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I have a community assembly dataset with 299 species at 15 sites. Im interested in correcting for the effect of spatial autocorrelation on beta-diversity (or species turnover). Dataset here.

There is an obvious effect of spatial distance between the sites and community dissimilarity. I have a completed a mantel correlogram to show this effect but now I’m a bit stuck on how to account for this effect or correct for beta diversity analyzes. And more importantly how does the effect of distance between sites compare to my environmental effect (precip)

#load libraries 
library (vegan)
library (fossil)
#load datasets
spp.list<-read.csv('Spatial Autocorrelation.csv', header=T)
rownames(spp.list)=spp.list$Site
sites.xy= spp.list[,(2:3)]
precip= spp.list[,(4)]
spp.list<-spp.list[,(5:303)]

#check for spatial autocorrelation and environmental correlation using Mantel Test

#build a species dissimilarity matrix 
dist.mat=vegdist (spp.list)

#build a geographic distance matrix for sites
geo.dist.mat=earth.dist(sites.xy)

#build a distance matrix for precip values
precip.dist <-dist (precip)
#identify the correlations between two matrices Matel Correlelogram
correlog<-mantel.correlog( dist.mat, geo.dist.mat, nperm=999 )
summary(correlog)
correlog
plot (correlog)

enter image description here

#partial Mantel Test including both distance and precipitation differences 
library (ecodist)
natt.pmgram<-pmgram (dist.mat, geo.dist.mat, precip.dist, nperm=999)
plot (natt.pmgram)

enter image description here

Im not sure how to interpret these correlograms. Does anyone have any suggestions/explanations? and can these analyses be used to correct for the obvious spatial auto-correlation issues in my dataset?

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  • $\begingroup$ Consider either adding data or its graphical representation. It is difficult to imagine how your data looks from the code only. $\endgroup$
    – mpiktas
    Dec 11, 2014 at 12:59
  • $\begingroup$ @mpiktas The dataset is linked in the question and the code is fully reproducible $\endgroup$
    – I Del Toro
    Dec 11, 2014 at 13:01
  • $\begingroup$ Sorry, missed the link. $\endgroup$
    – mpiktas
    Dec 11, 2014 at 13:05

1 Answer 1

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The first figure shows that species dissimilarity in the first two distance classes are significantly positively spatially correlated, whereas the forth distance class is negatively spatially correlated, with Holm's correction. However, I'd be a little concerned about fitting so many distance classes for the relatively few sites you seem to have (15, right?), are the bins adequately represented? The part I am not sure about is how you can have distance and precipitation simultaneously, with more distance classes (fig.2) than in distance alone (fig.1); because of that I was waiting to see if you get other answers, alas (at least for now), it may be too narrow of a topic.

Depending on whether you use univariate measure of beta-diversity or the entire dissimilarity matrix, you could use simple detrending or a combination of Moran Eigenvector Maps (MEM) with variance partitioning to analyze the relative importance of precipitation and spatial autocorrelation. Again, depending on your hypothesized correlation structure, asymmetric EM could be used: Blanchet et al. 2008 http://adn.biol.umontreal.ca/~numericalecology/Reprints/Blanchet_et_al_2008-EcoMod.pdf

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