rtrees

The goal of rtrees is to remove the barriers to derive phylogenies for a list of species from mega-trees. Basically, Phylomatic and more.

Installation

options(repos = c(
  rtrees = 'https://daijiang.r-universe.dev',
  CRAN = 'https://cloud.r-project.org'))
install.packages("rtrees")

The above code will also install one dependency {megatrees}, an R data package that hosts the megatrees used here.

Shinny app

There is also a Shinny app to get phylogenies without using R. However, given that I can only afford the free plan, the number of species to be inserted to the megatrees here will be limited to 1,000.

Mega-trees

Currently, rtrees provides mega-trees for the following taxonomic groups: amphibian, bird, fish, mammal, plant, reptile, and shark_ray. The mega-trees (or subset of 100 posterior phylogenies; 50 for fish to reduce the package size) are saved in the data package {megatrees}.

Taxon	# of species	# of trees	R object (in {megatrees})	Reference
Amphibian	7238	100	tree_amphibian_n100	Jetz and Pyron 2018
Bee	4651	1	tree_bee	Henríquez-Piskulich et al. 2023
	4651	100	tree_bee_n100	Henríquez-Piskulich et al. 2023
Bird	9993	100	tree_bird_n100	Jetz et al. 2012
Fish	11638	1	tree_fish_12k	Rabosky et al. 2018
	31516	50	tree_fish_32k_n50	Rabosky et al. 2018
Mammal	5831	100	tree_mammal_n100_phylacine	Faurby et al. 2018
	5911	100	tree_mammal_n100_vertlife	Upham et al. 2019
Plant	74531	1	tree_plant_otl	Brown and Smith 2018
Reptile (Squamate)	9755	100	tree_reptile_n100	Tonini et al. 2016
Shark, Ray, and Chimaera	1192	100	tree_shark_ray_n100	Stein et al. 2018

Usage examples

library(rtrees)
library(ape)

Prepare species data frame (optional)

The species lists which we want to have a phylogeny should be provided as a data frame with at least 3 columns: family, genus, and species. Their order does not matter. Here is an example for fish.

test_fish_list = tibble::tibble(
  species = c("Serrasalmus_geryi", "Careproctus_reinhardti", "Gobiomorphus_coxii", 
              "Periophthalmus_barbarus", "Prognichthys_glaphyrae", "Barathronus_bicolor", 
              "Knipowitschia_croatica", "Rhamphochromis_lucius", "Neolissochilus_tweediei", 
              "Haplochromis_nyanzae", "Astronesthes_micropogon", "Sanopus_reticulatus"),
  genus = c("Serrasalmus", "Careproctus", "Gobiomorphus", "Periophthalmus",
            "Prognichthys", "Barathronus", "Knipowitschia", "Rhamphochromis", 
            "Neolissochilus", "Haplochromis", "Astronesthes", "Sanopus"),
  family = c("Serrasalmidae", "Liparidae", "Eleotridae", "Gobiidae", 
             "Exocoetidae", "Aphyonidae", "Gobiidae", "Cichlidae", 
             "Cyprinidae", "Cichlidae", "Stomiidae", "Batrachoididae")
)

test_fish_list
#> # A tibble: 12 × 3
#>    species                 genus          family        
#>    <chr>                   <chr>          <chr>         
#>  1 Serrasalmus_geryi       Serrasalmus    Serrasalmidae 
#>  2 Careproctus_reinhardti  Careproctus    Liparidae     
#>  3 Gobiomorphus_coxii      Gobiomorphus   Eleotridae    
#>  4 Periophthalmus_barbarus Periophthalmus Gobiidae      
#>  5 Prognichthys_glaphyrae  Prognichthys   Exocoetidae   
#>  6 Barathronus_bicolor     Barathronus    Aphyonidae    
#>  7 Knipowitschia_croatica  Knipowitschia  Gobiidae      
#>  8 Rhamphochromis_lucius   Rhamphochromis Cichlidae     
#>  9 Neolissochilus_tweediei Neolissochilus Cyprinidae    
#> 10 Haplochromis_nyanzae    Haplochromis   Cichlidae     
#> 11 Astronesthes_micropogon Astronesthes   Stomiidae     
#> 12 Sanopus_reticulatus     Sanopus        Batrachoididae

