bioRxiv preprint doi: https://doi.org/10.1101/2020.05.30.125849; this version posted June 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

1 and habitat loss in Colombia

2 Authors: Pablo Jose Negret¹,², Martine Maron¹,², Richard A. Fuller², Hugh P. Possingham²,³,

3 James E.M. Watson¹,²,4, Jeremy S. Simmonds¹,²

4 ¹The University of Queensland, School of Earth and Environmental Sciences, Qld 4072,

5 Australia

6 ²The University of Queensland, Centre for Biodiversity and Conservation Science, Qld 4072,

7 Australia

8 ³The Nature Conservancy, South Brisbane, Queensland 4101, Australia

9 4Wildlife Conservation Society, Global Conservation Program, 2300 Southern Boulevard,

10 Bronx, NY 10460-1068, USA

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21 bioRxiv preprint doi: https://doi.org/10.1101/2020.05.30.125849; this version posted June 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

22 Abstract

23 Tropical forests harbor most of the planet’s terrestrial biodiversity, and their loss means

24 destruction of habitat for many species. Tropical deforestation continues at high rates in many

25 regions, but it is often reported only in terms of area lost or its impacts on high-profile

26 threatened species. We estimated the impact of both past and projected future deforestation

27 on habitat extent for the entire assemblage of forest-dependent across Colombia, the

28 country with more bird species than any other. Of the 550 forest-dependent species analysed,

29 Almost all (n=536; 96.5%) had lost habitat, and 18% had lost at least half of their habitat by

30 2015. We used the recently developed Loss Index (LI) to capture the severity of habitat loss

31 for the forest bird assemblage, discovering that the current LI for Colombia is 35, which

32 means 35% of bird species have lost at least 35% of their habitat. The national LI for

33 Colombia is projected to rise to 43 by 2040 if recent forest loss trends continue. There were

34 large regional differences; Caribe had an LI of 82 while for the Pacific it was 14. A threat

35 assessment for the regionally endemic species in the country showed that 12 (30%) of the

36 species that are projected to lose 50% or more of their historical habitat by 2040 are not

37 currently classified as threatened by the IUCN, suggesting that there are many species that

38 are not listed but that face an imminent extinction threat from habitat loss. This extensive

39 habitat depletion affecting entire species assemblages has significant implications for tropical

40 forest ecosystems, and risks eroding ecosystem function and ecosystem service provision.

41

42 Keywords: Extent of suitable habitat, forest-dependent species, range-restricted species,

43 threat status, threatened species

44

45 bioRxiv preprint doi: https://doi.org/10.1101/2020.05.30.125849; this version posted June 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

46 Introduction

47 Bird species have been experiencing rapid population declines worldwide (Inger et al. 2015;

48 Lindenmayer et al. 2018; Rosenberg et al. 2019), with habitat loss being one of the principal

49 drivers (Owens & Bennett 2000; Ford et al. 2009; Calvert et al. 2013). These population

50 declines and the local extirpation of species have been linked to a deterioration in the

51 function of ecosystems and the provision of ecosystem services, such as pollination and

52 insect control (Sekercioglu 2006; Gaston & Fuller 2008; Winfree et al. 2015). However, the

53 impact of habitat loss for entire bird assemblages has been little studied in tropical

54 ecosystems (Sekercioglu 2012), despite the fact that such ecosystems harbor most of the

55 planet’s terrestrial biodiversity (Gibson et al. 2011). Moreover, there is clear evidence that

56 species-rich assemblages such as those that characterise tropical forests play a critical role in

57 ecosystem function and service provision (Sekercioglu 2012; Gaston et al. 2018).

58 In the last two decades more than 2.3 million square kilometres of tropical forest have been

59 lost (Hansen et al. 2013; World Resources Institute 2018) and the destruction of these

60 habitats threatens the survival of forest specialist species (Donald et al. 2018; Symes et al.

61 2018; Watling et al. 2020). As tropical forests continue to decline in extent (Malhi et al.

62 2014), habitat for a huge number of species is being lost (Ceballos et al. 2017; Lovejoy

63 2017). However, we lack a clear picture of what this loss means for both whole assemblages

64 of species, and particular subsets of assemblages that are of conservation interest (e.g.

65 endemic species, functional groups; Simmonds et al. 2019).

66 Here, we assess the implications of forest loss for bird assemblages in Colombia, the country

67 with more bird species than any other (Ayerbe-Quiñones 2018), and where forest loss is

68 particularly acute (Negret et al. 2019). We estimate the impact of past and projected

69 deforestation on the extent of potential habitat for 550 forest-dependent bird species. bioRxiv preprint doi: https://doi.org/10.1101/2020.05.30.125849; this version posted June 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

70 Historical, recent, and projected future habitat loss for forest-dependent species was

71 calculated across Colombia, as well as for each biotic region, for species-rich taxonomic

72 groups of the broader assemblage (, ovenbirds, flycatchers and antbirds) and

73 separately for 69 regionally endemic forest-dependent species (defined as having ≥80% of

74 their global distribution in Colombia). In this way the impact of habitat loss was assessed for

75 all the forest-dependent species in the assemblage.

76

77 Methods

78 Study area

79 Colombia, in north western South America, is a tropical country of 1,142,000 km² with a

80 wide topographic range. As a result, the country has extraordinarily high vertebrate diversity

81 including >1900 species of birds (McMullan et al. 2010; Ayerbe-Quiñones 2018), 700

82 species of amphibians (Galeano et al. 2006) and 400 species of mammals (Ramirez-Chaves &

83 Suárez-Castro 2014). Natural forest covered more than 55% of its continental area in 2018

84 (World Resources Institute 2018).

