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  <front>
    <journal-meta>
<journal-id journal-id-type="publisher">WE</journal-id>
<journal-title-group>
<journal-title>Web Ecology</journal-title>
<abbrev-journal-title abbrev-type="publisher">WE</abbrev-journal-title>
<abbrev-journal-title abbrev-type="nlm-ta">Web Ecol.</abbrev-journal-title>
</journal-title-group>
<issn pub-type="epub">1399-1183</issn>
<publisher><publisher-name>Copernicus Publications</publisher-name>
<publisher-loc>Göttingen, Germany</publisher-loc>
</publisher>
</journal-meta>

    <article-meta>
      <article-id pub-id-type="doi">10.5194/we-16-17-2016</article-id><title-group><article-title>Incorporating natural and human factors in habitat modelling and spatial
prioritisation <?xmltex \hack{\break}?>for the <italic>Lynx lynx martinoi</italic></article-title>
      </title-group><?xmltex \runningtitle{Spatial prioritisation for \textit{Lynx lynx martinoi}}?><?xmltex \runningauthor{K.~Laze and A.~Gordon}?>
      <contrib-group>
        <contrib contrib-type="author" corresp="yes" rid="aff1 aff3">
          <name><surname>Laze</surname><given-names>K.</given-names></name>
          <email>m1.laze@outlook.com</email>
        <ext-link>https://orcid.org/0000-0002-2896-9548</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff2">
          <name><surname>Gordon</surname><given-names>A.</given-names></name>
          
        </contrib>
        <aff id="aff1"><label>1</label><institution>Leibniz Institute of Agriculture Development in Transition
Economies, Theodor-Lieser-Str. 2, <?xmltex \hack{\break}?>06120 Halle (Saale), Germany</institution>
        </aff>
        <aff id="aff2"><label>2</label><institution>School of Global, Urban and Social Studies, RMIT University, P.O. Box
2476, Melbourne 3001, Australia</institution>
        </aff>
        <aff id="aff3"><label>a</label><institution>now at: Polytechnic University of Albania, Faculty of Civil Engineering,
Department of Environmental Engineering, Rr. “M. Gjollesha”, No. 54, 1023
Tirana, Albania</institution>
        </aff>
      </contrib-group>
      <author-notes><corresp id="corr1">K. Laze (m1.laze@outlook.com)</corresp></author-notes><pub-date><day>2</day><month>February</month><year>2016</year></pub-date>
      
      <volume>16</volume>
      <issue>1</issue>
      <fpage>17</fpage><lpage>31</lpage>
      <history>
        <date date-type="received"><day>11</day><month>June</month><year>2015</year></date>
           <date date-type="rev-recd"><day>30</day><month>December</month><year>2015</year></date>
           <date date-type="accepted"><day>11</day><month>January</month><year>2016</year></date>
      </history>
      <permissions>
<license license-type="open-access">
<license-p>This work is licensed under a Creative Commons Attribution 3.0 Unported License. To view a copy of this license, visit <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/3.0/">http://creativecommons.org/licenses/by/3.0/</ext-link></license-p>
</license>
</permissions><self-uri xlink:href="https://we.copernicus.org/articles/16/17/2016/we-16-17-2016.html">This article is available from https://we.copernicus.org/articles/16/17/2016/we-16-17-2016.html</self-uri>
<self-uri xlink:href="https://we.copernicus.org/articles/16/17/2016/we-16-17-2016.pdf">The full text article is available as a PDF file from https://we.copernicus.org/articles/16/17/2016/we-16-17-2016.pdf</self-uri>


      <abstract>
    <p>Countries in south-eastern Europe are cooperating to
conserve a sub-endemic lynx species, <italic>Lynx lynx martinoi</italic>. Yet, the planning
of species conservation should go hand-in-hand with the planning and
management of (new) protected areas. <italic>Lynx lynx martinoi</italic> has a small,
fragmented distribution with a small total population size and an endangered
population. This study combines species distribution modelling with spatial
prioritisation techniques to identify conservation areas for <italic>Lynx lynx martinoi</italic>. The aim was to determine locations of high probability of
occurrence for the lynx, to potentially increase current protected areas by
20 % in Albania, the former Yugoslav Republic of Macedonia, Montenegro,
and Kosovo. The species distribution modelling used generalised linear
models with lynx occurrence and pseudo-absence data. Two models were
developed and fitted using the lynx data: one based on natural factors, and
the second based on factors associated with human disturbance. The
Zonation conservation planning software was then used to undertake spatial
prioritisations of the landscape using the first model composed of natural
factors as a biological feature, and (inverted) a second model composed of
anthropological factors such as a cost layer. The first model included
environmental factors as elevation, terrain ruggedness index, woodland and
shrub land, and food factor as chamois prey (occurrences) and had a
prediction accuracy of 82 %. Second model included anthropological
factors as agricultural land and had a prediction accuracy of 65 %.
Prioritised areas for extending protected areas for lynx conservation were
found primarily in the Albania–Macedonia–Kosovo and Montenegro–Albania–Kosovo
cross-border areas. We show how natural and human factors can be
incorporated into spatially prioritising conservation areas on a landscape
level. Our results show the importance of expanding the existing protected
areas in cross-border areas of core lynx habitat. The priority of these
cross-border areas highlight the importance international cooperation can
play in designing and implementing a coherent and long-term conservation
plan including a species conservation plan to securing the future of the
lynx.</p>
  </abstract>
    </article-meta>
  </front>
<body>
      

