Ecography 39: 001–009, 2016

doi: 10.1111/ecog.01961
 2015 The Authors. Ecography  2015 Nordic Society Oikos
Subject Editor: Brody Sandel. Editor-in-Chief: Miguel Araújo. Accepted 7 December 2015

NicheA: creating virtual species and ecological niches in

multivariate environmental scenarios

Huijie Qiao, A. Townsend Peterson, Lindsay P. Campbell, Jorge Soberón, Liqiang Ji

and Luis E. Escobar
H. Qiao and L. Ji, Key Laboratory of Animal Ecology and Conservation Biology, Inst. of Zoology, Chinese Academy of Sciences, Beijing, 100101
China. – A. T. Peterson (http://orcid.org/0000-0003-0243-2379), L. P. Campbell and J. Soberón, Biodiversity Inst., Univ. of Kansas, Lawrence,
KS 66045, USA. – L. E. Escobar ([email protected]), Minnesota Aquatic Invasive Species Research Center and Dept of Veterinary Population
Medicine, Univ. of Minnesota, St Paul, MN 55108, USA.

Robust methods by which to generate virtual species are needed urgently in the emerging field of distributional ecology
to evaluate performance of techniques for modeling ecological niches and species distributions and to generate new
questions in biogeography. Virtual species provide the opportunity to test hypotheses and methods based on known and
unbiased distributions. We present Niche Analyst (NicheA), a toolkit developed to generate virtual species following the
Hutchinsonian approach of an n-multidimensional space occupied by the species. Ecological niche models are generated,
analyzed, and visualized in an environmental space, and then projected to the geographic space in the form of continuous
or binary species distribution models. NicheA is implemented in a stable and user-friendly Java platform. The software,
online manual, and user support are freely available at < http://nichea.sourceforge.net >.

The ecological niche has been a central concept in mod- Basic ideas for measurement of niche characteristics
ern ecology (Hutchinson 1957, Leibold 1995, Holt 2009). were first proposed more than four decades ago (Colwell
G. Evelyn Hutchinson presented a formalization of niche and Futuyma 1971). Initial correlational niche modeling
concepts more than 50 yr ago (Hutchinson 1978), propos- approaches were outlined beginning in the 1970s (Green
ing relationships between ecological niches and geographic 1971, Hutchinson 1978), with enormous interest and
spaces (which he called ‘biotopes’; Soberón and Nakamura advancement in the 1990s and 2000s (Peterson et al. 2011).
2009); this linkage is known as the Hutchinsonian dual- More recently, techniques and toolkits have been developed
ity (Pulliam 2000, Colwell and Rangel 2009). However, to make these approaches more tractable (Abrams 1980,
tools for visualizing, exploring, and analyzing distributions Rödder and Engler 2011); in particular, these approaches
of species in these linked spaces have remained limited have been integrated in tools for model calibration (Phillips
(but see Duan et al. 2015 and Leroy et al. 2015). Recent and Dudík, 2008) and for comparative studies of eco-
years have seen massive increases in availability of data on logical niche models in ENMTools (Warren et al. 2008,
occurrences of species and important environmental dimen- 2010, Glor and Warren 2011) and NichePy (Bentlage and
sions, and researchers have developed correlational algo- Shcheglovitova 2012) software packages.
rithms by which to estimate ecological niches and explore The interplay of different factors in geographic (G) and
potential distributional areas (Peterson et al. 2011). These environmental (E) spaces can be explored via so-called ‘virtual
correlational models have been referred to as species distri- species’. Virtual species are made by software in the form of
bution models (Austin 2007, Pearson et al. 2007, Pearson simulated data that resemble real species, the researcher char-
2010), habitat models (Hirzel and Arlettaz 2003, Guisan acterizes a priori a limited and known set of causal factors to
and Thuiller 2005), or ecological niche models (Soberón create a ‘species’ of known niche characteristics. Niches and
and Peterson 2005, Peterson 2006). Soberón and Peterson distributions of virtual species can then be explored using
(2005) proposed the biological-abiotic-mobility (BAM) modeling techniques; numerous recent studies used virtual
scheme, a heuristic framework linking niche concepts and species to explore complicated questions in distributional
distributional areas. BAM highlights three important causal ecology (Hirzel et al. 2001, Elith and Graham 2009, Godsoe
factors of species’ distributions: the geographic distribution 2010, Rödder and Engler 2011, Barbet-Massin et al. 2012,
of suitable abiotic environmental conditions, the geographic Saupe et al. 2012, Owens et al. 2013, Meynard et al. 2013,
distribution of suitable biotic conditions, and the potential Miller 2014, Moudrý 2015). Virtual species allow research-
to reach areas by dispersal in relevant time periods. ers to avoid problems such as biases related to choice of

