Seminar Series in Quantitative Biology and Ecology


The seminar series in Quantitative Biology and Ecology is part of the Serrapilheira/ICTP-SAIFR TRAINING PROGRAM IN QUANTITATIVE BIOLOGY AND ECOLOGY. This Program trains young Brazilian and other Latin American scientists for world-class research on biology and ecology using the quantitative methods of mathematics, physics, and computer science. It strategically makes use of the country’s well-established excellence in mathematics and physics to tap into Brazil’s tremendous potential in life sciences.

The invited speakers of the Seminar Series cover different topics in Ecology and Biology, also showing the different theoretical and quantitative approaches they use in their research. The seminar series will happen regularly every Wednesday until the end of November. On special occasions, we might have seminars on other weekdays.

As part of our Training Program to prepare better scientists, we also organize Talks on transversal themes in Science (such as Women in Science, Mental Health in Science, Scientific Communication, among others). The Talks on transversal themes in Science will happen regularly every Monday until the end of November.

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Previous Seminars

Quantifying and integrating molecules for a more precise medicine (click to watch)
Speaker: Helder Nakaya – Albert Einstein Instituto Israelita de Ensino e Pesquisa
Date: July 28, 2022 14:30
Abstract: Diseases are mostly a consequence of an abnormality in multiple genes. Network Medicine investigates how genes interact to each other in complex intracellular and intercellular networks. The talk will show the recent advances on this emerging field of research and its impact on precision medicine and drug repositioning in Chikungunya, Zika, Malaria and Yellow Fever.

Theory, Models and Methods in Macroecology (click to watch)
Speaker: José Alexandre Felizola Diniz Filho – Universidade Federal de Goiás
Date: August 4, 2022 14:30
Abstract: Macroecology, as a relatively new field in Ecology, holds distinct methodological characteristics that lead to profound philosophical changes in the nature of evidence to support and build theories and models. One reason for this is the impracticability of controlled or manipulative experimental studies at broad spatial and temporal scales, as well as historical contingencies and the complexity of ecological dynamics at these scales. We follow here a model-based reasoning for building scientific theories and show in particular how computer simulation models, applied to different case studies in diversity gradients, can be successfully used in macroecology as mediating theory and data.

Assessing risks to biodiversity from climate change using macroecological and macroevolutionary models
Speaker: Andreas L. S. Meyer – University of Cape Town
Date: August 11, 2022 14:30
Abstract: Climate change is already causing local biodiversity losses, affecting ecosystems, and disrupting the life-supporting services they provide to people. However, our ability to forecast biodiversity responses and identify species most at risk from climate change remains insufficient. Here, I will explore how macroecological and macroevolutionary models can help us predict ecological and evolutionary responses of biodiversity to climate change. I will also show how simple, intuitive models can provide unprecedented information to assess risks and improve conservation prioritization and decision-making processes.

Unveiling complexity in ecology and evolution (click to watch)
Speaker: Flávia Maria Darcie Marquitti – Universidade Estadual de Campinas / ICTP-SAIFR
Date: August 18, 2022 14:30
Abstract: Mathematical and computational models are powerful tools to investigate patterns and delve into the processes behind them, making sense of the complexity of natural systems, from individuals to communities. In this talk, I will present the two main lines that guide my research: interaction networks and evolutionary models. In the first part, I will discuss how interactions across different levels of organization are shaped in nature and discuss the theoretical processes that may have resulted in observed interaction patterns. In the second part, I will address how genetic structure is important for the evolution of strategies and how the evolutionary process leaves signals in phylogenetic trees.

Tipping points and resilience: the case of the Amazonian ecosystems (click to watch)
Speaker: Marina Hirota – Universidade Federal de Santa Catarina
Date: August 25, 2022 14:30
Abstract: Not available.

Population genomics in space and time: insights from ancient DNA (click to watch)
Speaker: Prof Fernando Racimo – University of Copenhagen
Date: September 14, 2022 11:30
Abstract: The sequencing of ancient genomes has provided an unprecedented opportunity to study human evolutionary history over thousands of years, in different regions of the world. Here, I will describe several methods developed in our group to relate genomic data to informative parameters about population expansions, movement and adaptation, while explicitly accounting for both spatial and temporal dimensions. These include a new way to model the spread of ancestry in ancient genomes across a landscape, along with a new simulation framework for easily generating spatial simulations of arbitrary complexity. We have recently applied some of these methods to a new dataset including thousands of ancient human genomes and used them to infer major population movements over the past 13 millennia of Eurasian history.

