Current members
Group leader
Loïc’s research is focused on understanding and modelling past and future landscape dynamic and its link to biodiversity. His research provides fundamental knowledge in ecology and evolution of landscape biodiversity patterns and uses this knowledge to improve sustainable management of natural resources.
Coordinators
Lead scientist
Camille works at the interface of the research fields of biogeography, macroecology and evolution to understand the origin of marine biodiversity, its current distribution and its possible future under climate change and anthropogenic pressures. Camille investigates the spatial and temporal dynamics of marine assemblages by accounting for species identity, phylogenetic and functional diversity as well as the trophic interactions that connect species in ecosystems.
Teaching coordinator
Fabian is a lecturer and coordinates the teaching of the ecosystems and landscape evolution group. This includes several bachelor and master courses about environmental data science, eDNA for biodiversity monitoring, spatial analysis in R and basic and advanced landscape research. He is also involved in the coordination of two massive open online courses (MOOCs) about landscape ecology and environmental DNA (eDNA).
Wet-lab coordinator
Sarah is the wet lab coordinator, who will introduce everyone to the lab. She is the reference person in the group for the metabarcoding libraries development and optimisation. Her love of nature and being outdoors changed her focus to applying her skills from biotechnologies to monitoring biodiversity.
Admin and IT staff
Ankara del Carmen Marjatshang-Chen
Ankara runs the institute secretariat for ITES and is administrative assistant for two Professorships within the Institute, including the Chair of Ecosystems and Landscape Evolution. Ankara provides day-to-day administrative support, her responsibilities include reporting to the management, handling human resources and finances, organising and scheduling events, and acting as the point of contact between employees, guests and the various ETH bodies and services.
Gilbert assists the group with server installation and administration for users, groups, mailing lists, and the network management including the security handling. He does the setup and maintenance of the websites. He is responsible for hardware procurement and handling and does the basic and user specific installations including updates with Baramundi, including handover to new end-users or to the lab. In addition, he provides the end-user support, especially fore the more difficult cases.
Scientific staff
Meret is interested in the potential of environmental DNA (eDNA) as a powerful and rapidly evolving method for monitoring biodiversity in a time of rapid ecosystem change. The possibility of taking small, cost-effective sequencing devices into the field to generate real-time data is an exciting prospect for her. It increases the ease of access to generating data and creating scientific insights without depending on large laboratories that are often far from sampling sites. Her role is to help develop and test methods for the XPRIZE Rainforest competition to survey as much rainforest biodiversity as possible in a designated area of tropical rainforest within 24 hours. While the focus of her work is on the XPRIZE, she is excited to be developing these methods for future easy use in a broader context and further afield, say in the Arctic.
With his work, Thomas will explore the biogeodynamic processes driving life diversification within a joint research effort between the ELE group and the Department of Earth Sciences. In the investigation, he'll be utilizing machine learning techniques and computer simulations as his main tools. The primary focus is to develop fitness functions based on animal traits to represent species-environment and species-species interactions and to integrate these in existing modelling eco-evolutionary frameworks such as Gen3sis.
Postdoctoral researchers
Virginie’s research focuses on integrating molecular ecology tools via the use of environmental DNA (eDNA) to unravel the mechanisms shaping biodiversity patterns across ecosystems. Within the group, she is part of the SPI Greenfjord project, which plans to investigate the impact of melting glaciers on the marine ecosystem in Greenland fjords by relating physical properties and geochemical fluxes to biodiversity measured using eDNA metabarcoding. At the Arctic scale, she also aims at studying the spatial structure and drivers of marine food-webs properties.
Martina is interested in developing new methods for projects with an applied outcome. With her background in molecular biology she is therefore working on the CRISPeD project to help develop a CRISPR-Cas based method for rapid and efficient biodiversity monitoring via eDNA. Harnessing this novel approach should help advance real-time biodiversity and species monitoring.
external pageThéophile Sanchez
Théophile develops new approaches for the large-scale analysis of environmental DNA (eDNA) metabarcoding data. His work aims at replacing the current processing pipelines for taxonomic classification and sample classification with more automated and precise algorithms based on Deep Learning. These methods should help the community in ecology to improve biodiversity monitoring in order to find better management strategies for species and ecosystems. His research is part of the DNAi project, which involves the collaboration of the ETH, the Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), the Swiss Data Science Center (SDCS) and the Centre d’Écologie Fonctionnel et Évolutive (CEFE).
