16 May 19 May
From May 16, until May 19, 2022 - CIBIO-InBIO, Vairão, Portugal
University of Porto


From May 16, until May 19, 2022 - CIBIO-InBIO, Vairão, Portugal
(The course will take place in a classroom context)

Spatial conservation prioritization is a relatively new field which uses spatial data and quantitative techniques to support decision-making. Several methods and tools have been developed, two of the most popular being Marxan and Zonation, which solve two different mathematical problems: the minimum set and the maximal coverage, respectively.

This course aims to
1) introduce the main concepts underpinning spatial conservation prioritization;
2) distinguish the two major conservation problems: minimum set and the maximal coverage;
3) develop computational skills to use Marxan and Zonation programs;
4) Provide insights about different applications of these methods.


Day 1

Morning - 9h45 – 12h45


Introducing the lecturers, students, practical arrangements

What to expect from the course

Overview of the program

Preparing for the practical exercises

Installing R, R Studio, required R packages, QGIS and plugin CLUZ, Marxan and Zonation

Copying the exercise files from Dropbox to your local drive

Lecture1 – Spatial Conservation Prioritization

Convention on Biologic Diversity, and the Aichi Targets, the post-2020 Biodiversity Framework

The importance of space in conservation and restoration

Protected areas as a conservation tool

Systematic Conservation Planning: history and core principles

Mathematical characterization of conservation prioritization problems: minimum set vs maximal coverage

Types of conservation features: ecoregions, habitats, species distributions, phylogenetic, genetic and genomic data. Data sources.

Types and examples of spatial data used in conservation prioritization: point, polygon, raster

Practical – Introduction to spatial data and spatial analysis in R

Types of spatial data – vector and raster data

Import and process vector data

Importing and process raster data

Convert between vector and raster formats

Data projection systems and conversions

Afternoon - 14h45-17h45

Lecture 2– Introduction to Marxan

The Marxan objective function

Introduction to Marxan optimization - simulating annealing

Marxan´s input and output files

Practical – Understanding the Marxan algorithm

Optimization exercise with Excel

Day 2

Morning - 9h45 – 12h45

Practical - Using Marxan Software (part I)

Creating the planning Unit file (Pu.dat)

Creating the planning unit versus species matrix (puvsp.dat)

Using R with point (Gbif), polygon (IUCN) and raster (maxent .asc outputs) distribution data

Creating the species file (spec.dat)

Creating the boundary length file (bound.dat)

Afternoon - 14h45-17h45

Practical – Using Marxan Software (part II)

Run Marxan through R

Understand and calibrate Marxan parameters and interpret outputs

Display Marxan output and Interpret solutions

Design of planning scenarios: lock in/ out planning units, costs and connectivity

Import Marxan solutions to R for future analysis

Day 3

Morning - 9h45 – 12h45

Lecture 3 – Connectivity in spatial conservation prioritization

The importance of accounting for connectivity in spatial prioritization

Types of connectivity – Boundary Length, asymmetrical, longitudinal, lateral connectivity

Different ways to incorporate connectivity data in Marxan

Practical – Using Marxan Sofware (part III)

Create boundary files for different types of connectivity: asymmetrical, longitudinal and lateral

Run Marxan and exploring different results

Afternoon - 14h45-17h45

Lecture 4 –The Zonation framework

The Zonation framework

Zonation Meta-algorithm and cell-removal rules

Zonation Input and output files

Connectivity in Zonation: boundary length penalty, distribution smoothing, boundary quality penalty, directed connectivity, matrix connectivity, edge adjustment in connectivity

Using Zonation to spatial prioritization spanning the evolutionary continuum

Practical– Running Zonation (Part I)

Create Zonation input files

Run Zonation through command line

Day 4

Morning - 9h45 – 12h45

Practical– Running Zonation (Part II)

Analyze Zonation results: compare results with different cell-removal rules, connectivity options and biodiversity levels

Modify input files to accommodate phylogenetic diversity and intra-specific variation

Afternoon - 14h45-17h45

Practical– Running Zonation (Part III)

Post processing analysis and options

Discussion and Conclusions

Hours: 24


 9:45am to 17:45pm, lunch between 12:45-14:45


Silvia Carvalho (Coordinator) | CIBIO-InBIO | THEOECO/ BIODESERTS


Virgilio HermosoUniversity of Sevilla


The course will be open to a maximum number of 20 participants.


75% of available student slots are reserved for BIODIV students.
 Priority will be given to:
• 1st year and other PhD students attending the BIODIV Doctoral Program;
• PhD students attending other courses;
• Other post-graduate students and researchers.


Participation is free of charge for BIODIV students | 80€ (students) | 150€ (other participants). CIBIO-InBIO members will have an additional discount of 20%

Please note the rules apply for all BIODIV students


Registration deadline: March 31, 2022
All applicants will be notified about whether they are accepted until April 11, 2022

Fill out the application form and confirm that the following message appears:           

Thanks for your application!
Applicants will be informed of their acceptance by email.