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Online Supporting Material:
NICHE OPPORTUNITIES AND INVASION DYNAMICS IN
A DESERT ANNUAL COMMUNITY
Ginger R.H. Allington1,*, David N. Koons2, S. K. Morgan Ernest3, Michele R.
Schutzenhofer4 and Thomas J. Valone1
1Department
of Biology, Saint Louis University, St. Louis, MO 63103
Department of Wildland Resources and the Ecology Center, Utah State University,
Logan, UT 84322
3Department of Biology and the Ecology Center, Utah State University, Logan, UT
84322 11
4Division of Science & Mathematics, McKendree University, Lebanon, IL 62254
* Corresponding Author: gallingt@slu.edu, 314.724.3275
2
CONTENTS:
Appendix S1. Recent studies of biotic resistance.
Appendix S2. Abundance of the invader by plot over time.
Appendix S3. Results from the tiered approach to model selection.
Appendix S4. Schematic of treatment plots at the experimental site.
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21
APPENDIX S1: Recent studies of biotic resistance.
Table S1. Biotic resistance studies reviewed in Levine et al. (2004) (= L) and Parker et al. (2006)
22
(= P). ‘Years’ indicates the duration of the study, in years.
23
24
Study
Amsberry et al. 2000
Bakker & Wilson 2001
Barger et al. 2003
Barry et al. 2004
Beckstead & Parker 2003
Bell et al. 1987
Bellingham & Coomes 2003
Bergelson 1990
Biondini et al. 1998
Bock et al. 1984
Bork et al. 1998
Bossard & Rejmanek 1994
Bossard 1991
Bowers 1993
Brady et al. 1989
Bray et al. 2003
Cabin et al. 2000
Cadenasso et al. 2002
Callaway et al. 2001
Callaway et al. 2003
Callaway et al. 2004a
Callaway et al. 2004b
Carson & Root 1999
Case & Crawley 2000
Chaneton et al. 2002
D’Antonio & Mack 2001
D’Antonio 1993
D'Antonio et al. 1993
Detling 1998
DeWalt et al. 2004
Donlan 2003
Dormaar 1994
Dukes 2002
Erneberg 1999
Esler 1989
Evers 1998
Facelli 1989
Fahnestock & Detling 2002
Fowler 2002
Years
1.00
0.33
1.33
2.00
0.25
3.00
1.58
1.00
6.00
1.00
2.00
4.00
4.00
4.00
16.00
0.71
2.00
2.00
0.29
0.27
2.00
0.38
2.00
2.00
4.00
7.00
4.00
3.00
2.00
1.29
1.00
12.00
2.00
0.58
0.25
1.00
10.00
3.00
3.00
Review Source
L
L
L
P
L
P
L
P
P
P
P
P
L
P
P
L
P
P
L
L
L
L
P
L
P
L
L&P
P
P
P
P
P
L
L
P
P
P
P
P
Green et al. 2004
Greiling & Kichanan 2002
Grieshop & Nowierski 2002
Hamilton et al. 1999
Hayes & Holl 2003
Holmgren et al. 2000
Jesson et al. 2000
Keeley et al. 2003
Kelt & Valone 1995
Kennedy et al. 2002
Kimball & Schiffman 2003
Knops et al. 1999
Kucera 1956
Kuijper et al. 2004
Lambrinos 2002
Laycock 1967
Leader-Williams et al. 1987
Lenz & Facelli 2003
Levine 2001
Lindig-Cisneros & Zedler 2002
Lord 1990
Lym 1997
Lyons & Schwartz 2001
Marler et al. 1999
Mazia et al. 2001
McKnight & Hepp 1995
Meekins & McCarthy 2001
Parker 2001
Peart 1989a
Peart 1989b
Perrow et al. 1997
Pierson & Mack 1990
Popolizio et al. 1994
Prieur-Richard et al. 2000
Rachich & Reader 1999
Reinhart et al. 2003
Rice 1987
Rose et al. 1995
Rusch & Oesterheld 1997
Scherber et al. 2003
Schierenbeck et al. 1994
Schulz & Leininger 1990
Seabloom et al. 2003
Sheldon 1987
Siemann & Rogers 2003
Singer 1995
1.00
1.50
2.00
0.58
1.00
2.00
0.83
1.00
1.00
5.00
3.00
4.00
4.00
0.25
2.50
15.00
10.00
0.42
2.25
2.42
1.00
3.00
4.00
0.25
5.00
2.00
1.50
1.00
2.00
2.00
1.00
2.00
2.00
0.75
1.50
0.17
0.50
25.00
0.83
0.17
2.00
2.00
4.00
3.00
2.00
2.00
P
P
L
L
P
P
L
P
P
L
P
L
P
P
L&P
P
P
L
L
L
P
P
L
L
L
P
L
L
L
L&P
P
L &P
P
L
L&P
L
L&P
P
P
L&P
L&P
P
L
P
L&P
P
Stohlgren et al. 1999
Stohlgren et al. 1999
Thibaud et al. 1996
Valone et al. 2002
Vila & D’Antonio 1998
Walker et al. 2003
Yates et al. 2000
Yoshida & Allen 2001
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
1.00
1.00
1.50
20.00
1.00
13.00
1.00
0.25
P
P
L&P
P
L&P
P
P
L
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244
245
246
247
248
249
250
251
252
253
254
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255
256
APPENDIX S2: Abundance of the invader by plot over time.
