Electronic supplementary material – additional details on the dataset and preliminary analyses

Contents

1.  Constructing the dataset

2.  Species omitted from the analyses

3.  References for predictor variables & list of African land cover types

4.  Distribution of each predictor variable (Figure S1)

5.  OLS single predictor analyses (Table S1)

6.  OLS single predictor within biome analyses (Table S2a,b)

7.  Regression tree modeling (Figure S2)

8.  Generalised additive modeling (Figure S3)

9.  Variance inflation factors (Table S3)

10.  Correlograms (Figure S4a,b,c)

11.  F ratios for each term of each model of the non-spatial 95% confidence set (Table S4)

12.  Analyses using only species in the largest range size quartile (Table S5)

1. Constructing the dataset

References used in the construction of the distribution maps (see also Orme et al. 2005; 2006):

Brown, L., Urban, E. & Newman, K. (eds.) The Birds of Africa: Vol 1 (Academic Press, London, 1982).

Fry, C. & Keith, S. (eds.) The Birds of Africa: Vol 7 (Academic Press, London, 2004).

Fry, C., Keith, S. & Urban, E. (eds.) The Birds of Africa: Vol 6 (Academic Press, London, 2002).

Keith, S. & Fry, C. (eds.) The Birds of Africa: Vol 4 (Academic Press, London, 1992).

Keith, S., Urban, E. & Fry, C. (eds.) The Birds of Africa: Vol 3 (Academic Press, London, 2002).

Urban, E., Fry, C. & Keith, S. (eds.) The Birds of Africa: Vol 2 (Academic Press, London, 1982).

Urban, E., Keith, S. & Fry, C. (eds.) The Birds of Africa: Vol 5 (Academic Press, London, 1997).


2. Species and biomes omitted from the analyses

Minor biomes omitted from the analyses are: tropical & subtropical dry broadleaf forests (10 cells); temperate grasslands, savannas & shrublands (1); flooded grasslands & savannas (33); mediterreanean forests, woodlands & shrubs (3).

Omitted species (starred (*) species are sea birds that spend most of their life feeding at sea, but exist in the dataset for the Afrotropics because of breeding records from some of the omitted continental or island coastal cells).

