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Tree simulations and randomizations
Various packages in Mesquite can simulate or randomize trees,
allowing you to build statistical tests based on null distributions
or trees generated under some hypothesis.
Contents
Using results of simulations & randomizations
The simulated or randomized trees can be used or stored
in several ways:
- The trees can be stored into tree blocks in the current
file by choosing options in the Make New Trees Block
from submenu
of the Taxa&Trees menu.
- The trees may be used directly, at that moment, in
calculations. For example, if you make a Histogram for trees,
and
choose Simulated Trees as your source of trees,
the trees will be simulated and used in the chart without
being stored in the file.
- A series of many files can be saved, each one with
a different replicate of a block of simulated or randomized trees.
This is available through the Save Copies of Tree Blocks submenu of the Taxa&Trees menu menu
To replicate the results of a simulation or randomization, you can use
the Set Seed menu item to set the random number seed used. If
you are using the same conditions, including the same seed,
the simulations and randomizations should be reproducable.
Evolutionary Simulations of Trees
Species Trees
- Uniform speciation (Yule) (trees package)
— Generates tree by simple uniform probability speciation (a
Yule process). The chance of speciation
is equal for all tips. Options: total time depth of tree.
- Uniform speciation with sampling (TreeFarm
package) — Generates
a tree by Yule process, as above, but with to a total number
of species
greather
than in the taxa block. Extra species are then randomly sampled
out, to leave the tree with the appropriate number of species.
Barraclough & Nee (2001) discuss how this sampling alters
the branch length distribution of the tree.
Gene Trees
- Coalescent Trees (coalesce package) — Generates
tree by coalescence within a single panmictic population. Options:
Effective population size.
- Coalescence Contained within Current Tree
(coalesce package) — Generates tree by a simple coalescence
model of a neutral gene with constant population size, within
a current species tree from a Tree window or other tree context.
Branch lengths are assigned according to generation of coalescence.
The species tree used is a current tree found in a Tree Window
or other tree context.
Random Trees
- Equiprobable Trees (trees package)— Generates
trees randomly so that each possible labelled tree topology
is equally likely.
- Randomly Resolve Polytomies (TreeFarm package)
— Randomly resolves polytomies in tree. All possible resolutions
are equiprobable. Thus, if the tree is a polytomous bush, the
resulting resolved trees will be distributed equivalently to
that from the Equiprobable Trees module.
Randomized Trees
- Reshuffle Terminal Taxa (TreeFarm package)
— Shuffles (permutes) the taxa among the terminal nodes.
- Random Branch Moves (TreeFarm packages) — Performs a specified
number of randomly -chosen branch moves.
- Add Noise to Branch Lengths (TreeFarm package)
— Adds noise to branch lengths of tree. Noise is Normally distributed
with variance specified by user. Optionally, this variance is
proportional to current branch length. Negative branch lengths
are not allowed, and are changed to zero. Options: variance
of noise.
- Rarefy Tree (TreeFarm package) — Rarefies
tree by randomly deleting taxa. Options: how many excluded.
- Augment Tree Randomly (TreeFarm package)
— Augments tree by random placement of excluded taxa. Options:
whether branch lengths are to be considered; whether addition
is only to original branches
References
Barraclough, T.G. & S. Nee 2001. Phylogenetics and speciation. TRENDS
in Ecology and Evolution. 16:391-399.
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