For plant, fish, bird, and mammal, it is possible to prepare sp_list with function sp_list_df(); though you should check the results. It is possible to just provide the speices as a character vector for these taxon groups (or all genus in your species list are presented in the phylogeny).

sp_list_df(sp_list = c("Periophthalmus_barbarus", "Barathronus_bicolor"),
           taxon = "fish")
#> # A tibble: 2 × 4
#>   species                 genus          family     Family
#>   <chr>                   <chr>          <chr>      <chr> 
#> 1 Periophthalmus_barbarus Periophthalmus Gobiidae   <NA>  
#> 2 Barathronus_bicolor     Barathronus    Aphyonidae <NA>

Get phylogeny from one megatree

Once we have the species list ready, we can then derive a phylogeny from tree_fish.

test_tree = get_tree(sp_list = test_fish_list,
                     taxon = "fish",
                     scenario = "at_basal_node",
                     show_grafted = TRUE)
#> 
#> 6 species added at genus level (*)
#> 1 species have no co-family species in the mega-tree, skipped
#> (if you know their family, prepare and edit species list with `rtrees::sp_list_df()` may help): 
#> Barathronus_bicolor
plot(test_tree, no.margin = T)

No matter whether show_grafted is ‘TRUE’ or ‘FALSE’, the grafting information was saved along with the phylogeny and can be extracted with the following code:

# or use rtrees::get_graft_status(test_tree)
test_tree$graft_status
#> # A tibble: 12 × 3
#>    tip_label                species                 status                      
#>    <chr>                    <chr>                   <chr>                       
#>  1 Prognichthys_glaphyrae   Prognichthys_glaphyrae  exisiting species in the me…
#>  2 Rhamphochromis_lucius*   Rhamphochromis_lucius   grafted at genus level      
#>  3 Haplochromis_nyanzae*    Haplochromis_nyanzae    grafted at genus level      
#>  4 Knipowitschia_croatica*  Knipowitschia_croatica  grafted at genus level      
#>  5 Periophthalmus_barbarus  Periophthalmus_barbarus exisiting species in the me…
#>  6 Gobiomorphus_coxii       Gobiomorphus_coxii      exisiting species in the me…
#>  7 Careproctus_reinhardti   Careproctus_reinhardti  exisiting species in the me…
#>  8 Sanopus_reticulatus*     Sanopus_reticulatus     grafted at genus level      
#>  9 Astronesthes_micropogon* Astronesthes_micropogon grafted at genus level      
#> 10 Neolissochilus_tweediei* Neolissochilus_tweediei grafted at genus level      
#> 11 Serrasalmus_geryi        Serrasalmus_geryi       exisiting species in the me…
#> 12 <NA>                     Barathronus_bicolor     skipped as no co-family in …

Get a set of phylogenies from multiple posterior megatrees

The function rtrees::get_tree() can also work with a set of posterior megatrees with the option to use parallel computing for the whole process. The default number of cores to be used will be the available number of cores minus 2 (so that users can still perform other tasks on their computers at the same time). The output will be a set of generated phylogenies with class multiPhylo; the number of derived phylogenies will be the same as the input megatrees. For this scenario, we can use exactly the same code described above. For example, if we want to use the 100 randomly selected posterior phylogenies that have ~32k fish species, we can add the fish_tree = "all-taxon.

test_tree2 = get_tree(sp_list = test_fish_list,
                     taxon = "fish",
                     scenario = "at_basal_node",
                     show_grafted = TRUE,
                     fish_tree = "all-taxon")
#> Wow, all species are already in the mega-tree!
test_tree2
#> 50 phylogenetic trees
plot(ladderize(test_tree2[[1]]), no.margin = T)

