SUPPORTING INFORMATION
Figure S1. Sample-based rarefaction curves for a) all species, b) just endemics and c)
just non-endemics across land-uses. Small-dotted lines show the 95% confidence
intervals. The number of observed species richnesses is shown in front of the rarefaction
curves. The large dots in front of each graph show the estimated richness for each landuse, calculated using first order Jackknife.
Figure S2. Sample-based rarefaction curves for all (a-c), endemic (d-f) and non-endemic
(g-i) species across the different land-uses and regions: Montane (a, d and g), North (b, e
and h) and South (c, f and i). Small-dotted lines show the 95% confidence intervals.
Figure S3 Effect of canopy cover on the endemic (a), non-endemic (b) and total (c) number of species. The dots represent the values
observed and the lines represent the generalised linear models in the different regions. Regions are distinguished by colours: black –
Montane; dark grey – North; and light grey – South. All the models were selected by AICc, and canopy cover alone proved to be the best
predictor in all models apart from endemic species richness in the North, where the model performance was improved by the addiction of
the squared canopy cover.
Table S1. Characteristics of the bird species detected during the point counts. The taxonomy was adapted from Jones & Tye (2006) to
include recent taxonomic changes (Melo & Jones, 2008). Threat status according to IUCN’s 2011 Red List: LC – least concern; NT – near
threatened; VU – vulnerable; EN – endangered; CR – critically endangered. The weight refers to the average weight for the species or
subspecies, following the values obtained from the sources identified by the lowercase superscript letter. The feeding guild was
categorized according to Jones & Tye (2006) into: C – carnivore; F – frugivore; G – granivore; O - omnivore. In the last column, widespread
taxa (no) are distinguished from endemic species and subspecies. Species not detected during the point counts, but that are known to be
resident or breeders in the island’s terrestrial habitats are also included, although their characteristics are not shown.
Family
Scientific name
English name
Status
PHAETHONTIDAE
Phaethon lepturus
White-tailed Tropicbird
LC
ARDEIDAE
Bubulcus ibis
Cattle Egret
LC
THRESKIORNITHIDAE Bostrychia bocagei
Dwarf Ibis
CR
ACCIPITRIDAE
Milvus migrans
Black Kite
NT
754 a
C
No
Coturnix delegorguei histrionica
Harlequin Quail
LC
71.5 a
O
Subspecies
Francolinus afer
Red-necked Spurfowl
LC
Treron sanctithomae
São Tomé Green Pigeon
VU
227 b
F
Species
Columba malherbi
São Tomé Bronze-naped Pigeon NT
169 b
F
Species1
PHASIANIDAE
COLUMBIDAE
Weight (g)
Feeding guild
Endemic
No
365a
C
No
Species
No
Columba larvata simplex
Lemon Dove
LC
184.7 b,c
O
Subspecies
Columba thomensis
Maroon Pigeon
EN
440 a
F
Species
Streptopelia senegalensis
Laughing Dove
LC
81.5 a,c
G
No
Agapornis pullaria
Red-headed Lovebird
LC
39.5 a
F
No
Psittacus erithacus
Grey Parrot
LC
No
CUCULIDAE
Chrysococcyx cupreus insularum
Gulf of Guinea Emerald Cuckoo
LC
Subspecies
TYTONIDAE
Tyto alba thomensis
São Tomé Barn Owl
LC
Subspecies
STRIGIDAE
Otus hartlaubi
São Tomé Scops Owl
VU
80 a
C
Species
Zoonavena thomensis
São Tomé Spinetail
LC
8a
C
Species3
Cypsiurus parvus
Palm Swift
LC
14 a
C
No
Apus affinis bannermani