Virus and satellite in ecological coexistence (click to watch)
Speaker: Adriana L Sanz Garcia – Georgia Institute of Technology
Date: September 21, 2022 14:30
Abstract: Cooperation is a main driver of biological complexity at all levels. In the viral world, gene sharing among viral genomes, complementation between genomes or interactions within quasispecies are frequently observed. In this contribution, we explore the effects of flexible associations between fully fledged viruses and subviral entities, such as virus satellites, in viral dynamics and, in particular, in stable viral coexistence. We devise a mathematical model to compare different situations of competition between two viruses and to quantify how the association with a satellite qualitatively modifies dynamical equilibria. The relevant parameter is the invasion fitness of each virus or of the virus-satellite tandem, which in the model depends on the transmission rate of viruses and on their effect on host survival. In a virus-virus competition, one of the viruses becomes eventually extinct, recasting the competitive exclusion law of ecology. However, an association with a satellite might change the outcome of the competition in two ways, either to favor the less competitive virus (regardless of whether it is the helper virus or not) or to allow for the stable coexistence of the two viruses and the satellite. The virus-satellite association differs from other mechanisms proposed in ecology to date to enhance species coexistence. We hypothesize that such an association constitutes a parsimonious evolutionary pathway towards more stable cooperative associations, such as bipartite viral forms, a collaborative association unique to viruses.

Unraveling the complexity of the plasma membrane from studies of symmetric and asymmetric model membranes (click to watch)
Speaker: Thais A. Enoki – Cornell University
Date: September 27, 2022 14:30
Abstract: Cell membranes play important roles in cell function. The plasma membrane (PM) has the fundamental structure of a lipid bilayer, and has thousands lipid species that evolved to have physico-chemical properties that promote, for instance, a non-random lateral organization. This physical barrier protects the cell, and is composed of two leaflets of different lipid composition, thus is termed “asymmetric”. These PM leaflets have very different phase behavior. The exoplasmic leaflet, which faces the extracellular environment, is well studied using symmetric bilayers. The coexistence of liquid phases, named liquid disordered (Ld) and liquid ordered (Lo), is related to cell biology concepts of membrane rafts in the cell PM and is important to understand protein sorting and trafficking, membrane signal transduction, and viral assembly. We report a domain size transition tuned by the lipid composition, which can be explained by competing interactions between the line tension and dipole-dipole repulsion. In this transition, phase domain size abruptly changes without changes in the phase properties. Moreover, we observe notable patterns of modulated phases as the domain line tension decreases along the domain size transition. We also found a simple and accessible method to measure domain sizes below optical resolution (~200 nm). In contrast, the cytoplasmic leaflet lacks the high melting lipids, which with cholesterol could form the Lo phase. Thus, we need to consider a more complex model of the plasma membrane, which includes leaflets of distinct lipid composition. We first describe a new method to prepare asymmetric vesicles. Here, we use the hemifusion of giant unilamellar vesicles (GUVs) and a supported lipid bilayer (SLB) to engineer asymmetric GUVs, (aGUVs). We use different fluorescent dyes to monitor the inner and the outer leaflets of these unsupported aGUVs, and confirm that all newly exchanged lipids in the aGUVs are found in their outer leaflets. To model the plasma membrane, we prepare aGUVs that have one leaflet that phase separates into Ld+Lo phases, whereas the apposed leaflet forms a single fluid phase in an ordinary symmetric vesicle. For asymmetric vesicles, dye partition reveals induced ordered domains. We observed different cases where an ordered domain can induce order in the apposed leaflet. In addition, our results suggest that the induced ordered domains of the PM model are enriched in cholesterol. Therefore, the cytoplasmic leaflet may have “raft-like” domains induced by the exoplasmic leaflet.

Notification delay, a common problem on disease notification and how to correct it (click to watch)
Speaker: Leonardo Bastos – Programa de Computação Científica- Fiocruz
Date: October 4, 2022 14:30
Abstract: Notification delay in infectious disease surveillance consists in the time between the disease occurrence (symptoms onset) and the recording day. The second date refers to when the health system is aware of that case. Notification delay is a well-known problem in disease surveillance and usually the last days or weeks in a time series of disease counts tends to be ignored, otherwise a misunderstanding of the disease dynamic shall happen. However, this “solution” is far from optimal in an early warning system (EWS) for outbreaks, because the EWS would be too late to identify an outbreak. In this talk I will present a statistical approach to correct the delay that jointly model the delay and the time components proving predictions with uncertainty of the occur-but-not-yet-reported cases. The baseline model and some extensions will be presented and applied to different infectious diseases like COVID-19, dengue, chikungunya and malaria in Brazil. An R package is under development and will also be presented.