Add tips to user provided trees

It is also possible to derive a phylogeny based on a user provided tree. This can be particularly useful if we have things like Acer_spp that we want to insert to the basal node of the genus.

test_tree = ape::read.tree(text = "(((((((((Potentilla_intermedia:1.156097,Potentilla_gracilis:1.156097):9.169741,Potentilla_bipinnatifida:10.325839):10.466967,Potentilla_sterilis:20.792806):11.333216,Fragaria_virginiana:32.126022):6.026567,(((((Rosa_setigera:3.434279,Rosa_arkansana:3.434279):1.991106,Rosa_spinosissima:5.425386):0.993924,Rosa_acicularis:6.419309):6.730804,(Rosa_micrantha:0.188519,Rosa_canina:0.188519):12.961594):23.677485,(Agrimonia_gryposepala:4.730863,Agrimonia_parviflora:4.730863):32.096735):1.324992):6.47604,(Geum_urbanum:11.153303,Geum_rivale:11.153303):33.475326):1.449852,((((((((Rubus_semisetosus:3.10529,Rubus_glandicaulis:3.10529):0.957584,Rubus_steelei:4.062873):0.398394,Rubus_cuneifolius:4.461267):2.271628,Rubus_vagus:6.732895):0.023439,Rubus_superioris:6.756333):0.020104,(Rubus_multifer:4.287114,Rubus_elegantulus:4.287115):2.489323):0.025475,((Rubus_laciniatus:0.125186,Rubus_bifrons:0.125186):0.11903,Rubus_praecox:0.244216):6.557697):11.571849,(Rubus_parviflorus:14.85915,Rubus_odoratus:14.85915):3.514612):27.704718):16.915234,Filipendula_rubra:62.993714):13.354116,((((((((((Crataegus_dissona:0.081863,Crataegus_florifera:0.081863):0.49838,Crataegus_fulleriana:0.580243):1.434261,Crataegus_crus-galli:2.014503):0.177737,Crataegus_chrysocarpa:2.192239):0.051159,Crataegus_uniflora:2.243399):0.438351,Crataegus_persimilis:2.68175):4.697259,((Malus_toringo:6.472694,Malus_ioensis:6.472693):0.772012,Chaenomeles_speciosa:7.244705):0.134305):1.72489,Pyrus_communis:9.1039):0.313393,Amelanchier_spicata:9.417293):40.039557,((((((Prunus_pumila:6.189944,Prunus_nigra:6.189945):0.37487,Prunus_pensylvanica:6.564815):4.856241,(Prunus_padus:4.816999,Prunus_serotina:4.817):6.604057):29.162527,Sorbaria_sorbifolia:40.583584):2.924475,Rhodotypos_scandens:43.50806):2.718224,(Spiraea_X_bumalda:25.921582,Aruncus_dioicus:25.921583):20.304701):3.230567):26.89098);")

test_tree_sp = c("Rosa_sp", "Rubus_sp", "Amelanchier_sp", "Prunus_sp", "Sorbus_sp", "Potentilla_sp",
  "Potentilla_intermedia", "Potentilla_gracilis", "Potentilla_bipinnatifida", "Potentilla_sterilis", "Fragaria_virginiana", "Rosa_setigera", "Rosa_arkansana", "Rosa_spinosissima", "Rosa_acicularis", "Rosa_micrantha", "Rosa_canina", "Agrimonia_gryposepala", "Agrimonia_parviflora", "Geum_urbanum", "Geum_rivale", "Rubus_semisetosus", "Rubus_glandicaulis", "Rubus_steelei", "Rubus_cuneifolius", "Rubus_vagus", "Rubus_superioris", "Rubus_multifer", "Rubus_elegantulus", "Rubus_laciniatus", "Rubus_bifrons", "Rubus_praecox", "Rubus_parviflorus", "Rubus_odoratus", "Filipendula_rubra", "Crataegus_dissona", "Crataegus_florifera", "Crataegus_fulleriana", "Crataegus_crus-galli", "Crataegus_chrysocarpa", "Crataegus_uniflora", "Crataegus_persimilis", "Malus_toringo", "Malus_ioensis", "Chaenomeles_speciosa", "Pyrus_communis", "Amelanchier_spicata", "Prunus_pumila", "Prunus_nigra", "Prunus_pensylvanica", "Prunus_padus", "Prunus_serotina", "Sorbaria_sorbifolia", "Rhodotypos_scandens", "Spiraea_X_bumalda", "Aruncus_dioicus")

