bpec: Bayesian Phylogeographic and Ecological Clustering (BPEC)

Description Usage Arguments Details Value Note Author(s) References Examples

Description

Bayesian Phylogeographic and Ecological Clustering (BPEC) is aimed at identifying genetically, geographically and ecologically distinct population clusters and drawing inferences about ancestral locations. Given a dataset of DNA sequences (non-recombinant, typically mtDNA) and their respective geographical locations (longitude and latitude) along with additional environmental or phenotypic characteristics, the algorithm simultaneously draws inferences about the genealogy (in the form of a haplotype tree) and the population clustering. In addition, the algorithm identifies locations with high posterior probability of being ancestral.

Usage

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bpec(seqsFile, coordsFile, dims = 2, iter = 100000, postSamples = 100, 
     maxMig = 5, ds = 0, colorCode = c(7,5,6,3,2,8))

## S3 method for class 'bpec'
plot(x, GoogleEarth = 0, colorCode = c(7,5,6,3,2,8),...)
## S3 method for class 'bpec'
summary(object,...)
## S3 method for class 'bpec'
print(x,...)
## S3 method for class 'bpec'
mean(x,...)

Arguments

x

R object from bpec.mcmc run.

object

R object from bpec.mcmc run.

colorCode

A vector of color codes to use, ideally the same ones used in bpec.contourPlot.

seqsFile

The name of the NEXUS file in full, eg "SeqsFile.nex".

coordsFile

the name of the coordinate and sequence file in full, eg "CoordsLocs.txt".

maxMig

The maximum number of migration events (this means that the maximum number of clusters will be maxmig+1). The number you enter here is just an upper bound, so start with maxmig=6 and only increase it if you are really getting 7 clusters in return (which could mean that more clusters are appropriate). If, say, 4 clusters are needed, whether you use maxmig=6 or maxmig=10 (or similar), the number of clusters will collapse down to 4.

iter

The number of iterations for the MCMC sampler, must be a multiple of 10. You will need quite a large number here, like 100,000. Two MCMC chains will run, after which convergence is checked. If convergence has not been reached, the output will say "NO CONVERGENCE" and you should increase the number of iterations.

ds

This represents the parsimony relaxation parameter, with 0 being the minimum. Generally the higher ds, the more candidate trees are considered, but this comes at a computational cost. Start with ds=0 and increase to ds=1, etc, observing any changes.

postSamples

How many posterior samples per chain to save for use post-processing. A value of at least PostSamples=1000 would provide a reasonable assessment of posterior uncertainty. PostSamples must not be greater than iter/10. Also, only up to 20 saved (thinned) samples are used in the bpec.contourPlot function.

dims

The dimension, 2 for purely geographical data, +1 for each covariate (for example if environmental or phenotypic characteristics are also available).

GoogleEarth

If 1, .kml files are produced which can be opened with GoogleEarth.

...

Other default options.

Details

bpec requires 2 input files in order to run:

haplotypes.nex : The sequence file in NEXUS format. Sequence labels should either be integers, or contain unique integers which correspond to the labels in the CoordsLocsFile.txt. For example, '1', '1_label', 'label1_label' will all be treated as haplotype 1. NOTE: bpec will currently ignore unknown nucleotides in the inference.

coordsLocsFile.txt : For each observation, the coordinates (latitude and longitude, please use a +/- to indicate W or E), any other environmental or phenotypic covariates (the latitude and longitude MUST come first), plus the ID number of the haplotype (must match the number in the sequence NEXUS file). If more than one haplotype were found at a single location, these can be entered one after the other, eg:

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  36.88	-5.42	 24	 25
  37.00	-3.98	245	251	243	142	143	244	246	247
  43.35  1.48	153		

so, in the first location (lat/long 36.88, -5.42) you have 2 sampled individuals with haplotypes 24,25, in the second location eight individuals etc. Sequences don't necessarily need to be collapsed onto haplotypes, the program should take care of it.

The main function is bpec.mcmc and runs a Markov chain Monte Carlo sampler in order to obtain posterior samples for all the parameters simultaneously: the haplotype tree, the ancestral nodes, the number of population clusters as well as their means and covariances.

Three plotting functions are available. bpec.contourPlot shows the inferred population clusters superimposed on a world map. bpec.treePlot shows the Maximum A Posteriori rooted haplotype tree, indicating posterior cluster membership and number of times each haplotype was sampled. It can also output .kml files which can be loaded into Google Earth. bpec.CovariatesPlot shows the posterior density estimates for each additional covariate of each cluster.

