Supplemental Material:

Multiple factors influence plant richness and diversity in the cold and dry boreal forest of southwest Yukon, Canada

Authors: Shyam K. Paudel*, Craig R. Nitschke*†, Patrick O. Waeber, Suzanne W. Simard and John L. Innes

* Co-Primary authors

† Corresponding author: School of Ecosystem and Forest Sciences, University of Melbourne, 500 Yarra Blvd, Richmond, Victoria 3121, Australia. Email: ; Tel: +61 3 9035 6855.

Renyi’s Profile

Figure S1: Species accumulation curve

Diversity-Disturbance Relationships

Figure S2: Relationships between plant richness and diversity and plot age.

Figure S3: Relationships between plant richness and diversity and organic soil depth.

Figure S4: Relationships between plant richness and diversity and fermented layer depth.

Mixed Effects Modelling:

Goodness of Fit

Table S1: Goodness of fit for linear mixed-effects models of environmental variables

Effects plots

Figure S5: Effects plots for significant response variables on plant diversity and richness

Figure S6: Interaction plots for significant interactions between age and response variables on plant richness

Figure S1: Species accumulation curve. Species accumulation curve indicates that 60 plots were enough to capture ~90% of the plant species in the study area justifying the sampling intensity.

Figure S2: Relationships between plant diversity and plot age: (a) overall plant richness; (b) overall Simpson’s diversity; (c) tree richness; (d) shrub richness; (e) herb richness; (f) graminoid richness; (g) bryophyte richness; and, (h) lichen richness. Non-significant (ns) and significant relationships (†: P≤ 0.10; *: P≤ 0.05, **: P≤ 0.01; **8: P≤ 0.001) indicated along with coefficient of variation (R2) and the effective degrees of freedom (edf) for the regression smoother fitted by the GAMM model (k = 2). Dashed lines indicate the 95% confidence intervals for the fitted regression.

Figure S3: Relationships between plant diversity and organic soil depth (standardised): (a) overall plant richness; (b) overall Simpson’s diversity; (c) tree richness; (d) shrub richness; (e) herb richness; (f) graminoid richness; (g) bryophyte richness; and, (h) lichen richness. Non-significant (ns) and significant relationships (†: P≤ 0.10; *: P≤ 0.05, **: P≤ 0.01; **8: P≤ 0.001) indicated along with coefficient of variation (R2) and the effective degrees of freedom (edf) for the regression smoother fitted by the GAMM model (kmax = 2). Dashed lines indicate the 95% confidence intervals for the fitted model.

Figure S4: Relationships between plant diversity and fermented layer depth (F layer; standardised): (a) overall plant richness; (b) overall Simpson’s diversity; (c) tree richness; (d) shrub richness; (e) herb richness; (f) graminoid richness; (g) bryophyte richness; and, (h) lichen richness. Non-significant (ns) and significant relationships (†: P≤ 0.10; *: P≤ 0.05, **: P≤ 0.01; **8: P≤ 0.001) indicated along with coefficient of variation (R2) and the effective degrees of freedom (edf) for the regression smoother fitted by the GAMM model (k = 2). Dashed lines indicate the 95% confidence intervals for the fitted regression.

Table S1: Goodness of fit for linear mixed-effects models of environmental variables on species richness and plant functional types. Complete summary of fixed effects for full model shown in Table 4.

Trees / Shrubs / Herbs / Graminoids / Bryophytes / Lichens
Model Name / Null / Full / Null / Full / Null / Full / Null / Full / Null / Full / Null / Full
Fixed Effects / Est. (se) / Est. (se) / Est. (se) / Est. (se) / Est. (se) / Est. (se) / Est. (se) / Est. (se) / Est. (se) / Est. (se) / Est. (se) / Est. (se)
Intercept / 2.78 (0.13) / 2.84 (0.07) / 3.88 (0.42) / 4.08 (0.14) / 3.90 (0.56) / 3.77 (0.18) / 2.00 (0.26) / 1.98 (0.17) / 2.04 (0.18) / 2.28 (0.12) / 2.29 (0.14) / 2.28 (0.11)
Random Effects / VC / VC / VC / VC / VC / VC / VC / VC / VC / VC / VC / VC
Location / 0.08 (0.29) / 0.00 (0.00) / 0.94 (0.97) / 0.00 (0.00) / 2.02 (1.42) / 0.00 (0.00) / 0.49 (0.70) / 0.14 (0.37) / 0.22 (0.47) / 0.00 (0.00) / 0.06 (0.24) / 0.00 (0.00)
Residuals / 0.53 (0.73) / 0.35 (0.59) / 1.68 (1.30) / 1.42 (1.19) / 2.83 (1.68) / 2.75 (1.69) / 0.55 (0.74) / 0.56 (0.7) / 0.47 (0.68) / 0.39 (0.63) / 1.24 (1.11) / 1.03 (1.01)
Goodness of Fit
PCV (Location) / -100% / -100% / -100% / -71.4% / -100% / -100%
PCV (Residuals) / -34.0% / -15.5% / -2.8% / 1.8% / -17.0% / -18.2%
R2GLMM(m) / 45.3% / 48.3% / 36.2% / 23.4% / 43.9% / 21.8%
R2GLMM(c) / 45.3% / 48.3% / 36.2% / 38.8% / 43.9% / 21.8%
AIC / 210.4 / 174.7 / 320.3 / 299.5 / 368.3 / 355.4 / 222.0 / 218.4 / 204.3 / 184.4 / 282.5 / 265.8
BIC / 217.9 / 204.7 / 327.8 / 327.0 / 375.8 / 372.9 / 229.4 / 230.9 / 211.8 / 214.4 / 290.0 / 280.8
P: Null vs Full / 0.001 / 0.001 / 0.001 / 0.023 / 0.001 / 0.001

Est. (se), estimate (standard error); Location, locations of transects (L= 6); PCV, proportion of change in variance; R2GLMM(m), marginal variability explained by fixed effects; R2GLMM(c), conditional variability explained by full model; AIC, Akaike Information Criterion; BIC, Bayesian Information Criterion; VC, Variance Components; P, significance value based on likelihood ratio test.

Figure S5: Effects plots for significant response variables on plant diversity and richness. Shaded areas represent 95% confidence intervals: (a-c) Simpson’s Diversity Index; (d) total plant richness; (e-f) tree richness; (g-k) shrub richness; (l) bryophyte richness; (m-p) herb richness; (q-r) graminoid richness; and, (s-u) lichen richness. Response variables are presented as standardised values.

Figure S6: Interaction plots for significant interactions between age and response variables on plant richness. Interaction plots show the minimum (red) and maximum (blue) moderator values (i.e. plot age); shaded areas represent 95% confidence intervals: (a-c) tree richness; (d-f) bryophyte richness; and, (g) shrub richness. Response variables are presented as standardised values.