Abstract
20
Species distributions are frequently modeled using predictors that exceed the spatial scale 21
experienced by the focal species. Incorporating fine-scale environmental conditions is 22
therefore expected to lead to more realistic model predictions. However, the importance of the 23
variety in the existing fine-scale conditions on species distribution remains poorly assessed 24
although species can effectively utilize multiple microhabitats for behavioral adaptation to 25
withstand climate change impacts. Here, we developed a fine-scale species distribution model 26
based on ambient air conditions for the northern pika (Ochotona hyperborea), a small 27
lagomorph found in rocky landforms, to first understand the improvement in the model 28
performance from the conventional coarse-scale model. We then assessed how model 29
predictions alter by incorporating the rock-interstice microclimates that are found in their 30
habitats for the baseline (1981–2010) and future periods (2041–2100). The fine-scale model 31
performed better and overall predicted lower habitat suitability across the study area than the 32
coarse-scale model. Incorporation of rock-interstice microclimate increased the habitat 33
suitability markedly relative to predictions based on ambient conditions, which resulted in 34
predicting more suitable areas in lower elevations and more areas remaining suitable into the 35
future. This result suggests that the northern pika may withstand the negative impacts from 36
rising ambient temperatures by effectively utilizing rock interstices via behavioral adaptation. 37
Our findings highlight the importance of analyzing species distribution at fine scales and 38
considering local environmental heterogeneity, which helps species mitigate the adverse 39
impacts of climate change, for conservation under climate change. 40
HIGHLIGHTS 41
1. Species use a wide variety of microhabitats and experience thermal conditions existing 42
locally. 43
Author-formatted, not peer-reviewed document posted on 15/07/2024. DOI: https://doi.org/10.3897/arphapreprints.e131956
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2. In the northern pika, a cold-adapted lagomorph, fine-scale species distribution model 44
performed better than the coarse-scale model. 45
3. Complex topographical features that locally buffer ambient thermal conditions were 46
predicted to increase habitat suitability and elongate species persistence in the future. 47
4. Local environmental heterogeneity that helps species mitigate climate change impact will 48
be important for conservation. 49
50
Keywords
behavioral thermoregulation, climate change, microclimate, northern pika, species 51
distribution model, topography 52
53
54
Author-formatted, not peer-reviewed document posted on 15/07/2024. DOI: https://doi.org/10.3897/arphapreprints.e131956
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Introduction
55
Climate change is having a profound influence on species distribution worldwide. 56
Evidence from historical resurveys shows that species distribution limits are generally 57
expanding at the leading edge and contracting at the trailing edge towards higher elevations and 58
latitudes (Lenoir et al., 2020; Moritz et al., 2008) . These range shifts are predicted not only to 59
affect species extinction risks (Urban, 2015), but also ecosystem functions and services (Pecl 60
et al., 2017). It is therefore important in contemporary biogeography to assess accurately how 61
species will change their spatial distribution in the future and identify conservation priority 62
areas to mitigate those i mpacts. Species distribution model s (SDMs) have become extremely 63
useful in this role by relating species occurrence with environmental data and enabling forecasts 64
of how suitable habitats and associated distribution ranges will change over time (Elith & 65
Leathwick, 2009) . Yet, SDMs have been criticiz ed for analyzing species occurrence and 66
environment relationships at spatial resolutions that are often too coarse relative to the actual 67
scales at which species utilize those habitats . A review by Potter et al. (2013) showed that the 68
grid lengths of the environmental data used in previous studies were approximately 10,000 69
times larger than the body length of the focal animal species and 1,000 times in plants, 70
suggesting a strong spatial mismatch between the environmental data and the actual conditions 71
experienced by species. While some researchers argue that species distribution models aim to 72
model population-level rather than individual-level responses (Bennie et al., 2014), the issue of 73
scale mismatch in distribution modelling is still recognized as important when considering the 74
population dynamics for a wide range of taxa, such as small mammals, herpetofauna, and plants 75
(Nadeau et al., 2017) . Therefore, endeavors to develop SDMs that incorporate environmental 76
conditions at biologically relevant scales are warranted (Lembrechts et al., 2019). 77
The spatial resolution of SDMs is of concern particularly in rugged terrains where coarse-78
scale climate data cannot capture appropriately the fine-scale environmental conditions created 79
Author-formatted, not peer-reviewed document posted on 15/07/2024. DOI: https://doi.org/10.3897/arphapreprints.e131956
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by complex topographies (Austin & Van Niel, 2011). A growing body of literature has explored 80
the effect of resolution and spatial scale on SDMs (Franklin et al., 2013; Gillingham et al., 2012; 81
Guisan et al., 2007; Maclean & Early, 2023; Moudrý et al., 2023; Patiño et al., 2023; Randin et 82
al., 2009). Recent studies are further attempting to improve the performance and prediction 83
accuracy of fine -scale models by shifting from simply using downscaled climate data to 84
incorporating microclimates that are predicted based on in-situ thermal sensor measurements 85
(Haesen et al., 2023; Stark & Fridley, 2022) and remote sensing techniques (Stickley & 86
Fraterrigo, 2023). These studies show that incorporation of fine-scale conditions can improve 87
model performance and alter predictions of suitable areas, thus affecting the trajectory of 88
potential range shifts over time (e.g., Maclean & Early, 2023) . Therefore, relying solely on 89
coarse-scale models is problematic for conservation practice under climate change because it 90
can lead to poor decisions that overlook suitable areas when designing protected areas and 91
allocating resources for management. Further research is therefore required in this field because 92
a wide variety of environmental features create distinct climates at various spatial scales 93
(Morelli et al., 2017), and how species utilize and interact with them is system-specific (Shi et 94
al., 2016). 95
One of the perspectives still unexplored in this field , particularly for animals , is that a 96
given species can experience various fine -scale thermal conditions even within a single grid 97
cell as vertical structures also generate heterogenous conditions (e.g., Scheffers et al., 2014) . 98
Most previous studies have only considered the condition of a single vertical position, 99
overlooking the fine-grain heterogeneity in environmental condition s that likely influences 100
overall habitat suitability of a given location that an individual occupies . This is particularly 101
