generate_gene_tree_msc: Generate a gene tree based on the multi-species coalescent...

In castor: Efficient Phylogenetics on Large Trees

Generate a gene tree based on the multi-species coalescent model.

Description

Generate a random gene tree within a given species timetree, based on the multi-species coalescent (MSC) model. In this implementation of the MSC, every branch of the species tree has a specific effective population size (Ne) and a specific generation time (T), and gene alleles coalesce backward in time according to the Wright-Fisher model. This model does not account for gene duplication/loss, nor for hybridization or horizontal gene transfer. It is only meant to model "incomplete lineage sorting", otherwise known as "deep coalescence", which is one of the many mechanisms that can cause discordance between gene trees and species trees.

Usage

generate_gene_tree_msc( species_tree,
                        allele_counts              = 1, 
                        population_sizes           = 1,
                        generation_times           = 1,
                        mutation_rates             = 1,
                        gene_edge_unit             = "time",
                        Nsites                     = 1,
                        bottleneck_at_speciation   = FALSE,
                        force_coalescence_at_root  = FALSE,
                        ploidy                     = 1,
                        gene_tip_labels            = NULL)

Arguments

species_tree	Rooted timetree of class "phylo". The tree can include multifurcations and monofurcations. The tree need not necessarily be ultrametric, i.e. it may include extinct species. Edge lengths are assumed to be in time units.
allele_counts	Integer vector, listing the number of alleles sampled per species. Either NULL (1 allele per species), or a single integer (same number of alleles per species), or a vector of length Ntips listing the numbers of alleles sampled per species. In the latter case, the total number of tips in the returned gene tree will be equal to the sum of entries in allele_counts. Some entries in allele_counts may be zero (no alleles sampled from those species).
population_sizes	Integer vector, listing the effective population size on the edge leading into each tip/node in the species tree. Either NULL (all population sizes are 1), or a single integer (same population sizes for all edges), or a vector of length Ntips+Nnodes, listing population sizes for each clade's incoming edge (including the root). The population size for the root's incoming edge corresponds to the population size at the tree's stem (only relevant if force_coalescence_at_root=FALSE).
generation_times	Numeric vector, listing the generation time along the edge leading into each clade. Either NULL (all generation times are 1), or a single integer (same generation time for all edges) or a vector of length Ntips+Nnodes, listing generation times for each clade's incoming edge (including the root). The generation time for the root's incoming edge corresponds to the generation time at the tree's stem (only relevant if force_coalescence_at_root=FALSE).
mutation_rates	Numeric vector, listing the mutation rate (per site and per generation) along the edge leading into each clade. Either NULL (all mutation rates are 1), or a single integer (same mutation rate for all edges) or a vector of length Ntips+Nnodes, listing mutation rates for each clade's incoming edge (including the root). The mutation rate for the root's incoming edge corresponds to the mutation rate at the tree's stem (only relevant if force_coalescence_at_root=FALSE). The value of mutation_rates is only relevant if gene_edge_unit is "mutations_expected" or "mutations_random". Mutation rates represent probabilities, and so they must be between 0 and 1.
gene_edge_unit	Character, either "time", "generations", "mutations_expected" (expected mean number of mutations per site), or "mutations_random" (randomly generated mean number of mutations per site), specifying how edge lengths in the gene tree should be measured. By default, gene-tree edges are measured in time, as is the case for the input species tree.
Nsites	Integer, specifying the number of sites (nucleotides) in the gene. Only relevant when generating edge lengths in terms of random mutation counts, i.e. if gene_edge_unit=="mutations_random".
bottleneck_at_speciation	Logical. If TRUE, then all but one children at each node are assumed to have emerged from a single mutant individual, and thus all gene lineages within these bottlenecked species lineages must coalesce at a younger or equal age as the speciation event. Only the first child at each node is excluded from this assumption, corresponding to the "resident population" during the speciation event. This option deviates from the classical MSC model, and is experimental.
force_coalescence_at_root	Logical. If TRUE, all remaining orphan gene lineages that haven't coalesced before reaching the species-tree's root, will be combined at the root (via multiple adjacent bifurcations). If FALSE, coalescence events may extend beyond the species-tree's root into the stem lineage, as long as it takes until all gene lineages have coalesced.
ploidy	Integer, specifying the assumed genetic ploidy, i.e. number of gene copies per individual. Typically 1 for haploids, or 2 for diploids.
gene_tip_labels	Character vector specifying tip labels for the gene tree (i.e., for each of the sampled alleles) in the order of the corresponding species tips. Can also be NULL, in which case gene tips will be set to <species_tip_label>.<allele index>.

