Applied Methods in Community Ecology and Functional Ecology



This is a mostly practical course offering an overview on different community ecology and macroecological methods and software. These will include all steps of a research project, from the optimal sampling of communities to process inference from large-scale patterns of taxon, phylogenetic and functional diversity. Specific topics will be: (1) alpha, beta and gamma diversity; (2) estimating diversity from incomplete sampling; (3) partitioning taxonomic beta diversity; (4) community-assembly rules, (5) functional and phylogenetic diversity, (6) null models, (7) rarity and species abundance distribution. Finally, students will be asked to present own data and case studies.


This course can have a recognition of 6 ECTs for FCUL PhD students enrolling in it as part of their first doctoral year. For students only requiring 5 ECTs recognized in their specific PhD programmes  the last 6 hours of the course are not mandatory and the certificate will be on 'Topics in Applied methods in Community Ecology and Functional Ecology’.

Minimum formation: “Licenciatura” (bachelor) in Biology, Geography or related areas; (very) basic knowledge of R is required.


Directed to: PhD or MSc students in Ecology, Geography or related areas, and postdocs working in related topics

General Plan

  1.        Partitioning diversity into independent alpha, beta and gamma components - basic concepts and software (Species Diversity, Richness IV and R).
  2.        Partitioning beta diversity - multiplicative vs. additive measures of beta diversity and replacement vs richness differences components. Applications in PARTITION and R.
  3.        Estimating diversity from incomplete sampling - algorithms and applications with EstimateS and R.
  4.        Conceptual bases of community assembly theory.
  5.        Conceptual bases of functional and phylogenetic approaches in community ecology.
  6.        Computing functional and phylogenetic diversity (overview of the different indices and different R packages available and introduction to null models)
  7.        Rarity and Species Abundance Distribution Models (SADs) with new applications in R.
  8.        Student’s case studies.


Students fees.




Free for 1st year PhD students in the Doctoral program in Biology (FCUL), Biodiversity, Genetics and Evolution (BIODIV UL; UP) and Biology and Ecology of Global Changes (BEAG UL, UA) when the course counts credits for their formation, in which case the delivery of a final report done after the course is mandatory; 25 € for PhD students from institutions of the PEERS network (cE3c, CFE); 125 € for FCUL Master students and unemployed; 180 € for BTI, BI and other PhD students; 250 € for Professional and postdocs.

When the maximum number of students is reached 10 vacancies will be available for non-paying 1st year PhD students mentioned above, being, by order of preference: 1) cE3c students; 2) BIODIV students (not from cE3c); 3) FCUL students (not from cE3c); 4) BEAG students (not from FCUL).

Contacts for Inscription

Candidates should send a short CV and motivation letter explaining why they are interested in the course, including a brief description of their research projects. Send all information and requests to Paulo A. V. Borges (