257
258
Table S2. Abundance of E. cicutarium on rodent removal (-R), Dipodomys removal (-
259
D), and control (C) plots by year. Each column represents the total abundance for a
260
single plot; columns are labeled with their associated plot number. For 1982-2008
261
abundance is the total from 16 quadrats per plot. In 1978, 1980-82 eight quadrats were
262
counted per plot and in 1979 four quadrats were counted per plot; plot totals for those
263
years were multiplied by 2 or 4 to account for differences in sampling effort. Years 1980,
264
1990, 1996, 1999, 2000 and 2006 were very dry with low abundance of nearly all
265
annuals.
Year / Plot
1978
1979
1980
1981
1982
1983
1984
1985
1986
1987
1988
1989
1990
1991
1992
1993
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
2008
266
267
268
7
24
376
0
1848
162
373
3369
1636
259
916
128
21
2
1
0
0
15
6
0
132
586
0
0
127
212
589
108
136
0
318
181
-R
10
16
23
0
0
0
0
0
0
0
0
0
0
4
0
14
30
0
0
40
0
119
691
1
122
381
5
96
66
28
191
245
57
92
49
0
462
117
66
0
55
5
11
1
0
27
6
16
247
55
38
408
133
97
281
151
139
0
0
0
1101 1238 579
1737 1232 1658
0
0
0
0
0
0
587
445
427
404
92
286
1938 1191 1089
1197 1406 968
635
566
651
0
0
0
424
651
437
488
510
382
-D
3
0
0
0
0
0
2
14
0
74
453
44
155
43
0
4
24
78
56
0
450
758
1
0
291
131
393
810
603
0
438
462
15
0
0
0
0
2
0
0
0
1
2
103
4
0
0
0
0
0
1
0
10
57
0
0
100
21
782
383
270
0
256
191
19
0
4
0
0
6
8
430
137
150
328
2
458
0
4
31
71
244
195
0
1058
1039
14
0
500
99
735
802
562
0
512
308
C
21
0
0
0
0
0
3
14
7
10
38
0
149
4
0
1
12
18
35
0
291
857
0
0
384
120
902
1003
473
0
579
449
2
0
0
0
0
0
5
0
1
1
1
5
10
0
1
0
8
51
58
0
240
514
23
0
153
62
221
606
449
0
300
140
11
0
0
0
0
0
0
0
0
0
3
1
42
2
0
0
0
3
2
0
54
143
0
0
208
192
626
366
724
0
262
312
14
0
0
0
0
0
0
0
0
0
2
0
1
0
0
0
0
0
0
0
8
18
0
0
60
30
410
196
268
0
250
141
22
0
0
0
0
0
0
0
0
0
1
0
3
0
0
0
0
1
7
0
112
524
1
0
337
108
510
1150
587
0
818
362
269
APPENDIX S3. Results from the tiered approach to model selection.
270
271
272
273
274
275
276
277
278
279
280
Table S3-1. Comparison of GLMs with alternative parameterizations of a) rodent prevalence, b)
competition, and c) winter precipitation effects on Erodium cicutarium abundance during 19782008 at Portal, AZ. Considered variables included: the energy requirements of all rodents (AllE)
or Dipodomys rodents (DipoE) on each plot in each year, logged abundance of conspecifics on a
quadrat in the preceding year (z), logged native winter annual forb abundance on a quadrat in the
preceding (flag) or current year (f), and winter precipitation on the study area each year (ppt in
cm; see methods). A superscript of 2 indicates a quadratic effect, including first and second-order
terms. All models contained an intercept term, a negative binomial scaling parameter, and a zeroinflation parameter. K represents the total number of estimated parameters in a model. Evidence
for a model is inversely related to its ΔSIC, with ΔSIC = 0 having the best fit amongst
considered models. The p-value for tested coefficients in each model is also provided.
