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Research Group

Palaeogenomics and Biodiversity Conservation

Our research investigates the long-term exploitation of marine resources and the ways human activities have influenced the population dynamics of key marine species. By integrating archaeological, genomic, and ecological data, we aim to reconstruct historical patterns of resource use and their ecological consequences. Previous work has focused on the exploitation and decline of North Atlantic right whales (Eubalaena glacialis), Mediterranean monk seals (Monachus monachus), and the population dynamics of European sardine (Sardina pilchardus). Building on this foundation, current projects such as SEACHANGE and PALEOHAKE extend this approach to multiple pelagic species, including sardine, mackerel, and hake, from the Roman era to the present. Using advanced genomic and bioinformatic methods, this research provides a long-term perspective on human–marine interactions, offering valuable insights for sustainable management and conservation today.

Principal Investigator

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Paula Campos

Paula Cristina Fernandes Campos

Researcher

Paula Campos is a researcher specialized in ancient DNA applications to archaeological, paleontological and conservation biology questions. She received her degree in Biology in 2000, her MSc in Biodiversity and Genetic Resources in 2005 from the University of Porto and her PhD in Evolutionary Biology in 2009 from University of Copenhagen. As of January 2020, her publications include 2 theses, 4 book chapters, 1 technical report and 48 papers in international peer review journals. Of these, 15 were published in major multidisciplinary scientific journals including PNAS, Science and Nature, but also in specialized journals like Journal of Archaeological Science and Molecular Ecology. Paula is funded through FCT’s Individual Call to Scientific Employment Stimulus, CEEC2017.

RESEARCH GROUPS:

Research Projects

Ocean3R

PALEOHAKE

SARDINOMICS

SEACHANGE

Group members

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Inês M. dos Santos

Inês Moreira dos Santos

MSc Student

I have a bachelor’s degree in Applied Biology by the University of Minho and I am currently doing my master’s in Molecular Genetics by the same University. I have previously worked together with Minho’s School of Sciences in projects of scientific dynamization and communication, having been awarded a scholarship for my collaboration. I also have a special interest in History, Anthropology and Evolutionary Genetics, having done an internship in Population Genetics during my bachelor’s senior year.

RESEARCH GROUPS:
Paula2
Paula Campos

Paula Cristina Fernandes Campos

Researcher

Paula Campos is a researcher specialized in ancient DNA applications to archaeological, paleontological and conservation biology questions. She received her degree in Biology in 2000, her MSc in Biodiversity and Genetic Resources in 2005 from the University of Porto and her PhD in Evolutionary Biology in 2009 from University of Copenhagen. As of January 2020, her publications include 2 theses, 4 book chapters, 1 technical report and 48 papers in international peer review journals. Of these, 15 were published in major multidisciplinary scientific journals including PNAS, Science and Nature, but also in specialized journals like Journal of Archaeological Science and Molecular Ecology. Paula is funded through FCT’s Individual Call to Scientific Employment Stimulus, CEEC2017.

RESEARCH GROUPS:
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Rebecca Netels

Rebecca Netels

MSc Student
RESEARCH GROUPS:
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Rute Fonseca

Rute Andreia Rodrigues da Fonseca

Researcher

Rute Fonseca is an Assistant Professor at the University of Copenhagen, Denmark. She received her degree in Biochemistry in 2000 and her PhD in Computational Chemistry in 20016 from University of Porto. Rute uses computational tools to study molecular evolution in a variety of organisms. My recent work involves exploring large-scale genomic information on both modern and ancient DNA data sets. I am particularly interested in protein function evolution and how this impacts phenotypes.

RESEARCH GROUPS:
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Subramaniam Vijaykumar

Subramaniam Vijaykumar

MSc Student

Subramaniam Vijayakumar is a master’s student specializing in marine biotechnology and bioinformatics, currently conducting his master thesis at the Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto. His research focuses on uncovering the diet and gut microbiome of the Mediterranean monk seal (Monachus monachus) from the Desertas (Madeira) population using metabarcoding and metagenomic analyses. He also investigates the relationship between the seals’ diet and gilt-head seabream aquaculture production in Ribeira Brava.

