Implementation of ENFA Bio mapper
ENFA analysis is performed based on raster information layers in this software. Hence, the first step is to enter the data into the software. Maps are classified into two categories: maps of species presence points and maps of independent environmental variables. For this step, the correlation matrix of EGV maps was calculated. The correlation between the variables was less than the critical rate for deleting one of the variables. Therefore, all remaining variables were used for ENFA analysis.
Table 1. Investigation of the degree of correlation of independent environmental layers
Correlation matrix:
|
|
|
aspect
|
dem
|
land cover
|
river
|
road
|
slop
|
village
|
aspect
|
1
|
0.759
|
0.635
|
0.313
|
-0.306
|
0.597
|
-0.371
|
dem
|
0.759
|
1
|
0.831
|
0.399
|
-0.39
|
0.722
|
-0.482
|
Land cover
|
0.635
|
0.831
|
1
|
0.29
|
-0.318
|
0.659
|
-0.506
|
river
|
0.313
|
0.399
|
0.29
|
1
|
-0.191
|
0.28
|
-0.163
|
road
|
-0.306
|
-0.39
|
-0.318
|
-0.191
|
1
|
-0.169
|
0.467
|
slop
|
0.597
|
0.722
|
0.659
|
0.28
|
-0.169
|
1
|
-0.3
|
village
|
-0.371
|
-0.482
|
-0.506
|
-0.163
|
0.467
|
-0.3
|
1
|
After determining the degree of correlation, factor analysis of the ecological niche is performed. This analysis is similar to principal component analysis. The two important outputs of factor analysis of ecological nests are eigenvalues and score matrices, which contain the two main components of marginality and specialization, and must be carefully examined to understand the current situation ecologically.
Ecological Niche Factor Analysis (ENFA):
ENFA analysis forms the core of Bio mapper software. The ENFA analysis, similar to the Principal Component Analysis, calculates factors that explain much of the impact of species-independent environmental variables. Similar to principal component analysis, the calculated factors are not correlated with each other but are ecologically significant. The first column of the score matrix or eigenvector always represents 100% of the marginalization factor and 10 to 70% of the specialization factor, while the other columns, or in other words the number of independent environmental variables minus one, only represent the factor of specialization. The rows show the share of independent variables in each factor. In fact, in this matrix, the factors that explain sufficient information as well as the variables that show the highest coefficient (absolute value) will be very important in expressing the species distribution. Factors with a value of almost zero can be eliminated (Tables 3).
Table 2- Score matrix
Score matrix
|
|
|
|
|
|
|
|
1
|
2
|
3
|
4
|
5
|
6
|
7
|
aspect
|
-0.816
|
-0.172
|
0.077
|
-0.227
|
0.47
|
0.14
|
0.085
|
dem
|
-0.935
|
-0.122
|
0.051
|
-0.052
|
0.008
|
-0.133
|
-0.297
|
Land cover
|
-0.873
|
-0.092
|
0.18
|
0.11
|
-0.091
|
-0.385
|
0.169
|
river
|
-0.468
|
-0.181
|
-0.851
|
0.149
|
-0.011
|
0.011
|
0.029
|
road
|
0.507
|
-0.716
|
0.169
|
0.423
|
0.149
|
-0.003
|
-0.03
|
slop
|
-0.773
|
-0.375
|
0.178
|
-0.044
|
-0.361
|
0.309
|
0.047
|
village
|
0.628
|
-0.551
|
-0.125
|
-0.504
|
-0.078
|
-0.16
|
0.008
|
The first factor is marginalism and expresses the difference between the average habitat preference of a species or species distribution and the average habitat conditions or general distribution. In other words, this factor indicates the distance between the desired conditions of the target species and the prevailing conditions in the habitat. The value of marginalization is often between zero and one. Values close to zero indicate that the species tend to live in the mean conditions of the study area and there is no difference between the mean of the existing habitat and the species habitat. Values close to one indicate that the species lives in very special habitat. Marginality indicates the position of ecological niches in the environment. The second factor of ecological nests is specialization, which indicates the extent of ecological nests. Specialism is the ratio of variability or standard deviation of the general distribution to the variability or deviation of the species distribution. In other words, this factor is a measure of the range of environmental conditions that the species tolerates. In this case, values close to zero indicate that the target species can survive in a wide range of environmental conditions. High values of this factor indicate that the species is very specialized and lives in a narrow range of environmental conditions and, therefore, has a small ecological nest. The tolerance factor is the opposite of specialization and its values close to zero indicate the low tolerance of the species and its specialization. Conversely, On the contrary, the high values, while expressing the high tolerance of the species, indicate that the species does not need very special and special conditions in the habitat for life.