Gulf of Guinea Little Swift
LC
Subspecies
ALCEDINIDAE
Alcedo cristata thomensis
São Tomé Malachite Kingfisher
LC
Subspecies
MOTACILLIDAE
Amaurocichla bocagei
São Tomé Shortail
VU
Species
TURDIDAE
Turdus olivaceofuscus
São Tomé Thrush
NT
85 a,c,d
O
Species
SYLVIIDAE
Prinia molleri
São Tomé Prinia
LC
9.1 a,c
C
Species
MONARCHIDAE
Terpsiphone atrochalybeia
São Tomé Paradise Flycatcher
LC
13.8 a,c
C
Species
Anabathmis newtoni
São Tomé Sunbird
LC
7.5 a,c
O
Species
Dreptes thomensis
Giant Sunbird
VU
23 a,c
O
Species
Zosterops feae
São Tomé White-eye
VU
8.4 d
O
Species2
Zosterops lugubris
São Tomé Speirops
LC
17.2 c,d
O
Species
Oriolus crassirostris
São Tomé Oriole
VU
50 a
O
Species
PSITTACIDAE
APODIDAE
NECTARINIIDAE
ZOSTEROPIDAE
ORIOLIDAE
LANIIDAE
Lanius newtoni
São Tomé Fiscal
CR
STURNIDAE
Onychognathus fulgidus fulgidus
Chestnut-winged Starling
LC
118.5 a
O
Subspecies
Ploceus velatus peixotoi
Vitelline Masked Weaver
LC
19.3 c
O
Subspecies
Ploceus cucullatus
Village Weaver
LC
27.7 a,c
O
No
Ploceus grandis
Giant Weaver
LC
66 a,c
O
Species
Ploceus sanctithomae
São Tomé Weaver
LC
22.1 a,c
O
Species
Euplectes hordaceus
Fire-crowned Bishop
LC
23 a
O
No
Euplectes albonotatus
White-winged Widowbird
LC
Euplectes aureus
Golden-backed Bishop
LC
21.8 a,c
O
No
Estrilda astrild
Common Waxbill
LC
8.5 a
G
No
Uraeginthus angolensis
Southern Cordon-bleu
LC
9.7 a,c
G
No
Lonchura cucullata
Bronze Mannikin
LC
9.8 a
G
No
Vidua macroura
Pin-tailed Whydah
LC
15.5 a
G
No
Serinus mozambicus
Yellow-fronted Canary
LC
12.4 a,c
G
No
Serinus rufobrunneus thomensis
Príncipe Seedeater
LC
25 c,d
O
Species3
Serinus concolor
São Tomé Grosbeak
CR
PLOCEIDAE
ESTRILDIDAE
VIDUIDAE
FRINGILLIDAE
1
Species
No
Species
Shared with Annobon and Príncipe; 2 Recent split, with threat status still refering to previous species; 3 Shared with Príncipe. a (Hoyo et
al., 1992-2011); b (Carvalho unpublished data); c (Atkinson et al., 1994); d (Melo, 2006).
Table S2. Bird species’ observed abundance and frequency. Total values are shown together with the values obtained in each land-use (Old
– old-growth forest; Sec – secondary forest; Sha – shade plantation; Nfor – non-forested). Species are ordered according to overall
abundance rank, and frequency rank is also shown.
Species
Abundance
Frequency
Rank
Old
Sec
Sha
Nfor
TOTAL
Rank
Old
Sec
Sha
Nfor
TOTAL
Zosterops lugubris
1
113
255
198
131
697
3
35
67
55
35
192
Anabathmis newtoni
2
61
167
211
145
584
1
45
91
94
63
293
Prinia molleri
3
70
139
109
117
435
2
39
68
77
64
248
Estrilda astrild
4
0
18
72
310
400
9
0
3
18
45
66
Ploceus sanctithomae
5
61
149
125
48
383
5
29
61
59
21
170
Zosterops feae
6
51
107
65
80
303
11
9
15
10
8
42
Serinus rufobrunneus
7
36
82
82
80
280
4
24
55
53
47
179
Turdus olivaceofuscus
8
32
84
41
16
173
6
27
51
29
13
120
Terpsiphone atrochalybeia
9
25
50
59
23
157
7
22
37
41
16
116
Lonchura cucullata
10
0
0
18
110
128
18
0
0
3
10
13
Columba larvata
11
11
62
37
8
118
8
8
39
26
6
79
Oriolus crassirostris
12
43
19
0
0
62
10
33
15
0
0
48
Treron sanctithomae
13
11
26
16
3
56
14
11
9
6
3
29
Onychognathus fulgidus
14
6
24
8
9
47
13
5
14
5
6
30
Euplectes hordaceus
15
0
0
0
40
40
31
0
0
0
2
2
Streptopelia senegalensis
16
0
0
4
33
37
16
0
0
4
11
15
Ploceus grandis
17
2
15
15
4
36
12
2
13
13
3
31
Columba malherbi
18
1
9
8
12
30
15
1
8
6
12
27
Milvus migrans
