ID to the initial_edge_ID. Each row is an edge/branch.

  • $initial_edges_ID Vector of character strings. Provides the initial ID of edges/branches. Used to plot edge/branch IDs as labels with ape::edgelabels().

Details

The mapped phylogeny (densityMaps) is cut at a specific time in the past (i.e. the focal_time) and the current trait values of the overlapping edges/branches are extracted.

—– Extract trait_data —–

Most likely ranges are extracted from the posterior probabilities displayed in the densityMaps. The range with the highest probability is assigned to each tip and cut branches at focal_time.

True ML estimates will be used if tip_data and/or ace are provided as optional inputs. In practice the discrepancy is negligible.

—– Update the densityMaps —–

To obtain updated densityMaps alongside the trait data, set update_densityMaps = TRUE. The update consists in cutting off branches and mapping that are younger than the focal_time.

• When a branch with a single descendant tip is cut and keep_tip_labels = TRUE, the leaf left is labeled with the tip.label of the unique descendant tip.

• When a branch with a single descendant tip is cut and keep_tip_labels = FALSE, the leaf left is labeled with the node ID of the unique descendant tip.

• In all cases, when a branch with multiple descendant tips (i.e., a clade) is cut, the leaf left is labeled with the node ID of the MRCA of the cut-off clade.

The ancestral range mapping in densityMap ($tree$maps and $tree$mapped.edge) is updated accordingly by removing mapping associated with the cut off branches.

See also

cut_phylo_for_focal_time() cut_densityMaps_for_focal_time()

Associated main function: extract_most_likely_trait_values_for_focal_time()

Sub-functions for other types of trait data:

extract_most_likely_trait_values_from_contMap_for_focal_time() extract_most_likely_states_from_densityMaps_for_focal_time()

Author

Maël Doré

Examples

## Load biogeographic range data mapped on a phylogeny
data(eel_biogeo_data, package = "deepSTRAPP")

# Explore data
str(eel_biogeo_data, 1)
#> List of 9
#>  $ densityMaps           :List of 2
#>  $ densityMaps_all_ranges:List of 3
#>  $ trait_data_type       : chr "biogeographic"
#>  $ ace                   : num [1:60, 1:2] 0.361 0.524 0.623 0.334 0.47 ...
#>   ..- attr(*, "dimnames")=List of 2
#>  $ ace_all_ranges        : num [1:60, 1:3] 0.174 0.373 0.53 0.244 0.411 ...
#>   ..- attr(*, "dimnames")=List of 2
#>  $ BSM_output            :List of 2
#>  $ simmaps               :Class "multiPhylo"
#> List of 100
#>  $ best_model_fit        :List of 13
#>   ..- attr(*, "class")= chr "calc_loglike_sp_results"
#>  $ model_selection_df    :'data.frame':	6 obs. of  8 variables:
eel_biogeo_data$densityMaps # Two density maps: one per unique area: A, B.
#> $Density_map_A
#> Object of class "densityMap" containing:
#> 
#> (1) A phylogenetic tree with 61 tips and 60 internal nodes.
#> 
#> (2) The mapped posterior density of a discrete binary character
#>     with states (Not A, A).
#> 
#> 
#> $Density_map_B
#> Object of class "densityMap" containing:
#> 
#> (1) A phylogenetic tree with 61 tips and 60 internal nodes.
#> 
#> (2) The mapped posterior density of a discrete binary character
#>     with states (Not B, B).
#> 
#> 
eel_biogeo_data$densityMaps_all_ranges # Three density maps: one per range: A, B, and AB.
#> $Density_map_A
#> Object of class "densityMap" containing:
#> 
#> (1) A phylogenetic tree with 61 tips and 60 internal nodes.
#> 
#> (2) The mapped posterior density of a discrete binary character
#>     with states (Not A, A).
#> 
#> 
#> $Density_map_B
#> Object of class "densityMap" containing:
#> 
#> (1) A phylogenetic tree with 61 tips and 60 internal nodes.
#> 
#> (2) The mapped posterior density of a discrete binary character
#>     with states (Not B, B).
#> 
#> 
#> $Density_map_AB
#> Object of class "densityMap" containing:
#> 
#> (1) A phylogenetic tree with 61 tips and 60 internal nodes.
#> 
#> (2) The mapped posterior density of a discrete binary character
#>     with states (Not AB, AB).
#> 
#> 