Early View (EV): 1-EV

species (Barbet-Massin et al. 2012), biases and error in real- Core Team), Weka (Mark Hall et al. 2009), JAMA (Hicklin
world data sets (Saupe et al. 2012), and unknown true niche et al. 2012), GDAL (GDAL Development Team 2011),
dimensions (Broennimann et al. 2012). and QuickHull3D (Lloyd 2012; Supplementary material
Two software packages, SDMvspecies and virtualspecies Appendix 1). The platform is a window-based, user-friendly
(Duan et al. 2015 and Leroy et al. 2015), were presented application that executes on most common operating sys-
recently to permit researchers to design virtual species by tems (Fig. 1), including Microsoft Windows, Mac OS X,
several methods. SDMvspecies software can create virtual and some Linux releases, such as Ubuntu. The electronic
species based on ideas from four previous reports: niche user manual, which covers all of the functions implemented
syntheses (Hirzel et al. 2001), pick mean method (Jiménez- in NicheA, installation and user support, can be found at
Valverde and Lobo 2007), pick median method (Lobo and < http://nichea.sourceforge.net/ >.
Tognelli 2011), and artificial bell-shaped response method Because biotic interactions introduce enormous complex-
(Varela et al. 2014). In virtualspecies, users can generate ity, and relevant data are generally lacking (Soberón 2007,
virtual species by two approaches – defining response func- Colwell and Rangel 2009, Holt 2009), NicheA focuses on
tions for each environmental variable, and defining suitabil- non-interactive (scenopoetic) variables in Grinnellian niche
ity from a principal components analysis (PCA; Leroy et al. environments (Soberón 2007), thus effectively ignoring
2015). Both, virtualspecies and SDMvspecies, were written biotic interactions. Even when ecological niches are related
as R packages (R Development Core Team). to the environmental space (E), the current literature focuses
In this paper, we introduced a platform from which to on management, evaluation, and interpretation of ecologi-
explore Hutchinson’s duality in the context of the BAM cal niches in geographic space (G). To mitigate biases in
framework and other niche-related concepts, called Niche G, NicheA allows generating and displaying species’ niches
Analyst (NicheA). This freely available program allows users in E, and visualization of species’ distributions in linked E
to create virtual environmental spaces and species, and to and G spaces. Functions and action flows in NicheA are
analyze ecological niches in both multivariate environmental illustrated in Fig. 1.
and geographic spaces, effectively linking views of niche and NicheA assumes that species’ fundamental ecological
distribution. niches are convex in shape, as available evidence suggests
(Birch 1953, Maguire 1967, Hooper et al. 2008, Angilletta
2009, Soberón and Nakamura 2009). Niches can thus be
Description operationalized as minimum-volume ellipsoids (Van Aelst
and Rousseeuw 2009) or convex polyhedrons (Rissler and
NicheA is a cross-platform application released under a Apodaca 2007, Soberón and Nakamura, 2009, Lloyd 2012,
GNU Public License (GPL). NicheA is written in Java, Monahan and Tingley 2012). NicheA can generate such
combining several other libraries from R (R Development forms, calculate their volume, density, shape, position, and

Figure 1. Feasible action flows in NicheA, showing four function modules. 1) The left block is the workflow for creating and displaying a
background cloud with environmental layers supplied by the user. 2) The second block shows generation of occurrence data sets, displaying
them in E, and computing their attributes. 3) The third block shows a simple function used to design barriers in G. 4) The final block
contains processes related to interacting with other modeling algorithms. N ⫽ virtual niche; BC ⫽ background; ENMs ⫽ ecological niche
models.