85

86 Distribution ranges for forest-dependent species

87 We obtained distribution and ecological data for all native birds occurring in Colombia from

88 BirdLife International using the latest available range maps (BirdLife International &

89 Handbook of the Birds of the World 2018). These distribution maps are generated by experts

90 based on their knowledge and the available data for each species (BirdLife International &

91 Handbook of the Birds of the World 2018; IUCN Red List Technical Working Group 2019).

92 We then filtered our list to include only forest-dependent bird species following the Donald et bioRxiv preprint doi: https://doi.org/10.1101/2020.05.30.125849; this version posted June 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

93 al. (2018) definition of forest-dependent species: those whose listed habitat as defined by the

94 IUCN habitat classification scheme (https://www.iucnredlist.org/resources/habitat-

95 classification-scheme) included only the level 1 classification “Forest & Woodland”. After

96 filtering out non-forest and multi-habitat species, 550 forest-dependent species remained for

97 analysis. We adhered to the BirdLife taxonomic treatment.

98

99 Forest cover data

100 We used maps of forest cover in Colombia for four points in time (historical, 2000, 2015 and

101 2040) to determine the extent of suitable habitat inside each species’ range in each time

102 period. For the distribution of forest cover in 2000 and 2015 we used the 1 km² resolution

103 forest cover maps generated by Negret et al. (2019). For the historical distribution of forest

104 cover we used the map of historical cover of forest ecosystems in Colombia created by Etter

105 et al. (2017). This map used Landsat images for the country from 1972 – 1977, a combination

106 of different ecosystem maps (Etter 1998; Etter et al. 2006b) and information on the

107 distribution of areas of historical change where deforestation for agricultural land uses have

108 occurred, to define the potential distribution of the extent of forest cover if human

109 intervention and transformation had not occurred (Etter et al. 2006b, 2017). The resolution of

110 this forest cover map was 250 m² and so we generated a 1 km² grid covering Colombia to

111 match the resolution of the forest cover map generated by Negret et al. (2019), and calculated

112 the proportion of forest cover for each grid cell. We then defined grid cells with >30% forest

113 cover as forest and those with <30% as non-forest based on the threshold used by the

114 Colombian Institute of Hydrology, Meteorology and Environmental Studies – IDEAM

115 (Galindo et al. 2014; Negret et al. 2019). In forest landscapes that retain less than 30% forest

116 cover, bird species richness is markedly lower than those with greater cover (Ochoa-Quintero bioRxiv preprint doi: https://doi.org/10.1101/2020.05.30.125849; this version posted June 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

117 et al. 2015). Any pixel that was classified as non-forest using the historical forest cover layer

118 was treated as no forest for all subsequent time slices.

119

120 Forest cover change model

121 We simulated the spatial distribution of deforestation across Colombia in 2040, using a

122 cellular automata model developed in Dinamica EGO with parameters that allocate

123 deforestation on the basis of its empirical association with a set of predictor variables

124 (Soares-Filho et al. 2002, 2013) including; proximity to roads, rivers, mining concessions, oil

125 exploitation wells, distance to previous deforested areas, armed conflict intensity, distance to

126 coca plantations, the presence of protected areas, slope and elevation (Negret et al. 2019). To

127 do this, we assessed the association of the predictor variables with deforestation from 2000 to

128 2015 with the Bayesian weights of evidence method (Bonham-Carter 1994; Soares-Filho et

129 al. 2013). Then we used the weights of evidence coefficients from the spatial determinants of

130 forest change as inputs in a multi-stage process to model the spatial distribution of

131 deforestation pressure in the country (Soares-Filho et al. 2002, 2013; Negret et al. 2019). The

132 model used the weights of evidence coefficients, the 2015 forest cover map and the spatial

133 distribution of the biophysical and anthropogenic variables to produce a spatial map of

134 deforestation pressure. We then used an average annual deforestation rate calculated from the

135 2000 and 2015 forest cover maps and the deforestation pressure map to generate a forest

136 cover projection for 2040 using Dinamica EGO software (Teixeira et al. 2009; Molin et al.

137 2017). Although the published model included the effect of armed conflict in the context

138 previous to the signing of the peace deal with FARC, there has not been a cessation of

139 conflict in the country (Parkins 2019), so the same model was used.

140 bioRxiv preprint doi: https://doi.org/10.1101/2020.05.30.125849; this version posted June 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

141 Habitat loss across bird ranges

142 To estimate change in the extent of suitable habitat for each forest-dependent species at each

143 of the four points in time (Historical, 2000, 2015 and 2040), we assumed all forest inside

144 each species’ range was potential habitat. We quantified the total area of habitat for each

145 species in each time period, the loss through time, and the proportion of the estimated habitat

146 extent that the loss represented.

147

148 Deforestation impact on species assemblages

149 We estimated the impact of deforestation up to 2015 for all the forest-dependent species in

150 Colombia and for each biotic region. We also estimated the impact of deforestation for

151 regionally-endemic species (defined as having ≥80% of their range in Colombia) and for the

152 four most species-rich families (tanagers, ovenbirds, flycatchers and antbirds) to explore how

153 forest loss has variously affected these bird groups. Finally, we assessed the projected impact

154 of deforestation by 2040, for each biotic region, for the four species-rich taxonomic groups

155 and for all regionally-endemic species. We used the Loss Index (LI) to describe potential

156 natural habitat loss for the forest-dependent bird assemblages of Colombia (Simmonds et al.

157 2019). The LI is a metric where an LI of x, indicates that x% of species in an assemblage

158 have each lost at least x% of their potential natural habitat (Simmonds et al. 2019).