Marginality,
|
specialization,
|
tolerantly
|
664/0
|
366/12
|
489/0
|
Table 3. Table of scores and correlations between ecological niche factors analysis and independent environmental variables.
Score table
|
|
Ecogeographic maps
|
Factor 1 (54%)
|
Factor 2 (15%)
|
Factor 3 (12%)
|
Factor 4 (7%)
|
Factor 5 (6%)
|
Factor 6 (4%)
|
Factor 7 (2%)
|
aspect-box
|
--------
|
**
|
*
|
**
|
*****
|
*
|
*
|
dem-box
|
---------
|
*
|
*
|
*
|
0
|
*
|
***
|
land-box_cover
|
---------
|
*
|
**
|
*
|
*
|
****
|
**
|
river-box
|
-----
|
**
|
*********
|
*
|
0
|
0
|
0
|
road-box
|
+++++
|
*******
|
**
|
****
|
*
|
0
|
0
|
slop-box
|
--------
|
****
|
**
|
0
|
****
|
***
|
0
|
VILLAGE-box_FIN
|
++++++
|
******
|
*
|
*****
|
*
|
**
|
0
|
The first column represents 100% marginalization. The numbers in parentheses indicate the percentage of agent specialization. Signs (+) for the marginalization factor indicate that rams and ewes are present in habitats with values higher than the average habitat conditions, and signs (-) are the opposite. The number of symptoms indicates the degree of correlation. In the case of specialization, the sign (*) indicates the presence of rams and ewes in a narrow range of conditions. The number of these symptoms is a sign of a limited range of presence. The numbers zero indicate specialization as well as very low correlation.
Habitat suitability map:
A habitat suitability map is a map whose value of each cell is equal to the percentage of the desirability of that part of the habitat for the species. After performing ENFA analysis and obtaining the relevant outputs, the habitat suitability map can be calculated. The first step in calculating the habitat utility map is to calculate the Factor map. The results of this analysis are required to calculate the habitat utility map. The important point in this analysis is to determine the number of ENFA maps included in the Habitat suitability analysis. In Factor map analysis, the user determines how many ENFA maps are generated during this analysis. Of course, the Biomapper itself suggests the number of ENFA maps based on the Mc-Arthur broken wood criterion, but the user can determine this number himself based on the cumulative amount of variance justified by the factors.
Least cost path and circuit modeling approaches:
Two straightforward premises underlie the least cost path (LCP) to pass between two points involves encounters with topographic, natural, and/or cultural features that impede movement the optimal path of travel can be calculated by finding the one that passes between points with the minimum accumulation of these impediments or ‘costs’ (Atkinson et al. 2005; Berry, 2004; Collischonn and Pilar, 2001; Douglas, 1994; Lee and Stucky, 1998; van Leusen, 2002). LCP modeling identifies a single optimum solution for individuals of a species group to travel across a landscape. In many ways, the fact that LCP modeling produces one specified travel route has made this approach attractive to researchers but this modeling is not free from limitations.