Sarah is captivated about natural history museum collections - which are precious archives documenting the biodiversity. For her project, she highlights the value of those collections by exploiting museum specimens to develop a global genetic reference database of fishes and sharks. She will subsequently use this reference catalog to reanalyze eDNA metabarcoding samples collected over all oceans to determine fish and shark community composition.
external pageMarie-Ange Dahito
Marie-Ange is interested in mathematical programming and algorithm development for the resolution of complex real-world optimization problems. Her experience includes mixed-variable blackbox optimization and continuous nonlinear optimization. Strongly interested in environmental issues, her current research falls within the net zero initiative and focuses on using mathematical optimization tools to favour the energy transition in Switzerland while preserving biodiversity.
Lucie's research within the ACTNOW project (external pagehttps://www.actnow-project.eu/) focus on environmental DNA (eDNA) to monitor and assess the biodiversity of the Mediterranean Sea, offering unprecedented insights into its marine ecosystems. Lucie investigates the sanctuary effect of marine protected areas in the context of climate change and overfishing, with the goal of enhancing decision-making tools. By characterize the present marine biodiversity, her research also aims to detect new invaders and track their proliferation routes throughout the Mediterranean Sea.
Phd students
Yi investigates the drivers of mountain biodiversity. Globally, the biodiversity of different mountain regions varies notably. To attempt to have a better understanding of the processes shaping the patterns of montane biodiversity, he is working on the alpha and beta diversity patterns of plant groups across several mountain ranges, including the Rockies, Colombia, Hengduan, Madagascar, Alps, and New Zealand. His dissertation is co-supervised by Dr. Catherine Graham and Dr. Niklaus E. Zimmermann at WSL.
Wilhelmine’s research is focused on integrated mechanisms that have shaped biodiversity gradients of mammals, birds and amphibians globally. Hypotheses on the origin of biodiversity will be coupled with landscape dynamics to unravel large spatial patterns, such as the latitudinal diversity gradient. She will integrate ecological and evolutionary mechanisms with paleo-environmental reconstructions to simulate species distribution within a process-based model and compare them to extant biodiversity patterns.
Yaquan investigates what shapes the plant biodiversity and turnover in the Hengduan Mountains, China – an exceptional biodiversity hotspot outside the tropics. The historical (e.g. tectonic) and contemporary (e.g. climate) processes may have an integrated impact on the plant biodiversity patterns. Thus, one of the main aims of her Ph.D. project is disentangling these processes. Besides, she will also investigate functional and phylogenetic diversity to supplement taxonomic diversity, trying to get a holistic view of the biodiversity patterns and how they structured spatially.
In his PhD, Zili focuses on the macroevolution of the plant biodiversity in the Hengduan Mountains, China, which is a biodiversity hotspot. Different from a classical phylogenetic or population genetic analyses, in his study, taxonomy-centered sets of analyses will be carried out, contrasting sister species pairs regarding their geographic and ecological separation; along with analyzing of different genera and species richness across the Hengduan mountains, a better understanding of diversity which shaped Henduan mountains diversity as it is today can be outlined.
Dominik is broadly interested in aquatic ecosystems and especially in the application of environmental DNA (eDNA) based molecular methods. These methods allow us to uncover aquatic biodiversity in wide geographical areas (e.g. in a river catchment) with manageable effort. Dominik will use these techniques and focus on eDNA-metabarcoding to investigate the effects of river capture events on fish species assemblages and biodiversity in several rivers in Yunnan, China. His PhD is part of the BECCY - Project (Biodiversity, Earth, Climate Coupling in Yunnan), which combines various scientific disciplines to uncover the drivers of biodiversity in this hyper diverse region. Dominik's research is co-supervised by Prof. Florian Altermatt (EAWAG) and Prof.Loic Pelissier (ETH).
Shuo’s research interests are monitoring biodiversity and ecosystem globally and improving large-scale biodiversity modeling with the combination of satellite imagery and ground data. He tries to understand the connection between land cover shift and biodiversity using Remote Sensing, Environmental DNA, and Machine Learning methods. For this, he applies Remote sensing to estimate Essential Biodiversity Variables (defined by GEO BON) and develops other co-variables that have tight relationships with biodiversity and Environmental DNA, then applies Machine Learning methods to biodiversity mapping.
Julian studies the dependencies between geodynamic processes, the climate system and the biosphere over geological time by coupling models of the respective domains. A focus is given to the evolution of plant species and the resulting plant trait diversity and how they affect biosphere-geosphere interactions. His PhD is part of a joint research project of the Landscape Ecology group and the group of Geophysical Fluid Dynamics at the Department of Earth Sciences.
external pageMerin Reji Chacko
Merin’s research is focused on building a metaweb — a matrix encompassing all possible trophic interactions — of animal species in Switzerland based on data compilation, observations, molecular methods and modelling tools. The aim of her research is to better understand the robustness of ecosystems to global environmental change and ultimately develop novel indicators of biodiversity change in combination with ongoing monitoring programs.
