MONDAY 15th December 2025

WELCOME TO THE COURSE 

THEORETICAL BASES IN EVO-DEVO. MORNING SESSION: Ignacio Maeso

One of the central questions in the field of Biology is understanding the origin of the extraordinary morphological diversity of living forms. In recent decades, the study of disciplines such as molecular biology, evolutionary biology, genetics, and embryology has been promoted, providing compelling evidence that supports the vast conservation of the biological foundations of living organisms and their regulatory mechanisms. Specifically, studies on evolutionary developmental biology over the past decade have focused on understanding the hierarchy in signaling pathways and gene regulation, as well as the delineation of levels of biological organization based on genotypic and phenotypic modules that generate diversity. In this session presentation, I will develop these topics and introduce the course speakers in an integrative manner, following a common thread that will be the theoretical and empirical review of the evolutionary process.

ECO-EVO-DEVO. MORNING AND  AFTERNOON SESSIONS: Christoph Liedtke

In this session, I will highlight how transcriptomics (bulk RNA-seq) is a powerful approach for studying gene expression of plastic phenotypes in non-model organisms. I will introduce this technique and go through a hands-on practical of how to study the gene expression underlying plastic changes in pigmentation in amphibian larvae.

TRANSCRIPTOMICS IN EVO-DEVO. AFTERNOON SESSION: Isabel Almudí, María Roselló

In this session we will use RNA-seq toolkits to see how the evolutionary novelties have influenced the radiation of certain groups of animals, with a particular focus on the results we have obtained in the evolution of winged insects, the most diverse and numerous group of animals on the planet.

TUESDAY 16th December 2025

SINGLE CELL SPATIAL TRANSCRIPTOMICS. MORNING AND AFTERNOON SESSIONS: Jordi Solana; Aida Verdes

The session will be dedicated to the topic of single cell transcriptomics, with a structured approach to understanding its theoretical, molecular, and practical aspects. Beginning with a brief introduction to bulk transcriptomics (RNA-seq), we will lay the groundwork for comprehending single cell analysis. Subsequently, we will delve into the essentials of cell dissociation, explore the molecular basis of cell barcoding, and establish the foundational concepts behind the analysis methods used in single cell transcriptomics. To enhance comprehension, the session will also feature a hands-on practical exercise, allowing participants to actively engage with and visualize single cell information. Finally, we will see some practical applications of single cell transcriptomics to study stem cells and their evolution in different regenerating invertebrates such as cnidarians, annelids and planarians. In addition, we will explore on Spatial Transcriptomics, a powerful technology that allows to map and visualize the spatial location of whole transcriptomes within tissue sections. This allows us to connect specific molecules with particular anatomical features, tissues or even cell types, helping us to better understand the function and evolution of traits.

WEDNESDAY 17th December 2025

PHYLOGENOMICS. MORNING AND  AFTERNOON SESSIONS: Iker Irisarri; María Eleonora Rossi; Ana Riesgo

In this session we will give a general overview about phylogenomic and comparative genomic analyses explaining their differences from the classical phylogenetic approaches and, above all, why are they fundamental in evo-devo studies. With theoretical and hands-on practical exercises, we will understand all the basic tools available in phylogenomics (data acquisition, filtering, ortholog search, etc), including an introduction to synteny-based network analyses.

FUNCTIONAL GENOMICS IN EVO-DEVO. AFTERNOON SESSION: Juan Tena

In this session, we will discuss the ATAC-seq technique, which provides a map of open or accessible regions of the genome. These regions are usually active regions, mainly promoters and regulatory elements, so the results of this technique are extremely useful in studies related to gene regulation. In the theoretical part, we will discuss sample preparation and the main steps of data analysis, and in the practical part we will perform a simple analysis and visualize the results.

COURSE DINNER

THURSDAY 18th December 2025

FUNCTIONAL GENOMICS IN EVO-DEVO. MORNING SESSION: Marta Portela

In this session we will give a  a comprehensive introduction to gene regulatory networks (GRN). Through a combination of theory and hands-on exercises, participants will learn how regulatory interactions are identified, how to interpret network dynamics, and how these insights inform our understanding of cellular states, development, and evolution. The session will guide students through building the key components of a GRN—including coexpression matrices, cis-regulomes, and transcription factor–target databases—and show how to integrate these elements into a network that can be visualized and analyzed.

FUNCTIONAL GENOMICS IN EVO-DEVO. AFTERNOON SESSION: Manuel Irimia

A fundamental challenge in Biology is to understand how a single genome sequence can give rise to the extensive variety of cell and tissue types that compose a complex multicellular organism. Decades of research in cell and developmental biology have shown that this is achieved by tight transcriptional and post-transcriptional regulation of the genome during embryogenesis and adulthood. The primary outcome of this regulation is the transcriptome. Fortunately, the development of next-generation sequencing technologies more than a decade ago have allowed us to obtain highly detailed snapshots of the transcriptome of any given sample. From these data we can extract, for example, the quantitative regulation of gene expression and the qualitative diversification through alternative splicing. In this seminar, I will give an overview about comparative transcriptomic analyses, especially with respect to alternative splicing. 

CLOSING REMARKS.