important in the context of species adaptation to climate change since species may mitigate the 102
negative impacts by altering their behavior effectively to exploit local heterogeneity in climatic 103
conditions (Beever, O’Leary, et al., 2016), which may cascade to have broader implications for 104
Author-formatted, not peer-reviewed document posted on 15/07/2024. DOI: https://doi.org/10.3897/arphapreprints.e131956
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patterns in the overall distribution (Marske et al., 2023). Therefore, predicting habitat suitability 105
considering the variety of fine-scale conditions should improve the assessment of climate-106
induced species range shifts. 107
Pikas are small lagomorphs adapted to cold environments in montane ecosystems . 108
Various aspects of temperature, such as magnitude and variation, often act as strong drivers of 109
their distribution (Beever et al., 2010; Rodhouse et al., 2017) and abundance (Moyer-Horner et 110
al., 2016). Mounting evidence also suggest their vulnerability to recent climate change, with 111
field observations reporting local extinctions (Erb et al., 2011; Stewart et al., 2015) and range 112
contractions (Beever, Perrine, et al., 2016; Billman et al., 2021) . Other studies have predicted 113
future range contractions (Bhattacharyya et al., 2019; Schwalm et al., 2016). However, despite 114
occurring in complex t errain, previous studies modeling pika distribution have only used 115
coarse-scale climate data, possibly introducing bias into the habitat suitability predictions and 116
associated range shift estimates. 117
Some pika species belonging to the Pika subgenus dwell in rocky landforms such as talus 118
slopes, lava flows, and moraines. At the fine-scale, these rock-dwelling pikas experience duality 119
in thermal conditions as they utilize both the above-ground and sub-ground microhabitats. The 120
above-ground space is u sed for moving, vocalizing, foraging and collecting winter diet (i.e. 121
haypile), and pikas experience the local ambient air conditions during th ese activities. In 122
contrast, the sub-ground space in the rock interstices is used as the shelter (Gliwicz et al., 2005), 123
which provide pikas with cool and stable microclimates buffered from the ambient air 124
temperatures (Sakiyama et al., 2021; Varner & Dearing, 2014) . While both microhabitats are 125
essential for pikas, observations show that pikas respond flexibly to avoid the heat stress from 126
the local ambient air by utilizing rock interstices (Smith et al., 2016). Therefore, rock interstices 127
are considered a key f eature for their distribution by allowing the species to occur in 128
counterintuitive, low-elevation areas and for them to persist under climate change (Smith, 2020). 129
Author-formatted, not peer-reviewed document posted on 15/07/2024. DOI: https://doi.org/10.3897/arphapreprints.e131956
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Predicting the habitat suitability at fine-scales for both the above- and sub-ground space should 130
thus facilitate a more accurate assessment of their vulnerability to climate change while also 131
taking their adaptive capacity into account. 132
Here, we incorporate fine-scale thermal conditions in rocky landforms into SDMs to 133
predict the distribution of the northe rn pika Ochotona hyperborea in Hokkaido , Japan. We 134
evaluate how this incorporation changes model performance, suitable area prediction, and range 135
shift forecast from the conventional coarse-scale approach. In particular, we use macroclimate 136
data (30 arcsecs) and downscaled macroclimate data (3 arcsecs) to build the coarse-scale model 137
(hereafter macroclimate model) and the fine-scale model ( local-climate model), respectively, 138
and compare their performances and habitat suitability predictions across the whole distribution. 139
While the local-climate model considers the effects of fine-scale, above-ground temperature, 140
we further assessed the habitat suitability for the sub -ground space by incorporating rock-141
interstice microclimates into the predictions, which we modeled based on local thermal 142
measurements (Sakiyama & García Molinos, 2024). We then projected future range shifts for 143
the species and compared the area of suitable habitat between local-climate and microclimate-144
based predictions. We hypothesized that (1) the local -climate model will have higher model 145
performance than the macroclimate model ; (2) the local -climate model will predict habitat 146
suitability distinctively from the macroclimate model reflecting the complex topography ; (3) 147
the rock-interstice microclimate enhances the habitat suitability from the local-climate model 148
prediction; and (4) the rock-interstices retain the suitable habitats in future predictions. 149
Materials and methods
150
Study area and species distribution data 151
We modeled the distribution of northern pika populations in central Hokkaido, Japan, 152
because this is the core distribution area of the species in Japan and detailed fine-scale habitat 153
thermal measurements have been conducted in this area (Sakiyama et al., 2021; Sakiyama & 154
Author-formatted, not peer-reviewed document posted on 15/07/2024. DOI: https://doi.org/10.3897/arphapreprints.e131956
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García Molinos, 2024). The northern pika in Hokkaido is located at the southern margin of its 155
distribution and therefore its population is likely among the most vulnerable of the species to 156
climate warming. Although northerly neighboring populations are found across the Sea of Japan 157
in Sakhalin and Primorsky , the Hokkaido population is essentially a disjunct population . As 158
such, it is likely to respond to climate change by shifting upslope, but previous studies have not 159
predicted future distributions. 160
To model the distribution of northern pikas, we compiled occurrence data in central 161
Hokkaido from previous literature. Given almost all the compiled data comprised presence (but 162
not absence) locations, we decided to apply a presence-only algorithm for distribution modeling 163
(see Model Development section). We only used presence locations reported on high resolution 164
maps (i.e. 1/25,000 and 1/50,000 scale) for analysis since we were interested in modeling at 165
fine scales. Overall, a total of 305 presence points encompassing a wide elevational gradient 166
(50–2,210 m) were obtained from the literature (Table S1; Fig. S1a ). Survey years spanned 167
between 1963 and 2009 (Fig. S1a, b). Detection signs of northern pika presence were clearly 168
mentioned for almost all points (298 points, 97.7%), with the vocalization representing the main 169
Method
enabling detection of 241 points (79.0%). This suggests that the detection methods were 170
relatively consistent among different literature consulted. 171
As calibration extent for this study, we considered the area corresponding to the known 172
geographical range of the species comprising the continuous mountainous areas in central 173
Hokkaido delimited by the flatlands (i.e., river valleys) as the extent borders. Specifically, we 174
considered the Abira and Ishikari River systems as the western, the Teshio River system as the 175
northwestern, the Shokotsu River system and the Sea of Okhotsk as the northeastern, the 176
