Search

Research Team

Aquatic Ecology and Evolution

Aquatic Ecology and Evolution Research Group (AEE) integrates multi-disciplinary approaches to study different levels of organization of aquatic biodiversity: from the genome to organism level, populations, communities and ecosystems.

AEE group aims to unravel the patterns and processes driving diversity in aquatic systems and to understand the potential threats that anthropogenic stressors pose to biodiversity. Our previous investigations resulted in important contributions to the understanding of historical and contemporary evolutionary forces that govern genetic variation in nature, applying diverse molecular markers to multiple biological models, in particular, freshwater bivalves, fish and marine crustaceans. Our team also produced important ecological and conservation biology outputs, including status assessments, guidelines and research syntheses on aquatic species and habitats across the world. AEE works towards increasing public awareness and participation on biodiversity and conservation research, including participatory approaches like community-based conservation of marine resources.

Principal Investigator

Team Leader

Elsa Froufe, a Principal Investigator at CIIMAR, holds a Biology degree from Aveiro University (1997) and a PhD from the University of Porto (2006). With a strong background in genetics and evolutionary biology, Elsa’s work focuses on understanding aquatic biodiversity patterns and ecosystem complexities. Passionate about fostering scientific collaboration, she actively collaborates with a vast network of researchers as she is particularly interested in the application of integrative cross-discipline approaches to study different levels of aquatic biodiversity organization. In the last years she has been focused on the impact of climate changes in the aquatic biodiversity.

RESEARCH TEAMS:
Co-Principal Investigator
Research Grant

David Barros-García completed his PhD in Biology (2019) at the University of Vigo (Spain). His research interests are focused on phylogeography, evolution, integrative taxonomy and adaptation to the environment of deep-sea fishes. He obtained an Individual Call to Scientific Employment Stimulus as junior researcher from Fundação para a Ciência e a Tecnologia with a proposal based on genomics research of deep-sea teleosts to develop at the CIIMAR.

RESEARCH TEAMS:
Research Projects

A&BM

ATLANTIDA

BIOMETORE

ConBiOmics

CORAL

EdgeOmics

FRESHCO

INNOVMAR

MarInfo

MULTI-CRASH

Ocean3R

PerSeaVe

SeeingShore

Team members

Research Grant

Ana Matos has a BSc in Biology, a MSc in Cell and Molecular Biology, and a PhD in Biology from FCUP. Throughout her career, she has been involved in several aquatic research projects. The study of predator-prey interactions and the development of molecular markers to assess accurately and quickly the presence of potentially toxic cyanobacteria in freshwater systems are among those projects. Moreover, she also studied ascidians’ microbiome and its bioactive potential through the application of genomics, proteomics, and microbial approaches. Currently, she has a research grant to investigate freshwater bivalves’ adaptation to climate change effects (Edgeomics Project).

RESEARCH TEAMS:
MSc Student

Marine & Freshwater Projects Co-ordinator, Conservation Programmes, Zoological Society of London.
Ana works on a range of marine conservation projects that focus on community-based initiatives. Her project areas include ZSL’s Our Sea Our Life project (working with communities in Mozambique on the co-management of artisanal fisheries), and the Net-Works programme (empowering coastal communities in the developing world to collect and sell discarded fishing nets, which are recycled to make carpets). She holds a bachelor’s degree in Ocean Science from the University of Plymouth and is undertaking a master’s degree in Education for Sustainability with London South Bank University.

RESEARCH TEAMS:
Research Grant

André Gomes-dos-Santos graduated in Applied Biology in 2015 (Minho University), where he also obtained a Master’s degree in Ecology (2017). He concluded his PhD in Biology in 2023 (Porto University), during which he specialized in bioinformatics focused on whole genome assembly, phylogenomics, population genomics, and big data management. He has over 30 ISI-indexed publications in peer-review journals with nearly 100 different co-authors from 25 countries. His focus of research is the application of genomic sequencing outputs, implemented through computational biology, to understand the evolutionary dynamics and adaptations of freshwater mussels and other aquatic organisms.

RESEARCH TEAMS:
Researcher

Antonina dos Santos has over 20 years of scientific work in taxonomy and ecology of marine invertebrates. She graduated in Marine Biology and Fisheries at the University of Algarve and had her PhD in Biology (Ecology and Biosystematics) at the University of Lisbon in 2000.