Value

bpec object with the following variables.

Note

bpec.mcmc uses cexcept.h 2.0.1 (an interface for exception-handling in ANSI C) developed by Adam M. Costello and Cosmin Truta.

Author(s)

Ioanna Manolopoulou <[email protected]>, Axel Hille <[email protected]>

References

I. Manolopoulou and B.C. Emerson (2012). Phylogeographic ancestral inference using the coalescent model on haplotype trees. Journal of Computational Biology, 19(6), 745-755.

I. Manolopoulou, L. Legarreta, B.C. Emerson, S. Brooks, and S. Tavar? (2011). A Bayesian approach to phylogeographic clustering. Interface focus, rsfs20110054.

S.P. Brooks, I. Manolopoulou, and B.C. Emerson (2007). Assessing the Effect of Genetic Mutation - A Bayesian Framework for Determining Population History from DNA Sequence Data. Bayesian Statistics 8. Oxford University Press.

Adam M. Costello and Cosmin Truta (2008) cexcept.h exception handling interface in C, available at website http://www.nicemice.net/cexcept/.

Examples

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## Not run: 
# if you want to load the example burnet moth dataset
data(TransalpinaRawSeqs)
data(TransalpinaCoordsLocs)
rawSeqs = TransalpinaRawSeqs
coordsLocs = TransalpinaCoordsLocs

##if you want to use your own dataset, use setwd() to enter the correct folder, 
##then run the command below, changing the input parameters if necessary
 #rawSeqs = bpec.loadSeq('haplotypes.nex')
 #coordsLocs = bpec.loadCoords("coordsLocsFile.txt")

 ## to set phenotypic/environmental covariate names, use (as appropriate)
# colnames(CoordsLocs)[1:dims] = c('lat','long','cov1','cov2','cov3')  
## where dims is the corresponding number of measurements available 
## (2 for latitude and longitude only, add one for each additional available measurement) 
 
dims = 2 #this is 2 if you only have geographical longitude/latitude. 
#(add 1 for each environmental or phenotypic covariate)
maxMig = 5 #you will need a higher maximum number of migrations, suggest 7
ds = 0 #start with ds=0 and increase to 1 and then to 2
iter = 10000 #you will need far more iterations for convergence, start with 100,000
postSamples = 2 #you will need at least 100 saved posterior samples

#run the Markov chain Monte Carlo sampler
bpecout = bpec.mcmc(rawSeqs,coordsLocs,maxMig,iter,ds,postSamples,dims)

par(mar=c(0,0,0,0),pty="m",mfrow=c(1,2)) #No plot margins. Contours and tree side-by-side
# plot geographical cluster contour map
bpec.contourPlot(bpecout, GoogleEarth=0, mapType = 'plain') 

# plot tree network with cluster indicators
bpec.Tree = bpec.treePlot(bpecout)  

## if you want to load the example Brown Frog dataset
data(MacrocnemisRawSeqs)
data(MacrocnemisCoordsLocs)
RawSeqs = MacrocnemisRawSeqs
CoordsLocs = MacrocnemisCoordsLocs

dims = 8 #this is 2 if you only have geographical longitude/latitude. 
#(add 1 for each environmental or phenotypic covariate)
maxMig = 4 #you will need a higher maximum number of migrations, suggest 7
ds = 2 #start with ds=0 and increase to 1 and then to 2
iter = 10000 #you will need far more iterations for convergence, start with 100,000
postSamples = 2 #you will need at least 100 saved posterior samples

#run the Markov chain Monte Carlo sampler
bpecout = bpec.mcmc(rawSeqs,coordsLocs,maxMig,iter,ds,postSamples,dims)

par(mar=c(0,0,0,0),pty="m",mfrow=c(1,2))  #no plot margins, plot contours and tree side-by-side
# plot geographical cluster contour map
bpec.contourPlot(bpecout,GoogleEarth=0) 

# plot tree network with cluster indicators
bpec.Tree = bpec.treePlot(bpecout)   

# now also plot the environmental covariates
 par(mfrow=c(2,3)) #split the plot window into 2x3 to fit all the covariates
 bpec.covariatesPlot(bpecout) 
 
 bpec.Geo = bpec.geoTree(bpecout,file="GoogleEarthTree.kml")
 
## End(Not run)

BPEC documentation built on Aug. 23, 2017, 1:02 a.m.

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