Abashiri and the Tokachi River systems as the eastern, and the Pacific Ocean as the southern 177
borders of the extent (Fig. S1a). Next, we removed irrelevant land cover types from within the 178
study extent area such as urban land, agricultural fields, and aquatic area (e.g., lakes) since 179
Author-formatted, not peer-reviewed document posted on 15/07/2024. DOI: https://doi.org/10.3897/arphapreprints.e131956
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northern pikas require pristine montane conditions for inhabitation. The resulting filtered study 180
extent area covered approximately 21,000 km2 in central Hokkaido (Fig. S1a). 181
Model settings 182
To understand how difference s in spatial resolution s of climate data affect model 183
performances and predictions of species distribution, we constructed macroclimate ( coarse-184
scale) and local-climate (fine-scale) models (Fig. 1; Table S2). In the macroclimate model, we 185
used environmental predictors at a resolution of 30 arcsecs, which converts to a grid cell of 691 186
m by 926 m (longitude x latitude) and size of 639,682 m 2. We consider this setting to be a 187
coarse resolution for the northern pika because the ir home ran ge is much smaller, typically 188
within the range 1,822 –11,530 m 2 (n = 4; Onoyama et al., 1991) . We also note that, the 189
mountainous terrains of our study area are significant ly smoothed at this resolution, with 190
median and maximum elevational differences within one 30-arcsec grid cell as large as 182 m 191
and 770 m, respectively, when computed based on 10-times finer (3 arcsecs) elevation data (Fig. 192
S2). Since species occurrence-environment relationships might be confounded by such a large 193
degree of simplification, we developed our local climate model using environmental data at 3 194
arcsecs, which converts to a grid cell of 69.1 m by 92.6 m and size of 6,397 m 2. We consider 195
this setting to reflect the local ambient air conditions within individual home ranges. Based on 196
the local-climate model, we then generated two habitat suitability predictions to account for the 197
variety of fine -scale thermal conditions . The fir st corresponds to the model raw predictions 198
based on local-climate data and represents the above-ground habitat suitability. The second 199
prediction incorporates information on rock-interstice microclimates to further predict sub-200
ground habitat suitability. 201
Topographical and geological variables 202
We used the terrain slope angle as topographical predictor in the SDMs because it has 203
been shown to have a positive relationship with the northern pika distribution (Sakiyama et al., 204
Author-formatted, not peer-reviewed document posted on 15/07/2024. DOI: https://doi.org/10.3897/arphapreprints.e131956
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2021). We computed the slope angle raster in QGIS 3.34 (QGIS Development Team, 2023) 205
using the MERIT DEM (Yamazaki et al., 2017), a digital elevation model provided at a spatial 206
resolution of 3 arcsecs. Slope angles for the macroclimate setting were calculated using a DEM 207
aggregated to 30 arcsecs (Table S2). We also considered surface geology as a categorical binary 208
predictor because 99 % of the known distribution of the northern pika lies on igneous and 209
metamorphic rocks and moraines (Kawabe, 1992). To do so, we assigned whether any of these 210
geological types occurred per grid cell with in the study area based on the Seamless Digital 211
Geological Map of Japan (1:200,000) V2 (Geological Survey of Japan, National Institute of 212
Advanced Industrial Science and Technology, 2017) (Table S2). 213
Bioclimatic variables 214
To model and predict the distribution of northern pikas, w e computed the mean daily 215
temperature and mean diurnal range over July and August to account for the effects of thermal 216
magnitude and variation during the summer. We focused on summer conditions (i.e., July and 217
August) because the effects of climate change on cold-adapted species are likely to be 218
particularly strong during this season. Briefly (see Appendix S1 for a detailed explanation), we 219
first obtained climate data at 30 arcsecs using the chelsa-cmip6 R package, which provides 220
access to downscaled Global circulation model (GCM) projections (Karger et al., 2023). Four 221
GCMs that are known to reproduce well the climatic conditions of our study area were selected 222
(i.e. ACCESS-CM2, IPSL-CM6A-LR, MIROC6, and MRI-ESM2-0) (Shiogama et al., 2021). 223
We used climate data for 1981–2010 to model the baseline distribution. To create the 224
bioclimatic variables, we adapted the computation formulas used in ANUCLIM , a software 225
package used to build spatial climatic data (Xu & Hutchinson, 2011, 2013) , to the summer 226
season, and calculated mean summer temperature and mean summer diurnal range. The 227
resulting variables were then used for the macroclimate setting (Table S2). 228
For the local-climate setting, we downscaled the climate data obtained at 30 arcsecs to 3 229
Author-formatted, not peer-reviewed document posted on 15/07/2024. DOI: https://doi.org/10.3897/arphapreprints.e131956
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arcsecs as follows. Temperature data was downscaled using kriging with the krigR R package 230
(Davy & Kusch, 2021; Kusch & Davy, 2022) . This approach first models the relationship 231
between temperature and elevation at the coarse scale (30 arcsecs), which is then used to 232
interpolate the fine-scale temperature using elevation at the same target scale (3 arcsecs). We 233
used the raw MERIT DEM (Yamazaki et al., 2017) dataset, provided at 3 arcsecs, as the 234
elevation data for the fine-scale interpolation and the aggregated version at 30 arcsecs to model 235
the coarse-scale relationship (Table S2). 236
Finally, for the rock-interstice microclimate, we considered that northern pikas can utilize 237
sub-ground thermal conditions in rocky landforms, which are known to be buffered from the 238
ambient air temperature (Sakiyama and García Molinos, 2024). However, given the absence of 239
sufficient spatial distribution information regarding rocky landforms throughout our study 240
extent, we selected three representative regions where we had sufficient data separated by 241
elevational ranges: Biei (1,100–2,000 m), Shikaribetsu (600–1,250 m), and Oketo (400–800 m) 242
(Fig. 4). For Biei, we were able to map the rocky landforms directly using aerial images. For 243
Shikaribetsu and Oketo, we referred to the mapped occurrence of rocky landforms in previous 244
literature (Kojima, 2004; Kurumada, 201 0). For these regions, we then used an empirical 245
relationship between ambient and interstice temperatures previously derived from northern pika 246
taluses in our study area (Sakiyama and Garcia Molinos, 2024) to convert downscaled ambient 247
temperature into interstice temperature for each of the 3 arc second grid cells containing rocky 248
landforms (Fig. S3; Appendix S1). Here, our assumption is that northern pikas experience local 249
ambient climatic conditions in cells devoid of rocks since these landforms are patchily 250
distributed within each region. We validated our downscaling and microclimate incorporation 251
approach by comparing the thermal conditions measured in northern pika habitats with the 252
