The goal of rtrees is to remove the barriers to derive
phylogenies for a list of species from mega-trees. Basically,
Phylomatic and more.
rtrees just got an important update to speed it
up! Please try to install the latest version. If you see any problem,
please file a GitHub issue. Thanks!
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.
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.
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 stored as GitHub release assets
in the data package {megatrees} and
downloaded on demand via getter functions.
| Taxon | # of species | # of trees | How to load (in {megatrees}) |
Reference |
|---|---|---|---|---|
| Amphibian | 7238 | 100 | get_tree_amphibian_n100() |
Jetz and Pyron 2018 |
| Bee | 4651 | 1 | tree_bee |
Henríquez-Piskulich et al. 2023 |
| 4651 | 100 | get_tree_bee_n100() |
Henríquez-Piskulich et al. 2023 | |
| Butterfly | 2244 | 1 | tree_butterfly |
Kawahara et al. 2023 |
| Bird | 9993 | 100 | get_tree_bird_n100() |
Jetz et al. 2012 |
| 11017 | 1 | tree_bird_McTavish |
McTavish et al. 2025 | |
| Fish | 11638 | 1 | tree_fish_12k |
Rabosky et al. 2018 |
| 31516 | 50 | get_tree_fish_32k_n50() |
Rabosky et al. 2018 | |
| Mammal | 5831 | 100 | get_tree_mammal_n100_phylacine() |
Faurby et al. 2018 |
| 5911 | 100 | get_tree_mammal_n100_vertlife() |
Upham et al. 2019 | |
| Plant | 74531 | 1 | tree_plant_otl (default) |
Smith and Brown 2018 |
| 123182 | 1 | tree_plant_Carruthers |
Carruthers et al. 2026 | |
| 123182 | 100 | get_tree_plant_n100_Carruthers() |
Carruthers et al. 2026 | |
| Reptile (Squamate) | 9755 | 100 | get_tree_reptile_n100() |
Tonini et al. 2016 |
| Shark, Ray, and Chimaera | 1192 | 100 | get_tree_shark_ray_n100() |
Stein et al. 2018 |
library(rtrees)
library(ape)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 BatrachoididaeFor 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 × 3
#> species genus family
#> <chr> <chr> <chr>
#> 1 Periophthalmus_barbarus Periophthalmus Gobiidae
#> 2 Barathronus_bicolor Barathronus AphyonidaeOnce 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 Periophthalmus_barbarus Periophthalmus_barbarus exisiting species in the me…
#> 3 Gobiomorphus_coxii Gobiomorphus_coxii exisiting species in the me…
#> 4 Careproctus_reinhardti Careproctus_reinhardti exisiting species in the me…
#> 5 Sanopus_reticulatus* Sanopus_reticulatus grafted at genus level
#> 6 Serrasalmus_geryi Serrasalmus_geryi exisiting species in the me…
#> 7 Knipowitschia_croatica* Knipowitschia_croatica grafted at genus level
#> 8 Rhamphochromis_lucius* Rhamphochromis_lucius grafted at genus level
#> 9 Neolissochilus_tweediei* Neolissochilus_tweediei grafted at genus level
#> 10 Haplochromis_nyanzae* Haplochromis_nyanzae grafted at genus level
#> 11 Astronesthes_micropogon* Astronesthes_micropogon grafted at genus level
#> 12 <NA> Barathronus_bicolor skipped as no co-family in …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)
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:
processed_tree = rtrees::add_root_infor(tree, classification).rtrees::get_tree(sp_list_data_frame, processed_tree) to
derive the phylogeny for your species list.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 (**)
tree is specified, then taxon can be
ignored if all genus in the species list are presented in the
phylogeny.show_grafted = TRUE, species that are grafted will
have one or two * at the end of their names.
*.*s (i.e.,
**).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.tree can be a user provided tree, if so, set
tree_by_user = TRUE.?get_tree for more details.Feel free to test it. Contributions and suggestions are welcome. You can open an issue or send a pull request.
Li Daijiang. (2023). rtrees: an R package to assemble phylogenetic trees from megatrees. Ecography. e06643