159

160 Threat assessment for regionally-endemic species

161 We performed a threat assessment for the regionally-endemic species (defined as having

162 ≥80% of their range in Colombia) - for these species long-term survival is heavily dependent

163 on their persistence in Colombia. We used habitat loss as a proxy for population decline bioRxiv preprint doi: https://doi.org/10.1101/2020.05.30.125849; this version posted June 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

164 assuming that the rate of habitat loss was directly proportional to the rate of population

165 decline, such that a loss of 1% suitable habitat was equivalent to a 1% population decline

166 (Symes et al. 2018). We then determined the proportional population decline until 2015

167 (historical loss), the decline to 2040 (projected loss), and the decline between 2000 and 2015

168 (recent loss) for each species. Using these data, we identified the species that had lost more

169 than 20, 30, 50 and 80 percent of their population in the different timeframes (Historic,

170 projected and recent loss) and contrasted this loss with the threat classification thresholds of

171 population reduction from the IUCN Red List criterion A4 (IUCN Standards and Petitions

172 Committee 2019); Critically Endangered (>80% reduction), Endangered (>50% reduction),

173 Vulnerable (>30% reduction) and Near Threatened (>20% reduction). We are aware that

174 these thresholds refer to change over 10 years or 3 generations for classification purposes,

175 and use them here simply as a point of reference.

176 We also identified the species with area of occupancy of less than 3000, 2000, 500 and 10

177 km² in 2015 and in 2040 and contrasted this with the threat classification thresholds for extent

178 of area of occupancy from the IUCN Red List criterion B2 (IUCN Standards and Petitions

179 Committee 2019); Critically Endangered (<10 km²), Endangered (<500% km²), Vulnerable

180 (<2000% km²) and Near Threatened (<3000% km²). We defined the area of occupancy as the

181 area inside each species’ range with forest habitat.

182

183 Results

184 National level

185 The vast majority of forest-dependent birds (n=536; 96.5%) in Colombia had lost suitable

186 habitat by 2015 in comparison with their historical habitat extent (Fig. 1 & Supplementary

187 Fig. 1). The average loss of habitat was 24% (± 20 SD) by 2000, 27% (± 20.6 SD) by 2015, bioRxiv preprint doi: https://doi.org/10.1101/2020.05.30.125849; this version posted June 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

188 and we projected an average of 38% (± 26 SD) loss of habitat by 2040. Only 17% (n=35) of

189 the species that are projected to lose at least half their habitat in Colombia by 2040 (n=208)

190 are currently classified as threatened by the IUCN.

191

192 Deforestation impact on assemblages

193 The impact of deforestation on forest-dependent bird assemblages in Colombia was dramatic.

194 The Loss Index for the country was 35 (35% of Colombia’s forest-dependent species had lost

195 at least 35% of their suitable habitat by 2015) (see Supplementary Table 1 and 2 for full

196 details). Using the land use change model, the LI was projected to increase to 43 by 2040.

197 Moreover, 18% of the species (n=99) had lost more than half of their historical habitat in the

198 country by 2015 and 38% are projected to lose 50% or more of their habitat by 2040 (Fig. 2).

199 There were large differences in 2015 LI values for regions that differed in land-use intensity

200 and biogeographic characteristics (Fig. 3a). For example, in the Caribe region, the LI was 82.

201 This high LI value showed that forest loss had far-reaching effects on the majority of this

202 region’s forest avifauna, despite the fact that only 15 species occurring in the region are listed

203 as threatened. The LI dropped to 28 and 14 for the Amazon and Pacific regions, respectively,

204 where forest loss has not been as extensive (Fig. 3a). However, in the species rich Amazon

205 foothills, each km² of forest loss has the potential to affect up to 230 forest-dependent species

206 (Fig. 3a-b).

207 The region, which had the most forest-dependent species (491 species), had the

208 greatest projected increase in its LI, from 40 in 2015 to 54 in 2040 (Fig 3a). The region with

209 the highest LI by 2040 was Caribe with 90. The Amazon and the Pacific regions maintained

210 relatively low LI, 33 and 26 respectively, However the LI for the Pacific region almost

211 doubled from the value in 2015 (LI = 14). bioRxiv preprint doi: https://doi.org/10.1101/2020.05.30.125849; this version posted June 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

212 For regionally-endemic species, the LI was 43 in 2015 and is projected to be 53 by 2040 (Fig.

213 4a) (see Supplementary Table 1 for full details). This implies that more than half of

214 Colombia’s regionally-endemic species are projected to lose at least half of their habitat by

215 2040. The areas where deforestation is projected to affect more regionally-endemic species is

216 the north-east of the Antioquia department where deforestation has already affected the

217 habitat of more than 15 regionally-endemic species (Fig. 4b-c).

218 We also explored the LI for four of the largest species groups of Colombia’s forest-dependent

219 bird assemblages. Tanagers, which based on our assessment are the most species rich group

220 of forest-dependent species (61 species), had a LI of 43 in 2015, which increased to 51 when

221 projected forest loss by 2040 was included (Supplementary Fig. 2a). Ovenbirds (n=47) had a

222 LI of 38 in 2015 with a projected increase to 42 by 2040 (Supplementary Fig. 2b); flycatchers

223 (n=44) had a LI of 36 in 2015 projected to increase to 44 by 2040 (Supplementary Fig. 2c);

224 and antbirds (n=53) had a LI of 27 in 2015 projected to increase to 32 by 2040

225 (Supplementary Fig. 2d).