<sec id="Ch1.S1" sec-type="intro">
  <title>Introduction</title>
      <p>Many large carnivore species have declining population levels, and are listed
as endangered in the countries they inhabit (Wiegand et al., 1998;
Fernández et al., 2003; Kramer-Schadt et al., 2005). A prime example is
<italic>Lynx lynx martinoi</italic> that is one of nine subspecies (namely
<italic>Lynx, carpathicus, martinoi, dinniki, isabellinus, wardi, kozlovi, wrangeli, stroganovi</italic>) distributed in Europe, central Asia, and Russia
(Arx et al., 2004). In 2005, <italic>Lynx lynx martinoi</italic>
was shown to be a sub-species of the Eurasian lynx (<italic>Lynx lynx</italic>) using
genetic analysis (Breitenmoser-Würsten and Breitenmoser, 2001).
The <italic>Lynx lynx martinoi</italic> once populated a large area stretching from
Slovenia, Serbia and Croatia to Albania, the former Yugoslav Republic of
Macedonia, Montenegro, and Kosovo (Bojovič, 1978; Mirič, 1978; Large
Carnivore Initiative for Europe, 1997, 2004; Breitenmoser et al., 2008).
Today, the Balkan Lynx Recovery Program is contributing by collecting records
of the occurrences of individuals and populations of <italic>Lynx lynx martinoi</italic> in Albania, the former Yugoslav Republic of Macedonia, Kosovo, and
Montenegro (IUCN/SSC Cat Specialist Group, 2011; Balkan Lynx
Recovery Programme, 2015). The Balkan Lynx Recovery Programme has done work
analysing the distribution of the lynx population, the human factors
impacting its distribution and drawing and implementing strategies on the
conservation of the lynx (Balkan Lynx Strategy Group, 2008).
Explanatory factors impacting the spatial distribution of the <italic>Lynx lynx martinoi</italic>, and the prioritisation of areas in the landscape for the
conservation are less known and studied than other sub-species. The latest
population estimates is below 50 mature individuals, resulting in the
<italic>Lynx lynx martinoi</italic> being listed as critically endangered on the IUCN
Red List of Threatened Species on 19 November 2015 (IUCN, 2015).</p>
      <p>The <italic>Lynx lynx martinoi </italic>(henceforth referred to as “the lynx”)
occupies deciduous forests containing tree species of <italic>Fagus sylvatica</italic>, <italic>Quercus spp</italic>., <italic>Carpinus betulus</italic>, <italic>Ostrya carpinifolia</italic>, <italic>Fraxinus ornus. </italic>The lynx occupies coniferous
forests of <italic>Pinus spp.</italic>, of <italic>Abies spp.</italic>, as well as mixed forests of
fir and beech. It prefers elevated areas and uses mountain pastures for
hunting in summer. Preliminary results obtained from a study of
radio-telemetry in the Former Yugoslav Republic (FYR) of Macedonia revealed
that the lynx diet comprised of chamois (<italic>Rupicapra rupicapra</italic>;
24 %), European brown hare (<italic>Lepus europaeus</italic>; 12 %) and roe
deer (<italic>Capreolus capreolus</italic>; 64 %) (IUCN/SSC Cat
Specialist Group, 2012).</p>
      <p>Today, the most important threats to the lynx are a small population (less
than 50 individuals, increasing the risk of extinction from demographic
stochasticity), a limited prey base (caused by illegal hunting in Albania),
degradation of habitat (particularly in Albania and Kosovo), poaching
activities by humans and the isolation of smaller populations in a
fragmented landscape (IUCN/SSC Cat Specialist Group, 2012).</p>
      <p>The viability of a species in the landscape is fundamentally linked with
identification and delineation of its habitat. This is important for
determining both the distribution and abundance of the species as well as
for prioritising conservation activities targeting the species
(Boyce et al., 2016). Species distribution
models (SDMs)
are widely used to identify where habitat for a species is likely to occur and
to determine the core areas important for the conservation of species
(Zielinski et al., 2006). The advantage of SDMs is that based on a
given number of species records, the model can then make predictions on
large scales as to where the habitat for a species is likely to occur. SDMs
are increasingly using larger and more complex data sets of species due to
greater amounts of data being collected (e.g. radio telemetry), the
increased availability of environmental data from remote sensing and of
powerful techniques like generalised linear models and geographical
information system (GIS) to quantify species–environment relationships
(Johnson et al., 2004). Today, SDMs are the main tools
used to produce spatially explicit predictions regarding the relationships
between a species and its environment (Elith and Leathwick,
2009) at different spatial scales ranging from the local scale
(e.g. Johnson et al., 2004) to the global scale
(e.g. Thuiller et al., 2005). SDMs for one or more
species are now commonly used as inputs for spatial conservation
prioritisation, often focused on determining where new conservation areas
should occur in the landscape (Moilanen et al., 2006) using the software
of Zonation (Moilanen et al., 2012). Zonation software is an
approach to reduce uncertainties of SDM results (Guisan et al., 2013) that may potentially be used by
nature conservation decision making. SDM applications to support nature
conservation decision making is still needed, although critical habitat and
reserve selection are two of conservation domains where SDMs can be
increasingly valuable (see Guisan et al., 2013).</p>
      <p>Species present in existing protected areas are more likely to have viable
populations if the areas surrounding them are protected
(see, e.g. Fischer et al., 2006). Today, the
conservation efforts of the lynx are focused on collecting data for existing
population of the species, and on increasing the awareness of local human
populations (Ivanov et al., 2008) of the existence of the species
(Balkan Lynx Strategy Group, 2008). In addition, efforts have focused
on gathering data on species reproduction occurrences and on identifying
habitat for the species (e.g. in Montenegro, Balkan Lynx Recovery
Programme, 2015). Yet to our knowledge, there are no studies on the following: habitat
selection using a resource selection function (Boyce et al., 2016), developing a SDM, on animal behaviour and animal movement
(Patterson et al., 2008), or on conservation
prioritisation (Moilanen et al., 2006) for the lynx. A species
distribution modelling and conservation prioritisation approach can help
first identify the entire area of predicted habitat for the lynx to support
future data collection for the species and to identify core conservation
areas for the species that should be protected and priority areas for
managing given existing protected areas. We provided the first large-scale
SDM for the lynx to estimate the probability of occurrence of the species
throughout its range. The study area covered the full range of the current
habitat of the lynx in south-eastern Europe. We applied species distribution
modelling to understand how the lynx used natural resources (forests,
prey). Species distribution modelling was combined with a spatial
prioritisation approach to address questions such as the most effective
places to extend existing conservation areas (Moilanen et al., 2009) for the lynx.</p>
      <p>We aimed to develop SDM as a “model 1” composed of natural factors and “model 2” composed of anthropological factors: (1) to identify the areas of
estimated probability of occurrence for the lynx and natural factors that
explained the occurrence (records) of the lynx; (2) to understand the
impact of anthropogenic land-use activities on the lynx distribution. The
third aim was to identify priority areas for lynx conservation and to
determine the locations for the expansion of existing protected areas in the
study area.</p>
      <p>Finally, we used the lynx model 1 (selected from species distribution
modelling) derived from natural factors as a biological feature layer and
the lynx model 2 (selected from species distribution modelling) derived
from anthropogenic land-use activities as cost layer, respectively, in
Zonation conservation planning software (Moilanen et al., 2012).</p>
</sec>
<sec id="Ch1.S2">
  <title>Materials and methods</title>
<sec id="Ch1.S2.SS1">
  <title>Occurrence records of lynx and lynx prey</title>
      <p>Lynx data were collected by two domestic non-governmental organisations
(Sect. S0 in the Supplement) using a 50-question face-to-face interview with
key informants (i.e. hunters, game wardens, foresters, shepherds, livestock
breeders, beekeepers, cafeteria or market owners) in randomly selected
villages in the northern and eastern Albania (91 villages) and western the
FYR of Macedonia (154 villages) (Sect. S0) (Ivanov et al., 2008).
At least two people were randomly selected to be interviewed in each village
by Ivanov et al. (2008). A grid cell of 10 km <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10 km for
Albania and the FYR of Macedonia (henceforth “Macedonia”) was used based
on the lynx population and lynx population density in 2001 of the
publication of Arx et al. (2004) (Ivanov et al., 2008). The population density of the lynx was estimated to be between 0.65
and 1.09 in Albania and 2.06 in Macedonia in 2001 (see Sect. S0). The
spatial coverage of this survey was approximately 13 600 km<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:math></inline-formula> (i.e. 63
grid cells in Albania and 73 grid cells in Macedonia, Ivanov et al., 2008). The occurrence of the lynx and lynx prey (chamois, brown hare, roe
deer) was based on the “relative number of positive answers” of
interviewees on the species occurrences (Sect. <xref ref-type="disp-formula" rid="Ch1.E1"/> of the questionnaire
was on presence and distribution of large mammal species in the last 5 years; Sect. S0), in a 10 km <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10 km grid cell. A probable
occurrence (permanent occurrences in this study) was selected if there were
more than 50 % affirmative answers (to questions, e.g. on hard facts
like lynx tracks, stuffed lynx, prepared lynx pelts, lynx attacks on humans,
lynx attacks on domestic animals, more than one lynx or female with cubs
observed) of interviewees on the species occurrence in a grid cell of 10 km <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10 km (Ivanov et al., 2008). A possible occurrence
(temporal occurrences in this study) resulted if there were less than 50 % of affirmative answers of interviewees on the species occurrence in
a grid cell of 10 km <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10 km and no species occurrence if there were
no affirmative answers (i.e. on hard facts like lynx tracks, stuffed lynx,
prepared lynx pelts, lynx attacks on humans, lynx attacks on domestic
animals, more than one lynx or female with cubs observed) of the
interviewees on the species occurrences in a grid cell of 10 km <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10 km (Ivanov et al., 2008). See Sect. S0, for detailed information
on lynx data collected between 2006 and 2007, as well as for data on lynx distribution and lynx
data in 2001.</p>
      <p>The Balkan Lynx Recovery Programme collected the lynx prey occurrence records
consisting of species of brown hare, chamois and roe deer (Ivanov et
al., 2008). Roe deer occurrences were located mostly in the same grid cell of
10 km <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10 km of the lynx occurrences (Ivanov et al., 2008).
Brown hare and chamois had the widest and the smallest distribution,
respectively. Chamois and brown hare records were used in this study to
investigate any spatial effects of the smallest distribution of chamois and
the widest distribution of brown hare in the occurrence (records) of the
lynx in terms of neighbourhood scale of the best-performing model 1 (see
Model selection for the lynx). In total, 87 % of records of chamois
and 89 % of records of brown hare were located from approximately 2 to
23 km from the closest lynx occurrences. For more information on lynx prey
occurrence data collected between 2006 and 2007, see Sect. S0.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F1" specific-use="star"><caption><p>Locations of 109 lynx occurrence records in the study
area. Data were collected by the Balkan Lynx Recovery Programme.</p></caption>
          <?xmltex \igopts{width=398.338583pt}?><graphic xlink:href="https://we.copernicus.org/articles/16/17/2016/we-16-17-2016-f01.png"/>

        </fig>

      <p>We used 109 (39 permanent and 70 temporal) lynx occurrence records, 114
chamois occurrence records, 135 occurrence brown hare records in protected
areas and public-owned land, in our study area. The lynx occurrence records (109)
consisted of 37 lynx permanent occurrences records (25 in Macedonia
and 12 in Albania) and 72 lynx temporal occurrences records (36 in
Macedonia, 26 in Albania, 6 in Montenegro, and 4 in Kosovo). We
geo-referenced lynx occurrence records from for the lynx in Kosovo and
Montenegro from the maps of Arx et al. (2004), and lynx
occurrence records from 2006 to 2007 in Albania and Macedonia from the maps
of Ivanov et al. (2008) (Fig. 1). We also geo-referenced occurrence
records of species of lynx prey of a resolution 10 km <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10 km for
Albania and Macedonia from the maps of Ivanov et al. (2008), the
Balkan Lynx compendium (IUCN/SSC Cat Specialist Group, 2011). We
then obtained the coordinates of <inline-formula><mml:math display="inline"><mml:mi>X</mml:mi></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mi>Y</mml:mi></mml:math></inline-formula> of the lynx occurrences and of the
species of lynx prey (chamois and brown hare). We assigned a location for each
species (lynx, chamois, brown hare) within a 1 km <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 1 km grid cell
study unit by spatially joining the layer of the species occurrence record
and of the grid 1 km <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 1 km using Spatial Join of the Analysis Tool
in ArcGIS transferring the attribute of species occurrence record (<inline-formula><mml:math display="inline"><mml:mi>X</mml:mi></mml:math></inline-formula>, <inline-formula><mml:math display="inline"><mml:mi>Y</mml:mi></mml:math></inline-formula>) to
the 1 km <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 1 km grid (for each species i.e. lynx, chamois, brown
hare).</p>
      <p>We argue that the lynx may be anywhere in a 10  <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10 km cell; however, the
lynx is also thought to perceive forests up to 1 km apart as connected
(Kramer-Schadt et al., 2005). Thus we chose to undertake the study using
a spatial resolution of 1 km<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:math></inline-formula>.</p>
      <p>We used pseudo-absences to use our species distribution models. We selected
pseudo-absences following three criterion concerning the total number of
pseudo-absences, the number of locations of pseudo-absences from a given
cell of 1 km<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:math></inline-formula>, and the location of pseudo-absences in forest areas
(Sect. S1 in the Supplement).</p>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T1" specific-use="star"><caption><p>Hypothesis based on the literature for lynx</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="3">
     <oasis:colspec colnum="1" colname="col1" align="justify" colwidth="51.214961pt"/>
     <oasis:colspec colnum="2" colname="col2" align="justify" colwidth="170.716535pt"/>
     <oasis:colspec colnum="3" colname="col3" align="justify" colwidth="113.811024pt"/>
     <oasis:thead>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1">Model<?xmltex \hack{\hfill\break}?>hypothesis</oasis:entry>  
         <oasis:entry colname="col2">Description</oasis:entry>  
         <oasis:entry colname="col3">Reference</oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>  
         <oasis:entry colname="col1">Natural<?xmltex \hack{\hfill\break}?>environment</oasis:entry>  
         <oasis:entry colname="col2">The lynx need forests and land that provide suitable habitats for refuge, breed and food. The lynx needs elevated topography, stable, undisturbed, and well-connected forests to search for food, to breed refuge. The lynx uses sunny rocky areas as a refuge and hunts in meadows and highland pastures.</oasis:entry>  
         <oasis:entry colname="col3">Balkan Lynx Strategy Group, 2008; IUCN/SSC Cat Specialist Group, 2012</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Human<?xmltex \hack{\hfill\break}?>disturbance</oasis:entry>  
         <oasis:entry colname="col2">The lynx prefers to stay away from roads, urban areas, highly disturbed forested land (e.g. from logging) because of lower quality of habitat.</oasis:entry>  
         <oasis:entry colname="col3">Kramer-Schadt et al., 2005;<?xmltex \hack{\hfill\break}?>IUCN/SSC Cat Specialist<?xmltex \hack{\hfill\break}?>Group, 2012</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table></table-wrap>