values of each bioclimatic variable in the grid cells where those observations had been made 253
(see Appendix S2). Results confirmed that the local-climate data was moderately accurate in 254
Author-formatted, not peer-reviewed document posted on 15/07/2024. DOI: https://doi.org/10.3897/arphapreprints.e131956
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reflecting observed ambient temperature and that the microclimate data was highly accurate in 255
reflecting observed rock interstice temperatures (Fig. S4, 5). 256
Model development 257
We performed the distribution modeling analysis of northern pikas in Hokkaido using 258
maximum entropy (MaxEnt; Phillips et al., 2006) . Models were developed separately for the 259
macroclimate and the local -climate settings considering the years 1981–2010 as the baseline 260
period, thus using the presence points during this period for model fitting. Prior to model fitting, 261
we reduced the effect of spatial sampling bias by thinning the presence data using the spThin R 262
package (Aiello-Lammens et al., 2015) at a distance of 500 m as presence locations could be 263
viewed as independent at this distance considering the complex mountainous terrain and the 264
limited mobility of the northern pika . Considering that the diagonal distance of macroclimate 265
grid cells is larger than this thinning distance and duplicate sampling thus could occur, we 266
randomly selected a single point for each cell after thinning. This pre-selection process resulted 267
in a total of 80 presence points remaining. We generated 10,000 background points throughout 268
the study area, which are used in MaxEnt for characterizing the extant environmental conditions 269
within the study area. To avoid multicollinearity issues (Dormann et al., 2013) , we computed 270
the pairwise Pearson’s correlation coefficients among the continuous predictors and confirmed 271
that all pairs did not have a strong correlation (|r| > 0.7) (Fig. S6). 272
Since MaxEnt models with default settings can lead to overfitting (Anderson & Gonzalez, 273
2011), we initially tuned the model hyperparameters to control the complexity while fitting well 274
to the data. To do this, we used various hyperparameter combinations of feature classes, which 275
determines the shape of the response curves, and regularization multipliers, which controls the 276
model complexity (Phillips et al., 2006; Phillips & Dudík, 2008), and selected the combination 277
that resulted in the highest predicative accuracy. For the feature class, we considered linear (L), 278
quadratic (Q), product (P), and/or hinge (H) characteristics, and f or the regularization 279
Author-formatted, not peer-reviewed document posted on 15/07/2024. DOI: https://doi.org/10.3897/arphapreprints.e131956
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multipliers, we used values ranging from 0.2 to 2.0 with intervals of 0.2. The predictive 280
accuracy was assessed for each model by separating the presence data into training (80%) and 281
test (20%) data and computing the area under the receiver operating characteristic curve (AUC), 282
which indicates the accuracy condition on a range of 0 to 1 (Fielding & Bell, 1997). All tuning 283
processes were conducted using the optimizeModel function in the SDMtune R package 284
(Vignali et al., 2020) . After hyperparameter tuning, we evaluated the optimized model’s 285
predictive accuracy based on 5-fold cross validation using Continuous Boyce Index (Hirzel et 286
al., 2006), and compared these values among the model settings. 287
Comparing baseline predictions 288
For both the macroclimate and the local -climate m odels, w e predicted the habitat 289
suitability for the baseline period across the study area and compared the predicted suitability 290
by computing the difference. We also generated binarized maps of predicted species occurrence 291
(i.e. presence or absence) based on the habitat suitability prediction across the whole study area. 292
Since discriminant thresholds were likely to differ between the optimized models for the 293
macroclimate and local -climate and could be problematic for comparison, we instead used a 294
sensitivity analysis approach by applying a moving threshold from 0 to 1 at 0.01 increments to 295
discriminate presence or absence. Binary predictions were then compared between the 296
macroclimate and local-climate models by assessing the proportion of predicted presence areas 297
in the study area, calculated as the total amount of presence cells divided by the number of all 298
cells, for each moving threshold. We used p roportion instead of simply calculating the total 299
area of presence because the total study area was subtly different between the scales due to 300
processing procedures of environmental data. We then predicted the habitat suitability for the 301
sub-ground space for the three selected regions by replacing the local ambient temperatures by 302
the modeled rock interstice temperatures for the prediction of habitat suitability using the local-303
climate model . We consider this prediction to reflect the habitat suitability of the rock -304
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interstices within individual home ranges defined based on the relationship between 305
occurrences and ambient air temperatures. The resultant prediction was compared with those 306
based on the macroclimate and local-climate. 307
Hindcasting 308
We use a hindcasting approach t o evaluate the transferability of the models to project 309
distributions over time (see Nogués‐Bravo, 2009) by projecting the distribution of the species 310
to the past and comparing it to known past presence points from the same past period for 311
validation (Hodel et al., 2022). Although this approach is still rarely used in SDM studies (Yates 312
et al., 2018) , it allowed us to assess how confident we can be using the models to predict 313
distributions for a (past or future) time period different to that the model was calibrated for. We 314
projected the distribution of northern pikas for years 1961–1980, a period for which early 315
presence records are available (Table S1; Fig S1). The same procedures as the baseline climate 316
data were used for processing past data. We evaluated the model’s predicative accuracy via the 317
Continuous Boyce Index (Hirzel et al., 2006). 318
Future projection 319
To project the future distribution of the northern pika, we obtained climate data for two 320
future time periods, 2041–2070 and 2071–2100, considering two emission scenarios, SSP1-2.6 321
and SSP5-8.5, representing a globally sustainable and a fossil-fuel based development scenario, 322
respectively. We predicted the future distribution for the study extent based on the macroclimate 323
and local-climate models using the future bioclimatic data, which were processed based on the 324
same procedures for the baseline climate da ta (i.e., we assume that future topographical and 325
geological variables will remain the same as present ). We binarized the suitability predictions 326
to presence or absence by applying the same approach used for the baseline period to calculate 327
the proportion of presence areas. 328
Moreover, we also projected the future distribution of the northern pika for the three 329
Author-formatted, not peer-reviewed document posted on 15/07/2024. DOI: https://doi.org/10.3897/arphapreprints.e131956