226

227 Deforestation impact on individual species

228 Deforestation has been and is projected to have major impacts on several threatened and non-

229 threatened species in Colombia (Fig. 1 & 2) with 40% (n=208) of all forest-dependent species

230 projected to lose at least half of their habitat by 2040, and 15% (n=79) projected to lose 70%

231 or more of their habitat by 2040. The maximum proportional loss of habitat to 2015 and to

232 2040 among all the forest-dependent species was for the Giant Conebill (

233 binghami) with 99%. This species was also the one with the maximum proportional loss

234 between 2000 and 2015 (recent loss) with 63% of the remaining habitat to 2000 lost in this

235 period. The maximum projected proportional loss between 2015 and 2040 was for the bioRxiv preprint doi: https://doi.org/10.1101/2020.05.30.125849; this version posted June 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

236 ( ochracea) with 93% of its remaining habitat in 2015

237 projected to be lost in the period to 2040 (see Supplementary Table 2 for full details).

238 The maximum proportional loss of historical habitat for regional endemics to 2015 and to

239 2040 was for the Antioquia ( sernai), with 87% and 94% respectively. The

240 maximum proportional loss between 2000 and 2015 (recent loss) was for the Tolima Dove

241 ( conoveri), with 31% of the remaining habitat in 2000 lost in this period, and the

242 maximum proportional projected loss between 2015 and 2040 was for the Chestnut-capped

243 Piha (Lipaugus weberi) with 69% of the remaining habitat in 2015 projected to be lost in this

244 period (Fig. 5; see Supplementary Table 1 for full details).

245

246 Threat assessment for regionally-endemic species

247 Our threat assessment for the 69 regionally-endemic species showed that 49 species lost 20%

248 or more of their historical habitat by 2015, 40 species lost 30% or more, 18 species lost 50%

249 or more and one species lost more than 80%. When the projected loss until 2040 is included,

250 57 species are projected to lose 20% or more of their historical habitat by 2015, 54 species

251 are projected to lose 30% or more, 39 species are projected to lose 50% or more and 11

252 species are projected to lose more than 80% (Fig. 5). Of the 18 species that had lost 50% or

253 more of their historical habitat by 2015, six are not currently classified as threatened by the

254 IUCN, and of the 39 species that are projected to lose 50% or more of their historical habitat

255 by 2040, 12 are not currently classified as threatened by the IUCN (see Supplementary Table

256 3 for full details).

257 When considering recent loss only (2000 – 2015; i.e. not loss compared to historical

258 coverage) our results show that only two species lost more than 20% of their habitat.

259 However, when the projected loss between 2015 and 2040 is included in this assessment bioRxiv preprint doi: https://doi.org/10.1101/2020.05.30.125849; this version posted June 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

260 (2000 – 2040) 49 species are projected to lose 20% or more of their historical habitat by

261 2040, 37 species are projected to lose 30% or more and 15 species are projected to lose more

262 than 50% (Supplementary Fig. 3). Of the 15 species that are projected to lose, by 2040, 50%

263 or more of their remaining habitat in 2000, three are not currently classified as threatened by

264 the IUCN (see Supplementary Table 3 for full details).

265 Twenty-four species had less than 3000 km² of area of occupancy by 2015, 17 species had

266 less than 2000 km² and seven had less than 500 km². When this assessment is done based on

267 the projected extent of area of occupancy by 2040, 29 species had less than 3000 km² of area

268 of occupancy by 2040, 24 species had less than 2000 km², 10 had less than 500 km² and 1

269 had less than 10 km² (see Supplementary Table 3 for full details). Of the 24 species that are

270 projected to occupy less than 2000 km² by 2040, four are not currently classified as

271 threatened by the IUCN (see Supplementary Table 3 for full details).

272

273 Discussion

274 Our study highlights the importance of assessing the impact of deforestation on whole species

275 assemblages. We report a Loss Index (LI) of 35 for Colombia in 2015: 35% of the species

276 analysed had lost 35% or more of their historical habitat. If recent deforestation trends

277 continue, we estimate that LI will increase to 43 by 2040. Despite this ongoing attrition of

278 habitat, only 17% (n=35) of the species that are projected to lose 50% or more of their habitat

279 in Colombia by 2040 (n=208) are currently classified as threatened by the IUCN (2019b),

280 suggesting that there are many species that are facing an imminent extinction threat from

281 habitat loss even though they are not formally listed as threatened.

282

283 Depletion of Colombia’s forest bird habitat bioRxiv preprint doi: https://doi.org/10.1101/2020.05.30.125849; this version posted June 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

284 Deforestation has impacted almost all the forest-dependent bird species in the country

285 (n=536; 96.5%) but most still retain more than half of their historical habitat (n=451, 82%).

286 However, if deforestation trajectories continue, 40% (n=208) of the forest-dependent species

287 would lose half or more of their suitable habitat in the country by 2040 (Fig. 2). This is

288 particularly concerning for currently non-threatened species which comprise 83% of the

289 assemblage we explored, and which normally are not the focus of conservation initiatives.

290 When assessing only regionally-endemic species, our results show a more dramatic change

291 than the one observed for the entire forest-dependent bird assemblage. Seventy-four percent

292 (n=51) of the species retained at least half of their historical habitat in 2015, but if

293 deforestation trajectories continue, 57% (n=39) of the species would lose half or more of their

294 historical habitat by 2040 (Fig. 4a).

295 Our results also showed that forest-dependent tanagers were the bird family with the greatest

296 proportional loss of suitable habitat in the country to 2015 and projected to 2040. Tanagers

297 are particularly diverse in the Andes, which is one of the most heavily historically altered

298 regions of Colombia (Etter & van Wyngaarden 2000; Etter et al. 2006a). More knowledge of

299 the threats imposed by deforestation to habitat in the Andes is needed in order to

300 avoid their extinction.

