CBMA

Molecular Ecology and Biodiversity Group

In the Molecular Ecology and Biodiversity group we are broadly interested in the description and interpretation of the biological and ecological basis for the genetic diversity of natural populations and species over time and space. There are currently three main research topics addressed in our team: 1) molecular biodiversity, i.e. DNA barcoding and derived research, 2) comparative phylogeography of marine species at regional and global scales, and 3) population genetics of natural populations.

Molecular biodiversity projects seek to develop a reference library of DNA barcodes for marine life of Portugal, in order to improve the taxonomic knowledge of the target taxa, and to develop a suite of applications where routine identifications of species are required. My main research target organisms  and communities have been mostly crustaceans, fish and the marine benthos. Currently the focus is in the development and application high-thoughput sequencing DNA metabarcoding and eDNA metabarcoding for environmental monitoring  of marine organisms and communities.  

Current and past assignments

2008-present: Universidade do Minho, Braga – Assistant Professor, Department of Biology

2008-present: Centre of Molecular and Environmental Biology (CBMA) -  Permament researcher / group leader

2009-present: International Barcode of Life (www.ibol.org) – Portugal delegate and member of the International Scientific Collaboration Committee

2006-present Fish Barcode of Life (www.fishbol.org): Deputy-Chair and currently Chair of the European Regional Working Group

Lobo J, Shokralla S, Costa MH, Hajibabaei M, Costa FO (2017). DNA metabarcoding for high-throughput monitoring of estuarine macrobenthic communities Scientific Reports 7: 15618. doi:10.1038/s41598-017-15823-6

Hollatz C, Leite BR, Lobo J, Froufe H, Egas C, Costa FO (2017). Priming of a DNA metabarcoding approach for species identification and inventory in marine macrobenthic communities. Genome 60: 260-271.

Oliveira LM, Knebelsberger T, Landi M, Soares P, Raupach MJ, Costa FO (2016). Assembling and auditing a global DNA barcode reference library for European marine fishes. Journal of Fish Biology 89: 2741–2754. 

Lobo J, Costa PM, Teixeira MAL, Ferreira MS, Costa MH, Costa FO (2013). Enhanced primers for amplification of DNA barcodes from a broad range of marine metazoans. BMC Ecology 13: 34.

Costa FO, Landi M, Martins R, Costa MH, Costa ME, Carneiro M, Alves MJ, Steinke D, Carvalho GR (2012). A ranking system for reference libraries of DNA barcodes: Application to marine fish species from Portugal. PLoS One 7: e35858. 

Costa FO, Antunes PM (2012). The contribution of the Barcode of Life initiative to the discovery and monitoring of Biodiversity. In: Natural Resources, Sustainability and Humanity - A Comprehensive View. Mendonça, A. et al. (Ed.). pp. 37-68, Springer, Dordrecht. 

Costa FO, Carvalho GR (2010). New insights into molecular evolution: prospects from the Barcode of Life Initiative (BOLI). Theory in Biosciences 129: 149-157.

Costa FO, Henzler CM, Lunt DH, Whiteley N, Rock J (2009). Probing marine Gammarus (Amphipoda) taxonomy with DNA barcodes. Systematics & Biodiversity 7: 365-379.

Costa FO, Carvalho G.R. (2007). The Barcode of Life Initiative: synopsis and prospective societal impacts of DNA barcoding of Fish. Genomics, Society and Policy 3: 29-40.

Costa FO, deWaard, J. R., Boutillier, J., Ratnasingham S., Dooh R., Hajibabaei M., Hebert, P.D.N. (2007). Biological identifications through DNA barcodes: the case of the Crustacea. Can. J. Fish. Aquat. Sci. 64: 272-295.

2016- NEXT-SEA: Next generation monitoring of coastal ecosystems in a scenario of global change. Structured– Project R&D&I Norte-45-2015-02. Team Member

2016- DNAqua-Net: Developing new genetic tools for bio- assessment of aquatic ecosystems in Europe. COST Action CA 15219. Management Committee Member

2011- Benthic Estuarine Barcode (BEstBarcode): Development and application of massively paralelized sequencing for monitoring of estuarine macrobenthic communities. Funded by FCT, starting April 2011: Principal Investigator.