19
0
1
1
27
29
17
0
1
1
12
14
Ploceus velatus
20
0
0
19
9
28
20
0
0
5
6
11
Zoonavena thomensis
21
2
2
7
13
24
18
2
1
5
5
13
Dreptes thomensis
22
9
14
0
0
23
21
7
2
0
0
9
Vidua macroura
23
0
0
0
22
22
30
0
0
0
3
3
Serinus mozambicus
24
0
0
1
18
19
28
0
0
1
4
5
Agapornis pullaria
25
0
8
9
0
17
22
0
3
5
0
8
Ploceus cucullatus
26
0
0
0
15
15
24
0
0
0
6
6
Coturnix delegorguei
27
0
0
0
12
12
23
0
0
0
7
7
Cypsiurus parvus
28
0
0
0
11
11
24
0
0
0
6
6
Bubulcus ibis
29
0
0
6
2
8
24
0
0
4
2
6
Uraeginthus angolensis
30
0
0
2
5
7
24
0
0
2
4
6
Columba thomensis
31
1
1
2
0
4
29
1
1
2
0
4
Euplectes aureus
32
0
0
0
1
1
32
0
0
0
1
1
Otus hartlaubi
32
0
1
0
0
1
32
0
1
0
0
1
Table S3. Average number of species detected per point count across land-uses.
Groupings are according Tukey tests for GLMMs with a confidence interval of 95%.
All species
Endemic
Non-endemic
Old-growth
5.87a,b
5.55a
0.33c
Secondary
6.71a
5.85a
0.87b
Shade
6.40a,b
5.35a
1.05b
Non-forested
5.40b
3.53b
1.87a
Table S4. Results of the Indicator Species Analysis. For each species it is indicated the
land-use to which they are more strongly associated, their observed indicator value (IV)
and corresponding p-value. IV was calculated according to Dufrene and Legendre (1997).
The p-value corresponds to the proportion of randomized trials, using Monte Carlo
simulations with 4999 permutations, for which the indicator value was equal to or
exceeded IV. Species with a p-value smaller than 0.05 are highlighted in bold.
Species
Land-use
Indicator Value
p-value
Zosterops lugubris
Sec
29.9
0.511
Anabathmis newtoni
Sha
34.6
0.158
Prinia molleri
Sec
28.2
0.758
Estrilda astrild
Uns
77.5
<0.001
Ploceus sanctithomae
Sec
32.3
0.229
Zosterops feae
Old
21.3
0.685
Serinus rufobrunneus
Sec
26.0
0.939
Turdus olivaceofuscus
Sec
39.1
0.013
Terpsiphone atrochalybeia
Sha
35.6
0.039
Lonchura cucullata
Uns
21.5
0.173
Columba larvata
Sec
40.8
0.017
Oriolus crassirostris
Old
79.1
<0.001
Treron sanctithomae
Old
23.5
0.323
Onychognathus fulgidus
Sec
33.5
0.049
Euplectes hordaceus
Uns
8.3
1.000
Streptopelia senegalensis
Uns
22.3
0.149
Ploceus grandis
Sec
23.6
0.244
Columba malherbi
Uns
23.0
0.333
Milvus migrans
Uns
46.6
0.003
Ploceus velatus
Sha
17.0
0.263
Zoonavena thomensis
Uns
13.0
0.518
Dreptes thomensis
Old
32.9
0.008
Vidua macroura
Uns
16.7
0.235
Serinus mozambicus
Uns
23.7
0.082
Agapornis pullaria
Sha
22.1
0.100
Ploceus cucullatus
Uns
33.3
0.009
Coturnix delegorguei
Uns
25.0
0.054
Cypsiurus parvus
Uns
33.3
0.022
Bubulcus ibis
Sha
25.0
0.055
Uraeginthus angolensis
Uns
17.9
0.156
Columba thomensis
Sha
7.4
0.751
Euplectes aureus
Uns
8.3
1.000
Otus hartlaubi
Sec
8.3
1.000
Table S5. Models for explaining the proportion of endemic species per point count, ranked for AICc values. The generalised mixed-effects
models included five vegetation variables (CCV – canopy cover; CHE –canopy height; FBA – forest basal area; TSR – tree species richness;
UCV – understorey cover) plus land-use (LUS), and accounted the nestedness within regions. Kappa (K), delta (Ä) and sigma omega (Σω)
indicate respectively the “penalty” used to calculate the AICc value based on the number of parameters entered in the model, the
difference in AICc compared to the best model and the cumulative Akaike weight. The last columns show which variables were included in
each model.