301

302 Regional variation in impact of deforestation on assemblages

303 At a regional scale our results show that the Caribe region had the highest Loss Index value

304 (LI = 81) and had a mean historical habitat loss of 88% by 2015. This reflects high levels of

305 forest loss that is affecting most of the species in the assemblages in this region. Past studies

306 have also identified the Caribe as a priority region due to its high land conversion and low

307 protection levels (Forero-Medina & Joppa 2010; Negret et al. 2020), highlighting the bioRxiv preprint doi: https://doi.org/10.1101/2020.05.30.125849; this version posted June 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

308 importance of conservation aimed at reducing forest loss in this region. Colombia’s relatively

309 well-preserved Choco and Amazon regions had low LI values and the mean loss of historical

310 habitat was below 20% for both. These regions are characterized by high species richness

311 with Choco representing a hotspot for endemic birds (Mittermeier et al. 2004). The

312 maintenance of intactness in these regions is critical as diverse and intact species assemblages

313 underpin ecosystem functions such as seed dispersal, pollination, pest control and carbon

314 sequestration (Cardinale et al. 2012; Watson et al. 2018; Maxwell et al. 2019). The Andes

315 region, which was the most bird species rich, was also the region with a more drastic

316 projected change in the LI (from 40 to 54) and in mean habitat loss (35 to 54) when compared

317 to the other regions (Fig. 3a). Actions focused on preventing the loss of habitat for

318 endangered and range restricted species in this region are needed.

319 The west section of the Amazon foothills includes areas of very high species richness

320 (overlapping ranges of >200 forest-dependent birds in places) (Fig. 3). This region has

321 undergone a rapid increase in deforestation since the peace deal (Clerici et al. 2018; Murillo

322 Sandoval et al. 2020), so investment in management of protected areas and other effective

323 area-based conservation measures is a priority to avoid the loss of these rich bird

324 assemblages. Our results also showed that the central and eastern Andes are areas where

325 deforestation has substantially affected forest-dependent tanager species, while forest-

326 dependent antbirds were especially affected in the Amazon-Andes foothills in Putumayo.

327 Tanagers and antbirds provide important ecosystem services such as seed dispersal,

328 pollination and insect population regulation since their diet is mostly fruits and insects (Hilty

329 & Brown 1986; McMullan et al. 2010), making their effective conservation crucial for

330 ecosystem functioning and ecosystem service provision. Additionally, the north-east of the

331 Antioquia department is an area where projected deforestation will affect bird assemblages

332 that have a particularly high concentration of endemic species (Fig. 4). This region has been bioRxiv preprint doi: https://doi.org/10.1101/2020.05.30.125849; this version posted June 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

333 considerably affected by armed conflict, but there are several conservation initiatives and

334 research expeditions in this area after the peace deal (United Nations 2018). These

335 conservation initiatives would help protect the endemic bird species in this region.

336

337 Implications for species threat status

338 Half of the regionally-endemic species are currently not classified as threatened based on the

339 IUCN threatened species status criteria (see Supplementary Table 1 for full details) but our

340 analysis suggests that many of those species are facing significant habitat loss that could lead

341 to their extinction (Fig 5, Supplementary Fig 3). For example the Colombian Wren

342 (Pheugopedius columbianus) and the Stiles' Tapaculo (Scytalopus stilesi), which are currently

343 classified as Least Concern (LC), have already lost more than 60% of their habitat in

344 Colombia and are projected to lose more than 85% by 2040 (Fig 4). Targeted research for

345 these and other species with similar characteristics is needed in order to identify the factors

346 that are generating the reduction of their habitat and to determine if a revision of their Red

347 List classification is warranted. In contrast, loss of suitable habitat has been small for some

348 threatened and near threatened species in Colombia. This in part is associated to the fact that

349 some of these species inhabit less accessible areas (e.g., Wattled Curassow [Crax globulosa]

350 and Banded Ground-cuckoo [Neomorphus radiolosus]) or that have been the target of

351 successful conservation actions (e.g., Urrao Antpitta [Grallaria fenwickorum] and Gorgeted

352 Puffleg [Eriocnemis isabellae]) (Carantón-Ayala & Certuche-Cubillos 2010; ProAves 2019).

353 Moreover, our threat assessment for regionally-endemic species showed that accounting for

354 projected habitat loss can provide useful information of the species that need proactive

355 conservation interventions as projected loss would affect their habitat, population numbers

356 and threat status. bioRxiv preprint doi: https://doi.org/10.1101/2020.05.30.125849; this version posted June 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

357

358 Limitations of our analysis

359 While our method is a rapid way to assess and describe the impacts of deforestation to the

360 habitat of forest-dependent species, some limitations have to be noted. In predicting extent of

361 and change in potentially suitable habitat, the underlying maps, while the most

362 comprehensive and detailed up to date, likely contain commission and omission errors which

363 can lead to inaccurate forest change estimates (Rondinini et al. 2011; Ficetola et al. 2014;

364 Tracewski et al. 2016; Palacio et al. 2020). For some species in heavily historically altered

365 regions, like the Caribe (Etter & van Wyngaarden 2000; Etter et al. 2006a), mapped ranges

366 might be more consistent with the species’ current area of occupancy, reflecting the remnants

367 of the species pre-human range, and thus not account for range contractions which may have

368 occurred and been caused by historical habitat loss (e.g, Blue-billed Curassow [Crax

369 alberti]). Despite this, species in the tropics tend to have conservative niches, making

370 geographical and climatic barriers more effective (Janzen 1967; Brown 2014). This in turn

371 makes species distribution change less common. Additionally, species for which habitat

372 reduction represents the main extinction risk are normally those that are restricted to smaller

373 areas and have more specialized niches (Harris & Pimm 2008; Birand et al. 2012) so their

374 historical distributions can be better inferred. Even though this should be the case for the

375 majority of species, we are aware that there are information gaps in relation to the bird

376 communities present in some regions of the country, and that there are constant reports of

377 records beyond the known range and altitudinal limits for several species (Negret & Laverde-

