| AvoPhylo {avotrex} | R Documentation |
AvoPhylo: Building phylogenies based on the AvoTrex extinct bird trait database and BirdTree backbone
Description
Grafting extinct species onto BirdTree phylogenies using the AvoTrex database
Usage
AvoPhylo(ctrees, avotrex, tax, PER = 0.2, PER_FIXED = 0.75, Ntree,
n.cores = 1, cluster.ips = NULL)
Arguments
ctrees |
Either (i) object (of class multiPhylo) containing multiple
BirdTree phylogenies. Individual trees within the multiPhylo object must be
of class 'phylo', see the |
avotrex |
The AvoTrex extinct species phylogeny database. This database contains the information and commands required to graft the extinct species on to the BirdTree trees. |
tax |
The Jetz et al. (2012) BirdTree taxonomy .csv. Supplied as data within the package. |
PER |
Percentage/fraction for branch truncation based on random grafting
(see |
PER_FIXED |
Point along a branch (expressed as a fraction of the branch
length, rootward) to graft the species in the phylogeny database
( |
Ntree |
The number of trees to sample from the supplied number of
BirdTree trees (i.e., |
n.cores |
Number of cores used to build the phylogeny. Default is one (will run with parallel processing) |
cluster.ips |
Cluster location. Keep as default. |
Details
Function to build phylogenies incorporating the extinct species from the
AvoTrex extinct birds database (Sayol et al.). AvoTrex provides data on
geographical location, island endemicity, volancy, body size and standard
external and skeleton morphological measurements for 602 extinct bird
species. The AvoPhylo function provides a pipeline to incorporate the extinct
species from AvoTrex into the "BirdTree" phylogenies of extant birds (Jetz et
al. 2012). Utilising codes assigned to each species based on their known
taxonomic affinities, the function binds each species in turn to a provided
BirdTree phylogeny. Input phylogenies (i.e., BirdTree trees) must be of class
'phylo', see phylo.
BirdTree phylogenies can be sourced from: https://birdtree.org/
The species are grafted onto the tree in a set order provided in the column "Id_sps", as certain species need to be grafted onto the tree before other species. Some species are assigned to groups within the data. These species are assigned a code "xS" within the column "phylo_id2". These species groups consist of close relatives, whose exact taxonomic relationships are unknown. Therefore, the order in which they are joined is randomised. See Sayol et al. and Matthews et al. for further details.
As some of the codes (see table below) randomly place the given species
within a group of species, a genus, or a family, and some species groups are
randomised before grafting (see above), it is useful to run the grafting
procedure over a a number of trees to average out the randomisation.
Therefore, the function can be run in parallel using the argument
n.cores. Note that the function will run on one core as default and if
only one tree is supplied. Trees can also be randomly selected from a number
of trees by giving the function a group of trees using the argument
ctrees and then defining a smaller number using Ntree. If the
maximum number of trees is to be used, Ntree should equal
length(ctrees).
If Ntree > 1, a progress bar will be displayed.
A variety of different plotting options are available, see
the plot.avophylo documentation.
| Codes | Full name | Definition |
| S | Sister | Grafted as a sister to a known extant or extinct species already in the tree |
| SSG | Sister species group | Grafted as a sister to a group of extant and/or extinct species already in the tree |
| SGG | Sister genus group | Grafted as a sister to an entire extant or extinct genus (i.e., for the first grafted representative of an extinct genus) |
| SGG2 | Sister genus group 2 | Grafted as sister to multiple genera. This was for when a species was sister to a subfamily or some other large specific clade |
| SFG | Sister family group | Grafted as a sister to an entire extant or extinct family already present in the tree (i.e., for the first grafted representative of an extinct family) |
| SOG | Sister order group | Grafted as a sister to an entire order already present in the tree (i.e., for the first grafted representative of an extinct order) |
| RSG | Random species group | Grafted to a randomly selected species from a pre-defined group of species (i.e., from which is believed to have close affinities |
| RGG | Random genus group | Grafted to a randomly selected species from a given genus. For example, if an extinct species was believed to be a finch derived from a European finch species, but the exact sister species is unknown. |
| RGG2 | Random genus group 2 | Grafted to a randomly selected species from a group of genera (e.g. when all that is known is that the species is from a specific subfamily). Currently not used in the database, but the relevant functionality has been kept in the R script, as it could be useful for future studies. |
| RFG | Random family group | Grafted to a randomly selected species from a given family |
| RSGG | Random sister genus group | Grafted as sister to a randomly selected genus from a pre-defined group of genera |
| RSGG2 | Random sister genus group 2 | Grafted as sister to a randomly selected genus from a pre-defined family |
Value
The function returns an object of class 'multiAvophylo', which is a list consisting of N trees (each of class 'avophylo' and 'phylo') that were randomly selected from the supplied number. These trees have all had the extinct species from AvoTrex grafted on. For more details on the grafting, see: Sayol et al. (IN PREP).
References
Matthews et al. (IN REVIEW) The global loss of avian functional and phylogenetic diversity from extinctions in the Holocene and Late Pleistocene
Sayol et al. (IN PREP) The global loss of avian functional and phylogenetic diversity from extinctions in the Holocene and Late Pleistocene
Examples
# data(BirdTree_trees)
# data(BirdTree_tax)
# data(AvotrexPhylo)
# trees <- AvoPhylo(ctrees = BirdTree_trees,
# avotrex = AvotrexPhylo, PER = 0.2, PER_FIXED = 0.75,
# tax = BirdTree_tax, Ntree = 1, n.cores = 1, cluster.ips = NULL)
# class(trees)
# trees[[1]]
# class(trees[[1]])
#See the plot.avophylo documentation for the different available
#plotting options.