Monika’s PhD focuses on the use of environmental DNA in monitoring the effects of habitat loss and restoration on vertebrate communities. In particular, she is interested in applying eDNA metabarcoding to study patterns of catchment-scale vertebrate diversity in response to reforestation projects in Colombia. Through her research, she also aims to advance eDNA-based indicators of biodiversity to facilitate monitoring progress of restoration projects. Monika is a RESPONSE DP Fellow and her project is in collaboration with Dr. Arnaud Lyet at WWF US and Dr. Tony Dejean at SPYGEN.
Flurin is interested in biodiversity monitoring using environmental DNA (eDNA) and conservation. He is part of the team developing (species-)specific Crispr assays which should allow rapid detection of the target organisms and thus benefiting large-scale biodiversity monitoring. Flurin aims to investigate during his PhD the effectiveness of conservation measures based on the newly developed eDNA-based Crispr assay across catchments.
Romane’s research focuses on the application of environmental DNA (eDNA) in marine ecosystems to explore spatial variations of biodiversity at different temporal scales. She investigates the evolution of taxonomic, phylogenetic, and functional diversity in marine communities across different types of ecosystems in the Mediterranean Sea (tropical), Atlantic Ocean (temperate) and Arctic Ocean (polar), in areas under different levels of protection. She also aims to develop an innovative eDNA structure to perform autonomous sampling allowing to explore short-term temporal variations of biodiversity in those ecosystems.
Anouk investigates different monitoring methods for urban mammals, such as eDNA sampling, wildlife cameras and citizen science observations, based on their efficiency and effectiveness. She will analyze habitat and space use in squirrels and hedgehogs and other mammals in order to discover changes in distribution and abundance and to develop management and conservation strategies. The data analyzed in her dissertation has been collected in the citizen science projects StadtWildTiere and Wilde Nachbarn. Her dissertation is based at SWILD in Zurich and co-supervised by Prof. Loïc Pellissier (WSL and ETH), Prof. Holderegger (WSL) and Dr. Fabio Bontadina (SWILD).
Sherub’s research is focused on connecting the power of eDNA with spatial modelling in a landscape-scale wildlife assessment in Bhutan. A focus is given to developing spatial models to identify the area and period of Human-wildlife conflict using the occurrences data from eDNA. Moreover, through this research, he aims to advance eDNA-based monitoring of wildlife species to better understand their occupancy for management and conservation in Bhutan.
Sherub is currently a recipients of E4D Doctoral Scholarship and his research will be supervised by Prof. Loïc Pellissier (ETH).
Stefanie's research investigates global marine biodiversity patterns across indices, methods, functional groups, space and time. By concentrating on the gradient spanning from coastal regions to the open oceans, she aims to bridge the gaps in existing global models for plankton and fish, while also considering the role of seasonal dynamics in shaping biodiversity patterns. An important part of the project involves integrating a wide range of data sources — including traditional observations, environmental DNA (eDNA), and Omics data — to detect and interpret ecological patterns along major axes of variability in a range of integrative analyses. Her PhD is part of the BiOcean5D project, a major interdisciplinary project designed to better understand the impact of human activity on Europe's seas and coastlines. It is a joint research effort between the Ecosystem and Landscape Evolution group, the Environmental Physics group, and The Sunagawa Lab.
Associated PhD students
Julia investigates movement and behaviour of juvenile golden eagles during natal dispersal. Using supervised machine learning applied to GPS and accelerometer data transmitted from tagged birds on the one side and behaviour observations on the other side, she will classify golden eagle behaviours across space and time. Relating these to the spatiotemporal variation in abiotic and biotic conditions will help to better understand drivers of movement and behaviours of this iconic alpine species. The Swiss Alpine golden eagle project is part of the LifeTrack Golden Eagle Alps project coordinated by the Swiss Ornithological Institute and the Max Planck Institute for Animal Behaviour.
external pageLetizia Lamperti
The objective of Letizia's thesis is to harness a combination of machine learning approaches to support the development of a fast data pipeline that transforms eDNA metabarcoding data into ecological indicators for ecosystem monitoring.
Letizia will develop machine learning to improve the identification of the taxonomic composition of eDNA samples and to link eDNA composition to ecological indicators.
The project involves a collaboration between 3 labs (CEFE, EPHE - PSL ; ETH Zurich- WSL Birmensdorf ; TIMC-IMAG, Université Grenoble-Alpes) with complementary skills (ecology, genomics, modelling, artificial intelligence).