</sec>
<sec id="Ch1.S2.SS2">
  <title>Model selection for the lynx</title>
      <p>We developed species distribution models based on the permanent occurrences
data. The models were based on information-theoretic methods, which focus on
the search for a parsimonious model as the primary philosophy of statistical
inference (Burnham and Anderson, 2002; Johnson and Omland, 2004). We
identified a set of a priori hypotheses on the estimated probability of the lynx
occurrence that describe the natural conditions and resources required for
refuge, food and breeding of the lynx based on knowledge on ecology and
biology that exists for the Balkan lynx and Eurasian lynx <?xmltex \hack{\mbox\bgroup}?>(Table 1)<?xmltex \hack{\egroup}?>. We
split the variables for species distribution modelling into two categories,
namely “natural” and “human”, e.g. a “two dimensional” habitat model that
was developed for the brown bear in Spain (see Naves et al., 2003). The
“natural” hypothesis has environmental variables that are related with food
abundance of the lynx and forest connectivity. The “human disturbance”
hypothesis assumed that human activities (e.g. land-use activities and
roads) affect (lynx) mortality (Naves et al., 2003). Natural factors
consisted of layers such as forest cover, elevation and the terrain
ruggedness index (derived from slope of terrain), coniferous forests,
broadleaved forests mixed forests, pastures, bare rocks and transitional
shrub land-woodland composing model 1. The human variables comprised layers
such as agricultural land, urban land, burnt land, Euclidean distance to
road (i.e. proximity to roads), Euclidean distance to human settlements,
and village density composing model 2 (see Sect. S2 for details). The
layers depicting land cover, forest cover, roads and villages were
transformed into a set of neighbourhood variables (calculating the mean
value of the original variable within a specified neighbourhood radius
around the target cell) from 1 to 15 grid cells (corresponding to a radii of
1, 2, 3, 4, 5, 10, 15 km) and resulted in a total of 84
neighbourhood variables for potential use in the lynx models. The
neighbourhood variables helped obtain information about the scale at which
the lynx perceived the landscape and at which (natural) resources needed to
be available. For details on neighbourhood variables see Sect. S3. The
range of neighbourhood values (i.e. 1, 2, 3, 4, 5, 10, 15 km)
corresponded roughly to the known variation in home-range size of the
lynx (Bojovič, 1978; Balkan Lynx Strategy Group, 2008). We
removed all variables that were highly correlated (Pearson correlation test;
<inline-formula><mml:math display="inline"><mml:mi>r</mml:mi></mml:math></inline-formula> &gt; 0.7) and variables that did not show statistically significant
differences between occurrence and pseudo-absence locations of the lynx
(Kruskal–Wallis test; <inline-formula><mml:math display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula> &gt; 0.05) (Sect. S4). We calculated the
spatial autocorrelation of the dependent variable and for further details on
spatial autocorrelation see Sect. S5.</p>
</sec>
<sec id="Ch1.S2.SS3">
  <title>Model fitting</title>
      <p>We used generalised linear models (GLM) with logit-link to relate occurrence
and pseudo-absence data to sets of explanatory variables to predict the
probability of occurrence of the lynx in the study area. GLMs are an
extension of classic linear regression models (McCullagh and Nelder,
1989). We used binomial error structure (logistic regression) to account for
the lynx data structure. A logistic regression model predicts the
probability of the occurrence of the lynx (e.g. for food and or refuge) at
a given location within the study area. An estimated high probability of
occurrence of the lynx would indicate suitable habitat of the lynx (suitable
habitat is above the threshold value of the probability of occurrence of the
lynx that is estimated by the species distribution modelling; see Model
selection for the lynx and Model evaluation). All GLM (and resource
selection probability function (RSPF) models that calculate species habitat
selection are shown in Model evaluation) were fitted within the program R
2.9.0 (R Development Core Team, 2009).</p>
      <p>In total, we fitted 11 GLM candidate models for the lynx comprising the two
categories of variables (candidate models are in Sect. S6 and the results
of best models are in Sects. S7, S8). We selected the most parsimonious
model from 11 candidate models using the corrected Akaike information
criterion (AICc) for small samples (Johnson and Omland, 2004). The
uncertainty was assessed using AIC weights (e.g. Fernández et
al., 2006). AIC weights represented the relative likelihood of a model. AIC
weights was taken as the approximate probability that each model is the best
model out of the set of all proposed models (Anderson et al., 2000). We also
calculated the difference of corrected Akaike information
criterion <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">Δ</mml:mi></mml:math></inline-formula>AICc between competing candidate models (in Sect. S7).
We mapped out predictions of probability of lynx occurrences for the most
parsimonious model to identify the high probability values of lynx
occurrences (most suitable habitat) and the low probability values of lynx
occurrences (marginal and non-suitable habitat). We calculated the average
value of estimated probability values of the lynx occurrences from 0.50 (e.g. Naves et al., 2003) to 1.00 to select a threshold
(e.g. Liu et al., 2005). An estimated probability
value above the threshold value, e.g. of 0.5 would be a suitable habitat.
Marginal habitat and non-suitable habitats had values below or equal to this
threshold value, e.g. of 0.5 for the lynx. The layers of model 1 and of
model 2 were used as the biodiversity layer and cost layer, respectively, in
Zonation to identify conservation areas for the lynx.</p>
</sec>
<sec id="Ch1.S2.SS4">
  <title>Model evaluation</title>
      <p>We evaluated our models using three methods. First, all models were
evaluated by calculating the area under the receiver operating
characteristic curve (AUC). The value of AUC is from 0 to 1. A model with a value of AUC <inline-formula><mml:math display="inline"><mml:mo>≥</mml:mo></mml:math></inline-formula> 70 % performs well and a model with a high
value of AUC <inline-formula><mml:math display="inline"><mml:mo>≥</mml:mo></mml:math></inline-formula> 90 % indicates outstanding discrimination between
estimated high probability values of lynx occurrences (occurrences) and
estimated low probability values of lynx occurrences (pseudo-absences in
this study) (Hosmer and Lemeshow, 2000). We also calculated the
predictive accuracy of the most parsimonious (from all candidate models)
model using the deviance explained in percentage (<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi>D</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow></mml:math></inline-formula>). We
used cross-validation for logistic regression with a binary dependent
variable because we had only one data set to check if there was over-fitting
in the fitted models (e.g. Fernández et al., 2003;
Kanagaraj et al., 2011). Our data set was divided into 10 parts (folds) where
nine folds were used for fitting the model and the tenth fold was used for
testing the model. This was repeated 10 times so that each fold was used for
model testing. We considered the value of predicted probability (i.e.
“cross-validation estimate of accuracy”) which was calculated as an
average value of probability after testing the model 10 times. A predicted
probability value is from 0 to 1 (for details see DAAG package in R
Development Core Team, 2009). Second, we calculated the resource selection
probability function (RSPF) (Johnson et al., 2004; Lele et al., 2013;
Thurfjell et al., 2014) for 11 (GLM) candidate models. RSPF shows the
probability that an available natural resource unit, e.g. chamois prey,
is selected (Thurfjell et al., 2014) by the lynx when encountered.
We assessed the model fit (logistic regression with 39 permanent occurrences
and 39 pseudo-absences) for 11 RSPF candidate models using Hosmer–Lemeshow
test for goodness of fit by calculating the log-likelihood, the Bayesian
information criteria (BIC), and the chi-squared test statistic (<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi mathvariant="italic">χ</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> (Hosmer and Lemeshow, 2000). We calculated the <inline-formula><mml:math display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula> value for
11 RSPF candidate models to assess the statistical significance of 11 RSPF
candidate models (see, e.g. Johnson et al., 2004). We
ran the best RSPF model (out of 11 RSPF candidate models) with 10 permanent
occurrences and 10 randomly selected pseudo-absences i.e. we removed (at random) 25 % of 39 permanent occurrences of the lynx. We calculated the
Spearman correlation coefficient between the best RSPF model with 10
permanent occurrences and 10 randomly selected pseudo-absences and the best
RSPF model with 39 permanent occurrences and 39 randomly selected
pseudo-absences (i.e. no permanent occurrences removed). We removed
(at random) 51 % of 39 permanent occurrences and of 39 pseudo-absences of
the lynx. We ran the best RSPF model with 20 permanent occurrences and 20
randomly selected pseudo-absences of the lynx. The Spearman correlation
coefficient was then calculated between this RSPF model with 20 permanent
occurrences and 20 randomly selected pseudo-absences of the lynx and the
best RSPF model with 39 permanent occurrences and 39 randomly selected
pseudo-absences of the lynx. A high value of Spearman correlation
coefficient shows a strong prediction by the best RSPF candidate model (e.g. Johnson et al., 2004).</p>
      <p>We then applied the best RSPF model in the Step-Selection Function (SSF)
using Geospatial Modelling Environment (GME) (<uri>www.spatialecology.com/gme/</uri>).
The SSF is normally used with telemetry data of species involving randomly
walking of animal (see, e.g. Proulx et al., 2013). The SSF
links consecutive 39 lynx locations that are called (used) steps
(Thurfjell et al., 2014). We made three assumptions for the SSF.
Firstly, we assumed that our lynx data were as accurate as the telemetry data of
species for our data modelling (e.g. Johnson et al., 2008). Secondly, we assumed no seasonal variation for collected lynx data in
year 2006. We expected five “available” random steps for each of the lynx's
steps used (e.g. <italic>lynx canadensis</italic> in Thurfjell et al., 2014). For each used
and random steps, we calculated the step length and turning angles using
non-linear functions (for details, see Beyer, 2015). Thirdly, we
assumed an exponential function to calculate the lynx step length with a
different single rate parameter and we assumed wrapped Cauchy function
