Electronic Supplementary Material (ESM) for Davis et al. “The utilization of
phylogeny in assessing species’ phenological response to global climate change”
Figure S1. Composite phylogenies of 167 and 323 flowering plant species from Chinnor,
England (A) and Concord, USA (B) depicted in Figure 2 of the main text. Red and blue dots
at nodes represent less and more phenologically responsive clades, respectively, based on
their ability to track their flowering times to seasonal temperature variation. Solid colored
dots indicate those clades that have demonstrated a significant tracking response. A null
distribution of mean flowering time tracking for each node in the phylogeny was generated
by 9999 randomizations (‘node.mn’ in Phylocom). Observed clade values that ranked ≤ 250
(p ≤ 0.05) indicated significantly strong trackers while values that ranked ≥ 9750 (p ≤ 0.05)
indicated significantly weak trackers. Open dots indicate marginally significant clades (p ≤
0.10). Each of the clades exhibiting these tracking responses is further highlighted in pink
and blue and referenced numerically to its clade name. Subclades of interest are labeled
with the more familiar, and more inclusive, clade to which they belong followed by pro
parte (p.p.).
Figure S2. Composite phylogeny of 100 European bird species depicted in Figure 3 of the
main text. Solid red dots indicate clades that have declined significantly from 1990-2000
(results were similar for the earlier interval 1970-1990); solid blue dots indicate clades
that have increased significantly. A null distribution of mean change in abundance for each
clade in the phylogeny was generated by 9999 randomizations (‘node.mn’ in Phylocom).
Observed clade values that ranked ≤ 250 (p ≤ 0.05) were considered to have significantly
declined in abundance while values that ranked ≥ 9750 (p ≤ 0.05) were considered to have
significantly increased in abundance. Open dots indicate marginally significant clades (p ≤
0.10). Each of these clades is further highlighted in pink or blue and referenced numerically
to its clade name. Subclades of interest are labeled with the more familiar, and more
inclusive, clade to which they belong followed by pro parte (p.p.).
Traits
Concord, USA
Non-native status
Invasive status
Flowering time tracking
Flowering time shift (19002006)
Chinnor, England
Non-native status
Invasive status
Non-native status
Invasive status
Flowering time tracking
Flowering time shift (19542000)
Flowering time tracking
Flowering time shift (19542000)
Poales
n
Mean Obs.
Rankbldj
-
587
587
167
1
200
2884
0.0002
0.0400
0.5768
342
2143
0.4286
377
377
873
1584
0.1746
0.3168
323
94
0.0188
323
377
4446
972
0.8892
0.1943
377
1783
0.3567
323
154
0.0307
323
4305
0.8609
-
Poales
Poales
Poales
excluded
Poales
excluded
Poales
Poales
Poales
excluded
Poales
excluded
p-value
Table S1. Phylogenetic signal of non-native species status and phenological response traits
when accounting for phylogenetic uncertainty. Each trait was analyzed across a set of 50
trees with polytomies resolved randomly. Branch lengths were adjusted for estimated
divergence time. Mean obs. rank of the 50 iterations is presented in the table. A high mean
obs. rank indicates trait overdispersion. A low mean obs. rank indicates trait clustering (i.e.,
phylogenetic signal). Significance of observed rank based on a two-tail test: significant obs.
rank < 250, > 9750 = P, 0.05, marginally significant obs. rank < 500, > 9500 = P, 0.10.
Traits
Non-native status
Invasive status
Flowering time tracking
Flowering time shift (19542000)
n
377
377
Obs.
Rankbldj
1266
4163
p-value
0.2532
0.2532
Obs.
RankBL1
440
9906
pvalue
0.0880
0.0188
377
3890
0.7780
56
0.0112
377
4054
0.8108
8150
0.3700
Table S2. Phylogenetic signal of non-native species status and phenological response traits
for Chinnor, England with the Poales clade included. Phylogenetic signal was tested by
comparing the rank of the observed mean standard deviation (obs. rank) calculated across
all nodes in the community phylogeny to a null distribution of mean standard deviations
based on 9999 iterations of trait values arranged randomly across the phylogeny tips.
These analyses were conducted with branch lengths adjusted for estimated divergence
times (obs. rankbldj) and with branch lengths set to 1 (obs. rankBL1). A high obs. rank
indicates trait overdispersion. A low mean obs. rank indicates trait clustering. Significance
of observed rank based on a two-tail test: significant obs. rank < 250, > 9750 = P, 0.05,
marginally significant obs. rank < 500, > 9500 = P, 0.10.