378 R. 2014; Gomez-Bernal et al. 2015; Negret et al. 2015). Based on this we decided not to

379 generate further altitudinal range refinements for the species analysed, making our estimates

380 of the impact of deforestation to the habitat and population size of forest-dependent species

381 conservative. bioRxiv preprint doi: https://doi.org/10.1101/2020.05.30.125849; this version posted June 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

382 There is also a lack of understanding of habitat preferences for some species (e.g., Magdalena

383 Tapaculo [Scytalopus rodriguezi]), especially species with highly specialised habitat

384 requirements or that exist at very low densities within suitable habitat. For example, based on

385 our results the Banded Ground-cuckoo (Neomorphus radiolosus), which is categorized as

386 Endangered (EN), has retained more than half of its habitat. However, the extent of suitable

387 habitat for the species might be lower than our estimates suggest as it is a species present in

388 low densities, and for which ecological characteristics are poorly understood (Hilty & Brown

389 1986; McMullan et al. 2010; Ayerbe-Quiñones 2018). This is because our broad

390 classification of potential ‘habitat’ – forest – does not allow us to account for species-specific

391 specialisation (although this is accounted for broadly by restricting habitat amount

392 calculations to within the current range of where species occur). Consequently, while our

393 results represent an improvement on existing knowledge in the majority of cases, each

394 assessment must be judged carefully and in combination with on the ground information if

395 possible. Finally, our results should be used in context with each species’ particular

396 circumstances, considering other threats such as the impacts of selective logging (Isaac &

397 Cowlishaw 2004; Mayor et al. 2015), hunting (Isaac & Cowlishaw 2004; Benítez-López et al.

398 2017), and wildlife trade (Symes et al. 2018) which will likely cause substantial reductions in

399 some species, as would occur in any normal IUCN assessment process.

400

401 Conclusion

402 Our results show the importance of holistic assessments of the impact of deforestation on

403 whole species assemblages. We show the level of historical and recent reduction in habitat

404 for non-threatened forest-dependent species in Colombia is comparable to that of threatened

405 species and we argue that monitoring of both threatened and non-threatened species must be bioRxiv preprint doi: https://doi.org/10.1101/2020.05.30.125849; this version posted June 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

406 done in tandem. Moreover, many of the non-threatened species that have already lost half or

407 more of their potential habitat in Colombia are considered ‘common’ (e.g., Basileuterus

408 tristriatus[Three-striped Warbler]) or ‘abundant’ (e.g., Grey-breasted Wood-wren

409 [Henicorhina leucophrys]) (Hilty & Brown 1986; McMullan et al. 2010). Common and

410 abundant species represent the bulk of individuals in forest assemblages and their ecological

411 roles are fundamental for ecosystem functioning (Sekercioglu 2006; Gaston & Fuller 2008)

412 and the provision of ecosystem services (Sekercioglu 2012; Gaston et al. 2018). Their

413 extirpation can reduce income for local communities in ecotourism (Maldonado et al. 2018),

414 reduce pest control in nearby agroforest and agricultural landscapes (Sekercioglu 2012) and

415 reduce pollination and seed dispersal of fruiting and timber trees in adjacent agricultural

416 landscapes (Gaston & Fuller 2008).

417 While identifying and halting the underlying causes of deforestation is fundamental to avoid

418 the extinction of forest-dependent species, improving the protection for species under

419 imminent risk is necessary in the short term to avoid their extinction. Understanding future

420 threats to species based on projected impacts of deforestation is therefore an important tool

421 which helps to generate better conservation plans and actions to protect focal species of

422 otherwise unseen risk. We believe the methodological framework applied in this study can

423 provide a rapid way to generate an initial evaluation of the state of entire species assemblages

424 in other biodiverse countries and regions where field data is not complete or available.

425

426

427

428

429 bioRxiv preprint doi: https://doi.org/10.1101/2020.05.30.125849; this version posted June 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

430 References

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552 Negret PJ, Garzón O, Stevenson PR, Laverde- O, Gar On O. 2015. New ecological 553 information for the Black Tinamou (Tinamus osgoodi hershkovitzi). The Auk 132:533– 554 539. 555 Negret PJ, Laverde-R. O. 2014. The enigmatic Black Tinamou: Do distribution, climate, and 556 vocalizations reveal more than one species? The Auk 132:132–139. 557 Negret PJ, Sonter L, Watson JEM, Possingham H, Jones KR, Cesar S, Ochoa-Quintero JM, 558 Maron M. 2019. Emerging evidence that armed conflict and coca cultivation influence 559 deforestation patterns. Biological Conservation.239. DOI: 560 https://doi.org/10.1016/j.biocon.2019.07.021 561 Ochoa-Quintero JM, Gardner TA, Rosa I, de Barros Ferraz SF, Sutherland WJ. 2015. 562 Thresholds of species loss in Amazonian deforestation frontier landscapes. Conservation 563 Biology 29:440–451. 564 Owens IPF, Bennett PM. 2000. Ecological basis of extinction risk in birds: Habitat loss 565 versus human persecution and introduced predators. Proceedings of the National 566 Academy of Sciences 97:12144–12148. 567 Palacio RD, Negret PJ, Velasquez-Tibata J, Jacobson AP. 2020. A data-driven geospatial 568 workflow to improve mapping species distributions and assessing extinction risk under 569 the IUCN Red List. bioRxiv. DOI: 10.1017/CBO9781107415324.004 570 Parkins J. 2019. Former Farc commanders say they are returning to war despite 2016 peace 571 deal. The Guardian. Bogota, Colombia. Available from 572 https://www.theguardian.com/world/2019/aug/29/ex-farc-rebels-announce-offensive- 573 despite-peace-deal-colombia-video. 574 ProAves. 2019. ProAves Foundation. Available from http://www.proaves.org/proaves- 575 reserves/?lang=en. 576 Ramirez-Chaves H, Suárez-Castro A. 2014. Adiciones y cambios a la lista de mamíferos de 577 Colombia: 500 especies registradas para el territorio nacional. Mammalogy Notes 1:31– 578 34. 579 Rondinini C et al. 2011. Global habitat suitability models of terrestrial mammals. 580 Philosophical transactions of the Royal Society of London. Series B, Biological sciences 581 366:2633–2641. 582 Rosenberg K V. et al. 2019. Decline of the North American avifauna. Science 366:120–124. 583 Sekercioglu CH. 2006. Increasing awareness of avian ecological function. Trends in Ecology 584 and Evolution 21:464–471. 585 Sekercioglu CH. 2012. Bird functional diversity and ecosystem services in tropical forests, 586 agroforests and agricultural areas. Journal of Ornithology 153:153–161. 587 Simmonds JS, Watson JEM, Salazar A, Maron M. 2019. A composite measure of habitat loss 588 for entire assemblages of species. Conservation Biology 33:1438–1447. 589 Soares-Filho B, Rodrigues H, Follador M. 2013. A hybrid analytical-heuristic method for 590 calibrating land-use change models. Environmental Modelling and Software 43:80–87. 591 Elsevier Ltd. Available from http://dx.doi.org/10.1016/j.envsoft.2013.01.010. 592 Soares-Filho BS, Coutinho Cerqueira G, Lopes Pennachin C. 2002. DINAMICA - A bioRxiv preprint doi: https://doi.org/10.1101/2020.05.30.125849; this version posted June 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