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selected regions to assess how microclimate contributes to retaining suitable conditions in the 330
future. When processing the future microclimate data, we assumed that the buffering effect of 331
the rock interstices (i.e., the empirical relationship between local ambient and rock -interstice 332
temperatures) will remain invariable over time. We believe that this assumption is robust 333
because the field thermal measurements from which this relationship was derived contained a 334
large elevational gradient of 350–2200 m and the model residual was stable across the ambient 335
temperature gradient (Sakiyama and Garcia Molinos, 2024) , although we note that some 336
extrapolation did occur for some lower elevation areas where future conditions exceeded the 337
observed thermal gradient. We binarized the suitability predictions for both local-climate and 338
microclimate using the maximum true skill statistic computed for the local-climate model. The 339
consensus among the resulting binarized predictions from each of the four GCMs was then 340
computed by considering a cell as present whenever that cell was predicted as presen t by two 341
or more individual GCMs (i.e., ≥50% consensus) . The consensus predictions in the selected 342
regions were compared visually between the local-climate and microclimate-based predictions 343
for each period and emission scenarios. 344
Results
345
Model performance and variable importance 346
Both the macroclimate and local-climate models converged to the same hyperparameter 347
combinations for the best -fit model comprising an LQP feature class and a regularization 348
parameter value of 2. Using these hyperparameters, the Continuous Boyce Index was 0.73 and 349
0.80 for the macroclimate and local-climate models, respectively (Table 1). This indicates that 350
the continuous predictions reflected the species distribution well and that the local-climate 351
model was more accurate than the macroclimate model. 352
Mean summer temperature was the most important predictor explaining the northern pika 353
distribution in both models with a permutation importance of 74.5 % and 76.2 % for the 354
Author-formatted, not peer-reviewed document posted on 15/07/2024. DOI: https://doi.org/10.3897/arphapreprints.e131956
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macroclimate and local-climate models, respectively (Fig. S 7). Mean summer temperature 355
decreased occurrence probability in both models, indicating that the northern pika is more likely 356
to be present in cooler areas. However, we detected a slightly steeper slope in the response 357
curve of the local-climate model, which indicates that the local -climate model fitted towards 358
cooler conditions than the macroclimate model (Fig. S8). In both models, surface geology was 359
the second most important predictor with 20% and 18 % of permutation importance , 360
respectively (Fig. S7), and a positive relationship with occurrence probability (Fig. S8). The 361
permutation contribution of daily thermal range and slope was less than 5% in both models (Fig. 362
S7). 363
Habitat suitability for the baseline period 364
The negative effect of mean summer temperature was reflected in the habitat suitability 365
predictions at the whole distribution scale in both models, with higher elevations predicted as 366
highly suitable areas and the suitability lowering gradually towards downslope (Fig. 2 a,b). 367
Specifically, large mountain ranges such as the Daisetsuzan and Hidaka Mountain Ranges , 368
which contain summits over 2 ,000 m , as well as mountains in the Eastern Daisetsu region 369
(elevation of the main peaks 1,800–2,000 m) were recognized as the most suitable areas. Mid- 370
to high -elevation mountain ranges, such as the Yubari-Ashibetsu (1,600–1,720 m) , Teshio 371
(1,400–1,600 m), Ashoro (1,200–1,300 m), and Shikaribestu Mountains (1,100–1,250 m), were 372
predicted as areas with moderate to high suitability . Finally, low-elevation mountains were 373
predicted to be low in habitat suitability for northern pikas in almost all regions although some 374
presence points were reported from such areas (e.g. central and northeastern region s). One 375
exception was the Samani-Erimo region, which was predicted to have high suitability despite 376
the region being predominated by low elevations (Fig. 2a,b). 377
As we compared the macroclimate-based and local-climate based predictions, the former 378
was generally higher in habitat suitability than the latter across the study area (Fig. 2c). The 379
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difference in suitability was relatively large in the mountainous areas, particularly in the slopes 380
rather than the summits, with suitability differences up to 0.5. However, habitat suitability from 381
the local-climate based were also higher than the macroclimate -based predictions in some 382
mountainous areas as well as the Samani-Erimo region. The habitat suitability difference was 383
relatively small in low elevations. 384
The proportion of predicted presence areas for both models indicated similar curves along 385
the moving binarization threshold (Fig. 3a). The curve inverse shape means that, while the 386
whole study area is discriminated as present when the threshold is zero, a large proportion 387
becomes absent at relatively low thresholds, although a small proportion of the study area 388
remains present until the threshold becomes o ne. In other words, while most of the study area 389
is predicted to have low suitability, some areas have distinctively high values. Comparing the 390
curves between the models, the proportion of presence areas was higher in the macroclimate-391
based prediction than in the local -climate based prediction across the whole range of 392
binarization threshold (Fig. 3a). This suggests that the macroclimate model predicted a larger 393
area of suitable habitat than the local-climate model regardless of the binarization threshold. 394
In the three selected regions, the habitat suitability based on the macroclimate and local-395
climate showed a gradually changing pattern , likely reflecting the elevation difference. In 396
contrast, accounting for the rock interstice microclimate in local-climate predictions boosted 397
the habitat suitability distinctively within these regions (Fig. 4). For instance, while the habitat 398
suitability in Biei was relatively high given its high elevation in both the macroclimate - and 399
local-climate-based predictions, the rocky landforms further increased the suitability to mostly 400
reaching a suitability of 1 (Fig. 4 ). This trend was more evident in Shikaribetsu , the mid -401
elevation region, where the predicted suitability reached as high as 0.99 in the microclimate -402
based predictions despite the surrounding landscape having suitability less than 0.5 (Fig. 4). In 403
Oketo, the low-elevation region, the total area that increased in suitability was relatively small 404
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given the limited area of rocky landforms, but the predicted suitability within rocky landforms 405
reached as high as 0.66 (Fig. 4). The maximum values of predicted suitability based on the 406
macroclimate and local-climate models were 0.55 and 0.41 in Shikaribetsu and 0.24 and 0.25 407
in Oketo, respectively. In all these three regional-scale predictions, the habitat suitability was 408
