phangorn (version 2.1.1)

dist.p: Pairwise Polymorphism P-Distances from DNA Sequences

Description

This function computes a matrix of pairwise uncorrected polymorphism p-distances. Polymorphism p-distances include intra-individual site polymorphisms (2ISPs; e.g. "R") when calculating genetic distances.

Usage

dist.p(x, cost="polymorphism", ignore.indels=TRUE)

Arguments

x

a matrix containing DNA sequences; this must be of class "phyDat" (use as.phyDat to convert from DNAbin objects).

cost

A cost matrix or "polymorphism" for a predefined one.

ignore.indels

a logical indicating whether gaps are treated as fifth state or not. Warning, each gap site is treated as a characters, so an an indel that spans a number of base positions would be treated as multiple character states.

Value

an object of class dist.

Details

The polymorphism p-distances (Potts et al. 2014) have been developed to analyse intra-individual variant polymorphism. For example, the widely used ribosomal internal transcribed spacer (ITS) region (e.g. Alvarez and Wendel, 2003) consists of 100's to 1000's of units within array across potentially multiple nucleolus organising regions (Bailey et al., 2003; Goeker and Grimm, 2008). This can give rise to intra-individual site polymorphisms (2ISPs) that can be detected from direct-PCR sequencing or cloning . Clone consensus sequences (see Goeker and Grimm, 2008) can be analysed with this function.

References

Alvarez, I., and J. F. Wendel. (2003) Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution, 29, 417--434.

Bailey, C. D., T. G. Carr, S. A. Harris, and C. E. Hughes. (2003) Characterization of angiosperm nrDNA polymorphism, paralogy, and pseudogenes. Molecular Phylogenetics and Evolution 29, 435--455.

Goeker, M., and G. Grimm. (2008) General functions to transform associate data to host data, and their use in phylogenetic inference from sequences with intra-individual variability. BMC Evolutionary Biology, 8:86.

Potts, A.J., T.A. Hedderson, and G.W. Grimm. (2014) Constructing phylogenies in the presence of intra-individual site polymorphisms (2ISPs) with a focus on the nuclear ribosomal cistron. Systematic Biology, 63, 1--16

See Also

dist.dna, dist.hamming

Examples

data(Laurasiatherian)
laura = as.DNAbin(Laurasiatherian)

dm <- dist.p(Laurasiatherian, "polymorphism")

########################################################
# Dealing with indel 2ISPs
# These can be coded using an "x" in the alignment. Note
# that as.character usage in the read.dna() function.
#########################################################
cat("3 5",
    "No305     ATRA-",
    "No304     ATAYX",
    "No306     ATAGA",
    file = "exdna.txt", sep = "\n")
(ex.dna <- read.dna("exdna.txt", format = "sequential", as.character=TRUE))
dat= phyDat(ex.dna, "USER", levels=unique(as.vector(ex.dna)))
dist.p(dat)