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other attributes, and quantify similarity among multiple Outputs
niches in terms of overlap in n-dimensional environmental
spaces. NicheA generates ecological niche models for virtual Different functions in NicheA have different outputs. The
species in E in the form of ellipsoids or polyhedrons, and main output, which is defined as the virtual niche, N, in
projects results to G. However, in view of the heterogeneous NicheA, is a folder including the following files: geographic
distribution of populations within the niche with high spe- coordinates of occurrences (ll.txt), plane coordinates (xy.txt),
cies abundance in core areas of the niche and low species environmental values of the occurrences (values.txt), and the
abundance at the edges (Martínez-Meyer et al. 2012, Lira- species’ geographic distribution in both GeoTIFF (present.
Noriega and Manthey 2014), NicheA can relax polyhedron tiff) and PNG (present.png) formats. Models can be gener-
assumptions, allowing projection of species distributions ated in binary and continuous formats. Continuous models
based on continuous or logistic functions (Lira-Noriega and based distribution of suitability using linear and logistic func-
Manthey 2014, Leroy et al. 2015). tions as in Leroy et al. (2015), but incorporating the ability
Niches of virtual species can be generated using three dif- of applying such functions to all the environmental condi-
ferent options. 1) Virtual niches can be created based on an tions available or restricted to environments falling inside
ellipsoid drawn manually selecting the shape, position, and the virtual niche based on a hyperdimensional ellipsoid.
size of ellipsoids using the widget in the software interface, Niches from virtual species in the form of ellipsoids can be
which allows ellipsoid manipulation from the computer’s exported in editable (.elp) and non-editable formats (.mve),
mouse or via writing the ellipsoid’s dimension for detailed that contain the elements of the ellipsoid (the centroid and
estimations; then, this niche can be exported to the geog- the covariance matrix) and are readable in NicheA.
raphy using the ‘Create a virtual N’ tool in the ‘Toolbox’ of Occurrence points drawn randomly from within a vir-
NicheA. 2) Ecological niches can also be generated based tual niche can be exported as a table with geographic coor-
on environmental parameters (e.g. temperature range) under dinates mirroring a continuous model with areas of high or
diverse suitability distributions established by the user using low suitability, arranging column labels in formats required
the ‘Virtual species – parameter’ tool. 3) Users interested in by popular ecological niche modeling software packages
generating virtual niches incorporating specific geographic (e.g. Maxent and OpenModeller; Phillips and Dudík 2008,
areas can create a virtual species based on geographic coordi- Muñoz et al. 2011; Supplementary material Appendix 3c).
nates resembling the site of interest using the ‘Generate N(s) Models of the virtual species in continuous format from
from occurrences’ tool. other ecological niche modeling software platforms can be
Furthermore, using NicheA, it is possible to increase evaluated in NicheA using the Partial-ROC AUC and AIC
complexity of virtual species by, for example, generating dis- metrics (Peterson et al. 2008 and Warren and Seifert 2011;
persal barriers in G and exploring associated configurations Supplementary material Appendix 3d and e). Continuous
in E, to simulate geographic configurations of species distri- models in raster format can also be converted to binary
butions and biogeography. Thus, users are able to generate based on nine threshold methods (Supplementary material
virtual species of known, user-selected fundamental niche Appendix 3f ). As complementary outputs, NicheA offers
characteristics; NicheA functions are summarized in Table 1. tables and figures associated with several analytical tools,
These tools are available in NicheA ver. 3.0 9.14.2015, and including niche overlap measurements in E, and descriptive
steps to develop virtual species are described in Table 2 and statistics of environmental variables, occurrence points, and
Supplementary material Appendix 2. model evaluation (Supplementary material Appendix 3g).