LCP modeling assumes a traveler has complete knowledge of the landscape they are traversing (McRae et al. 2008) and operates under the assumption that they will be both able and willing to select the lowest single path cost based on this knowledge. However, individuals can be isolated in landscapes, unaware of potential matrix heterogeneity they will experience as they disperse across a landscape, making them unable to select a single optimum route. Even when individuals have landscape knowledge, various factors can lead to divergences from optimum path selection. For instance, optimum paths can become blocked or closed to dispersers. Moreover, individual travel preferences can change; across species “individuals rarely use a single optimum route” and thus LCP “fails to incorporate variation in individual behavior” (Pinto and Keitt, 2009).
Circuit modeling attempts to move away from the limits of LCP modeling’s reflection of the movement cost accrued by a single individual by using a concept of resistance distance that incorporates both the minimum movement distance (or cost) and the availability of alternative pathways. Unlike least-cost path modeling, as additional links are added, individuals do not necessarily travel shorter paths but have more pathways available to them (McRae et al. 2008).
Three interconnected layers of theory underlie circuit modeling: graph theory, network theory, and circuit theory (and associated with this is random walk theory). In short, graph theory is the branch of mathematics concerned with connections among discrete objects; network theory applies graph theory with a focus on properties of real-world networks, their structural dynamics, and the relationship between their structure and function; and circuit theory applies network theory to quantify connectivity in circuited systems that respond positively to the presence of alternative pathways (Rayfield et al. 2011). Random walk theory facilitates circuit theory’s application to species movement in a landscape by assuming random dispersal of species, the fates of random walkers on circuits can be predicted by resistance, conductance, effective resistance, effective conductance, current, and voltage (see McRae et al. 2008; Shah and McRae, 2008 for a more detailed description of measures).
Applying circuit theory to find optimal paths:
Circuit theory uses theory-based theory to model the communication of wildlife populations in the appearance of heterogeneous lands. This software is the most common application that models the movement and flow of genes for plants and animals, as well as identifies important areas for conservation and connection between habitats. Circuit theory uses land use data to predict and identify habitat relationships. Electrical circuits are networks consisting of nodes that are connected by electrical components that conduct current. According to Ohm's law, when a voltage (V) is established between two nodes, the total current flow depends on the amount of voltage and the resistance of the resistors (Mertzanis et al. 2006). In this theory, electrical nodes are considered as habitat spots, current movement as the movement of individuals, and resistors between nodes are considered as habitat paths or corridors. Increasing the number of parallel resistors increases the current flowing through the nodes. Increasing the number or extent of habitat spots connecting populations and habitats also increases the likelihood of movement and communication between them. Landscape circuit theory considers the surface as a conductive surface in which each pixel is converted into an electrical node and an electrical circuit is formed by connecting adjacent nodes (Roever et al. 2013). The results of this theory are current and voltage maps. The intensity of the electric current indicates the possibility of movement of people in the landscape. In addition, by using the flow map, it is possible to identify important corridors and communication areas in the landscape. Voltage, which indicates the amount of electric current flux difference between two nodes in a circuit, can also be used to predict the probability of an individual arriving from a point in the circuit to a specific destination, or in other words, to predict the success rate of individuals. (Srisang et al. 2007). The superiority of this model over other common analytical models that study habitat relationships is in identifying multiple pathways for species distribution (Minor and Urban, 2007). The advantage of this method is that if one or more of the diffusion and migration routes are lost at some point, the importance of the other remaining predicted routes increases. More importantly, the communication models resulting from this theory are very close to how the species move in the landscape. The idea of using habitat suitability models to calculate resistance is that in the landscape, pixels with desirable habitat characteristics, such as low human population density and the absence of roads, have little resistance to species passage, while Pixels with poor habitat characteristics such as agricultural land, high human population density, and roads show high resistance to species movement (Minor and Urban, 2007). This means that there is an inverse relationship between resistance and habitat suitability. Therefore, the relevant layer can be used to prepare the resistance layer (Hirzel et al. 2007). The inverse resistance layer is the habitat utility layer. Where the value of the pixels is high, it means that there are many obstacles to the movement of the species and the species is less inclined to move in those directions.