2010 - METAFISHCODE: Fish genetic diversity and meta-species phylogeography at global and regional scales: implications for fisheries management. Funded by FCT, starting April 2010: Principal Investigator.

2010- Patterns and processes of (neutral and adaptive) variation in the honey bee (Apis mellifera iberiensis) hybrid zone of the Iberian Peninsula: a population genetics approach integrating population genomics and landscape genetics. Funded by FCT. Project Partner. 

2008- LusoMarBoL - Integrating molecular approaches into marine biodiversity research in Portugal: implementing DNA barcoding and investigating phylogeographic patterns. Funded by FCT: Principal Investigator.

2008- LusoAquaBarcode - Implementing DNA barcoding into aquatic biodiversity research in Portugal and priming new macrobenthos monitoring tools). European Reintegration Grant, Funded by EC, starting September 2008: Principal Investigator.

Selection of 15 papers

Lobo J, Ferreira MS, Antunes IC, Teixeira MAL, Borges LMS, Sousa R, Gomes PA, Costa MH, Cunha MR, Costa FO (2017) Contrasting morphological and DNA barcode suggested species boundaries among shallow-water amphipod fauna from the southern European Atlantic coast. Genome 60: 147-157.

Borges LMS, Hollatz C, Lobo J, Cunha AM, Vilela AP, Calado G, Coelho R, Costa AC, Ferreira MG, Costa MH, Costa FO (2016). With a little help from DNA barcoding: investigating the diversity of Gastropoda from the Portuguese coast. Scientific Reports 6, 20226.

Lobo J, Teixeira MAL, Borges LMS, Ferreira MSG, Hollatz C, Gomes PA, Sousa R, Ravara A, Costa MH, Costa FO (2016). Starting a DNA barcode reference library for shallow water polychaetes from the southern European Atlantic coast. Molecular Ecology Resources 16: 298-313.

Carneiro M, Martins R, Landi M, Costa FO (2014). Updated checklist of marine fishes (Chordata: Craniata) from Portugal and the proposed extension of the Portuguese continental shelf. European Journal of Taxonomy 73: 1-73.

Knebelsberger T, Landi M, Neumann H, Kloppmann M, Sell A, Campbell PD, Laakmann S, Raupach MJ, Carvalho GR, Costa FO (2014). A reliable DNA barcode reference library for the identification of the North European shelf fish fauna. Molecular Ecology Resources 14: 1060-1071. doi: 10.1111/1755-0998.12238

Lobo J, Costa PM, Teixeira MAL, Ferreira MS, Costa MH, Costa FO (2013). Enhanced primers for amplification of DNA barcodes from a broad range of marine metazoans. BMC Ecology 13: 34.

Costa FO, Landi M, Martins R, Costa MH, Costa ME, Carneiro M, Alves MJ, Steinke D, Carvalho GR (2012). A ranking system for reference libraries of DNA barcodes: Application to marine fish species from Portugal. PLoS One 7: e35858. 

Borges LMS, Sivrikaya H, le Roux A, Shipway R, Cragg SM, Costa FO (2012). Investigating the taxonomy and systematics of marine wood borers (Bivalvia: Teredinidae) combining evidence from morphology, DNA barcodes and nuclear locus sequences. Invertebrate Systematics 26: 572–582.

Matzen da Silva J, Creer S, dos Santos A, Costa AC, Cunha MR, Costa FO, Carvalho GR (2011). Systematic and evolutionary insights derived from mtDNA COI barcode diversity in the Decapoda (Crustacea: Malacostraca). PLoS One 6: e19449.

Costa FO, Henzler CM, Lunt DH, Whiteley N, Rock J (2009). Probing marine Gammarus (Amphipoda) taxonomy with DNA barcodes. Systematics & Biodiversity 7: 365-379.

Costa FO, Carvalho GR (2007). The Barcode of Life Initiative: synopsis and prospective societal impacts of DNA barcoding of Fish. Genomics, Society and Policy 3: 29-40.

Costa FO, deWaard JR, Boutillier J, Ratnasingham S, Dooh R, Hajibabaei M, Hebert, PDN (2007). Biological identifications through DNA barcodes: the case of the Crustacea. Can. J. Fish. Aquat. Sci. 64: 272-295.