Environmental variables Scientific workflow management system

Two input data formats are used in NicheA to character- Functions in NicheA are connected by the outputs. In other
ize environmental landscapes: GeoTIFF and ESRI ASCII words, an output from one function can be an input of
raster grid layers. NicheA uses data held in these inputs to another function. NicheA provides a novel method to man-
draw a background cloud that characterizes the universe age connections among functions via a scientific workflow
of environments available to a virtual species. According management system that composes and executes series of
to the scientific question and user preferences, environ- computational or data manipulation steps (Fig. 2). Using
mental variables can be from original (e.g. temperature), this tool, users can carry out a complex analysis process, and
summarized (i.e. principal components; Supplementary these workflows can be shared, reused, and adapted. Users
material Appendix 3a), or virtual environments. NicheA can download shared workflows via the workflows reposi-
displays the distribution of the virtual niche in E based tory (Supplementary material Appendix 3h). Users can also
on one, two, or three dimensions (Supplementary mate- design their own workflows, and share them with other
rial Appendix 3b). One dimension displays are the density scientists to develop replicable ecological niche analyses.
and range occupied by the virtual species with respect to
each variable, whereas two and three dimensions are visu- Virtual species example
alized in the virtual scenario. Users can calibrate models
and generate multivariate analyses in NicheA using the The process to generate virtual species within NicheA is
n dimensions of E; however, the cost of overfitting and simple, as we will illustrate by means of some worked exam-
redundant data layers in analyses should be considered ple analyses. A basic workflow of this example is available
(Peterson 2007). as a default in NicheA for new users. First, we created an

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Table 1. Analytical tools available in NicheA.

Function Tool Description

Background data Principal component analysis Generate a principal component analysis (PCA) from selected raster
layers; result is a ‘background’ folder to generate a 2D or 3D
environmental space. This function also generates figures and tables
summarizing the analysis and correlation among variables and the R
script employed during the analysis.
Draw background – folder Select a background cloud from folder created during the PCA to display
a 3D environmental space.
Draw background – files Select a background cloud from raster layers selected by the user to
display a 2D or 3D environmental space.
Niche simulation Open (N)s Open one or several ecological niche (N) models from NicheA (folders)
or other software output (GeoTIFF/ASCII rasters).
Design barriers Open a geographic map that allows the user to create geographic
barriers. Areas selected will result in a portion of the virtual niche.
Clear scenario Remove all items from the current environmental space.
Create a virtual N Export the virtual niche to the geography based in the current editable
ellipsoid (i.e. white ellipsoid with colorful vertexes).
Generate virtual N(s) from Draw a virtual species from a coma delimited file (.csv) including the
occurrences species’ name, longitude, and latitude.
Generate virtual N(s) from ellipsoid Draw a virtual species from a previous saved minimum-volume ellipsoid
file (.mve) not editable.
Virtual species – parameter Create a virtual species based on selected physiological parameters.
User can determine the physiological limits of the virtual species and
the distribution of the frequency (i.e. uniform, normal, binomial,
poisson).
Save current selection Save current ellipsoid selection (.elp) for posterior edition in NicheA.
Open a selection Open an editable virtual niche (.elp).
Open selections Open more than one virtual niche (.elp).
Niche analysis tools Quantify niche overlap Measure the hypervolume overlap of two or more ellipsoids or
convex-polyhedrons.
N attributes Features of the virtual niche.
Import/export Export to ENMs Generate occurrence points from the virtual species to be used in
different ecological niche model software. Occurrences can be drawn
from areas with high or low probability based on a logistic function.
All occurrences can be exported with different suitability values and
then converted from point to raster using the ‘Convert points to raster’
tool.
Close N/ Close N: remove virtual niches from the background.
export N as continuous raster/ Export N as continuous raster: generate a species distribution model in
export MVE configurations GeoTIFF raster format with continuous values of the distance to the
niche centroid.
Export MVE configurations: export virtual niche as ellipsoid file (.elp) to
be open and edit later in an environmental space in NicheA.
Post-ENM analysis Threshold calculator Generate binary maps from continuous models based on 10 different
functions. Binary model and occurrences are required. Environmental
rasters can also be thresholded to show suitable areas according to
each environmental variable.
Occurrence statistics Describe the density distribution in environmental terms of the virtual
niche, according to geographic coordinates, a binary niche model,
and the environmental values available in the study area.
Change the range of the ENM’s Normalization technique to convert continuous model from values
result ranging between 0 and 100 or between 0 and 1.
Calculate AUC value of partial-area Useful for model comparison. Determines if the continuous models
ROC approaches predict independent occurrences better than by chance, considering
the area predicted in a binary format. Diverse binary thresholds can
be tested. Continuous models and occurrences are required (Peterson
2012).
Calculate AIC/BIC values Useful for model comparison. Determine Akaike information criterion
values of Maxent models (Phillips and Dudík 2008) for model
comparisons (Warren and Seifert 2011).
Utility functions Raster conversion Convert raster from GeoTIFF to ASCII files and vice versa.
Variable statistics Maximum, mean, minimum, and range values of the environmental
variables selected.
Read data from multiple raster Extract values from different environmental variables based on one
layers geographic coordinate.
Variable normalization/ Two methods available for normalization of environmental variables for
standardization better visualization of the background to create the virtual niche.
Set no data value Allows users to change the no data value of raster files to fit with
different software requirements.
Convert points to raster Convert occurrence points to raster file.