Pathogen dynamics across scales: from strain diversity to climate forcing (click to watch)
Speaker: Pamela Martinez Vargas – University of Illinois at Urbana-Champaign
Date: October 5, 2022 14:30
Abstract: The ecological and evolutionary mechanisms that influence the population dynamics of infectious diseases remain an active area of research of relevance to fundamental biology and applied public health. Temporal and spatial changes in infectious disease dynamics are difficult to anticipate due to the effects of environmental and climate drivers on the transmission of pathogens, and the complex diversity that these microorganisms exhibit. To address these challenges, I use mathematical models to study (1) how pathogen diversity interacts and interferes with intervention strategies and (2) how environmental and demographic factors shape the population dynamics of infectious diseases in space and time.

Structure and dynamics of complex parasite-host networks and their consequences for disease outbreaks
Speaker: Cecilia Siliansky de Andreazzi – Department of Biodiversity, Ecology and Evolution of the Complutense University of Madrid and Instituto Oswaldo Cruz -FIOCRUZ
Date: October 6, 2022 14:30
Abstract: Ecological communities are structured in networks of interacting species that shape and are shaped by ecological and evolutionary processes. To raise the challenge of understanding the mechanisms driving parasite spillover and disease outbreaks, we still need to develop approaches that capture the eco-evolutionary feedbacks connecting landscape use and community-level dynamics to the population-level processes that shape species abundances and trait evolution. In this talk I will discuss the effects of parasite-host coevolution on network structure and dynamics, how deforestation-driven changes affect parasite-host networks and if the reconfiguration of interactions amplifies or dilutes the risk of parasite spillover.

Emergent properties of behavioral coordination: slime molds, disease control, and plasmid evolution
Speaker: Fernando Rossine – Biomedical Informatics, Harvard Medical School
Date: October 12, 2022 14:30
Abstract: Not available.

The developmental basis of biological diversity: lessons from mammalian skin
Speaker: Ricardo Mallarino – Princeton University
Date: October 26, 2022 14:30
Abstract: The overall goal of my laboratory is to understand the molecular mechanisms by which phenotypic traits are established and elucidate how these processes are modified during evolutionary time to produce the spectacular phenotypic diversity seen in nature. To achieve this, we develop genomic and experimental approaches in non-traditional model species and focus on questions relating to patterning and the evolution of novelty in the mammalian skin. Mammalian skin is a powerful model because it exhibits remarkable diversity in structure and function across species, is experimentally accessible/tractable, and the molecular mechanisms underlying its formation are well characterized. In this talk, I’ll describe our recent work aimed at understanding two distinct spatially patterned phenomena during skin development (1) color pattern formation in rodents, and (2) formation of gliding membranes in marsupials. I’ll discuss how we are using a variety of approaches, including experimental embryology, transcriptomic and epigenomic profiling, comparative genomics, functional genetics, and imaging, to uncover gene function and understand mechanisms of evolutionary change. Together, by focusing on developmental mechanisms, our work seeks to provide a comprehensive roadmap for linking genotype and phenotype at an unprecedented mechanistic and conceptual level.

Patterns, processes, correlations, and causality: what is behind species and phenotypic diversification in vertebrates? (click to watch)
Speaker: Gustavo Burin – Department of Sciences (Division of Vertebrates) Natural History Museum – London/UK
Date: November 03, 2022 14:30
Abstract: Biodiversity has constantly changed in myriad ways throughout the history of life on Earth. Diversification, the balance between speciation and extinction, is influenced by many variables, including environmental and biological factors, and so are species’ phenotypes. During the several millions of years of a given lineage’s lifespan, we expect that the factors driving diversification dynamics will also change in relative importance. Identifying and quantifying how these factors drive diversity trajectories are therefore crucial to our understanding of past and current biodiversity. A plethora of macroevolutionary methods and techniques have been proposed to address increasingly complex questions about the drivers of diversification dynamics. However, several conceptual and methodological gaps still prevent researchers from directly examining phenomena of interest. One important issue is that most approaches are based on correlation tests and lack an assessment of the causal relationships between each system’s components, meaning that observed patterns cannot be causally inferred. This is especially true for complex systems with many interacting components. My work aims to address these gaps by both using multiple sources of information and implementing new approaches specifically developed to test for causality in time series to macroevolutionary data. To accomplish this, I use both diversification and phenotypical evolution dynamics to address fundamental questions in Macroevolution, drawing hypotheses from the observed patterns that can be tested using ecological information such as niche space occupation, and past and current geographical distributions. I will show some of my studies using tetrapods, a group with plenty of molecular, fossil, and ecological information available that makes them very useful to help me tackle most of my questions.