Species restricted to the omitted
coastal/lakeside cells
Species / Order / Family
Alectoris chukar / Galliformes / Phasianidae
Coracias garrulus / Coraciiformes / Coraciidae
Alcedo thomensis / Coraciiformes / Alcedinidae
Alcedo nais / Coraciiformes / Alcedinidae
Cuculus canorus / Cuculiformes / Cuculidae
Psittacula echo / Psittaciformes / Psittacidae
Collocalia elaphra / Apodiformes / Apodidae
Collocalia francica / Apodiformes / Apodidae
Zoonavena thomensis / Apodiformes / Apodidae
Apus alexandri / Apodiformes / Apodidae
Otus hartlaubi / Strigiformes / Strigidae
Otus brucei / Strigiformes / Strigidae
Otus magicus / Strigiformes / Strigidae
Otus pauliani / Strigiformes / Strigidae
Columba thomensis / Columbiformes / Columbidae
Columba pollenii / Columbiformes / Columbidae
Columba malherbii / Columbiformes / Columbidae
Columba mayeri / Columbiformes / Columbidae
Treron sanctithomae / Columbiformes / Columbidae
Treron pembaensis / Columbiformes / Columbidae
Alectroenas sganzini / Columbiformes / Columbidae
Alectroenas pulcherrima / Columbiformes / Columbidae
Atlantisia rogersi / Gruiformes / Rallidae
Gallinula nesiotis / Gruiformes / Rallidae
Charadrius sanctaehelenae / Ciconiiformes / Charadriidae
Dromas ardeola / Ciconiiformes / Glareolidae
Catharacta antarctica * / Ciconiiformes / Laridae
Catharacta lonnbergi * / Ciconiiformes / Laridae
Stercorarius pomarinus * / Ciconiiformes / Laridae
Stercorarius parasiticus * / Ciconiiformes / Laridae
Sterna vittata / Ciconiiformes / Laridae
Anous minutus / Ciconiiformes / Laridae
Gygis alba / Ciconiiformes / Laridae
Milvus milvus / Ciconiiformes / Accipitridae
Falco punctatus / Ciconiiformes / Falconidae
Falco araea / Ciconiiformes / Falconidae
Phaethon aethereus / Ciconiiformes / Phaethontidae
Phaethon rubricauda / Ciconiiformes / Phaethontidae
Phaethon lepturus / Ciconiiformes / Phaethontidae
Morus capensis / Ciconiiformes / Sulidae
Morus serrator / Ciconiiformes / Sulidae
Sula dactylatra / Ciconiiformes / Sulidae
Phalacrocorax coronatus / Ciconiiformes / Phalacrocoracidae
Phalacrocorax neglectus / Ciconiiformes / Phalacrocoracidae
Phalacrocorax nigrogularis / Ciconiiformes / Phalacrocoracidae
Ardeola grayii / Ciconiiformes / Ardeidae
Fregata magnificens / Ciconiiformes / Fregatidae
Fregata aquila / Ciconiiformes / Fregatidae
Fregata minor * / Ciconiiformes / Fregatidae
Fregata ariel * / Ciconiiformes / Fregatidae
Eudyptes chrysocome / Ciconiiformes / Spheniscidae
Spheniscus demersus / Ciconiiformes / Spheniscidae
Macronectes giganteus * / Ciconiiformes / Procellariidae
Pterodroma brevirostris * / Ciconiiformes / Procellariidae
Pterodroma aterrima / Ciconiiformes / Procellariidae
Pterodroma macroptera * / Ciconiiformes / Procellariidae
Pterodroma feae / Ciconiiformes / Procellariidae
Pterodroma mollis * / Ciconiiformes / Procellariidae
Pterodroma incerta * / Ciconiiformes / Procellariidae
Pachyptila vittata * / Ciconiiformes / Procellariidae
Pachyptila salvini * / Ciconiiformes / Procellariidae
Pachyptila turtur * / Ciconiiformes / Procellariidae
Bulweria bulwerii * / Ciconiiformes / Procellariidae
Procellaria aequinoctialis * / Ciconiiformes / Procellariidae
Procellaria cinerea * / Ciconiiformes / Procellariidae
Calonectris diomedea * / Ciconiiformes / Procellariidae
Puffinus pacificus * / Ciconiiformes / Procellariidae
Puffinus carneipes * / Ciconiiformes / Procellariidae
Puffinus gravis * / Ciconiiformes / Procellariidae
Puffinus griseus * / Ciconiiformes / Procellariidae
Puffinus assimilis * / Ciconiiformes / Procellariidae
Puffinus persicus * / Ciconiiformes / Procellariidae
Pelecanoides urinatrix * / Ciconiiformes / Procellariidae
Diomedea exulans * / Ciconiiformes / Procellariidae
Diomedea amsterdamensis * / Ciconiiformes / Procellariidae
Diomedea chlororhynchos * / Ciconiiformes / Procellariidae
Phoebetria fusca * / Ciconiiformes / Procellariidae
Phoebetria palpebrata * / Ciconiiformes / Procellariidae
Garrodia nereis * / Ciconiiformes / Procellariidae
Pelagodroma marina * / Ciconiiformes / Procellariidae
Fregetta grallaria * / Ciconiiformes / Procellariidae
Oceanodroma castro * / Ciconiiformes / Procellariidae
Lanius newtoni / Passeriformes / Laniidae
Oriolus crassirostris / Passeriformes / Corvidae
Coracina typica / Passeriformes / Corvidae
