distinguish effects of geographic and ecological isolation on differentiation

Populations can be genetically isolated by both geographic distance and by differences in their ecology or environment that decrease the rate of successful migration. Empirical studies often seek to investigate the relationship between genetic differentiation and some ecological variable(s) while accounting for geographic distance, but common approaches to this problem (such as the partial Mantel test) have a number of drawbacks. In this article, we present a Bayesian method that enables users to quantify the relative contributions of geographic distance and ecological distance to genetic differentiation between sampled populations or individuals. We model the allele frequencies in a set of populations at a set of unlinked loci as spatially correlated Gaussian processes, in which the covariance structure is a decreasing function of both geographic and ecological distance. Parameters of the model are estimated using a Markov chain Monte Carlo algorithm. We call this method Bayesian Estimation of Differentiation in Alleles by Spatial Structure and Local Ecology (BEDASSLE), and have implemented it in a user-friendly format in the statistical platform R. We demonstrate its utility with a simulation study and empirical applications to human and teosinte datasets.

http://arxiv.org/abs/1302.3274

R tools for spatial analysis

1. http://www.openair-project.org/Default.aspx

2. http://metvurst.wordpress.com/

Stamen maps with spplot

Several R packages provide an interface to query map services (Google Maps,Stamen Maps or OpenStreetMap) to obtain raster images from them. As far as I know, there are three packages devoted to this task: RgoogleMaps,OpenStreetMap and ggmap. The latter two are increasingly popular with a wide collection of providers.

Species distribution models in R

http://www.molecularecologist.com/2013/04/species-distribution-models-in-r/#more-3017

OpenStreetMap package of R - get beautiful maps

The bigest change in the new version is the addition of dozens of tile servers, giving the user the option of many different map looks, including those from Bing, MapQuest and Apple.

nm = c("osm", "maptoolkit-topo",
"waze", "mapquest", "mapquest-aerial",
"bing", "stamen-toner", "stamen-terrain",
"stamen-watercolor", "osm-german", "osm-wanderreitkarte",
"mapbox", "esri", "esri-topo",
"nps", "apple-iphoto", "skobbler",
 "opencyclemap", "osm-transport",
"osm-public-transport", "osm-bbike", "osm-bbike-german")

png(width=1200,height=2200)
par(mfrow=c(6,4))
for(i in 1:length(nm)){
 print(nm[i])
 map = openmap(c(lat= 38.05025395161289,   lon= -123.03314208984375),
   c(lat= 36.36822190085111,   lon= -120.69580078125),
   minNumTiles=9,type=nm[i])
 plot(map)
 title(nm[i],cex.main=4)
}
dev.off()

http://blog.fellstat.com/?p=356

visualization of biological data in Google Earth using R2G2, an R CRAN package

Arrigo, N., Albert, L. P., Mickelson, P. G. and Barker, M. S. (2012), Quantitative visualization of biological data in Google Earth using R2G2, an R CRAN package. Molecular Ecology Resources. doi: 10.1111/1755-0998.12012

making maps with R

http://www.molecularecologist.com/2012/09/making-maps-with-r/

A Geospatial Modelling Approach Integrating Archaeobotany and Genetics to Trace the Origin and Dispersal of Domesticated Plants

Background

The study of the prehistoric origins and dispersal routes of domesticated plants is often based on the analysis of either archaeobotanical or genetic data. As more data become available, spatially explicit models of crop dispersal can be used to combine different types of evidence.

Methodology/Principal Findings

We present a model in which a crop disperses through a landscape that is represented by a conductance matrix. From this matrix, we derive least-cost distances from the geographical origin of the crop and use these to predict the age of archaeological crop remains and the heterozygosity of crop populations. We use measures of the overlap and divergence of dispersal trajectories to predict genetic similarity between crop populations. The conductance matrix is constructed from environmental variables using a number of parameters. Model parameters are determined with multiple-criteria optimization, simultaneously fitting the archaeobotanical and genetic data. The consilience reached by the model is the extent to which it converges around solutions optimal for both archaeobotanical and genetic data. We apply the modelling approach to the dispersal of maize in the Americas.

Conclusions/Significance

The approach makes possible the integrative inference of crop dispersal processes, while controlling model complexity and computational requirements.

van Etten J, Hijmans RJ (2010) A Geospatial Modelling Approach Integrating Archaeobotany and Genetics to Trace the Origin and Dispersal of Domesticated Plants. PLoS ONE 5(8): e12060. doi:10.1371/journal.pone.0012060

Get Historical Climate Data from KNMI Climate Explorer

http://thebiobucket.blogspot.ca/2012/09/get-historical-climate-data-from-knmi.html

Map biodiversity records with rgbif and ggmap packages in R

Another example for geographic mapping in R

http://vijaybarve.wordpress.com/2012/07/23/map-biodiversity-records-with-rgbif-and-ggmap-packages-in-r/

Reclass ascii grid with awk

http://kariert.wordpress.com/

I had to reclass a large number of grids (20000+) on a server without any GIS installed.So my choice was awk.

BEGIN {FS=" ";}
 {
 if (NR < 7) print $0;
 else{
 for(i=1;i<=NF;i++)
 {
 if ($i == "-9999") res=-9999;
 else if ($i < a) res=0;
 else res=1;
 printf "%s ", res;
 } printf "\n";
 }
}

The script requires as a parameter a a threshold. Every value below this threshold is classified as 0 and every value above as 1. No data values (-9999) are not affected. Once the script is saved to reclass.awk, it can be calle with:

awk -v a=0.4 -f reclass.awk ingrid.asc > outgrid.asc

really nice map generated by R

http://dsparks.wordpress.com/2012/07/18/mapping-public-opinion-a-tutorial/

a good example of two dimensional density plot on a map

http://xccds1977.blogspot.de/2012/06/ggmap.html

chinese GIS data resources

Chinees GIS resources

Here is a list of useful Chinese GIS resources:

1. CHGIS (download and CD)
2. China Dimensions
3. CloudMade (dowload)
4. GRASS-Wiki

Training manual on spatial analysis of plant diversity and distribution

http://www.bioversityinternational.org/index.php?id=19&user_bioversitypublications_pi1[showUid]=5052

A tutorial for DivaGIS.

link ecologic niche models with intra-specific genetic variation

Climate envelope modelling reveals intraspecific relationships among flowering phenology, niche breadth and potential range size in Arabidopsis thaliana

http://evol-eco.blogspot.de/2012/05/putting-ecological-niche-models-to-good.html

current and historical climate data set for ecological modeling

https://www.climond.org/Default.aspx

Geophylogenies and geological map

1. Geophylogenies and the Map of Life

2. Space, time, form: viewing the Tree of Life

GenGIS - tool for generating map for trees

GenGIS

nice spatial plot

http://stevemosher.wordpress.com/2012/03/22/metadata-dubuque-and-uhi/