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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

IMG_20250724_134117
Paula F. Campos

Paula F. Campos

Group Leader

Paula Campos is a researcher specializing in the application of ancient DNA to archaeological, palaeontological, and conservation biology questions. She obtained her degree in Biology in 2000, her Master’s degree in Biodiversity and Genetic Resources from the University of Porto in 2005, and her PhD in Evolutionary Biology from the University of Copenhagen in 2009.

Her publications include two theses, five book chapters, one technical report, and 64 peer-reviewed articles in international journals. Of these, 18 have been published in leading multidisciplinary scientific journals, including PNAS, Science, and Nature, as well as in specialized journals such as Journal of Archaeological Science, Molecular Ecology, and Antiquity

RESEARCH GROUPS:

Research Projects

Ocean3R

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:
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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:

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).