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Table 2. Steps to create virtual species using NicheA. Next, we collected 100 occurrences drawn at random
Steps Process Tool from N and generated new virtual niches from this sample.
The niche estimates that resulted were projected to geog-
Step 1 Generate background Principal component analysis,
draw background – folder raphy according to models based on a minimum-volume
Step 2 Draw virtual species Draw a virtual niche manually ellipsoid and a convex polyhedron. A detailed example and
using the widget in the left explanation are in the online manual (Supplementary mate-
panel of NicheA, generate rial Appendix 3j). Figure 3 illustrates the completed outputs
virtual N(s) from occurrences
or virtual species – parameter
of the process above.
Step 3 Import virtual species Save current selection To display the E and G link, which is a function unique
(ellipsoid), export to ENMs to NicheA, we generated geographic barriers (e.g. ocean, des-
(coordinates), export N as ert, river) for the virtual species in the geographic view, and
continuous raster (map), used the ‘Design barriers’ tool to divide G into four subsets
export MVE configurations
(ellipsoid) that could then be displayed in E (Fig. 4, 5). Finally, we mea-
Step 4 Virtual species analyses Design barriers, quantify niches sured the overlap between the resulting minimum-volume
overlap, N attributes, ellipsoids from the geographic footprint, as divided by the
threshold calculator hypothesized geographic barriers. Details of this process can
be found in the online manual (Supplementary material
environmental background using 19 bioclimatic variables Appendix 3k).
from the WorldClim climate data archive (Hijmans et al. Additional analytical tools in multivariate environmen-
2005) at 10’ spatial resolution. In NicheA, we calculated tal spaces, and the use of NicheA to manage other ENM
the principal components of the 19 variables, and drew a outputs are described in detail in NicheA’s user manual
background cloud using the first 3 principal components in (< http://nichea.sourceforge.net/ >). Video tutorials and case
the E viewer. Then, we created a virtual niche using widgets studies are available in both English and Spanish (< http://
from the NicheA interface to draw an ellipsoid representing bit.ly/1O9tmaQ >).
a virtual species’ niche (Supplementary material Appendix
3i; Fig. 2). To save the virtual species, we used the ‘Create a
virtual N’ tool. We then visualized the virtual niche, N, in Discussion
the geographic space based on environmental values inside
the minimum-volume ellipsoid we created, and projected NicheA provides a GUI-based tool by which to generate
the environments corresponding to a convex polyhedron virtual species based on physiological ranges, geographic
from the same ellipsoid to the geography. coordinates generated by the user, or a manual selection

Figure 2. NicheA interface. (A) The set of tool options by which to generate, analyze, and manage ecological niche models in environmen-
tal space. (B) Widget by which to generate virtual species manually using the mouse to move the bars or via entering specific dimensions
of the niche. (C) Environmental space window where ecological niches can be viewed in a three-dimensional environmental scenario as a
background cloud (gray points) with three virtual ecological niches (green, yellow, and red ellipsoids).