Her main area of work has been the study of decapod larvae, focusing her studies on taxonomy, larval dispersal and recruitment. Besides that she has also done some important work on the taxonomy of adults having already described four new species of shrimp to science (Bresilia saldanhai, Periclimenaeus aurae, Lysmata jundalini and Macrobrachium pantanalense). Recently she created GelAvista, a citizen science project to study jellyfish. She has been involved in many scientific projects subject to competitive tendering national and European multidisciplinary, 5 of which as coordinator. The results of her scientific activities are reflected in the publication of over 60 scientific articles published in international journals. She have also guided many students from graduates to masters theses, doctoral and post-doc from Portugal, Spain, Italy and Brazil among others. It has been chief scientist on more than 15 multidisciplinary oceanographic campaigns off the Portuguese coast. Also it is editor of the ICES Identification Leaflets for Plankton and academic editor of PeerJ.

RESEARCH TEAMS:
Research Grant

David Barros-García completed his PhD in Biology (2019) at the University of Vigo (Spain). His research interests are focused on phylogeography, evolution, integrative taxonomy and adaptation to the environment of deep-sea fishes. He obtained an Individual Call to Scientific Employment Stimulus as junior researcher from Fundação para a Ciência e a Tecnologia with a proposal based on genomics research of deep-sea teleosts to develop at the CIIMAR.

RESEARCH TEAMS:
Researcher

I’m interested in biogeography, evolutionary biology and conservation, and have worked with a variety of terrestrial and aquatic taxa. My academic theses have focused on analysing evolutionary and biogeographic patterns at different spatial and time scales using GIS, ecological niche-based models and genetics, mostly of terrestrial and semi-aquatic desert herpetofauna from West Africa. I also did some work with fish and freshwater mussels. Presently I am studying the distribution and evolution of freshwater biodiversity of North African semi-arid regions and how it contrasts with terrestrial patterns. I have accumulated hundreds of fieldwork days in expeditions to remote locations, mostly Africa, and strive for balance among exploration, conservation, learning and hypothesis-based scientific thinking.

RESEARCH TEAMS:
Research Technician

Elza Fonseca is a Researcher at CIIMAR. She holds a BSc in Biochemistry (2010) and a MSc in Bioengineering (2013) from the University of Minho, and a PhD in Biology (2020) awarded by the Faculty of Sciences, University of Porto. Her research interests focus on Molecular & Cellular Biology, Comparative & Functional Genomics, and Evolutionary Biology. She is particularly interested in studying nuclear receptors as one of the largest superfamilies of transcription factors unique to metazoans and responsible for regulating biological processes such as cell differentiation, development, metabolism, and reproduction.

RESEARCH TEAMS:
Researcher

Fernando Tuya is Associate Professor (“Profesor Titular”) at the Universidad de Las Palmas de G.C., since February 2018, after a “Ramón y Cajal” (2010-2015) tenure-track position and two postdoctoral positions at the Centre for Marine Ecosystems Research, Edith Cowan University (Australia, 2006-2008) and CIIMAR, Universidade do Porto (Portugal, 2009-2010). In 2015, I was awarded the I3 certification by the MINECO, according to the merits obtained in the first 4 years of the “Ramón y Cajal” tenure-track position.

Motivation of research: the necessity of searching for models that aim to explain patterns in the organization of benthic marine assemblages through ecosystems across different scales of space, time and taxonomy. More specifically, my research focuses in ecological interactions in and around marine habitats to tease apart the often-complex interactions that cause patterns of species distributions in nature. This approach allows transferring basic ecological knowledge into the sustainable management of marine ecosystems.

RESEARCH TEAMS:
PhD Student

Giulia Secci graduated in Biology in 2014 and obtained her Master degree in Marine Biology in 2016, both achieved in the University of Cagliari. She has been awarded with a PhD mixed grant from FCT. She is carrying out her work in the AEE (Aquatic Ecology and Evolution), AGE (Animal Genetic and Evolution) laboratories at CIIMAR and in the Institute of Zoology of Karl-Franzens University in Graz (Austria), under the supervision of Elsa Froufe, Filipe Castro and Steven Weiss. Her work uses grayling (Thymallus) species to study patterns of population structure, phylogeny and phylogeography using full mitogenomes as well as mechanisms of adaptation by building low-coverage genomes.

RESEARCH TEAMS:
Research Technician

Research Assistant at IPMA. Performs research support activity in the scientific area of Information Systems and Technologies, within the scope of the EMODnet Biology project. Organization and formatting of biodiversity data sets for the its availability on the EMODnet data portal, using the formats Darwin Core, EurOBIS, OBIS & OBIS-ENV, WoRMS.

RESEARCH TEAMS:
Research Grant

Jérémy Huet has got a Master degree in conservation biology since 2007. He has worked on community-based projects from protecting marine biodiversity and sawfish in Guinea-Bissau to diversifying habitats for wild plants with local volunteer groups in the Balkans. Hosted by CIIMAR in Porto since 2014, he is now working for the Zoological Society of London on a fishery co-management project in Mozambique: Our Sea Our Life. This innovative project supports Community Fisheries Councils to manage marine reserves and diversify livelihoods through oyster farming and saving groups.