Costa FO, Neuparth T, Theodorakis CW, Costa MH, Shugart LR (2004). RAPD analysis of southern populations of Gammarus locusta: comparison with allozyme data and ecological inferences. Mar. Ecol. Progr. Ser. 277: 197-207.

Costa FO, Costa MH (2000) Review of the ecology of Gammarus locusta (L.). Pol. Arch. Hydrobiol. 48: 541-559.

Costa FO, Costa MH (1999). Life history of the amphipod Gammarus locusta in the Sado Estuary (Portugal). Acta Oecologica 20: 305-314.

Costa FO, Antunes PM (2012). The contribution of the Barcode of Life initiative to the discovery and monitoring of Biodiversity. In: Natural Resources, Sustainability and Humanity - A Comprehensive View. Mendonça, A. et al. (Ed.). pp. 37-68, Springer, Dordrecht.

Carvalho GR, Creer S, Allen MJ, Costa FO, Tsigenopoulos, CS, Le Goff-Vitry M, Magoulas AM, Medlin L, Metfies K (2010). Genomics in the discovery and monitoring of marine biodiversity. In: Introduction to Marine Genomics. M. Cock et al. (ed.), pp. 1-32. Springer, Netherlands.

Post-doctoral fellows

Sofia Duarte (2016-ongoing) - Metabarcoding of meio- and macrobenthic estuarine communities: performance assessment and implementation in monitoring programmes.

Claudia Hollatz (started March 2014, concluded) - Metabarcoding of estuarine macrobenthic communities of Portugal. 

Cátia Bartilotti (started April 2010, concluded) – Phylogeny, phylogeography and ontogeny of the worldwide distributed shrimp genus Plesionika: contrasting molecular and morphology-based approaches.

Luisa Borges (started January 2009). Molecular biodiversity and advanced monitoring tools for use in macrobenthic communities in Portuguese costal ecosystems.

Monica Landi (started January 2009, concluded). Molecular biodiversity and meta-species phylogeography of fish from the NE Atlantic and the Mediterranean.

Manuela Parente (starting June 2007, concluded). Biodiversity and evolution of brown seaweeds from Portuguese waters and adjacent oceanographic regions. Institute of Marine Research, Portugal.

Ph.D. students

Barbara Daniela Rocha Leite (2016-ongoing). Monitoring coastal benthic colonization of artificial substrates with the support of DNA metabarcoding approaches.

Maria Fais (2015-ongoing). Development of a metabarcoding approach for investigating the coupled dynamics of estuarine meio- and macrobenthic communities.

Dora Sofia Martins Henriques (2013-ongoing). Genomic phylogeography and demographic history of the Iberian honeybee (Apis mellifera iberiensis). (Co-supervisor)

Pedro Emanuel Ferreira dos Reis Vieira (2012-2017). Associations between genetic and community diversity in Northeast Atlantic rocky shore environments: the case of the peracarids. (Co-supervisor)

Jorge Lobo Arteaga (2011-2016). Molecular biodiversity and advanced monitoring tools for macrobenthic communities of Portuguese coastal ecosystems.

Julio César Chávez Galarza (2011-2016). Population genomics and landscape genetics of the Iberian honey bee (Apis mellifera iberiensis). (Co-supervisor)

Joana Matzen (2006-2011): Biodiversity and molecular evolution of crustaceans from bathyal ecosystems of the Portuguese margin. Ph.D. Thesis in Biology, Universidade de Aveiro, Portugal. (Co-supervisor)

MSc.

 • Ilisa Antunes - Masters Degree in Ecology

• Luis Manuel Oliveira - Masters Degree in Ecology 

• Ana Paula Vilela - Masters Degree in Ecology 

• Barbara Leite - Masters Degree in Molecular Genetics 

• Nuno Gomes - Masters Degree in Ecology 

• Soraia Castro- Masters Degree in Ecology 

• Marcos Teixeira –Masters Degree in Ecology

 • Artur Oliveira –Masters Degree in Biotechnology of Medicinal Plants

Grantees

íris Sampaio (2011). Research Fellowship in the scope of LusoAquaBarcode

Undergraduate students

Ana Margarida Cunha (2011). Final BSc project.

Nuno Gomes (2011). Final BSc. project