predicted in a more detailed and complex manner in the fine-scale (3 arc sec) predictions than 409
that in the coarse -scale (30 arc sec) predictions as evidenced by the variation in habitat 410
suitability of the local-climate and microclimate predict ions within the coarse-scale grid cells 411
(Fig. 4). 412
Hindcasting and future projection 413
In the hindcasting analysis, both macroclimate and local-climate models had Continuous 414
Boyce Index values well above zero (Table 1), suggesting that the models were a ccurate in 415
predicting past distributions. This result supports the transferability of these models to predict 416
distributional change over time . Accordingly, we were able to predict future distributions for 417
both model settings with confidence. 418
Both models indicated inverse curves in the proportion of presence areas in the future 419
(Fig. 3b). Comparing with the baseline proportions, future distribution was predicted to 420
decrease by more than 60% in in both time periods and emission scenarios considered (Fig S9). 421
Between the two future time periods, the difference in the habitat decrease rate was relatively 422
small under the SSP1-2.6 scenario, suggesting that presence areas will decrease until 2041–423
2070 but will then remain relatively stable until 2071–2100. However, the habitat decrease was 424
apparent under the SSP5-8.5 scenario, suggesting that suitable habitats will continue to decrease 425
until 2071–2100. (Fig. 3b; S9). 426
Patterns of predicted distributional change largely differed among the three selected 427
regions between the local-climate an d microclimate -based predictions . Based on the local -428
climate, predicted presences were found in Biei in both future time periods and scenarios and 429
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in Shikaribetsu under the SSP1-2.6 scenario, while none were found in Oketo under all future 430
settings (Fig. 5). Conversely, predicted presences were found in almost all regions in all future 431
settings when accounting for rock interstice microclimates , except in Oketo for the far future 432
under the SSP5-8.5 scenario (Fig. 5). Discrepancies between local-climate and microclimate-433
based predictions were high towards the lower elevations and under the higher carbon emission 434
scenario (SSP5-8.5). 435
Discussion
436
We developed distribution model s for the northern pika that incorporate d fine-scale 437
temperatures experienced by the species to assess how model performances and predictions 438
change from a conventional model based on coarse-scale conditions . Our results show that 439
predictive accuracy was higher for the fine-scale model. We also found that the predicted 440
habitat suitability varied among regions and at smaller spatial scales in the fine-scale prediction. 441
These results confirm that accounting for fine-scale environments can lead to distinct and more 442
complex predictions than those obtained from a coarse-scale model and that solely depending 443
on coarse-scale predictions can result in biased predictions that overlook potential suitable 444
habitats. 445
There are two possible reasons that likely contributed to the higher predictive accuracy 446
in the fine-scale model. First, model response curves showed some important differences in the 447
modeled relationship between occurrence and the environmental predictors . While mean 448
temperature had a dominant negative effect on the distribution in both models (Fig. S7; S8), a 449
response also observed in a previous study (Sakiyama et al., 2021) , the response curve was 450
steeper in the local-climate model. This indicates that the model fitted towards cooler conditions, 451
which may be reflecting the actual response of the northern pika more accurate ly than th e 452
macroclimate model. Interestingly, our input data for the distribution model indicated that many 453
of the occurrence points in higher elevations were located in areas higher than its surroundings 454
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and thus had cooler temperatures at the fine-scale (Fig. S10). Although we referred to presence 455
points recorded in previous literature, it remains unclear whether this trend is due to a potential 456
sampling bias in convex topographies such as ridgelines and mountain tops. We believe that 457
assessing species distribution at fine-scales could introduce its scale-dependent issues, which 458
requires attention as more fine-scale SDMs are developed (Mitchell et al., 2017). Second, the 459
quality of the predictors may have also had an effect on model accuracy . Even when coarse- 460
and fine-scale models exhibit the same relationship between occurrence and environment, the 461
validated accuracy is likely to decrease if predictors are generalized at the coarse-scale. Instead, 462
fine-scale predictors are more likely to accurately represent true environmental conditions, 463
which could have resulted in higher predictive accuracy by resolving better local complex 464
topographies. Thus, the overall increase in accuracy of the local-climate model can be attributed 465
to these small refinements in the modeled relationship and predictors. In general, our results are 466
in agreement with recent studies finding higher performance in SDMs incorporating fine-scale 467
climates (Haesen et al., 2023; Stark & Fridley, 2022). 468
Our results showed that incorporating fine-scale environments into SDMs resulted in a 469
decrease of suitable areas compared to the coarse-scale prediction. This is likely due to 470
differences in the modeled response of mean summer temperature between the models. Such 471
differences likely emerged from the local -climate model being fitted towards cooler 472
temperatures relative to the coarser macroclimate model resulting in lower predicted occurrence 473
probabilities at certain temperatures or elevations. Consequently, this leads to a greater area of 474
predicted presence in the macroclimate model along the moving threshold when binarizing the 475
habitat suitability predictions . In previous literature, fine-scale models have resulted in both 476
greater (Stickley & Fraterrigo, 2023) and smaller suitable areas (Franklin et al., 2013; Haesen 477
et al., 2023) . Hence, the difference in the predicted habitat area resulting from incorporating 478
fine-scale environments into S DMs may be s pecific to each study system and the scale -479
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dependent relationship between the occurrence records and environmental predictors used in 480
the model . Furthermore, in our study, both models projected drastic future declines in the 481
northern pika distribution, with over half of the suitable habitats predicted to disappear by mid-482
century. This suggests that, similar to other pika species, northern pikas in Hokkaido are 483
vulnerable to climate change (Beever et al., 2011; Bhattacharyya et al., 2019). Importantly, the 484
predicted change in species distribution depended strongly on the future period and emission 485
scenario. This result stresses the need to enforce effective policies for greenhouse gas emission 486
mitigation and to guide effective conservation of the species by protecting areas that will 487
account for the effect of climate change and maintain its distribution in the future. 488