Map of main nodes
Habitat maps show the resistance of each pixel of the land landscape to the conductivity of the flow conductor (SalmanMahiny and Kamyab, 2011). This map shows spots or polygons (usually the main habitats) that indicate the degree of habitat connection they are modeled (Roever et al. 2013). Here, about fifty major nodes are shown as high-habitat patches and as a map of the main nodes.
Since the electrical circuit program uses data in ASCII format, after preparing the layers in the Idrisi environment, their format became the desired format.
Execution of electrical circuits program
By converting habitat raster pixels to nodes and connecting each of them to the nearest adjacent nodes, the program forms networks and calculates the intensity of the flow through the nodes (communication or the possibility of propagation of individuals). Slowly the electrical current between the nodes is calculated based on the average resistance or the average amount of conductivity between the nodes. Because the selected raster map of the habitats showed the resistance of the study area, the relationship was calculated based on the mean resistance. Circuit theory uses one of the following four methods to calculate the relationship between nodes.
1- Pairwise: In this method, the relationship between the two nodes (pixels) is calculated. In this method, one node is optionally connected to the output (Ground) and the other node to a current source of one ampere (Source), and the current passing through the two nodes is calculated and this process is repeated between all pairs of nodes.
2-: One - to - all in this method, one node is connected to the current source of one ampere and the other nodes are connected to the ground and the process is repeated for each node.
-: All-to-one in this model, one node is connected to the ground and the other nodes are connected to a current source of one ampere. This method is a good alternative to the first method. Especially when the goal is to map important communication areas between multiple habitats.
4-Advanced mode: In this method, the user has the option to specify any number of input (Source) and output (Ground) for the electric current in the landscape (Roever et al. 2013). In this study, the third model was used to calculate the electric current. Because it shows important areas for habitat communication better than the other three models, it also runs faster and requires less memory.
Preparation of electric current map (corridors between two habitats)
Here, the One - to - all method is used to determine the optimal network model of corridors and the results of the implementation of circuit theory in the form of a flow intensity map for rams and ewes are shown in Figure 8. In this model, the value of each pixel indicates the intensity of the current passing through that pixel (node) or in other words the probability of the species moving from one habitat spot to other spots. Warmer (brown) colors indicate higher flow intensities than diffusers, which can be seen in different parts of the study area. As we move towards lighter browns, the flow rate decreases, and consequently the probability of propagation decrease. In bold areas, the probability of species movement is very high, but the small width of some areas makes communication very vulnerable.
Identifying the areas where the movement of the flow, or in other words the movement of the species through the narrow zone, is one of the most important results of the flow maps for the target species. These important communication areas, called pinch points, are the most sensitive and vulnerable parts of the communication network because the elimination or reduction of habitats in these areas can disrupt or cut off communication in the whole area.
Habitat corridor modeling
Least-cost modeling is a method used for measuring the effective distance, rather than the Euclidian distance, between habitat patches. This method has been used in planning to assess the connectivity of existing or proposed reserves. GIS technology is an important tool for conducting least-cost analyses. Typically, a resistance surface in raster format is the input to the least-cost modeling. This resistance surface is derived from one or more spatially explicit variables such as animal-habitat relationships distance to development or other avoided areas, topography, physical barriers such as fences, roads, or streams. GIS habitat layers in polygon or grid format are weighted according to the expected resistance encountered by an organism when moving across the surface and linear features are then merged with the weighted resistance surface. Care must be taken when adding narrow features to the resistance surface to ensure that the narrow features are completely connected. ‘Cracks’ in narrow linear features may allow the least-cost path to incorrectly pass through an area with high resistance.
We used CorridorDesigner software in ArcGIS 10.2 to model habitat corridors. CorridorDesigner identifies least-cost corridors between termini (start–end locations). We identified a terminus in each core area as the set of all potential population patches within the core area.