(see Beyer, 2015) to calculate lynx turning angles. We simulated
our SSF model 30 times. We calculated the number of lynx steps
predicted by each SSF model simulation. We then overlapped the predicted
lynx steps by each SSF model simulation with predicted probability of
occurrence of the lynx (above the threshold of estimated probability of
occurrence of the lynx; see Model fitting) by our best GLM model. We
selected the SSF model simulation with the highest number of lynx steps overlapped with predicted probability of occurrence of the lynx (above
the threshold of the estimated probability of occurrence of the lynx) to
calculate the mean of step length of the lynx. We compared the step length
mean (in km) of the selected SSF model simulation with the range (radius in
km) of neighbourhood variables of our best GLM models. We also overlapped
the predicted lynx steps by the selected SSF model simulation with
the prioritised conservation areas of 10 and 20 % by Zonation.
Third, we randomly removed 1, 2, 4, 8, and 16 permanent occurrences and
replaced the same number of removed permanent occurrences (1, 2, 4, 8, and
16) with randomly selected locations (no presence) from 136 cells of 10 km <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10 km
of the lynx survey of Ivanov et al. (2008) and we ran the best
GLM model. We did the same for combined permanent and temporal lynx
occurrences (see Sect. S9 in the Supplement).</p>
      <p>Finally, we collected information on evidence for lynx presence (photos) in
the study area. We used Google Earth, ArcGIS and information about the
locations evidence of lynx presence gathered in the study area to overlap
with the predicted probability of occurrence of the lynx (see Evaluation of
GLM models). This information was collected in National Park Rugova in 2015,
western Kosovo, in Munella Mountain in 2014, in Thethi National Park, and in
Thira in 2015, northern Albania, in Pelister National Park in 2013, and in
Mavrovo National Park in 2015, Macedonia (Balkan Lynx Recovery
Programme, 2014). In Albania, all lynx photos in 2014 were taken by
camera traps that were placed from 1 to 2 km from each other covering an
area of 400 km<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:math></inline-formula> (Balkan Lynx Recovery Programme, 2014).</p>
</sec>
<sec id="Ch1.S2.SS5">
  <title>Prioritisation of landscape for lynx conservation</title>
      <p>The conservation planning software package “Zonation” (Moilanen et al., 2012) was used to identify well-connected
habitat in the landscape suitable for lynx conservation (see Sect. S10
for the Zonation configuration settings used). Although Zonation is designed
for prioritising areas with multiple species, it is also appropriate to use
with a single species. Here, we utilise features of Zonation which allow us
explore locations for extending existing conservation areas while accounting
for connectivity (of the lynx habitat). The main output of Zonation is a
landscape prioritisation in the form of a raster map where each raster cell
is ranked in terms of its importance in providing lynx habitat. Thus,
Zonation can be used to identify locations in the landscape that should be
protected to ensure the conservation of the lynx. Using Zonation we examined
the extent to which existing protected areas in the four countries
overlapped the most important areas for lynx conservation as predicted by
Zonation. We then undertook a separate Zonation analysis to examine how
these protected areas should be expanded to maximise conservation benefits
to the lynx.</p>
      <p>We used the species distribution model derived from natural factors as the
primary input for Zonation. The core-area variant of the Zonation algorithm
was used (Moilanen et al., 2005), which minimizes biological loss by
iteratively picking a cell <inline-formula><mml:math display="inline"><mml:mi>i</mml:mi></mml:math></inline-formula>, for removal that has the smallest biological
loss, <inline-formula><mml:math display="inline"><mml:mi mathvariant="italic">δ</mml:mi></mml:math></inline-formula> until all cells have been removed. For a single species, the
biological loss is determined by
            <disp-formula id="Ch1.E1" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi mathvariant="italic">δ</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:msub><mml:mi>Q</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mfenced open="(" close=")"><mml:mi>S</mml:mi></mml:mfenced></mml:mrow><mml:mrow><mml:msub><mml:mi>c</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>.</mml:mo></mml:mrow></mml:math></disp-formula>
          The function <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>Q</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>(</mml:mo><mml:mi>S</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> identifies the proportion of the remaining
distribution of lynx habitat located in cell <inline-formula><mml:math display="inline"><mml:mi>i</mml:mi></mml:math></inline-formula>, out of in the remaining cells
to be prioritised, <inline-formula><mml:math display="inline"><mml:mi>S</mml:mi></mml:math></inline-formula>. When a part of the distribution of the species is
removed by Zonation, the proportion located in each remaining cell is
raised, which results in Zonation attempting to maintain core areas of lynx
habitat until the process of cell removal was finished. <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is the cost
associated cell <inline-formula><mml:math display="inline"><mml:mi>i</mml:mi></mml:math></inline-formula> (Moilanen, 2007). We used the species distribution model derived from human factors to generate the cost layer. This was chosen as
all the factors in this model were thought to be detrimental to the lynx,
and we inverted the layer so that areas with low values of the estimated
probability of the lynx occurrence (marginal and non-suitable habitat; see
Model selection for the lynx and Model evaluation) had a high cost, and areas
with high values of estimated probability of the lynx occurrence (suitable
habitat) had a low cost of lynx conservation. (This means that suitable
habitats are less expensive to maintain, manage, and conserve the lynx
habitat located in natural and semi-natural forests compared to non-suitable
habitats located in agricultural areas for the lynx. We assume the land
conversion from non-preferred agricultural land to preferred forested land
would be associated with a high cost for the conservation of the lynx).</p>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T2" specific-use="star"><caption><p>The summary of the GLM models of estimated probability of
lynx occurrences used for the Zonation analysis and the model selection
estimators. Model 1 composed of natural factors was used as the habitat
layer in the Zonation analysis the output of model 2 composed of
anthropological factors was inverted and used as the cost layer in Zonation.
Neighbourhood area is the scale; AICc <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> corrected Akaike's information
criterion; Akaike <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>w</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> Akaike weight; <inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi>D</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> deviance
explained; CV <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> cross validation; AUC <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> area under curve <inline-formula><mml:math display="inline"><mml:mi>i</mml:mi></mml:math></inline-formula>. For each
model the coefficients and their sign is shown along with their standard
errors and statistically significance.</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="11">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="left"/>
     <oasis:colspec colnum="3" colname="col3" align="left"/>
     <oasis:colspec colnum="4" colname="col4" align="left"/>
     <oasis:colspec colnum="5" colname="col5" align="left"/>
     <oasis:colspec colnum="6" colname="col6" align="left"/>
     <oasis:colspec colnum="7" colname="col7" align="left"/>
     <oasis:colspec colnum="8" colname="col8" align="left"/>
     <oasis:colspec colnum="9" colname="col9" align="left"/>
     <oasis:colspec colnum="10" colname="col10" align="left"/>
     <oasis:colspec colnum="11" colname="col11" align="left"/>
     <oasis:thead>
       <oasis:row>  
         <oasis:entry colname="col1">Model</oasis:entry>  
         <oasis:entry colname="col2">Neighbourhood</oasis:entry>  
         <oasis:entry colname="col3">AUC</oasis:entry>  
         <oasis:entry colname="col4"><inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi>D</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col5">CV</oasis:entry>  
         <oasis:entry colname="col6">AIC <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>w</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col7">AICc</oasis:entry>  
         <oasis:entry colname="col8">Variables</oasis:entry>  
         <oasis:entry colname="col9">Coefficients</oasis:entry>  
         <oasis:entry colname="col10">Standard errors</oasis:entry>  
         <oasis:entry colname="col11"><inline-formula><mml:math display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula> value</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2">area (km<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:math></inline-formula>)</oasis:entry>  
         <oasis:entry colname="col3">(%)</oasis:entry>  
         <oasis:entry colname="col4">(%)</oasis:entry>  
         <oasis:entry colname="col5">(%)</oasis:entry>  
         <oasis:entry colname="col6">(%)</oasis:entry>  
         <oasis:entry colname="col7"/>  
         <oasis:entry colname="col8"/>  
         <oasis:entry colname="col9">of coefficients</oasis:entry>  
         <oasis:entry colname="col10"/>  
         <oasis:entry colname="col11"/>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2"/>  
         <oasis:entry colname="col3"/>  
         <oasis:entry colname="col4"/>  
         <oasis:entry colname="col5"/>  
         <oasis:entry colname="col6"/>  
         <oasis:entry colname="col7"/>  
         <oasis:entry colname="col8">ELEV</oasis:entry>  
         <oasis:entry colname="col9"><inline-formula><mml:math display="inline"><mml:mrow><mml:mo>+</mml:mo><mml:mn>0.0018</mml:mn></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col10">0.0006</oasis:entry>  
         <oasis:entry colname="col11">0.006</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2"/>  
         <oasis:entry colname="col3"/>  
         <oasis:entry colname="col4"/>  
         <oasis:entry colname="col5"/>  
         <oasis:entry colname="col6"/>  
         <oasis:entry colname="col7"/>  
         <oasis:entry colname="col8">TRIR</oasis:entry>  
         <oasis:entry colname="col9"><inline-formula><mml:math display="inline"><mml:mrow><mml:mo>+</mml:mo><mml:mn>0.007</mml:mn></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col10">0.044</oasis:entry>  
