1. Non-metric multi-dimensional scaling (NMDS): How do species compositions compare between site types in the 1st survey period?

NMDS (McCune and Grace 2002) is a non-parametric ordination technique useful for community data, which is often non-normal. Here, I used a detrended correspondence analysis (DCA, McCune and Grace 2002, Leps and Smilauer 2003) to determine the length of the species turnover gradient (~3.5). This result, as well as the large number of zeros present in this dataset suggested NMDS would likely be the most appropriate ordination method. I ran the NMDS starting from a random configuration (PC-ORD ver. 5.0 McCune and Mefford 1999) using Bray-Curtis distance measure, in 5-dimensions with monte carlo simulations and determined that 3 dimensions were appropriate for my data (to minimize stress). I then ran a principal component analysis (PCA) and used this output as starting configuration for my final NMDS run to reduce instability. This final run used only one iteration in 3-dimensions with Bray-Curtis distance and used PCA starting coordinates.

The results of the NMDS indicate a grouping of sites in ordination space, with "02-poor" and "03-mesic" sites on the right side of Axis 1 and "01-rich" sites on the left side of Axis 1. 

Axis 1 may indicate a moisture/nutrient gradient with Pinus albicaulis and Cladina/Cladonia sp. on the right hand side, and Abies lasciocarpa, Streptopus lanceolatus, Rubus pedatus and Vaccinium ovalifolium on the left. Sites are indicated on the graph by triangles colour-coded by site type. however, there are no species vectors to help explain Axis 3.

2. Multi-response permutation procedure (MRPP): Are the communities in site series "01", "02" and "03 significantly different from one another?

Multi-response permutation procedure is a useful technique to determine whether groups in an ordination are significantly different from each other (MRPP, McCune and Grace 2002). This test was run on the sites grouped by "01", "02" and "03" from the original survey period to determine if there was significantly different community types prior to disturbance and determine baseline relationships between the three site series. Pair-wise comparisons indicate that the "01-rich" sites are significantly different from all others ("02": T=-4.30 P=0.001, "03": T=-5.07, P<0.001), but "02-poor" and "03-mesic" were not significantly different from each other in the initial survey (T=0.30, P=0.53) (alpha=0.017).

3. Indicator Species Analysis: What species characterize each site type from the initial survey period?

Indicator species analysis (McCune and Grace 2002) was used to determine which species are most abundant and 'faithful' to each site series group ("01","02" and "03"). This describes which species characterize a community. Only the "01-rich" group and "02-poor" groups show significant indicator species. The communities found in "03-mesic" do not have species of high abundance and "faithfulness" to that group. "02-poor" sites are characterized by Whitebark pine (P.albicaulis), Cassiope mertensiana, Hieracium scouleri var. albertinum and stereocaulon paschale. These species are all associated with drier sites (Beaudry et al 1999, Parish et al 1996). "01-rich" sites were characterized by Rubus pedatus, Streptopus lanceolatus and Rhytidiopsis robusta, which are all commonly found on moist sites or in general in subalpine areas (Rhytidiopsis) (Pojar and Mackinnon 1994). 

References:

Beaudry, L., Coupe, R., Delong, C. and Pojar, J. 1999. Plant indicator guide for northern British Columbia: Boreal, Sub-boreal and Subalpine biogeoclimatic zones. Province of British Columbia. Crown publications, Victoria, BC.

Leps, J. and Smilauer, P. 2003. Multivariate analysis of ecological data using CANOCO. Cambridge University Press. Cambridge, UK.

McCune, B. and Grace, J.B. 2002. Analysis of ecological communities. MJM Software Design, Gleneden Beach, Oregon

McCune, B. and Mefford., M. J., 1999. PC-ORD. Multivariate Analysis of Ecological Data., Version 5.0, MjM Software, Gleneden Beach, Oregon, U.S.A.

Parish, R., Coupe, R., and Lloyd, D. 1996. Plants of southern interior British Columbia and the inland Northwest. Lone Pine Publishing.

Pojar, J. and MacKinnon, A. 1994. Plants of coastal British Columbia. Lone Pine Publishing.