Dear R-listers,

I'm trying to compare beta diversity of bacteria in soil in relation to
land use (factor with four levels). I've got two dissimilarity matrices
(using the mothur platform): Jaccard and Bray-Curtis. Jaccard estiamation
is based on shared species, whereas Bray Curtis also takes into account the
abundance of each species within each site. I use first anosim() and
adonis() to see if species composition among land uses differ and then
betadisper() to look at variation within each land use.

ANOSIM:

anosim(bray_curtis,land_use)
Call:
anosim(dat = bray_curtis, grouping = land_use)
Dissimilarity:

ANOSIM statistic R: 0.1724
Significance: 0.012

Based on 999 permutations

anosim(jaccard,land_use)
Call:
anosim(dat = jclass, grouping = LUSE)
Dissimilarity:

ANOSIM statistic R: 0.1766
Significance: 0.001

Based on 999 permutations

ADONIS:
adonis(bray_curtis~land_use)
Call:
adonis(formula = bray_curtis ~ land_use)

Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
land_use 3 1.1238 0.37460 1.6893 0.15326 0.016 *
Residuals 28 6.2090 0.22175 0.84674
Total 31 7.3328 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

adonis(jaccard~land_use)
Call:
adonis(formula = jaccard ~ land_use)

Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
land_use 3 1.325 0.44166 1.158 0.11037 0.003 **
Residuals 28 10.679 0.38140 0.88963
Total 31 12.004 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

BETADISPER:
BC<-betadisper(bray_curtis,land_use)
Homogeneity of multivariate dispersions

Call: betadisper(d = bray_curtis, group = land_use)

No. of Positive Eigenvalues: 31
No. of Negative Eigenvalues: 0

Average distance to centroid:
1L 2L OP UL
0.4267 0.4359 0.4634 0.4086

Eigenvalues for PCoA axes:
PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 PCoA7 PCoA8 PCoA9 PCoA10 PCoA11
2.0644 0.4832 0.4528 0.3611 0.3026 0.2731 0.2228 0.2172 0.2040 0.1939
0.1766
PCoA12 PCoA13 PCoA14 PCoA15 PCoA16 PCoA17 PCoA18 PCoA19 PCoA20 PCoA21
PCoA22
0.1711 0.1605 0.1575 0.1481 0.1388 0.1345 0.1323 0.1260 0.1245 0.1182
0.1171
PCoA23 PCoA24 PCoA25 PCoA26 PCoA27 PCoA28 PCoA29 PCoA30 PCoA31
0.1151 0.1075 0.1019 0.0968 0.0948 0.0904 0.0866 0.0820 0.0773

anova(BC)
Analysis of Variance Table

Response: Distances
Df Sum Sq Mean Sq F value Pr(>F)
Groups 3 0.012521 0.0041737 0.5399 0.6589
Residuals 28 0.216461 0.0077308


JAC<-betadisper(jaccard,land_use)
Homogeneity of multivariate dispersions

Call: betadisper(d = jaccard, group = land_use)

No. of Positive Eigenvalues: 31
No. of Negative Eigenvalues: 0

Average distance to centroid:
1L 2L OP UL
0.5698 0.5844 0.5906 0.5645

Eigenvalues for PCoA axes:
PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 PCoA7 PCoA8 PCoA9 PCoA10 PCoA11
0.8231 0.5371 0.4680 0.4306 0.4209 0.4063 0.4040 0.3950 0.3922 0.3884
0.3860
PCoA12 PCoA13 PCoA14 PCoA15 PCoA16 PCoA17 PCoA18 PCoA19 PCoA20 PCoA21
PCoA22
0.3833 0.3781 0.3768 0.3714 0.3682 0.3650 0.3605 0.3577 0.3538 0.3488
0.3478
PCoA23 PCoA24 PCoA25 PCoA26 PCoA27 PCoA28 PCoA29 PCoA30 PCoA31
0.3403 0.3385 0.3364 0.3327 0.3302 0.3202 0.3188 0.3143 0.3097

anova(JAC)
Analysis of Variance Table

Response: Distances
Df Sum Sq Mean Sq F value Pr(>F)
Groups 3 0.0035553 0.00118510 2.8792 0.05364 .
Residuals 28 0.0115251 0.00041161


My interpretation of these results is that there are siginificant
differences among land uses for both dissimilarity measures (based on the
anosim() results).
The results from adonis() tell also that species composition among land
uses is different (i.e. the centroids of spp composition among land uses
are different). Together, I could then say that species composition differ
among land uses in terms of presence/absence of species (Jaccard), and also
when species abundance is taken into account (Bray Curtis). Is this correct?

>From the betadisper() results then I would say that even though species
composition is different among land uses, the variation WITHIN each land
use is similar (ie beta diversity). But this would only be the case for tht
Bray-Curtis dissimilarity. How can then I interpret the significant
(P=0.05) result for the Jaccard index? Is it that species composition
changes more between sites within at least one of the land uses compared to
the others?

Any help much appreciated.

-- 
Larisa Lee Cruz
Laboratory of Geographical Ecology
School of Biological Sciences
Seoul National University

	[[alternative HTML version deleted]]