With a strong background in chemistry, having completed a Master’s in Chemistry, Subramaniam is currently studying in the Joint Master’s Programme in Marine Biotechnology under the prestigious Erasmus Mundus EU-CONEXUS program, gaining valuable international research experience. His expertise spans a broad range of areas, including organic, physical, and analytical chemistry, microbial cultures, genetic analysis, structural biology, and computational drug discovery, leveraging advanced computational tools for data analysis and modeling.”

As a voting member of the EU-CONEXUS JMPMB Student Board and patent holder for anti-cancer aminothiazole derivatives, Subramaniam is passionate about advancing research in marine bioactive compounds, with a focus on health, aquaculture, and sustainability

RESEARCH GROUPS:

Main publications

DNA from cetariae fish remains confirms sardine ( Sardina pilchardus ) use and local population continuity in Northwestern Iberia since Roman times.

Espregueira Themudo, G., Fernández-Fernández, A., Abad, P.V., Nóvoa, A.A.R., Fernández-Rodriguez, C., de Agüero, E.G.-G., da Fonseca, R.R., Campos, P.F.

2025
The complete mitochondrial genome of the extinct Caribbean monk seal (Neomonachus tropicalis) confirms its taxonomic position and the monophyly of the genus Neomonachus.

Espregueira Themudo, G., Rey-Iglesia, A., Campos, P.F.

2024Mar Biol 171, 195
Population Genomics Reveals the Underlying Structure of the Small Pelagic European Sardine and Suggests Low Connectivity within Macaronesia.

da Fonseca, R.R., Campos, P.F., Rey-Iglesia, A., Barroso, G. V., Bergeron, L.A., Nande, M., Tuya, F., Abidli, S., Pérez, M., Riveiro, I., Carrera, P., Jurado-Ruzafa, A., G. Santamaría, M.T., Faria, R., Machado, A.M., Fonseca, M.M., Froufe, E., C. Castro, L.F.

2024Genes (Basel) 15, 170.
Building a Portuguese Coalition for Biodiversity Genomics.

Marques, JP, Alves, PC, Amorim, IR, Lopes RJ, Moura, M, Meyers, G, Sim-sim, M, Sousa-Santos, C, Alves, MJ, Borges, PAV, Brown, T, Carneiro, C, Carrapato, C, Ceríaco, L, Ciofi, C, Silva, L. Diedericks, G, Diroma, MA, Farelo, L. Formenti, G, Gil, F, Grilo, M, Ianucci, A, Leitão, H, Máguas, C, McCartney, A, Mendes, S, Moreno, J, Morselli, M, MOuton, A, Natali, C, Pereira, F, Rego, R, Resendes, R, Roxo, G, Svardal, H, Trindade, H, Vicente, S, Winkler, S, Alvarenga, M, Amaral, A, Antunes, A, Campos, PF, Canário, A, Castilho, C, Castro, LF, Crottini, A, Cunha, M, Themudo, G, Esteves, P, Faria, R, Fernandes, C, Ledoux, JB, LOuto, B, Magalhães, S, Paulo, O, Pearson, G, Pimenta, J, Pina-Martins, F, Santos, T, Serrão, E, Melo-Ferreira J, Sousa, V

2024npj Biodiversity
How genomics can help biodiversity conservation. Trends in Genetics.

