palmatifoliae: _Oxalis_ section _Palmatifoliae_

In phyloclim: Integrating Phylogenetics and Climatic Niche Modeling

Description

This is a data set of Oxalis sect. Palmatifoliae derived from a larger scale study by Heibl & Renner (2012). The sites data frame gives the coordinates (WGS1984) of the sites where Oxalis sect. Palmatifoliae has been collected. These were taken as presence points in distribution modeling and the list of predicted niche occupancy profiles (PNO). Finally, tree holds a phylogenetic hypothesis for the section extracted from a relaxed molecular clock model of the phylogeny of Oxalidales based approx. 7500 bp of chloroplast and nuclear markers. For 19 bioclimatic variables summarizing temperature and precipiation and five species of Oxalis, the suitability or probability of occurence is given along the environmental gradients.

Usage

	data(PNO)
	data(sites)
	data(tree)
	

Format

sites

a data frame representing 290 collections of Oxalis sect. Palmatifoliae.

PNO

a list consisting of 19 matrixes. Each matrix corresponds to an environmental variable and contains the predicted niche occupancy profile (PNO) for each species of Oxalis sect. Palmatifoliae, whereby column 1 of each matrix gives the values of the environmental variable and columns 2-6 give probabilites of occurance of each species along the environmental gradient in column 1.

tree

an object of class "phylo" (see Value section of read.tree).

Source

Heibl, C. & S.S. Renner. Arid-adapted Distribution models and a dated phylogeny for Chilean Oxalis species reveal occupation of new habitats by different lineages, not rapid adaptive radiation. 2012. Syst. Biol. 61(5): 823-834.

Examples

# 290 collections of Palmatifoliae
# --------------------------------
data(sites)
plot(sites$long, sites$lat,
  xlab = "Longitude", ylab = "Latitude")

## PNO profiles along 19 bioclimatic variables
## -------------------------------------------
data(PNO); names(PNO)
temp <- names(PNO)[1]
plotPNO(PNO[[temp]], xlab = temp)

## phylogenetic hypothesis for Palmatifoliae
## -----------------------------------------
data(tree)
plot(tree)

Example output

Loading required package: ape
Loading required package: raster
Loading required package: sp

Attaching package: 'raster'

The following objects are masked from 'package:ape':

    rotate, zoom

 [1] "AnnualMeanTemperature"         "MeanDiurnalRange"             
 [3] "Isothermality"                 "TemperatureSeasonality"       
 [5] "MaxTemperatureWarmestMonth"    "MinTemperatureColdestMonth"   
 [7] "TemperatureAnnualRange"        "MeanTemperatureWettestQuarter"
 [9] "MeanTemperatureDriestQuarter"  "MeanTemperatureWarmestQuarter"
[11] "MeanTemperatureColdestQuarter" "AnnualPrecipitation"          
[13] "PrecipitationWettestMonth"     "PrecipitationDriestMonth"     
[15] "PrecipitationSeasonality"      "PrecipitationWettestQuarter"  
[17] "PrecipitationDriestQuarter"    "PrecipitationWarmestQuarter"  
[19] "PrecipitationColdestQuarter"  

phyloclim documentation built on May 2, 2019, 8:07 a.m.