plot(get_tree(sp_list = test_tree_sp, tree = test_tree, taxon = "plant",
              show_grafted = T, tree_by_user = T), type = "fan")
#> Not all genus can be found in the phylogeny.
#> Warning: For user provided phylogeny, without a classification for all genus of species in the phylogeny,
#>               it is unlikely to find the most recent ancestor for genus and family; here we proceed the phylogeny
#>               by adding root information for genus and family that can be found in the phylogeny or species list but
#>               we recommend to prepare the phylogeny using `add_root_info()` with a classification
#>               data frame with all tips first.
#> 
#> 5 species added at genus level (*)
#> 1 species added at family level (**)

Pay attention to the warning message there. Because not all genera in the species list are presented in the megatree, it is impossible to find the most recent ancestor for genus and family that are missing from the megatree. Therefore, for user-provided phylogenies, here is the recommended steps:

1. Get the classification information (a data frame with two columns: genus and family) for all genera presented in the species list and the megatree.
2. Prepare the species list as a data frame with three columns: species, genus, and family using the classification information.
3. Process the megatree using function processed_tree = rtrees::add_root_infor(tree, classification).
4. Pass the processed megatree to rtrees::get_tree(sp_list_data_frame, processed_tree) to derive the phylogeny for your species list.

Bind missing species to specified places

It is also possible to specify a particular species to bind with by specifying columns close_sp and/or close_genus.

test_tree_sp_df = sp_list_df(test_tree_sp, "plant")
test_tree_sp_df$close_sp = NA
test_tree_sp_df$close_sp[1] = "Rosa_acicularis" # bind Rosa_sp to here
plot(get_tree(sp_list = test_tree_sp_df, tree = test_tree, taxon = "plant",
              show_grafted = T, tree_by_user = T), type = "fan")
#> Not all genus can be found in the phylogeny.
#> Warning: For user provided phylogeny, without a classification for all genus of species in the phylogeny,
#>               it is unlikely to find the most recent ancestor for genus and family; here we proceed the phylogeny
#>               by adding root information for genus and family that can be found in the phylogeny or species list but
#>               we recommend to prepare the phylogeny using `add_root_info()` with a classification
#>               data frame with all tips first.
#> 
#> 5 species added at genus level (*)
#> 1 species added at family level (**)

Some notes

• If tree is specified, then taxon can be ignored if all genus in the species list are presented in the phylogeny.
• If a species does not have a co-family species in the mega-tree, it will be skipped.
• If show_grafted = TRUE, species that are grafted will have one or two * at the end of their names.
  • If it is grafted at the genus level, one *.
  • If it is grafted at the family level, two *s (i.e., **).
• The default scenario is at_basal_node, which will graft species at the genus/family basal node.
  • random_below_basal will randomly select a downstream node to attach the new tip.
  • If only one species in the mega-tree that is in the same genus/family of the new tip, then the new tip will be grafted at the middle of this species’ branch for all scenarios.
• The tree can be a user provided tree, if so, set tree_by_user = TRUE.
• See ?get_tree for more details.

Contribution

Feel free to test it. Contributions and suggestions are welcome. You can open an issue or send a pull request.

Citation

Li Daijiang. (2023). rtrees: an R package to assemble phylogenetic trees from megatrees. Ecography.