# Set focal time to 10 Mya
focal_time <- 10

# ----- Example 1: Using only unique areas ----- #

## Extract trait data and update densityMaps for the given focal_time

# Extract from the densityMaps
eel_biogeo_data_10My <- extract_most_likely_ranges_from_densityMaps_for_focal_time(
   densityMaps = eel_biogeo_data$densityMaps,
   # ace = eel_biogeo_data$ace,
   focal_time = focal_time,
   update_densityMaps = TRUE)
#> WARNING: No ancestral character estimates (ace) for internal nodes have been provided. Using most likely ranges extracted from the densityMaps instead.
#> WARNING: No tip data have been provided. Using ranges extracted from the densityMaps instead.

## Print trait data
str(eel_biogeo_data_10My, 1)
#> List of 4
#>  $ trait_data     : Named chr [1:52] "B" "B" "B" "A" ...
#>   ..- attr(*, "names")= chr [1:52] "Moringua_edwardsi" "Kaupichthys_nuchalis" "69" "Venefica_proboscidea" ...
#>  $ focal_time     : num 10
#>  $ trait_data_type: chr "biogeographic"
#>  $ densityMaps    :List of 2
eel_biogeo_data_10My$trait_data
#>             Moringua_edwardsi          Kaupichthys_nuchalis 
#>                           "B"                           "B" 
#>                            69          Venefica_proboscidea 
#>                           "B"                           "A" 
#>                            74              Anguilla_bicolor 
#>                           "B"                           "B" 
#>             Anguilla_japonica             Serrivomer_beanii 
#>                           "B"                           "A" 
#>        Nemichthys_scolopaceus      Kaupichthys_hyoproroides 
#>                           "A"                           "A" 
#>            Dysomma_anguillare        Simenchelys_parasitica 
#>                           "A"                           "A" 
#>         Gnathophis_longicauda         Facciolella_gilbertii 
#>                           "B"                           "A" 
#>          Nettastoma_melanurum          Gavialiceps_taeniola 
#>                           "A"                           "A" 
#>            Uroconger_lepturus        Bathyuroconger_vicinus 
#>                           "A"                           "A" 
#>          Rhynchoconger_flavus        Saurenchelys_fierasfer 
#>                           "A"                           "A" 
#>                            91                            94 
#>                           "B"                           "B" 
#>      Scolecenchelys_breviceps          Myrichthys_maculosus 
#>                           "B"                           "B" 
#>                            99          Myrichthys_breviceps 
#>                           "B"                           "B" 
#>   Brachysomophis_crocodilinus      Pisodonophis_cancrivorus 
#>                           "A"                           "A" 
#>          Ichthyapus_ophioneus         Myrichthys_magnificus 
#>                           "A"                           "B" 
#>        Oxyconger_leptognathus           Gymnothorax_moringa 
#>                           "A"                           "A" 
#>         Gymnothorax_castaneus Gymnothorax_pseudothyrsoideus 
#>                           "A"                           "A" 
#>                           111            Gymnothorax_kidako 
#>                           "A"                           "A" 
#>   Gymnothorax_flavimarginatus      Uropterygius_micropterus 
#>                           "A"                           "A" 
#>            Scuticaria_tigrina        Congresox_talabonoides 
#>                           "A"                           "A" 
#>                           115            Cynoponticus_ferox 
#>                           "A"                           "A" 
#>                Ariosoma_anago Parabathymyrus_macrophthalmus 
#>                           "B"                           "B" 
#>           Ariosoma_balearicum                           119 
#>                           "B"                           "B" 
#>             Serrivomer_sector           Paraconger_notialis 
#>                           "A"                           "B" 
#>             Moringua_javanica                  Elops_saurus 
#>                           "A"                           "B" 
#>          Megalops_cyprinoides                 Albula_vulpes 
#>                           "B"                           "B" 

## Plot density maps as overlay of all range posterior probabilities

# Plot initial density maps with ACE pies
plot_densityMaps_overlay(densityMaps = eel_biogeo_data$densityMaps, fsize = 0.7)
abline(v = max(phytools::nodeHeights(eel_biogeo_data$densityMaps[[1]]$tree)[,2]) - focal_time,
       col = "red", lty = 2, lwd = 2)


# Plot updated densityMaps with ACE pies
plot_densityMaps_overlay(eel_biogeo_data_10My$densityMaps, fsize = 0.7)


# ----- Example 2: Using all ranges ----- #

## Extract trait data and update densityMaps_all_ranges for the given focal_time

# Extract from the densityMaps
eel_biogeo_data_10My <- extract_most_likely_ranges_from_densityMaps_for_focal_time(
  densityMaps = eel_biogeo_data$densityMaps_all_ranges,
  # ace = eel_biogeo_data$ace_all_ranges,
  focal_time = focal_time,
  update_densityMaps = TRUE)
#> WARNING: No ancestral character estimates (ace) for internal nodes have been provided. Using most likely ranges extracted from the densityMaps instead.
#> WARNING: No tip data have been provided. Using ranges extracted from the densityMaps instead.