593 stochastic cellular automata model designed to simulate the landscape dynamics in an 594 Amazonian colonization frontier. Ecological Modelling 154:217–235. 595 Symes WS, Edwards DP, Miettinen J, Rheindt FE, Carrasco R. 2018. Combined impacts of 596 deforestation and wildlife trade on tropical biodiversity are severely underestimated. 597 Nature Communications 9. DOI: https://doi.org/10.1038/s41467-018-06579-2 598 Teixeira AMG, Soares-Filho BS, Freitas SR, Metzger JP. 2009. Modeling landscape 599 dynamics in an Atlantic Rainforest region: Implications for conservation. Forest 600 Ecology and Management 257:1219–1230. 601 Tracewski Ł, Butchart SHM, Di Marco M, Ficetola GF, Rondinini C, Symes A, Wheatley H, 602 Beresford AE, Buchanan GM. 2016. Toward quantification of the impact of 21st- 603 century deforestation on the extinction risk of terrestrial vertebrates. Conservation 604 Biology 30:1070–1079. 605 United Nations. 2018. Bio Anori: A Reconciliation Expedition. Available from 606 https://colombia.unmissions.org/en/bio-anorí-reconciliation’-expedition. 607 Watling JI et al. 2020. Support for the habitat amount hypothesis from a global synthesis of 608 species density studies. Ecology Letters 23:674–681. 609 Watson JEM et al. 2018. The exceptional value of intact forest ecosystems. Nature Ecology 610 and Evolution 2:599–610. 611 Winfree R, Fox JW, Williams NM, Reilly JR, Cariveau DP. 2015. Abundance of common 612 species, not species richness, drives delivery of a real-world ecosystem service. Ecology 613 Letters 18:626–635. 614 World Resources Institute. 2018. Global Forest Watch. Available from 615 https://www.globalforestwatch.org/dashboards/country/COL. 616 617 Acknowledgements

618 We are grateful to R.D. Palacio, J.R. Allan and K.R. Jones, for providing constructive 619 feedback and discussion around elements of this study. Funding: This work was supported 620 by the Colombian Administrative Department of Science, Technology and Innovation 621 (Colciencias).

622

623 Authors’ contributions

624 P.J.N. conceived and designed the study with J.S.S., M.M. and J.E.M.W suggestions. P.J.N. 625 implemented the analysis. All the authors contributed to subsequent drafts and gave final 626 approval for publication.

627 bioRxiv preprint doi: https://doi.org/10.1101/2020.05.30.125849; this version posted June 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

628 Data Availability

629 Supplementary Table 1,2 & 3 will be made available upon request, previous to its deposition 630 in an open-access repository with the peer-reviewed version of this study. Requests should be 631 sent to the corresponding author.

632 bioRxiv preprint doi: https://doi.org/10.1101/2020.05.30.125849; this version posted June 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

633 Figures 634 635 Figure 1. (a) Loss of extent of potential habitat for forest-dependent Colombian birds. Change in 636 suitable habitat for each of the 550 species, until 2015 and the projected loss by 2040, split by each 637 species’ current IUCN Red-list status: critically endangered (CR), endangered (EN), vulnerable (VU), 638 near threatened (NT), and least concern (LC). The circles represent the historical extent of suitable 639 habitat within the range of each species, the triangles the extent in 2015 and the asterisks the projected 640 extent for 2040; the lines are drawn between the circle and triangle for the same species to highlight 641 the species-specific change, the same for the dashed lines between the circles and asterisks. (b) The 642 same figure but only showing species with historical extent of suitable habitat smaller than 5000 km². 643 In this graph the horizontal black dotted lines represent the thresholds for classification as vulnerable 644 (VU) (2000 km²), endangered (EN) (500 km²) and critically endangered (CR) (10 km²) based on the 645 IUCN criterion B2. 646 647 648 (a) 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 bioRxiv preprint doi: https://doi.org/10.1101/2020.05.30.125849; this version posted June 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