Details

This function assumes that Kingman's coalescent assumption is met, i.e. that the effective population size is much larger than the number of allele lineages coalescing within any given branch.

The function assumes that the species tree is a time tree, i.e. with edge lengths given in actual time units. To simulate gene trees in coalescence time units, choose population_sizes and generation_times accordingly (this only makes sense if the product of population_sizes \times generation_times is the same everywhere). If species_tree is ultrametric and gene_edge_unit=="time", then the gene tree will be ultrametric as well.

If gene_edge_unit is "mutations_random", then the number of generations elapsed along each time segment is translated into a randomly distributed number of accumulated mutations, according to a binomial distribution where the probability of success is equal to the mutation rate and the number of trials is equal to the number of generations multiplied by Nsites; this number of mutations is averaged across all sites, i.e. the edge lengths in the returned gene tree always refer to the mean number of mutations per site. In cases where the mutation rate varies across the species tree and a single gene edge spans multiple species edges, the gene edge length will be a sum of multiple binomially distributed mutation counts (again, divided by the number of sites), corresponding to the times spent in each species edge.

Value

A named list with the following elements:

success	Logical, indicating whether the gene tree was successfully generated. If FALSE, the only other value returned is error.
tree	The generated gene tree, of class "phylo". This tree will be rooted and bifurcating. It is only guaranteed to be ultrametric if species_tree was ultrametric.
gene_tip2species_tip	Integer vector of length NGtips (where NGtips is the number of tips in the gene tree), mapping gene-tree tips to species-tree tips.
gene_node2species_edge	Integer vector of length NGnodes (where NGnodes is the number of internal nodes in the gene tree), mapping gene-tree nodes (=coalescence events) to the species-tree edges where the coalescences took place.
gene_clade_times	Numeric vector of size NGtips+NGnodes, listing the time (total temporal distance from species root) of each tip and node in the gene tree. The units will be the same as the time units assumed for the species tree. Note that this may include negative values, if some gene lineages coalesce at a greater age than the root.
error	Character, containing an explanation of the error that occurred. Only included if success==FALSE.

Author(s)

Stilianos Louca

References

J. H. Degnan, N. A. Rosenberg (2009). Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends in Ecology & Evolution. 24:332-340.

B. Rannala, Z. Yang (2003). Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics. 164:1645-1656.

See Also

generate_random_tree, generate_gene_tree_msc_hgt_dl

Examples

# Simulate a simple species tree
parameters   = list(birth_rate_factor=1)
Nspecies     = 10
species_tree = generate_random_tree(parameters,max_tips=Nspecies)$tree

# Simulate a haploid gene tree within the species tree
# Assume the same population size and generation time everywhere
# Assume the number of alleles samples per species is poisson-distributed
results = generate_gene_tree_msc(species_tree, 
                                 allele_counts      = rpois(Nspecies,3),
                                 population_sizes   = 1000,
                                 generation_times   = 1,
                                 ploidy             = 1);
if(!results$success){
    # simulation failed
    cat(sprintf("  ERROR: %s\n",results$error))
}else{
    # simulation succeeded
    gene_tree = results$tree
    cat(sprintf("  Gene tree has %d tips\n",length(gene_tree$tip.label)))
}

castor documentation built on June 29, 2024, 9:08 a.m.