Traits
n1
Branch lengths scaled to
approximate time
Flowering time shift
(1954-2000)
Flowering time tracking
Branch lengths set to one
Flowering time shift
(1954-2000)
Flowering time tracking
Non-native vs. Native
pn2 n3 estimate
t
value
322 44 11
-0.45
322 44 11
-0.14
322 44 11
0.48
322 44 11
-0.14
1.09
8.94
1.80
7.04
Invasive vs. Native
pestimate
t
value
0.2804
-5.40
0.0000
0.00
0.2980
-5.78
0.0000
-0.06
5.93 0.0000
0.12 0.9011
6.83 0.0000
1.55 0.1269
Non-invasive non-native vs. Native
estimate
t
p-value
0.40
0.92
0.3616
-0.16
-9.93
0.0000
2.33
4.67
0.0000
-0.16
-7.51
0.0000
Table S3. Correlations of phenological response traits for non-native species from Chinnor, England with the Poales clade
included. Analyses were conducted with branch lengths adjusted for time and branch lengths set to one. Trait correlations of
these phenological response traits (i.e., flowering time shift and flowering time tracking) and non-native/native classes were
tested using generalized estimating equations (see main text). n = species sample size within each class: 1) natives, 2) nonnative non-invasives and 3) invasives
Traits
Concord,
Massachusetts
Flowering time
shift (19002006)
Flowering time
tracking
Chinnor, England
Flowering time
shift (19542000)
Flowering time
tracking
Flowering time
shift (19542000)
Flowering time
tracking
Non-native vs. Native
Poales
-
n1
n2 n3 estimate
259 72 11
134 28
5
p-value
estimate
0.50
0.56
0.4167
13.55
6.26 0.0000
-1.08
0.3438
1.18
-0.11
4.22
0.0003
-0.19
0.0138
2.94
-0.10
0.0010
3.82
322 44 11
-0.48
Poales
322 44 11
-0.13
271 41 11
-0.49
271 41 11
-0.08
1.15
8.13
0.97
4.27
t
pvalue
t
Poales
Poales
excluded
Poales
excluded
Invasive vs. Native
Non-invasive nonnative vs. Native
pestimate
t
value
0.3139
-5.57
6.16 0.0000
0.0000
0.00
0.12 0.7841
-0.15
0.3837
-5.45
5.81 0.0000
0.81
0.0019
0.02
0.53 0.5964
-0.11
0.42
Table S4. Correlations of phenological response traits for non-native species accounting for phylogenetic uncertainty. Each
analysis was run using 50 different trees with polytomies resolved randomly. Branch lengths were adjusted for time after
resolution. Trait correlations of these phenological response traits (i.e., flowering time shift and flowering time tracking) and
non-native/native classes were tested using generalized estimating equations (see main text). The mean of the 50 iterations
are presented in the table. n = species sample size within each class: 1) natives, 2) non-native non-invasives and 3) invasives.
0.95 0.2595
9.15 0.0000
1.47 0.2305
5.25 0.0002
Traits
Concord, USA
Flowering
time shift
(19002006)
Flowering
time
tracking
Chinnor,
England
Flowering
time shift
(19542000)
Flowering
time
tracking
Non-native vs. Native
n1
n2 n3 estimate
t
p-value
Invasive vs. Native
estimate
t
p-value
Non-invasive non-native
vs. Native
estimate
t
p-value
245 65 11 1.42
1.64
0.11
9.57
5.17
<.0001
0.004
0.004
0.99
126 25 5
-3.68
0.0001
-0.080
-1.02
0.32
-0.12
-3.69
0.001
271 41 11 0.56
1.15
0.2559
-5.74
-6.55
<.0001
2.55
4.78
<.0001
271 41 11 -0.13
-6.24
<.0001
-0.05
-1.44
0.1565
-0.15
-6.67
<.0001
-0.12
Table S5. Phylogenetic correlations of two phenological response traits across non-native and native species’ classes in
Concord, USA and Chinnor, England. Phylogentic branch lengths have been adjusted to one. Trait correlations of these
phenological response traits (i.e., flowering time shift and flowering time tracking) and non-native/native classes were tested
using generalized estimating equations (see main text). n = species sample size within each class: 1) natives, 2) non-native
non-invasives and 3) invasives.
Traits
Habitat specificity
Thermal maximum
Natal dispersal
Change in migration date
Migration distance
Overwinter in Africa
Number of broods
Farmland habitat
Northernmost latitude
Sexual dichromatism
European population size
Body mass
Change in abundance (19701990)
n
38
38
45
98
98
98
98
98
98
98
98
98
96
Change in abundance 1990-2000
estimate
t
p-value
-1.28
-7.26
0.0012
0.39
4.98
0.0055
-0.18
-0.82
0.4445
-2.81
-12.59
0.0000
-0.77
-5.85
0.0001
-0.65
-4.94
0.0003
0.29
3.66
0.0033
-0.43
-2.95
0.0122
0.03
1.58
0.1404
-0.17
-1.27
0.2276
-0.10
-1.09
0.2954
0.07
0.33
0.7451
0.23
5.88
0.0001
Change in abundance 1970-1990
estimate
t
p-value
-0.45
-1.91
0.1208
0.02
0.22
0.8347
0.00
0.00
0.9995
-1.18
-4.54
0.0007
-0.60
-4.43
0.0009
-0.93
-6.93
0.0000
0.13
1.65
0.1248
-0.70
-4.62
0.0006
-0.05
-3.16
0.0085
-0.10
-0.68
0.5099
0.11
1.06
0.3099
0.86
4.55
0.0007
-
-
-
Table S6. Univariate regression analyses of trait correlations with change in abundance in European birds. The individual
regression between each trait and change in abundance (calculated over two time periods: 1970-1990, 1990-2000) was tested
using generalized estimating equations. Estimates indicate the direction and magnitude of the correlation. n = species sample
size.