         <oasis:entry colname="col11">0.866</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Model 1</oasis:entry>  
         <oasis:entry colname="col2">50.2</oasis:entry>  
         <oasis:entry colname="col3">82.6</oasis:entry>  
         <oasis:entry colname="col4">16.76</oasis:entry>  
         <oasis:entry colname="col5">71.8</oasis:entry>  
         <oasis:entry colname="col6">50</oasis:entry>  
         <oasis:entry colname="col7">88.5</oasis:entry>  
         <oasis:entry colname="col8">CHP</oasis:entry>  
         <oasis:entry colname="col9"><inline-formula><mml:math display="inline"><mml:mrow><mml:mo>+</mml:mo><mml:mn>2.293</mml:mn></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col10">1.620</oasis:entry>  
         <oasis:entry colname="col11">0.156</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2"/>  
         <oasis:entry colname="col3"/>  
         <oasis:entry colname="col4"/>  
         <oasis:entry colname="col5"/>  
         <oasis:entry colname="col6"/>  
         <oasis:entry colname="col7"/>  
         <oasis:entry colname="col8">TRANP</oasis:entry>  
         <oasis:entry colname="col9"><inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>935.9</oasis:entry>  
         <oasis:entry colname="col10">356.1</oasis:entry>  
         <oasis:entry colname="col11">0.008</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2"/>  
         <oasis:entry colname="col3"/>  
         <oasis:entry colname="col4"/>  
         <oasis:entry colname="col5"/>  
         <oasis:entry colname="col6"/>  
         <oasis:entry colname="col7"/>  
         <oasis:entry colname="col8">Intercept</oasis:entry>  
         <oasis:entry colname="col9"><inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>1.383</oasis:entry>  
         <oasis:entry colname="col10">1.256</oasis:entry>  
         <oasis:entry colname="col11">0.271</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Model 2</oasis:entry>  
         <oasis:entry colname="col2">314</oasis:entry>  
         <oasis:entry colname="col3">65.2</oasis:entry>  
         <oasis:entry colname="col4"><inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.27</oasis:entry>  
         <oasis:entry colname="col5">59</oasis:entry>  
         <oasis:entry colname="col6">&lt; 0.01</oasis:entry>  
         <oasis:entry colname="col7">104.6</oasis:entry>  
         <oasis:entry colname="col8">AGLRP</oasis:entry>  
         <oasis:entry colname="col9"><inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>832.5</oasis:entry>  
         <oasis:entry colname="col10">336.8</oasis:entry>  
         <oasis:entry colname="col11">0.014</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2"/>  
         <oasis:entry colname="col3"/>  
         <oasis:entry colname="col4"/>  
         <oasis:entry colname="col5"/>  
         <oasis:entry colname="col6"/>  
         <oasis:entry colname="col7"/>  
         <oasis:entry colname="col8">Intercept</oasis:entry>  
         <oasis:entry colname="col9"><inline-formula><mml:math display="inline"><mml:mrow><mml:mo>+</mml:mo><mml:mn>0.740</mml:mn></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col10">0.376</oasis:entry>  
         <oasis:entry colname="col11">0.049</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table><table-wrap-foot><p>Note: ELEV is the elevation, TRIR is the index terrain neighbourhood, TRANP
is the transitional land neighbourhood in percentage, CHP is chamois
presence, AGLRP is agriculture land neighbourhood.</p></table-wrap-foot></table-wrap>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T3" specific-use="star"><caption><p>The summary of the best RSPF models of lynx habitat used
for the SSF model and the model selection estimators. Neighbourhood area is
the scale; maximum likelihood estimates with nonparametric bootstrap
standard errors (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi>B</mml:mi><mml:mo>=</mml:mo></mml:mrow></mml:math></inline-formula> 99), BIC <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> Bayesian information criteria, AIC <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> Akaike's
information criterion; <inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi mathvariant="italic">χ</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup><mml:mo>=</mml:mo></mml:mrow></mml:math></inline-formula> chi-squared test
statistic, <inline-formula><mml:math display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula> value <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> model statistically significance.
For the best model the coefficients and their sign is shown along with their standard errors
and statistically significance.</p></caption><oasis:table frame="topbot"><?xmltex \begin{scaleboxenv}{.95}[.95]?><oasis:tgroup cols="11">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="left"/>
     <oasis:colspec colnum="3" colname="col3" align="left"/>
     <oasis:colspec colnum="4" colname="col4" align="left"/>
     <oasis:colspec colnum="5" colname="col5" align="left"/>
     <oasis:colspec colnum="6" colname="col6" align="left"/>
     <oasis:colspec colnum="7" colname="col7" align="left"/>
     <oasis:colspec colnum="8" colname="col8" align="left"/>
     <oasis:colspec colnum="9" colname="col9" align="right"/>
     <oasis:colspec colnum="10" colname="col10" align="right"/>
     <oasis:colspec colnum="11" colname="col11" align="right"/>
     <oasis:thead>
       <oasis:row>  
         <oasis:entry colname="col1">Model</oasis:entry>  
         <oasis:entry colname="col2">Neighbourhood</oasis:entry>  
         <oasis:entry colname="col3">Log-</oasis:entry>  
         <oasis:entry colname="col4">BIC</oasis:entry>  
         <oasis:entry colname="col5">AIC</oasis:entry>  
         <oasis:entry colname="col6"><inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi mathvariant="italic">χ</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col7"><inline-formula><mml:math display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula> value</oasis:entry>  
         <oasis:entry colname="col8">Variables</oasis:entry>  
         <oasis:entry colname="col9">Coefficients</oasis:entry>  
         <oasis:entry colname="col10">Standard errors</oasis:entry>  
         <oasis:entry colname="col11"><inline-formula><mml:math display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula> value</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2">area (km<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">likelihood</oasis:entry>  
         <oasis:entry colname="col4"/>  
         <oasis:entry colname="col5"/>  
         <oasis:entry colname="col6"/>  
         <oasis:entry colname="col7"/>  
         <oasis:entry colname="col8"/>  
         <oasis:entry colname="col9">of coefficients</oasis:entry>  
         <oasis:entry colname="col10"/>  
         <oasis:entry colname="col11"/>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>  
         <oasis:entry colname="col1">Model 1</oasis:entry>  
         <oasis:entry colname="col2">50.2</oasis:entry>  
         <oasis:entry colname="col3"><inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>93.34</oasis:entry>  
         <oasis:entry colname="col4">205</oasis:entry>  
         <oasis:entry colname="col5">196.6</oasis:entry>  
         <oasis:entry colname="col6">17.36</oasis:entry>  
         <oasis:entry colname="col7">0.026</oasis:entry>  
         <oasis:entry colname="col8">ELEV</oasis:entry>  
         <oasis:entry colname="col9">3.033e<inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>03</oasis:entry>  
         <oasis:entry colname="col10">6.989e<inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>04</oasis:entry>  
         <oasis:entry colname="col11">&lt; 0.0001</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2"/>  
         <oasis:entry colname="col3"/>  
         <oasis:entry colname="col4"/>  
         <oasis:entry colname="col5"/>  
         <oasis:entry colname="col6"/>  
         <oasis:entry colname="col7"/>  
         <oasis:entry colname="col8">TRIR</oasis:entry>  
         <oasis:entry colname="col9">1.021e<inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>02</oasis:entry>  
         <oasis:entry colname="col10">4.067e<inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>02</oasis:entry>  
         <oasis:entry colname="col11">0.801</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2"/>  
         <oasis:entry colname="col3"/>  
         <oasis:entry colname="col4"/>  
         <oasis:entry colname="col5"/>  
         <oasis:entry colname="col6"/>  
         <oasis:entry colname="col7"/>  
         <oasis:entry colname="col8">CHP</oasis:entry>  
         <oasis:entry colname="col9">7.789e<inline-formula><mml:math display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula>02</oasis:entry>  
         <oasis:entry colname="col10">1.168e<inline-formula><mml:math display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula>02</oasis:entry>  
         <oasis:entry colname="col11">&lt; 0.0001</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2"/>  
         <oasis:entry colname="col3"/>  
         <oasis:entry colname="col4"/>  
         <oasis:entry colname="col5"/>  
         <oasis:entry colname="col6"/>  
         <oasis:entry colname="col7"/>  
         <oasis:entry colname="col8">TRANP</oasis:entry>  
         <oasis:entry colname="col9"><inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>1.187e<inline-formula><mml:math display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula>03</oasis:entry>  
         <oasis:entry colname="col10">1.436e<inline-formula><mml:math display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula>02</oasis:entry>  
         <oasis:entry colname="col11">&lt; 0.0001</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2"/>  
         <oasis:entry colname="col3"/>  
         <oasis:entry colname="col4"/>  
         <oasis:entry colname="col5"/>  
         <oasis:entry colname="col6"/>  
         <oasis:entry colname="col7"/>  
         <oasis:entry colname="col8">Intercept</oasis:entry>  
         <oasis:entry colname="col9"><inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>2.021e<inline-formula><mml:math display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula>01</oasis:entry>  
         <oasis:entry colname="col10">5.273e<inline-formula><mml:math display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula>00</oasis:entry>  
         <oasis:entry colname="col11">&lt; 0.0001</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup><?xmltex \end{scaleboxenv}?></oasis:table><?xmltex \begin{scaleboxenv}{.95}[.95]?><table-wrap-foot><p>Note: ELEV is the elevation, TRIR is the index terrain neighbourhood, TRANP
is the transitional land neighbourhood in percentage, CHP is chamois
presence, AGLRP is agriculture land neighbourhood.</p></table-wrap-foot><?xmltex \end{scaleboxenv}?></table-wrap>