Coracina newtoni / Passeriformes / Corvidae
Dicrurus aldabranus / Passeriformes / Corvidae
Dicrurus fuscipennis / Passeriformes / Corvidae
Dicrurus waldenii / Passeriformes / Corvidae
Terpsiphone atrochalybeia / Passeriformes / Corvidae
Terpsiphone corvina / Passeriformes / Corvidae
Terpsiphone bourbonnensis / Passeriformes / Corvidae
Batis poensis / Passeriformes / Corvidae
Monticola solitarius / Passeriformes / Muscicapidae
Nesocichla eremita / Passeriformes / Muscicapidae
Turdus olivaceofuscus / Passeriformes / Muscicapidae
Turdus bewsheri / Passeriformes / Muscicapidae
Humblotia flavirostris / Passeriformes / Muscicapidae
Horizorhinus dohrni / Passeriformes / Muscicapidae
Copsychus sechellarum / Passeriformes / Muscicapidae
Saxicola tectes / Passeriformes / Muscicapidae
Oenanthe monacha / Passeriformes / Muscicapidae
Onychognathus frater / Passeriformes / Sturnidae
Lamprotornis ornatus / Passeriformes / Sturnidae
Hirundo rustica / Passeriformes / Hirundinidae
Hirundo perdita / Passeriformes / Hirundinidae
Psalidoprocne fuliginosa / Passeriformes / Hirundinidae
Hypsipetes crassirostris / Passeriformes / Pycnonotidae
Hypsipetes parvirostris / Passeriformes / Pycnonotidae
Hypsipetes borbonicus / Passeriformes / Pycnonotidae
Cisticola incanus / Passeriformes / Cisticolidae
Cisticola haesitatus / Passeriformes / Cisticolidae
Prinia molleri / Passeriformes / Cisticolidae
Speirops lugubris / Passeriformes / Zosteropidae
Speirops brunneus / Passeriformes / Zosteropidae
Speirops leucophoeus / Passeriformes / Zosteropidae
Zosterops vaughani / Passeriformes / Zosteropidae
Zosterops mayottensis / Passeriformes / Zosteropidae
Zosterops mouroniensis / Passeriformes / Zosteropidae
Zosterops ficedulinus / Passeriformes / Zosteropidae
Zosterops griseovirescens / Passeriformes / Zosteropidae
Zosterops borbonicus / Passeriformes / Zosteropidae
Zosterops olivaceus / Passeriformes / Zosteropidae
Zosterops chloronothos / Passeriformes / Zosteropidae
Zosterops modestus / Passeriformes / Zosteropidae
Nesillas aldabrana / Passeriformes / Sylviidae
Nesillas longicaudata / Passeriformes / Sylviidae
Nesillas brevicaudata / Passeriformes / Sylviidae
Nesillas mariae / Passeriformes / Sylviidae
Acrocephalus brevipennis / Passeriformes / Sylviidae
Bebrornis sechellensis / Passeriformes / Sylviidae
Hippolais caligata / Passeriformes / Sylviidae
Sylvia atricapilla / Passeriformes / Sylviidae
Sylvia conspicillata / Passeriformes / Sylviidae
Mirafra ashi / Passeriformes / Alaudidae
Alauda razae / Passeriformes / Alaudidae
Nectarinia hartlaubii / Passeriformes / Nectariniidae
Nectarinia newtonii / Passeriformes / Nectariniidae
Nectarinia thomensis / Passeriformes / Nectariniidae
Nectarinia balfouri / Passeriformes / Nectariniidae
Nectarinia dussumieri / Passeriformes / Nectariniidae
Nectarinia humbloti / Passeriformes / Nectariniidae
Nectarinia comorensis / Passeriformes / Nectariniidae
Nectarinia coquerellii / Passeriformes / Nectariniidae
Nectarinia pembae / Passeriformes / Nectariniidae
Passer hispaniolensis / Passeriformes / Passeridae
Passer iagoensis / Passeriformes / Passeridae
Passer insularis / Passeriformes / Passeridae
Carpospiza brachydactyla / Passeriformes / Passeridae
Ploceus princeps / Passeriformes / Passeridae
Ploceus victoriae / Passeriformes / Passeridae
Ploceus grandis / Passeriformes / Passeridae
Ploceus sanctithomae / Passeriformes / Passeridae
Foudia eminentissima / Passeriformes / Passeridae
Foudia rubra / Passeriformes / Passeridae
Foudia sechellarum / Passeriformes / Passeridae
Padda oryzivora / Passeriformes / Passeridae
Serinus rufobrunneus / Passeriformes / Fringillidae
Neospiza concolor / Passeriformes / Fringillidae
Emberiza socotrana / Passeriformes / Fringillidae
Rowettia goughensis / Passeriformes / Fringillidae
Nesospiza acunhae / Passeriformes / Fringillidae
Nesospiza wilkinsi / Passeriformes / Fringillidae
Species found only in omitted biomes
Vanellus indicus / Ciconiiformes / Charadriidae
Sula leucogaster / Ciconiiformes / Sulidae
Pterodroma baraui / Ciconiiformes / Procellariidae
Xenopirostris damii / Passeriformes / Corvidae
Pycnonotus leucogenys / Passeriformes / Pycnonotidae
Bebrornis rodericanus / Passeriformes / Sylviidae
Foudia flavicans / Passeriformes / Passeridae