At the regional scale, the incorporation of the rock-interstice microclimate provided 489
distinct predictions for both the baseline and future. Overall, the cooler conditions provided by 490
rock-interstices resulted in the microclimate predictions markedly enhancing habitat suitability 491
compared to t he local-climate based prediction in all three regions. This demonstrates that a 492
single location (grid cell) can exhibit dual habitat suitability due to the existence of diverse 493
thermal conditions in complex topograph ies. However , what are the implications for the 494
northern pika distribution? In rocky landforms, the habitat suitability can simply be categorized 495
into three combinations based on the local -climate and microclimate conditions: high -high, 496
low-high, and low-low. The combination of high-low suitability was not observed because rock 497
interstices were always cooler than local ambient conditions , hence more suitable. Northern 498
pikas are expected to be present in areas with high-high suitability, and absent from areas with 499
low-low suitability . However, whether areas with low-high suitability serve as functional 500
habitats for northern pikas will likely depend on the extent to which the rock interstice condition 501
mitigates the impact of poor thermal ambient conditions, which should be strongly linked to the 502
capacity of northern pika s to adapt their thermoregulation behavior. Previous studies have 503
indicated that northern pika s utilize above-ground space during the cooler times of the day 504
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(Onoyama, 1 991); a behavior also observed in American pika stud ies (Smith et al., 2016) . 505
Additionally, research on the American pika suggests that it regulates body temperature by 506
reducing above-ground activities and retreating into rock interstices (MacArthur & Wang, 507
1974). Thus, the northern pika may exhibit high behavioral flexibility to respond to unfavorable 508
ambient conditions, enabling them to inhabit areas with low-high suitability. Consequently, the 509
actual overall suitability of a given rocky landform should be influenced by a more complex 510
combination of these two suitability conditions (above and below ground). 511
Despite its simplicity, our approach to predict microclimate-based habitat suitability is 512
innovative because it enables detecting potential suitable habitats that are likely to be 513
overlooked in predictions based solely on ambient conditions, especially in the lower elevations. 514
Therefore, this approach can be used as a first -cut approach to identify potential priority areas 515
for conservation. Assessing occupancy patterns in areas with low-high suitability will be 516
therefore important for resource allocation , although the large elevational range of observed 517
presence of the northern pika, despite their cold adaptation, already suggests they are inhabiting 518
such counterintuitive areas perhaps through behavioral adaptation. Moreover, this approach has 519
implications for identifying climate change refugia for the northern pika as all three regions 520
were predicted to contain areas supported by rock interstice microclimate in the future despite 521
the deterioration of local-climate conditions. Areas with favorable microclimates that support 522
species persistence under a changing climate (i.e., microrefugia) are often cryptic (Provan & 523
Bennett, 2008), and therefore, extensive identification of such areas based on spatial data should 524
facilitate effective protection of vulnerable populations. In our case, however, the current lack 525
of an extensive dataset reporting presence of rocky landforms in our study area limits such 526
endeavors. Therefore, further refinements in geospatial data are warranted for predicting 527
potential microrefugia. Deeper understanding of the behavioral responses of the northern pika 528
to ambient and rock interstice thermal conditions will also be important to assess the reliability 529
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of behavioral adaptation in driving species distribution patterns (Marske et al., 2023). 530
The importance of f ine-scale SDMs are being increasingly recognized as they often 531
provide distinct predictions from conventional scales and information in fine-scale predictions 532
are essential for improving downstream objectives, such as designing effective conservation 533
plans under climate change (Nadeau et al., 2022) . In this study, the local-climate model 534
prediction proved to be valuable for achieving such objectives as it provided distinct habitat 535
suitability predictions. Additionally, an important implication of fine-scale SDMs is their role 536
in filling the gap between predictions and observations of ongoing species range shifts (Chen 537
et al., 2011). This is because conventional approaches have been criticized for overestimating 538
range shifts due to the lack of consideration for the fine-scale climates that may facilitate species 539
persistence in warmer regions (Pearson, 2006). Therefore, it is important to validate whether 540
fine-scale models effectively reduce d overestimation by conducting ground-truthing surveys. 541
A study by Maclean and Early (2023) exemplifies this, demonstrating that fine-scale predictions 542
reduced the number of species at extinction risk and were in agreement with the actual observed 543
patterns, while coarse-scale predictions estimated several species to become extinct. 544
One of t he limitations of our study is that, despite using the downscaled macroclimate 545
data, we still rely on a simplified representation of time and space to develop the fine-scale 546
models. Rocky landforms exhibit high heterogeneity, with ambient air and rock interstice 547
temperatures varying depending on height and depth, respectively, and changing across seasons 548
(Benedict et al., 2020; Millar et al., 2016; Smith, 2020) . In this regard, our study may still be 549
considered as a coarse-scale representation of reality in time and space. Like other SDM studies, 550
our model relies on the correlative relationships between presences and climatic and 551
topographical predictors. Studies have demonstrated that predicted distributions are altered by 552
incorporating biotic interactions (Bateman et al., 2012), dispersal settings (Zurell et al., 2016), 553
and lineage information (Zhang et al., 2021) into the models. Therefore , further research is 554
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needed to incorporate these aspects into the prediction of the distribution of the northern pika. 555
In conclusion, the incorporation of fine-scale climate data into SDMs yielded contrasting 556
predictions to the coarse -scale prediction . Future distribution s were predicted to decrease 557
increasingly with both further away time horizons and higher emission scenarios considered , 558
stressing the impo rtance of enforcing effective mitigation measures to curve greenhouse gas 559
emissions. Together, this information is essential for the conservation of northern pika s in 560
Hokkaido, as previous studies have not assessed such impacts. Incorporation of rock-interstice 561
microclimate data significantly increased the habitat suitability and predicted more suitable 562
habitats for both the baseline and future. Behavioral adaptation is considered crucial for the 563