This thesis is part of Artificial Intelligence for the Sciences (AI4theSciences) doctoral program run by Université PSL.
Bastiaan researches links between aquatic and terrestrial food webs in Swiss forests. The structure of food webs is crucial for maintaining biodiversity, while this is heavily influenced by global changes, both in climate and land management. However, terrestrial, aquatic and interconnected food webs may respond differently to these changes. During his PhD project, Bastiaan will utilize field work, mesocosms, feeding experiments, stable isotope and fatty acid analysis in order to unravel the effects of forest management and climate change on links between aquatic and terrestrial food webs. Bastiaan’s PhD is a part of the Blue-Green Biodiversity project and he is supervised by prof. dr. Martin Gossner (WSL), prof. dr. Carsten Schubert (EAWAG) and prof. dr. Loïc Pelissier (ETH).
Dominic Stemmler
Dominic is investigating the effect of continental collisions and break ups on species traits and biodiversity patters under constant atmospheric conditions. To explore the parameter space and possible feedback loops over deep time simulations more efficiently, a focus is on building a pipeline and coupling for the models of these different domains which include plate tectonic and global palaeogeography, climatic general circulation and downscaling as well as spatially-explicit biological process models.
Visting PhD students
Wenjun Zhong
As a visiting PhD student, Wenjun focuses on fish biodiversity facets (taxonomic, functional and genetic diversity) and distribution models using environmental DNA (eDNA). During his studying period, he hopes to address the changes and response mechanisms of fish biodiversity distribution patterns influenced by human activities. At present, he has some experience in field sampling, laboratory operation and bioinformatics analysis. After participating in the study of coastal China, Yangtze River and other provincial rivers, he will work with BECCY project participants to complete the relevant analysis of the three parallel rivers in the Hengduan Mountains.
Wenqi Song
Wenqi focuses on large-scale species patterns and the mechanisms underlying them. During his studying period, he hopes to understand the species richness pattern and phylogenetic structure in East Eurasia and their relationship with the environment factors and evolutionary history. In addition, he also pays attention to changes in species richness and species composition in China and the reasons for species changes.
Jiagang Zhao
Jiagang focuses on the evolutionary history and driving factors of plant diversity in China during the Cenozoic. She has compiled plant fossil data in China during the Cenozoic. By comparing results of quantitative reconstruction using plant fossils and Gen3sis outputs, she will reconstruct the spatial patterns of plant diversity in China during this period and further explore how deep-time environmental dynamics and biological processes to shape these patterns.
Master students
Mudit Joshi
In his Master's thesis, Mudit delves into the deep-time dynamics of plant macroevolution in response to climate shifts and bio-geodynamic processes. Employing the R-based mechanistic model Gen3sis, he simulates and assesses biodiversity changes across diverse climate trajectories over the past 400 million years. This research provides critical insights into the impact of historical landscape transformations, driven by climate and plate tectonics, on current biodiversity, with potential implications for future predictions.
Laura Perez
With a background both in social geography as well as environmental sciences, Laura's interest lies in interdisciplinary research. Her master thesis focuses on the influence of human activities on the presence and occupancy of urban mammals in the city of Zurich. From the urban gradient and human presence to socio-economic factors, there are numerous variables that can more or less predict the distribution of these mammals. Her goal is to better understand these dynamics.
Deniz Imir
As a master student in biology, Deniz is interested in understanding the mechanisms that have shaped biodiversity and will influence its future evolution. His research project investigates the impact of past geological events, such as glaciation or tectonic movement, on plant communities' biodiversity in mountainous areas. To do this, he compares in-field measures of biodiversity with statistical estimation to evaluate the influence of geology on community speciation. This project will hopefully contribute to our understanding of how the past has influenced the current state of biodiversity.
Bachelor students
Lea Ott
For her Bachelor’s thesis, Lea is using statistical models to identify catchment-specific biodiversity hotspots and investigate the drivers that influence biodiversity patterns. Her analysis includes different species groups as well as red list species and examines how a range of environmental and anthropogenic factors influence local biodiversity. In doing so, Lea aims to contribute to the fight against biodiversity loss in Switzerland.
Interns
Darina is a zoologist and bioinformatician using genetic and genomic tools to understand the ecology, evolution and diversity of both animal and plant species. In our group, she will focus on a comparison of two sequencing methods, the Illumina MiSeq and the MinION nanopore sequencing. She will examine their effectiveness, accuracy and their differences regarding the application in the environmental DNA (eDNA) metabarcoding in mammals. She will work mainly with mammalian eDNA samples collected in Bhutan.