RESEARCH TEAMS:
Research Grant

Lígia Faria de Sousa graduated in Biology in 2012 in the Sciences Faculty of Lisbon University (FCUL) and has a Master degree in Scientific Illustration achieved in 2015. She works in the description of the morphology of decapod crustacean larvae, and has been collaborating in the Portuguese citizen science program GelAvista since 2016.

RESEARCH TEAMS:
PhD Student

Manuel Lopes-Lima is currently the (IUCN/SSC) Coordinator of the Red List Authority on Freshwater Bivalves within the Mollusk Specialist Group. His research interests are related with the global conservation of freshwater mussels including phylogeny, genetic diversity and ecophysiology. He is also an active promoter of international research efforts around this faunistic group.

RESEARCH TEAMS:
Researcher

Rita F. T. Pires has a PhD in Marine Sciences by the University of Lisbon (2022) and a master degree in Marine Biology (specialization in Marine Ecology and Conservation) by the University of Algarve (2010). Since 2011, as a research assistant at the Portuguese Institute for Sea and Atmosphere, she has been working on ecology and taxonomy of marine zooplankton. She specialized in the identification of decapod crustacean and fish larvae, and jellyfish. Since 2016, she also collaborates on the Portuguese citizen science program GelAvista, for the monitoring of jellyfish. Her research interests also include biological oceanography, larval dispersal and connectivity processes, biophysical modelling and scientific dissemination. In her PhD, she focused on biophysical modelling studies for decapod larvae for the northeastern Atlantic – western Mediterranean area.

RESEARCH TEAMS:
MSc Student

Tea graduated as Bachelor of Biology – Microbiology at the Faculty of Natural Sciences and Mathematics, University of Sarajevo. Currently, she is doing a Master’s degree in Biodiversity, Genetics and Evolution at the Faculty of Sciences, University of Porto. Her master’s thesis aims to: i) characterise the parasite community of West African crocodile (Crocodylus suchus) and Guinea baboon (Papio papio) along an aridity gradient; ii) analyse environmental drivers of parasite diversity and turnover; iii) predict potential shifts in parasite diversity distribution in these species. Her interests are biodiversity conservation, evolutionary biology, microbiology, genetics, biogeography, herpetology, and marine biology.

RESEARCH TEAMS:

Main publications

A novel assembly pipeline and functional annotations for targeted sequencing: A case study on the globally threatened Margaritiferidae (Bivalvia: Unionida).

Gomes‐dos‐Santos, A., Froufe, E., Pfeiffer, J. M., Johnson, N. A., Smith, C. H., Machado, A. M., ... & Lopes Lima, M.

2023Molecular Ecology Resources.
Multilocus species delimitation analyses show junior synonyms and deep-sea unknown species of genus Gaidropsarus (Teleostei: Gadiformes) in the North Atlantic/Mediterranean Sea area.

Barros-García, D., Comesaña, Á. S., Bañón, R., Baldó, F., Arronte, J. C., Froufe, E., & De Carlos, A.

2022Mar Biol 169, 131.
Morphological description of the first protozoeal stage of the deep-sea shrimps Aristeus antennatus and Gennadas elegans with a key.

Carreton, M., Dos Santos, A., De Sousa, L.F. Rotllant, G., Company, J.B.

2020Scientific Reports 10, 11178
Freshwater mussels (Bivalvia: Unionidae) from the rising sun (Far East Asia): phylogeny, systematics, and distribution.

Lopes-Lima, M., Hattori, A., Kondo, T., Lee, J. H., Kim, S. K., Shirai, A., ... & Froufe, E.

2020Molecular Phylogenetics and Evolution, 146, 106755.
Evaluating a species phylogeny using ddRAD SNPs: Cyto-nuclear discordance and introgression in the salmonid genus Thymallus (Salmonidae).

Secci-Petretto, G., Englmaier, G. K., Weiss, S. J., Antonov, A., Persat, H., Denys, G. P., ... & Froufe, E.

2023Molecular Phylogenetics and Evolution, 178, 107654
Joint species distribution models unveil co‐occurrences between freshwater mussels and their fish hosts.

da Silva, J. P., Goncalves, D. V., Garcia‐Raventós, A., Lopes‐Lima, M., Varandas, S., Froufe, E., Teixeira, A., Hui, F. K.C., Filipe, A. F., Sousa. R.

2023Journal of Biogeography 50, no. 4: 730-742
PacBio Hi-Fi genome assembly of the Iberian dolphin freshwater mussel Unio delphinus Spengler, 1793.

Gomes-dos-Santos, A., Lopes-Lima, M., Machado, M. A., Teixeira, A., C. Castro, L. F., & Froufe, E.

2023Scientific Data, 10(1), 340.