      <p>The boundary quality penalty (BQP) function of Zonation was used in our
analysis to incorporate spatial aggregation into the areas prioritised for
the lynx for conservation. When using the BQP, Eq. (<xref ref-type="disp-formula" rid="Ch1.E1"/>) is replaced by a
more complex equation to determine the cell removal rule (for details see Moilanen, 2007). This allowed the habitat value of each cell to be
adjusted based on proportion of the cells containing habitat within a
specified neighbourhood around a given focal cell. The BQP is characterised
by an effect radius and a response curve. The effect radius specifies the size of the neighbourhood
used in calculating the BQP. For the lynx we used an effect radius
determined by the radius of the neighbourhood variable used in the best
fitting model 1; this value was 4 km<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:math></inline-formula>( corresponding to 50.2 km<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>. The
response curve specifies how the local quality of a focal cell changes when
different proportions of areas with high probability of lynx occurrences are
lost from within the effect radius, and it is related to the sensitivity of the
lynx to fragmentation of its habitat (Moilanen and Wintle,
2007; Gordon et al., 2009). The BQP curve used for this analysis is given in
the Supplement (Sect. S10). The Zonation analysis was done using
maps with the same 1 km<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:math></inline-formula> resolution as used in the species distribution
modelling.</p>
      <p>Finally, Zonation was run in both “constrained” and “unconstrained”
mode. In the unconstrained mode, the algorithm can pick cells purely based
on Eq. (<xref ref-type="disp-formula" rid="Ch1.E1"/>). In the constrained model we included the current protected
areas using Zonation's mask function (Moilanen et al., 2012).
This forced the raster cells in the protected areas to have the highest
rankings to determine areas to extend the current set of protected
areas.</p>
</sec>
</sec>
<sec id="Ch1.S3">
  <title>Results</title>
      <p>The spatial autocorrelation at the model grain of 1 km for the occurrences
of the lynx was statistically insignificant (<inline-formula><mml:math display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula> value &lt; 0.001). The
model 1 showed the highest accuracy (AUC <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 82 %) and performed
better than model 2 (AUC <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 65 %) in terms of model selection (the
lowest value of AICc) and accuracy (Table 2). The higher value of AUC for
the model 1 suggests that model 1 shows a relatively clear pattern of
estimated high probability of the lynx occurrences with respect to natural
factors (elevation, terrain index, chamois prey occurrences). The lower
value of AUC for the model 2 shows that the estimated probability of lynx
occurrences is more conditioned by natural factors (e.g. the abundance of
chamois prey) than by human disturbance i.e. agricultural land. This model 1 has an AIC weight of 50 % showing that this model is likely the best
performing model from the 11 GLM models (see Model selection of the lynx).
The models performed best at the neighbourhood scale of 50.2 km<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:math></inline-formula> (a
radius of 4 km). The model 1 neighbourhood scale (a radius of 4 km) implied
that the lynx selected habitat (primarily for food and refuge), if the
natural resources and prey were available at the range of approximately 50 km<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:math></inline-formula>.
This scale matches to the estimations of home-range of the lynx
(e.g. Bojovič 1978). This model 1 showed that the estimated
probability of occurrence for the lynx increased with elevation (ME), steep
terrain (TRIR), and areas with abundant prey (chamois, CHP) and decreased
with well-connected transitional land (TRAN) that presents the change of
forest management from woodland (taller trees, higher tree volume) to
shrub-land (shorter trees, lower tree volume) (Table 2).<?xmltex \hack{\newpage}?></p>
      <p>The selected model 2 indicated that the estimated probability of the
occurrence for the lynx decreased in human modified landscapes (i.e. in
agricultural land). Agriculture land had a negative impact and the greatest
effect (Table 2) on the lynx habitat. The selected neighbourhood scale of
this model 2 was 314 km<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:math></inline-formula> (a radius of 10 km). This scale indicated the
scale at which the lynx avoids agricultural areas.</p>
      <p>The models with combined permanent and temporal occurrences indicated that
the lynx selected areas well-connected with forests at the range of
approximately 50 km<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:math></inline-formula> and avoid agricultural and urban areas at the
range of 707 km<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:math></inline-formula>. The results of the best models with combined
permanent and temporal occurrences are in Sects. S7–S9 and S11–S12 in the Supplement.</p>
<sec id="Ch1.S3.SS1">
  <title>Evaluation of GLM models</title>
      <p>The best RSPF model (selected model) was model 1 at the range of
approximately 50 km<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:math></inline-formula>. This model fully agreed with the best GLM models
in terms of sign of coefficients and of variables. RSPF model 1 is
statistically significant (<inline-formula><mml:math display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula> value of 0.026) with a negative value of
log-likelihood of 93.3, with a value of <inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi mathvariant="italic">χ</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow></mml:math></inline-formula> of 17.3 and the lowest
value of AIC of 196.6 from 11 RSPF models. The neighbourhood scale of this
RSPF model 1 has a radius of 4 km, implying that the natural resources and prey
are available and encountered by the lynx at the range of approximately 50 km<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:math></inline-formula>,
the lynx selects these natural resources, e.g. for food (Table 3).
The Spearman correlation coefficient between the best RSPF model (no
permanent presence removed) and the best RSPF model, removing 25 % of the
permanent occurrences, was 0.93. The Spearman correlation coefficient
between the best RSPF model (no permanent presence removed) and the best
RSPF model, removing 51 % of the permanent occurrences, was also 0.93,
indicating strong prediction by the best RSPF model (see Model evaluation).
We simulated SSF with the selected RSPF model (model 1). We selected SSF
model simulation with 222 predicted lynx steps as the best SSF model simulation. We overlapped 222 predicted lynx steps by the best SSF
model simulation with predicted probability of occurrence of lynx with <inline-formula><mml:math display="inline"><mml:mi>H</mml:mi></mml:math></inline-formula>&gt;0.65 (threshold) of best GLM model (model 1 in Table 2). The selected SSF
simulation had the highest number of steps of 36 % and a mean step length
of 3.3 km for 222 predicted lynx steps by 30 SSF model simulations. The mean
step length of 3.3 km corresponds closely to the radius of 4 km of our
neighbourhood variables (at range of approximately 50 km<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> for our best
GLM models (Table 2). We mapped out the predicted probability of occurrence
of the lynx (<inline-formula><mml:math display="inline"><mml:mi>H</mml:mi></mml:math></inline-formula> &gt; 0.65) by the best RSPF model and predicted
probability of occurrence of lynx with <inline-formula><mml:math display="inline"><mml:mi>H</mml:mi></mml:math></inline-formula> &gt; 0.65 by our best GLM
model. We found that maps of the best RSPF model and best GLM model were
very alike (Fig. S9 in the Supplement). Predicted probability of
occurrence of lynx with <inline-formula><mml:math display="inline"><mml:mi>H</mml:mi></mml:math></inline-formula> &gt; 0.65 by best RSPF model and predicted
probability of occurrence of lynx with <inline-formula><mml:math display="inline"><mml:mi>H</mml:mi></mml:math></inline-formula> &gt; 0.65 by our best GLM
model resulted in 11.9 and 11.8 % of the entire study area,
respectively. This indicates GLM model adequately predicted the probability of
occurrences of the lynx.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F2" specific-use="star"><caption><p>The estimated probability of occurrence of the lynx <bold>(a)</bold> in
the cross-border area of Montenegro, Albania, and Kosovo, <bold>(b)</bold> in the cross
border area of Albania, Macedonia, and Kosovo <bold>(c)</bold> model 1 (biological feature
used in Zonation), <bold>(d)</bold> model 2 (cost layer used inverted in Zonation) and
existing terrestrial protected areas. The numbers (1), (2), (3), (4), (5),
(6) identifies approximately areas of the lynx photos captured in Kosovo (in
year 2015), 27 and 21 photos in Albania (in year 2014 and in winter time
between 2014 and 2015, respectively) and 37 photos (in 2015) in (5) and
photos in (6) (in year 2013) in Macedonia, respectively. These areas are
approximately selected by using Google Earth 2015 and village geographical
data of Albania.</p></caption>
          <?xmltex \igopts{width=398.338583pt}?><graphic xlink:href="https://we.copernicus.org/articles/16/17/2016/we-16-17-2016-f02.png"/>