Traits
Habitat specificity
Thermal maximum
Change in migration date
European population size
n
38
38
38
38
Change in abundance 1990-2000
estimate
t
p-value
-0.59
-3.71
0.0989
0.29
4.66
0.0717
-2.97
-12.53
0.0166
0.07
1.51
0.3081
Change in abundance 1970-1990
estimate
t
p-value
-0.41
-1.57
0.2326
-0.03
-0.32
0.7757
-0.47
-1.19
0.3356
-
Table S7. Multivariate regression analyses of trait correlations with abundance change in European birds using generalized
estimating equations. All traits listed were included as co-variates in the regression model. Estimates indicate the direction
and magnitude of the correlation. n = species sample size.
Chinnor, England
Taxon
Rubiaceae
Rosaceae p.p.
(Prunus, Malus,
Sorbus)
Rosaceae p.p.
(Geum, Rosa)
Ranunculaceae p.p.
(Ranuculus)
Ranunculaceae p.p.
(Clematis,
Ranuculus)
Onagraceae
Lamiales
Fabaceae p.p.
(Trifolium)
Campanulaceae
Asteraceae p.p.
(Senecio, Solidago)
Apiales
Asterales
Betulaceae
Brassicaceae
Caryophyllaceae p.p.
(Cerastium,
Stellaria)
Caryophyllales
Dipsacales
Euphorbiaceae
Fabaceae p.p. (Vicia,
Lathyrus)
Orchidaceae
n
5
Concord, USA
mean SD rank Taxon
1.25 0.10 1100 Rubiaceae
7
1.55
10
0.58
5
1.29
Rosaceae p.p. (Prunus,
0.22
8
Amelanchier)
Rosaceae p.p. (Rosa,
0.00 7943 Potentilla)
Ranunculaceae p.p.
0.22 657 (Ranunculus)
Ranuculaceae (Clematis,
Ranuculus)
Onagraceae
Lamiales
Fabaceae p.p.
(Trifolium)
Campanulaceae
Asteraceae p.p. (Senecio,
Solidago)
Apiaceae
Asparagales
Papaveraceae
Primulaceae
n
4
mean SD rank
1.42 0.04 786
5
1.36
0.07
857
4
0.77
0.05 8119
3
1.55
0.12
9
4
14
0.87
0.77
0.79
0.01 7715
0.28 8324
0.01 9233
5
2
1.24
0.74
0.02 2527
0.07 7644
405
7
6
40
1.30
0.75
0.55
0.11 635
0.31 6134
0.07 9711
5
2
0.84
-0.02
0.23 5102
0.13 9371
21
13
54
4
15
0.60
0.39
0.26
1.39
1.18
0.16 8941
0.49 9374
0.13 9996
0.12 479
0.09 334
14
4
7
2
4
0.74
0.84
1.19
1.59
1.19
0.11 800
0.23 7489
0.26 2715
0.07 743
0.05 3292
6
25
10
4
1.38
0.34
0.93
1.34
0.13 295 Ericaceae
15
0.04 9965 Cornus
3
0.20 3389 Plantaginaceae
5
0.22 753 Malvaceae/Brassicaceae 3
1.28
0.78
0.80
0.85
0.12 542
0.45 8057
0.21 7956
0.00 7290
4
12
0.48
0.60
0.10 8354
0.06 8457
Plantaginaceae
Sapindaceae
Saxifragales
12
4
6
0.85
1.51
1.34
0.15 4759
0.10 176
0.02 399
Table S8. Clade means for flowering time tracking in Concord and Chinnor (see also Figure 2 in the main text). Mean values are corrected for
phylogenetic relatedness and branch lengths. Means have been standardized by their respective phylogenetically corrected community means:
a mean of >1 is inferred to be a good tracker, and a mean of <1 is inferred to be a poor tracker. The standard deviation (SD) of these means is
also phylogenetically corrected. Significance of means was tested by comparing the rank of the observed mean (rank) to a null distribution
based on 9999 iterations of trait values arranged randomly across the clade tips. A significantly low rank indicates that the clade is composed of
good trackers, whereas a significantly high rank indicates that the clade is composed of poor trackers. Significance of observed rank is based on
a two-tail test (i.e., significant rank < 250, > 9750 = P, 0.05; marginally significant rank < 500, > 9500 = P, 0.10). n = number of terminal taxa.