Comparison of species included and omitted from the analyses

Species numbers / Proportion of species
Order / Included / Omitted / Included / Omitted
Anseriformes / 22 / 0 / 0.0115 / 0
Apodiformes / 22 / 4 / 0.0115 / 0.0235
Bucerotiformes / 25 / 0 / 0.0131 / 0
Ciconiiformes / 218 / 61 / 0.1144 / 0.3588
Coliiformes / 6 / 0 / 0.0031 / 0
Columbiformes / 33 / 8 / 0.0173 / 0.0471
Coraciiformes / 51 / 3 / 0.0268 / 0.0176
Cuculiformes / 35 / 1 / 0.0184 / 0.0059
Galliformes / 52 / 1 / 0.0273 / 0.0059
Gruiformes / 55 / 2 / 0.0289 / 0.0118
Musophagiformes / 23 / 0 / 0.0121 / 0
Passeriformes / 1177 / 85 / 0.6178 / 0.5000
Piciformes / 87 / 1 / 0.0457 / 0.0059
Psittaciformes / 22 / 4 / 0.0115 / 0.0235
Strigiformes / 58 / 0 / 0.0304 / 0
Struthioniformes / 1 / 0 / 0.0005 / 0
Trogoniformes / 3 / 0 / 0.0016 / 0
Turniciformes / 5 / 0 / 0.0026 / 0
Upupiformes / 10 / 0 / 0.0052 / 0
Total / 1905 / 170


3. References used to construct the predictor variables

Human population density: Center for International Earth Science Information Network (CIESIN) (2003) Gridded Population of the World (GPW), Version 2. Available at http://sedac.ciesin.columbia.edu/plue/gpw.

Mean annual temperature: New M., Lister D., Hulme M., Makin I. 2002 A high-resolution data set of surface climate over global land areas. Climate Research, 21, 1-25.

Mean annual actual evapotranspiration: University of Delaware Global Climate Resource Pages (UD GCRP) Available at http://climate.geog.udel.edu/~climate/html_pages/download.html.

Mean elevation: US Geological Survey (USGS) National Center for Earth Resources Observation & Science (2003) Global 30-arc-second elevation data set (GTOPO30). Available at http://edcdaac.usgs.gov/gtopo30/gtopo30.asp.

Landscape heterogeneity: US Geological Survey (USGS) National Center for Earth Resources Observation & Science (2003) Africa land cover characterisation data base v2.0 (GLCC). Available at

http://edc2.usgs.gov/glcc/afdoc2_0.php#olso. There are 96 land cover types in the GLCC v.2 database. 34 of them are represented in the Afrotropical realm, and are listed below.