669 670 (b) 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 bioRxiv preprint (which wasnotcertifiedbypeerreview)istheauthor/funder.Allrightsreserved.Noreuseallowedwithoutpermission. 700 Figure 2. (a) Histogram of the number of forest-dependent birds (n=550 species) with different proportions of historical habitat loss until 2015 and (b) the 701 projected for 2040 in Colombia. Continues lines represent a smoothed count estimate, vertical dashed lines show the mean habitat loss. doi:

702 https://doi.org/10.1101/2020.05.30.125849 703 704 (a) (b) 705 706 707 708 709 ; 710 this versionpostedJune24,2020. 711 712 713 714 715 716 The copyrightholderforthispreprint 717 718 719 720 721 bioRxiv preprint (which wasnotcertifiedbypeerreview)istheauthor/funder.Allrightsreserved.Noreuseallowedwithoutpermission. 722 Figure 3. (a) Habitat loss index (LI) and histogram of the number of forest-dependent birds against percentage of historical habitat loss until 2015 (black) and 723 the projected for 2040 (orange) for Colombia and its different biotic regions. Vertical dashed lines in the histograms show the mean habitat loss. In the centre 724 a map of the number of forest-dependent birds potentially affected by habitat loss in different regions of Colombia (dark grey; remnant forest habitat, light doi:

725 grey; non forest habitat; colour key; number of species that potentially lost natural habitat) to 2015 (b) and from 2015 to 2040. Caribe (n=170 species); Andes https://doi.org/10.1101/2020.05.30.125849 726 (n=491 species); Orinoquía (n=213 species); Amazonas (n=301 species); Pacific (n=285 species). 727 728 (a) (c) 729 730 731 732 733 ; this versionpostedJune24,2020. 734 735 736 737 The copyrightholderforthispreprint bioRxiv preprint doi: https://doi.org/10.1101/2020.05.30.125849; this version posted June 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

738 Figure 4. (a) Histogram of the number of regionally-endemic forest-dependent birds (n=69) against 739 the percentage of historical habitat loss until 2105 and the projected for 2040 in Colombia. The 740 vertical black dashed lines show the mean habitat loss. Continuous lines represent a smoothed count 741 estimate. (b) Habitat loss index (LI) and map of the number of regionally-endemic forest-dependent 742 birds potentially affected by habitat loss in different regions of Colombia (dark grey; remnant forest 743 habitat, light grey; non-forest habitat; colour key; number of species that potentially lost natural 744 habitat) for 2015 and (c) 2040. 745 746 (a) 747 748 749 750 751 752 753 754 (b) (c) 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 bioRxiv preprint doi: https://doi.org/10.1101/2020.05.30.125849; this version posted June 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

774 Figure 5. Population declines from habitat loss. The blue bar is the habitat loss until 2000, the orange 775 bar the habitat loss until 2015 and the red bar the projected habitat loss by 2040. This graph only 776 shows the 69 regionally-endemic forest-dependent species. Vertical lines represent the thresholds for 777 classification as near threatened (NT) (20%), vulnerable (VU) (30%), endangered (EN) (50%), and 778 critically endangered (CR) (80%) based on the IUCN criterion A4. In parenthesis IUCN category in 779 2019. 780 781 782 783 784 785

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799 bioRxiv preprint doi: https://doi.org/10.1101/2020.05.30.125849; this version posted June 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

800 Supplementary material:

801 Supplementary Table 1, 2 & 3 are in an excel file 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 bioRxiv preprint doi: https://doi.org/10.1101/2020.05.30.125849; this version posted June 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

833 Supplementary Figure 1. (a) Loss of extent of suitable habitat in Colombia for regionally-endemic 834 forest-dependent birds. Change in suitable habitat for each of the 69 species until 2040, split by their 835 current IUCN Red-list status: critically endangered (CR), endangered (EN), vulnerable (VU), near 836 threatened (NT), and least concern (LC). The circles represent the historical extent of suitable habitat 837 within the range of each species, the triangles the extent in 2015 and the asterisks the projected extent 838 for 2040; the lines are drawn between the circle and triangle for the same species to highlight the 839 species-specific change, the same for the dashed lines between the circles and asterisks. 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 bioRxiv preprint doi: https://doi.org/10.1101/2020.05.30.125849; this version posted June 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

868 Supplementary Figure 2. Habitat loss index values (LI), map of the locations of potential lost natural 869 habitat (shaded pixels), and histogram of the number of forest-dependent species against percentage 870 of historical habitat loss until 2105 (black) and the projected for 2040 (orange) in Colombia for 4 871 major bird groups. Dashed lines show the mean habitat loss by 2015 and the projected by 2040 (a) 872 Tanagers (Thraupidae, n = 61 species), (b) Antbirds (Thamnophilidae, n = 53 species), (c) Ovenbirds 873 (Furnariidae, n = 47 species) and (d) Flycatchers (Tyrannidae, n = 43 species). In the maps, dark grey 874 depicts remanent forest habitat, light grey non forest habitat and the colour key, the number of species 875 that potentially lost natural habitat. 876 877 (a) 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 (b) 894 895 896 897 898 899 900 901 902 903 bioRxiv preprint doi: https://doi.org/10.1101/2020.05.30.125849; this version posted June 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

904 (c) 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 (d) 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 bioRxiv preprint doi: https://doi.org/10.1101/2020.05.30.125849; this version posted June 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

937 Supplementary Figure 3. Population declines from habitat loss. The blue bar is the habitat loss from 938 2000 to 2015, and the red bar the projected habitat loss by 2040. This graph only shows the 69 939 regionally-endemic forest-dependent species. Vertical lines represent the thresholds for classification 940 as near threatened (NT) (20%), vulnerable (VU) (30%), endangered (EN) (50%), and critically 941 endangered (CR) (80%) based on the IUCN criterion A4. In parenthesis IUCN category in 2019. 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964