Variables in the model
Rank
AICc
k
Δ
ω
Σω
1
44.00
3
0.00
0.136
0.136
x
2
44.30
5
0.30
0.117
0.253
x
3
44.85
4
0.85
0.089
0.342
x
4
45.29
6
1.28
0.071
0.413
x
5
45.35
4
1.35
0.069
0.482
x
x
6
46.02
6
2.02
0.049
0.531
x
x
7
46.06
4
2.06
0.048
0.579
x
8
46.21
6
2.21
0.045
0.624
x
9
46.69
5
2.69
0.035
0.659
x
CCV CHE FBA REG LUS TSR UCV
x
x
x
x
x
x
x
x
x
x
10
46.80
5
2.80
0.033
0.692
x
11
46.90
7
2.90
0.032
0.724
x
12
47.33
5
3.33
0.026
0.750
x
x
13
47.38
7
3.38
0.025
0.775
x
x
14
47.57
6
3.57
0.023
0.798
x
15
47.82
7
3.82
0.020
0.818
x
x
16
48.62
6
4.61
0.014
0.832
x
x
17
48.91
8
4.91
0.012
0.844
x
18
48.98
8
4.98
0.011
0.855
x
19
49.27
7
5.27
0.010
0.865
x
20
49.43
3
5.43
0.009
0.874
x
21
49.64
6
5.64
0.008
0.882
x
22
49.65
7
5.65
0.008
0.890
23
49.68
5
5.68
0.008
0.898
24
49.69
7
5.69
0.008
0.906
25
49.94
4
5.94
0.007
0.913
26
50.01
5
6.01
0.007
0.920
27
50.27
9
6.27
0.006
0.926
x
x
x
28
50.97
9
6.97
0.004
0.930
x
x
x
29
51.03
4
7.03
0.004
0.934
30
51.06
9
7.06
0.004
0.938
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
31
51.23
6
7.23
0.004
0.942
x
x
32
51.26
6
7.26
0.004
0.946
33
51.27
5
7.27
0.004
0.950
x
34
51.27
7
7.27
0.004
0.954
x
35
51.33
8
7.33
0.003
0.957
x
36
51.33
8
7.33
0.003
0.960
x
37
51.50
6
7.50
0.003
38
51.65
7
7.65
39
51.79
3
40
51.80
41
x
x
0.963
x
x
0.003
0.966
x
7.79
0.003
0.969
8
7.80
0.003
0.972
51.93
5
7.93
0.003
0.975
x
42
52.20
8
8.19
0.002
0.977
x
43
52.20
10
8.20
0.002
0.979
44
52.27
8
8.27
0.002
0.981
45
52.43
10
8.43
0.002
0.983
46
52.73
6
8.73
0.002
0.985
47
52.94
4
8.94
0.002
0.987
48
53.16
10
9.16
0.001
0.988
49
53.38
6
9.38
0.001
0.989
x
50
53.43
8
9.43
0.001
0.990
x
51
53.46
9
9.46
0.001
0.991
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
52
53.57
7
9.57
0.001
0.992
x
x
53
53.58
7
9.58
0.001
0.993
x
x
54
53.93
9
9.93
0.001
0.994
x
x
x
55
54.30
9
10.30
0.001
0.995
x
x
x
56
54.33
9
10.33
0.001
0.996
x
x
x
x
57
54.42
11
10.42
0.001
0.997
x
x
x
x
58
54.67
5
10.67
0.001
0.998
59
54.82
7
10.82
0.001
0.999
60
55.63
8
11.63
0.000
0.999
61
55.70
4
11.70
0.000
0.999
62
55.94
10
11.94
0.000
0.999
63
56.96
5
12.96
0.000
0.999
64
56.99
3
12.99
0.000
0.999
65
57.17
6
13.17
0.000
0.999
x
66
57.54
5
13.54
0.000
0.999
x
67
57.77
5
13.77
0.000
0.999
x
x
68
58.55
7
14.55
0.000
0.999
x
x
69
58.86
6
14.86
0.000
0.999
x
x
x
70
59.03
6
15.03
0.000
0.999
x
x
x
71
59.14
7
15.13
0.000
0.999
x
72
59.19
7
15.19
0.000
0.999
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
73
59.58
6
15.58
0.000
0.999
x
x
74
59.80
7
15.80
0.000
0.999
x
x
75
60.29
8
16.29
0.000
0.999
x
x
x
x
76
60.70
8
16.70
0.000
0.999
x
x
x
x
77
60.74
4
16.74
0.000