## Print trait data
str(eel_biogeo_data_10My, 1)
#> List of 4
#>  $ trait_data     : Named chr [1:52] "AB" "AB" "B" "A" ...
#>   ..- attr(*, "names")= chr [1:52] "Moringua_edwardsi" "Kaupichthys_nuchalis" "69" "Venefica_proboscidea" ...
#>  $ focal_time     : num 10
#>  $ trait_data_type: chr "biogeographic"
#>  $ densityMaps    :List of 3
eel_biogeo_data_10My$trait_data
#>             Moringua_edwardsi          Kaupichthys_nuchalis 
#>                          "AB"                          "AB" 
#>                            69          Venefica_proboscidea 
#>                           "B"                           "A" 
#>                            74              Anguilla_bicolor 
#>                          "AB"                           "B" 
#>             Anguilla_japonica             Serrivomer_beanii 
#>                           "B"                           "A" 
#>        Nemichthys_scolopaceus      Kaupichthys_hyoproroides 
#>                           "A"                           "A" 
#>            Dysomma_anguillare        Simenchelys_parasitica 
#>                           "A"                          "AB" 
#>         Gnathophis_longicauda         Facciolella_gilbertii 
#>                           "B"                           "A" 
#>          Nettastoma_melanurum          Gavialiceps_taeniola 
#>                           "A"                           "A" 
#>            Uroconger_lepturus        Bathyuroconger_vicinus 
#>                           "A"                           "A" 
#>          Rhynchoconger_flavus        Saurenchelys_fierasfer 
#>                          "AB"                           "A" 
#>                            91                            94 
#>                           "B"                           "B" 
#>      Scolecenchelys_breviceps          Myrichthys_maculosus 
#>                           "B"                           "B" 
#>                            99          Myrichthys_breviceps 
#>                           "B"                           "B" 
#>   Brachysomophis_crocodilinus      Pisodonophis_cancrivorus 
#>                           "A"                           "A" 
#>          Ichthyapus_ophioneus         Myrichthys_magnificus 
#>                           "A"                           "B" 
#>        Oxyconger_leptognathus           Gymnothorax_moringa 
#>                           "A"                           "A" 
#>         Gymnothorax_castaneus Gymnothorax_pseudothyrsoideus 
#>                           "A"                           "A" 
#>                           111            Gymnothorax_kidako 
#>                           "A"                           "A" 
#>   Gymnothorax_flavimarginatus      Uropterygius_micropterus 
#>                           "A"                           "A" 
#>            Scuticaria_tigrina        Congresox_talabonoides 
#>                           "A"                           "A" 
#>                           115            Cynoponticus_ferox 
#>                           "A"                           "A" 
#>                Ariosoma_anago Parabathymyrus_macrophthalmus 
#>                          "AB"                           "B" 
#>           Ariosoma_balearicum                           119 
#>                          "AB"                           "B" 
#>             Serrivomer_sector           Paraconger_notialis 
#>                          "AB"                           "B" 
#>             Moringua_javanica                  Elops_saurus 
#>                           "A"                           "B" 
#>          Megalops_cyprinoides                 Albula_vulpes 
#>                          "AB"                           "B" 

## Plot density maps as overlay of all range posterior probabilities

# Plot initial density maps with ACE pies
root_age <- max(phytools::nodeHeights(eel_biogeo_data$densityMaps_all_ranges[[1]]$tree)[,2])
plot_densityMaps_overlay(densityMaps = eel_biogeo_data$densityMaps_all_ranges, fsize = 0.7)
abline(v =  root_age - focal_time,
       col = "red", lty = 2, lwd = 2)


# Plot updated densityMaps with ACE pies
plot_densityMaps_overlay(eel_biogeo_data_10My$densityMaps, fsize = 0.7)