inhabitance of the northern pikas at lower elevations, which is important for the conservation 564
of the northern pika because its distribution is often considered to be restricted to the alpine 565
zone. Based on these results, we advocate for the identification of rocky landforms and their 566
integration into conservation planning to effectively leverage microclimates in conservation 567
efforts. 568
569
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Acknowledgements
570
This study was supported by the JSPS KAKENHI Grant Number JP22J10191, grant-in-aid of 571
The Zoshinkai Fund for Protection of Endangered Animals, and grant-in-aid of The Inui 572
Memorial Trust for Research on Animal Science, Japan. 573
DECLARATION OF COMPETING INTEREST 574
The authors have no competing interests to declare. 575
CRediT AUTHORSHIP CONTRIBUTION STATEMENT 576
TS contributed to conceptualization and design o f methodology, data analysis, funding 577
acquisition, and writing the original draft; TS and JGM contributed to discussion of results, 578
writing the final manuscript and gave final approval for publication. 579
DATA AVAILABILITY 580
Data will be made available on request. 581
SUPPLEMENTAL MATERIAL 582
The following materials are available as part of the online article at 583
https://escholarship.org/uc/fb. 584
Appendix S1. Derivation of the bioclimatic variables. 585
Appendix S2. Validation of the bioclimatic variables. 586
Table S1. List of previous literature reporting the northern pika distribution in Hokkaido. 587
Table S2. Procedures for generating the environmental variables. 588
Fig. S1. Geographical map of the presence points used in this study. 589
Fig. S2. A boxplot indicating the elevational difference within macroclimate grid cells. 590
Fig. S3. The modeled relationship between mean ambient and rock interstice temperatures. 591
Fig. S4. Scatterplots used for validating the bioclimatic variables. 592
Fig. S5. Validation plots of the bioclimatic variables used in the study. 593
Fig. S6. Result of the correlation analysis. 594
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Fig. S7. Permutation importance of the model predictors. 595
Fig. S8. Response plots of the model predictors. 596
Fig. S9. Percentage of presence areas predicted to change in the future from the baseline period. 597
Fig. S10. Elevational difference between the macroclimate and local-scale cells at the presence 598
points. 599
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Tables 864
Table 1. Optimized hyperparameters and Continuous Boyce Index values of the best macroclimate and local-climate models. 865
Model Feature class Regularization multiplier Continuous Boyce index Hindcast Continuous Boyce index
Macroclimate LQP 2.0 0.73 0.82
Local-climate LQP 2.0 0.80 0.96
866
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Figures 868
869
870
Figure 1. Schematic diagram describing the different model and prediction settings of the 871
study. First, distribution modeling was conducted at two spatial resolutions: coarse (30 872
arcsecs) and fine (3 arcsecs). We used the macroclimate data in the coarse-scale setting to 873
reflect the conditions often used in traditional SDM studies. In the fine-scale setting, we used 874
the downscaled macroclimate data or the local-climate data, which we considered to represent 875
the local ambient conditions. Second, we predicted the baseline habitat suitability based on 876
these models. At the fine-scale, we further predicted the habitat suitability using the rock-877
interstice microclimate data, which we predicted based on empirical thermal measurements. 878
Third, we conducted a hindcasting analysis to evaluate the original models’ capability of 879
predicting species distribution over time. Fourth, we projected the future distribution based on 880
macroclimate, local-climate, and microclimate, considering four Global circulation models 881
and two emission scenarios. 882
883
Author-formatted, not peer-reviewed document posted on 15/07/2024. DOI: https://doi.org/10.3897/arphapreprints.e131956
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884
Figure 2. Predicted habitat suitability of the whole distribution of the northern pika in 885
Hokkaido, Japan based on (a) macroclimate and (b) local-climate models. In (c), the habitat 886
suitability difference between these two predictions (Local – Macro) is provided. Black points 887
represent presence locations. In (d), the elevation of central Hokkaido is shown in the 888
background. The black border line denotes the model’s calibration extent with blue areas 889
within representing areas that were excluded from the analysis (see Methods for details). 890
891
Author-formatted, not peer-reviewed document posted on 15/07/2024. DOI: https://doi.org/10.3897/arphapreprints.e131956
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892
Figure 3. Proportion of the study extent area predicted as present area along the binarization 893
threshold applied as a moving window at 0.01 increments (see Methods for details) for the (a) 894
baseline and (b) future periods. The lines and shade colors represent model settings (orange = 895
macroclimate, green = local-climate). The future panels are divided by time period (2041–896
2070 and 2071–2100) and emission scenario (SSP1-2.6 and SSP5-8.5), while the filled 897
envelopes represent the range of the future proportions of presence area predicted for the four 898
Global circulation models. 899
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Author-formatted, not peer-reviewed document posted on 15/07/2024. DOI: https://doi.org/10.3897/arphapreprints.e131956
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901
Figure 4. Predicted habitat suitability of the northern pika in (starting from top row) the Biei, 902
Shikaribetsu, and Oketo regions based on (starting from left column) the macroclimate, local-903
climate, and microclimate. Areas with rocky landforms are depicted by black lines in the 904
microclimate panels. The elevation for each region is shown in the last column. 905
906
Author-formatted, not peer-reviewed document posted on 15/07/2024. DOI: https://doi.org/10.3897/arphapreprints.e131956
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907
Figure 5 Predicted future distribution of the northern pika in the Biei, Shikaribetsu, and 908
Oketo regions based on the consensus approach. The 1st and 2nd columns represent predictions 909
for the 2041–2070 and 2071–2100 under the SSP1-2.6 scenario, and the 3rd and 4th those 910
under the SSP5-8.5 scenario. Dark gray areas represent areas suitable for the baseline period 911
that are predicted to become unsuitable in the future, while light gray areas represent areas 912
unsuitable for the baseline period. Areas with rocky landforms are depicted by the black lines. 913
The light blue areas represent suitable habitats supported by the local climate outside rocky 914
landforms. Within rocky landforms, the dark blue areas represent suitable habitats supported 915
by both the local-climate and microclimate, whereas the pink areas represent those supported 916
only by microclimate. 917
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Author-formatted, not peer-reviewed document posted on 15/07/2024. DOI: https://doi.org/10.3897/arphapreprints.e131956
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