Value / Ecosystem
1 / Urban
2 / Low Sparse Grassland
8 / Bare Desert
11 / Semi Desert
14 / Inland Water
22 / Cool Conifer Forest
28 / Montane Tropical Forests
29 / Seasonal Tropical Forest
31 / Crops and Town
32 / Dry Tropical Woods
33 / Tropical Rainforest
34 / Tropical Degraded Forest
36 / Rice Paddy and Field
40 / Cool Grasses and Shrubs
41 / Hot and Mild Grasses and Shrubs
43 / Savanna (Woods)
45 / Marsh Wetland
47 / Dry Woody Scrub
50 / Sand Desert
51 / Semi Desert Shrubs
53 / Barren Tundra
56 / Forest and Field
58 / Fields and Woody Savanna
59 / Succulent and Thorn Scrub
62 / Narrow Conifers
72 / Mangrove
76 / Crop and Water Mixtures
78 / Southern Hemisphere Mixed Forest
90 / Rain Green Tropical Forest
91 / Woody Savanna
92 / Broadleaf Crops
93 / Grass Crops
94 / Crops, Grass, Shrubs
95 / Evergreen Tree Crop


Figure S1 – Distribution of each of the predictor variables. Grey cells are those omitted from the analyses.

Abbreviations as follows: ELEV: mean elevation (metres); AET: mean annual actual evapotranspiration (mm); TEMP: mean annual temperature (°C); ELEVR: elevational range (log(metres)); LandHet: landscape heterogeneity (number of co-occurring ecosystem types); BiomeHet: biome heterogeneity (number of biome edges); HPD: human population density (log(people per km2)).


Preliminary analyses to determine the minimum adequate model

Single-predictor ordinary least squares (OLS) regression was carried out to assess the consistency and robustness of the multivariate analyses subsequently performed and to compare the significance and directions of slopes obtained from each mode of analysis (Table S1). Human population density is included here although ultimately was not used in the main analyses.

With one categorical and six continuous variables, there are a great many higher-order and interaction terms possible in the maximal model. To restrict analyses to manageable levels, preliminary studies were made to identify which terms were sensible and relevant to include. Single-predictor analyses by biome indicated the significant modulating effect of this factor (Tables S2a,b).

Variables which are repeatedly found nested together in tree models are potential candidates for interaction terms. Following tree modelling, two additional interaction terms were included in the maximal model, AET with temperature and AET with elevational range (Figure S2).

Generalised additive models (GAMs) were also used to determine whether any of the explanatory variables required higher-order terms to describe their relationship with ω. GAMs fit non-parametric smoothers through the data and their graphical representation facilitates decisions on whether a higher-order term or a transformation is necessary. This, plus the increase in degrees of freedom necessary to fit the smoother, indicates whether or not a linear term is sufficient. A multivariate GAM was fitted using all of the continuous variables as well as interaction terms identified through tree modelling. The GAMs indicated that no relationship benefited from description using higher-order terms (Figure S3).


Table S1 – Regression statistics for the single-predictor non-spatial analyses.

Elevational range and human population density have been log-transformed.

Significance codes: p<0.0001 ***, 0.0001≤p<0.001 **, 0.001≤p<0.01 *, 0.01≤p<0.05 ·, p≥0.05 n.s.

Predictor / Slope / ±SE / F 1,2016 / T / P / R2
Mean elevation / 0.00014 / 0.00003 / 18.85 / 4.34 / *** / 0.00927
Mean annual AET / -0.00071 / 0.00004 / 329.10 / -18.14 / *** / 0.14030
Mean annual temperature / 0.00600 / 0.00413 / 2.11 / 1.45 / n,s / 0.00105
Elevational range / 0.16734 / 0.01412 / 140.50 / 11.85 / *** / 0.06516
Landscape heterogeneity / -0.01651 / 0.00367 / 20.28 / -4.50 / *** / 0.00947
Biome heterogeneity / 0.19294 / 0.01400 / 190.00 / 13.79 / *** / 0.08614
Human population density / -0.00117 / 0.00925 / 0.02 / -0.13 / n.s / 0.00001


Table S2 – (A) Mean values of each predictor by biome. Shaded values are not significantly different from one another under TukeyHSD criteria. For logit (ω), biomes 1 and 7 and biomes 10 and 13 are not significantly different from each other.