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Figure 3. Process by which to generate a virtual species’ niche. (A) Virtual species niche based on an ellipsoid generated manually (white
ellipsoid) using NicheA’s widgets to specify external vertices as environmental semi-axes X, Y, and Z (red points) and the niche centroid
(green point). (B) Final virtual ecological niche in the form of a minimum volume ellipsoid (MVE; yellow ellipsoid). (C) Convex polyhe-
dron from the virtual ecological niche (CP; green lines). (D) Points falling inside the virtual ecological niche (red points).

of hypothetical environmental spaces occupied by the vir- and geographic spaces. NicheA provides users with tools
tual species. NicheA allows users to explore the Hutchinson with which to explore G and E spaces for virtual spe-
duality through visualizations of linked environmental cies, as opposed to the manipulations in G only typical of

Figure 4. Linking environmental and geographic spaces using NicheA. (A) Virtual ecological niche based on a minimum-volume ellipsoid
(yellow). (B) Geographic distribution corresponding to the minimum-volume ellipsoid (yellow). (C) Virtual ecological niche based on a
convex-polyhedron (green). (D) Geographic distribution corresponding to the convex-polyhedron (green). Notice that niche estimation
using minimum-volume ellipsoid generates broader predictions compared to convex-polyhedron.

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Figure 5. Linking environmental and geographic space using barriers. (A) Virtual species’ niche in geographic space showing different por-
tions of the original fundamental niche. The original virtual species’ potential distribution split into distinct populations: North America
(red), South America (green), South Africa (yellow), and Australia (blue). (B) Each ellipsoid represents a sub-portion of the species’ funda-
mental niche. Notice that although populations of different continents are spatially distant their niches overlap broadly in E.

geographic information systems applications. NicheA gen- and Leroy et al. 2015), NicheA has a GUI to manage the
erates virtual species based on five approaches: minimum- virtual species’ niche in a multidimensional environmental
volume ellipsoids, convex polyhedrons, physiological ranges, space (Table 3), something we found critical for robust study
and linear and logistic functions (Leroy et al. 2015). Virtual design and accurate interpretation of outputs (Escobar et al.
niches are displayed in one, two, or three environmental 2014). Beyond creating virtual niches in an environmental
dimensions, but analyses can be developed in any number space from a variety of possibilities (e.g. manual or via occur-
of dimensions. rence data), NicheA allows the user to analyze the features
Furthermore, NicheA is a toolkit including several inde- of the virtual niche and to visualize and evaluate continuous
pendent functions with which to analyze the complexity of model outputs from diverse ecological niche model algo-
ecological niche models. Such functions can be arranged, rithms (e.g. Maxent). A virtual niche from NicheA can also
exported, and imported in the form of a workflow. By merg-
ing different functions via this tool, users can analyze diverse Table 3. Environmental scenario manipulation in NicheA using the
problems creatively, without the limitations of single-func- computer’s mouse.
tion applications. Thus, NicheA is a workbench at which
Operation Commands
users can address a variety of questions related to species’
ecological niches and geographic distributions. Rotate scenario Left click ⫹ mouse movement
Compared to existing tools for creating virtual species Zoom in/out scenario Alt ⫹ left click ⫹ mouse movement
including SDMvspecies and virtualspecies (Duan et al. 2015 Move scenario Right click ⫹ mouse movement

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Supplementary material (Appendix ECOG-01961 at < www.

ecography.org/appendix/ecog-01961 >). Appendix 1–3.

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