        </fig>

      <?xmltex \floatpos{t}?><fig id="Ch1.F3" specific-use="star"><caption><p>Priority locations for extending current protected areas
for lynx conservation <bold>(a)</bold> in the cross-border area of Montenegro,
Albania, and Kosovo; <bold>(b)</bold> in the cross border area of Albania, Macedonia, and
Kosovo; <bold>(c)</bold> the top 10 and 20 % of the landscape for lynx
conservation as prioritised by Zonation constrained to the current protected
areas (dashed lines); <bold>(d)</bold> result of unconstrained solution by Zonation.</p></caption>
          <?xmltex \igopts{width=398.338583pt}?><graphic xlink:href="https://we.copernicus.org/articles/16/17/2016/we-16-17-2016-f03.png"/>

        </fig>

      <p>Finally, we found that predicted lynx steps by SSF model increased
from 36 % in areas with high probability of lynx occurrence (<inline-formula><mml:math display="inline"><mml:mi>H</mml:mi></mml:math></inline-formula> &gt; 0.65)
to 50 % in areas with low probability of lynx
occurrence (<inline-formula><mml:math display="inline"><mml:mi>H</mml:mi></mml:math></inline-formula> &gt; 0.50 to <inline-formula><mml:math display="inline"><mml:mi>H</mml:mi></mml:math></inline-formula> &lt; 0.65), estimated by our best
GLM model (Fig. 2c). We overlapped 222 predicted steps by the selected SSF
simulation with prioritised conservation areas of 10 and 20 % by
Zonation. We found approximately 20 and 56 % of all steps inside of
prioritised conservation areas of 10 and 20 % by Zonation,
respectively (Fig. 3). We also simulated SSF model with RSPF model 2
including agricultural land at the range of 314 km<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:math></inline-formula>. Then, we
overlapped 195 lynx steps predicted by the SSF model (with RSPF model 2)
simulation with predicted probability of occurrences of the lynx with
<inline-formula><mml:math display="inline"><mml:mi>H</mml:mi></mml:math></inline-formula> &gt; 0.50 (threshold of estimated probability of occurrences of the lynx) for the
GLM model 2 (see Table 2). We found that 89 % of all steps predicted by
this SSF model (with RSPF model of anthropological factors) simulation were
associated with no agricultural land.</p>
      <p>The change of AICc was below 2 (<inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">Δ</mml:mi></mml:math></inline-formula>AICc &lt;2) between models of
the best GLM model (model 1 in Table 2) with 1, 2 randomly removed permanent
occurrences and the best GLM model (no permanent occurrences removed).
Models with randomly removed 4, 8, and 16 permanent occurrences had a change
of AICc above 2 (<inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">Δ</mml:mi></mml:math></inline-formula>AICc &gt; 2) compared to our best GLM
model (see Model evaluation). Results are shown in Sect. S9.</p>
      <p>All evidence of the lynx overlaps with areas with high probability of
lynx occurrences of <inline-formula><mml:math display="inline"><mml:mi>H</mml:mi></mml:math></inline-formula> &gt; 0.65 and with areas with low probability
of lynx occurrences (marginal habitat) of <inline-formula><mml:math display="inline"><mml:mi>H</mml:mi></mml:math></inline-formula> &gt; 0.50 and <inline-formula><mml:math display="inline"><mml:mi>H</mml:mi></mml:math></inline-formula> &lt; 0.65
in Fig. 2 and in Sect. S11. Four pieces of evidence numbered (1), (2), (5) and (6)
were inside of protected areas, and numbers (3) and (4) were in the surrounding protected
areas. Evidence piece (3) was 12 km, and evidence pieces (4) was a 5 km (straight line) far
from the closest protected area boundary (see Fig. 2b).</p>
</sec>
<sec id="Ch1.S3.SS2">
  <title>Lynx habitat maps</title>
      <p>We mapped out the estimated probability of occurrence of the lynx in the
model 1 and model 2 (Table 2; Fig. 2). The cut-off value in the estimated
probability of occurrence of the lynx (predicted habitat suitability, <inline-formula><mml:math display="inline"><mml:mi>H</mml:mi></mml:math></inline-formula>) in
the model 1 was <inline-formula><mml:math display="inline"><mml:mi>H</mml:mi></mml:math></inline-formula> &gt; 0.65 and in model 2 <inline-formula><mml:math display="inline"><mml:mi>H</mml:mi></mml:math></inline-formula> &gt; 0.50. This
cut-off enabled us to distinguish areas with high probability of lynx
occurrence (e.g. for model 1 <inline-formula><mml:math display="inline"><mml:mi>H</mml:mi></mml:math></inline-formula> &gt; 0.65) from areas with low
probability of lynx occurrence (e.g. for model 1 <inline-formula><mml:math display="inline"><mml:mi>H</mml:mi></mml:math></inline-formula> &lt; 0.65)
(see, e.g. Naves et al., 2003). Areas with high probability of lynx
occurrence (suitable habitat) tended to occur in forested areas and areas
with high elevation, while areas with low probability of lynx occurrence
(marginal and non-suitable habitat) was concentrated in low land and
non-forested land (i.e. agricultural land; the expansion of agricultural
land may decrease the areas of areas with estimated high probability of lynx
occurrence of the lynx in the study area). Patches with estimated high
probability of lynx occurrence were fragmented and divided by areas of
estimated low probability of lynx occurrence.</p>
      <p>The areas with estimated high probability of lynx occurrence was spatially
distributed over all four countries in the study area. Two large areas with
estimated high probability of lynx occurrence, one spanning Montenegro,
Kosovo, and Albania, the other spanning Albania, Kosovo, and the FYR of Macedonia
is a key finding of this analysis (indicated by the zoomed-in maps in (a) and (b) in Fig. 2). The areas with estimated high probability of lynx occurrence
outside protected areas were identified within Albania, which may ensure the
connection of two multi-border areas of Albania, Montenegro, and Kosovo in
the north and Albania, Macedonia, and Kosovo in centre of the study area,
respectively. Areas with estimated high probability of lynx occurrence were
also identified in the cross-border between Macedonia and Greece.</p>
      <p>The areas with probability of the lynx occurrence (<inline-formula><mml:math display="inline"><mml:mi>H</mml:mi></mml:math></inline-formula> &gt; 0.65)
predicted by the model 1 and model 2, respectively, overlapped (i.e. map (c) and map (d) in Fig.2). The model 1 and model 2 showed insignificant
value of correlation (Spearman correlation; <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>r</mml:mi><mml:mo>=</mml:mo></mml:mrow></mml:math></inline-formula> 0.013). Areas of overlap in
both models indicated the presence of forested elevated land (model 1) as
well as less agricultural land (model 2). These areas tended to occur
predominantly in Macedonia and Albania and in western Kosovo.</p>
      <p>The areas with estimated high probability of lynx occurrence for the lynx
were identified in protected areas that had forested elevated areas and species of lynx prey (model 1) and have little or no agriculture land (model 2).
This indicated that protected areas were well-located for lynx
conservation. The areas with estimated probability values from <inline-formula><mml:math display="inline"><mml:mi>H</mml:mi></mml:math></inline-formula> &gt; 0.50
to <inline-formula><mml:math display="inline"><mml:mi>H</mml:mi></mml:math></inline-formula> &lt; 0.65 in protected areas can still be
beneficial for the lynx (e.g. the photos of lynx were collected in Pelister
National Park; (6) in Map (b) in Fig. 2 in 2013 (Balkan Lynx Recovery
Programme, 2014).</p>
</sec>
<sec id="Ch1.S3.SS3">
  <title>Prioritisation of the landscape for lynx conservation</title>
      <p>Areas prioritised by Zonation (unconstrained solution) were concentrated in
the centre and north of the study area with the majority of the top 20 % solution occurring in the cross border areas of
Montenegro–Albania–Kosovo, Albania–Macedonia, as well as in Macedonia and
Montenegro.</p>
      <p>Constraining the Zonation solution with the current protected areas forced
all protected areas to be in the top 20 % solution (and most in the
top 10 %) (Fig. 3c). The constrained (Fig. 3c) and unconstrained
solutions (Fig. 3d) were similar. This indicated again that the existing
protected areas occurred in high priority locations for lynx
conservation. The major differences between constrained and unconstrained
solutions were a reduction in some of high priority areas in Albania,
Macedonia, and between Albania and Macedonia border areas.</p>
      <p>In the constrained solution, high priority rankings have been assigned to
new areas outside the current protected areas in western Macedonia, the
north and east of Albania as well as in northern and western Montenegro,
(Fig. 3c). These new areas within the top 20 % landscape
prioritisation connected the two protected areas situated in the
Albania–Montenegro–Kosovo cross-border area (Fig. 3a) and the
Albania–Macedonia–Kosovo cross-border area (Fig. 3b).
Prioritised areas in Macedonia and Albania tended to be fragmented.</p>
      <p>The number of steps predicted by SSF in top 10 % Zonation solution was
larger for Macedonia compared to Albania, with Kosovo having a small share
and no share for Montenegro (Fig. 4, light grey components of columns). The
top 20 % solution increased the difference between Macedonia and three
other countries (Albania, Montenegro, and Kosovo), with Macedonia having the
largest share of 68.2 % (Fig. 4).
<?xmltex \hack{\vspace{-3mm}}?></p>
</sec>
</sec>
<sec id="Ch1.S4">
  <title>Discussion</title>
      <p>We used a GLM with an information-theoretic approach for testing a set of a priory hypothesis
on the estimated probability of occurrences of lynx. This modelling approach
helped us to identify the factors that determine the distribution of the
lynx. Our models with permanent occurrences (the number of positive answers
was above 50 % affirmative answers collected on lynx by interviewers for
a cell of 10 km <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10 km) and combined permanent and temporal lynx
occurrences (the number of positive answers was below 50 % affirmative
answers collected on lynx by interviewers for a cell of 10 km <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10 km)
showed that distribution of the lynx is determined by the abundance of
environmental resources, high elevation, slope, the presence of forested and
pastureland, and of lynx prey (chamois). Other studies on the Iberian lynx
(<italic>Lynx pardinus</italic>) have also found that the lynx in Spain was conditionally distributed by
natural resources, shrubs and rocky areas (Fernández et al., 2006)
and pastureland (Fernández et al., 2003). The GLM models are used in
habitat modelling of large-carnivore species because they are an effective
modelling approach for SDMs performing well with adequate species data and
handling non-linear responses between species occurrences and environmental
variables (Kanagaraj et al., 2013). There are many approaches
of species distribution modelling such as Maxent (Phillips
et al., 2006) that uses presence-only data of species, niche models like
ecological niche factor analysis (ENFA) (Hirzel et al., 2004)
that estimates species home-range, resource selection functions (RSFs) and
resource selection probability functions (RSPFs) (Lele et al., 2013) that calculates habitat selection of species. GLMs deal with
autocorrelation of species data, multi-collinearity of variables and with
model performance using very few species occurrence records, though GLMs do
not show disadvantages (see, e.g. Kanagaraj et al., 2013).
Another issue concerning species distribution modelling including GLMs is on
the concept of “habitat” (a good discussion is provided by Gaillard et
al., 2010). In this study, we applied RSPF model (model 1) to calculate the
probability of occurrence of the lynx to compare explicitly with probability
of occurrence of the lynx estimated by our best GLM model (model 1). We
found that results obtained by best RSPF model and by best GLM model were
very similar in the terms of model type, i.e. “natural” vs. “human” model,
number and type of explanatory variables and sign of coefficients (see Table 2)
and the maps (Fig. 2c and Fig. S9). These findings indicated that the
predictions of RSPF model and GLM model were consistent with known
information of lynx occurrences in the cross-border area between Albania and
Macedonia (Breitenmoser et al., 2008) and of lynx
occurrences in Albania, Macedonia, and Kosovo (see evidence of lynx
collected from 2013 to 2015 in Albania and Macedonia shown in Figs. 2a, b and S11a, b).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F4"><caption><p>The number of predicted steps by the SSF model for the lynx in
the top 10 and 20 % of the Zonation solution constrained to the
current protected areas aggregated for each country.</p></caption>
        <?xmltex \igopts{width=236.157874pt}?><graphic xlink:href="https://we.copernicus.org/articles/16/17/2016/we-16-17-2016-f04.png"/>