Evolution of complex traits: from genotypes to phenotypes to ecosystem services. (click to watch)
Speaker: Ana Paula Aprigio Assis – Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo
Date: November 09, 2022 14:30
Abstract: My research explores how ecological and evolutionary processes interact to determine populations’ responses to environmental change. Adaptive responses are determined by the magnitude and direction of selection, but also by patterns of variation and genetic covariation among traits. Throughout my career, I have studied how these two components (selection and genetic variation) interact to determine the direction and rate of evolution. To study this, I use a combination of empirical and theoretical approaches based on quantitative genetics and ecological theory.

The shape of vocal communication in a non-human primate
Speaker: Daniel Y. Takahashi – Instituto do Cérebro, Universidade Federal do Rio Grande no Norte
Date: November 16, 2022 14:30
Abstract: Primate societies coordinate group actions by communicating with each other. Often such coordination is achieved by exchanging vocalization with each other. When the vocalization itself is modulated by other vocalizations, i.e., a feedback loop is established, a complex dependence of calls emerges where what one animal vocalizes depends on the history of its own vocalization. (1) How can we understand the dynamics and neural basis of vocal interactions that are subject to dynamic interactions? Vocal communication changes during development together with changes in the entire body and social environment. The change in vocalization affects the body and social environment and vice-versa in such a way that we cannot understand vocal development by decoupling one factor from the other. Hence, it is natural to ask (2) What do we mean by understanding vocal development when the body, brain, and environment are all dependent on each other? A general characteristic during the development of vocalization in vocal-learning primates is the existence of sudden non-linear changes in the call acoustics from an immature vocalization stage to a mature vocalization stage. (3) How can we explain the nonlinearity in the vocal development of these animals? In this talk, using marmoset monkey vocal behavior and mathematical modeling I will show that we can approach the three questions posed above.

From systems biology to evolutionary predictions
Speaker: Fernanda Pinheiro – Fondazione Human Technopole
Date: November 17, 2022 14:30
Abstract: Urgent challenges of modern medicine require understanding evolutionary processes. But how can we distill the seemingly overwhelming complexity of biological evolution into simple, quantitative frameworks that can ultimately generate evolutionary predictions? In this talk, I will explore the interface of systems biology and evolution to address this question in the context of antibiotic resistance. Bacteria evolve resistance to antibiotics through multiple mechanisms, which allow them to grow under conditions they should not. At its core, antibiotic resistance is an exercise in bacterial growth. Yet, the question of how resistance evolution affects cell growth at different drug levels is still open. I will present a fitness model that predicts growth rates of common resistance mutants from their effects on cell metabolism. The model integrates drug action and evolutionary response into bacterial growth laws. It predicts evolutionary trajectories of dosage-dependent growth rates and resistance levels, as well as the prevalent resistance mechanism depending on drug and nutrient levels. These predictions are confirmed by empirical growth inhibition curves and genomic data of E. coli populations. In a broader context, I will discuss how metabolic models linking systems biology, ecology and evolution can become a tool for predictions.

Upcoming Seminars

Microbiota interactions with the plant immune system

Paulo Teixeira

Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo

November 23, 2022 14:30

Abstract: Plants have a sophisticated immune system to fend off invaders and prevent diseases. Yet, they are normally inhabited by thousands of microbial species, many of which have beneficial effects on the host. How plants mount effective defenses against pathogens while allowing the colonization of commensals remains poorly understood. In this talk, I will discuss how the plant immune system interacts with the microbiome, highlighting recent findings regarding the suppression of plant immunity by commensal microbes.

Informal Meetings

During the period of September 12 – December 2, 2022, 28 distinguished international researchers in the fields of biology and ecology will be participating in the advanced module of the Serrapilheira/ICTP-SAIFR Training Program in Quantitative Biology and Ecology. In order to discuss common research interests which may lead to future collaborations, ICTP-SAIFR is organizing weekly informal meetings of Brazilian PhD students, postdocs and professors with these distinguished researchers.

The informal meetings will occur for a few hours in the late afternoon of one day during the visit of the researcher. The precise dates will be decided later, and if you would like to participate in one or more of these informal meetings, please fill out the application form at least one month before the visit of the researcher. You can request to participate in up to 10 informal meetings, and you will be asked to order in priority from 1 to 10 the researchers whom you would like to meet.

The application form and the list of names and dates of the visiting researchers are at


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