K
ΔSIC
DipoE
4
0
< 0.001
AllE
4
169.2
0.001
Intercept only
3
172.4
z + flag
5
0
both < 0.001
z
4
498.6
< 0.001
flag
4
1348.8
< 0.001
f
4
1394.6
< 0.001
Intercept only
3
1524.3
ppt + ppt2
5
0
Intercept only
3
187.5
ppt
4
195.4
Model
p
a)
b)
c)
281
282
283
284
285
286
287
288
289
both < 0.001
0.45
290
291
292
293
294
295
296
Table S3-2. A global model with additive and plausible interactive effects of the rodent
prevalence, competition, and winter precipitation covariates that performed best in the first tier
of analysis (see Table S3-1: DipoE×flag + DipoE×(ppt+ppt2) + flag×(ppt+ppt2) + z×(ppt+ppt2);
where a × indicates an interaction, including the interaction term and all underlying additive
terms). Alternative versions of the global GLM were compared with and without a zero-inflation
(ZI) parameter, and with either the Poisson distribution or the NB1 or NB2 parameterizations of
the negative binomial distribution using SIC (Hilbe 2011).
with ZI
without ZI
Poisson
NB1
X
15
0
X
14
9.4
X
15
947.0
X
14
990.2
X
14
20704.0
X
13
110762.1
X
X
X
297
298
299
300
301
302
303
ΔSIC
K
X
X
X
NB2
Table S3-3. Likelihood ratio tests for the significance of adding ‘quadrat within plot within
treatment’ (spatial) and ‘year’ random effects to the global model (DipoE×flag +
DipoE×(ppt+ppt2) + flag×(ppt+ppt2) + z×(ppt+ppt2)) with a zero-inflation term and NB1
parameterization of the negative binomial distribution (see Table S3-2). A p-value < 0.05
indicates rejection of the simpler model in favor of the more complicated model (i.e., that with
more random effects).
Model
p
no random effects vs. year
< 0.001
no random effects vs. spatial
< 0.001
no random effects vs. year + spatial
< 0.001
year vs. year + spatial
< 0.001
spatial vs. year + spatial
< 0.001
Table S3-4. Results from a stepwise removal of fixed-effect parameters in the global GLMM with crossed random effects for ‘quadrat
within plot within treatment’ and ‘year’ (listed as model 1, see also Table S3-3). Parameters were removed based on p-values, one-byone, until all covariates in the GLMM were significant (α > 0.05). The crossed random effects were included in all of the GLMMs at
this final stage of analysis. Here, ‘Int’ denotes the intercept, and × indicates an interaction term only – the underlying additive terms
are listed separately. All other notation is as listed in Table S3-1.
Stepwise removal of parameters →
Model # and p-values associated with parameters in the model
Parameters
1. p
2. p
3. p
4. p
Int
< 0.001 < 0.001 < 0.001 < 0.001
DipoE
z
5. p
6. p
7. p
8. p
9. p
10. p
< 0.001 < 0.001 < 0.001
< 0.001
< 0.001
< 0.001
< 0.001 < 0.001 < 0.001 < 0.001
< 0.001 < 0.001 < 0.001
< 0.001
< 0.001
< 0.001
< 0.001 < 0.001 < 0.001 < 0.001
< 0.001 < 0.001 < 0.001
< 0.001
< 0.001
< 0.001
flag
0.281
0.167
0.991
0.759
0.543
ppt
0.002
0.001
0.002
0.002
0.002 < 0.001 < 0.001
0.001
< 0.001
< 0.001
ppt2
0.010
0.010
0.010
0.010
0.010
0.010
0.004
0.004
DipoE×flag
0.138
0.272
0.109
0.265
DipoE×ppt
0.133
0.142
0.560
DipoE×ppt2
0.672
0.700
0.404
z×ppt
0.051
z×ppt2
< 0.001
0.187
0.335
0.004
0.004
0.259
0.563
0.036
0.140
0.118
0.128
0.003 < 0.001
0.001
0.001
0.001
flag ×ppt
0.507
0.336
flag ×ppt2
0.332
0.217
APPENDIX S4. Schematic of treatment plots
FIGURE S4. Schematic of treatment plots at the experimental site. Plots in light grey
text were not included in these analyses as they have not received the same treatment for
the entire duration of the study.