5. Theissinger, K., Fernandes, C., Formenti, G., Bista, I., Berg, P.R., Bleidorn, C., Bombarely, A., Crottini, A., Gallo, G.R., Godoy, J.A., Jentoft, S., Malukiewicz, J., Mouton, A., Oomen, R.A., Paez, S., Palsbøll, P.J., Pampoulie, C., Ruiz-López, M.J., Secomandi, S., Svardal, H., Theofanopoulou, C., de Vries, J., Waldvogel, A.-M., Zhang, G., Jarvis, E.D., Bálint, M., Ciofi, C., Waterhouse, R.M., Mazzoni, C.J., Höglund, J., Aghayan, S.A., Alioto, T.S., Almudi, I., Alvarez, N., Alves, P.C., Amorim do Rosario, I.R., Antunes, A., Arribas, P., Baldrian, P., Bertorelle, G., Böhne, A., Bonisoli-Alquati, A., Boštjančić, L.L., Boussau, B., Breton, C.M., Buzan, E., Campos, P.F., Carreras, C., Castro, L.Fi.C., Chueca, L.J., Čiampor, F., Conti, E., Cook-Deegan, R., Croll, D., Cunha, M. V., Delsuc, F., Dennis, A.B., Dimitrov, D., Faria, R., Favre, A., Fedrigo, O.D., Fernández, R., Ficetola, G.F., Flot, J.-F., Gabaldón, T., Agius, D.R., Giani, A.M., Gilbert, M.T.P., Grebenc, T., Guschanski, K., Guyot, R., Hausdorf, B., Hawlitschek, O., Heintzman, P.D., Heinze, B., Hiller, M., Husemann, M., Iannucci, A., Irisarri, I., Jakobsen, K.S., Klinga, P., Kloch, A., Kratochwil, C.F., Kusche, H., Layton, K.K.S., Leonard, J.A., Lerat, E., Liti, G., Manousaki, T., Marques-Bonet, T., Matos-Maraví, P., Matschiner, M., Maumus, F., Mc Cartney, A.M., Meiri, S., Melo-Ferreira, J., Mengual, X., Monaghan, M.T., Montagna, M., Mysłajek, R.W., Neiber, M.T., Nicolas, V., Novo, M., Ozretić, P., Palero, F., Pârvulescu, L., Pascual, M., Paulo, O.S., Pavlek, M., Pegueroles, C., Pellissier, L., Pesole, G., Primmer, C.R., Riesgo, A., Rüber, L., Rubolini, D., Salvi, D., Seehausen, O., Seidel, M., Studer, B., Theodoridis, S., Thines, M., Urban, L., Vasemägi, A., Vella, A., Vella, N., Vernes, S.C., Vernesi, C., Vieites, D.R., Wheat, C.W., Wörheide, G., Wurm, Y., Zammit, G.,

2023
Assessing microplastic exposure of the Critically Endangered Mediterranean monk seal (Monachus monachus) on a remote oceanic island.

McIvor, A.J., Pires, R., Lopes, C., Raimundo, J., Campos, P.F., Pais, M.P., Canning-Clode, J., Dinis, A.,

2023Science of The Total Environment 856, 159077.
The population genomic legacy of the second plague pandemic.

Gopalakrishnan, S., Ebenesersdóttir, S.S., Lundstrøm, I.K.C., Turner-Walker, G., Moore, K.H.S., Luisi, P., Margaryan, A., Martin, M.D., Ellegaard, M.R., Magnússon, Ó.þ., Sigurðsson, Á., Snorradóttir, S., Magnúsdóttir, D.N., Laffoon, J.E., van Dorp, L., Liu, X., Moltke, I., Ávila-Arcos, M.C., Schraiber, J.G., Rasmussen, S., Juan, D., Gelabert, P., de-Dios, T., Fotakis, A.K., Iraeta-Orbegozo, M., Vågene, Å.J., Denham, S.D., Christophersen, A., Stenøien, H.K., Vieira, F.G., Liu, S., Günther, T., Kivisild, T., Moseng, O.G., Skar, B., Cheung, C., Sandoval-Velasco, M., Wales, N., Schroeder, H., Campos, P.F., Guðmundsdóttir, V.B., Sicheritz-Ponten, T., Petersen, B., Halgunset, J., Gilbert, E., Cavalleri, G.L., Hovig, E., Kockum, I., Olsson, T., Alfredsson, L., Hansen, T.F., Werge, T., Willerslev, E., Balloux, F., Marques-Bonet, T., Lalueza-Fox, C., Nielsen, R., Stefánsson, K., Helgason, A., Gilbert, M.T.P.

2022Current Biology.
Mitogenomics of the endangered Mediterranean monk seal (Monachus monachus) reveals dramatic loss of diversity and supports historical gene flow between Atlantic and eastern Mediterranean populations.

Rey-Iglesia, A., Gaubert, P., Espregueira Themudo, G., Pires, R., De la Fuente, C., Freitas, L., ...Campos, P. F.

2020Zoological Journal of the Linnean Society.
The genetic history of whaling in the Cantabrian Sea during the 13th–18th centuries: Were North Atlantic right whales (Eubalaena glacialis) the main target species?

Rey-Iglesia, A., Martínez-Cedeira, J., López, A., Fernández, R., Campos, P.F. (2018).

2018JAS Reports, 18, (393-398).