0.999
78
60.76
4
16.76
0.000
0.999
79
60.92
7
16.91
0.000
0.999
80
61.08
6
17.08
0.000
0.999
81
61.11
8
17.11
0.000
0.999
82
61.13
6
17.13
0.000
0.999
83
61.30
5
17.30
0.000
0.999
84
61.37
4
17.36
0.000
0.999
85
61.53
8
17.53
0.000
0.999
x
x
x
86
61.94
8
17.94
0.000
0.999
x
x
x
87
61.95
8
17.95
0.000
0.999
x
x
x
x
88
62.03
6
18.03
0.000
0.999
x
x
89
62.11
9
18.11
0.000
0.999
90
62.30
7
18.30
0.000
0.999
x
x
91
62.37
5
18.37
0.000
0.999
x
x
92
62.38
5
18.37
0.000
0.999
93
62.44
9
18.44
0.000
0.999
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
94
62.73
8
18.73
0.000
0.999
95
62.81
7
18.81
0.000
0.999
96
62.82
4
18.82
0.000
0.999
x
97
62.88
7
18.88
0.000
0.999
x
98
63.04
7
19.04
0.000
0.999
x
x
99
63.21
7
19.20
0.000
0.999
x
x
100
63.32
6
19.32
0.000
0.999
101
63.36
6
19.36
0.000
0.999
x
102
63.49
3
19.49
0.000
0.999
x
103
63.60
10
19.60
0.000
0.999
x
x
x
104
63.64
9
19.64
0.000
0.999
x
x
x
105
63.65
7
19.65
0.000
0.999
106
63.69
9
19.69
0.000
0.999
107
63.70
5
19.70
0.000
0.999
108
64.12
9
20.12
0.000
0.999
x
109
64.25
10
20.25
0.000
0.999
x
110
64.30
2
20.29
0.000
0.999
111
64.30
10
20.30
0.000
0.999
112
64.36
8
20.36
0.000
0.999
113
64.49
9
20.49
0.000
0.999
114
64.67
9
20.67
0.000
0.999
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
115
64.88
9
20.87
0.000
0.999
x
x
116
64.90
8
20.90
0.000
0.999
117
64.91
8
20.91
0.000
0.999
118
65.13
8
21.13
0.000
0.999
119
65.66
11
21.66
0.000
0.999
x
120
65.81
11
21.81
0.000
0.999
x
121
65.83
10
21.83
0.000
0.999
122
66.46
11
22.46
0.000
0.999
123
66.55
10
22.55
0.000
0.999
124
66.60
10
22.60
0.000
0.999
125
66.79
10
22.78
0.000
126
66.98
9
22.98
127
67.89
12
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
0.999
x
x
x
x
0.000
0.999
x
x
x
23.89
0.000
0.999
x
x
x
128
68.64
11
24.64
0.000
0.999
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
REFERENCES
Atkinson, P.W., Dutton, J.S., Peet, N.B. & Sequeira, V.A.S. (1994) A study of the birds, small
mammals, turtles and medicinal plants of São Tomé and Príncipe. BirdLife
International, Cambridge.
del Hoyo, J., Elliott, A., Sargatal, J. & Christie, D.A. (1992-2011) Handbook of the birds of the
world. Lynx editions, Barcelona.
Dufrene, M. & Legendre, P. (1997) Species assemblages and indicator species: The need
for a flexible asymmetrical approach. Ecological Monographs, 67, 345-366.
Jones, P. & Tye, A. (2006) The birds of São Tomé and Príncipe, with Annobón: islands of the
Gulf of Guinea. British Ornithologists' Union, Oxford.
Melo, M. (2007) Bird speciation in the Gulf of Guinea island system. PhD dissertation,
University of Edinburgh, Edinburgh.