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.
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.
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 organizing 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
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))
#> [,1] [,2] [,3] [,4] [,5]
#> No305 "a" "t" "r" "a" "-"
#> No304 "a" "t" "a" "y" "x"
#> No306 "a" "t" "a" "g" "a"
dat <- phyDat(ex.dna, "USER", levels=unique(as.vector(ex.dna)))
dist.p(dat)
#> No305 No304
#> No304 4
#> No306 3 4
unlink("exdna.txt")