• Advanced Courses in Life Sciences

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Online Course – 1st Edition

Introduction to Geographic Analyses of Biodiversity

May 24th-28th, 2021


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This course will be delivered live online

This course will be taught using a combination of live (synchronous) sessions on Zoom and tasks to be completed in between live sessions on the Slack platform.
The live sessions will be recorded and available to the participants for a limited period of time. However, attendance at the live sessions is required as this course is mostly hands-on.


Course Introduction to Geographic Analyses of BiodiversityCourse Overview

In this course instructors will introduce different conceptual biological reasons why it might be interesting to examine biodiversity data in a geographic context, focusing on the relationships between species richness, trait similarity and phylogeny, as well as patterns of turnover in those relationships. In this overview, they will discuss what these can reveal about patterns of community assembly, in situ diversification vs immigration, as well as the potential connections between these patterns and environmental/climatic/elevational gradients.

In this workshop, instructors will cover how to obtain the various types of data (geographic, environmental/climatic and elevation; morphological and phylogenetic), how to work with them in R, the metrics of diversity, and how to map them for purposes of visualization and how to conduct the statistical analyses, taking geography into account.

This workshop is primarily intended for (but is not exclusive to) graduate students and postdocs with a degree in biological sciences.

The instructors will supply datasets but participants are encouraged to bring (or download) geographic information, phylogeny and morphological data.

Check the full program here


Some familiarity with R is strongly recommended (and will be needed to follow the workshop).

Participants must have a personal computer (Windows, Mac, Linux). The use of a webcam and headphones is strongly recommended, and a good internet connection.




May 24th-28th, 2021

Schedule and Course length

Online live sessions from Monday to Friday from 15:00 to 17:00 and from 19:00 to 21:00 (Madrid time zone).

Participants are expected to work on exercises between the live sessions each day.

30 hours

This course is equivalent to 1 ECTS (European Credit Transfer System) at the Life Science Zurich Graduate School.

The recognition of ECTS by other institutions depends on each university or school.




Places are limited to 18 participants and will be occupied by strict registration order.

Participants who have completed the course will receive a certificate at the end of it.

Pascal Title instructor for Transmitting Science

Dr. Pascal Title

Stony Brook University

Miriam Zelditch instructor for Transmitting Science

Dr. Miriam Zelditch

University of Michigan

Donald L Swiderski instructor for Transmitting Science

Dr. Donald L. Swiderski

University of Michigan

Haris Saslis coordinator for Transmitting Science

Dr. Haris Saslis
Transmitting Science

Soledad De Esteban-Trivigno Transmitting Science coordinator

Dr. Soledad De Esteban-Trivigno

Transmitting Science

Iris Menéndez coordinator for Transmitting Science

Iris Menéndez

Universidad Complutense de Madrid


Introduction to ecoPhyloMapper

  • We will demonstrate how to work with the multiple types of data so that all can be integrated in the analysis of geographic patterns of biodiversity.  One major hurdle is to align all the types of data, which can be done using the tools in ecoPhyloMapper, an R package with tools that facilitate the manipulation of these datasets. We also provide tools for calculating a variety of metrics per grid cell, and for generating turnover patterns in taxonomic, phylogenetic and multivariate trait space. The novelty of the R package lies in the data structures and helper tools, as well as in the spatial grid metrics intended for multivariate morphological data.

Sources and types of data

  • Geographic
    • We will briefly discuss the types of biodiversity data one might come across: Primary biodiversity data such as occurrence records, expert range maps (IUCN), suitability surfaces from SDM’s, etc. We will discuss how these fit into the ecoPhyloMapper framework (for instance, use occurrences directly, or make polygons from them?).
  • Environmental
    • We will briefly discuss types of environmental data, online sources of those data, and how to obtain and import them into R. Among the types of data we will cover are rasterized climate data and polygon land cover types, from sources such as Worldclim, Chelsa, EarthEnv, and Bio-Oracle.
  • Phylogenetic
    • We will discuss the main formats for phylogenetic trees that can be imported into R, where to obtain them, and how to work with multiple trees, including how to produce the maximum credibility tree from a Bayesian posterior distribution of trees.
  • Morphological
    • We will briefly introduce the formats for size and shape data, and how to produce the formats needed to integrate both univariate and multivariate morphological data with geographic and phylogenetic data.

Producing an ecoPhyloMapper object

  • We will review the main considerations for constructing a ecoPhyloMapper object, including (1) spatial resolution, (2) grid type, (2) spatial projection and how they capture what you are trying to measure.

Working with phylogenies

  • We will present an overview of what you can infer from phylogenies, such as what “patristic distance” means, and what the “diversification rate” statistic (DR) means and what you can learn from phylogenetic signal and the geographic structure of phylogenetic turnover.

Working with shape data: An introduction to geometric morphometrics

  • We will briefly summarize the basics of shape analysis, including the collection of landmark and semilandmark data, extracting shape and size data from them, and measuring distances between shapes and sizes.

Measuring biodiversity

  • We will first present an overview of metrics of biodiversity and how they are related to each other, and what these mean for interpreting their geographic distributions, and how to visualize these on a map using ecoPhyloMapper.

Statistical analysis (SARS models)

  • We will present an introduction to statistical methods for analyzing relationships among the metrics of biodiversity (Spatial autoregressive models), including how to obtain a random sample from the grid cells of the map, determine the best model for the error term (to take spatial autocorrelation into account in the statistical analysis), and plot the relationships between variables.


  • Course Fee
  • Early bird (until April 30th, 2021):
  • 545 €
    (436 € for Ambassador Institutions)
  • Regular (after April 30th, 2021):
  • 620 €
    (496 € for Ambassador Institutions)
  • The price is VAT included.
    After registration you will receive confirmation of your acceptance in the course. Payment is not required during registration.

You can check the list of Ambassador Institutions. If you want your institution to become a Transmitting Science Ambassador please contact us at communication@transmittingscience.com


Discounts are not cumulative and apply only on the Course Fee. We offer the possibility of paying in two instalments (contact courses@transmittingscience.com).

Former participants will have a 5 % discount on the Course Fee.

20 % discount on the Course Fee is offered for members of some organizations (Ambassador Institutions). If you want to apply to this discount please indicate it in the Registration form (proof will be asked later).

Unemployed scientists living in Spain may benefit from a 40 % discount on the Course Fee. If you would like to enquire about this discount, please contact the course coordinator. That would apply for a maximum of 2 places and they will be covered by strict registration order.