      </fig>

      <p>We checked our lynx data (see Lynx data) quality and detectability of our
best GLM model by randomly removing a different number of permanent
occurrences and a different number of combined permanent and temporal
occurrences and replaced removed lynx occurrences with no lynx occurrence
records (see Model evaluation). We found that our best model performed
consistently worse than our best GLM model (<inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">Δ</mml:mi></mml:math></inline-formula>AICc &gt; 1;
CV &lt; 0.71) after we randomly removed permanent lynx occurrences
(Sect. S9) showing that lynx permanent occurrences could be better
identified than lynx temporal occurrences. Overall, the lynx showed clear
patterns of areas with high probability of its occurrences with respect to
natural resources. Our findings demonstrate that using fine resolution
environmental data (elevation, forest, land) helps detect areas with high
probability of occurrence of species even if we use coarse resolution
species data. Our results of Step Selection Function (SSF) model showed that
lynx prefers to inhabit mostly in the cross-border area of Albania, Macedonia, and Kosovo. We suggest SSF or any resource selection models that
tackle the autocorrelation problems of telemetry data (see, e.g. Johnson et
al., 2008) to be used with new radio-telemetry data of lynx that are
collected (personal communication with Gjorge Ivanov) to understand the
animal behaviour and movement. This could be a new research area for
organisation teams (see Sect. S0) working on the lynx data
collection and lynx conservation.</p>
      <p>This study clearly demonstrated the conservation areas for the lynx. We
assessed potential key conservation areas for lynx conservation in
south-eastern Europe and provided a large-scale study of the estimation of
probability of occurrence of the lynx in four post-socialist countries of
Albania, Macedonia, Montenegro, and Kosovo. This is an important step forward
for designing conservation plans for large carnivores in countries that
experienced massive political and socioeconomic changes
(Radeloff et al., 2013). Our study identified the two
cross-border areas between Albania and Macedonia and between Albania,
Montenegro, and Kosovo in Fig. 3a and b for
conservation of this enigmatic species. These results suggest that a close
and effective cooperation of the governments of Albania, Macedonia,
Montenegro, and Kosovo is required for lynx conservation in these
cross-border areas (shown in box (a) and (b) in Fig. 3). The
cross-border area between Albania and Macedonia is the key-conservation area
identified by local and international organisation in terms of forest
conservation, of local population awareness and engagement in nature
conservation and of nature conservation at national and international level
(see Sect. S0.1).</p>
      <p>Our model results using the lynx occurrence records from questionnaires are
also supported by direct observation records of the lynx subspecies (box (a) and (b) in Fig. 2). Our results may also be used for identifying new
areas for intensive research. This may also help meeting targets of the
Convention on Biodiversity Conservation of 17 % of terrestrial
ecosystems and of no unknown species to go extinction (e.g. the lynx) by
2020 by governments. These findings support well the cross-border
cooperation that has already started between Albania and Macedonia in 1990s
(see Sect. S0.1).</p>
      <p>This paper showed a full workflow starting with lynx occurrence data,
applying species distribution modelling and combining it with spatial
prioritisation of locations for lynx conservation. Our study is added to
the existing literature of conservation science that has used generalised
linear models and Zonation (see, e.g. Kujala et al., 2013).
We separated natural and human factors to estimate the probability of the
lynx occurrences and then to map “natural” and “human” model (the lynx
habitat maps were based on “natural” and “human” factors, respectively).
These “natural” and “human” maps served as the biological feature layer and
the cost layer (“human” model was inverted), respectively, in Zonation
software. We assessed, thus, the conservation areas of the lynx. This helped
to show where to extend the existing protected areas and to potentially
create new protected areas (and buffer zones) for lynx conservation.</p>
      <p>The needs of lynx for forests and pastures (pastures, prey, well-connected
forests were potentially selected habitats of the lynx for refuge and food)
could be jeopardised by humans. We observed disturbed forests near stable
forests and in protected areas and their surroundings (Sect. S13).
Similar results were found in the case of Ukraine and Romania
(post-socialist countries). In Romania, the high logging rates were likely
trigged by rapid changes in institutions and ownership that resulted in
forest decrease inside protected areas, which in turn, caused an increasing
fragmentation of forest cover in the protected areas (Knorn et
al., 2012).</p>
<sec id="Ch1.S4.SS1">
  <title>Recommendations for lynx conservation</title>
      <p>This study showed lynx conservation areas and predicted lynx steps by SSF were spread between Albania and Macedonia (Figs. 3 and 4). This
indicates that these countries have similar responsibilities for the
conservation of the lynx populations and habitat. Albania and Macedonia
currently have the largest lynx populations and both countries share the
largest part of predicted steps of lynx by SSP in the top 10 % of the
landscape prioritised for lynx conservation (Fig. 4). Because of the
existing lynx populations in Albania and Macedonia, both countries will be
required to make all efforts to maintain these populations. Albania and
Macedonia can collaborate to ensure a single long-term conservation plan of
their cross-border areas, for example, to collaborate on preparing a species
conservation plan. In addition, the results of our species distribution
modelling and landscape prioritisation indicate that both countries may need
to address the following factors: (i) the conserving of existing areas with
high probability of lynx occurrence through forest conservation measures
such as incentive programs to reduce the forested areas for forest
harvesting and firewood (e.g. firewood is still important source for heating
in rural areas in Albania; Laze, 2014); such
an incentive program may compensate local people for the switching from wood
harvesting to forest conservation (i.e. from resource to biodiversity
forest ecosystem service); (ii) well-managed hunting activities such as
limiting or halting chamois, brown hare and roe deer hunting at fixed times
of the year; (iii) sustainable planning for the use of agriculture and
pasture land; (iv) the collecting of constant seasonal and yearly lynx data
using the advance monitoring system (radio-telemetry); (v) expansion of
protected areas and the addition of new protected areas in locations such as
the cross-border areas but also inside of Albania, Macedonia, Kosovo, and
Montenegro (Fig. 3). This last point could help the lynx disperse from the
north to the centre of the study area. This is because any lynx individual
matters for the existing small population of the lynx. (Data collection on
Carpathian lynx occurrence in the north of the study area (primarily Montenegro)
can be useful to identify any potential overlapped areas of the distribution
between Carpathian lynx and the lynx; yet, this is not our study objective).</p>
      <p>Our results suggest that conservation efforts in the countries of our study
could be oriented towards increasing the size of existed protected areas and
their surrounding-buffer areas. This, however, will require a closer
inter-country collaboration because the most promising areas for lynx
conservation extend over the country borders. The expansion of protected
areas must be associated with the conservation of forests, the reduction of
human disturbance in the prioritised areas as well as with the connectivity
of habitat patches for the lynx in their cross-border areas. This is because
the lynx prefers larger areas of undisturbed forests, moves a great deal
within its home-range (Balkan Lynx Strategy Group, 2008) to satisfy
its needs for refuge, food and breeding as well as it is sensitive to
anthropogenic land changes. We highlight here the relevance of large-area
for the production of the lynx quoting as follows:<disp-quote>
  <p>Although isolation is
of great importance in the production of new species, on the
whole I am inclined to believe that largeness of area is still more
important, especially for the production of species which shall prove
capable of enduring for a long period, and of spreading widely (Darwin, 2011).</p>
</disp-quote></p>
</sec>
</sec>

      
      </body>
    <back><app-group>
        <supplementary-material position="anchor"><p><bold>The Supplement related to this article is available online at <inline-supplementary-material xlink:href="http://dx.doi.org/10.5194/we-16-17-2016-supplement" xlink:title="pdf">doi:10.5194/we-16-17-2016-supplement</inline-supplementary-material>.</bold></p></supplementary-material>
        </app-group><ack><title>Acknowledgements</title><p>We are grateful to all those that made the data available on the internet for
the lynx and environmental and human data available in 2008 (to K. Laze) as well as to J. Stadler, R. Brandl, and one anonymous reviewer for their comments. This manuscript was designed in
October 2011, when K. Laze was a doctoral student at Leibniz Institute of
Agriculture Development in Transition Economies, Germany. A. Gordon was supported
by funding from the Australian Research Council Centre of Excellence for
Environmental Decisions.<?xmltex \hack{\newline}?><?xmltex \hack{\newline}?>
Edited by: J. Stadler<?xmltex \hack{\newline}?>
Reviewed by: R. Brandl and one anonymous referee</p></ack><ref-list>
    <title>References</title>

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    <!--<article-title-html>Incorporating natural and human factors in habitat modelling and spatial
prioritisation for the <i>Lynx lynx martinoi</i></article-title-html>
<abstract-html><p class="p">Countries in south-eastern Europe are cooperating to
conserve a sub-endemic lynx species, <i>Lynx lynx martinoi</i>. Yet, the planning
of species conservation should go hand-in-hand with the planning and
management of (new) protected areas. <i>Lynx lynx martinoi</i> has a small,
fragmented distribution with a small total population size and an endangered
population. This study combines species distribution modelling with spatial
prioritisation techniques to identify conservation areas for <i>Lynx lynx
martinoi</i>. The aim was to determine locations of high probability of
occurrence for the lynx, to potentially increase current protected areas by
20 % in Albania, the former Yugoslav Republic of Macedonia, Montenegro,
and Kosovo. The species distribution modelling used generalised linear
models with lynx occurrence and pseudo-absence data. Two models were
developed and fitted using the lynx data: one based on natural factors, and
the second based on factors associated with human disturbance. The
Zonation conservation planning software was then used to undertake spatial
prioritisations of the landscape using the first model composed of natural
factors as a biological feature, and (inverted) a second model composed of
anthropological factors such as a cost layer. The first model included
environmental factors as elevation, terrain ruggedness index, woodland and
shrub land, and food factor as chamois prey (occurrences) and had a
prediction accuracy of 82 %. Second model included anthropological
factors as agricultural land and had a prediction accuracy of 65 %.
Prioritised areas for extending protected areas for lynx conservation were
found primarily in the Albania–Macedonia–Kosovo and Montenegro–Albania–Kosovo
cross-border areas. We show how natural and human factors can be
incorporated into spatially prioritising conservation areas on a landscape
level. Our results show the importance of expanding the existing protected
areas in cross-border areas of core lynx habitat. The priority of these
cross-border areas highlight the importance international cooperation can
play in designing and implementing a coherent and long-term conservation
plan including a species conservation plan to securing the future of the
lynx.</p></abstract-html>
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